Strategy to discover diverse optimal molecules in the small molecule universe.

Science.gov (United States)

Rupakheti, Chetan; Virshup, Aaron; Yang, Weitao; Beratan, David N

2015-03-23

The small molecule universe (SMU) is defined as a set of over 10(60) synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework ( Virshup et al. J. Am. Chem. Soc. 2013 , 135 , 7296 - 7303 ) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 10(5) molecules.

[Molecular characteristics of Clustered Regularly Interspaced Short Palindromic Repeat in Shigella].

Science.gov (United States)

Xue, Zerun; Wang, Yingfang; Duan, Guangcai; Yang, Haiyan; Xi, Yuanlin; Wang, Pengfei; Wang, Linlin; Guo, Xiangjiao

2015-08-01

To detect the molecular characteristics of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) in Shigella and to analyze the distribution of CRISPR related to the time of isolation. Of the 52 Shigella strains, 41 were isolated from Henan, 6 from Jiangxi and 5 isolated from Beijing. Both CRISPR locus of S1, S2, S3 and S4 in Shigella were detected by polymerase chain reaction (PCR). The PCR products were sequenced and compared. The positive rates of CRISPR locus in Shigella were 33.69% (S1), 50.00% (S2), 82.69% (S3) and 73.08% (S4), respectively. Two subtypes were discovered in S1 and S3 locus. Three subtypes were discovered in S2 locus. Four different subtypes were discovered in S4 locus. The isolates from Henan strains were divided into two groups by the time of isolation. Distributions of S1 were different, before or after 2004, on Shigella. S1 could not be detected after 2004. There were no statistical differences of S2, S3 and S4 in two groups. Different CRISPR subtypes or Shigella were discovered. A significant correlation was noticed between the CRISPR S1 related to the time of isolation but not between S2, S3 or S4 on the time of isolation.

Comparative studies on different molecular methods for ...

African Journals Online (AJOL)

The present study aims to evaluate two molecular methods for epidemiological typing of multi drug resistant Klebsiella pneumoniae isolated from Mansoura Hospitals. In this study, a total of 300 clinical isolates were collected from different patients distributed among Mansoura Hospitals, Dakahlia governorate, Egypt.

Discovering Alaska's Salmon: A Children's Activity Book.

Science.gov (United States)

Devaney, Laurel

This children's activity book helps students discover Alaska's salmon. Information is provided about salmon and where they live. The salmon life cycle and food chains are also discussed. Different kinds of salmon such as Chum Salmon, Chinook Salmon, Coho Salmon, Sockeye Salmon, and Pink Salmon are introduced, and various activities on salmon are…

Medicinal benefits of marine invertebrates: sources for discovering natural drug candidates.

Science.gov (United States)

De Zoysa, Mahanama

2012-01-01

Marine invertebrates are one of the major groups of organisms, which could be diversified under the major taxonomic groups of Porifera, Cnidaria, Mollusca, Arthropoda, Echinodermata, and many other minor phyla. To date, range of medicinal benefits and a significant number of marine natural products (MNPs) have been discovered from marine invertebrates. Seafood diet from edible marine invertebrates such as mollusks and crustaceans has been linked with various medicinal benefits to improve human health. Among marine invertebrates, spongers from phylum Porifera is the most dominant group responsible for discovering large number of MNPs, which have been used as template to develop therapeutic drugs. MNPs isolated from invertebrates have shown wide range of therapeutic properties including antimicrobial, antioxidant, antihypertensive, anticoagulant, anticancer, anti-inflammatory, wound healing and immune modulator, and other medicinal effects. Therefore, marine invertebrates are rich sources of chemical diversity and health benefits for developing drug candidates, cosmetics, nutritional supplements, and molecular probes that can be supported to increase the healthy life span of human. Copyright © 2012 Elsevier Inc. All rights reserved.

Discovering Hands - México

OpenAIRE

Salamanca Cárdenas, Daniela; Castelblanco Domínguez, Junio Andrés; Aguilar Ardila, Laura Andrea

2016-01-01

El modelo de Discovering Hands ha sido reconocido internacionalmente como un proyecto innovador que se ha expandido por diferentes países del mundo, como Austria, y se ha empezado a estudiar la propuesta en países como República Checa, India y Colombia. (Discovering Hands, 2016). Esto se debe a que no solo mejora el tratamiento de cáncer de mama, sino que también reduce los costos totales de tratamiento de la enfermedad y aumenta la fuerza laborar de los países donde esté presente. Al represe...

Heterogeneity of mammary lesions represent molecular differences

International Nuclear Information System (INIS)

Namba, Ruria; Gregg, Jeffrey P; Maglione, Jeannie E; Davis, Ryan R; Baron, Colin A; Liu, Stephenie; Carmack, Condie E; Young, Lawrence JT; Borowsky, Alexander D; Cardiff, Robert D

2006-01-01

Human breast cancer is a heterogeneous disease, histopathologically, molecularly and phenotypically. The molecular basis of this heterogeneity is not well understood. We have used a mouse model of DCIS that consists of unique lines of mammary intraepithelial neoplasia (MIN) outgrowths, the premalignant lesion in the mouse that progress to invasive carcinoma, to understand the molecular changes that are characteristic to certain phenotypes. Each MIN-O line has distinguishable morphologies, metastatic potentials and estrogen dependencies. We utilized oligonucleotide expression arrays and high resolution array comparative genomic hybridization (aCGH) to investigate whole genome expression patterns and whole genome aberrations in both the MIN-O and tumor from four different MIN-O lines that each have different phenotypes. From the whole genome analysis at 35 kb resolution, we found that chromosome 1, 2, 10, and 11 were frequently associated with whole chromosome gains in the MIN-Os. In particular, two MIN-O lines had the majority of the chromosome gains. Although we did not find any whole chromosome loss, we identified 3 recurring chromosome losses (2F1-2, 3E4, 17E2) and two chromosome copy number gains on chromosome 11. These interstitial deletions and duplications were verified with a custom made array designed to interrogate the specific regions at approximately 550 bp resolution. We demonstrated that expression and genomic changes are present in the early premalignant lesions and that these molecular profiles can be correlated to phenotype (metastasis and estrogen responsiveness). We also identified expression changes associated with genomic instability. Progression to invasive carcinoma was associated with few additional changes in gene expression and genomic organization. Therefore, in the MIN-O mice, early premalignant lesions have the major molecular and genetic changes required and these changes have important phenotypic significance. In contrast, the changes

The Universe for all to discover

Science.gov (United States)

Ortiz-Gil, A.; Ballesteros, F.; Espinós, H.; Fernández-Soto, A.; Lanzara, M.; Moya, M. J.; Navarro, J.

2015-05-01

In the title of this paper, we have changed the slogan of the International Year of Astronomy, ``The Universe yours to discover" to ``The Universe for all to discover" in order to emphasize the need to think about broader audiences when we plan astronomical activities at school or during outreach events. The strategy we propose follows what is known as the Universal Design for Learning (UDL). UDL allows to reach to the general public as well as to audiences which might be regarded as ``special" because they have some disability. It has been shown that everybody has a preferred style of learning (some remember better what they see, others what they hear or what they touch) and therefore, everybody is more or less able under the different styles of learning. Through this talk I am going to outline some of the principles of the UDL that can be applied in the teaching and communication of Astronomy, along with an example of its implementation in the project ``A Touch of the Universe".

Did the ancient egyptians discover Algol?

Science.gov (United States)

Jetsu, L.; Porceddu, S.; Porceddu, S.; Lyytinen, J.; Kajatkari, P.; Markkanen, T.; Toivari-Viitala, J.

2013-02-01

Fabritius discovered the first variable star, Mira, in 1596. Holwarda determined the 11 months period of Mira in 1638. Montanari discovered the next variable star, Algol, in 1669. Its period, 2.867 days, was determined by Goodricke (178). Algol was associated with demon-like creatures, "Gorgon" in ancient Greek and "ghoul" in ancient Arab mythology. This indicates that its variability was discovered much before 1669 (Wilk 1996), but this mythological evidence is ambiguous (Davis 1975). For thousands of years, the Ancient Egyptian Scribes (AES) observed stars for timekeeping in a region, where there are nearly 300 clear nights a year. We discovered a significant periodicity of 2.850 days in their calendar for lucky and unlucky days dated to 1224 BC, "the Cairo Calendar". Several astrophysical and astronomical tests supported our conclusion that this was the period of Algol three millennia ago. The "ghoulish habits" of Algol could explain this 0.017 days period increase (Battersby 2012).

Distinct molecular subtypes of uterine leiomyosarcoma respond differently to chemotherapy treatment.

Science.gov (United States)

An, Yang; Wang, Shuzhen; Li, Songlin; Zhang, Lulu; Wang, Dayong; Wang, Haojie; Zhu, Shibai; Zhu, Wan; Li, Yongqiang; Chen, Wenwu; Ji, Shaoping; Guo, Xiangqian

2017-09-11

Uterine leiomyosarcoma (ULMS) is an aggressive form of soft tissue tumors. The molecular heterogeneity and pathogenesis of ULMS are not well understood. Expression profiling data were used to determine the possibility and optimal number of ULMS molecular subtypes. Next, clinicopathological characters and molecular pathways were analyzed in each subtype to prospect the clinical applications and progression mechanisms of ULMS. Two distinct molecular subtypes of ULMS were defined based on different gene expression signatures. Subtype I ULMS recapitulated low-grade ULMS, the gene expression pattern of which resembled normal smooth muscle cells, characterized by overexpression of smooth muscle function genes such as LMOD1, SLMAP, MYLK, MYH11. In contrast, subtype II ULMS recapitulated high-grade ULMS with higher tumor weight and invasion rate, and was characterized by overexpression of genes involved in the pathway of epithelial to mesenchymal transition and tumorigenesis, such as CDK6, MAPK13 and HOXA1. We identified two distinct molecular subtypes of ULMS responding differently to chemotherapy treatment. Our findings provide a better understanding of ULMS intrinsic molecular subtypes, and will potentially facilitate the development of subtype-specific diagnosis biomarkers and therapy strategies for these tumors.

MRI and pathological features of different molecular subtypes of breast cancers

International Nuclear Information System (INIS)

Yu Yang; Huo Tianlong; Lai Yunyao; Hong Nan

2014-01-01

Objective: To investigate the MRI and pathological features of different molecular subtypes of breast cancer. Methods: The data of 202 patients who underwent primary breast cancer resection were retrospectively reviewed. All of the patients had MRI preoperatively. The molecular subtypes of breast cancer defined by immunohistochemistry were classified as basal-like, luminal and HER-2 overexpression. Morphology (including mass or non-mass like enhancement, shape and margin of masses, unifocal or multifocal masses) and enhancement characteristics on MRI, histologic types and grades of tumors were analyzed with Chi-square test, exact test, Fisher exact test, Kruskal-Wallis H test, and Wilcoxon test. Results: Among the 202 patients, 34 were basal-like, 144 were luminal and 24 were HER-2 overexpression. The number of mass cases in each subtype was 29, 133 and 19 respectively,making no significant difference (χ 2 =4.136, P=0.126). As for the shape of basal-like lesions,8 were round,19 were lobular and 2 were irregular, while this distribution was 23, 58, 52 in luminal subtype and 1, 11, 7 in HER-2 overexpression subtype (χ 2 =13.391, P<0.05). The margin was also strikingly different among three groups (smooth, spiculate, irregular): 20, 5, 4 respectively in basal-like, 27, 53, 53 respectively in luminal, and 4, 7, 8 respectively in HER-2 overexpression (χ 2 =28.515, P<0.01). 52.6% (10/19) of HER-2 overexpression cases were multifocal, while only 6.9% (2/29) of luminal and 8.0% (24/133) of basal-like ones were multifocal (χ 2 =16.140, P<0.01). Characteristics in dynamic contrast-enhanced MRI were statistically different, with homogeneous, heterogeneous, and rim enhancement 0, 13, 16 respectively in basal-like cases, 28, 93, 11 respectively in luminal cases and 2, 11, 6 respectively in HER-2 overexpression cases (P<0.01). However, the difference for enhancement curve did not reach significance (P =0.457). Histologic types were significantly different among molecular

Laboratory Information Systems in Molecular Diagnostics: Why Molecular Diagnostics Data are Different.

Science.gov (United States)

Lee, Roy E; Henricks, Walter H; Sirintrapun, Sahussapont J

2016-03-01

Molecular diagnostic testing presents new challenges to information management that are yet to be sufficiently addressed by currently available information systems for the molecular laboratory. These challenges relate to unique aspects of molecular genetic testing: molecular test ordering, informed consent issues, diverse specimen types that encompass the full breadth of specimens handled by traditional anatomic and clinical pathology information systems, data structures and data elements specific to molecular testing, varied testing workflows and protocols, diverse instrument outputs, unique needs and requirements of molecular test reporting, and nuances related to the dissemination of molecular pathology test reports. By satisfactorily addressing these needs in molecular test data management, a laboratory information system designed for the unique needs of molecular diagnostics presents a compelling reason to migrate away from the current paper and spreadsheet information management that many molecular laboratories currently use. This paper reviews the issues and challenges of information management in the molecular diagnostics laboratory.

Discovering the Solar System

Science.gov (United States)

Jones, Barrie W.

1999-04-01

Discovering the Solar System Barrie W. Jones The Open University, Milton Keynes, UK Discovering the Solar System is a comprehensive, up-to-date account of the Solar System and of the ways in which the various bodies have been investigated and modelled. The approach is thematic, with sequences of chapters on the interiors of planetary bodies, on their surfaces, and on their atmospheres. Within each sequence there is a chapter on general principles and processes followed by one or two chapters on specific bodies. There is also an introductory chapter, a chapter on the origin of the Solar System, and a chapter on asteroids, comets and meteorites. Liberally illustrated with diagrams, black and white photographs and colour plates, Discovering the Solar System also features: * tables of essential data * question and answers within the text * end of section review questions with answers and comments Discovering the Solar System is essential reading for all undergraduate students for whom astronomy or planetary science are components of their degrees, and for those at a more advanced level approaching the subject for the first time. It will also be of great interest to non-specialists with a keen interest in astronomy. A small amount of scientific knowledge is assumed plus familiarity with basic algebra and graphs. There is no calculus. Praise for this book includes: ".certainly qualifies as an authoritative text. The author clearly has an encyclopedic knowledge of the subject." Meteorics and Planetary Science ".liberally doused with relevant graphs, tables, and black and white figures of good quality." EOS, Transactions of the American Geophysical Union ".one of the best books on the Solar System I have seen. The general accuracy and quality of the content is excellent." Journal of the British Astronomical Association

Discovering genes underlying QTL

Energy Technology Data Exchange (ETDEWEB)

Vanavichit, Apichart [Kasetsart University, Kamphaengsaen, Nakorn Pathom (Thailand)

2002-02-01

A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

What if Fleming had not discovered penicillin?

Science.gov (United States)

Alharbi, Sulaiman Ali; Wainwright, Milton; Alahmadi, Tahani Awad; Salleeh, Hashim Bin; Faden, Asmaa A; Chinnathambi, Arunachalam

2014-09-01

What would have happened had Alexander Fleming not discovered penicillin in 1928? Perhaps the obvious answer is that, someone else would have discovered penicillin during 1930s and the Oxford group, would still have purified it sometime in the early 1940s. Here, however, in this counterfactual account of the penicillin story, it is argued that without Fleming, penicillin might still be undiscovered and the antibiotic age would never have dawned. As a result, many of the recent developments in medicine, such as organ transplantation, might have been delayed or, at best, made more hazardous. Penicillin might have come onto the scene a few years later but, had Fleming overlooked the discovery, it seems certain that penicillin would not have saved countless Allied lives, during and after D-Day. Instead of having enjoyed fifty and more years of the antibiotic age, it is argued here, that we would have had to rely upon highly developed sulphonamides, so-called "supasulfas", and other chemically-derived antibacterial drugs. Indeed, it might be the case that, even well into this new millennium, the antibiotic age has yet to dawn, and medicine is still waiting for someone to chance upon penicillin. Here we discuss what might have happened had Fleming not discovered penicillin and come to the conclusion that the medical armoury available today would have been far different and might have relied solely upon highly developed varieties of sulphonamides or similar, synthetic, non-antibiotic antibacterial agents.

The distribution of 14C-chitosan by different molecular weight in mice

International Nuclear Information System (INIS)

Kim, Kwang Yoon; Kim, Young Ho; Bom, Hee Seung; Kim, Ji Yeul; Kim, Hee Kyung; Roh, Young Bok; Nishimura, Yoshikazu

1998-01-01

Chitosan is a nontoxic natural chealtor which was made by chitin, and reduced a contamination of radiostrontium in animals. In this experiment, a different molecular weight of C-14 chitosan was intravenously administered to mice, and then the distribution of C-14 chitosan in the body was observed. Male mice (8 to 10 weeks, body weight of 30 to 35g) of ICR strain were used. C-14 chitosan, mice was sacrificed at the 6th hour, 1st, 3rd, 5th, and 7th day. Beta radioactivities in the blood, liver, kidney, liver, muscle, testis, and urine was measured using a liquid scintillation analyzer. Most of the C-14 chitosan was excreted through urine within 6 hours. Biodistribution of C-14 chitosan was similar despite the difference of molecular weight. Higher distributions of radioactivities were found in the liver, kidney, spleen. The relative concentration in tissue increased for the 6 hours and then decreased. In conclusion, most of C-14 chitosan was excreted through urine despite the difference of molecular weight. and, low molecular weight of C-14 chitosan showed higher distribution than high molecular weight of C-14 chitosan in tissues

Molecular simulations in electrochemistry : Electron and proton transfer reactions mediated by flavins in different molecular environments

NARCIS (Netherlands)

Kılıç, M.

2014-01-01

The aim of this thesis is to address specific questions about the role of solvent reorganization on electron transfer in different environments and about the calculation of acidity constant, as well. Particularly, we focus on molecular simulation of flavin in water and different protein (BLUF and

Development of PNTDs synthesized from monomers with different molecular length and analysis of molecular damages by heavy ion

International Nuclear Information System (INIS)

Kawashima, Hajime; Kodaira, Satoshi; Ihara, Daisuke; Yasuda, Nakahiro; Kusumoto, Tamon; Mori, Yutaka; Yamauchi, Tomoya; Kobayashi, Keiichi; Benton, Eric

2017-01-01

Our interests for years lay to investigate the reason why CR-39 polymer has such high sensitivity as plastic nuclear track detector (PNTD) on chemical structural aspects. We developed three PNTDs from three diacrylate compounds as monomers bearing different molecular length as well as different numbers of internal ether bonds. The polymer products obtained were colorless and transparent with 3-D molecular structures as CR-39 and different lattice structures each other. Our purpose of the current study was to investigate structural damages caused in newly prepared PNTDs and CR-39 by irradiation of Nitrogen ion (6 MeV/n, fluence of 5 x 10 11 cm -2 ). The structural damage by irradiation was analyzed by the magnitude of the relative absorbance of specific functional groups such as ester, C=O, ether and C-H bonds by means of FT-IR (ATR) method. The correlation between the relative absorbance and the molecular length of the monomers were discussed. (author)

Discovering a misaligned CO outflow related to the red MSX source G034.5964-01.0292

Science.gov (United States)

Paron, S.; Ortega, M. E.; Petriella, A.; Rubio, M.

2014-07-01

Aims: The red MSX source G034.5964-01.0292 (MSXG34), catalogued as a massive young stellar object, was observed in molecular lines with the aim of discovering and studying molecular outflows. Methods: We mapped a region of 3'× 3' centred at MSXG34 using the Atacama Submillimeter Telescope Experiment in the 12CO J = 3-2 and HCO+J = 4-3 lines with an angular and spectral resolution of 22'' and 0.11 km s-1. Additionally, public 13CO J = 1-0 and near-IR UKIDSS data obtained from the Galactic Ring Survey and the WFCAM Sciencie Archive were analysed. Results: We found that the 12CO spectra towards the YSO present a self-absorption dip, as is common in star-forming regions, and spectral wings that indicate outflow activity. The HCO+ was detected only towards the MSXG34 position at vLSR ~ 14.2 km s-1, in coincidence with the 12CO absorption dip and approximately with the velocity of previous ammonia observations. HCO+ and NH3 are known to be enhanced in molecular outflows. When we analysed the spectral wings of the 12CO line, we discovered misaligned red- and blue-shifted molecular outflows associated with MSXG34. The near-IR emission shows a cone-like nebulosity composed of two arc-like features related to the YSO, which might be due to a cavity cleared in the circumstellar material by a precessing jet. This can explain the misalignment in the molecular outflows. From the analysis of the 13CO J = 1-0 data we suggest that the YSO is very likely related to a molecular clump ranging between 10 and 14 km s-1. This suggests that MSXG34, with an associated central velocity of about 14 km s-1, may be located in the background of this clump. Thus, the blue-shifted outflow is probably deflected by the interaction with dense gas along the line of sight. From a spectral energy distribution analysis of MSXG34 we found that its central object probably is an intermediate-mass protostar.

Discovering workflow nets using integer linear programming

NARCIS (Netherlands)

van Zelst, S.J.; van Dongen, B.F.; van der Aalst, W.M.P.; Verbeek, H.M.W.

Process mining is concerned with the analysis, understanding and improvement of business processes. Process discovery, i.e. discovering a process model based on an event log, is considered the most challenging process mining task. State-of-the-art process discovery algorithms only discover local

Radiodegradation process in PVDF with different molecular weight

International Nuclear Information System (INIS)

Silva, L.; Batista, A.S.M.; Nascimento, J.P.; Furtado, C.A.; Faria, L.O.

2017-01-01

Poly(vinylidene fluoride) (PVDF) is a semi-crystalline polymer with several industrial applications due to its mechanical, ferroelectric and biocompatibility properties. Due to the particularity of some of its applications this polymer is exposed to high energy radiation, for example in the aerospace industry and with biomaterial, in sterilization processes. In this sense it is of interest studies that evaluate the radiodegradation of this material, as a way to predict its mechanical behavior after processes of exposure to gamma radiation. In this study the radioresistance of PVDF with different molecular weights is evaluated, considering that large molecular chains can provide greater resistance than smaller chains. Method: PVDF samples with different molecular weights were produced by the solvent dilution process. They were irradiated with gamma doses of 100, 300, 500, 1000 and 2000 kGy with a source of cobalt in the Laboratório de Irradiação Gama (LIG) of the Centro de Desenvolvimento da Tecnologia Nuclear (CDTN). FTIR, UV-Vis, DSC and XRD analyzes were used to evaluate the induced radiodegradation processes immediately after irradiation and one month later. Results: The FTIR and UV-Vis analyzes showed formation of unsaturations in the polymer chains. The DSC technique showed a drop in the crystalline fraction of the polymer confirmed by the XRD technique. Conclusion: Post-irradiation sample evaluations are discussed in terms of the effect of high energy ionizing radiation on polymeric mate-rials for industrial and biomedical use for safety in quality assurance and performance in service. (author)

Radiodegradation process in PVDF with different molecular weight

Energy Technology Data Exchange (ETDEWEB)

Silva, L.; Batista, A.S.M., E-mail: adriananuclear@yahoo.com.br [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil); Nascimento, J.P.; Furtado, C.A.; Faria, L.O. [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)

2017-07-01

Poly(vinylidene fluoride) (PVDF) is a semi-crystalline polymer with several industrial applications due to its mechanical, ferroelectric and biocompatibility properties. Due to the particularity of some of its applications this polymer is exposed to high energy radiation, for example in the aerospace industry and with biomaterial, in sterilization processes. In this sense it is of interest studies that evaluate the radiodegradation of this material, as a way to predict its mechanical behavior after processes of exposure to gamma radiation. In this study the radioresistance of PVDF with different molecular weights is evaluated, considering that large molecular chains can provide greater resistance than smaller chains. Method: PVDF samples with different molecular weights were produced by the solvent dilution process. They were irradiated with gamma doses of 100, 300, 500, 1000 and 2000 kGy with a source of cobalt in the Laboratório de Irradiação Gama (LIG) of the Centro de Desenvolvimento da Tecnologia Nuclear (CDTN). FTIR, UV-Vis, DSC and XRD analyzes were used to evaluate the induced radiodegradation processes immediately after irradiation and one month later. Results: The FTIR and UV-Vis analyzes showed formation of unsaturations in the polymer chains. The DSC technique showed a drop in the crystalline fraction of the polymer confirmed by the XRD technique. Conclusion: Post-irradiation sample evaluations are discussed in terms of the effect of high energy ionizing radiation on polymeric mate-rials for industrial and biomedical use for safety in quality assurance and performance in service. (author)

Discovering Wavelets

CERN Document Server

Aboufadel, Edward

1999-01-01

An accessible and practical introduction to wavelets. With applications in image processing, audio restoration, seismology, and elsewhere, wavelets have been the subject of growing excitement and interest over the past several years. Unfortunately, most books on wavelets are accessible primarily to research mathematicians. Discovering Wavelets presents basic and advanced concepts of wavelets in a way that is accessible to anyone with only a fundamental knowledge of linear algebra. The basic concepts of wavelet theory are introduced in the context of an explanation of how the FBI uses wavelets

Discovering frequently recurring movement sequences in team-sport athlete spatiotemporal data.

Science.gov (United States)

Sweeting, Alice J; Aughey, Robert J; Cormack, Stuart J; Morgan, Stuart

2017-12-01

Athlete external load is typically analysed from predetermined movement thresholds. The combination of movement sequences and differences in these movements between playing positions is also currently unknown. This study developed a method to discover the frequently recurring movement sequences across playing position during matches. The external load of 12 international female netball athletes was collected by a local positioning system during four national-level matches. Velocity, acceleration and angular velocity were calculated from positional (X, Y) data, clustered via one-dimensional k-means and assigned a unique alphabetic label. Combinations of velocity, acceleration and angular velocity movement were compared using the Levenshtein distance and similarities computed by the longest common substring problem. The contribution of each movement sequence, according to playing position and relative to the wider data set, was then calculated via the Minkowski distance. A total of 10 frequently recurring combinations of movement were discovered, regardless of playing position. Only the wing attack, goal attack and goal defence playing positions are closely related. We developed a technique to discover the movement sequences, according to playing position, performed by elite netballers. This methodology can be extended to discover the frequently recurring movements within other team sports and across levels of competition.

Multi-Scale Molecular Deconstruction of the Serotonin Neuron System.

Science.gov (United States)

Okaty, Benjamin W; Freret, Morgan E; Rood, Benjamin D; Brust, Rachael D; Hennessy, Morgan L; deBairos, Danielle; Kim, Jun Chul; Cook, Melloni N; Dymecki, Susan M

2015-11-18

Serotonergic (5HT) neurons modulate diverse behaviors and physiology and are implicated in distinct clinical disorders. Corresponding diversity in 5HT neuronal phenotypes is becoming apparent and is likely rooted in molecular differences, yet a comprehensive approach characterizing molecular variation across the 5HT system is lacking, as is concomitant linkage to cellular phenotypes. Here we combine intersectional fate mapping, neuron sorting, and genome-wide RNA-seq to deconstruct the mouse 5HT system at multiple levels of granularity-from anatomy, to genetic sublineages, to single neurons. Our unbiased analyses reveal principles underlying system organization, 5HT neuron subtypes, constellations of differentially expressed genes distinguishing subtypes, and predictions of subtype-specific functions. Using electrophysiology, subtype-specific neuron silencing, and conditional gene knockout, we show that these molecularly defined 5HT neuron subtypes are functionally distinct. Collectively, this resource classifies molecular diversity across the 5HT system and discovers sertonergic subtypes, markers, organizing principles, and subtype-specific functions with potential disease relevance. Copyright © 2015 Elsevier Inc. All rights reserved.

Caught in the act: discovering secreted proteins from fungi and oomycetes in action

DEFF Research Database (Denmark)

Roth, Doris; Grell, Morten Nedergaard; Jensen, Annette Bruun

Host-microbe relationships largely rely on secreted proteins like enzymes, virulence factors and antimicrobial peptides. To discover proteins secreted by microbe and host during the interaction with each other, we produced dual-organism cDNA libraries from three different fungus- or oomycete-infe......, by applying a similar strategy with a fungus-only library. As a result, we will show that our approach is widely applicable and allows us to deepen the understanding a variety of different host-microbe systems.......Host-microbe relationships largely rely on secreted proteins like enzymes, virulence factors and antimicrobial peptides. To discover proteins secreted by microbe and host during the interaction with each other, we produced dual-organism cDNA libraries from three different fungus- or oomycete...

Learning Faster by Discovering and Exploiting Object Similarities

Directory of Open Access Journals (Sweden)

Tadej Janež

2013-03-01

Full Text Available In this paper we explore the question: “Is it possible to speed up the learning process of an autonomous agent by performing experiments in a more complex environment (i.e., an environment with a greater number of different objects?” To this end, we use a simple robotic domain, where the robot has to learn a qualitative model predicting the change in the robot's distance to an object. To quantify the environment's complexity, we defined cardinal complexity as the number of objects in the robot's world, and behavioural complexity as the number of objects' distinct behaviours. We propose Error reduction merging (ERM, a new learning method that automatically discovers similarities in the structure of the agent's environment. ERM identifies different types of objects solely from the data measured and merges the observations of objects that behave in the same or similar way in order to speed up the agent's learning. We performed a series of experiments in worlds of increasing complexity. The results in our simple domain indicate that ERM was capable of discovering structural similarities in the data which indeed made the learning faster, clearly superior to conventional learning. This observed trend occurred with various machine learning algorithms used inside the ERM method.

Discovering and Exploring State-based Models for Multi-perspective Processes

NARCIS (Netherlands)

van Eck, M.L.; Sidorova, N.; van der Aalst, W.M.P.; La Rosa, M.; Loos, P.; Pastor, O.

2016-01-01

Process mining provides fact-based insights into process behaviour captured in event data. In this work we aim to discover models for processes where different facets, or perspectives, of the process can be identified. Instead of focussing on the events or activities that are executed in the context

Molecular selectivity of graphene-enhanced Raman scattering.

Science.gov (United States)

Huang, Shengxi; Ling, Xi; Liang, Liangbo; Song, Yi; Fang, Wenjing; Zhang, Jin; Kong, Jing; Meunier, Vincent; Dresselhaus, Mildred S

2015-05-13

Graphene-enhanced Raman scattering (GERS) is a recently discovered Raman enhancement phenomenon that uses graphene as the substrate for Raman enhancement and can produce clean and reproducible Raman signals of molecules with increased signal intensity. Compared to conventional Raman enhancement techniques, such as surface-enhanced Raman scattering (SERS) and tip-enhanced Raman scattering (TERS), in which the Raman enhancement is essentially due to the electromagnetic mechanism, GERS mainly relies on a chemical mechanism and therefore shows unique molecular selectivity. In this paper, we report graphene-enhanced Raman scattering of a variety of different molecules with different molecular properties. We report a strong molecular selectivity for the GERS effect with enhancement factors varying by as much as 2 orders of magnitude for different molecules. Selection rules are discussed with reference to two main features of the molecule, namely its molecular energy levels and molecular structures. In particular, the enhancement factor involving molecular energy levels requires the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies to be within a suitable range with respect to graphene's Fermi level, and this enhancement effect can be explained by the time-dependent perturbation theory of Raman scattering. The enhancement factor involving the choice of molecular structures indicates that molecular symmetry and substituents similar to that of the graphene structure are found to be favorable for GERS enhancement. The effectiveness of these factors can be explained by group theory and the charge-transfer interaction between molecules and graphene. Both factors, involving the molecular energy levels and structural symmetry of the molecules, suggest that a remarkable GERS enhancement requires strong molecule-graphene coupling and thus effective charge transfer between the molecules and graphene. These conclusions are further

Distinct molecular features of different macroscopic subtypes of colorectal neoplasms.

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Kenichi Konda

Full Text Available Colorectal adenoma develops into cancer with the accumulation of genetic and epigenetic changes. We studied the underlying molecular and clinicopathological features to better understand the heterogeneity of colorectal neoplasms (CRNs.We evaluated both genetic (mutations of KRAS, BRAF, TP53, and PIK3CA, and microsatellite instability [MSI] and epigenetic (methylation status of nine genes or sequences, including the CpG island methylator phenotype [CIMP] markers alterations in 158 CRNs including 56 polypoid neoplasms (PNs, 25 granular type laterally spreading tumors (LST-Gs, 48 non-granular type LSTs (LST-NGs, 19 depressed neoplasms (DNs and 10 small flat-elevated neoplasms (S-FNs on the basis of macroscopic appearance.S-FNs showed few molecular changes except SFRP1 methylation. Significant differences in the frequency of KRAS mutations were observed among subtypes (68% for LST-Gs, 36% for PNs, 16% for DNs and 6% for LST-NGs (P<0.001. By contrast, the frequency of TP53 mutation was higher in DNs than PNs or LST-Gs (32% vs. 5% or 0%, respectively (P<0.007. We also observed significant differences in the frequency of CIMP between LST-Gs and LST-NGs or PNs (32% vs. 6% or 5%, respectively (P<0.005. Moreover, the methylation level of LINE-1 was significantly lower in DNs or LST-Gs than in PNs (58.3% or 60.5% vs. 63.2%, P<0.05. PIK3CA mutations were detected only in LSTs. Finally, multivariate analyses showed that macroscopic morphologies were significantly associated with an increased risk of molecular changes (PN or LST-G for KRAS mutation, odds ratio [OR] 9.11; LST-NG or DN for TP53 mutation, OR 5.30; LST-G for PIK3CA mutation, OR 26.53; LST-G or DN for LINE-1 hypomethylation, OR 3.41.We demonstrated that CRNs could be classified into five macroscopic subtypes according to clinicopathological and molecular differences, suggesting that different mechanisms are involved in the pathogenesis of colorectal tumorigenesis.

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

International Nuclear Information System (INIS)

Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

2013-01-01

Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts

Providing a New Model for Discovering Cloud Services Based on Ontology

Directory of Open Access Journals (Sweden)

B. Heydari

2017-12-01

Full Text Available Due to its efficient, flexible, and dynamic substructure in information technology and service quality parameters estimation, cloud computing has become one of the most important issues in computer world. Discovering cloud services has been posed as a fundamental issue in reaching out high efficiency. In order to do one’s own operations in cloud space, any user needs to request several various services either simultaneously or according to a working routine. These services can be presented by different cloud producers or different decision-making policies. Therefore, service management is one of the important and challenging issues in cloud computing. With the advent of semantic web and practical services accordingly in cloud computing space, access to different kinds of applications has become possible. Ontology is the core of semantic web and can be used to ease the process of discovering services. A new model based on ontology has been proposed in this paper. The results indicate that the proposed model has explored cloud services based on user search results in lesser time compared to other models.

Metagenomic approach for discovering new pathogens in infection disease outbreaks

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Emanuela Giombini

2011-09-01

Full Text Available Viruses represent the most abundant biological components on earth.They can be found in every environment, from deep layers of oceans to animal bodies.Although several viruses have been isolated and sequenced, in each environment there are millions of different types of viruses that have not been identified yet.The advent of nextgeneration sequencing technologies with their high throughput capabilities make possible to study in a single experiment all the community of microorganisms present in a particular sample “microbioma”.They made more feasible the application of the metagenomic approach, by which it is also possible to discover and identify new pathogens, that may pose a threat to public health.This paper summarizes the most recent applications of nextgeneration sequencing to discover new viral pathogens during the occurrence of infection disease outbreaks.

A concurrent multiscale micromorphic molecular dynamics

International Nuclear Information System (INIS)

Li, Shaofan; Tong, Qi

2015-01-01

In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation

Molecular and functional definition of the developing human striatum.

Science.gov (United States)

Onorati, Marco; Castiglioni, Valentina; Biasci, Daniele; Cesana, Elisabetta; Menon, Ramesh; Vuono, Romina; Talpo, Francesca; Laguna Goya, Rocio; Lyons, Paul A; Bulfamante, Gaetano P; Muzio, Luca; Martino, Gianvito; Toselli, Mauro; Farina, Cinthia; Barker, Roger A; Biella, Gerardo; Cattaneo, Elena

2014-12-01

The complexity of the human brain derives from the intricate interplay of molecular instructions during development. Here we systematically investigated gene expression changes in the prenatal human striatum and cerebral cortex during development from post-conception weeks 2 to 20. We identified tissue-specific gene coexpression networks, differentially expressed genes and a minimal set of bimodal genes, including those encoding transcription factors, that distinguished striatal from neocortical identities. Unexpected differences from mouse striatal development were discovered. We monitored 36 determinants at the protein level, revealing regional domains of expression and their refinement, during striatal development. We electrophysiologically profiled human striatal neurons differentiated in vitro and determined their refined molecular and functional properties. These results provide a resource and opportunity to gain global understanding of how transcriptional and functional processes converge to specify human striatal and neocortical neurons during development.

Growth response of microorganisms to different molecular fractions of lignite

Energy Technology Data Exchange (ETDEWEB)

Polman, J.K.; Breckenridge, C.R.; Dugan, P.R.; Quigley, D.R.

1990-01-01

Our research is primarily concerned with isolating and characterizing microbes which are able to dissimilate coal and convert it to other useful chemicals. This quarter, general growth responses of microorganisms cultivated in the presence of different molecular weight fractions of lignite coal were examined. Aerobic and anaerobic environmental samples from a variety of ecological niches were used as inocula. Growth of the microorganisms in these samples on the following types of media was tested: COAL medium, containing alkali-solubilized whole coal; THFI medium, containing the alkali-solubilized, tetrahydrofuran-insoluble, macromolecular portion of whole coal; THFS medium, containing the THF-soluble, low molecular weight portion of whole coal; and CON medium, void of any coal constituent. Overall results indicated that the presence of the THF-soluble, low molecular weight coal fraction enhanced the growth yield and the variety of aerobic microorganisms compared to the other coal fractions or the control medium. Conversely, anaerobic microbes grew best on media which contained the macromolecular fraction. 12 refs., 5 tabs.

Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma

Science.gov (United States)

2013-01-01

Background Differential gene expression (DGE) analysis is commonly used to reveal the deregulated molecular mechanisms of complex diseases. However, traditional DGE analysis (e.g., the t test or the rank sum test) tests each gene independently without considering interactions between them. Top-ranked differentially regulated genes prioritized by the analysis may not directly relate to the coherent molecular changes underlying complex diseases. Joint analyses of co-expression and DGE have been applied to reveal the deregulated molecular modules underlying complex diseases. Most of these methods consist of separate steps: first to identify gene-gene relationships under the studied phenotype then to integrate them with gene expression changes for prioritizing signature genes, or vice versa. It is warrant a method that can simultaneously consider gene-gene co-expression strength and corresponding expression level changes so that both types of information can be leveraged optimally. Results In this paper, we develop a gene module based method for differential gene expression analysis, named network-based differential gene expression (nDGE) analysis, a one-step integrative process for prioritizing deregulated genes and grouping them into gene modules. We demonstrate that nDGE outperforms existing methods in prioritizing deregulated genes and discovering deregulated gene modules using simulated data sets. When tested on a series of smoker and non-smoker lung adenocarcinoma data sets, we show that top differentially regulated genes identified by the rank sum test in different sets are not consistent while top ranked genes defined by nDGE in different data sets significantly overlap. nDGE results suggest that a differentially regulated gene module, which is enriched for cell cycle related genes and E2F1 targeted genes, plays a role in the molecular differences between smoker and non-smoker lung adenocarcinoma. Conclusions In this paper, we develop nDGE to prioritize

Proton transport properties of poly(aspartic acid) with different average molecular weights

Energy Technology Data Exchange (ETDEWEB)

Nagao, Yuki, E-mail: ynagao@kuchem.kyoto-u.ac.j [Department of Mechanical Systems and Design, Graduate School of Engineering, Tohoku University, 6-6-01 Aoba Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Imai, Yuzuru [Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-cho, Aoba-ku, Sendai 980-8575 (Japan); Matsui, Jun [Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan); Ogawa, Tomoyuki [Department of Electronic Engineering, Graduate School of Engineering, Tohoku University, 6-6-05 Aoba Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Miyashita, Tokuji [Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan)

2011-04-15

Research highlights: Seven polymers with different average molecular weights were synthesized. The proton conductivity depended on the number-average degree of polymerization. The difference of the proton conductivities was more than one order of magnitude. The number-average molecular weight contributed to the stability of the polymer. - Abstract: We synthesized seven partially protonated poly(aspartic acids)/sodium polyaspartates (P-Asp) with different average molecular weights to study their proton transport properties. The number-average degree of polymerization (DP) for each P-Asp was 30 (P-Asp30), 115 (P-Asp115), 140 (P-Asp140), 160 (P-Asp160), 185 (P-Asp185), 205 (P-Asp205), and 250 (P-Asp250). The proton conductivity depended on the number-average DP. The maximum and minimum proton conductivities under a relative humidity of 70% and 298 K were 1.7 . 10{sup -3} S cm{sup -1} (P-Asp140) and 4.6 . 10{sup -4} S cm{sup -1} (P-Asp250), respectively. Differential thermogravimetric analysis (TG-DTA) was carried out for each P-Asp. The results were classified into two categories. One exhibited two endothermic peaks between t = (270 and 300) {sup o}C, the other exhibited only one peak. The P-Asp group with two endothermic peaks exhibited high proton conductivity. The high proton conductivity is related to the stability of the polymer. The number-average molecular weight also contributed to the stability of the polymer.

Molecular machines with bio-inspired mechanisms.

Science.gov (United States)

Zhang, Liang; Marcos, Vanesa; Leigh, David A

2018-02-26

The widespread use of molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular machines-which by and large function as switches-and the machines of the macroscopic world, which utilize the synchronized behavior of integrated components to perform more sophisticated tasks than is possible with any individual switch. Should we try to make molecular machines of greater complexity by trying to mimic machines from the macroscopic world or instead apply unfamiliar (and no doubt have to discover or invent currently unknown) mechanisms utilized by biological machines? Here we try to answer that question by exploring some of the advances made to date using bio-inspired machine mechanisms.

Effect of torsion angle on electronic transport through different anchoring groups in molecular junction

International Nuclear Information System (INIS)

Xia Caijuan; Fang Changfeng; Zhao Peng; Xie Shijie; Liu Desheng

2009-01-01

By applying nonequilibrium Green's function formalism combined with first-principles density functional theory, we investigate effect of torsion angle on electronic transport properties of 4,4 ' -biphenyl molecule connected with different anchoring groups (dithiocarboxylate and thiol group) to Au(111) electrodes. The influence of the HOMO-LUMO gaps and the spatial distributions of molecular orbitals on the quantum transport through the molecular device are discussed. Theoretical results show that the torsion angle plays important role in conducting behavior of molecular devices. By changing the torsion angle between two phenyl rings, namely changing the magnitude of the intermolecular coupling effect, a different transport behavior can be observed in these two systems.

Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.

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Judith Somekh

2012-12-01

Full Text Available We propose a Conceptual Model-based Systems Biology framework for qualitative modeling, executing, and eliciting knowledge gaps in molecular biology systems. The framework is an adaptation of Object-Process Methodology (OPM, a graphical and textual executable modeling language. OPM enables concurrent representation of the system's structure-the objects that comprise the system, and behavior-how processes transform objects over time. Applying a top-down approach of recursively zooming into processes, we model a case in point-the mRNA transcription cycle. Starting with this high level cell function, we model increasingly detailed processes along with participating objects. Our modeling approach is capable of modeling molecular processes such as complex formation, localization and trafficking, molecular binding, enzymatic stimulation, and environmental intervention. At the lowest level, similar to the Gene Ontology, all biological processes boil down to three basic molecular functions: catalysis, binding/dissociation, and transporting. During modeling and execution of the mRNA transcription model, we discovered knowledge gaps, which we present and classify into various types. We also show how model execution enhances a coherent model construction. Identification and pinpointing knowledge gaps is an important feature of the framework, as it suggests where research should focus and whether conjectures about uncertain mechanisms fit into the already verified model.

Exploring RNA structure by integrative molecular modelling

DEFF Research Database (Denmark)

Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice

2010-01-01

RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based...... on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...

SMART design to control over conformation and molecular packing in blue luminescent oligofluorenes

Science.gov (United States)

Yu, Meng-Na; Ou, Chang-Jin; Liu, Bin; Xie, Ling-Hai; Lin, Jin-Yi; Wang, Sha-Sha; Wei, Ying; Huang, Wei

2018-01-01

The uncertainty evolution of conformation and molecular packing from solution to film is key challenge for the repeatability of procedures in organic optoelectronics. Herein, we observed the noncovalent force at the bulky groups to decode the supramolecular steric hindrance (SSH) effect and to propose synergistically molecular attractor-repulsor theory (SMART). The fine difference between ideal and real bulks were described and the SSH effect have been proved by two comparable stat-of-the-art models. The SMART design guide us to discover blue oligo/polydiarylfluorenes with beta phase as well as nanosheets with the paradigm of Interdigital Lipid Bilayer-like (ILB) mode. SMART address one kind of AR molecules with potential controllable behaviors. The design of bulk-withdraw and bulk-rich will exhibit the unreplaceable role in morphology-directed design that is just like the role of donor-acceptor molecular design of organic polymer semiconductors.

Molecular nature of alpha-globin genes in the Saudi population

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J. Francis Borgio

2015-11-01

Full Text Available Alpha-thalassemia (α-thal is a disorder caused by the deletion of single or double α-globin genes, and/or point mutations in the α-globin genes. There are 2 common types of α-globin genes; HBA2 and HBA1. Recently, it has been discovered that the HBA2 gene is replaced by a unique HBA12 gene convert in 5.7% of the Saudi population. The α-globin genes have been emerging as a molecular target for the treatment of β-thalassemia (β-thal. Hence, it is essential to understand the molecular nature of α-globin genes to treat the most prevalent hemoglobin disorders, such as sickle cell disease, α-thal, and β-thal prevalent in the Kingdom of Saudi Arabia. Thirty-two different α-globin genotypes have been observed in the Saudi population. This review outlines the classification of the α-globin genes on the basis of their molecular nature and complex combinations of α-globin genes, and their variants predominant in Saudis.

Molecular Genotype Identification of Different Chickens: Major Histocompatibility Complex

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Hongzhi Wang

2014-09-01

Full Text Available Chicken is a main poultry in China. Molecular breeding for disease resistance plays an important role in the control of diseases, especially infectious diseases. Choice of genes for disease resistance is the key technology of molecular breeding. The major histocompatibility complex (MHC is of great interest to poultry breeding scientists for its extraordinary polymorphism and close relation with traits of resistance against infectious diseases. The MHC-B haplotype plays an important role in the study of disease resistance in chicken. The traditional chicken MHC-B haplotype is commonly defined by serologic reactions of erythrocytes and the majority of studies have been conducted in Leghorn and broiler but study about other chicken breeds is little. In this study, firstly, the microsatellite marker LEI0258 which is located within the MHC was sequenced by using target sequence capture assay in different chicken breeds, and then according to the number of repeated structures and polymorphic sequences in microsatellite, sequence information for the region defined by LEI0258 was obtained for different haplotypes. Afterwards, we identified the relation between MHC-B haplotypes and disease resistance. Collectively, these observed results provided the reference data for disease-resistant breeding association with blood type and for further study of MHC gene function in poultry.

Nitroproteins in Human Astrocytomas Discovered by Gel Electrophoresis and Tandem Mass Spectrometry

Science.gov (United States)

Peng, Fang; Li, Jianglin; Guo, Tianyao; Yang, Haiyan; Li, Maoyu; Sang, Shushan; Li, Xuejun; Desiderio, Dominic M.; Zhan, Xianquan

2015-12-01

Protein tyrosine nitration is involved in the pathogenesis of highly fatal astrocytomas, a type of brain cancer. To understand the molecular mechanisms of astrocytomas and to discover new biomarkers/therapeutic targets, we sought to identify nitroproteins in human astrocytoma tissue. Anti-nitrotyrosine immunoreaction-positive proteins from a high-grade astrocytoma tissue were detected with two-dimensional gel electrophoresis (2DGE)-based nitrotyrosine immunoblots, and identified with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Fifty-seven nitrotyrosine immunopositive protein spots were detected. A total of 870 proteins (nitrated and non-nitrated) in nitrotyrosine-immunopositive 2D gel spots were identified, and 18 nitroproteins and their 20 nitrotyrosine sites were identified with MS/MS analysis. These nitroproteins participate in multiple processes, including drug-resistance, signal transduction, cytoskeleton, transcription and translation, cell proliferation and apoptosis, immune response, phenotypic dedifferentiation, cell migration, and metastasis. Among those nitroproteins that might play a role in astrocytomas was nitro-sorcin, which is involved in drug resistance and metastasis and might play a role in the spread and treatment of an astrocytoma. Semiquantitative immune-based measurements of different sorcin expressions were found among different grades of astrocytomas relative to controls, and a semiquantitative increased nitration level in high-grade astrocytoma relative to control. Nitro-β-tubulin functions in cytoskeleton and cell migration. Semiquantitative immunoreactivity of β-tubulin showed increased expression among different grades of astrocytomas relative to controls and semiquantitatively increased nitration level in high-grade astrocytoma relative to control. Each nitroprotein was rationalized and related to the corresponding functional system to provide new insights into tyrosine nitration and its potential role in the

Medulloblastoma: Molecular Genetics and Animal Models

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Corey Raffel

2004-07-01

Full Text Available Medulloblastoma is a primary brain tumor found in the cerebellum of children. The tumor occurs in association with two inherited cancer syndromes: Turcot syndrome and Gorlin syndrome. Insights into the molecular biology of the tumor have come from looking at alterations in the genes altered in these syndromes, PTC and APC, respectively. Murine models of medulloblastoma have been constructed based on these alterations. Additional murine models that, while mimicking the appearance of the human tumor, seem unrelated to the human tumor's molecular alterations have been made. In this review, the clinical picture, origin, molecular biology, murine models of medulloblastoma are discussed. Although a great deal has been discovered about this tumor, the genetic alterations responsible for tumor development in a majority of patients have yet to be described.

Molecular type channeling of relativistic electrons in crystals

International Nuclear Information System (INIS)

Vyatkin, E.G.; Filimonov, Yu.M.; Taratin, A.M.; Vorobiev, S.A.

1983-01-01

Channeling of relativistic electrons in direction in a diamond crystal and the channeling radiation spectra are investigated using computer simulation by the binary collision model and using the model of a continuum potential of the atomic rows. In a computer experiment the atomic- and molecular-type states of channeled elcetrons are revealed, and the orientational dependence of the electron trapping probability in these states is obtained. The peculiarities revealed of the angular distributions and radiation spectra of electrons in the molecular-type states allow to discover these states in the experiment. (author)

Lung eQTLs to Help Reveal the Molecular Underpinnings of Asthma

NARCIS (Netherlands)

Hao, Ke; Bosse, Yohan; Nickle, David C.; Pare, Peter D.; Postma, Dirkje S.; Laviolette, Michel; Sandford, Andrew; Hackett, Tillie L.; Daley, Denise; Hogg, James C.; Elliott, W. Mark; Couture, Christian; Lamontagne, Maxime; Brandsma, Corry-Anke; van den Berge, Maarten; Koppelman, Gerard; Reicin, Alise S.; Nicholson, Donald W.; Malkov, Vladislav; Derry, Jonathan M.; Suver, Christine; Tsou, Jeffrey A.; Kulkarni, Amit; Zhang, Chunsheng; Vessey, Rupert; Opiteck, Greg J.; Curtis, Sean P.; Timens, Wim; Sin, Don D.

2012-01-01

Genome-wide association studies (GWAS) have identified loci reproducibly associated with pulmonary diseases; however, the molecular mechanism underlying these associations are largely unknown. The objectives of this study were to discover genetic variants affecting gene expression in human lung

Time Domains of the Hypoxic Ventilatory Response and Their Molecular Basis

Science.gov (United States)

Pamenter, Matthew E.; Powell, Frank L.

2016-01-01

Ventilatory responses to hypoxia vary widely depending on the pattern and length of hypoxic exposure. Acute, prolonged, or intermittent hypoxic episodes can increase or decrease breathing for seconds to years, both during the hypoxic stimulus, and also after its removal. These myriad effects are the result of a complicated web of molecular interactions that underlie plasticity in the respiratory control reflex circuits and ultimately control the physiology of breathing in hypoxia. Since the time domains of the physiological hypoxic ventilatory response (HVR) were identified, considerable research effort has gone toward elucidating the underlying molecular mechanisms that mediate these varied responses. This research has begun to describe complicated and plastic interactions in the relay circuits between the peripheral chemoreceptors and the ventilatory control circuits within the central nervous system. Intriguingly, many of these molecular pathways seem to share key components between the different time domains, suggesting that varied physiological HVRs are the result of specific modifications to overlapping pathways. This review highlights what has been discovered regarding the cell and molecular level control of the time domains of the HVR, and highlights key areas where further research is required. Understanding the molecular control of ventilation in hypoxia has important implications for basic physiology and is emerging as an important component of several clinical fields. PMID:27347896

Photocuring of stimulus responsive membranes for controlled-release of drugs having different molecular weights

International Nuclear Information System (INIS)

Ng, Loo-Teck; Nakayama, Hiroshi; Kaetsu, Isao; Uchida, Kumao

2005-01-01

Intelligent drug delivery membranes were prepared by photocuring poly(acrylic acid) coatings onto poly(2-hydroxyethyl methacrylate) membranes each with model drugs of different molecular weights being incorporated. pH-responsive release behaviours of the model drugs which included sodium salicylate, nicotinamide, nicotinic acid, methylene blue, brilliant green and crystal violet were investigated. Only the membrane with methylene blue incorporated showed a clear pH-responsive release and other drug-incorporated membranes showed no intelligent behaviour. These phenomena were explained in terms of the difference in diffusivity of drugs through polymer matrices of the membranes attributable to the difference in the molecular weights of drugs

Photocuring of stimulus responsive membranes for controlled-release of drugs having different molecular weights

Energy Technology Data Exchange (ETDEWEB)

Ng, Loo-Teck [School of Science, Food and Horticulture, University of Western Sydney, Locked bag 1797, Penrith South DC, NSW 1797 (Australia)]. E-mail: l.ng@uws.edu.au; Nakayama, Hiroshi [Department of Nuclear Engineering, Faculty of Science and technology, Kinki University, Kowakae, 3-4-1, Higashi-Osaka 577-8502 (Japan); Kaetsu, Isao [Department of Nuclear Engineering, Faculty of Science and technology, Kinki University, Kowakae, 3-4-1, Higashi-Osaka 577-8502 (Japan)]. E-mail: kaetsu@ned.kindai.ac.jp; Uchida, Kumao [Department of Nuclear Engineering, Faculty of Science and technology, Kinki University, Kowakae, 3-4-1, Higashi-Osaka 577-8502 (Japan)

2005-06-01

Intelligent drug delivery membranes were prepared by photocuring poly(acrylic acid) coatings onto poly(2-hydroxyethyl methacrylate) membranes each with model drugs of different molecular weights being incorporated. pH-responsive release behaviours of the model drugs which included sodium salicylate, nicotinamide, nicotinic acid, methylene blue, brilliant green and crystal violet were investigated. Only the membrane with methylene blue incorporated showed a clear pH-responsive release and other drug-incorporated membranes showed no intelligent behaviour. These phenomena were explained in terms of the difference in diffusivity of drugs through polymer matrices of the membranes attributable to the difference in the molecular weights of drugs.

Decision mining revisited - Discovering overlapping rules

NARCIS (Netherlands)

Mannhardt, Felix; De Leoni, Massimiliano; Reijers, Hajo A.; Van Der Aalst, Wil M P

2016-01-01

Decision mining enriches process models with rules underlying decisions in processes using historical process execution data. Choices between multiple activities are specified through rules defined over process data. Existing decision mining methods focus on discovering mutually-exclusive rules,

Decision Mining Revisited - Discovering Overlapping Rules

NARCIS (Netherlands)

Mannhardt, F.; De Leoni, M.; Reijers, H.A.; van der Aalst, W.M.P.; Nurcan, S.; Soffer, P.; Bajec, M.; Eder, J.

2016-01-01

Decision mining enriches process models with rules underlying decisions in processes using historical process execution data. Choices between multiple activities are specified through rules defined over process data. Existing decision mining methods focus on discovering mutually-exclusive rules,

Molecular characterization and genetic diversity of different genotypes of Oryza sativa and Oryza glaberrima

Directory of Open Access Journals (Sweden)

Caijin Chen

2017-11-01

Conclusions: Genetic diversity studies revealed that 50 rice types were clustered into different subpopulations whereas three genotypes were admixtures. Molecular fingerprinting and 10 specific markers were obtained to identify the 53 rice genotypes. These results can facilitate the potential utilization of sibling species in rice breeding and molecular classification of O. sativa and O. glaberrima germplasms.

A systematic framework to discover pattern for web spam classification

OpenAIRE

Jelodar, Hamed; Wang, Yongli; Yuan, Chi; Jiang, Xiaohui

2017-01-01

Web spam is a big problem for search engine users in World Wide Web. They use deceptive techniques to achieve high rankings. Although many researchers have presented the different approach for classification and web spam detection still it is an open issue in computer science. Analyzing and evaluating these websites can be an effective step for discovering and categorizing the features of these websites. There are several methods and algorithms for detecting those websites, such as decision t...

Opposite photo-induced deformations in azobenzene-containing polymers with different molecular architecture: Molecular dynamics study

International Nuclear Information System (INIS)

Ilnytskyi, Jaroslav M.; Neher, Dieter; Saphiannikova, Marina

2011-01-01

Photo-induced deformations in azobenzene-containing polymers (azo-polymers) are central to a number of applications, such as optical storage and fabrication of diffractive elements. The microscopic nature of the underlying opto-mechanical coupling is yet not clear. In this study, we address the experimental finding that the scenario of the effects depends on molecular architecture of the used azo-polymer. Typically, opposite deformations in respect to the direction of light polarization are observed for liquid crystalline and amorphous azo-polymers. In this study, we undertake molecular dynamics simulations of two different models that mimic these two types of azo-polymers. We employ hybrid force field modeling and consider only trans-isomers of azobenzene, represented as Gay-Berne sites. The effect of illumination on the orientation of the chromophores is considered on the level of orientational hole burning and emphasis is given to the resulting deformation of the polymer matrix. We reproduce deformations of opposite sign for the two models being considered here and discuss the relevant microscopic mechanisms in both cases.

Molecular Characterization of Clostridium difficile Isolates in China From 2010 to 2015

Directory of Open Access Journals (Sweden)

Xiao-shu Liu

2018-04-01

Full Text Available Clostridium difficile infection (CDI has become a worldwide public health problem causing high mortality and a large disease burden. Molecular typing and analysis is important for surveillance and infection control of CDI. However, molecular characterization of C. difficile across China is extremely rare. Here, we report on the toxin profiles, molecular subtyping with multilocus sequence typing (MLST and PCR ribotyping, and epidemiological characteristics of 199 C. difficile isolates collected between 2010 through 2015 from 13 participating centers across China. We identified 35 STs and 27 ribotypes (RTs among the 199 C. difficile isolates: ST35 (15.58%, ST3 (15.08%, ST37 (12.06%, and RT017 (14.07%, RT001 (12.06%, RT012 (11.56% are the most prevalent. One isolate with ST1 and 8 isolates with ST 11 were identified. We identified a new ST in this study, denoted ST332. The toxin profile tcdA+tcdB+tcdC+tcdR+tcdE+CDT- (65.83% was the predominant profile. Furthermore, 11 isolates with positive binary toxin genes were discovered. According to the PCR ribotyping, one isolate with RT 027, and 6 isolates with RT 078 were confirmed. The epidemiological characteristics of C. difficile in China shows geographical differences, and both the toxin profile and molecular types exhibit great diversity across the different areas.

Implications of storing urinary DNA from different populations for molecular analyses.

Directory of Open Access Journals (Sweden)

Angela Cannas

2009-09-01

Full Text Available Molecular diagnosis using urine is established for many sexually transmitted diseases and is increasingly used to diagnose tumours and other infectious diseases. Storage of urine prior to analysis, whether due to home collection or bio-banking, is increasingly advocated yet no best practice has emerged. Here, we examined the stability of DNA in stored urine in two populations over 28 days.Urine from 40 (20 male healthy volunteers from two populations, Italy and Zambia, was stored at four different temperatures (RT, 4 degrees C, -20 degrees C & -80 degrees C with and without EDTA preservative solution. Urines were extracted at days 0, 1, 3, 7 and 28 after storage. Human DNA content was measured using multi-copy (ALU J and single copy (TLR2 targets by quantitative real-time PCR. Zambian and Italian samples contained comparable DNA quantity at time zero. Generally, two trends were observed during storage; no degradation, or rapid degradation from days 0 to 7 followed by little further degradation to 28 days. The biphasic degradation was always observed in Zambia regardless of storage conditions, but only twice in Italy.Site-specific differences in urine composition significantly affect the stability of DNA during storage. Assessing the quality of stored urine for molecular analysis, by using the type of strategy described here, is paramount before these samples are used for molecular prognostic monitoring, genetic analyses and disease diagnosis.

Effect of the different chain transfer agents on molecular weight and optical properties of poly(methyl methacrylate)

Science.gov (United States)

Çetinkaya, Onur; Demirci, Gökhan; Mergo, Paweł

2017-08-01

Investigation of molecular weight and optical properties of poly(methyl metacrylate) (PMMA) polymerized in house with different chain transfer agents was studied. Isopropyl alcohol (IPA), n-butyl mercaptan (nBMC) and pentamethyl disilane (PMDS) were used as chain transfer agents. The molecular weight (Mw) of PMMA samples were measured by Ostwald viscometer. Mw of bulk polymer samples were decreased with increase the concentration of chain transfer agents (CTA). Since reactivity of used CTAs is not same, molecular weights of samples which were produced with different type of CTA but same concentration of CTA was varied. Higher concentration of n-BMC showed higher scattering. Transmission of samples could not be correlated with different concentration of CTA. Refractive index of samples was not affected by concentration of CTA nevertheless higher molecular weight of CTA showed higher refractive index.

A molecular recombination map of Antirrhinum majus

Directory of Open Access Journals (Sweden)

Hudson Andrew

2010-12-01

Full Text Available Abstract Background Genetic recombination maps provide important frameworks for comparative genomics, identifying gene functions, assembling genome sequences and for breeding. The molecular recombination map currently available for the model eudicot Antirrhinum majus is the result of a cross with Antirrhinum molle, limiting its usefulness within A. majus. Results We created a molecular linkage map of A. majus based on segregation of markers in the F2 population of two inbred lab strains of A. majus. The resulting map consisted of over 300 markers in eight linkage groups, which could be aligned with a classical recombination map and the A. majus karyotype. The distribution of recombination frequencies and distorted transmission of parental alleles differed from those of a previous inter-species hybrid. The differences varied in magnitude and direction between chromosomes, suggesting that they had multiple causes. The map, which covered an estimated of 95% of the genome with an average interval of 2 cM, was used to analyze the distribution of a newly discovered family of MITE transposons and tested for its utility in positioning seven mutations that affect aspects of plant size. Conclusions The current map has an estimated interval of 1.28 Mb between markers. It shows a lower level of transmission ratio distortion and a longer length than the previous inter-species map, making it potentially more useful. The molecular recombination map further indicates that the IDLE MITE transposons are distributed throughout the genome and are relatively stable. The map proved effective in mapping classical morphological mutations of A. majus.

UPLC-based metabonomic applications for discovering biomarkers of diseases in clinical chemistry.

Science.gov (United States)

Zhao, Ying-Yong; Cheng, Xian-Long; Vaziri, Nosratola D; Liu, Shuman; Lin, Rui-Chao

2014-10-01

Metabonomics is a powerful and promising analytic tool that allows assessment of global low-molecular-weight metabolites in biological systems. It has a great potential for identifying useful biomarkers for early diagnosis, prognosis and assessment of therapeutic interventions in clinical practice. The aim of this review is to provide a brief summary of the recent advances in UPLC-based metabonomic approach for biomarker discovery in a variety of diseases, and to discuss their significance in clinical chemistry. All the available information on UPLC-based metabonomic applications for discovering biomarkers of diseases were collected via a library and electronic search (using Web of Science, Pubmed, ScienceDirect, Springer, Google Scholar, etc.). Metabonomics has been used in clinical chemistry to identify and evaluate potential biomarkers and therapeutic targets in various diseases affecting the liver (hepatocarcinoma and liver cirrhosis), lung (lung cancer and pneumonia), gastrointestinal tract (colorectal cancer) and urogenital tract (prostate cancer, ovarian cancer and chronic kidney disease), as well as metabolic diseases (diabetes) and neuropsychiatric disorders (Alzheimer's disease and schizophrenia), etc. The information provided highlights the potential value of determination of endogenous low-molecular-weight metabolites and the advantages and potential drawbacks of the application of UPLC-based metabonomics in clinical setting. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Discovering Authentication Credentials in Volatile Memory of Android Mobile Devices

OpenAIRE

Apostolopoulos , Dimitris; Marinakis , Giannis; Ntantogian , Christoforos; Xenakis , Christos

2013-01-01

Part 5: Adoption Issues in e/m-Services; International audience; This paper investigates whether authentication credentials in the volatile memory of Android mobile devices can be discovered using freely available tools. The experiments that we carried out for each application included two different sets: In the first set, our goal was to check if we could recover our own submitted credentials from the memory dump of the mobile device. In the second set of experiments, the goal was to find pa...

Molecular Dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

Energy Technology Data Exchange (ETDEWEB)

Tringe, J.W., E-mail: tringe2@llnl.gov [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Ileri, N. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Levie, H.W. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Stroeve, P.; Ustach, V.; Faller, R. [Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Renaud, P. [Swiss Federal Institute of Technology, Lausanne, (EPFL) (Switzerland)

2015-08-18

Highlights: • WGA proteins in nanochannels modeled by Molecular Dynamics and Monte Carlo. • Protein surface coverage characterized by atomic force microscopy. • Models indicate transport characteristics depend strongly on surface coverage. • Results resolve of a four orders of magnitude difference in diffusion coefficient values. - Abstract: We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage. Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.

The impact of different phytosterols on the molecular dynamics in the hydrophobic/hydrophilic interface phosphatidylcholine- liposomes

DEFF Research Database (Denmark)

Hellgren, Lars; Sandelius, A.S.

2001-01-01

Plant sterols differ from cholesterol in having an alkyl group at Delta -24, and, in the case of stigmasterol, also a Delta -22 double bond. The effects of 10 mol% of three plant sterols (campesterol, fl-sitosterol, stigmasterol) and cholesterol on the molecular dynamics and phase behavior...... in multilamellar liposomes made from different phosphatidylcholine (PC) molecular species have been compared, utilizing the fluorescent probe Laurdan (2-dimethyl-amino-6-laurylnaphthalene). Laurdan reports the molecular mobility in the hydrophilic/hydrophobic interface of the membrane by determining the rate...... of dipolar relaxation of water molecules close to the glycerol backbone of PC. Our results showed that the Delta -24 alkyl group of plant sterols did not affect their ability to reduce molecular mobility in this region of the PC membranes. However, the plant sterols had a decreased capacity compared...

Did Viking discover life on Mars?

Science.gov (United States)

Klein, H. P.

1999-01-01

A major argument in the claim that life had been discovered during the Viking mission to Mars is that the results obtained in the Labeled Release (LR) experiment are analogous to those observed with terrestrial microorganisms. This assertion is critically examined and found to be implausible.

The discovered preference hypothesis - an empirical test

DEFF Research Database (Denmark)

Lundhede, Thomas; Ladenburg, Jacob; Olsen, Søren Bøye

Using stated preference methods for valuation of non-market goods is known to be vulnerable to a range of biases. Some authors claim that these so-called anomalies in effect render the methods useless for the purpose. However, the Discovered Preference Hypothesis, as put forth by Plott [31], offers...... an nterpretation and explanation of biases which entails that the stated preference methods need not to be completely written off. In this paper we conduct a test for the validity and relevance of the DPH interpretation of biases. In a choice experiment concerning preferences for protection of Danish nature areas...... as respondents evaluate more and more choice sets. This finding supports the Discovered Preference Hypothesis interpretation and explanation of starting point bias....

Gender differences in skeletal muscle substrate metabolism - molecular mechanisms and insulin sensitivity

DEFF Research Database (Denmark)

Lundsgaard, Annemarie; Kiens, Bente

2014-01-01

higher insulin sensitivity of female skeletal muscle can be related to gender-specific regulation of molecular metabolism will be topic for discussion. Gender differences in muscle fiber type distribution and substrate availability to and in skeletal muscle are highly relevant for substrate metabolism...

Molecular perspectives in differentiated thyroid cancer.

Science.gov (United States)

Buffet, C; Groussin, L

2015-02-01

Progress in understanding the molecular genetics of thyroid cancer in the last 20 years has accelerated recently with the advent of high-throughput sequencing technologies known as Next-Generation Sequencing. Besides classical molecular abnormalities involving the MAPK (Mitogen Activated Protein Kinase) and PI3K (PhosphoInositide 3-Kinase) pathways that play a key role in follicular-derived thyroid tumorigenesis, new molecular abnormalities have been discovered. The major advances in recent years have been the discovery of new somatic driver gene point mutations (such as RASAL1 [RAS protein activator Like 1] mutations in follicular cancer) and/or mutations that have prognostic value (such as TERT [Telomerase reverse transcriptase] promoter mutations); new chromosomal rearrangements, usually having close connection with exposure to ionizing radiation (such as ALK [Anaplastic Lymphoma Kinase] rearrangements); and deregulation of some gene or microRNA expression representing a molecular signature. Progress made in understanding the molecular mechanisms of thyroid cancer offers new perspectives for the diagnosis of the benign or malignant status of a thyroid nodule, to refine prognosis and offer new perspectives of targeted therapy for radioiodine-refractory cancers. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Molecular hydrogen jets from the Orion nebula

International Nuclear Information System (INIS)

Taylor, K.N.R.; Storey, J.W.V.; Zealey, W.J.

1984-01-01

In an attempt to understand the relationship of the recently discovered complex of Herbig Haro objects in Orion to the IR sources in this region, the authors have carried out a survey of the molecular hydrogen S(1) line distribution. The observations have led to the discovery of a previously unsuspected structure of finger-like filaments of H 2 emission extending radially outwards from a common centre at IRC9. (author)

Discovering functional interdependence relationship in PPI networks for protein complex identification.

Science.gov (United States)

Lam, Winnie W M; Chan, Keith C C

2012-04-01

Protein molecules interact with each other in protein complexes to perform many vital functions, and different computational techniques have been developed to identify protein complexes in protein-protein interaction (PPI) networks. These techniques are developed to search for subgraphs of high connectivity in PPI networks under the assumption that the proteins in a protein complex are highly interconnected. While these techniques have been shown to be quite effective, it is also possible that the matching rate between the protein complexes they discover and those that are previously determined experimentally be relatively low and the "false-alarm" rate can be relatively high. This is especially the case when the assumption of proteins in protein complexes being more highly interconnected be relatively invalid. To increase the matching rate and reduce the false-alarm rate, we have developed a technique that can work effectively without having to make this assumption. The name of the technique called protein complex identification by discovering functional interdependence (PCIFI) searches for protein complexes in PPI networks by taking into consideration both the functional interdependence relationship between protein molecules and the network topology of the network. The PCIFI works in several steps. The first step is to construct a multiple-function protein network graph by labeling each vertex with one or more of the molecular functions it performs. The second step is to filter out protein interactions between protein pairs that are not functionally interdependent of each other in the statistical sense. The third step is to make use of an information-theoretic measure to determine the strength of the functional interdependence between all remaining interacting protein pairs. Finally, the last step is to try to form protein complexes based on the measure of the strength of functional interdependence and the connectivity between proteins. For performance evaluation

Scientists Discover Sugar in Space

Science.gov (United States)

2000-06-01

. Glycolaldehyde is a simpler molecular cousin to table sugar, the scientists say. The sugar molecule was detected in a large cloud of gas and dust some 26,000 light-years away, near the center of our Galaxy. Such clouds, often many light-years across, are the material from which new stars are formed. Though very rarified by Earth standards, these interstellar clouds are the sites of complex chemical reactions that occur over hundreds of thousands or millions of years. So far, about 120 different molecules have been discovered in these clouds. Most of these molecules contain a small number of atoms, and only a few molecules with eight or more atoms have been found in interstellar clouds. The 12 Meter Telescope "Finding glycolaldehyde in one of these interstellar clouds means that such molecules can be formed even in very rarified conditions," said Hollis. "We don't yet understand how it could be formed there," he added. "A combination of more astronomical observations and theoretical chemistry work will be required to resolve the mystery of how this molecule is formed in space." "We hope this discovery inspires renewed efforts to find even more kinds of molecules, so that, with a better idea of the total picture, we may be able to deduce the details of the prebiotic chemistry taking place in interstellar clouds," Hollis said. The discovery was made by detecting faint radio emission from the sugar molecules in the interstellar cloud. Molecules rotate end-for-end, and as they change from one rotational energy state to another, they emit radio waves at precise frequencies. The "family" of radio frequencies emitted by a particular molecule forms a unique "fingerprint" that scientists can use to identify that molecule. The scientists identified glycolaldehyde by detecting six frequencies of radio emission in what is termed the millimeter-wavelength region of the electromagnetic spectrum -- a region between more-familiar microwaves and infrared radiation. The NRAO 12 Meter Telescope

Hypoglycemic effect of polysaccharides with different molecular weight of Pseudostellaria heterophylla

Science.gov (United States)

2013-01-01

Abstracts Background The aims of this study were to evaluate the antidiabetic activity and to detect molecular size of Pseudostellaria heterophylla polysaccharide (PHP). Pseudostellaria heterophylla is a medicine extensively used in traditional Chinese medicine formulas to treat diabetes and its complications. Methods Molecular weight of PHP was determined by gel permeation chromatography combined with phenol-sulphuric acid method and the monosaccharides composition was determined by HPLC with a precolumn derivatization. Four polysaccharides with different molecular weight were compared for hypoglycemic active on two animal models both high does alloxan induced type1 diabetic mellitus (T1DM) and high-fat/lower does streptozotocin induced type2 diabetic mellitus (T2DM). Blood sugar, glucose tolerance, and insulin tolerance were detected. Rat serum IL-1β, IL-2, IL-10, Leptin, TNF-α, Acrp30 and CRP were also analyzed by sandwich-ELISA approaches to preliminary probe the hypoglycemic mechanism of PHP. Results The hypoglycemic effects related to molecular size of polysaccharide were more effective against T2DM than T1DM. PHP comprise four monosaccharides of galacturonic acid, glucose, galactose and arabinos. T2DM rats daily receiving oral dose of polysaccharide(100 ~ 400 mg/kg) with 50 ~ 210 kDa molecular weight (PF40) could not only significantly lower blood sugar but also reduce total triglyceride level in serum. PF40 improves in insulin tolerance inhibited the expression of some biomarkers including inflammatory cytokine TNF-α and elevated anti-inflammatory cytokine IL-10, regulated adiponectin Acrp30 and leptin. Conclusions PF40 prevent the cascade of inflammatory events in the treatment of T2DM to block overweight progresses to obesity. PMID:24131482

Discovering Technicolor

DEFF Research Database (Denmark)

R. Andersen, J.; Antipin, O.; Azuelos, G.

2011-01-01

We provide a pedagogical introduction to extensions of the Standard Model in which the Higgs is composite. These extensions are known as models of dynamical electroweak symmetry breaking or, in brief, Technicolor. Material covered includes: motivations for Technicolor, the construction of underly...... the relevant experimental benchmarks for Vanilla, Running, Walking, and Custodial Technicolor, and a natural fourth family of leptons, by laying out the framework to discover these models at the Large Hadron Collider....... of underlying gauge theories leading to minimal models of Technicolor, the comparison with electroweak precision data, the low energy effective theory, the spectrum of the states common to most of the Technicolor models, the decays of the composite particles and the experimental signals at the Large Hadron...... Collider. The level of the presentation is aimed at readers familiar with the Standard Model but who have little or no prior exposure to Technicolor. Several extensions of the Standard Model featuring a composite Higgs can be reduced to the effective Lagrangian introduced in the text. We establish...

Discovering Multimodal Behavior in Ms. Pac-Man through Evolution of Modular Neural Networks.

Science.gov (United States)

Schrum, Jacob; Miikkulainen, Risto

2016-03-12

Ms. Pac-Man is a challenging video game in which multiple modes of behavior are required: Ms. Pac-Man must escape ghosts when they are threats and catch them when they are edible, in addition to eating all pills in each level. Past approaches to learning behavior in Ms. Pac-Man have treated the game as a single task to be learned using monolithic policy representations. In contrast, this paper uses a framework called Modular Multi-objective NEAT (MM-NEAT) to evolve modular neural networks. Each module defines a separate behavior. The modules are used at different times according to a policy that can be human-designed (i.e. Multitask) or discovered automatically by evolution. The appropriate number of modules can be fixed or discovered using a genetic operator called Module Mutation. Several versions of Module Mutation are evaluated in this paper. Both fixed modular networks and Module Mutation networks outperform monolithic networks and Multitask networks. Interestingly, the best networks dedicate modules to critical behaviors (such as escaping when surrounded after luring ghosts near a power pill) that do not follow the customary division of the game into chasing edible and escaping threat ghosts. The results demonstrate that MM-NEAT can discover interesting and effective behavior for agents in challenging games.

Discovering English with the Sketch Engine

Science.gov (United States)

Thomas, James

2014-01-01

"Discovering English with the Sketch Engine" is the title of a new book (Thomas, 2014) which introduces the use of corpora in language study, teaching, writing and translating. It focuses on using the Sketch Engine to identify patterns of normal usage in many aspects of English ranging from morphology to discourse and pragmatics. This…

Molecular magnets physics and applications

CERN Document Server

Bartolomé, Juan; Fernández, Julio F

2013-01-01

This book provides an overview of the physical phenomena discovered in magnetic molecular materials over the last 20 years. It is written by leading scientists having made the most important contributions to this active area of research. The main topics of this book are the principles of quantum tunneling and quantum coherence of single-molecule magnets (SMMs), phenomena which go beyond the physics of individual molecules, such as the collective behavior of arrays of SMMs, the physics of one-dimensional singleâ€"chain magnets and magnetism of SMMs grafted on substrates.

Discovering context-aware conditional functional dependencies

Institute of Scientific and Technical Information of China (English)

Yuefeng DU; Derong SHEN; Tiezheng NIE; Yue KOU; Ge YU

2017-01-01

Conditional functional dependencies(CFDs) are important techniques for data consistency.However,CFDs are limited to 1) provide the reasonable values for consistency repairing and 2) detect potential errors.This paper presents context-aware conditional functional dependencies(CCFDs) which contribute to provide reasonable values and detect potential errors.Especially,we focus on automatically discovering minimal CCFDs.In this paper,we present context relativity to measure the relationship of CFDs.The overlap of the related CFDs can provide reasonable values which result in more accuracy consistency repairing,and some related CFDs are combined into CCFDs.Moreover,we prove that discovering minimal CCFDs is NP-complete and we design the precise method and the heuristic method.We also present the dominating value to facilitate the process in both the precise method and the heuristic method.Additionally,the context relativity of the CFDs affects the cleaning results.We will give an approximate threshold of context relativity according to data distribution for suggestion.The repairing results are approved more accuracy,even evidenced by our empirical evaluation.

A knowledge-based integrated approach for discovering and repairing declare maps

NARCIS (Netherlands)

Maggi, F.M.; Jagadeesh Chandra Bose, R.P.; Aalst, van der W.M.P.; Salinesi, C.; Norrie, M.C.; Pastor, O.

2013-01-01

Process mining techniques can be used to discover process models from event data. Often the resulting models are complex due to the variability of the underlying process. Therefore, we aim at discovering declarative process models that can deal with such variability. However, for real-life event

Decision Mining Revisited – Discovering Overlapping Rules

NARCIS (Netherlands)

Mannhardt, F.; de Leoni, M.; Reijers, H.A.; van der Aalst, W.M.P.

2016-01-01

Decision mining enriches process models with rules underlying decisions in processes using historical process execution data. Choices between multiple activities are specified through rules defined over process data. Existing decision mining methods focus on discovering mutually-exclusive rules,

Discovering Mira Ceti: Celestial Change and Cosmic Continuity

Science.gov (United States)

Hatch, Robert Alan

In the short narrative that follows I introduce two new heroes. Although we begin with Fabricius's first sighting in 1596, the new pivot point in the drama is the collaboration between Hevelius and Boulliau that began around 1660. As it happens, Learned Europe paid little attention to Mira in the generation after the first scattered sightings of 1596, indeed, nearly 70 years passed before the New Star was given a working identity. Like Columbus discovering America, Fabricius and Holwarda saw different things - for convenience, I call them Fabricius's Star and Holwarda's Star. Hevelius's Historiola (Danzig, 1662) and Boulliau's Ad astronomos (Paris, 1667) presented a different vision. It made Mira famous. As I shall argue, if Hevelius gave Mira a history, Boulliau gave Mira a future.5 In the end, the New Star not only challenged the ancient cosmos, it became an enduring icon for the New Science, a returning reminder of celestial continuity and cosmic order.

Growing Self-Estemm and Discovering Intelligences through Oral Production

Directory of Open Access Journals (Sweden)

Ochoa Dora Liliana

2002-08-01

Full Text Available After having applied a needs analysis in an eleventh grade course of English, I could notice that there was a big lack of security and self-confidence in the students. They expressed in different data-gathering instruments their fear when speaking in front of the class. Also, they talked about their insecurity when pronouncing English and the need for more opportunities for developing speaking. Therefore, the implementation of an innovation in class was carried out in order to respond to the students¿ needs and make them discover their talents. The implementation was successful and students improved some areas of their communicative competence.

Einstein@Home discovers a radio-quiet gamma-ray millisecond pulsar.

Science.gov (United States)

Clark, Colin J; Pletsch, Holger J; Wu, Jason; Guillemot, Lucas; Kerr, Matthew; Johnson, Tyrel J; Camilo, Fernando; Salvetti, David; Allen, Bruce; Anderson, David; Aulbert, Carsten; Beer, Christian; Bock, Oliver; Cuéllar, Andres; Eggenstein, Heinz-Bernd; Fehrmann, Henning; Kramer, Michael; Kwang, Shawn A; Machenschalk, Bernd; Nieder, Lars; Ackermann, Markus; Ajello, Marco; Baldini, Luca; Ballet, Jean; Barbiellini, Guido; Bastieri, Denis; Bellazzini, Ronaldo; Bissaldi, Elisabetta; Blandford, Roger D; Bloom, Elliott D; Bonino, Raffaella; Bottacini, Eugenio; Brandt, Terri J; Bregeon, Johan; Bruel, Philippe; Buehler, Rolf; Burnett, Toby H; Buson, Sara; Cameron, Rob A; Caputo, Regina; Caraveo, Patrizia A; Cavazzuti, Elisabetta; Cecchi, Claudia; Charles, Eric; Chekhtman, Alexandre; Ciprini, Stefano; Cominsky, Lynn R; Costantin, Denise; Cutini, Sara; D'Ammando, Filippo; De Luca, Andrea; Desiante, Rachele; Di Venere, Leonardo; Di Mauro, Mattia; Di Lalla, Niccolò; Digel, Seth W; Favuzzi, Cecilia; Ferrara, Elizabeth C; Franckowiak, Anna; Fukazawa, Yasushi; Funk, Stefan; Fusco, Piergiorgio; Gargano, Fabio; Gasparrini, Dario; Giglietto, Nico; Giordano, Francesco; Giroletti, Marcello; Gomez-Vargas, Germán A; Green, David; Grenier, Isabelle A; Guiriec, Sylvain; Harding, Alice K; Hewitt, John W; Horan, Deirdre; Jóhannesson, Guðlaugur; Kensei, Shiki; Kuss, Michael; La Mura, Giovanni; Larsson, Stefan; Latronico, Luca; Li, Jian; Longo, Francesco; Loparco, Francesco; Lovellette, Michael N; Lubrano, Pasquale; Magill, Jeffrey D; Maldera, Simone; Manfreda, Alberto; Mazziotta, Mario N; McEnery, Julie E; Michelson, Peter F; Mirabal, Nestor; Mitthumsiri, Warit; Mizuno, Tsunefumi; Monzani, Maria Elena; Morselli, Aldo; Moskalenko, Igor V; Nuss, Eric; Ohsugi, Takashi; Omodei, Nicola; Orienti, Monica; Orlando, Elena; Palatiello, Michele; Paliya, Vaidehi S; de Palma, Francesco; Paneque, David; Perkins, Jeremy S; Persic, Massimo; Pesce-Rollins, Melissa; Porter, Troy A; Principe, Giacomo; Rainò, Silvia; Rando, Riccardo; Ray, Paul S; Razzano, Massimiliano; Reimer, Anita; Reimer, Olaf; Romani, Roger W; Saz Parkinson, Pablo M; Sgrò, Carmelo; Siskind, Eric J; Smith, David A; Spada, Francesca; Spandre, Gloria; Spinelli, Paolo; Thayer, Jana B; Thompson, David J; Torres, Diego F; Troja, Eleonora; Vianello, Giacomo; Wood, Kent; Wood, Matthew

2018-02-01

Millisecond pulsars (MSPs) are old neutron stars that spin hundreds of times per second and appear to pulsate as their emission beams cross our line of sight. To date, radio pulsations have been detected from all rotation-powered MSPs. In an attempt to discover radio-quiet gamma-ray MSPs, we used the aggregated power from the computers of tens of thousands of volunteers participating in the Einstein@Home distributed computing project to search for pulsations from unidentified gamma-ray sources in Fermi Large Area Telescope data. This survey discovered two isolated MSPs, one of which is the only known rotation-powered MSP to remain undetected in radio observations. These gamma-ray MSPs were discovered in completely blind searches without prior constraints from other observations, raising hopes for detecting MSPs from a predicted Galactic bulge population.

Discovering Science through Art-Based Activities

Science.gov (United States)

Alberts, Rebecca

2010-01-01

Art and science are intrinsically linked; the essence of art and science is discovery. Both artists and scientists work in a systematic but creative way--knowledge and understanding are built up through pieces of art or a series of labs. In the classroom, integrating science and visual art can provide students with the latitude to think, discover,…

Dipicolinate salt of imidazole: Discovering its structure and properties using different experimental methodologies and quantum chemical investigations

Science.gov (United States)

Thirumurugan, R.; Anitha, K.

2018-03-01

A novel organic proton transfer complex of imidazolium dipicolinate (ID) has been synthesized and it was grown as single crystals using slow evaporation method. The molecular structure of synthesized compound and vibrational modes of its functional groups were confirmed by (1H and 13C) NMR, FTIR and FT-Raman spectroscopic studies, respectively. Single crystal X-ray diffraction (SCXRD) analysis confirmed the orthorhombic system with noncentrosymmetric (NCS), P212121, space group of grown ID crystal. UV-Vis-NIR spectral study confirmed its high optical transparency within the region of 285-1500 nm. Powder second harmonic generation (SHG) efficiency of ID crystal was confirmed and it was 6.8 times that of KDP crystal. TG-DTA and DSC analysis revealed the higher thermal stability of grown crystal as 249 °C. The dielectric response and mechanical behaviour of grown crystal were studied effectively. Density functional theory calculations were performed to probe the relationship between the structure and its properties including molecular optimization, Mulliken atomic charge distribution, frontier molecular orbital (FMOs) and molecular electrostatic potential map (MEP) analysis and first hyperpolarizability. All these experimental and computational results were discussed in this communication and it endorsed the ID compound as a potential NLO candidate could be employed in optoelectronics device applications in near future.

Using high throughput experimental data and in silico models to discover alternatives to toxic chromate corrosion inhibitors

International Nuclear Information System (INIS)

Winkler, D.A.; Breedon, M.; White, P.; Hughes, A.E.; Sapper, E.D.; Cole, I.

2016-01-01

Highlights: • We screened a large library of organic compounds as replacements for toxic chromates. • High throughput automated corrosion testing was used to assess inhibitor performance. • Robust, predictive machine learning models of corrosion inhibition were developed. • Models indicated molecular features contributing to performance of organic inhibitors. • We also showed that quantum chemistry descriptors do not correlate with performance. - Abstract: Restrictions on the use of toxic chromate-based corrosion inhibitors have created important issues for the aerospace and other industries. Benign alternatives that offer similar or superior performance are needed. We used high throughput experiments to assess 100 small organic molecules as potential inhibitors of corrosion in aerospace aluminium alloys AA2024 and AA7075. We generated robust, predictive, quantitative computational models of inhibitor efficiency at two pH values using these data. The models identified molecular features of inhibitor molecules that had the greatest impact on corrosion inhibition. Models can be used to discover better corrosion inhibitors by screening libraries of organic compounds for candidates with high corrosion inhibition.

Layer-specific morphological and molecular differences in neocortical astrocytes and their dependence on neuronal layers.

Science.gov (United States)

Lanjakornsiripan, Darin; Pior, Baek-Jun; Kawaguchi, Daichi; Furutachi, Shohei; Tahara, Tomoaki; Katsuyama, Yu; Suzuki, Yutaka; Fukazawa, Yugo; Gotoh, Yukiko

2018-04-24

Non-pial neocortical astrocytes have historically been thought to comprise largely a nondiverse population of protoplasmic astrocytes. Here we show that astrocytes of the mouse somatosensory cortex manifest layer-specific morphological and molecular differences. Two- and three-dimensional observations revealed that astrocytes in the different layers possess distinct morphologies as reflected by differences in cell orientation, territorial volume, and arborization. The extent of ensheathment of synaptic clefts by astrocytes in layer II/III was greater than that by those in layer VI. Moreover, differences in gene expression were observed between upper-layer and deep-layer astrocytes. Importantly, layer-specific differences in astrocyte properties were abrogated in reeler and Dab1 conditional knockout mice, in which neuronal layers are disturbed, suggesting that neuronal layers are a prerequisite for the observed morphological and molecular differences of neocortical astrocytes. This study thus demonstrates the existence of layer-specific interactions between neurons and astrocytes, which may underlie their layer-specific functions.

Possible origin of Saturn's newly discovered outer ring

International Nuclear Information System (INIS)

Moehlmann, D.

1986-01-01

Within a planetogonic model the self-gravitationally caused formation of pre-planetary and pre-satellite rings from an earlier thin disk is reported. The theoretically derived orbital radii of these rings are compared with the orbital levels in the planetary system and the satellite systems of Jupiter, Saturn and Uranus. From this comparison it is concluded that at the radial position of Saturn's newly discovered outer ring an early pre-satellite ring of more or less evolved satellites could have existed. These satellites should have been disturbed in their evolution by the gravitation of the neighbouring massive satellite Titan. The comparison also may indicate similarities between the asteroidal belt and the newly discovered outer ring of Saturn

Discovering Phonemes of Bidayuh

Directory of Open Access Journals (Sweden)

Jecky Misieng

2012-07-01

Full Text Available There are generally three views of the notion of a phoneme. The structuralist view of the phoneme focuses on this language phenomenon as a phonetic reality. In discovering phonemes of a language, phonologists who hold this view will look for minimal contrasting pairs as a way to determine contrasting sounds of that language. They will also look for allophones or two sounds of the same phoneme which may appear in complementary distribution. This paper will discuss the possible application of the structuralist approach to analyzing the phonemes of a dialect of Bidayuh, one of the Malayo-Polynesian languages spoken in the northern region of Borneo.

Institute for Molecular Medicine Research Program

Energy Technology Data Exchange (ETDEWEB)

Phelps, Michael E [Univ. of California, Los Angeles, CA (United States)

2012-12-14

The objectives of the project are the development of new Positron Emission Tomography (PET) imaging instrumentation, chemistry technology platforms and new molecular imaging probes to examine the transformations from normal cellular and biological processes to those of disease in pre-clinical animal models. These technology platforms and imaging probes provide the means to: 1. Study the biology of disease using pre-clinical mouse models and cells. 2. Develop molecular imaging probes for imaging assays of proteins in pre-clinical models. 3. Develop imaging assays in pre-clinical models to provide to other scientists the means to guide and improve the processes for discovering new drugs. 4. Develop imaging assays in pre-clinical models for others to use in judging the impact of drugs on the biology of disease.

Effect of alkali lignins with different molecular weights from alkali pretreated rice straw hydrolyzate on enzymatic hydrolysis.

Science.gov (United States)

Li, Yun; Qi, Benkun; Luo, Jianquan; Wan, Yinhua

2016-01-01

This study investigated the effect of alkali lignins with different molecular weights on enzymatic hydrolysis of lignocellulose. Different alkali lignins fractions, which were obtained from cascade ultrafiltration, were added into the dilute acid pretreated (DAP) and alkali pretreated (AP) rice straws respectively during enzymatic hydrolysis. The results showed that the addition of alkali lignins enhanced the hydrolysis and the enhancement for hydrolysis increased with increasing molecular weights of alkali lignins, with maximum enhancement being 28.69% for DAP and 20.05% for AP, respectively. The enhancement was partly attributed to the improved cellulase activity, and filter paper activity increased by 18.03% when adding lignin with highest molecular weight. It was found that the enhancement of enzymatic hydrolysis was correlated with the adsorption affinity of cellulase on alkali lignins, and the difference in surface charge and hydrophobicity of alkali lignins were responsible for the difference in affinity between cellulase and lignins. Copyright © 2015 Elsevier Ltd. All rights reserved.

Einstein@Home discovers a radio-quiet gamma-ray millisecond pulsar

Science.gov (United States)

Clark, Colin J.; Pletsch, Holger J.; Wu, Jason; Guillemot, Lucas; Kerr, Matthew; Johnson, Tyrel J.; Camilo, Fernando; Salvetti, David; Allen, Bruce; Anderson, David; Aulbert, Carsten; Beer, Christian; Bock, Oliver; Cuéllar, Andres; Eggenstein, Heinz-Bernd; Fehrmann, Henning; Kramer, Michael; Kwang, Shawn A.; Machenschalk, Bernd; Nieder, Lars; Ackermann, Markus; Ajello, Marco; Baldini, Luca; Ballet, Jean; Barbiellini, Guido; Bastieri, Denis; Bellazzini, Ronaldo; Bissaldi, Elisabetta; Blandford, Roger D.; Bloom, Elliott D.; Bonino, Raffaella; Bottacini, Eugenio; Brandt, Terri J.; Bregeon, Johan; Bruel, Philippe; Buehler, Rolf; Burnett, Toby H.; Buson, Sara; Cameron, Rob A.; Caputo, Regina; Caraveo, Patrizia A.; Cavazzuti, Elisabetta; Cecchi, Claudia; Charles, Eric; Chekhtman, Alexandre; Ciprini, Stefano; Cominsky, Lynn R.; Costantin, Denise; Cutini, Sara; D’Ammando, Filippo; De Luca, Andrea; Desiante, Rachele; Di Venere, Leonardo; Di Mauro, Mattia; Di Lalla, Niccolò; Digel, Seth W.; Favuzzi, Cecilia; Ferrara, Elizabeth C.; Franckowiak, Anna; Fukazawa, Yasushi; Funk, Stefan; Fusco, Piergiorgio; Gargano, Fabio; Gasparrini, Dario; Giglietto, Nico; Giordano, Francesco; Giroletti, Marcello; Gomez-Vargas, Germán A.; Green, David; Grenier, Isabelle A.; Guiriec, Sylvain; Harding, Alice K.; Hewitt, John W.; Horan, Deirdre; Jóhannesson, Guðlaugur; Kensei, Shiki; Kuss, Michael; La Mura, Giovanni; Larsson, Stefan; Latronico, Luca; Li, Jian; Longo, Francesco; Loparco, Francesco; Lovellette, Michael N.; Lubrano, Pasquale; Magill, Jeffrey D.; Maldera, Simone; Manfreda, Alberto; Mazziotta, Mario N.; McEnery, Julie E.; Michelson, Peter F.; Mirabal, Nestor; Mitthumsiri, Warit; Mizuno, Tsunefumi; Monzani, Maria Elena; Morselli, Aldo; Moskalenko, Igor V.; Nuss, Eric; Ohsugi, Takashi; Omodei, Nicola; Orienti, Monica; Orlando, Elena; Palatiello, Michele; Paliya, Vaidehi S.; de Palma, Francesco; Paneque, David; Perkins, Jeremy S.; Persic, Massimo; Pesce-Rollins, Melissa; Porter, Troy A.; Principe, Giacomo; Rainò, Silvia; Rando, Riccardo; Ray, Paul S.; Razzano, Massimiliano; Reimer, Anita; Reimer, Olaf; Romani, Roger W.; Saz Parkinson, Pablo M.; Sgrò, Carmelo; Siskind, Eric J.; Smith, David A.; Spada, Francesca; Spandre, Gloria; Spinelli, Paolo; Thayer, Jana B.; Thompson, David J.; Torres, Diego F.; Troja, Eleonora; Vianello, Giacomo; Wood, Kent; Wood, Matthew

2018-01-01

Millisecond pulsars (MSPs) are old neutron stars that spin hundreds of times per second and appear to pulsate as their emission beams cross our line of sight. To date, radio pulsations have been detected from all rotation-powered MSPs. In an attempt to discover radio-quiet gamma-ray MSPs, we used the aggregated power from the computers of tens of thousands of volunteers participating in the Einstein@Home distributed computing project to search for pulsations from unidentified gamma-ray sources in Fermi Large Area Telescope data. This survey discovered two isolated MSPs, one of which is the only known rotation-powered MSP to remain undetected in radio observations. These gamma-ray MSPs were discovered in completely blind searches without prior constraints from other observations, raising hopes for detecting MSPs from a predicted Galactic bulge population. PMID:29503868

Breast cancer in Ethiopia: evidence for geographic difference in the distribution of molecular subtypes in Africa.

Science.gov (United States)

Hadgu, Endale; Seifu, Daniel; Tigneh, Wondemagegnhu; Bokretsion, Yonas; Bekele, Abebe; Abebe, Markos; Sollie, Thomas; Merajver, Sofia D; Karlsson, Christina; Karlsson, Mats G

2018-02-14

Breast cancer is a heterogeneous disease with several morphological and molecular subtypes. Widely accepted molecular classification system uses assessment of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and proliferation marker Ki67. Few studies have been conducted on the incidence and molecular types of breast cancer in Sub-Saharan Africa. Previous studies mainly from Western and Central Africa, showed breast cancer to occur at younger ages and to present with aggressive features, such as high-grade, advanced stage and triple-negative phenotype (negative for ER, PR and HER2). Limited data from East Africa including Ethiopia however shows hormone receptor negative tumors to account for a lower proportion of all breast cancers than has been reported from elsewhere in Africa. In this study from Tikur Anbessa Specialized Hospital, 114 breast cancer patients diagnosed between 2012 and 2015 were enrolled. ER, PR, Ki67 and HER2 receptor status were assessed using immunohistochemistry from tissue microarrays. FISH was used for assessment of gene amplification in all equivocal tumor samples and for confirmation in HER2-enriched cases. The distribution of molecular subtypes was: Luminal A: 40%; Luminal B: 26%; HER2-enriched: 10%; TNBC: 23%. ER were positive in 65% of all tumors and 43% the cases were positive for PR. There was statistically significant difference in median age at diagnosis between the molecular subtypes (P molecular subtypes in different age ranges with Luminal B subtype being more common at younger ages (median = 36) and Luminal A subtype more prevalent at older ages (median = 42). There were no statistically significant differences in tumor grade, histology, and stage between the molecular subtypes of breast cancer. The present study detected Luminal A breast cancer to be the most common subtype and reveals a relatively low rate of hormone receptor negative and TNBC. Our findings and

New jump mechanisms for dumbbell and induced migration of point defects by molecular dynamics simulation

International Nuclear Information System (INIS)

Doan, N.V.; Pontikis, V.; Tenenbaum, A.

1978-01-01

The induced migration of the (100) - dumbbell is studied using the molecular dynamics simulation. Two new types of jumps are discovered for the dumbbell: first the jump takes place through an intermediate crowdion configuration (110), then the crowdion is converted into the dumbbell configuration with some other orientation. The threshold energy is found for different knocked-on directions. The dependence of the interstitial jump frequency on the incident electron energy is determined for copper. The induced interstitial migration shows a maximum value, but for an electron energy around 15 Kev. The effect of new jump mechanisms on the effective recombination volume is discussed

Two Newly Discovered Plants in Taiwan

OpenAIRE

Tian-Chuan Hsu; Jia-Jung Lin; Shih-Wen Chung

2009-01-01

Two herbs are newly discovered in Taiwan. Limnophila fragrans (G. Forst.) Seem. (Scrophulariaceae), native in SE Asia, is recognized from southern lowlands. Anagallis minima (L.) E. H. L. Krause (Primulaceae), native in N America and Europe, was found from northern mountainous region at low altitudes. In this study, descriptions, line drawings, color photos and a distribution map of the two species are provided.

Gene discovery in glioma in the context of molecular reclassification of tumors

Directory of Open Access Journals (Sweden)

Khushboo Irshad

2015-12-01

Full Text Available Conventional classification of tumors, especially in terms of staging and grading is of immense importance for both prognostication as well as management strategies. However it is not a perfect system and there are many instances where tumor behaviour does not correspond to what is expected. In addition, with the onset of targeted therapy, the identification of the distinct molecular target in a subset of tumors becomes a marker of tumor behaviour as well as a target of therapy. This leads to the concept of molecular subclassification of tumors where molecular markers further refine and in some cases, alter conventional classification. We would be presenting this concept in relation to glial tumors, especially in the context of molecular markers discovered in our laboratory.

[Neonatal hyperbilirubinemia and molecular mechanisms of jaundice].

Science.gov (United States)

Jirsa, M; Sticová, E

2013-07-01

The introductory summarises the classical path of heme degradation and classification of jaundice. Subsequently, a description of neonatal types of jaundice is given, known as Crigler Najjar, Gilberts, DubinJohnson and Rotor syndromes, emphasising the explanation of the molecular mechanisms of these metabolic disorders. Special attention is given to a recently discovered molecular mechanism of the Rotor syndrome. The mechanism is based on the inability of the liver to retrospectively uptake the conjugated bilirubin fraction primarily excreted into the blood, not bile. A reduced ability of the liver to uptake the conjugated bilirubin contributes to the development of hyperbilirubinemia in common disorders of the liver and bile ducts and to the toxicity of xenobiotics and drugs using transport proteins for conjugated bilirubin.

Molecular musings in microbial ecology and evolution.

Science.gov (United States)

Case, Rebecca J; Boucher, Yan

2011-11-10

A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology.The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology.The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology).The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies

Chandra Discovers Cosmic Cannonball

Science.gov (United States)

2007-11-01

One of the fastest moving stars ever seen has been discovered with NASA's Chandra X-ray Observatory. This cosmic cannonball is challenging theories to explain its blistering speed. Astronomers used Chandra to observe a neutron star, known as RX J0822-4300, over a period of about five years. During that span, three Chandra observations clearly show the neutron star moving away from the center of the Puppis A supernova remnant. This remnant is the stellar debris field created during the same explosion in which the neutron star was created about 3700 years ago. Chandra X-ray Image of RX J0822-4300 in Puppis A Chandra X-ray Image of RX J0822-4300 in Puppis A By combining how far it has moved across the sky with its distance from Earth, astronomers determined the neutron star is moving at over 3 million miles per hour. At this rate, RX J0822-4300 is destined to escape from the Milky Way after millions of years, even though it has only traveled about 20 light years so far. "This star is moving at 3 million miles an hour, but it's so far away that the apparent motion we see in five years is less than the height of the numerals in the date on a penny, seen from the length of a football field," said Frank Winkler of Middlebury College in Vermont. "It's remarkable, and a real testament to the power of Chandra, that such a tiny motion can be measured." Labeled Image of RX J0822-4300 in Puppis A Labeled Image of RX J0822-4300 in Puppis A "Just after it was born, this neutron star got a one-way ticket out of the Galaxy," said co-author Robert Petre of NASA's Goddard Space Flight Center in Greenbelt, Md. "Astronomers have seen other stars being flung out of the Milky Way, but few as fast as this." So-called hypervelocity stars have been previously discovered shooting out of the Milky Way with speeds around one million miles per hour. One key difference between RX J0822-4300 and these other reported galactic escapees is the source of their speed. The hypervelocity stars are

Molecular diversity and hypoglycemic polypeptide-P content of Momordica charantia in different accessions and different seasons.

Science.gov (United States)

Tian, Miao; Zeng, Xiang-Qing; Song, Huan-Lei; Hu, Shan-Xin; Wang, Fu-Jun; Zhao, Jian; Hu, Zhi-Bi

2015-04-01

Momordica charantia (MC) has been used for treating diabetes mellitus from ancient times in Asia, Africa and South America. There are many MC accessions in local markets. Polypeptide-P as a main hypoglycemic component in MC was first studied in this experiment to illustrate the different contents in MC of different accessions and different harvesting times. Nineteen MC accessions collected from different regions were clustered into three groups using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) molecular markers. Content of polypeptide-P in the tested MC accessions was detected by western blot (WB) method. The WB results revealed that polypeptide-P was detected in MC accessions harvested in June and July but not in September and October. Furthermore, Polypeptide-P content corresponded well with the MC accessions. Our results suggest that the MC accessions and the harvesting times or the weather during harvest play significant roles in high content of polypeptide-P. © 2014 Society of Chemical Industry.

Challenges in service mining : record, check, discover

NARCIS (Netherlands)

Aalst, van der W.M.P.; Daniel, F.; Dolog, P.; Li, Q.

2013-01-01

Process mining aims to discover, monitor and improve real processes by extracting knowledge from event logs abundantly available in today’s information systems. Although process mining has been applied in hundreds of organizations and process mining techniques have been embedded in a variety of

The Magic of Mathematics Discovering the Spell of Mathematics

CERN Document Server

Pappas, Theoni

2011-01-01

Delves into the world of ideas, explores the spell mathematics casts on our lives, and helps you discover mathematics where you least expect it. Be spellbound by the mathematical designs found in nature. Learn how knots may untie the mysteries of life. Be mesmerized by the computer revolution. Discover how the hidden forces of mathematics hold architectural structures together connect your telephone calls help airplanes get off the ground solve the mysteries of the living cell. See how some artists use a mathematical palette in their works and how many writers draw upon the wealth of its ideas

A Combination of 3D-QSAR, Molecular Docking and Molecular Dynamics Simulation Studies of Benzimidazole-Quinolinone Derivatives as iNOS Inhibitors

Directory of Open Access Journals (Sweden)

Peixun Liu

2012-09-01

Full Text Available Inducible Nitric Oxide Synthase (iNOS has been involved in a variety of diseases, and thus it is interesting to discover and optimize new iNOS inhibitors. In previous studies, a series of benzimidazole-quinolinone derivatives with high inhibitory activity against human iNOS were discovered. In this work, three-dimensional quantitative structure-activity relationships (3D-QSAR, molecular docking and molecular dynamics (MD simulation approaches were applied to investigate the functionalities of active molecular interaction between these active ligands and iNOS. A QSAR model with R2 of 0.9356, Q2 of 0.8373 and Pearson-R value of 0.9406 was constructed, which presents a good predictive ability in both internal and external validation. Furthermore, a combined analysis incorporating the obtained model and the MD results indicates: (1 compounds with the proper-size hydrophobic substituents at position 3 in ring-C (R3 substituent, hydrophilic substituents near the X6 of ring-D and hydrophilic or H-bond acceptor groups at position 2 in ring-B show enhanced biological activities; (2 Met368, Trp366, Gly365, Tyr367, Phe363, Pro344, Gln257, Val346, Asn364, Met349, Thr370, Glu371 and Tyr485 are key amino acids in the active pocket, and activities of iNOS inhibitors are consistent with their capability to alter the position of these important residues, especially Glu371 and Thr370. The results provide a set of useful guidelines for the rational design of novel iNOS inhibitors.

Two Newly Discovered Plants in Taiwan

Directory of Open Access Journals (Sweden)

Tian-Chuan Hsu

2009-11-01

Full Text Available Two herbs are newly discovered in Taiwan. Limnophila fragrans (G. Forst. Seem. (Scrophulariaceae, native in SE Asia, is recognized from southern lowlands. Anagallis minima (L. E. H. L. Krause (Primulaceae, native in N America and Europe, was found from northern mountainous region at low altitudes. In this study, descriptions, line drawings, color photos and a distribution map of the two species are provided.

Modern classification of neoplasms: reconciling differences between morphologic and molecular approaches

International Nuclear Information System (INIS)

Berman, Jules

2005-01-01

For over 150 years, pathologists have relied on histomorphology to classify and diagnose neoplasms. Their success has been stunning, permitting the accurate diagnosis of thousands of different types of neoplasms using only a microscope and a trained eye. In the past two decades, cancer genomics has challenged the supremacy of histomorphology by identifying genetic alterations shared by morphologically diverse tumors and by finding genetic features that distinguish subgroups of morphologically homogeneous tumors. The Developmental Lineage Classification and Taxonomy of Neoplasms groups neoplasms by their embryologic origin. The putative value of this classification is based on the expectation that tumors of a common developmental lineage will share common metabolic pathways and common responses to drugs that target these pathways. The purpose of this manuscript is to show that grouping tumors according to their developmental lineage can reconcile certain fundamental discrepancies resulting from morphologic and molecular approaches to neoplasm classification. In this study, six issues in tumor classification are described that exemplify the growing rift between morphologic and molecular approaches to tumor classification: 1) the morphologic separation between epithelial and non-epithelial tumors; 2) the grouping of tumors based on shared cellular functions; 3) the distinction between germ cell tumors and pluripotent tumors of non-germ cell origin; 4) the distinction between tumors that have lost their differentiation and tumors that arise from uncommitted stem cells; 5) the molecular properties shared by morphologically disparate tumors that have a common developmental lineage, and 6) the problem of re-classifying morphologically identical but clinically distinct subsets of tumors. The discussion of these issues in the context of describing different methods of tumor classification is intended to underscore the clinical value of a robust tumor classification. A

Discovering approximate-associated sequence patterns for protein-DNA interactions

KAUST Repository

Chan, Tak Ming

2010-12-30

Motivation: The bindings between transcription factors (TFs) and transcription factor binding sites (TFBSs) are fundamental protein-DNA interactions in transcriptional regulation. Extensive efforts have been made to better understand the protein-DNA interactions. Recent mining on exact TF-TFBS-associated sequence patterns (rules) has shown great potentials and achieved very promising results. However, exact rules cannot handle variations in real data, resulting in limited informative rules. In this article, we generalize the exact rules to approximate ones for both TFs and TFBSs, which are essential for biological variations. Results: A progressive approach is proposed to address the approximation to alleviate the computational requirements. Firstly, similar TFBSs are grouped from the available TF-TFBS data (TRANSFAC database). Secondly, approximate and highly conserved binding cores are discovered from TF sequences corresponding to each TFBS group. A customized algorithm is developed for the specific objective. We discover the approximate TF-TFBS rules by associating the grouped TFBS consensuses and TF cores. The rules discovered are evaluated by matching (verifying with) the actual protein-DNA binding pairs from Protein Data Bank (PDB) 3D structures. The approximate results exhibit many more verified rules and up to 300% better verification ratios than the exact ones. The customized algorithm achieves over 73% better verification ratios than traditional methods. Approximate rules (64-79%) are shown statistically significant. Detailed variation analysis and conservation verification on NCBI records demonstrate that the approximate rules reveal both the flexible and specific protein-DNA interactions accurately. The approximate TF-TFBS rules discovered show great generalized capability of exploring more informative binding rules. © The Author 2010. Published by Oxford University Press. All rights reserved.

Y(4143) is probably a molecular partner of Y(3930)

International Nuclear Information System (INIS)

Liu Xiang; Zhu Shilin

2009-01-01

After discussing the various possible interpretations of the Y(4143) signal observed by the CDF collaboration in the J/ψφ mode, we tend to conclude that Y(4143) is probably a D s *D s * molecular state with J PC =0 ++ or 2 ++ while Y(3930) is its D*D* molecular partner as predicted in our previous work [X. Liu, Z. G. Luo, Y. R. Liu, and Shi-Lin Zhu, Eur. Phys. J. C 61, 411 (2009)]. Both the hidden-charm and open-charm two-body decays occur through the rescattering of the vector components within the molecular states while the three- and four-body open-charm decay modes are forbidden kinematically. Hence, their widths are narrow naturally. CDF, BABAR and Belle collaborations may have discovered heavy molecular states already. We urge experimentalists to measure their quantum numbers and explore their radiative decay modes in the future.

Molecular Form Differences Between Prostate-Specific Antigen (PSA) Standards Create Quantitative Discordances in PSA ELISA Measurements

Science.gov (United States)

McJimpsey, Erica L.

2016-02-01

The prostate-specific antigen (PSA) assays currently employed for the detection of prostate cancer (PCa) lack the specificity needed to differentiate PCa from benign prostatic hyperplasia and have high false positive rates. The PSA calibrants used to create calibration curves in these assays are typically purified from seminal plasma and contain many molecular forms (intact PSA and cleaved subforms). The purpose of this study was to determine if the composition of the PSA molecular forms found in these PSA standards contribute to the lack of PSA test reliability. To this end, seminal plasma purified PSA standards from different commercial sources were investigated by western blot (WB) and in multiple research grade PSA ELISAs. The WB results revealed that all of the PSA standards contained different mass concentrations of intact and cleaved molecular forms. Increased mass concentrations of intact PSA yielded higher immunoassay absorbance values, even between lots from the same manufacturer. Standardization of seminal plasma derived PSA calibrant molecular form mass concentrations and purification methods will assist in closing the gaps in PCa testing measurements that require the use of PSA values, such as the % free PSA and Prostate Health Index by increasing the accuracy of the calibration curves.

Impact of Molecular Subtypes in Muscle-invasive Bladder Cancer on Predicting Response and Survival after Neoadjuvant Chemotherapy.

Science.gov (United States)

Seiler, Roland; Ashab, Hussam Al Deen; Erho, Nicholas; van Rhijn, Bas W G; Winters, Brian; Douglas, James; Van Kessel, Kim E; Fransen van de Putte, Elisabeth E; Sommerlad, Matthew; Wang, Natalie Q; Choeurng, Voleak; Gibb, Ewan A; Palmer-Aronsten, Beatrix; Lam, Lucia L; Buerki, Christine; Davicioni, Elai; Sjödahl, Gottfrid; Kardos, Jordan; Hoadley, Katherine A; Lerner, Seth P; McConkey, David J; Choi, Woonyoung; Kim, William Y; Kiss, Bernhard; Thalmann, George N; Todenhöfer, Tilman; Crabb, Simon J; North, Scott; Zwarthoff, Ellen C; Boormans, Joost L; Wright, Jonathan; Dall'Era, Marc; van der Heijden, Michiel S; Black, Peter C

2017-10-01

An early report on the molecular subtyping of muscle-invasive bladder cancer (MIBC) by gene expression suggested that response to neoadjuvant chemotherapy (NAC) varies by subtype. To investigate the ability of molecular subtypes to predict pathological downstaging and survival after NAC. Whole transcriptome profiling was performed on pre-NAC transurethral resection specimens from 343 patients with MIBC. Samples were classified according to four published molecular subtyping methods. We developed a single-sample genomic subtyping classifier (GSC) to predict consensus subtypes (claudin-low, basal, luminal-infiltrated and luminal) with highest clinical impact in the context of NAC. Overall survival (OS) according to subtype was analyzed and compared with OS in 476 non-NAC cases (published datasets). Gene expression analysis was used to assign subtypes. Receiver-operating characteristics were used to determine the accuracy of GSC. The effect of GSC on survival was estimated by Cox proportional hazard regression models. The models generated subtype calls in expected ratios with high concordance across subtyping methods. GSC was able to predict four consensus molecular subtypes with high accuracy (73%), and clinical significance of the predicted consensus subtypes could be validated in independent NAC and non-NAC datasets. Luminal tumors had the best OS with and without NAC. Claudin-low tumors were associated with poor OS irrespective of treatment regimen. Basal tumors showed the most improvement in OS with NAC compared with surgery alone. The main limitations of our study are its retrospective design and comparison across datasets. Molecular subtyping may have an impact on patient benefit to NAC. If validated in additional studies, our results suggest that patients with basal tumors should be prioritized for NAC. We discovered the first single-sample classifier to subtype MIBC, which may be suitable for integration into routine clinical practice. Different molecular

Integrative genome-wide expression profiling identifies three distinct molecular subgroups of renal cell carcinoma with different patient outcome

Directory of Open Access Journals (Sweden)

Beleut Manfred

2012-07-01

Full Text Available Abstract Background Renal cell carcinoma (RCC is characterized by a number of diverse molecular aberrations that differ among individuals. Recent approaches to molecularly classify RCC were based on clinical, pathological as well as on single molecular parameters. As a consequence, gene expression patterns reflecting the sum of genetic aberrations in individual tumors may not have been recognized. In an attempt to uncover such molecular features in RCC, we used a novel, unbiased and integrative approach. Methods We integrated gene expression data from 97 primary RCC of different pathologic parameters, 15 RCC metastases as well as 34 cancer cell lines for two-way nonsupervised hierarchical clustering using gene groups suggested by the PANTHER Classification System. We depicted the genomic landscape of the resulted tumor groups by means of Single Nuclear Polymorphism (SNP technology. Finally, the achieved results were immunohistochemically analyzed using a tissue microarray (TMA composed of 254 RCC. Results We found robust, genome wide expression signatures, which split RCC into three distinct molecular subgroups. These groups remained stable even if randomly selected gene sets were clustered. Notably, the pattern obtained from RCC cell lines was clearly distinguishable from that of primary tumors. SNP array analysis demonstrated differing frequencies of chromosomal copy number alterations among RCC subgroups. TMA analysis with group-specific markers showed a prognostic significance of the different groups. Conclusion We propose the existence of characteristic and histologically independent genome-wide expression outputs in RCC with potential biological and clinical relevance.

The impact of computer science in molecular medicine: enabling high-throughput research.

Science.gov (United States)

de la Iglesia, Diana; García-Remesal, Miguel; de la Calle, Guillermo; Kulikowski, Casimir; Sanz, Ferran; Maojo, Víctor

2013-01-01

The Human Genome Project and the explosion of high-throughput data have transformed the areas of molecular and personalized medicine, which are producing a wide range of studies and experimental results and providing new insights for developing medical applications. Research in many interdisciplinary fields is resulting in data repositories and computational tools that support a wide diversity of tasks: genome sequencing, genome-wide association studies, analysis of genotype-phenotype interactions, drug toxicity and side effects assessment, prediction of protein interactions and diseases, development of computational models, biomarker discovery, and many others. The authors of the present paper have developed several inventories covering tools, initiatives and studies in different computational fields related to molecular medicine: medical informatics, bioinformatics, clinical informatics and nanoinformatics. With these inventories, created by mining the scientific literature, we have carried out several reviews of these fields, providing researchers with a useful framework to locate, discover, search and integrate resources. In this paper we present an analysis of the state-of-the-art as it relates to computational resources for molecular medicine, based on results compiled in our inventories, as well as results extracted from a systematic review of the literature and other scientific media. The present review is based on the impact of their related publications and the available data and software resources for molecular medicine. It aims to provide information that can be useful to support ongoing research and work to improve diagnostics and therapeutics based on molecular-level insights.

MICRO-STRUCTURAL INVESTIGATION OF SOME ARTIFACTS DISCOVERED AT POROLISSUM

Directory of Open Access Journals (Sweden)

MUNTEANU Mihai

2014-09-01

Full Text Available the paper presents the investigation of two fragments of roman bronze artefacts, discovered during archaeological works performed at Porolissum, an important military and economical point on the northern limes of Dacia Province. One of the analyzed fragments (Mi1 was taken from a consistent fragment of a Roman bronze statue, while the second (Mi2 was among a lot of small metal pieces, discovered in the same investigated area. Using highly sophisticated micro-structural analysing techniques – X-Ray diffraction, the paper investigates the possibility that the Mi2 fragment may have belonged to the same statue from which the sample Mi1 was taken

Probing molecular orientations in thin films by x-ray photoelectron spectroscopy

Science.gov (United States)

Li, Y.; Li, P.; Lu, Z.-H.

2018-03-01

A great number of functional organic molecules in active thin-film layers of optoelectronic devices have highly asymmetric structures, such as plate-like, rod-like, etc. This makes molecular orientation an important aspect in thin-films as it can significantly affect both the optical and electrical performance of optoelectronic devices. With a combination of in-situ ultra violet photoelectron spectroscopy (UPS) and x-ray photoelectron spectroscopy (XPS) investigations for organic molecules having a broad range of structural properties, we discovered a rigid connection of core levels and frontier highest occupied molecular orbital levels at organic interfaces. This finding opens up opportunities of using X-ray photoemission spectroscopy as an alternative tool to UPS for providing an easy and unambiguous data interpretation in probing molecular orientations.

A strategy to discover new organizers identifies a putative heart organizer.

Science.gov (United States)

Anderson, Claire; Khan, Mohsin A F; Wong, Frances; Solovieva, Tatiana; Oliveira, Nidia M M; Baldock, Richard A; Tickle, Cheryll; Burt, Dave W; Stern, Claudio D

2016-08-25

Organizers are regions of the embryo that can both induce new fates and impart pattern on other regions. So far, surprisingly few organizers have been discovered, considering the number of patterned tissue types generated during development. This may be because their discovery has relied on transplantation and ablation experiments. Here we describe a new approach, using chick embryos, to discover organizers based on a common gene expression signature, and use it to uncover the anterior intestinal portal (AIP) endoderm as a putative heart organizer. We show that the AIP can induce cardiac identity from non-cardiac mesoderm and that it can pattern this by specifying ventricular and suppressing atrial regional identity. We also uncover some of the signals responsible. The method holds promise as a tool to discover other novel organizers acting during development.

On a New Technique for Discovering Variable Stars

Directory of Open Access Journals (Sweden)

Mironov A. V.

2003-12-01

Full Text Available A technique for discovering variable stars based on the calculation of the correlation coefficients is proposed. Applications of the technique are shown on the results of numerical experiments and on the Hipparcos photometric data.

Molecular outflows in the L1641 region of Orion

International Nuclear Information System (INIS)

Morgan, J.A.

1990-01-01

Little is known about the interaction between molecular outflows associated with young stellar objects and the parent molecular cloud that produced them. This is because molecular outflows are a recently discovered phenomenon and, so, have not had their global properties studied in great detail and molecular clouds were not mapped to sufficiently high spatial resolution to resolve the interaction. The interaction between molecular outflows and the L1641 molecular cloud is addressed by both identifying and mapping all the molecular outflows as well as the detailed structure of the cloud. Candidate molecular outflows were found from single point 12-CO observations of young stellar objects identified from the IRAS survey data. The candidate sources were then mapped to confirm their molecular outflow nature. From these maps, molecular outflow characteristics such as their morphology, orientation, and energetics were determined. In addition, the Orion molecular cloud was mapped to compare directly with the molecular outflows. The molecular outflows identified were found to have rising infrared spectra, radio continuum emission that suggests a stellar wind or optically thick H II region, and molecular line strengths that indicate that they are embedded within a very dense environment. The lack of an optical counterpart for many molecular outflows suggests that they occur at the earliest stages of stellar evolution. The lack of an optical counterpart for many molecular outflows suggest that they occur at the earliest stages of stellar evolution. The orientations of the molecular outflows appear to lie in no preferred direction and they have shapes that indicate that the molecular cloud is responsible for determining their direction and collimation

Corrected placement of Mus-Rattus fossil calibration forces precision in the molecular tree of rodents

OpenAIRE

Kimura, Yuri; Hawkins, Melissa T. R.; McDonough, Molly M.; Jacobs, Louis L.; Flynn, Lawrence J.

2015-01-01

Time calibration derived from the fossil record is essential for molecular phylogenetic and evolutionary studies. Fossil mice and rats, discovered in the Siwalik Group of Pakistan, have served as one of the best-known fossil calibration points in molecular phylogenic studies. Although these fossils have been widely used as the 12 Ma date for the Mus/Rattus split or a more basal split, conclusive paleontological evidence for the nodal assignments has been absent. This study analyzes newly reco...

How to Discover the Rogers–Ramanujan Identities

Indian Academy of Sciences (India)

IAS Admin

The purpose of this article is to introduce you to the. Rogers–Ramanujan identities, by discussing an approach to discover them. When you see that they appear from a very simple generalization of the simplest possible in- finite continued fraction, that in turn is related to the celebrated Fibonacci sequence, perhaps you may ...

A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms

Science.gov (United States)

Trujillo, Caleb M.; Anderson, Trevor R.; Pelaez, Nancy J.

2015-01-01

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do explanations made by experts from different biology subdisciplines at a university support the validity of this model? Guided by the modeling framework of R. S. Justi and J. K. Gilbert, the validity of an initial model was tested by asking seven biologists to explain a molecular mechanism of their choice. Data were collected from interviews, artifacts, and drawings, and then subjected to thematic analysis. We found that biologists explained the specific activities and organization of entities of the mechanism. In addition, they contextualized explanations according to their biological and social significance; integrated explanations with methods, instruments, and measurements; and used analogies and narrated stories. The derived methods, analogies, context, and how themes informed the development of our final MACH model of mechanistic explanations. Future research will test the potential of the MACH model as a guiding framework for instruction to enhance the quality of student explanations. PMID:25999313

Trend of different molecular markers in the last decades for studying human migrations.

Science.gov (United States)

Kundu, Sharbadeb; Ghosh, Sankar Kumar

2015-02-10

Anatomically modern humans are known to have widely migrated throughout history. Different scientific evidences suggest that the entire human population descended from just several thousand African migrants. About 85,000 years ago, the first wave of human migration was out of Africa, that followed the coasts through the Middle East, into Southern Asia via Sri Lanka, and in due course around Indonesia and into Australia. Another wave of migration between 40,000 and 12,000 years ago brought humans northward into Europe. However, the frozen north limited human expansion in Europe, and created a land bridge, "Bering land bridge", connecting Asia with North America about 25,000 years ago. Although fossil data give the most direct information about our past, it has certain anomalies. So, molecular archeologists are now using different molecular markers to trace the "most recent common ancestor" and also the migration pattern of modern humans. In this study, we have studied the trend of molecular markers and also the methodologies implemented in the last decades (2003-2014). From our observation, we can say that D-loop region of mtDNA and Y chromosome based markers are predominant. Nevertheless, mtDNA, especially the D-loop region, has some unique features, which makes it a more effective marker for tracing prehistoric footprints of modern human populations. Although, natural selection should also be taken into account in studying mtDNA based human migration. As per technology is concerned, Sanger sequencing is the major technique that is being used in almost all studies. But, the emergence of different cost-effective-and-easy-to-handle NGS platforms has increased its popularity over Sanger sequencing in studying human migration. Copyright © 2014. Published by Elsevier B.V.

GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data.

Science.gov (United States)

Schulz, Tizian; Stoye, Jens; Doerr, Daniel

2018-05-08

Hi-C sequencing offers novel, cost-effective means to study the spatial conformation of chromosomes. We use data obtained from Hi-C experiments to provide new evidence for the existence of spatial gene clusters. These are sets of genes with associated functionality that exhibit close proximity to each other in the spatial conformation of chromosomes across several related species. We present the first gene cluster model capable of handling spatial data. Our model generalizes a popular computational model for gene cluster prediction, called δ-teams, from sequences to graphs. Following previous lines of research, we subsequently extend our model to allow for several vertices being associated with the same label. The model, called δ-teams with families, is particular suitable for our application as it enables handling of gene duplicates. We develop algorithmic solutions for both models. We implemented the algorithm for discovering δ-teams with families and integrated it into a fully automated workflow for discovering gene clusters in Hi-C data, called GraphTeams. We applied it to human and mouse data to find intra- and interchromosomal gene cluster candidates. The results include intrachromosomal clusters that seem to exhibit a closer proximity in space than on their chromosomal DNA sequence. We further discovered interchromosomal gene clusters that contain genes from different chromosomes within the human genome, but are located on a single chromosome in mouse. By identifying δ-teams with families, we provide a flexible model to discover gene cluster candidates in Hi-C data. Our analysis of Hi-C data from human and mouse reveals several known gene clusters (thus validating our approach), but also few sparsely studied or possibly unknown gene cluster candidates that could be the source of further experimental investigations.

Helium Adsorption on Carbon Nanotube Bundles with Different Diameters:. Molecular Dynamics Simulation

Science.gov (United States)

Majidi, R.; Karami, A. R.

2013-05-01

We have used molecular dynamics simulation to study helium adsorption capacity of carbon nanotube bundles with different diameters. Homogeneous carbon nanotube bundles of (8,8), (9,9), (10,10), (11,11), and (12,12) single walled carbon nanotubes have been considered. The results indicate that the exohedral adsorption coverage does not depend on the diameter of carbon nanotubes, while the endohedral adsorption coverage is increased by increasing the diameter.

Molecular Form Differences Between Prostate-Specific Antigen (PSA) Standards Create Quantitative Discordances in PSA ELISA Measurements

Science.gov (United States)

McJimpsey, Erica L.

2016-01-01

The prostate-specific antigen (PSA) assays currently employed for the detection of prostate cancer (PCa) lack the specificity needed to differentiate PCa from benign prostatic hyperplasia and have high false positive rates. The PSA calibrants used to create calibration curves in these assays are typically purified from seminal plasma and contain many molecular forms (intact PSA and cleaved subforms). The purpose of this study was to determine if the composition of the PSA molecular forms found in these PSA standards contribute to the lack of PSA test reliability. To this end, seminal plasma purified PSA standards from different commercial sources were investigated by western blot (WB) and in multiple research grade PSA ELISAs. The WB results revealed that all of the PSA standards contained different mass concentrations of intact and cleaved molecular forms. Increased mass concentrations of intact PSA yielded higher immunoassay absorbance values, even between lots from the same manufacturer. Standardization of seminal plasma derived PSA calibrant molecular form mass concentrations and purification methods will assist in closing the gaps in PCa testing measurements that require the use of PSA values, such as the % free PSA and Prostate Health Index by increasing the accuracy of the calibration curves. PMID:26911983

[Molecular characterization of Echinococcus granulosus isolates obtained from different hosts].

Science.gov (United States)

Erdoğan, Emrah; Özkan, Bora; Mutlu, Fatih; Karaca, Serkan; Şahin, İzzet

2017-01-01

Echinococcus granulosus is a parasite that can be seen throughout the world. So far, five species of genus Echinococcus have been identified as parasite in people: E.granulosus, E.multilocularis, E.vogeli, E.oligarthrus, E.shiquicus. Larval (metacestod) form of parasite settles in internal organs of hoofed animals (cattle, goats, pigs, horses, sheep, etc.) and human; the adult form is found in small intestine of final host, canine. Disease caused by parasite called as "Cystic echinococcosis" (CE) is an important health problem and causes economic losses in many countries including our country that livestock is common. Infective eggs cause infections in intermediate hosts by taking oral way and rarely inhalation. Received egg opens in the stomach and intestines of intermediate host and oncosphere is released. Oncosphere quickly reaches the lamina propria of the villus epithelium by its histolytic enzymes and hooks. It usually transported from here to the liver and lungs, less frequently, muscle, brain, spleen, kidney and to other organs through the veins. By molecular studies, five species have been validated taxonomically and 10 different variants or strains of E.granulosus have been identified. Host and developmental differences between strains may negatively affect control studies and fight against the parasite. This study aimed to determinate E.granulosus strains obtained from cyst material of different intermediate hosts from different regions of Turkey by molecular methods. In the study, 25 human, 8 cattle, 6 sheep and 2 goat cysts material has been collected. Total genomic DNA was isolated from protoscoleces in cyst fluid and analyzed by PCR with COX-1 (L) and COX-1 (S) genes specific primers. DNA sequence analysis for each PCR product has been made. DNA sequence analysis results evaluated phylogenetically by MEGA analyze and BLAST software. As a result of this study, all isolates were identified as E.granulosus sensu stricto (G1) by DNA sequence analysis. CE

A new screening method for discovering antibacterial agents from ...

African Journals Online (AJOL)

A new screening method for discovering antibacterial agents from filamentous fungi. ... African Journal of Biotechnology ... Keywords: Drug-resistant bacterial pathogens, novel antibiotics; screening method, filamentous fungi products ...

Association of radionuclides with different molecular size fractions in soil solution: implications for plant uptake

International Nuclear Information System (INIS)

Nisbet, A.F.; Shaw, S.; Salbu, B.

1993-01-01

The feasibility of using hollow fibre ultrafiltration to determine the molecular size distribution of radionuclides in soil solution was investigated. The physical and chemical composition of soil plays a vital role in determining radionuclide uptake by plant roots. Soil solution samples were extracted from loam, peat and sand soils that had been artificially contaminated with 137 Cs, 90 Sr, 239 Pu and 241 Am six years previously as part of a five-year lysimeter study on radionuclide uptake to crops. Ultrafiltration of soil solution was performed using hollow fibre cartridges with a nominal molecular weight cut off of 3 and 10 kD. The association of 137 Cs, 90 Sr, 239 Pu and 241 Am with different molecular size fractions of the soil solution is discussed in terms of radionuclide bioavailability to cabbage grown in the same three soils. 137 Cs and 90 Sr were present in low molecular weight forms and as such were mobile in soil and potentially available for uptake by the cabbage. In contrast, a large proportion (61-87%) of the 239 Pu and 241 Am were associated with colloidal and high molecular weight material and therefore less available for uptake by plant roots. The contribution from low molecular weight species of 239 Pu and 241 Am to the total activity in soil solution decreased in the order loam ≥ peat ≥ sand. Association of radionuclides with low molecular weight species of less than 3 kD did not, however, automatically imply availability to plants. (author)

[Crosslinking sodium hyaluronate gel with different ratio of molecular weight for subcutaneous injection: animal experimental study and clinical trials subcutaneous injection].

Science.gov (United States)

Ran, Weizhi; Wang, Xiaoli; Hu, Yuefei; Gao, Songying; Yang, Yahong; Sun, Jian; Sun, Shuming; Liu, Zhongmei; Wang, Jiangling

2015-05-01

To investigate the biocompatibility and degradation rate of crosslinking sodium hyaluronate gel with different ratio of molecular weight, so as to choose the effective, safe and totally degraded hyaluronate gel for aesthetic injection. (1) Compound colloid was formed by cross-linking the divinyl sulphone and sodium hyaluronate with different molecular weight (4 x 10(5), 8 x 10(5), 10 x 10(5), 12 x 10(5)). (2) Healthy level KM mice was randomly divided into two groups to receive hyaluronic acid gel or liquid injection. Each group was subdivided into three subgroup to receive hyaluronic acid with different molecular weight. The biocompatibility and degradation rate, of hyaluronate were observed at 7, 90, 180 days after injection. At the same time, different molecular weight of sodium hyaluronate gel is sealed or exposed respectively under the low temperature preservation to observe its natural degradation rate. (3) The most stable colloid was selected as aesthetic injector for volunteers to observe the aesthetic effect. The sodium hyaluronate gel with molecular of 4 x 10(5) was completely degraded 90 days later. The sodium hyaluronate gel with molecular of 8 x 10(5) was completely degraded 180 days later. The sodium hyaluronate gel with molecular of 10 x 10(5) was degraded to 90.0% after 180 days. The sodium hyaluronate liquid can be degraded completely within 7 days. The colloid could be kept for at least 12 months when sealed under low temperature, but was totally degraded when exposed for I d. Sodium hyaluronate gel with molecular 10 x 10(5) was confirmed to be kept for at least 6 months in animal experiment and clinical trials. Under the same condition of material ratio, the higher the molecular weight is, the lower the degradation rate is. But the liquidity of gel is not good for injection when molecular weight is too large. It suggests that Sodium hyaluronate gel with molecular 10 x 10(5) maybe the best choice in cosmetic injections.

Analysing and Rationalising Molecular and Materials Databases Using Machine-Learning

Science.gov (United States)

de, Sandip; Ceriotti, Michele

Computational materials design promises to greatly accelerate the process of discovering new or more performant materials. Several collaborative efforts are contributing to this goal by building databases of structures, containing between thousands and millions of distinct hypothetical compounds, whose properties are computed by high-throughput electronic-structure calculations. The complexity and sheer amount of information has made manual exploration, interpretation and maintenance of these databases a formidable challenge, making it necessary to resort to automatic analysis tools. Here we will demonstrate how, starting from a measure of (dis)similarity between database items built from a combination of local environment descriptors, it is possible to apply hierarchical clustering algorithms, as well as dimensionality reduction methods such as sketchmap, to analyse, classify and interpret trends in molecular and materials databases, as well as to detect inconsistencies and errors. Thanks to the agnostic and flexible nature of the underlying metric, we will show how our framework can be applied transparently to different kinds of systems ranging from organic molecules and oligopeptides to inorganic crystal structures as well as molecular crystals. Funded by National Center for Computational Design and Discovery of Novel Materials (MARVEL) and Swiss National Science Foundation.

Probing molecular orientations in thin films by x-ray photoelectron spectroscopy

Directory of Open Access Journals (Sweden)

Y. Li

2018-03-01

Full Text Available A great number of functional organic molecules in active thin-film layers of optoelectronic devices have highly asymmetric structures, such as plate-like, rod-like, etc. This makes molecular orientation an important aspect in thin-films as it can significantly affect both the optical and electrical performance of optoelectronic devices. With a combination of in-situ ultra violet photoelectron spectroscopy (UPS and x-ray photoelectron spectroscopy (XPS investigations for organic molecules having a broad range of structural properties, we discovered a rigid connection of core levels and frontier highest occupied molecular orbital levels at organic interfaces. This finding opens up opportunities of using X-ray photoemission spectroscopy as an alternative tool to UPS for providing an easy and unambiguous data interpretation in probing molecular orientations.

Scientists discover planetary system similar to our own

CERN Multimedia

2003-01-01

'An international team of scientists has discovered a planet and star that may share the same relationship as Jupiter and our Sun, the closest comparison that researchers have found since they began their search for extra-solar planets nearly a decade ago' (1 page).

An approach for discovering keywords from Spanish tweets using Wikipedia

Directory of Open Access Journals (Sweden)

Daniel AYALA

2016-05-01

Full Text Available Most approaches to keywords discovery when analyzing microblogging messages (among them those from Twitter are based on statistical and lexical information about the words that compose the text. The lack of context in the short messages can be problematic due to the low co-occurrence of words. In this paper, we present a new approach for keywords discovering from Spanish tweets based on the addition of context information using Wikipedia as a knowledge base. We present four different ways to use Wikipedia and two ways to rank the new keywords. We have tested these strategies using more than 60000 Spanish tweets, measuring performance and analyzing particularities of each strategy.

Scientists discover how deadly fungal microbes enter host cells

OpenAIRE

Whyte, Barry James

2010-01-01

A research team led by scientists at the Virginia Bioinformatics Institute at Virginia Tech has discovered a fundamental entry mechanism that allows dangerous fungal microbes to infect plants and cause disease.

A comparative cellular and molecular biology of longevity database.

Science.gov (United States)

Stuart, Jeffrey A; Liang, Ping; Luo, Xuemei; Page, Melissa M; Gallagher, Emily J; Christoff, Casey A; Robb, Ellen L

2013-10-01

Discovering key cellular and molecular traits that promote longevity is a major goal of aging and longevity research. One experimental strategy is to determine which traits have been selected during the evolution of longevity in naturally long-lived animal species. This comparative approach has been applied to lifespan research for nearly four decades, yielding hundreds of datasets describing aspects of cell and molecular biology hypothesized to relate to animal longevity. Here, we introduce a Comparative Cellular and Molecular Biology of Longevity Database, available at ( http://genomics.brocku.ca/ccmbl/ ), as a compendium of comparative cell and molecular data presented in the context of longevity. This open access database will facilitate the meta-analysis of amalgamated datasets using standardized maximum lifespan (MLSP) data (from AnAge). The first edition contains over 800 data records describing experimental measurements of cellular stress resistance, reactive oxygen species metabolism, membrane composition, protein homeostasis, and genome homeostasis as they relate to vertebrate species MLSP. The purpose of this review is to introduce the database and briefly demonstrate its use in the meta-analysis of combined datasets.

Retinal ganglion cells with distinct directional preferences differ in molecular identity, structure, and central projections.

Science.gov (United States)

Kay, Jeremy N; De la Huerta, Irina; Kim, In-Jung; Zhang, Yifeng; Yamagata, Masahito; Chu, Monica W; Meister, Markus; Sanes, Joshua R

2011-05-25

The retina contains ganglion cells (RGCs) that respond selectively to objects moving in particular directions. Individual members of a group of ON-OFF direction-selective RGCs (ooDSGCs) detect stimuli moving in one of four directions: ventral, dorsal, nasal, or temporal. Despite this physiological diversity, little is known about subtype-specific differences in structure, molecular identity, and projections. To seek such differences, we characterized mouse transgenic lines that selectively mark ooDSGCs preferring ventral or nasal motion as well as a line that marks both ventral- and dorsal-preferring subsets. We then used the lines to identify cell surface molecules, including Cadherin 6, CollagenXXVα1, and Matrix metalloprotease 17, that are selectively expressed by distinct subsets of ooDSGCs. We also identify a neuropeptide, CART (cocaine- and amphetamine-regulated transcript), that distinguishes all ooDSGCs from other RGCs. Together, this panel of endogenous and transgenic markers distinguishes the four ooDSGC subsets. Patterns of molecular diversification occur before eye opening and are therefore experience independent. They may help to explain how the four subsets obtain distinct inputs. We also demonstrate differences among subsets in their dendritic patterns within the retina and their axonal projections to the brain. Differences in projections indicate that information about motion in different directions is sent to different destinations.

Molecular Responses to the Zika Virus in Mosquitoes

Directory of Open Access Journals (Sweden)

Catalina Alfonso-Parra

2018-05-01

Full Text Available The Zika virus (ZIKV, originally discovered in 1947, did not become a major concern until the virus swept across the Pacific and into the Americas in the last decade, bringing with it news of neurological complications and birth defects in ZIKV affected areas. This prompted researchers to dissect the molecular interactions between ZIKV and the mosquito vector in an attempt to better understand not only the changes that occur upon infection, but to also identify molecules that may potentially enhance or suppress a mosquito’s ability to become infected and/or transmit the virus. Here, we review what is currently known regarding ZIKV-mosquito molecular interactions, focusing on ZIKV infection of Aedes aegypti and Aedes albopictus, the primary species implicated in transmitting ZIKV during the recent outbreaks.

The early years of molecular biology: personal recollections.

Science.gov (United States)

Holliday, Robin

2003-05-01

The early years of molecular biology were characterized by a strong interaction between theory and experiment. This included the elucidation of the structure of DNA itself; genetic fine structure, recombination and repair; DNA replication; template-directed protein synthesis; the universality of the triplet genetic code, and the co-linearity of the DNA sequence of structural genes and the sequence of amino acids in proteins. The principle of co-linearity was later modified when split genes were discovered. It is suggested that accurate splicing of gene transcripts might also be template directed. In 1958 Crick proposed a 'central dogma' of molecular biology stating that information could not be transmitted from proteins to DNA. Nevertheless, proteins can chemically modify DNA, and this is now known to have strong effects on gene expression.

Genetic and Molecular Differences in Prostate Carcinogenesis between African American and Caucasian American Men

Directory of Open Access Journals (Sweden)

Shiv Srivastava

2013-07-01

Full Text Available Prostate cancer is the most common non-skin cancer and the second leading cause of cancer-related death for men in the United States. Prostate cancer incidence and associated mortality are highest in African American men in comparison to other races. The observed differences in incidence and disease aggressiveness at presentation support a potential role for different pathways of prostate carcinogenesis between African American and Caucasian men. This review focuses on some of the recent molecular biology discoveries, which have been investigated in prostate carcinogenesis and their likely contribution to the known discrepancies across race and ethnicity. Key discussion points include the androgen receptor gene structure and function, genome-wide association studies and epigenetics. The new observations of the ethnic differences of the ERG oncogene, the most common prostate cancer gene, are providing new insights into ERG based stratification of prostate cancers in the context of ethnically diverse patient populations. This rapidly advancing knowledge has the likely potential to benefit clinical practice. Current and future work will improve the ability to sub-type prostate cancers by molecular alterations and lead to targeted therapy against this common malignancy.

Discussing the low fraction of disk-bearing T Tauri stars discovered near to the Sh2-296 nebula

Science.gov (United States)

Gregorio-Hetem, Jane

2015-08-01

A multiband study has been developed by our team in the direction of young star clusters associated to the Sh2-296 nebula aiming to unveil the star formation history of this galactic molecular cloud that shows a mixing of different age stellar groups. A sample of 58 pre-main sequence stars has been recently discovered by us in this region (Fernandes et al. 2015, MNRAS in press), based on optical spectral features. Only 41% of the sample shows evidence of IR excess revealing the presence of circumstellar disks. It is interesting to note that the targets were revealed by their strong X-ray emission, typically found in T Tauri stars (TTs) (Santos-Silva et al. 2015, in preparation) . In this case, it would be expected a larger number of disk-bearing stars and also the fraction of circumstellar emission (fc = Ldisk/Ltotal ) should be more significant in these objects. However, we verified that only 12% of the sample has fc > 30%. This low fraction is quite rare compared to most young star-forming regions, suggesting that some external factor has accelerated the disc dissipation. In the present work we explore the circumstellar structure of a subsample of 8 TTs associated to Sh2-296. The TTs were selected on the basis of their high circumstellar emission, which is estimated by SED fitting that uses near- to mid-IR data extracted from available catalogues (WISE, AKARI, MSX). The circumstellar characteristics are confronted to interstellar environment by comparing the stellar spatial distribution with 12CO maps (Nanten Survey, Fukui et al. ). Most of the TTs are projected against moderate molecular emission (33 Jy), but some of them are found in regions of lower levels of gas distribution (3.8 Jy). The similarities and differences found among the studied objects are discussed in order to better understand the formation and evolution of protostellar disks of the selected sample and their role in the star formation scenario nearby Sh2-296

Top quark discovered

International Nuclear Information System (INIS)

Anon.

1995-01-01

Nine months after a careful announcement of tentative evidence for the long-awaited sixth 'top' quark, physicists from the CDF and DO experiments at Fermilab's Tevatron proton-antiproton collider declared on 2 March that they had finally discovered the top quark. Last year (June 1994, page 1), the CDF experiment at the Tevatron reported a dozen candidate top events. These, said CDF, had all the characteristics expected of top, but the difficulties of extracting the tiny signal from a trillion proton-antiproton collisions made them shy of claiming a discovery. For its part, the companion DO Tevatron experiment reported a few similar events but were even more guarded about their interpretation as top quarks. Just after these hesitant announcements, performance at the Tevatron improved dramatically last summer. After the commissioning of a new linear accelerator and a magnet realignment, the machine reached a new world record proton-antiproton collision luminosity of 1.28 x 10 31 per sq cm per s, ten times that originally planned. Data began to pour in at an unprecedented rate and the data sample grew to six trillion collisions. Luminosity has subsequently climbed to 1.7 x 10 31 . The top quark is the final letter in the alphabet of Standard Model particles. According to this picture, all matter is composed of six stronglyinteracting subnuclear particles, the quarks, and six weakly interacting particles, the leptons. Both sextets are neatly arranged as three pairs in order of increasing mass. The fifth quark, the 'beauty' or 'b' quark, was also discovered at Fermilab, back in 1977. Since then physicists have been eagerly waiting for the top to turn up, but have been frustrated by its heaviness - the top is some 40 times the mass of its 'beautiful' partner. Not only is the top quark the heaviest by far, but it is the only quark which has been actively hunted. After the quarry was glimpsed last year, the net has now been

Discovering Alzheimer Genetic Biomarkers Using Bayesian Networks

Directory of Open Access Journals (Sweden)

Fayroz F. Sherif

2015-01-01

Full Text Available Single nucleotide polymorphisms (SNPs contribute most of the genetic variation to the human genome. SNPs associate with many complex and common diseases like Alzheimer’s disease (AD. Discovering SNP biomarkers at different loci can improve early diagnosis and treatment of these diseases. Bayesian network provides a comprehensible and modular framework for representing interactions between genes or single SNPs. Here, different Bayesian network structure learning algorithms have been applied in whole genome sequencing (WGS data for detecting the causal AD SNPs and gene-SNP interactions. We focused on polymorphisms in the top ten genes associated with AD and identified by genome-wide association (GWA studies. New SNP biomarkers were observed to be significantly associated with Alzheimer’s disease. These SNPs are rs7530069, rs113464261, rs114506298, rs73504429, rs7929589, rs76306710, and rs668134. The obtained results demonstrated the effectiveness of using BN for identifying AD causal SNPs with acceptable accuracy. The results guarantee that the SNP set detected by Markov blanket based methods has a strong association with AD disease and achieves better performance than both naïve Bayes and tree augmented naïve Bayes. Minimal augmented Markov blanket reaches accuracy of 66.13% and sensitivity of 88.87% versus 61.58% and 59.43% in naïve Bayes, respectively.

Molecular analysis of interactions between dendrimers and asymmetric membranes at different transport stages.

Science.gov (United States)

He, XiaoCong; Qu, ZhiGuo; Xu, Feng; Lin, Min; Wang, JiuLing; Shi, XingHua; Lu, TianJian

2014-01-07

Studying dendrimer-biomembrane interactions is important for understanding drug and gene delivery. In this study, coarse-grained molecular dynamics simulations were performed to investigate the behaviors of polyamidoamine (PAMAM) dendrimers (G4 and G5) as they interacted with asymmetric membranes from different sides of the bilayer, thus mimicking different dendrimer transport stages. The G4 dendrimer could insert into the membrane during an equilibrated state, and the G5 dendrimer could induce pore formation in the membrane when the dendrimers interacted with the outer side (outer interactions) of an asymmetric membrane [with 10% dipalmitoyl phosphatidylserine (DPPS) in the inner leaflet of the membrane]. During the interaction with the inner side of the asymmetric membrane (inner interactions), the G4 and G5 dendrimers only adsorbed onto the membrane. As the membrane asymmetry increased (e.g., increased DPPS percentage in the inner leaflet of the membrane), the G4 and G5 dendrimers penetrated deeper into the membrane during the outer interactions and the G4 and G5 dendrimers were adsorbed more tightly onto the membrane for the inner interactions. When the DPPS content reached 50%, the G4 dendrimer could completely penetrate through the membrane from the outer side to the inner side. Our study provides molecular understanding and reference information about different dendrimer transport stages during drug and gene delivery.

Molecular differences in transition zone and peripheral zone prostate tumors

Science.gov (United States)

Sinnott, Jennifer A.; Rider, Jennifer R.; Carlsson, Jessica; Gerke, Travis; Tyekucheva, Svitlana; Penney, Kathryn L.; Sesso, Howard D.; Loda, Massimo; Fall, Katja; Stampfer, Meir J.; Mucci, Lorelei A.; Pawitan, Yudi; Andersson, Sven-Olof; Andrén, Ove

2015-01-01

Prostate tumors arise primarily in the peripheral zone (PZ) of the prostate, but 20–30% arise in the transition zone (TZ). Zone of origin may have prognostic value or reflect distinct molecular subtypes; however, it can be difficult to determine in practice. Using whole-genome gene expression, we built a signature of zone using normal tissue from five individuals and found that it successfully classified nine tumors of known zone. Hypothesizing that this signature captures tumor zone of origin, we assessed its relationship with clinical factors among 369 tumors of unknown zone from radical prostatectomies (RPs) and found that tumors that molecularly resembled TZ tumors showed lower mortality (P = 0.09) that was explained by lower Gleason scores (P = 0.009). We further applied the signature to an earlier study of 88 RP and 333 transurethral resection of the prostate (TURP) tumor samples, also of unknown zone, with gene expression on ~6000 genes. We had observed previously substantial expression differences between RP and TURP specimens, and hypothesized that this might be because RPs capture primarily PZ tumors, whereas TURPs capture more TZ tumors. Our signature distinguished these two groups, with an area under the receiver operating characteristic curve of 87% (P zones. Zone of origin may be important to consider in prostate tumor biomarker research. PMID:25870172

Non-Adiabatic Molecular Dynamics Methods for Materials Discovery

Energy Technology Data Exchange (ETDEWEB)

Furche, Filipp [Univ. of California, Irvine, CA (United States); Parker, Shane M. [Univ. of California, Irvine, CA (United States); Muuronen, Mikko J. [Univ. of California, Irvine, CA (United States); Roy, Saswata [Univ. of California, Irvine, CA (United States)

2017-04-04

The flow of radiative energy in light-driven materials such as photosensitizer dyes or photocatalysts is governed by non-adiabatic transitions between electronic states and cannot be described within the Born-Oppenheimer approximation commonly used in electronic structure theory. The non-adiabatic molecular dynamics (NAMD) methods based on Tully surface hopping and time-dependent density functional theory developed in this project have greatly extended the range of molecular materials that can be tackled by NAMD simulations. New algorithms to compute molecular excited state and response properties efficiently were developed. Fundamental limitations of common non-linear response methods were discovered and characterized. Methods for accurate computations of vibronic spectra of materials such as black absorbers were developed and applied. It was shown that open-shell TDDFT methods capture bond breaking in NAMD simulations, a longstanding challenge for single-reference molecular dynamics simulations. The methods developed in this project were applied to study the photodissociation of acetaldehyde and revealed that non-adiabatic effects are experimentally observable in fragment kinetic energy distributions. Finally, the project enabled the first detailed NAMD simulations of photocatalytic water oxidation by titania nanoclusters, uncovering the mechanism of this fundamentally important reaction for fuel generation and storage.

Fast Ss-Ilm a Computationally Efficient Algorithm to Discover Socially Important Locations

Science.gov (United States)

Dokuz, A. S.; Celik, M.

2017-11-01

Socially important locations are places which are frequently visited by social media users in their social media lifetime. Discovering socially important locations provide several valuable information about user behaviours on social media networking sites. However, discovering socially important locations are challenging due to data volume and dimensions, spatial and temporal calculations, location sparseness in social media datasets, and inefficiency of current algorithms. In the literature, several studies are conducted to discover important locations, however, the proposed approaches do not work in computationally efficient manner. In this study, we propose Fast SS-ILM algorithm by modifying the algorithm of SS-ILM to mine socially important locations efficiently. Experimental results show that proposed Fast SS-ILM algorithm decreases execution time of socially important locations discovery process up to 20 %.

FAST SS-ILM: A COMPUTATIONALLY EFFICIENT ALGORITHM TO DISCOVER SOCIALLY IMPORTANT LOCATIONS

Directory of Open Access Journals (Sweden)

A. S. Dokuz

2017-11-01

Full Text Available Socially important locations are places which are frequently visited by social media users in their social media lifetime. Discovering socially important locations provide several valuable information about user behaviours on social media networking sites. However, discovering socially important locations are challenging due to data volume and dimensions, spatial and temporal calculations, location sparseness in social media datasets, and inefficiency of current algorithms. In the literature, several studies are conducted to discover important locations, however, the proposed approaches do not work in computationally efficient manner. In this study, we propose Fast SS-ILM algorithm by modifying the algorithm of SS-ILM to mine socially important locations efficiently. Experimental results show that proposed Fast SS-ILM algorithm decreases execution time of socially important locations discovery process up to 20 %.

Starlight detectives how astronomers, inventors, and eccentrics discovered the modern universe

CERN Document Server

Hirshfeld, Alan

2014-01-01

NBC News “Top Science and Tech Books of the Year" selectionScientific American/FSG “Favorite Science Books of the Year" selectionNature.com “Top Reads of the Year" selectionKirkus Reviews “Best Books of the Year" selectionDiscover magazine “Top 5 Summer Read"“A masterful balance of science, history and rich narrative." —Discover magazine“Hirshfeld tells this climactic discovery of the expanding universe with great verve and sweep, as befits a story whose scope, characters and import leave

Unveiling the Structural Origin of the High Carrier Mobility of a Molecular Monolayer on Boron Nitride

OpenAIRE

Xu, Rui; He, Daowei; Zhang, Yuhan; Wu, Bing; Liu, Fengyuan; Meng, Lan; Liu, Jun-Fang; Wu, Qisheng; Shi, Yi; Wang, Jinlan; Nie, Jia-Cai; Wang, Xinran; He, Lin

2014-01-01

Very recently, it was demonstrated that the carrier mobility of a molecular monolayer dioctylbenzothienobenzothiophene (C8-BTBT) on boron nitride can reach 10 cm2/Vs, the highest among the previously reported monolayer molecular field-effect transistors. Here we show that the high-quality single crystal of the C8-BTBT monolayer may be the key origin of the record-high carrier mobility. We discover that the C8-BTBT molecules prefer layer-by-layer growth on both hexagonal boron nitride and grap...

Electrospinning and characterization of polyamide 66 nanofibers with different molecular weights

Directory of Open Access Journals (Sweden)

Lilia Muller Guerrini

2009-06-01

Full Text Available Polyamide 66 (PA66 nanofibers of different molecular weights were obtained by electrospinning of formic acid solutions. An ionic salt, NaCl, was also added to the solutions to increase the conductivity. PA66 concentrations between 15-17 wt.(%/v and electrical fields between 2.0 and 2.5 kV/cm were the best conditions to produce the smallest nanofibers; however, the addition of NaCl increased the fibers average diameters.The characterization of the fibers was done by scanning electron microscopy (SEM, differential scanning calorimetry (DSC, wide angle X rays diffraction (WAXD and Fourier Transformed Infrared (FTIR. As the molecular weight decreased, the nanofibers average diameters also decreased; however, critical number average and weight average molecular weights were necessary for electrospinning. As the amounts of carboxyl terminal groups (CTG increased, the nanofibers average diameters decreased; however, above CTG's critical values of 8.7 x 10-5 mol.g-1 no electrospinning was possible. The addition of ionic salt increased the electrical conductivity of the solutions and increased the nanofibers' average diameters. By DSC, residual solvent in all the electrospun mats was found; two melting endotherms, one between 248 and 258 °C and the other one between 258 and 267 °C, depending on the sample were also observed. These endotherms were attributed to the melting, re-crystallization and re-melting of the PA66 α-phase. The nanofibers had low % of crystallinity compared to a textile fiber. By WAXS and FTIR, confirmation of the presence of α-phase crystals, of small dimensions and highly imperfect and of a very small amount of β and γ-phases crystals in the nanofibers structure was obtained.

New perspectives in the Fischer-Tropsch synthesis using cobalt supported on mesoporous molecular sieves; Novas perspectivas na sintese de Fischer-Tropsch usando cobalto suportado em peneiras moleculares mesoporosas

Energy Technology Data Exchange (ETDEWEB)

Souza, M.J.B.; Silva, A.O.S. [Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN (Brazil). Dept. de Engenharia Quimica; Fernandes Junior, V.J.; Araujo, A.S. [Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN (Brazil). Dept. de Quimica

2004-07-01

The conversion of synthesis gas to liquid products via Fischer-Tropsch synthesis (FTS) is an important process in the generation of clean fuels of sulfur and nitrogen compounds. Catalysts based on iron are very used in the conventional process due its cheap manufacture price. Recently the use of cobalt as promoter gave good results. MCM-41 mesoporous materials were discovered by Mobil scientists in the nineties and ever since they have great successes as support and catalyst in several processes of the oil industry as catalytic cracking, reformer and hydrotreating. In this work are presented new alternatives for FTS with the use of cobalt supported on molecular sieves of the type MCM-41. A comparative study with the usual catalysts based on silica was accomplished with different levels of cobalt. (author)

Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations

DEFF Research Database (Denmark)

Paavilainen, S.; Rog, T.; Vattulainen, I.

2011-01-01

We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile......, no significant bending or stretching of nanocellulose is discovered. Considerations of atomic-scale interaction patterns bring about that the twisting arises from hydrogen bonding within and between the chains in a fibril....

Surface properties of heat-induced soluble soy protein aggregates of different molecular masses.

Science.gov (United States)

Guo, Fengxian; Xiong, Youling L; Qin, Fang; Jian, Huajun; Huang, Xiaolin; Chen, Jie

2015-02-01

Suspensions (2% and 5%, w/v) of soy protein isolate (SPI) were heated at 80, 90, or 100 °C for different time periods to produce soluble aggregates of different molecular sizes to investigate the relationship between particle size and surface properties (emulsions and foams). Soluble aggregates generated in these model systems were characterized by gel permeation chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Heat treatment increased surface hydrophobicity, induced SPI aggregation via hydrophobic interaction and disulfide bonds, and formed soluble aggregates of different sizes. Heating of 5% SPI always promoted large-size aggregate (LA; >1000 kDa) formation irrespective of temperature, whereas the aggregate size distribution in 2% SPI was temperature dependent: the LA fraction progressively rose with temperature (80→90→100 °C), corresponding to the attenuation of medium-size aggregates (MA; 670 to 1000 kDa) initially abundant at 80 °C. Heated SPI with abundant LA (>50%) promoted foam stability. LA also exhibited excellent emulsifying activity and stabilized emulsions by promoting the formation of small oil droplets covered with a thick interfacial protein layer. However, despite a similar influence on emulsion stability, MA enhanced foaming capacity but were less capable of stabilizing emulsions than LA. The functionality variation between heated SPI samples is clearly related to the distribution of aggregates that differ in molecular size and surface activity. The findings may encourage further research to develop functional SPI aggregates for various commercial applications. © 2015 Institute of Food Technologists®

An ensemble heterogeneous classification methodology for discovering health-related knowledge in social media messages.

Science.gov (United States)

Tuarob, Suppawong; Tucker, Conrad S; Salathe, Marcel; Ram, Nilam

2014-06-01

The role of social media as a source of timely and massive information has become more apparent since the era of Web 2.0.Multiple studies illustrated the use of information in social media to discover biomedical and health-related knowledge.Most methods proposed in the literature employ traditional document classification techniques that represent a document as a bag of words.These techniques work well when documents are rich in text and conform to standard English; however, they are not optimal for social media data where sparsity and noise are norms.This paper aims to address the limitations posed by the traditional bag-of-word based methods and propose to use heterogeneous features in combination with ensemble machine learning techniques to discover health-related information, which could prove to be useful to multiple biomedical applications, especially those needing to discover health-related knowledge in large scale social media data.Furthermore, the proposed methodology could be generalized to discover different types of information in various kinds of textual data. Social media data is characterized by an abundance of short social-oriented messages that do not conform to standard languages, both grammatically and syntactically.The problem of discovering health-related knowledge in social media data streams is then transformed into a text classification problem, where a text is identified as positive if it is health-related and negative otherwise.We first identify the limitations of the traditional methods which train machines with N-gram word features, then propose to overcome such limitations by utilizing the collaboration of machine learning based classifiers, each of which is trained to learn a semantically different aspect of the data.The parameter analysis for tuning each classifier is also reported. Three data sets are used in this research.The first data set comprises of approximately 5000 hand-labeled tweets, and is used for cross validation of the

Pulsed recording of anisotropy and holographic polarization gratings in azo-polymethacrylates with different molecular architectures

DEFF Research Database (Denmark)

Forcén, Patricia; Oriol, Luis; Alcala, Rafael

2008-01-01

Recording of anisotropy and holographic polarization gratings using 532 nm, 4 ns light pulses has been carried out in thin films of polymers with the same azobenzene content (20 wt %) and different molecular architectures. Random and block copolymers comprising azobenzene and methylmethacrylate (...

Re-discovering indigenous knowledge – Ulwazi Lwemveli for ...

African Journals Online (AJOL)

Therefore, the imperative to re-discover and re-store IK cannot be underestimated since building on this knowledge is particularly effective in helping to reach those living in rural communities. This knowledge is often the main asset they control, and certainly one with which they are more familiar. The case studies discussed ...

Discovering disease-associated genes in weighted protein-protein interaction networks

Science.gov (United States)

Cui, Ying; Cai, Meng; Stanley, H. Eugene

2018-04-01

Although there have been many network-based attempts to discover disease-associated genes, most of them have not taken edge weight - which quantifies their relative strength - into consideration. We use connection weights in a protein-protein interaction (PPI) network to locate disease-related genes. We analyze the topological properties of both weighted and unweighted PPI networks and design an improved random forest classifier to distinguish disease genes from non-disease genes. We use a cross-validation test to confirm that weighted networks are better able to discover disease-associated genes than unweighted networks, which indicates that including link weight in the analysis of network properties provides a better model of complex genotype-phenotype associations.

Effect of polar surfaces on organic molecular crystals

Science.gov (United States)

Sharia, Onise; Tsyshevskiy, Roman; Kuklja, Maija; University of Maryland College Park Team

Polar oxide materials reveal intriguing opportunities in the field of electronics, superconductivity and nanotechnology. While behavior of polar surfaces has been widely studied on oxide materials and oxide-oxide interfaces, manifestations and properties of polar surfaces in molecular crystals are still poorly understood. Here we discover that the polar catastrophe phenomenon, known on oxides, also takes place in molecular materials as illustrated with an example of cyclotetramethylene tetranitramine (HMX) crystals. We show that the surface charge separation is a feasible compensation mechanism to counterbalance the macroscopic dipole moment and remove the electrostatic instability. We discuss the role of surface charge on degradation of polar surfaces, electrical conductivity, optical band-gap closure and surface metallization. Research is supported by the US ONR (Grants N00014-16-1-2069 and N00014-16-1-2346) and NSF. We used NERSC, XSEDE and MARCC computational resources.

[Early effectiveness of discover cervical artificial disc replacement in treatment of cervical spondylosis].

Science.gov (United States)

Qian, Yufeng; Xue, Feng; Sheng, Xiaowen; Lu, Jianmin; Chen, Bingqian

2012-03-01

To investigate the early effectiveness of the Discover cervical artificial disc replacement in treating cervical spondylosis. Qualified for the selective standard, 24 patients with cervical spondylosis were treated between March 2010 and March 2011. Of 24 patients, 13 patients underwent anterior cervical decompression and fusion (ACDF) (ACDF group, between March 2010 and September 2010) and 11 patients underwent Discover cervical artificial disc replacement (CADR group, between September 2010 and March 2011). There was no significant difference in gender, age, disease duration, lesions typing, and affected segments between 2 groups (P > 0.05). The operative time, blood loss, and complications were recorded. Japanese Orthopaedic Association (JOA) scores, Neck Disability Index (NDI) scores, and Odom's scores were used to evaluate the postoperative effectiveness. In CADR group, the cervical range of motion (ROM) in all directions, and prosthesis eccentricity were measured before and after operation. Symptoms disappeared and no complication occurred after operation in the patients of 2 groups. The patients were followed up 12 to 18 months (mean, 15.3 months) in ACDF group and 6 to 12 months (mean, 9.6 months) in CADR group. The NDI scores in CADR group were significantly higher than those in ACDF group at 1, 3, and 6 months (P 0.05). According to Odom's score at last follow-up, the results were excellent in 6 cases, good in 4 cases, and fair in 3 cases with an excellent and good rate of 76.92% in ACDF group, and were excellent in 9 cases, good in 1 case, and poor in 1 case with an excellent and good rate of 90.91% in CADR group, showing no significant difference (chi2 = 3.000, P = 0.223). The patients in CADR group had significant limit of cervical joint ROM in flexion and extension and right bending at 1 month (P value (P < 0.05). Meanwhile, ROM in left bending were bigger than that in right bending in replaced segment and upper segment (P < 0.05), and the ROM

New open cluster candidates discovered in the XSTPS-GAC survey

Science.gov (United States)

Guo, Jin-Cheng; Zhang, Hua-Wei; Zhang, Hui-Hua; Liu, Xiao-Wei; Yuan, Hai-Bo; Huang, Yang; Wang, Song; Chen, Li; Zhao, Hai-Bin; Liu, Ji-Feng; Chen, Bing-Qiu; Xiang, Mao-Sheng; Tian, Zhi-Jia; Huo, Zhi-Ying; Wang, Chun

2018-03-01

The Xuyi Schmidt Telescope Photometric Survey of the Galactic Anti-center (XSTPS-GAC) is a photometric sky survey that covers nearly 6000 deg2 towards the Galactic Anti-center (GAC) in the g, r, i bands. Half of its survey field is located on the Galactic Anti-center disk, which makes XSTPS-GAC highly suitable to search for new open clusters in the GAC region. In this paper, we report new open cluster candidates discovered in this survey, as well as properties of these open cluster candidates, such as age, distance and reddening, derived by isochrone fitting in the color-magnitude diagram (CMD). These open cluster candidates are stellar density peaks detected in the star density maps by applying the method from Koposov et al. Each candidate is inspected in terms of its true color image composed from three XSTPS-GAC band images. Then its CMD is checked, in order to identify whether the central region stars have a clear isochrone-like trend differing from background stars. The parameters derived from isochrone fitting for these candidates are mainly based on three band photometry of XSTPS-GAC. Moreover, when these new candidates are able to be seen clearly in 2MASS data, their parameters are also derived based on the 2MASS (J – H, J) CMD. There are a total of 320 known open clusters rediscovered and 24 new open cluster candidates discovered in this work. Furthermore, the parameters of these new candidates, as well as another 11 previously known open clusters, are properly determined for the first time.

Molecular pathobiology of thyroid neoplasms.

Science.gov (United States)

Tallini, Giovanni

2002-01-01

Tumors of thyroid follicular cells provide a very interesting model to understand the development of human cancer. It is becoming apparent that distinct molecular events are associated with specific stages in a multistep tumorigenic process with good genotype/ phenotype correlation. For instance, mutations of the gsp and thyroid-stimulating hormone receptor genes are associated with benign hyperfunctioning thyroid nodules and adenomas while alterations of other specific genes, such as oncogenic tyrosine kinase alterations (RET/PTC, TRK) in papillary carcinoma and the newly discovered PAX8/peroxisome proliferator-activated receptor gamma rearrangement, are distinctive features of cancer. Although activating RAS mutations occur at all stages of thyroid tumorigenesis, evidence is accumulating that they may also play an important role in tumor progression, a role that is well documented for p53. Environmental factors (iodine deficiency, ionizing radiations) have been shown to play a crucial role in promoting the development of thyroid cancer, influencing both its genotypic and phenotypic features. It is possible that the follicular thyroid cell has unique ways to respond to DNA damage. Similarly to leukemia or sarcomas (and unlike most epithelial cancers), numerous specific rearrangements are being discovered in thyroid cancer suggesting preferential activation of DNA repair instead of cell death programs after environmentally induced genetic alterations.

The Design, Synthesis, and Study of Solid-State Molecular Rotors: Structure/Function Relationships for Condensed-Phase Anisotropic Dynamics

Science.gov (United States)

Vogelsberg, Cortnie Sue

Amphidynamic crystals are an extremely promising platform for the development of artificial molecular machines and stimuli-responsive materials. In analogy to skeletal muscle, their function will rely upon the collective operation of many densely packed molecular machines (i.e. actin-bound myosin) that are self-assembled in a highly organized anisotropic medium. By choosing lattice-forming elements and moving "parts" with specific functionalities, individual molecular machines may be synthesized and self-assembled in order to carry out desirable functions. In recent years, efforts in the design of amphidynamic materials based on molecular gyroscopes and compasses have shown that a certain amount of free volume is essential to facilitate internal rotation and reorientation within a crystal. In order to further establish structure/function relationships to advance the development of increasingly complex molecular machinery, molecular rotors and a molecular "spinning" top were synthesized and incorporated into a variety of solid-state architectures with different degrees of periodicity, dimensionality, and free volume. Specifically, lamellar molecular crystals, hierarchically ordered periodic mesoporous organosilicas, and metal-organic frameworks were targeted for the development of solid-state molecular machines. Using an array of solid-state nuclear magnetic resonance spectroscopy techniques, the dynamic properties of these novel molecular machine assemblies were determined and correlated with their corresponding structural features. It was found that architecture type has a profound influence on functional dynamics. The study of layered molecular crystals, composed of either molecular rotors or "spinning" tops, probed functional dynamics within dense, highly organized environments. From their study, it was discovered that: 1) crystallographically distinct sites may be utilized to differentiate machine function, 2) halogen bonding interactions are sufficiently

The role of molecular diagnostic testing in the management of thyroid nodules.

Science.gov (United States)

Moore, Maureen D; Panjwani, Suraj; Gray, Katherine D; Finnerty, Brendan M; Zarnegar, Rasa; Fahey, Thomas J

2017-06-01

Fine needle aspiration (FNA) with cytologic examination remains the standard of care for investigation of thyroid nodules. However, as many as 30% of FNA samples are cytologically indeterminate for malignancy, which confounds clinical management. To reduce the burden of repeat diagnostic testing and unnecessary surgery, there has been extensive investigation into molecular markers that can be detected on FNA specimens to more accurately stratify a patient's risk of malignancy. Areas covered: In this review, the authors discuss recent evidence and progress in molecular markers used in the diagnosis of thyroid cancer highlighting somatic gene alterations, molecular technologies and microRNA analysis. Expert commentary: The goal of molecular markers is to improve diagnostic accuracy and aid clinicians in the preoperative management of thyroid lesions. Modalities such as direct mutation analysis, mRNA gene expression profiling, next-generation sequencing, and miRNA expression profiling have been explored to improve the diagnostic accuracy of thyroid nodule FNA. Although no perfect test has been discovered, molecular diagnostic testing has revolutionized the management of thyroid nodules.

Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating.

Science.gov (United States)

Barba-Montoya, Jose; Dos Reis, Mario; Yang, Ziheng

2017-09-01

Fossil calibrations are the utmost source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis. The quality of calibrations is thus expected to have a major impact on divergence time estimates even if a huge amount of molecular data is available. In Bayesian molecular clock dating, fossil calibration information is incorporated in the analysis through the prior on divergence times (the time prior). Here, we evaluate three strategies for converting fossil calibrations (in the form of minimum- and maximum-age bounds) into the prior on times, which differ according to whether they borrow information from the maximum age of ancestral nodes and minimum age of descendent nodes to form constraints for any given node on the phylogeny. We study a simple example that is analytically tractable, and analyze two real datasets (one of 10 primate species and another of 48 seed plant species) using three Bayesian dating programs: MCMCTree, MrBayes and BEAST2. We examine how different calibration strategies, the birth-death process, and automatic truncation (to enforce the constraint that ancestral nodes are older than descendent nodes) interact to determine the time prior. In general, truncation has a great impact on calibrations so that the effective priors on the calibration node ages after the truncation can be very different from the user-specified calibration densities. The different strategies for generating the effective prior also had considerable impact, leading to very different marginal effective priors. Arbitrary parameters used to implement minimum-bound calibrations were found to have a strong impact upon the prior and posterior of the divergence times. Our results highlight the importance of inspecting the joint time prior used by the dating program before any Bayesian dating analysis. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Molecular evidence for gender differences in the migratory behaviour of a small seabird.

Directory of Open Access Journals (Sweden)

Renata J Medeiros

Full Text Available Molecular sexing revealed an unexpectedly strong female bias in the sex ratio of pre-breeding European Storm Petrels (Hydrobates pelagicus, attracted to playback of conspecific calls during their northwards migration past SW Europe. This bias was consistent across seven years, ranging from 80.8% to 89.7% female (mean annual sex ratio ± SD = 85.5% female ±4.1%. The sex ratio did not differ significantly from unity (i.e., 50% female among (i Storm Petrel chicks at a breeding colony in NW France, (ii adults found dead on beaches in Southern Portugal, (iii breeding birds attending nest burrows in the UK, captured by hand, and (iv adults captured near a breeding colony in the UK using copies of the same sound recordings as used in Southern Europe, indicating that females are not inherently more strongly attracted to playback calls than males. A morphological discriminant function analysis failed to provide a good separation of the sexes, showing the importance of molecular sexing for this species. We found no sex difference in the seasonal or nocturnal timing of migration past Southern Europe, but there was a significant tendency for birds to be caught in sex-specific aggregations. The preponderance of females captured in Southern Europe suggests that the sexes may differ in migration route or in their colony-prospecting behaviour during migration, at sites far away from their natal colonies. Such differences in migration behaviour between males and females are poorly understood but have implications for the vulnerability of seabirds to pollution and environmental change at sea during the non-breeding season.

Molecular Genetic of Atopic dermatitis: An Update

Science.gov (United States)

Al-Shobaili, Hani A.; Ahmed, Ahmed A.; Alnomair, Naief; Alobead, Zeiad Abdulaziz; Rasheed, Zafar

2016-01-01

Atopic dermatitis (AD) is a chronic multifactorial inflammatory skin disease. The pathogenesis of AD remains unclear, but the disease results from dysfunctions of skin barrier and immune response, where both genetic and environmental factors play a key role. Recent studies demonstrate the substantial evidences that show a strong genetic association with AD. As for example, AD patients have a positive family history and have a concordance rate in twins. Moreover, several candidate genes have now been suspected that play a central role in the genetic background of AD. In last decade advanced procedures similar to genome-wide association (GWA) and single nucleotide polymorphism (SNP) have been applied on different population and now it has been clarified that AD is significantly associated with genes of innate/adaptive immune systems, human leukocyte antigens (HLA), cytokines, chemokines, drug-metabolizing genes or various other genes. In this review, we will highlight the recent advancements in the molecular genetics of AD, especially on possible functional relevance of genetic variants discovered to date. PMID:27004062

32 CFR 644.533 - Contamination discovered after return of land to owner, or sale.

Science.gov (United States)

2010-07-01

... 32 National Defense 4 2010-07-01 2010-07-01 true Contamination discovered after return of land to owner, or sale. 644.533 Section 644.533 National Defense Department of Defense (Continued) DEPARTMENT OF... Other Contamination from Proposed Excess Land and Improvements § 644.533 Contamination discovered after...

Real-time reflectance-difference spectroscopy of GaAs molecular beam epitaxy homoepitaxial growth

Energy Technology Data Exchange (ETDEWEB)

Lastras-Martínez, A., E-mail: alm@cactus.iico.uaslp.mx, E-mail: alastras@gmail.com; Ortega-Gallegos, J.; Guevara-Macías, L. E.; Nuñez-Olvera, O.; Balderas-Navarro, R. E.; Lastras-Martínez, L. F. [Instituto de Investigación en Comunicación Optica, Universidad Autónoma de San Luis Potosí, Alvaro Obregón 64, San Luis Potosí, SLP 78000 (Mexico); Lastras-Montaño, L. A. [IBM T. J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Lastras-Montaño, M. A. [Department of Electrical and Computer Engineering, University of California, Santa Barbara, Santa Barbara, California 93106 (United States)

2014-03-01

We report on real time-resolved Reflectance-difference (RD) spectroscopy of GaAs(001) grown by molecular beam epitaxy, with a time-resolution of 500 ms per spectrum within the 2.3–4.0 eV photon energy range. Through the analysis of transient RD spectra we demonstrated that RD line shapes are comprised of two components with different physical origins and determined their evolution during growth. Such components were ascribed to the subsurface strain induced by surface reconstruction and to surface stoichiometry. Results reported in this paper render RD spectroscopy as a powerful tool for the study of fundamental processes during the epitaxial growth of zincblende semiconductors.

Strontium-90 Error Discovered in Subcontract Laboratory Spreadsheet. Topical Report

International Nuclear Information System (INIS)

Brown, D.D.; Nagel, A.S.

1999-07-01

West Valley Demonstration Project health physicists and environment scientists discovered a series of errors in a subcontractor's spreadsheet being used to reduce data as part of their strontium-90 analytical process

Discovering More Accurate Frequent Web Usage Patterns

OpenAIRE

Bayir, Murat Ali; Toroslu, Ismail Hakki; Cosar, Ahmet; Fidan, Guven

2008-01-01

Web usage mining is a type of web mining, which exploits data mining techniques to discover valuable information from navigation behavior of World Wide Web users. As in classical data mining, data preparation and pattern discovery are the main issues in web usage mining. The first phase of web usage mining is the data processing phase, which includes the session reconstruction operation from server logs. Session reconstruction success directly affects the quality of the frequent patterns disc...

Water models based on a single potential energy surface and different molecular degrees of freedom

Science.gov (United States)

Saint-Martin, Humberto; Hernández-Cobos, Jorge; Ortega-Blake, Iván

2005-06-01

Up to now it has not been possible to neatly assess whether a deficient performance of a model is due to poor parametrization of the force field or the lack of inclusion of enough molecular properties. This work compares several molecular models in the framework of the same force field, which was designed to include many-body nonadditive effects: (a) a polarizable and flexible molecule with constraints that account for the quantal nature of the vibration [B. Hess, H. Saint-Martin, and H. J. C. Berendsen, J. Chem. Phys. 116, 9602 (2002), H. Saint-Martin, B. Hess, and H. J. C. Berendsen, J. Chem. Phys. 120, 11133 (2004)], (b) a polarizable and classically flexible molecule [H. Saint-Martin, J. Hernández-Cobos, M. I. Bernal-Uruchurtu, I. Ortega-Blake, and H. J. C. Berendsen, J. Chem. Phys. 113, 10899 (2000)], (c) a polarizable and rigid molecule, and finally (d) a nonpolarizable and rigid molecule. The goal is to determine how significant the different molecular properties are. The results indicate that all factors—nonadditivity, polarizability, and intramolecular flexibility—are important. Still, approximations can be made in order to diminish the computational cost of the simulations with a small decrease in the accuracy of the predictions, provided that those approximations are counterbalanced by the proper inclusion of an effective molecular property, that is, an average molecular geometry or an average dipole. Hence instead of building an effective force field by parametrizing it in order to reproduce the properties of a specific phase, a building approach is proposed that is based on adequately restricting the molecular flexibility and/or polarizability of a model potential fitted to unimolecular properties, pair interactions, and many-body nonadditive contributions. In this manner, the same parental model can be used to simulate the same substance under a wide range of thermodynamic conditions. An additional advantage of this approach is that, as the force

Vitroprocines, new antibiotics against Acinetobacter baumannii, discovered from marine Vibrio sp. QWI-06 using mass-spectrometry-based metabolomics approach

Science.gov (United States)

Liaw, Chih-Chuang; Chen, Pei-Chin; Shih, Chao-Jen; Tseng, Sung-Pin; Lai, Ying-Mi; Hsu, Chi-Hsin; Dorrestein, Pieter C.; Yang, Yu-Liang

2015-08-01

A robust and convenient research strategy integrating state-of-the-art analytical techniques is needed to efficiently discover novel compounds from marine microbial resources. In this study, we identified a series of amino-polyketide derivatives, vitroprocines A-J, from the marine bacterium Vibrio sp. QWI-06 by an integrated approach using imaging mass spectroscopy and molecular networking, as well as conventional bioactivity-guided fractionation and isolation. The structure-activity relationship of vitroprocines against Acinetobacter baumannii is proposed. In addition, feeding experiments with 13C-labeled precursors indicated that a pyridoxal 5‧-phosphate-dependent mechanism is involved in the biosynthesis of vitroprocines. Elucidation of amino-polyketide derivatives from a species of marine bacteria for the first time demonstrates the potential of this integrated metabolomics approach to uncover marine bacterial biodiversity.

Small molecules make big differences: molecular doping effects on electronic and optical properties of phosphorene

International Nuclear Information System (INIS)

Jing, Yu; Tang, Qing; He, Peng; Zhou, Zhen; Shen, Panwen

2015-01-01

Systematical computations on the density functional theory were performed to investigate the adsorption of three typical organic molecules, tetracyanoquinodimethane (TCNQ), tetracyanoethylene (TCNE) and tetrathiafulvalene (TTF), on the surface of phosphorene monolayers and thicker layers. There exist considerable charge transfer and strong non-covalent interaction between these molecules and phosphorene. In particular, the band gap of phosphorene decreases dramatically due to the molecular modification and can be further tuned by applying an external electric field. Meanwhile, surface molecular modification has proven to be an effective way to enhance the light harvesting of phosphorene in different directions. Our results predict a flexible method toward modulating the electronic and optical properties of phosphorene and shed light on its experimental applications. (paper)

Dynamic molecular oxygen production in cometary comae

Science.gov (United States)

Yao, Yunxi; Giapis, Konstantinos P.

2017-05-01

Abundant molecular oxygen was discovered in the coma of comet 67P/Churyumov-Gerasimenko. Its origin was ascribed to primordial gaseous O2 incorporated into the nucleus during the comet's formation. This thesis was put forward after discounting several O2 production mechanisms in comets, including photolysis and radiolysis of water, solar wind-surface interactions and gas-phase collisions. Here we report an original Eley-Rideal reaction mechanism, which permits direct O2 formation in single collisions of energetic water ions with oxidized cometary surface analogues. The reaction proceeds by H2O+ abstracting a surface O-atom, then forming an excited precursor state, which dissociates to produce O2-. Subsequent photo-detachment leads to molecular O2, whose presence in the coma may thus be linked directly to water molecules and their interaction with the solar wind. This abiotic O2 production mechanism is consistent with reported trends in the 67P coma and raises awareness of the role of energetic negative ions in comets.

The Use of a Performance Assessment for Identifying Gifted Lebanese Students: Is DISCOVER Effective?

Science.gov (United States)

Sarouphim, Ketty M.

2009-01-01

The purpose of this study was to investigate the effectiveness of DISCOVER, a performance- based assessment in identifying gifted Lebanese students. The sample consisted of 248 students (121 boys, 127 girls) from Grades 3-5 at two private schools in Beirut, Lebanon. Students were administered DISCOVER and the Raven Standard Progressive Matrices…

Metabolomics reveals distinct, antibody-independent, molecular signatures of MS, AQP4-antibody and MOG-antibody disease.

Science.gov (United States)

Jurynczyk, Maciej; Probert, Fay; Yeo, Tianrong; Tackley, George; Claridge, Tim D W; Cavey, Ana; Woodhall, Mark R; Arora, Siddharth; Winkler, Torsten; Schiffer, Eric; Vincent, Angela; DeLuca, Gabriele; Sibson, Nicola R; Isabel Leite, M; Waters, Patrick; Anthony, Daniel C; Palace, Jacqueline

2017-12-06

The overlapping clinical features of relapsing remitting multiple sclerosis (RRMS), aquaporin-4 (AQP4)-antibody (Ab) neuromyelitis optica spectrum disorder (NMOSD), and myelin oligodendrocyte glycoprotein (MOG)-Ab disease mean that detection of disease specific serum antibodies is the gold standard in diagnostics. However, antibody levels are not prognostic and may become undetectable after treatment or during remission. Therefore, there is still a need to discover antibody-independent biomarkers. We sought to discover whether plasma metabolic profiling could provide biomarkers of these three diseases and explore if the metabolic differences are independent of antibody titre. Plasma samples from 108 patients (34 RRMS, 54 AQP4-Ab NMOSD, and 20 MOG-Ab disease) were analysed by nuclear magnetic resonance spectroscopy followed by lipoprotein profiling. Orthogonal partial-least squares discriminatory analysis (OPLS-DA) was used to identify significant differences in the plasma metabolite concentrations and produce models (mathematical algorithms) capable of identifying these diseases. In all instances, the models were highly discriminatory, with a distinct metabolite pattern identified for each disease. In addition, OPLS-DA identified AQP4-Ab NMOSD patient samples with low/undetectable antibody levels with an accuracy of 92%. The AQP4-Ab NMOSD metabolic profile was characterised by decreased levels of scyllo-inositol and small high density lipoprotein particles along with an increase in large low density lipoprotein particles relative to both RRMS and MOG-Ab disease. RRMS plasma exhibited increased histidine and glucose, along with decreased lactate, alanine, and large high density lipoproteins while MOG-Ab disease plasma was defined by increases in formate and leucine coupled with decreased myo-inositol. Despite overlap in clinical measures in these three diseases, the distinct plasma metabolic patterns support their distinct serological profiles and confirm that these

Molecular characterization of velogenic viscerotropic Ranikhet (Newcastle) disease virus from different outbreaks in desi chickens

OpenAIRE

Dhaygude, V. S.; Sawale, G. K.; Chawak, M. M.; Bulbule, N. R.; Moregaonkar, S. D.; Gavhane, D. S.

2017-01-01

Aim: Diagnosis of velogenic viscerotropic Ranikhet disease from six different flocks of desi chicken in and around Mumbai by gross and histopathological examination, isolation of virus and molecular methods. Materials and Methods: A total of 25 carcasses (varying between 2 and 6 carcasses from each flock) of six different flocks of adult desi chicken were subjected to necropsy examination for diagnosis of the disease during the span of a year (2014-2015). After thorough gross examination,...

Screening individual hybridomas by microengraving to discover monoclonal antibodies

Science.gov (United States)

Ogunniyi, Adebola O; Story, Craig M; Papa, Eliseo; Guillen, Eduardo; Love, J Christopher

2014-01-01

The demand for monoclonal antibodies (mAbs) in biomedical research is significant, but the current methodologies used to discover them are both lengthy and costly. Consequently, the diversity of antibodies available for any particular antigen remains limited. Microengraving is a soft lithographic technique that provides a rapid and efficient alternative for discovering new mAbs. This protocol describes how to use microengraving to screen mouse hybridomas to establish new cell lines producing unique mAbs. Single cells from a polyclonal population are isolated into an array of microscale wells (~105 cells per screen). The array is then used to print a protein microarray, where each element contains the antibodies captured from individual wells. The antibodies on the microarray are screened with antigens of interest, and mapped to the corresponding cells, which are then recovered from their microwells by micromanipulation. Screening and retrieval require approximately 1–3 d (9–12 d including the steps for preparing arrays of microwells). PMID:19528952

Discovering the secrets of the Olifants sediments

CSIR Research Space (South Africa)

Petersen, C

2012-07-01

Full Text Available is an important component of an aquatic ecosystem in that it provides habitat, feed- ing and spawning areas for aquatic fauna such as fish and benthic Discovering the secrets of THE OLIFANTS SEDIMENTS The polluted Upper Olifants River, in Mpumalanga, has... the distribution of bed material sizes. This allows for the determination ? Top right: The Koffie- spruit, a tributary of the Upper Olifants River. Middle right: Bank erosion was evident throughout the Koffiespruit study reach. This section of river...

Summary different routes for procurement of molecular sieves type AL-SBA-15

International Nuclear Information System (INIS)

Figueiroa, D.S.; Santos, J.O.P.N.; Medeiros, C.D.; Sousa, B.V.

2012-01-01

The search for new materials to assist industrial development, especially in the chemical industry has been growing more and more. Molecular sieves are great examples of these materials that aim the improvement of various chemical processes. The present work aimed to synthesize the molecular sieve Al-SBA-15 by two different synthesis procedures. In procedure A was used a temperature of 40°C for 24 hours during stirring process. For B process the stirring procedure was done at room temperature. The molar composition of reactants was: 1.0 SiO 2 : 0.04 Al 2 O 3 :0.0168 EO 20 PO 70 EO 20 : 5.85 HCl: 160 H 2 O. The pH of the reaction gel was adjusted to 7 and after the gel was putted under 100 deg C for 48 hours for the heat treatment. Then the sample was calcined under flowing air at 500° C for 6 hours. By techniques such as XRD and SEM, it was confirmed the formation of the hexagonal mesoporous structure, with an orderly distribution of its pores, also indicating the successful incorporation of aluminum into the hexagonal structure of the catalyst support. (author)

Energy transformation in molecular electronic systems: Comprehensive progress report, 1986--1989

International Nuclear Information System (INIS)

Kasha, M.

1989-01-01

Our research focuses on discovering the fundamental issues in proton-transfer and charge-transfer excitations in model systems, with an eye on which molecular systems will serve as the best guide to biological systems. This report addresses an intramolecular proton transfer classification system, proton-transfer potentials, proton-transfer spectroscopy of benzanilides, proton-transfer in aminosalicylates, proton-transfer in lumichrome, development of proton-transfer lasers, and triplet excitation enhancement via proton-transfer tunneling. 6 refs., 2 figs

Tumor microvascular changes in antiangiogenic treatment : Assessment by magnetic resonance contrast media of different molecular weights

NARCIS (Netherlands)

Turetschek, K; Preda, A; Novikov, [No Value; Brasch, RC; Weinmann, HJ; Wunderbaldinger, P; Roberts, TPL

Purpose: To test magnetic resonance (MR) contrast media of different molecular weights (MWs) for their potential to characterize noninvasively microvascular changes in an experimental tumor treatment model. Materials and Methods: MD-MBA-435, a poorly differentiated human breast cancer cell line, was

DISCOVER-AQ: an innovative approach to study the vertical distribution of air quality constituents in the Earth's atmosphere

Science.gov (United States)

Wisthaler, Armin; Crawford, James H.; Müller, Markus; Mikoviny, Tomas; Cady-Pereira, Karen E.

2014-05-01

DISCOVER-AQ (Deriving Information on Surface Conditions from Column and Vertically Resolved Observations Relevant to Air Quality) is a multi-year NASA research project to improve remote sensing of air quality from space. Satellite-based measurements of air pollutants typically provide information integrated over the total atmospheric column while it is the lowermost part of the atmosphere that is of interest from a public health perspective. DISCOVER-AQ has implemented a new field observation strategy to collect a comprehensive dataset on the vertical distribution of air pollutants in the atmosphere. In situ measurements from the NASA P-3B Airborne Science Laboratory generate profile information of air quality constituents over a set of selected ground monitoring sites. Ground and profile information is tied to column information collected by active and passive remote sensors looking downward from a second King Air aircraft flying higher in the atmosphere above the P-3B. Vertical profiles of air pollutants are measured repetitively during different times of the day and under different meteorological conditions occurring in the timeframe of 1-month field campaigns. Targeted regions in the U.S. affected by poor air quality include the Washington/Baltimore metropolitan area (June/July 2011), the San Joaquin Valley in California (January/February 2013), the Houston metropolitan area (September 2013) and the Northern Front Range area in Colorado (June/July 2014). Herein, we will present the DISCOVER-AQ project to the European community and show preliminary analyses of the obtained data. The latter will focus on non-methane hydrocarbons and ammonia, being the species measured by our newly developed airborne PTR-ToF-MS instrument (see session AS4.17). In situ ammonia data collected over the San Joaquin Valley are in promising agreement with satellite data obtained from the Tropospheric Emission Spectrometer (TES). Web site: http://discover-aq.larc.nasa.gov/ Funding

The Spy VI child : A newly discovered Neandertal infant

NARCIS (Netherlands)

Crevecoeur, Isabelle; Bayle, Priscilla; Rougier, Helene; Maureille, Bruno; Higham, Thomas; van der Plicht, Johannes; De Clerck, Nora; Semal, Patrick

2010-01-01

Spy cave (Jemeppe-sur-Sambre Belgium) is reputed for the two adult Neandertal individuals discovered in situ in 1886 Recent reassessment of the Spy collections has allowed direct radiocarbon dating of these individuals The sorting of all of the faunal collections has also led to the discovery of the

Molecular taxonomy provides new insights into anopheles species of the neotropical arribalzagia series.

Directory of Open Access Journals (Sweden)

Giovan F Gómez

Full Text Available Phylogenetic analysis of partial mitochondrial cytochrome oxidase c subunit I (COI and nuclear internal transcribed spacer 2 (ITS2 sequences were used to evaluate initial identification and to investigate phylogenetic relationships of seven Anopheles morphospecies of the Arribalzagia Series from Colombia. Phylogenetic trees recovered highly supported clades for An. punctimaculas.s., An. calderoni, An. malefactor s.l., An. neomaculipalpus, An. apicimacula s.l., An. mattogrossensis and An. peryassui. This study provides the first molecular confirmation of An. malefactorfrom Colombia and discovered conflicting patterns of divergence for the molecular markers among specimens from northeast and northern Colombia suggesting the presence of two previously unrecognized Molecular Operational Taxonomic Units (MOTUs. Furthermore, two highly differentiated An. apicimacula MOTUs previously found in Panama were detected. Overall, the combined molecular dataset facilitated the detection of known and new Colombian evolutionary lineages, and constitutes the baseline for future research on their bionomics, ecology and potential role as malaria vectors.

Discovering potential Streptomyces hormone producers by using disruptants of essential biosynthetic genes as indicator strains.

Science.gov (United States)

Thao, Nguyen B; Kitani, Shigeru; Nitta, Hiroko; Tomioka, Toshiya; Nihira, Takuya

2017-10-01

Autoregulators are low-molecular-weight signaling compounds that control the production of many secondary metabolites in actinomycetes and have been referred to as 'Streptomyces hormones'. Here, potential producers of Streptomyces hormones were investigated in 40 Streptomyces and 11 endophytic actinomycetes. Production of γ-butyrolactone-type (IM-2, VB) and butenolide-type (avenolide) Streptomyces hormones was screened using Streptomyces lavendulae FRI-5 (ΔfarX), Streptomyces virginiae (ΔbarX) and Streptomyces avermitilis (Δaco), respectively. In these strains, essential biosynthetic genes for Streptomyces hormones were disrupted, enabling them to respond solely to the externally added hormones. The results showed that 20% of each of the investigated strains produced IM-2 and VB, confirming that γ-butyrolactone-type Streptomyces hormones are the most common in actinomycetes. Unlike the γ-butyrolactone type, butenolide-type Streptomyces hormones have been discovered in recent years, but their distribution has been unclear. Our finding that 24% of actinomycetes (12 of 51 strains) showed avenolide activity revealed for the first time that the butenolide-type Streptomyces hormone is also common in actinomycetes.

Molecular and genetic aspects of odontogenic tumors: a review.

Science.gov (United States)

Garg, Kavita; Chandra, Shaleen; Raj, Vineet; Fareed, Wamiq; Zafar, Muhammad

2015-06-01

Odontogenic tumors contain a heterogeneous collection of lesions that are categorized from hamartomas to benign and malignant neoplasms of inconstant aggressiveness. Odontogenic tumors are usually extraordinary with assessed frequency of short of 0.5 cases/100,000 population for every year. The lesions such as odontogenic tumors are inferred from the components of the tooth-structuring contraption. They are discovered solely inside the maxillary and mandibular bones. This audit speaks to experiences and cooperation of the molecular and genetic variations connected to the development and movement of odontogenic tumors which incorporate oncogenes, tumor-silencer genes, APC gene, retinoblastoma genes, DNA repair genes, onco-viruses, development components, telomerase, cell cycle controllers, apoptosis-related elements, and regulators/conttrollers of tooth development. The reasonable and better understanding of the molecular components may prompt new ideas for their detection and administrating a better prognosis of odontogenic tumors.

Real-time reflectance-difference spectroscopy of GaAs molecular beam epitaxy homoepitaxial growth

Directory of Open Access Journals (Sweden)

A. Lastras-Martínez

2014-03-01

Full Text Available We report on real time-resolved Reflectance-difference (RD spectroscopy of GaAs(001 grown by molecular beam epitaxy, with a time-resolution of 500 ms per spectrum within the 2.3–4.0 eV photon energy range. Through the analysis of transient RD spectra we demonstrated that RD line shapes are comprised of two components with different physical origins and determined their evolution during growth. Such components were ascribed to the subsurface strain induced by surface reconstruction and to surface stoichiometry. Results reported in this paper render RD spectroscopy as a powerful tool for the study of fundamental processes during the epitaxial growth of zincblende semiconductors.

Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

Science.gov (United States)

Li, Jianwei; Nowak, Piotr; Otto, Sijbren

2013-06-26

Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

Molecular origin of differences in hole and electron mobility in amorphous Alq3--a multiscale simulation study.

Science.gov (United States)

Fuchs, Andreas; Steinbrecher, Thomas; Mommer, Mario S; Nagata, Yuki; Elstner, Marcus; Lennartz, Christian

2012-03-28

In order to determine the molecular origin of the difference in electron and hole mobilities of amorphous thin films of Alq(3) (meridional Alq(3) (tris(8-hydroxyquinoline) aluminium)) we performed multiscale simulations covering quantum mechanics, molecular mechanics and lattice models. The study includes realistic disordered morphologies, polarized site energies to describe diagonal disorder, quantum chemically calculated transfer integrals for the off-diagonal disorder, inner sphere reorganization energies and an approximative scheme for outer sphere reorganization energies. Intermolecular transfer rates were calculated via Marcus-theory and mobilities were simulated via kinetic Monte Carlo simulations and by a Master Equation approach. The difference in electron and hole mobility originates from the different localization of charge density in the radical anion (more delocalized) compared to the radical cation (more confined). This results in higher diagonal disorder for holes and less favourable overlap properties for the hole transfer integrals leading to an overall higher electron mobility.

Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques.

Science.gov (United States)

Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M; Prates, Luciana L; Yu, Peiqiang

2017-08-05

The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HED N/OM ), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular Convergence of Infrared Vision in Snakes

Science.gov (United States)

Yokoyama, Shozo; Altun, Ahmet; DeNardo, Dale F.

2011-01-01

It has been discovered that the transient receptor potential ankyrin 1 (TRPA1) proteins of Boidae (boas), Pythonidae (pythons), and Crotalinae (pit vipers) are used to detect infrared radiation, but the molecular mechanism for detecting the infrared radiation is unknown. Here, relating the amino acid substitutions in their TRPA1 proteins and the functional differentiations, we propose that three parallel amino acid changes (L330M, Q391H, and S434T) are responsible for the development of infrared vision in the three groups of snakes. Protein modeling shows that the three amino acid changes alter the structures of the central region of their ankyrin repeats. PMID:20937734

Yes, Aboriginal Australians can and did discover the variability of Betelgeuse

Science.gov (United States)

Schaefer, Bradley E.

2018-04-01

Recently, a widely publicized claim has been made that the Aboriginal Australians discovered the variability of the red star Betelgeuse in the modern Orion, plus the variability of two other prominent red stars: Aldebaran and Antares. This result has excited the usual healthy skepticism, with questions about whether any untrained peoples can discover the variability and whether such a discovery is likely to be placed into lore and transmitted for long periods of time. Here, I am offering an independent evaluation, based on broad experience with naked-eye sky viewing and astro-history. I find that it is easy for inexperienced observers to detect the variability of Betelgeuse over its range in brightness from V = 0.0 to V = 1.3, for example in noticing from season-to-season that the star varies from significantly brighter than Procyon to being greatly fainter than Procyon. Further, indigenous peoples in the Southern Hemisphere inevitably kept watch on the prominent red star, so it is inevitable that the variability of Betelgeuse was discovered many times over during the last 65 millennia. The processes of placing this discovery into a cultural context (in this case, put into morality stories) and the faithful transmission for many millennia is confidently known for the Aboriginal Australians in particular. So this shows that the whole claim for a changing Betelgeuse in the Aboriginal Australian lore is both plausible and likely. Given that the discovery and transmission is easily possible, the real proof is that the Aboriginal lore gives an unambiguous statement that these stars do indeed vary in brightness, as collected by many ethnographers over a century ago from many Aboriginal groups. So I strongly conclude that the Aboriginal Australians could and did discover the variability of Betelgeuse, Aldebaran, and Antares.

Controlling molecular condensation/diffusion of copper phthalocyanine by local electric field induced with scanning tunneling microscope tip

Science.gov (United States)

Nagaoka, Katsumi; Yaginuma, Shin; Nakayama, Tomonobu

2018-02-01

We have discovered the condensation/diffusion phenomena of copper phthalocyanine (CuPc) molecules controlled with a pulsed electric field induced by the scanning tunneling microscope tip. This behavior is not explained by the conventional induced dipole model. In order to understand the mechanism, we have measured the electronic structure of the molecule by tunneling spectroscopy and also performed theoretical calculations on molecular orbitals. These data clearly indicate that the molecule is positively charged owing to charge transfer to the substrate, and that hydrogen bonding exists between CuPc molecules, which makes the molecular island stable.

Transient Changes in Molecular Geometries and How to Model Them

DEFF Research Database (Denmark)

Dohn, Asmus Ougaard

Light-induced chemical processes are accompanied by molecular motion on the femtosecond time scale. Uncovering this dynamical motion is central to understanding the chemical reaction on a fundamental level. This thesis focuses on the aspects of excess excitation energy dissipation via dynamic...... observe how the wide distribution of ground state geometries is responsible for decoherence, and that the solvent cage actually facilitates coherent motion, by blocking the newly discovered vibrational mode. We furthermore observe a non-specific, rotational solvent response to the excitation. The second...

Different molecular organization of two carotenoids, lutein and zeaxanthin, in human colon epithelial cells and colon adenocarcinoma cells

Science.gov (United States)

Grudzinski, Wojciech; Piet, Mateusz; Luchowski, Rafal; Reszczynska, Emilia; Welc, Renata; Paduch, Roman; Gruszecki, Wieslaw I.

2018-01-01

Two cell lines, human normal colon epithelial cells (CCD 841 CoTr) and human colon adenocarcinoma cells (HT-29) were cultured in the presence of exogenous carotenoids, either zeaxanthin or lutein. Both carotenoids demonstrated cytotoxicity with respect to cancer cells but not to normal cells. Cells from both the cell lines were analyzed with application of fluorescence lifetime imaging microscopy and Raman scattering microscopy. Both imaging techniques show effective incorporation of carotenoid molecules into growing cells. Comparison of the Raman scattering and fluorescence lifetime characteristics reveals different molecular organization of carotenoids in the carcinoma and normal cells. The main difference consists in a carotenoid aggregation level which is substantially lower in the carcinoma cells as compared to the normal cells. Different molecular organization of carotenoids was interpreted in terms of a different metabolism of normal and carcinoma cells and has been concluded to provide a possibility of cancer diagnosis based on spectroscopic analyses.

A WARM MOLECULAR HYDROGEN TAIL DUE TO RAM-PRESSURE STRIPPING OF A CLUSTER GALAXY

International Nuclear Information System (INIS)

Sivanandam, Suresh; Rieke, Marcia J.; Rieke, George H.

2010-01-01

We have discovered a remarkable warm (130-160 K) molecular hydrogen tail with a H 2 mass of approximately 4 x 10 7 M sun extending 20 kpc from a cluster spiral galaxy, ESO 137-001, in Abell 3627. At least half of this gas is lost permanently to the intracluster medium, as the tail extends beyond the tidal radius of the galaxy. We also detect a hot (400-550 K) component in the tail that is approximately 1% of the mass. The large H 2 line to IR continuum luminosity ratio in the tail indicates that star formation is not a major excitation source and that the gas is possibly shock-heated. This discovery confirms that the galaxy is currently undergoing ram-pressure stripping, as also indicated by its previously discovered X-ray and Hα tails. We estimate that the galaxy is losing its warm H 2 gas at a rate of ∼2-3 M sun yr -1 . The true mass-loss rate is likely higher if we account for cold molecular gas and atomic gas. We predict that the galaxy will lose most of its gas in a single pass through the core and place a strong upper limit on the ram-pressure timescale of 1 Gyr. We also study the star-forming properties of the galaxy and its tail. We identify most of the previously discovered external Hα sources within the tail in our 8 μm data but not in our 3.6 μm data; IRS spectroscopy of the region containing these Hα sources also reveals aromatic features typically associated with star formation. From the positions of these H II regions, it appears that star formation is not occurring throughout the molecular hydrogen tail but only immediately downstream of the galaxy. Some of these H II regions lie outside the tidal radius of the galaxy, indicating that ram-pressure stripping can be a source of intracluster stars.

Astronomers Discover Fastest-Spinning Pulsar

Science.gov (United States)

2006-01-01

discovered in 1982. For reference, the fastest speeds of common kitchen blenders are 250-500 Hz. The scientists say the object's fast rotation speed means that it cannot be any larger than about 20 miles across. According to Hessels, "If it were any larger, material from the surface would be flung into orbit around the star." The scientists' calculation assumed that the neutron star contains less than two times the mass of the Sun, an assumption that is consistent with the masses of all known neutron stars. The spinning pulsar has a companion star that orbits it once every 26 hours. The companion passes in front of the pulsar, eclipsing the pulsar about 40 percent of the time. The long eclipse period, probably due to bloating of the companion, makes it difficult for the astronomers to learn details of the orbital configuration that would allow them to precisely measure the masses of the pulsar and its companion. "If we could pin down these masses more precisely, we could then get a better limit on the size of the pulsar. That, in turn, would then give us a better figure for the true density inside the neutron star," explained Ingrid Stairs, an assistant professor at the University of British Columbia and another collaborator on the work. Competing theoretical models for the types and distributions of elementary particles inside neutron stars make widely different predictions about the pressure and density of such an object. "We want observational data that shows which models fit the reality of nature," Hessels said. If the scientists can't use PSR J1748-2446ad to do that, they are hopeful some of its near neighbors will yield the data they seek. Using the GBT, the astronomers so far have found 30 new fast "millisecond pulsars" in the cluster Terzan 5, making 33 pulsars known in the cluster in total. This is the largest number of such pulsars ever found in a single globular cluster. Dense globular clusters of stars are excellent places to find fast-rotating millisecond

CORNELL: CLEO discovers B meson penguins

Energy Technology Data Exchange (ETDEWEB)

Anon.

1993-06-15

The CLEO collaboration at Cornell's CESR electron-positron storage ring has discovered a rare type of B meson decay in which only a high energy photon and a K* meson are produced. These decays provide the first unambiguous evidence for an alternative route for heavy quark decay that has been given the whimsical name ''penguin diagram''. In the mid-1970s penguin diagrams were proposed to explain the puzzling strangeness quantum number selection rules in the decay of K mesons. At the same time it was realized that penguin diagrams could also be important in the CP violation seen in neutral K meson decay. CP violation, an asymmetry between matter and antimatter, is an essential ingredient in understanding why there is much more matter than antimatter in the universe. CP violation introduces a definite direction to the arrow of time, which could otherwise point equally forwards or backwards. In addition, penguin decays are very sensitive to some extensions of the Standard Model of weak decay. Although penguin diagrams were first proposed to explain an effect in K meson decay, the K system gives no unique signature for them, and verification of penguin processes meant looking elsewhere. In the Standard Model, quarks decay under the influence of the weak force, emitting a W boson. Since the W is charged, the charge of the initial quark differs from that of the final quark, so the charge of the quark changes as well as its flavour.

Functioning and nonfunctioning thyroid adenomas involve different molecular pathogenetic mechanisms.

Science.gov (United States)

Tonacchera, M; Vitti, P; Agretti, P; Ceccarini, G; Perri, A; Cavaliere, R; Mazzi, B; Naccarato, A G; Viacava, P; Miccoli, P; Pinchera, A; Chiovato, L

1999-11-01

The molecular biology of follicular cell growth in thyroid nodules is still poorly understood. Because gain-of-function (activating) mutations of the thyroid-stimulating hormone receptor (TShR) and/or Gs alpha genes may confer TSh-independent growth advantage to neoplastic thyroid cells, we searched for somatic mutations of these genes in a series of hyperfunctioning and nonfunctioning follicular thyroid adenomas specifically selected for their homogeneous gross anatomy (single nodule in an otherwise normal thyroid gland). TShR gene mutations were identified by direct sequencing of exons 9 and 10 of the TShR gene in genomic DNA obtained from surgical specimens. Codons 201 and 227 of the Gs alpha gene were also analyzed. At histology, all hyperfunctioning nodules and 13 of 15 nonfunctioning nodules were diagnosed as follicular adenomas. Two nonfunctioning thyroid nodules, although showing a prevalent microfollicular pattern of growth, had histological features indicating malignant transformation (a minimally invasive follicular carcinoma and a focal papillary carcinoma). Activating mutations of the TShR gene were found in 12 of 15 hyperfunctioning follicular thyroid adenomas. In one hyperfunctioning adenoma, which was negative for TShR mutations, a mutation in codon 227 of the Gs alpha gene was identified. At variance with hyperfunctioning thyroid adenomas, no mutation of the TShR or Gs alpha genes was detected in nonfunctioning thyroid nodules. In conclusion, our findings clearly define a different molecular pathogenetic mechanism in hyperfunctioning and nonfunctioning follicular thyroid adenomas. Activation of the cAMP cascade, which leads to proliferation but maintains differentiation of follicular thyroid cells, typically occurs in hyperfunctioning thyroid adenomas. Oncogenes other than the TShR and Gs alpha genes are probably involved in nonfunctioning follicular adenomas.

DeBi: Discovering Differentially Expressed Biclusters using a Frequent Itemset Approach

Directory of Open Access Journals (Sweden)

Vingron Martin

2011-06-01

Full Text Available Abstract Background The analysis of massive high throughput data via clustering algorithms is very important for elucidating gene functions in biological systems. However, traditional clustering methods have several drawbacks. Biclustering overcomes these limitations by grouping genes and samples simultaneously. It discovers subsets of genes that are co-expressed in certain samples. Recent studies showed that biclustering has a great potential in detecting marker genes that are associated with certain tissues or diseases. Several biclustering algorithms have been proposed. However, it is still a challenge to find biclusters that are significant based on biological validation measures. Besides that, there is a need for a biclustering algorithm that is capable of analyzing very large datasets in reasonable time. Results Here we present a fast biclustering algorithm called DeBi (Differentially Expressed BIclusters. The algorithm is based on a well known data mining approach called frequent itemset. It discovers maximum size homogeneous biclusters in which each gene is strongly associated with a subset of samples. We evaluate the performance of DeBi on a yeast dataset, on synthetic datasets and on human datasets. Conclusions We demonstrate that the DeBi algorithm provides functionally more coherent gene sets compared to standard clustering or biclustering algorithms using biological validation measures such as Gene Ontology term and Transcription Factor Binding Site enrichment. We show that DeBi is a computationally efficient and powerful tool in analyzing large datasets. The method is also applicable on multiple gene expression datasets coming from different labs or platforms.

Successful application of virtual screening and molecular dynamics simulations against antimalarial molecular targets

Directory of Open Access Journals (Sweden)

Renata Rachide Nunes

Full Text Available The main challenge in the control of malaria has been the emergence of drug-resistant parasites. The presence of drug-resistant Plasmodium sp. has raised the need for new antimalarial drugs. Molecular modelling techniques have been used as tools to develop new drugs. In this study, we employed virtual screening of a pyrazol derivative (Tx001 against four malaria targets: plasmepsin-IV, plasmepsin-II, falcipain-II, and PfATP6. The receiver operating characteristic curves and area under the curve (AUC were established for each molecular target. The AUC values obtained for plasmepsin-IV, plasmepsin-II, and falcipain-II were 0.64, 0.92, and 0.94, respectively. All docking simulations were carried out using AutoDock Vina software. The ligand Tx001 exhibited a better interaction with PfATP6 than with the reference compound (-12.2 versus -6.8 Kcal/mol. The Tx001-PfATP6 complex was submitted to molecular dynamics simulations in vacuum implemented on an NAMD program. The ligand Tx001 docked at the same binding site as thapsigargin, which is a natural inhibitor of PfATP6. Compound TX001 was evaluated in vitro with a P. falciparum strain (W2 and a human cell line (WI-26VA4. Tx001 was discovered to be active against P. falciparum (IC50 = 8.2 µM and inactive against WI-26VA4 (IC50 > 200 µM. Further ligand optimisation cycles generated new prospects for docking and biological assays.

Nuclear fission discovered fifty years ago

International Nuclear Information System (INIS)

Weis, M.

1988-01-01

Fifty years ago, Otto Hahn, Lise Meitner and Fritz Strassmann discovered the process of nuclear fission which, more than other scientific discoveries to date, profoundly has changed the world and continues to influence our life significantly: This discovery made the up to then incontestable physicists' view of the atom as an inseparable whole suddenly shatter to pieces. It has brought about the invaluable advantages of a peaceful utilization of nuclear energy, and at the same time put scientists in the position to build the most terrible weapon ever, threatening mankind and earth with complete destruction. All this certainly is reason enough to recall the scientists, their work and the spirit of the time. (orig.) [de

Discovering network behind infectious disease outbreak

Science.gov (United States)

Maeno, Yoshiharu

2010-11-01

Stochasticity and spatial heterogeneity are of great interest recently in studying the spread of an infectious disease. The presented method solves an inverse problem to discover the effectively decisive topology of a heterogeneous network and reveal the transmission parameters which govern the stochastic spreads over the network from a dataset on an infectious disease outbreak in the early growth phase. Populations in a combination of epidemiological compartment models and a meta-population network model are described by stochastic differential equations. Probability density functions are derived from the equations and used for the maximal likelihood estimation of the topology and parameters. The method is tested with computationally synthesized datasets and the WHO dataset on the SARS outbreak.

Temperature dependence of viscoelasticity of crystalline cellulose with different molecular weights added to silicone elastomer

Science.gov (United States)

Sugino, Naoto; Nakajima, Shinya; Kameda, Takao; Takei, Satoshi; Hanabata, Makoto

2017-08-01

Silicone elastomers ( polydimethylsiloxane _ PDMS) are widely used in the field of imprint lithography and microcontactprinting (μCP). When performing microcontactprinting, the mechanical properties of the PCMS as a base material have a great influence on the performance of the device. Cellulose nanofibers having features of high strength, high elasticity and low coefficient of linear expansion have attracted attention in recent years due to their characteristics. Therefore, three types of crystalline cellulose having different molecular weights were added to PDMS to prepare a composite material, and dynamic viscoelasticity was measured using a rheometer. The PDMS with the highest molecular weight crystalline cellulose added exhibited smaller storage modulus than PDMS with other molecular weight added in all temperature ranges. Furthermore, when comparing PDMS to which crystalline cellulose was added and PDMS which is not added, the storage modulus of PDMS to which cellulose was added in the low temperature region was higher than that of PDMS to which it was not added, but it was reversed in the high temperature region It was a result. When used in a low temperature range (less than 150 ° C.), it can be said that cellulose can function as a reinforcing material for PDMS.

Discovering objects in a blood recipient information system.

Science.gov (United States)

Qiu, D; Junghans, G; Marquardt, K; Kroll, H; Mueller-Eckhardt, C; Dudeck, J

1995-01-01

Application of object-oriented (OO) methodologies has been generally considered as a solution to the problem of improving the software development process and managing the so-called software crisis. Among them, object-oriented analysis (OOA) is the most essential and is a vital prerequisite for the successful use of other OO methodologies. Though there are already a good deal of OOA methods published, the most important aspect common to all these methods: discovering objects classes truly relevant to the given problem domain, has remained a subject to be intensively researched. In this paper, using the successful development of a blood recipient information system as an example, we present our approach which is based on the conceptual framework of responsibility-driven OOA. In the discussion, we also suggest that it may be inadequate to simply attribute the software crisis to the waterfall model of the software development life-cycle. We are convinced that the real causes for the failure of some software and information systems should be sought in the methodologies used in some crucial phases of the software development process. Furthermore, a software system can also fail if object classes essential to the problem domain are not discovered, implemented and visualized, so that the real-world situation cannot be faithfully traced by it.

Molecular dynamics simulations of a fully hydrated dipalmitoyl phosphatidylcholine bilayer with different macroscopic boundary conditions and parameters

NARCIS (Netherlands)

Tieleman, D.P; Berendsen, H.J.C.

1996-01-01

We compared molecular dynamics simulations of a bilayer of 128 fully hydrated phospholipid (DPPC) molecules, using different parameters and macroscopic boundary conditions. The same system was studied under constant pressure, constant volume, and constant surface tension boundary conditions, with

ISLSCP II IGBP DISCover and SiB Land Cover, 1992-1993

Data.gov (United States)

National Aeronautics and Space Administration — This data set describes the geographic distributions of 17 classes of land cover based on the International Geosphere-Biosphere DISCover land cover legend (Loveland...

Discovering and explaining work-family strategies of parents in Luxembourg

NARCIS (Netherlands)

Zhelyazkova, Nevena

2014-01-01

The presented analysis discovers and explains typical patterns of work-family reconciliation for parents who had a child in the same period (2003) and in the same country (Luxembourg), thus facing the same macroeconomic and institutional conditions. Work-family trajectories are reconstructed as

Louis Pasteur, language, and molecular chirality. I. Background and dissymmetry.

Science.gov (United States)

Gal, Joseph

2011-01-01

Louis Pasteur resolved sodium ammonium (±)-tartrate in 1848, thereby discovering molecular chirality. Although hindered by the primitive state of organic chemistry, he introduced new terminology and nomenclature for his new science of molecular and crystal chirality. He was well prepared for this task by his rigorous education and innate abilities, and his linguistic achievements eventually earned him membership in the supreme institution for the French language, the Académie française. Dissymmetry had been in use in French from the early 1820s for disruption or absence of symmetry or for dissimilarity or difference in appearance between two objects, and Pasteur initially used it in the latter connotation, without any reference to handedness or enantiomorphism. Soon, however, he adopted it in the meaning of chirality. Asymmetry had been in use in French since 1691 but Pasteur ignored it in favor of dissymmetry. The two terms are not synonymous but it is not clear whether Pasteur recognized this difference in choosing the former over the latter. However, much of the literature mistranslates his dissymmetry as asymmetry. Twenty years before Pasteur the British polymath John Herschel proposed that optical rotation in the noncrystalline state is due to the "unsymmetrical" [his term] nature of the molecules and later used dissymmetrical for handed. Chirality, coined by Lord Kelvin in 1894 and introduced into chemistry by Mislow in 1962, has nearly completely replaced dissymmetry in the meaning of handedness, but the use of dissymmetry continues today in other contexts for lack of symmetry, reduction of symmetry, or dissimilarity. Copyright © 2010 Wiley-Liss, Inc.

Molecular Dynamics Simulation of Solidification of Pd-Ni Clusters with Different Nickel Content

Directory of Open Access Journals (Sweden)

Chen Gang

2014-01-01

Full Text Available Molecular dynamics simulation has been performed for investigating the glass transition of Pd-Ni alloy nanoparticles in the solidification process. The results showed that the Pd-Ni nanoparticles with composition far from pure metal should form amorphous structure more easily, which is in accordance with the results of the thermodynamic calculation. There are some regular and distorted fivefold symmetry in the amorphous Pd-Ni alloy nanoparticles. The nanoclusters with bigger difference value between formation enthalpies of solutions and glasses will transform to glass more easily than the other Pd-Ni alloy nanoclusters.

Molecular and genetic aspects of odontogenic tumors: a review

Directory of Open Access Journals (Sweden)

Kavita Garg

2015-06-01

Full Text Available Odontogenic tumors contain a heterogeneous collection of lesions that are categorized from hamartomas to benign and malignant neoplasms of inconstant aggressiveness. Odontogenic tumors are usually extraordinary with assessed frequency of short of 0.5 cases/100,000 population for every year. The lesions such as odontogenic tumors are inferred from the components of the tooth-structuring contraption. They are discovered solely inside the maxillary and mandibular bones. This audit speaks to experiences and cooperation of the molecular and genetic variations connected to the development and movement of odontogenic tumors which incorporate oncogenes, tumor-silencer genes, APC gene, retinoblastoma genes, DNA repair genes, onco-viruses, development components, telomerase, cell cycle controllers, apoptosis-related elements, and regulators/controllers of tooth development. The reasonable and better understanding of the molecular components may prompt new ideas for their detection and administrating a better prognosis of odontogenic tumors.

Shining Light on the Differences in Molecular Structural Chemical Makeup and the Cause of Distinct Degradation Behavior Between Malting- and Feed- Type Barley Using Synchrotorn FTIR Microspectroscopy: A Novel Approach

International Nuclear Information System (INIS)

Yu, P.; Doiron, K.; Liu, D.

2008-01-01

The objective of this study was to use advanced synchrotron-sourced FTIR microspectroscopy (SFTIRM) as a novel approach to identify the differences in protein and carbohydrate molecular structure (chemical makeup) between these two varieties of barley and illustrate the exact causes for their significantly different degradation kinetics. Items assessed included (1) molecular structural differences in protein amide I to amide II intensities and their ratio within cellular dimensions, (2) molecular structural differences in protein secondary structure profile and their ratios, and (3) molecular structural differences in carbohydrate component peak profile. Our hypothesis was that molecular structure (chemical makeup) affects barley quality, fermentation, and degradation behavior in both humans and animals. Using SFTIRM, the protein and carbohydrate molecular structural chemical makeup of barley was revealed and identified. The protein molecular structural chemical makeup differed significantly between the two varieties of barleys. No difference in carbohydrate molecular structural chemical makeup was detected. Harrington was lower than Valier in protein amide I, amide II, and protein amide I to amide II ratio, while Harrington was relatively higher in model-fitted protein a-helix and β-sheet, but lower in the others (β-turn and random coil). These results indicated that it is the molecular structure of protein (chemical makeup) that may play a major role in the different degradation kinetics between the two varieties of barleys (not the molecular structure of carbohydrate). It is believed that use of the advanced synchrotron technology will make a significant step and an important contribution to research in examining the molecular structure (chemical makeup) of plant, feed, and seeds.

Discovering Patterns in Brain Signals Using Decision Trees

Directory of Open Access Journals (Sweden)

Narusci S. Bastos

2016-01-01

Full Text Available Even with emerging technologies, such as Brain-Computer Interfaces (BCI systems, understanding how our brains work is a very difficult challenge. So we propose to use a data mining technique to help us in this task. As a case of study, we analyzed the brain’s behaviour of blind people and sighted people in a spatial activity. There is a common belief that blind people compensate their lack of vision using the other senses. If an object is given to sighted people and we asked them to identify this object, probably the sense of vision will be the most determinant one. If the same experiment was repeated with blind people, they will have to use other senses to identify the object. In this work, we propose a methodology that uses decision trees (DT to investigate the difference of how the brains of blind people and people with vision react against a spatial problem. We choose the DT algorithm because it can discover patterns in the brain signal, and its presentation is human interpretable. Our results show that using DT to analyze brain signals can help us to understand the brain’s behaviour.

Newly Discovered Items of the Zoomorphic Style from the Left Bank of the Lower Dniester

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Sinika Vitalij S.

2017-09-01

Full Text Available The article presents an overview of items corresponding to the Scythian zoomorphic style discovered at barbaric and ancient sites of the Northwestern Black Sea Region, and a publication of two new findings. They were discovered on the left bank of the Lower Dniester. The first item discovered at Parkany-II settlement is a fragment of a bronze horse plaque (its lower part crafted in the shape of a "rooster"-hippocampus. The other artifact discovered near Tokmazeya village also represents a horse plaque with an image of a cat predator's head. Presently, there are no counterparts of the images on these findings in the Northwestern Black Sea Region, which is the westmost periphery of the Scythian steppe culture. These fragments of horse apparel broaden our knowledge of the Scythian "bestiary" in the region. Besides, apart from the other items of material culture, the published findings confirm the presence of Scythian population at settlement sites, which contradicts the generally accepted opinion on the exclusively nomadic cattle breeding lifestyle of the Scythians in 5th –4th centuries B.C.

Common Subcluster Mining in Microarray Data for Molecular Biomarker Discovery.

Science.gov (United States)

Sadhu, Arnab; Bhattacharyya, Balaram

2017-10-11

Molecular biomarkers can be potential facilitators for detection of cancer at early stage which is otherwise difficult through conventional biomarkers. Gene expression data from microarray experiments on both normal and diseased cell samples provide enormous scope to explore genetic relations of disease using computational techniques. Varied patterns of expressions of thousands of genes at different cell conditions along with inherent experimental error make the task of isolating disease related genes challenging. In this paper, we present a data mining method, common subcluster mining (CSM), to discover highly perturbed genes under diseased condition from differential expression patterns. The method builds heap through superposing near centroid clusters from gene expression data of normal samples and extracts its core part. It, thus, isolates genes exhibiting the most stable state across normal samples and constitute a reference set for each centroid. It performs the same operation on datasets from corresponding diseased samples and isolates the genes showing drastic changes in their expression patterns. The method thus finds the disease-sensitive genesets when applied to datasets of lung cancer, prostrate cancer, pancreatic cancer, breast cancer, leukemia and pulmonary arterial hypertension. In majority of the cases, few new genes are found over and above some previously reported ones. Genes with distinct deviations in diseased samples are prospective candidates for molecular biomarkers of the respective disease.

US NSF: scientists discover planetary system similar to our own

CERN Multimedia

2003-01-01

An international team of scientists has discovered a planet and star that may share the same relationship as Jupiter and our Sun, the closest comparison that researchers have found since they began their search for extra-solar planets nearly a decade ago (1 page).

СD44+/CD24- markers of cancer stem cells in patients with breast cancer of different molecular subtypes.

Science.gov (United States)

Chekhun, S V; Zadvorny, T V; Tymovska, Yu O; Anikusko, M F; Novak, O E; Polishchuk, L Z

2015-03-01

To determine frequency of tumors with immunohistochemical markers of cancer stem cells (CSC) CD44+/CD24- in patients with breast cancer (BC) of different molecular subtype and to evaluate their prognostic value. Surgical material of 132 patients with BC stage I-II, age from 23 to 75 years, mean age - 50.2 ± 3.1 years was studied. Clinical, immunohistochemical (expression CD44+/CD24-), morphological, statistical. BC is characterized by heterogeneity of molecular subtypes and expression of markers (CD44+/CD24-). Immunohistochemical study of expression of CSC markers in surgical material has detected their expression in 34 (25.4%) patients with BC of different molecular subtypes. The highest frequency of cells with expression of CSC marker was observed in patients with basal molecular subtype (44.8% patients). Most of BC patients with phenotype CD44+/CD24 had stage I of tumor process (34.3%). Statistical processing of data has showen that Yule colligation coefficient equaled 0.28 (р > 0.05) that argues poor correlation between stage of tumor process and number of tumors with positive expression of CSC markers. Statistical processing of data has showen high correlation between presence of cells with expression of CSC markers and metastases of BC in regional lymph nodes (Yule colligation coefficient equals 0.943; р molecular subtype depending on expression of CSC CD44+/CD24- markers was detected. Survival of patients with basal BC was reliably higher at lack in tumors of cells with CSC markers CD44+/CD24- and, correspondingly, lower at presence of such cells (р markers was not determined (р > 0.05). Significance of tumor cells with markers CD44+/CD24- within the limits of molecular subtype of BC may be additional criterion for advanced biological characteristic of BC, and in patients with BC of basal molecular subtype - for predictive evaluation of individual potential of tumor to aggressive clinical course.

Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

International Nuclear Information System (INIS)

Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

1992-09-01

Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

Molecular regulation of plant cell wall extensibility

Science.gov (United States)

Cosgrove, D. J.

1998-01-01

Gravity responses in plants often involve spatial and temporal changes in cell growth, which is regulated primarily by controlling the ability of the cell wall to extend. The wall is thought to be a cellulose-hemicellulose network embedded in a hydrated matrix of complex polysaccharides and a small amount of structural protein. The wall extends by a form of polymer creep, which is mediated by expansins, a novel group of wall-loosening proteins. Expansins were discovered during a molecular dissection of the "acid growth" behavior of cell walls. Expansin alters the rheology of plant walls in profound ways, yet its molecular mechanism of action is still uncertain. It lacks detectable hydrolytic activity against the major components of the wall, but it is able to disrupt noncovalent adhesion between wall polysaccharides. The discovery of a second family of expansins (beta-expansins) sheds light on the biological role of a major group of pollen allergens and implies that expansins have evolved for diverse developmental functions. Finally, the contribution of other processes to wall extensibility is briefly summarized.

Genomic Analyses Reveal Demographic History and Temperate Adaptation of the Newly Discovered Honey Bee Subspecies Apis mellifera sinisxinyuan n. ssp.

Science.gov (United States)

Chen, Chao; Liu, Zhiguang; Pan, Qi; Chen, Xiao; Wang, Huihua; Guo, Haikun; Liu, Shidong; Lu, Hongfeng; Tian, Shilin; Li, Ruiqiang; Shi, Wei

2016-05-01

Studying the genetic signatures of climate-driven selection can produce insights into local adaptation and the potential impacts of climate change on populations. The honey bee (Apis mellifera) is an interesting species to study local adaptation because it originated in tropical/subtropical climatic regions and subsequently spread into temperate regions. However, little is known about the genetic basis of its adaptation to temperate climates. Here, we resequenced the whole genomes of ten individual bees from a newly discovered population in temperate China and downloaded resequenced data from 35 individuals from other populations. We found that the new population is an undescribed subspecies in the M-lineage of A. mellifera (Apis mellifera sinisxinyuan). Analyses of population history show that long-term global temperature has strongly influenced the demographic history of A. m. sinisxinyuan and its divergence from other subspecies. Further analyses comparing temperate and tropical populations identified several candidate genes related to fat body and the Hippo signaling pathway that are potentially involved in adaptation to temperate climates. Our results provide insights into the demographic history of the newly discovered A. m. sinisxinyuan, as well as the genetic basis of adaptation of A. mellifera to temperate climates at the genomic level. These findings will facilitate the selective breeding of A. mellifera to improve the survival of overwintering colonies. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Discovering Multidimensional Structure in Relational Data

DEFF Research Database (Denmark)

Jensen, Mikael Rune; Holmgren, Thomas; Pedersen, Torben Bach

2004-01-01

On-Line Analytical Processing (OLAP) systems based on multidimensional databases are essential elements of decision support. However, most existing data is stored in “ordinary” relational OLTP databases, i.e., data has to be (re-) modeled as multidimensional cubes before the advantages of OLAP to...... algorithms for discovering multidimensional schemas from relational databases. The algorithms take a wide range of available metadata into account in the discovery process, including functional and inclusion dependencies, and key and cardinality information....... tools are available. In this paper we present an approach for the automatic construction of multidimensional OLAP database schemas from existing relational OLTP databases, enabling easy OLAP design and analysis for most existing data sources. This is achieved through a set of practical and effective...

Discovering the Library with Google Earth

Directory of Open Access Journals (Sweden)

Michaela Brenner

2008-06-01

Full Text Available Libraries need to provide attractive and exciting discovery tools to draw patrons to the valuable resources in their catalogs. The authors conducted a pilot project to explore the free version of Google Earth as such a discover tool for Portland State Library’s digital collection of urban planning documents. They created eye-catching placemarks with links to parts of this collection, as well as to other pertinent materials like books, images, and historical background information. The detailed how-to-do part of this article is preceded by a discussion about discovery of library materials and followed by possible applications of this Google Earth project.

Primary malignant melanoma of the urinary bladder: clinical, morphological, and molecular analysis of five cases.

Science.gov (United States)

Karabulut, Yasemin Y; Erdogan, Seyda; Sayar, Hamide; Ergen, Ali; Ertoy Baydar, Dilek

2016-12-01

The aim of our study was to evaluate the clinical and morphological features of primary malignant melanomas of the urinary bladder. We obtained information on five such cases from three different institutions. These were three men and two women between 52 and 76 years of age. Three tumors presented with hematuria, one with dysuria, and one was discovered incidentally on imaging studies. All were invasive to muscularis propria on transuretral resections performed for diagnosis. Neoplastic cells showed variable patterns (large cell epithelioid, small cell diffuse, storiform, or mixed) in different tumors. Pigmentation was prominent in all except one case. Each case was labeled diffusely for S-100, HMB-45, and Melan-A. Pan-cytokeratin showed a perinuclear dot-like reaction in two tumors. Three cases showed the BRAF mutation in molecular studies. Two patients were already metastatic at the time of diagnosis. Two patients died, one is alive with disease after 15 months, and two patients are disease free at 1 and 5 years of surveillance.

CORNELL: CLEO discovers B meson penguins

International Nuclear Information System (INIS)

Anon.

1993-01-01

The CLEO collaboration at Cornell's CESR electron-positron storage ring has discovered a rare type of B meson decay in which only a high energy photon and a K* meson are produced. These decays provide the first unambiguous evidence for an alternative route for heavy quark decay that has been given the whimsical name ''penguin diagram''. In the mid-1970s penguin diagrams were proposed to explain the puzzling strangeness quantum number selection rules in the decay of K mesons. At the same time it was realized that penguin diagrams could also be important in the CP violation seen in neutral K meson decay. CP violation, an asymmetry between matter and antimatter, is an essential ingredient in understanding why there is much more matter than antimatter in the universe. CP violation introduces a definite direction to the arrow of time, which could otherwise point equally forwards or backwards. In addition, penguin decays are very sensitive to some extensions of the Standard Model of weak decay. Although penguin diagrams were first proposed to explain an effect in K meson decay, the K system gives no unique signature for them, and verification of penguin processes meant looking elsewhere. In the Standard Model, quarks decay under the influence of the weak force, emitting a W boson. Since the W is charged, the charge of the initial quark differs from that of the final quark, so the charge of the quark changes as well as its flavour

New variable stars discovered in the fields of three Galactic open clusters using the VVV survey

Science.gov (United States)

Palma, T.; Minniti, D.; Dékány, I.; Clariá, J. J.; Alonso-García, J.; Gramajo, L. V.; Ramírez Alegría, S.; Bonatto, C.

2016-11-01

This project is a massive near-infrared (NIR) search for variable stars in highly reddened and obscured open cluster (OC) fields projected on regions of the Galactic bulge and disk. The search is performed using photometric NIR data in the J-, H- and Ks- bands obtained from the Vista Variables in the Vía Láctea (VVV) Survey. We performed in each cluster field a variability search using Stetson's variability statistics to select the variable candidates. Later, those candidates were subjected to a frequency analysis using the Generalized Lomb-Scargle and the Phase Dispersion Minimization algorithms. The number of independent observations range between 63 and 73. The newly discovered variables in this study, 157 in total in three different known OCs, are classified based on their light curve shapes, periods, amplitudes and their location in the corresponding color-magnitude (J -Ks ,Ks) and color-color (H -Ks , J - H) diagrams. We found 5 possible Cepheid stars which, based on the period-luminosity relation, are very likely type II Cepheids located behind the bulge. Among the newly discovered variables, there are eclipsing binaries, δ Scuti, as well as background RR Lyrae stars. Using the new version of the Wilson & Devinney code as well as the "Physics Of Eclipsing Binaries" (PHOEBE) code, we analyzed some of the best eclipsing binaries we discovered. Our results show that these studied systems turn out to be ranging from detached to double-contact binaries, with low eccentricities and high inclinations of approximately 80°. Their surface temperatures range between 3500 K and 8000 K.

Electronic structure and partial charge distribution of Doxorubicin in different molecular environments.

Science.gov (United States)

Poudel, Lokendra; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Podgornik, Rudolf; Steinmetz, Nicole F; Ching, Wai-Yim

2015-05-18

The electronic structure and partial charge of doxorubicin (DOX) in three different molecular environments-isolated, solvated, and intercalated in a DNA complex-are studied by first-principles density functional methods. It is shown that the addition of solvating water molecules to DOX, together with the proximity to and interaction with DNA, has a significant impact on the electronic structure as well as on the partial charge distribution. Significant improvement in estimating the DOX-DNA interaction energy is achieved. The results are further elucidated by resolving the total density of states and surface charge density into different functional groups. It is concluded that the presence of the solvent and the details of the interaction geometry matter greatly in determining the stability of DOX complexation. Ab initio calculations on realistic models are an important step toward a more accurate description of the long-range interactions in biomolecular systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thymolipoma combined with hyperthyroidism discovered by neurological symptoms.

Science.gov (United States)

Takahashi, Hidenobu; Harada, Masahiko; Kimura, Masakazu; Kato, Harubumi

2007-04-01

Thymolipomas are rare slow-growing mediastinal thymic neoplasms. Most cases are asymptomatic and are sometimes discovered as a huge mass on chest x-ray films. A few cases have been discovered during examinations for other diseases. We report the second case of thymolipoma combined with hyperthyroidism in the English language literature. Neurological symptoms suddenly appeared in a 45-year-old woman. Central nervous system disorder was suggested but no significant abnormalities were found on brain MR nor were there any neurological signs. Several months later, neurological and systemic examinations on admission revealed hyperthyroidism and an anterior mediastinal tumor, 9.0x5.0x3.0 cm in size on chest CT films. Despite treatment of hyperthyroidism by medication, her neurological symptoms remained. Neurologists recommended resection of the mediastinal tumor. Malignancy could not be ruled out because of the irregularity of the tumor appearance on contrast-enhanced chest CT. Furthermore, the tumor appeared to be attached to the ascending aorta, so cytological and/or pathological diagnosis by CT-guided needle biopsy before operation were contraindicated. Extended thymectomy was performed in May 2005. The pathological diagnosis was benign thymolipoma consisting of mature fatty tissue and thymic tissue structures with Hassall's corpuscles. Her neurological symptoms seemed slightly but not markedly improved. The relationship between thymolipoma and hyperthyroidism is still unknown.

[Discover potential inhibitors of 5-LOX and LTA4H from Rhei Radix et Rhizoma, Notopterygii Rhizoma et Radix and Genitana Macrophyllae Radix based on molecular simulation methods].

Science.gov (United States)

Gu, Yu; Zhang, Xu; Chen, Yan-Kun; Zhao, Bo-Wen; Zhang, Yan-Ling

2017-12-01

5-lipoxygenase (5-LOX) and leukotriene A4 hydrolase (LTA4H), as the major targets of 5-LOX branch in the arachidonic acid (AA) metabolic pathway, play an important role in the treatment of inflammation. Rhei Radix et Rhizoma, Notopterygii Rhizoma et Radix and Genitana Macrophyllae Radix have clear anti-inflammation activities. In this paper, the targets of 5-LOX and LTA4H were used as the research carrier, and Hiphop module in DS4.0 (Discovery studio) was used to construct ingredients database for preliminary screening of three traditional Chinese medicines based on target inhibitor pharmacophore, so as to obtain 5-LOX and LTA4H potential active ingredients. The ingredients obtained in initial pharmacophore screening were further screened by using CDOCKER module, and the screening rules were established based on the score of initial compound and the key amino acids to obtain 12 potential 5-LOX inhibitors and 7 potential LTA4H inhibitors. To be more specific, the potential 5-LOX inhibitors included 6 ingredients in Rhei Radix et Rhizoma, such as procyanidins B2-3,3'-O-double gallate and revandchinone 2; four ingredients in notopterygium, such as dodecanoic acid and so on. On the other hand, potential LTA4H inhibitors included revandchinone 1, revandchinone 4 in Rhei Radix et Rhizoma, tridecanoic acid, tetracosanoic acid and methyl eicosanoate in Notopterygii Rhizoma et Radix, montanic acid methyl ester and N-docosanoyl-O-aminobenzoate in Genitana Macrophyllae Radix and so on. The molecular simulation methods were highly efficient and time-saving to obtain the potential inhibitors of 5-LOX and LTA4H, which could provide assistance for discovering the chemical quality indicators of anti-inflammatory efficacy of three Chinese herbs, and may be helpful to promote the whole-process quality control of three Chinese herbs. Copyright© by the Chinese Pharmaceutical Association.

Tools and strategies for discovering novel enzymes and metabolic pathways

Directory of Open Access Journals (Sweden)

John A. Gerlt

2016-12-01

Full Text Available The number of entries in the sequence databases continues to increase exponentially – the UniProt database is increasing with a doubling time of ∼4 years (2% increase/month. Approximately 50% of the entries have uncertain, unknown, or incorrect function annotations because these are made by automated methods based on sequence homology. If the potential in complete genome sequences is to be realized, strategies and tools must be developed to facilitate experimental assignment of functions to uncharacterized proteins discovered in genome projects. The Enzyme Function Initiative (EFI; previously supported by U54GM093342 from the National Institutes of Health, now supported by P01GM118303 developed web tools for visualizing and analyzing (1 sequence and function space in protein families (EFI-EST and (2 genome neighbourhoods in microbial and fungal genomes (EFI-GNT to assist the design of experimental strategies for discovering the in vitro activities and in vivo metabolic functions of uncharacterized enzymes. The EFI developed an experimental platform for large-scale production of the solute binding proteins (SBPs for ABC, TRAP, and TCT transport systems and their screening with a physical ligand library to identify the identities of the ligands for these transport systems. Because the genes that encode transport systems are often co-located with the genes that encode the catabolic pathways for the transported solutes, the identity of the SBP ligand together with the EFI-EST and EFI-GNT web tools can be used to discover new enzyme functions and new metabolic pathways. This approach is demonstrated with the characterization of a novel pathway for ethanolamine catabolism.

Hydrothermal vent fields discovered in the southern Gulf of California clarify role of habitat in augmenting regional diversity.

Science.gov (United States)

Goffredi, Shana K; Johnson, Shannon; Tunnicliffe, Verena; Caress, David; Clague, David; Escobar, Elva; Lundsten, Lonny; Paduan, Jennifer B; Rouse, Greg; Salcedo, Diana L; Soto, Luis A; Spelz-Madero, Ronald; Zierenberg, Robert; Vrijenhoek, Robert

2017-07-26

Hydrothermal vent communities are distributed along mid-ocean spreading ridges as isolated patches. While distance is a key factor influencing connectivity among sites, habitat characteristics are also critical. The Pescadero Basin (PB) and Alarcón Rise (AR) vent fields, recently discovered in the southern Gulf of California, are bounded by previously known vent localities (e.g. Guaymas Basin and 21° N East Pacific Rise); yet, the newly discovered vents differ markedly in substrata and vent fluid attributes. Out of 116 macrofaunal species observed or collected, only three species are shared among all four vent fields, while 73 occur at only one locality. Foundation species at basalt-hosted sulfide chimneys on the AR differ from the functional equivalents inhabiting sediment-hosted carbonate chimneys in the PB, only 75 km away. The dominant species of symbiont-hosting tubeworms and clams, and peripheral suspension-feeding taxa, differ between the sites. Notably, the PB vents host a limited and specialized fauna in which 17 of 26 species are unknown at other regional vents and many are new species. Rare sightings and captured larvae of the 'missing' species revealed that dispersal limitation is not responsible for differences in community composition at the neighbouring vent localities. Instead, larval recruitment-limiting habitat suitability probably favours species differentially. As scenarios develop to design conservation strategies around mining of seafloor sulfide deposits, these results illustrate that models encompassing habitat characteristics are needed to predict metacommunity structure. © 2017 The Authors.

Discover 4-H Clubs: The Essential Resource for 4-H

Science.gov (United States)

MacArthur, Stacey; Nelson, Cindy; Brower, Naomi; Memmott, Margie; Peterson, Gaelynn

2016-01-01

Obstacles facing new 4-H volunteers include time constraints and difficulty finding project-specific information, resources, and opportunities available for club members. As a solution to these obstacles and an aid for assisting volunteers in becoming confident in delivering information to youth, content experts produced Discover 4-H Clubs, a…

REVIEW: Discovering Statistics Using SPSS for Windows ANDY FIELD (2000)

OpenAIRE

SHARMA, Reviewed By Ashok

2015-01-01

The book "Discovering Statistics Using SPSS for Windows" is exactly that! Since it calculates amazingly fast, in the recent years, the computer has become the most useful and helpful tool for the researchers in almost every field of knowledge - be it open and distance education, psychology, sociology, management or else.

Simultaneously Discovering and Localizing Common Objects in Wild Images.

Science.gov (United States)

Wang, Zhenzhen; Yuan, Junsong

2018-09-01

Motivated by the recent success of supervised and weakly supervised common object discovery, in this paper, we move forward one step further to tackle common object discovery in a fully unsupervised way. Generally, object co-localization aims at simultaneously localizing objects of the same class across a group of images. Traditional object localization/detection usually trains specific object detectors which require bounding box annotations of object instances, or at least image-level labels to indicate the presence/absence of objects in an image. Given a collection of images without any annotations, our proposed fully unsupervised method is to simultaneously discover images that contain common objects and also localize common objects in corresponding images. Without requiring to know the total number of common objects, we formulate this unsupervised object discovery as a sub-graph mining problem from a weighted graph of object proposals, where nodes correspond to object proposals, and edges represent the similarities between neighbouring proposals. The positive images and common objects are jointly discovered by finding sub-graphs of strongly connected nodes, with each sub-graph capturing one object pattern. The optimization problem can be efficiently solved by our proposed maximal-flow-based algorithm. Instead of assuming that each image contains only one common object, our proposed solution can better address wild images where each image may contain multiple common objects or even no common object. Moreover, our proposed method can be easily tailored to the task of image retrieval in which the nodes correspond to the similarity between query and reference images. Extensive experiments on PASCAL VOC 2007 and Object Discovery data sets demonstrate that even without any supervision, our approach can discover/localize common objects of various classes in the presence of scale, view point, appearance variation, and partial occlusions. We also conduct broad

Molecularly Imprinted Membranes

Science.gov (United States)

Trotta, Francesco; Biasizzo, Miriam; Caldera, Fabrizio

2012-01-01

Although the roots of molecularly imprinted polymers lie in the beginning of 1930s in the past century, they have had an exponential growth only 40–50 years later by the works of Wulff and especially by Mosbach. More recently, it was also proved that molecular imprinted membranes (i.e., polymer thin films) that show recognition properties at molecular level of the template molecule are used in their formation. Different procedures and potential application in separation processes and catalysis are reported. The influences of different parameters on the discrimination abilities are also discussed. PMID:24958291

Potato agriculture, late blight science, and the molecularization of plant pathology.

Science.gov (United States)

Turner, R Steven

2008-01-01

By the mid-1980s nucleic-acid based methods were penetrating the farthest reaches of biological science, triggering rivalries among practitioners, altering relationships among subfields, and transforming the research front. This article delivers a "bottom up" analysis of that transformation at work in one important area of biological science, plant pathology, by tracing the "molecularization" of efforts to understand and control one notorious plant disease -- the late blight of potatoes. It mobilizes the research literature of late blight science as a tool through which to trace the changing typography of the research front from 1983 to 2003. During these years molecularization intensified the traditional fragmentation of the late blight research community, even as it dramatically integrated study of the causal organism into broader areas of biology. In these decades the pathogen responsible for late blight, the oomycete "Phytophthora infestans," was discovered to be undergoing massive, frightening, and still largely unexplained genetic diversification -- a circumstance that lends the episode examined here an urgency that reinforces its historiographical significance as a case-study in the molecularization of the biological sciences.

Molecular Evolution and Expansion Analysis of the NAC Transcription Factor in Zea mays

Science.gov (United States)

Fan, Kai; Wang, Ming; Miao, Ying; Ni, Mi; Bibi, Noreen; Yuan, Shuna; Li, Feng; Wang, Xuede

2014-01-01

NAC (NAM, ATAF1, 2 and CUC2) family is a plant-specific transcription factor and it controls various plant developmental processes. In the current study, 124 NAC members were identified in Zea mays and were phylogenetically clustered into 13 distinct subfamilies. The whole genome duplication (WGD), especially an additional WGD event, may lead to expanding ZmNAC members. Different subfamily has different expansion rate, and NAC subfamily preference was found during the expansion in maize. Moreover, the duplication events might occur after the divergence of the lineages of Z. mays and S. italica, and segmental duplication seemed to be the dominant pattern for the gene duplication in maize. Furthermore, the expansion of ZmNAC members may be also related to gain and loss of introns. Besides, the restriction of functional divergence was discovered after most of the gene duplication events. These results could provide novel insights into molecular evolution and expansion analysis of NAC family in maize, and advance the NAC researches in other plants, especially polyploid plants. PMID:25369196

Pancreatic sarcoidosis discovered during Whipple procedure.

Science.gov (United States)

Cook, Jonathan; Spees, Tanner; Telefus, Phillip; Ranaudo, Jeffrey M; Carryl, Stephen; Xiao, Philip

2013-04-04

Pancreatic sarcoidosis is a rare variant of systemic sarcoidosis, with cases described in literature as recently as January 2010. We present here a case of pancreatic involvement with non-caseating granulomas discovered on laparotomy in a patient with a preoperative diagnosis of pancreatic carcinoma. Computer tomography scan without contrast revealed a well-marginated smooth-shaped tumor in the head of the pancreas morphologically consistent with malignancy. During Whipple procedure, the mass was found to be a large lymph node that contained numerous non-caseating granulomas. Radiologically and clinically, non-caseating granulomas of the pancreas are often misdiagnosed as malignant tumor. Special attention given to this differential diagnosis by surgeons, pathologists and clinicians can avoid misdiagnosis and unnecessary treatment. Published by Oxford University Press and JSCR Publishing Ltd. All rights reserved. © The Author 2013.

A study on EUV reticle surface molecular contamination under different storage conditions in a HVM foundry fab

Science.gov (United States)

Singh, SherJang; Yatzor, Brett; Taylor, Ron; Wood, Obert; Mangat, Pawitter

2017-03-01

The prospect of EUVL (Extreme Ultraviolet Lithography) insertion into HVM (High Volume Manufacturing) has never been this promising. As technology is prepared for "lab to fab" transition, it becomes important to comprehend challenges associated with integrating EUVL infrastructure within existing high volume chip fabrication processes in a foundry fab. The existing 193nm optical lithography process flow for reticle handling and storage in a fab atmosphere is well established and in-fab reticle contamination concerns are mitigated with the reticle pellicle. However EUVL reticle pellicle is still under development and if available, may only provide protection against particles but not molecular contamination. HVM fab atmosphere is known to be contaminated with trace amounts of AMC's (Atmospheric Molecular Contamination). If such contaminants are organic in nature and get absorbed on the reticle surface, EUV photon cause photo-dissociation resulting into carbon generation which is known to reduce multilayer reflectivity and also degrades exposure uniformity. Chemical diffusion and aggregation of other ions is also reported under the e-beam exposure of a EUV reticle which is known to cause haze issues in optical lithography. Therefore it becomes paramount to mitigate absorbed molecular contaminant concerns on EUVL reticle surface. In this paper, we have studied types of molecular contaminants that are absorbed on an EUVL reticle surface under HVM fab storage and handling conditions. Effect of storage conditions (gas purged vs atmospheric) in different storage pods (Dual pods, Reticle Clamshells) is evaluated. Absorption analysis is done both on ruthenium capping layer as well as TaBN absorber. Ru surface chemistry change as a result of storage is also studied. The efficacy of different reticle cleaning processes to remove absorbed contaminant is evaluated as well.

Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data.

Science.gov (United States)

Ren, Zhonglu; Wang, Wenhui; Li, Jinming

2016-02-01

Identifying colon cancer subtypes based on molecular signatures may allow for a more rational, patient-specific approach to therapy in the future. Classifications using gene expression data have been attempted before with little concordance between the different studies carried out. In this study we aimed to uncover subtypes of colon cancer that have distinct biological characteristics and identify a set of novel biomarkers which could best reflect the clinical and/or biological characteristics of each subtype. Clustering analysis and discriminant analysis were utilized to discover the subtypes in two different molecular levels on 153 colon cancer samples from The Cancer Genome Atlas (TCGA) Data Portal. At gene expression level, we identified two major subtypes, ECL1 (expression cluster 1) and ECL2 (expression cluster 2) and a list of signature genes. Due to the heterogeneity of colon cancer, the subtype ECL1 can be further subdivided into three nested subclasses, and HOTAIR were found upregulated in subclass 2. At DNA methylation level, we uncovered three major subtypes, MCL1 (methylation cluster 1), MCL2 (methylation cluster 2) and MCL3 (methylation cluster 3). We found only three subtypes of CpG island methylator phenotype (CIMP) in colon cancer instead of the four subtypes in the previous reports, and we found no sufficient evidence to subdivide MCL3 into two distinct subgroups.

A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms

Science.gov (United States)

Trujillo, Caleb M.; Anderson, Trevor R.; Pelaez, Nancy J.

2015-01-01

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do…

On reliable discovery of molecular signatures

Directory of Open Access Journals (Sweden)

Björkegren Johan

2009-01-01

Full Text Available Abstract Background Molecular signatures are sets of genes, proteins, genetic variants or other variables that can be used as markers for a particular phenotype. Reliable signature discovery methods could yield valuable insight into cell biology and mechanisms of human disease. However, it is currently not clear how to control error rates such as the false discovery rate (FDR in signature discovery. Moreover, signatures for cancer gene expression have been shown to be unstable, that is, difficult to replicate in independent studies, casting doubts on their reliability. Results We demonstrate that with modern prediction methods, signatures that yield accurate predictions may still have a high FDR. Further, we show that even signatures with low FDR may fail to replicate in independent studies due to limited statistical power. Thus, neither stability nor predictive accuracy are relevant when FDR control is the primary goal. We therefore develop a general statistical hypothesis testing framework that for the first time provides FDR control for signature discovery. Our method is demonstrated to be correct in simulation studies. When applied to five cancer data sets, the method was able to discover molecular signatures with 5% FDR in three cases, while two data sets yielded no significant findings. Conclusion Our approach enables reliable discovery of molecular signatures from genome-wide data with current sample sizes. The statistical framework developed herein is potentially applicable to a wide range of prediction problems in bioinformatics.

Two Herbig-Haro objects discovered by narrow-band CCD imagery

International Nuclear Information System (INIS)

Ogura, Katsuo

1990-01-01

Two new Herbig-Haro objects, HH 132 and HH 133, have been discovered by CCD imagery behind interference filters on and just off the forbidden S II lines in the red. They are located in Puppis R2 and in Vela R2. Possible locations of their exciting sources are discussed. 12 refs

Discovering EEG resting state alterations of semantic dementia.

Science.gov (United States)

Grieder, Matthias; Koenig, Thomas; Kinoshita, Toshihiko; Utsunomiya, Keita; Wahlund, Lars-Olof; Dierks, Thomas; Nishida, Keiichiro

2016-05-01

Diagnosis of semantic dementia relies on cost-intensive MRI or PET, although resting EEG markers of other dementias have been reported. Yet the view still holds that resting EEG in patients with semantic dementia is normal. However, studies using increasingly sophisticated EEG analysis methods have demonstrated that slightest alterations of functional brain states can be detected. We analyzed the common four resting EEG microstates (A, B, C, and D) of 8 patients with semantic dementia in comparison with 8 healthy controls and 8 patients with Alzheimer's disease. Topographical differences between the groups were found in microstate classes B and C, while microstate classes A and D were comparable. The data showed that the semantic dementia group had a peculiar microstate E, but the commonly found microstate C was lacking. Furthermore, the presence of microstate E was significantly correlated with lower MMSE and language scores. Alterations in resting EEG can be found in semantic dementia. Topographical shifts in microstate C might be related to semantic memory deficits. This is the first study that discovered resting state EEG abnormality in semantic dementia. The notion that resting EEG in this dementia subtype is normal has to be revised. Copyright © 2016 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Molecular profiling of synchronous and metachronous cancers of the pancreas reveal molecular mimicry between samples from the same patient.

Science.gov (United States)

Talbott, Vanessa A; Yeo, Charles J; Brody, Jonathan R; Witkiewicz, Agnieszka K

2012-07-01

Pancreatic ductal adenocarcinoma (PDA) is rarely a survivable disease. In rare cases, separate synchronous tumors are discovered at the time of resection, while in others, patients present with a metachronous cancer after prior surgical resection. Studying molecular markers of synchronous and metachronous lesions may aid to clarify the biology of this often deadly disease. Two patients presented with synchronous tumors (each one with a tumor in the pancreatic head/neck and the other in the tail, designated patients A and B). An additional patient (patient C) underwent an R0 resection for PDA of the head and recurred 1.5 y later with PDA in the tail. Genomic DNA was laser capture microdissected (LCM) from the tumor and molecular analysis was performed. K-ras status and loss of heterozygosity (LOH) were determined from multiple specimens for each case. All samples from each patient harbored identical K-ras mutations. In patient A, the tumor at the head of the pancreas had more clonal genetic instability as reflected by LOH analysis over multiple LCM samples. Patient B had more genetic instability in the tail lesion compared with the neck. Patient C had virtually the identical molecular profile in both tumors, supporting the notion that both tumors were related. We conclude that the synchronous and metachronous tumors likely are initiated from identical precursor lesions and/or events (i.e., K-ras mutations). Future studies will need to investigate if these tumors will respond similarly to adjuvant therapies targeted against the clonal molecular events in the tumor. Copyright © 2012 Elsevier Inc. All rights reserved.

Hydrophobic ampersand hydrophilic: Theoretical models of solvation for molecular biophysics

International Nuclear Information System (INIS)

Pratt, L.R.; Tawa, G.J.; Hummer, G.; Garcia, A.E.; Corcelli, S.A.

1996-01-01

Molecular statistical thermodynamic models of hydration for chemistry and biophysics have advanced abruptly in recent years. With liquid water as solvent, salvation phenomena are classified as either hydrophobic or hydrophilic effects. Recent progress in treatment of hydrophilic effects have been motivated by continuum dielectric models interpreted as a modelistic implementation of second order perturbation theory. New results testing that perturbation theory of hydrophilic effects are presented and discussed. Recent progress in treatment of hydrophobic effects has been achieved by applying information theory to discover models of packing effects in dense liquids. The simplest models to which those ideas lead are presented and discussed

Discovering the quantum universe the role of particle colliders

CERN Document Server

2006-01-01

What does "Quantum Universe" mean? To discover what the universe is made of and how it works is the challenge of particle physics. "Quantum Universe" defines the quest to explain the universe in terms of quantum physics, which governs the behavior of the microscopic, subatomic world. It describes a revolution in particle physics and a quantum leap in our understanding of the mystery and beauty of the universe.

Fuzzy method of recognition of high molecular substances in evidence-based biology

Science.gov (United States)

Olevskyi, V. I.; Smetanin, V. T.; Olevska, Yu. B.

2017-10-01

Nowadays modern requirements to achieving reliable results along with high quality of researches put mathematical analysis methods of results at the forefront. Because of this, evidence-based methods of processing experimental data have become increasingly popular in the biological sciences and medicine. Their basis is meta-analysis, a method of quantitative generalization of a large number of randomized trails contributing to a same special problem, which are often contradictory and performed by different authors. It allows identifying the most important trends and quantitative indicators of the data, verification of advanced hypotheses and discovering new effects in the population genotype. The existing methods of recognizing high molecular substances by gel electrophoresis of proteins under denaturing conditions are based on approximate methods for comparing the contrast of electrophoregrams with a standard solution of known substances. We propose a fuzzy method for modeling experimental data to increase the accuracy and validity of the findings of the detection of new proteins.

Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase

Directory of Open Access Journals (Sweden)

Beata Szefler

2016-10-01

Full Text Available Glucose oxidase (GOx is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H2O2. GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI. The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD study of the PEI ligand (C14N8_07_B22 and the GOx enzyme (3QVR was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1 of −5.8 kcal/mol and (LIG2 of −4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1 and on its surface (LIG2 were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase.

Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase.

Science.gov (United States)

Szefler, Beata; Diudea, Mircea V; Putz, Mihai V; Grudzinski, Ireneusz P

2016-10-27

Glucose oxidase (GOx) is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state) to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H₂O₂). GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI). The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD) study of the PEI ligand (C14N8_07_B22) and the GOx enzyme (3QVR) was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1) of -5.8 kcal/mol and (LIG2) of -4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1) and on its surface (LIG2) were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase.

Discovering the cosmos with small spacecraft the American explorer program

CERN Document Server

Harvey, Brian

2018-01-01

Explorer was the original American space program and Explorer 1 its first satellite, launched in 1958. Sixty years later, it is the longest continuously running space program in the world, demonstrating to the world how we can explore the cosmos with small spacecraft. Almost a hundred Explorers have already been launched.  Explorers have made some of the fundamental discoveries of the Space Age.Explorer 1 discovered Earth’s radiation belts. Later Explorers surveyed the Sun, the X-ray and ultraviolet universes, black holes, magnetars and gamma ray bursts. An Explorer found the remnant of the Big Bang. One Explorer chased and was the first to intercept a comet. The program went through a period of few launches during the crisis of funding for space science in the 1980s. However, with the era of ‘faster, cheaper, better,’ the program was reinvented, and new exiting missions began to take shape, like Swift and the asteroid hunter WISE.  Discovering the Cosmos with Small Spacecraft gives an account of ...

The ratio of high-molecular weight adiponectin and total adiponectin differs in preterm and term infants.

Science.gov (United States)

Yoshida, Tomohide; Nagasaki, Hiraku; Asato, Yoshihide; Ohta, Takao

2009-05-01

Adiponectin consists of three subspecies (high-, middle- and low-molecular weight adiponectin). Among these, high-molecular weight adiponectin (H-adn) is suggested to be an active form of this protein. To assess the relationship between H-adn and postnatal growth in preterm infants (PIs), serum H-adn and total adiponectin (T-adn) were measured in 46 PIs at birth and at corrected term, and 26 term infants (TI) at birth. T-adn and H-adn concentrations, and the ratio of H-adn to T-adn (H/T-adn) were significantly greater in TI and PI at corrected term than in PI at birth (p adn and H-adn concentrations in PI at corrected term were similar to those in TI, but H/T-adn in PI at corrected term was less than that in TI (p adn and serum concentrations of T- and H-adn in PI at corrected term were different from those in TI. These data suggest that quality of early postnatal growth in PIs is different from that in normally developed TI. Postnatal growth accompanying adipose tissue similar to TI may be important for PI to prevent future development of cardiovascular disease.

Characteristics and bioactivities of different molecular weight polysaccharides from camellia seed cake.

Science.gov (United States)

Xu, Zhou; Li, Xu; Feng, Shiling; Liu, Jing; Zhou, Lijun; Yuan, Ming; Ding, Chunbang

2016-10-01

Four polysaccharides, namely COP-1, COP-2, COP-3 and COP-4, were ultrafiltrated from crud Camellia oleifera seed cake polysaccharides (COP-c), purified, and characterized, including the determination of antioxidant and antiproliferative activities. Their molecular weights were 7.9, 36, 83 and 225kDa, respectively. All COPs showed the similar FT-IR spectrums, but significant differentials in monosaccharide components. COP-2 exhibited the highest radical scavenging abilities. COP-1 has the strongest metal chelating capabilities. Although with higher molecular weight, COP-4 showed the poorest antioxidant abilities. These results suggested appreciate molecular weight COP possessed a better antioxidant activities. Additionally, all COPs had non-significant antiproliferative abilities in HaLa and HepG2 cells. Copyright © 2016 Elsevier B.V. All rights reserved.

Interspecies comparison of probiotics isolated from different animals

Directory of Open Access Journals (Sweden)

Amr M. Abdou

2018-02-01

Full Text Available Aim: The aim of the current study was to isolate and identify naturally occurring probiotic Lactobacillus species in different animals with the different environmental background including fish, and farm animals to investigate interspecies differences in probiotics on the species level. Materials and Methods: A total of 44 fecal and milk samples were collected under aseptic conditions from cattle, buffalo, camel, sheep, goats, and fish. The samples were cultured, and the isolated strains were confirmed biochemically and molecularly using 16S rRNA multiplex polymerase chain reaction (PCR analysis following DNA extraction from the bacterial isolates. Results: A total of 31 isolates identified as lactobacilli were isolated from cattle milk, goat feces, sheep feces, fish feces, buffalo milk, camel milk, and goats' milk. Lactobacillus species were identified based on the size of the PCR product. The results showed that different species were different in their lactobacilli content. At the same time, there were some differences between individuals of the same species. Conclusion: The diversity of probiotic strains isolated from different animal species implies different types of benefits to the host. Although it would be both money - and time-consuming research, discovering the benefit of each of these strains may provide very important information for the health of both human and animal. Furthermore, transferring these beneficial effects either to individuals within the same species or between different species would be of great importance.

Molecular Aspects of H. pylori-Related MALT Lymphoma

Directory of Open Access Journals (Sweden)

Scott R. Owens

2011-01-01

Full Text Available Helicobacter pylori-related extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue is a paradigm for malignancy arising in an inflammatory background. While the diagnosis of H. pylori gastritis is often straightforward, distinction between severe gastritis and early lymphoma can be difficult and requires careful assessment of clinical findings in addition to histological features and immunohistochemical results. A number of cytogenetic abnormalities have been discovered in H. pylori-related lymphomas and several have clinical importance, related to the responsiveness of lymphoma to H. pylori eradication therapy, but routine molecular studies are not widely utilized. While molecular methods may be used in equivocal cases, a trial of conservative therapy is warranted given the propensity for these lymphomas to regress with eradication of the organism. Once therapy is initiated, care must be taken to avoid a premature assignment of disease refractoriness because complete response can take several months to more than a year. Cases truly refractory to H. pylori eradication therapy may be treated with adjuvant chemoradiation with a high response rate.

Discovering Communicable Scientific Knowledge from Spatio-Temporal Data

Science.gov (United States)

Schwabacher, Mark; Langley, Pat; Norvig, Peter (Technical Monitor)

2001-01-01

This paper describes how we used regression rules to improve upon a result previously published in the Earth science literature. In such a scientific application of machine learning, it is crucially important for the learned models to be understandable and communicable. We recount how we selected a learning algorithm to maximize communicability, and then describe two visualization techniques that we developed to aid in understanding the model by exploiting the spatial nature of the data. We also report how evaluating the learned models across time let us discover an error in the data.

Interactive Gaussian Graphical Models for Discovering Depth Trends in ChemCam Data

Science.gov (United States)

Oyen, D. A.; Komurlu, C.; Lanza, N. L.

2018-04-01

Interactive Gaussian graphical models discover surface compositional features on rocks in ChemCam targets. Our approach visualizes shot-to-shot relationships among LIBS observations, and identifies the wavelengths involved in the trend.

The role of positive selection in determining the molecular cause of species differences in disease

Directory of Open Access Journals (Sweden)

Foord Steven M

2008-10-01

Full Text Available Abstract Background Related species, such as humans and chimpanzees, often experience the same disease with varying degrees of pathology, as seen in the cases of Alzheimer's disease, or differing symptomatology as in AIDS. Furthermore, certain diseases such as schizophrenia, epithelial cancers and autoimmune disorders are far more frequent in humans than in other species for reasons not associated with lifestyle. Genes that have undergone positive selection during species evolution are indicative of functional adaptations that drive species differences. Thus we investigate whether biomedical disease differences between species can be attributed to positively selected genes. Results We identified genes that putatively underwent positive selection during the evolution of humans and four mammals which are often used to model human diseases (mouse, rat, chimpanzee and dog. We show that genes predicted to have been subject to positive selection pressure during human evolution are implicated in diseases such as epithelial cancers, schizophrenia, autoimmune diseases and Alzheimer's disease, all of which differ in prevalence and symptomatology between humans and their mammalian relatives. In agreement with previous studies, the chimpanzee lineage was found to have more genes under positive selection than any of the other lineages. In addition, we found new evidence to support the hypothesis that genes that have undergone positive selection tend to interact with each other. This is the first such evidence to be detected widely among mammalian genes and may be important in identifying molecular pathways causative of species differences. Conclusion Our dataset of genes predicted to have been subject to positive selection in five species serves as an informative resource that can be consulted prior to selecting appropriate animal models during drug target validation. We conclude that studying the evolution of functional and biomedical disease differences

Molecular docking and molecular dynamics simulation studies on Thermus thermophilus leucyl-tRNA synthetase complexed with different amino acids and pre-transfer editing substrates

Directory of Open Access Journals (Sweden)

Rayevsky A. V.

2016-02-01

Full Text Available Aim. To investigate the structural bases for the amino acid selectivity of the Thermus thermophilus leucyl-tRNA synthetase (LeuRSTT aminoacylation site and to disclose the binding pattern of pre-transfer editing substrates. Methods. Eight amino acids proposed as semi-cognate substrates for aminoacylation and eight aminoacyl-adenylates (formed from AMP and eight amino acids were prepared in zwitterions form. The protein structure with a co-crystallized substrate in the aminoacylation site [PDBID: 1OBH] was taken from RCSB. Docking settings and evaluation of substrate efficiency were followed by twofold docking function analysis for each conformation with Gold CCDC. The molecular dynamics simulation was performed using Gromacs. The procedures of relaxation and binding study were separated in two different subsequent simulations for 50ns and 5ns. Results. The evaluation of substrate efficiency for 8 amino acids by twofold docking function analysis, based on score values,has shown that the ligands of LeuRSTT can be positioned in the following order: Leu>Nva>Hcy>Nle>Met>Cys>Ile >Val. MD simulation has revealed lower electrostatic interactions of isoleucine with the active site of the enzyme compared with those for norvaline and leucine. In the case of aminoacyl-adenylates no significant differences were found based on score values for both GoldScore and Asp functions. Molecular dynamics of leucyl-, isoleucyl- and norvalyl-adenylates showed that the most stable and conformationally favorable is leucine, then follow norvaline and isoleucine. It has been also found that the TYR43 of the active site covers carboxyl group of leucine and norvaline like a shield and deflected towards isoleucine, allowing water molecules to come closer. Conclusions. In this study we revealed some structural basis for screening unfavorable substrates by shape, size and flexibility of a radical. The results obtained for different amino acids by molecular docking and MD studies

Discovering Sentinel Rules for Business Intelligence

Science.gov (United States)

Middelfart, Morten; Pedersen, Torben Bach

This paper proposes the concept of sentinel rules for multi-dimensional data that warns users when measure data concerning the external environment changes. For instance, a surge in negative blogging about a company could trigger a sentinel rule warning that revenue will decrease within two months, so a new course of action can be taken. Hereby, we expand the window of opportunity for organizations and facilitate successful navigation even though the world behaves chaotically. Since sentinel rules are at the schema level as opposed to the data level, and operate on data changes as opposed to absolute data values, we are able to discover strong and useful sentinel rules that would otherwise be hidden when using sequential pattern mining or correlation techniques. We present a method for sentinel rule discovery and an implementation of this method that scales linearly on large data volumes.

Molecular modeling study on tunnel behavior in different histone deacetylase isoforms.

Directory of Open Access Journals (Sweden)

Sundarapandian Thangapandian

Full Text Available Histone deacetylases (HDACs have emerged as effective therapeutic targets in the treatment of various diseases including cancers as these enzymes directly involved in the epigenetic regulation of genes. However the development of isoform-selective HDAC inhibitors has been a challenge till date since all HDAC enzymes possess conserved tunnel-like active site. In this study, using molecular dynamics simulation we have analyzed the behavior of tunnels present in HDAC8, 10, and 11 enzymes of class I, II, and IV, respectively. We have identified the equivalent tunnel forming amino acids in these three isoforms and found that they are very much conserved with subtle differences to be utilized in selective inhibitor development. One amino acid, methionine of HDAC8, among six tunnel forming residues is different in isoforms of other classes (glutamic acid (E in HDAC10 and leucine (L in HDAC 11 based on which mutations were introduced in HDAC11, the less studied HDAC isoform, to observe the effects of this change. The HDAC8-like (L268M mutation in the tunnel forming residues has almost maintained the deep and narrow tunnel as present in HDAC8 whereas HDAC10-like (L268E mutation has changed the tunnel wider and shallow as observed in HDAC10. These results explained the importance of the single change in the tunnel formation in different isoforms. The observations from this study can be utilized in the development of isoform-selective HDAC inhibitors.

The Brain Mechanisms Underlying the Cognitive Benefits of Bilingualism may be Extraordinarily Difficult to Discover

Directory of Open Access Journals (Sweden)

Kenneth R. Paap

2014-12-01

Full Text Available The hypothesis that coordinating two or more languages leads to an enhancement in executive functioning has been intensely studied for the past decade with very mixed results. The purpose of this review and analysis is to consider why it has been (and will continue to be difficult to discover the brain mechanisms underlying any cognitive benefits to bilingualism. Six reasons are discussed: 1 the phenomenon may not actually exist; 2 the cognitive neuroscientists investigating bilingual advantages may have been studying the wrong component of executive functioning; 3 most experiments use risky small numbers of participants and are underpowered; 4 the neural differences between groups do not align with the behavioral differences; 5 neural differences sometimes suffer from valence ambiguity, that is, disagreements whether “more” implies better or worse functioning and 6 neural differences often suffer from kind ambiguity, that is, disagreements regarding what type of mental events the pattern of activation in a region-of-interest actually reflects.

Discovering and Promoting Commodity Health Attributes: Programs and Issues

OpenAIRE

Carman, Hoy F.

2007-01-01

There is a growing consumer segment demanding healthy foods and diets, health and nutrition messages can expand food demand, and governments in the U.S. and EU, faced with increasing obesity and associated health outcomes, want consumers to have reliable information to choose healthy diets. California commodity organizations, charged with expanding the demand for almonds, avocados, strawberries and walnuts, are funding health and nutrition research as a means to discover a unique selling prop...

"The molecular basis of aging": the Boehringer Ingelheim Fonds 95th International Titisee Conference.

Science.gov (United States)

Garinis, George A; Patil, Christopher K; Schumacher, Björn

2007-01-01

Nearly 20 years ago, researchers discovered that lifespan can be extended by single-gene mutations in the nematode worm Caenorhabditis elegans. Further studies revealed that the mechanisms governing aging in the smallest organisms have been evolutionarily conserved and may operate in human beings. Since then, the field of biogerontology has expanded considerably, learning from - and contributing to - such disparate fields as cell signaling, metabolism, endocrinology, and a wide range of human diseases including cancer. To date, newly discovered connections and novel interdisciplinary approaches gradually unify what once seemed unrelated observations between seemingly disparate research areas. While this unification is far from complete, several overlapping themes have clearly emerged. At the 95th International Titisee Conference, devoted to "The Molecular Basis of Aging," 60 of the world's pre-eminent biogerontologists shared their most recent findings in the biology of aging, and discussed interdisciplinary connections between diverse fields.

Discover Earth: an earth system science program for libraries and their communities

Science.gov (United States)

Dusenbery, P.

2011-12-01

The view from space has deepened our understanding of Earth as a global, dynamic system. Instruments on satellites and spacecraft, coupled with advances in ground-based research, have provided us with astonishing new perspectives of our planet. Now more than ever, enhancing the public's understanding of Earth's physical and biological systems is vital to helping citizens make informed policy decisions especially when they are faced with the consequences of global climate change. While the focus for education reform is on school improvement, there is considerable research that supports the role that out-of-school experiences can play in student achievement. Libraries provide an untapped resource for engaging underserved youth and their families in fostering an appreciation and deeper understanding of science and technology topics. The Space Science Institute's National Center for Interactive Learning (NCIL) in partnership with the American Library Association (ALA), the Lunar and Planetary Institute (LPI), and the National Girls Collaborative Project (NGCP) have received funding from NSF to develop a national project called the STAR Library Education Network: a hands-on learning program for libraries and their communities (or STAR-Net for short). STAR stands for Science-Technology, Activities and Resources. STAR-Net includes two exhibitions: Discover Earth and Discover Tech. The Discover Earth exhibition will focus on local earth science topics-such as weather, water cycle, and ecosystem changes-as well as a global view of our changing planet. The main take-away message (or Big Idea) for this exhibition is that the global environment changes - and is changed by - the host community's local environment. The project team is testing whether this approach will be a good strategy for engaging the public, especially in rural America. This presentation will provide an overview of the Discover Earth project and how it is integrating climate change ideas into the exhibit

Discovery of energetic molecular ions (NO+ and O2+) in the storm time ring current

International Nuclear Information System (INIS)

Klecker, B.; Moebius, E.; Hovestadt, D.; Scholer, M.; Gloeckler, G.; Ipavich, F.M.

1986-01-01

A few hours after the onset of a large geomagnetic storm on September 4, 1984, energetic molecular ions in the mass range 28--32, predminantly NO + and O 2 + , have been discovered in the outer ring current at L--7. The data have been obtained with the time-of-flight spectrometer SULEICA on the AMPTE/IRM spacecraft. We find at 160 keV/e a mean abundance ratio of the molecular ions relative to O + ions of 0.031 +- 0.004. During quiet times no molecular ions are observed, the 1 sigma upper limit of the ratio derived by averaging over several quiet periods is 0.003. The observations demonstrate the injection of ionospheric plasma into the storm time ring current and the subsequent acceleration to energies of several hundred keV on a time scale of a few hours after the onset of the magnetic storm

A novel tree-based algorithm to discover seismic patterns in earthquake catalogs

Science.gov (United States)

Florido, E.; Asencio-Cortés, G.; Aznarte, J. L.; Rubio-Escudero, C.; Martínez-Álvarez, F.

2018-06-01

A novel methodology is introduced in this research study to detect seismic precursors. Based on an existing approach, the new methodology searches for patterns in the historical data. Such patterns may contain statistical or soil dynamics information. It improves the original version in several aspects. First, new seismicity indicators have been used to characterize earthquakes. Second, a machine learning clustering algorithm has been applied in a very flexible way, thus allowing the discovery of new data groupings. Third, a novel search strategy is proposed in order to obtain non-overlapped patterns. And, fourth, arbitrary lengths of patterns are searched for, thus discovering long and short-term behaviors that may influence in the occurrence of medium-large earthquakes. The methodology has been applied to seven different datasets, from three different regions, namely the Iberian Peninsula, Chile and Japan. Reported results show a remarkable improvement with respect to the former version, in terms of all evaluated quality measures. In particular, the number of false positives has decreased and the positive predictive values increased, both of them in a very remarkable manner.

Life in the salinity gradient: Discovering mechanisms behind a new biodiversity pattern

Science.gov (United States)

Telesh, Irena; Schubert, Hendrik; Skarlato, Sergei

2013-12-01

A recently discovered paradoxical maximum of planktonic protistan species in the salinity gradient of the Baltic Sea revealed an inverse trend of species number/salinity relation in comparison to the previously accepted species-minimum model for macrozoobenthos. Here, we review long-term data on organisms of different size classes and ecological groups to show that eukaryotic and prokaryotic microbes in plankton demonstrate a maximum species richness in the challenging zone of the critical salinity 5-8, where the large-bodied bottom dwellers (macrozoobenthos, macroalgae and aquatic higher plants) experience large-scale salinity stress which leads to an impoverished diversity. We propose a new conceptual model to explain why the diversity of small, fast-developing, rapidly evolving unicellular plankton organisms benefits from relative vacancy of brackish-water ecological niches and impaired competitiveness therein. The ecotone theory, Hutchinson's Ecological Niche Concept, species-area relationships and the Intermediate Disturbance Hypothesis are considered as a theoretical framework for understanding extinctions, speciation and variations in the evolution rates of different aquatic species in ecosystems with the pronounced salinity gradient.

CO near the Pleiades: encounter of a star cluster with a small molecular cloud

International Nuclear Information System (INIS)

Bally, J.; White, R.E.

1986-01-01

Although there is a large amount of interstellar matter near the Pleiades star cluster, the observed dust and gas is not a remnant of the placental molecular cloud from which the star cluster was formed. Carbon monoxide (CO) associated with the visible reflection nebulae was discovered by Cohen (1975). Its radial velocity differs from that of the cluster by many times the cluster escape velocity, which implies that the cloud-cluster association is the result of a chance encounter. This circumstance and the proximity of the Pleiades to the sun creates an unique opportunity for study of interstellar processes at high spatial resolution. To study the molecular component of the gas, a 1.7 square degree field was mapped with the ATandT Bell Laboratories 7-meter antenna (1.7' beam) on a 1' grid in the J=1.0 C(12)O line, obtaining over 6000 spectra with 50 kHz resolution. The cloud core was mapped in the J=1-0 line of C(13)O. Further observations include an unsuccessful search for CS (J=2-1) at ATandT BL, and some C(12)O J=2-1 spectra obtained at the Millimeter Wave Observatory of the University of Texas

CO near the Pleiades: Encounter of a star cluster with a small molecular cloud

Science.gov (United States)

Bally, J.; White, R. E.

1986-01-01

Although there is a large amount of interstellar matter near the Pleiades star cluster, the observed dust and gas is not a remnant of the placental molecular cloud from which the star cluster was formed. Carbon monoxide (CO) associated with the visible reflection nebulae was discovered by Cohen (1975). Its radial velocity differs from that of the cluster by many times the cluster escape velocity, which implies that the cloud-cluster association is the result of a chance encounter. This circumstance and the proximity of the Pleiades to the sun creates an unique opportunity for study of interstellar processes at high spatial resolution. To study the molecular component of the gas, a 1.7 square degree field was mapped with the AT&T Bell Laboratories 7-meter antenna (1.7' beam) on a 1' grid in the J=1.0 C(12)O line, obtaining over 6,000 spectra with 50 kHz resolution. The cloud core was mapped in the J=1-0 line of C(13)O. Further observations include an unsuccessful search for CS (J=2-1) at AT&T BL, and some C(12)O J=2-1 spectra obtained at the Millimeter Wave Observatory of the University of Texas.

CWI cryptanalyst discovers new cryptographic attack variant in Flame spy malware

NARCIS (Netherlands)

M.M.J. Stevens (Marc); R.J.F. Cramer (Ronald)

2012-01-01

htmlabstractCryptanalyst Marc Stevens from the Centrum Wiskunde & Informatica (CWI) in Amsterdam, known for breaking the https security in 2008 using a cryptanalytic attack on MD5, analyzed the recent Flame virus this week. He discovered that for this spy malware an as yet unknown cryptographic

A non-parametric hierarchical model to discover behavior dynamics from tracks

NARCIS (Netherlands)

Kooij, J.F.P.; Englebienne, G.; Gavrila, D.M.

2012-01-01

We present a novel non-parametric Bayesian model to jointly discover the dynamics of low-level actions and high-level behaviors of tracked people in open environments. Our model represents behaviors as Markov chains of actions which capture high-level temporal dynamics. Actions may be shared by

Biochemical, physiological and molecular responses of Ricinus communis seeds and seedlings to different temperatures: a multi-omics approach

NARCIS (Netherlands)

Ribeiro de Jesus, P.R.

2015-01-01

Biochemical, physiological and molecular responses of Ricinus communis seeds and seedlings to different temperatures: a multi-omics approach

by Paulo Roberto Ribeiro de Jesus

The main objective of this thesis was to provide a detailed

Orbits of the Asteroids Discovered at the Molėtai Observatory in 2000–2004

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Černis K.

2014-12-01

Full Text Available The paper presents statistics of the asteroids observed and discovered at the Molėtai Observatory, Lithuania in 2000–2004 within the project for astrometric observations of the near-Earth objects (NEOs, the main belt asteroids and comets. CCD observations of asteroids were obtained with the 35/51 cm Maksutov-type meniscus telescope and the 1.65 m Ritchey-Chretien reflector. In the Minor Planet Circulars and the Minor Planet Electronic Circulars (2000–2004 we published 6629 astrometric positions of 1114 asteroids. Among them 78 were newly discovered asteroids at Molėtai, a few NEOs were found by our team independently. For the 67 asteroids discovered at Molėtai the precise orbits were calculated. Because of small number of observations, a few asteroids have low-precision orbits and some asteroids have been lost. For seven objects we present their ephemerides for 2015.

Pillars of Creation among Destruction: Star Formation in Molecular Clouds near R136 in 30 Doradus

Science.gov (United States)

Kalari, Venu M.; Rubio, Mónica; Elmegreen, Bruce G.; Guzmán, Viviana V.; Zinnecker, Hans; Herrera, Cinthya N.

2018-01-01

We present new sensitive CO(2–1) observations of the 30 Doradus region in the Large Magellanic Cloud. We identify a chain of three newly discovered molecular clouds that we name KN1, KN2, and KN3 lying within 2–14 pc in projection from the young massive cluster R136 in 30 Doradus. Excited H2 2.12 μm emission is spatially coincident with the molecular clouds, but ionized Brγ emission is not. We interpret these observations as the tails of pillar-like structures whose ionized heads are pointing toward R136. Based on infrared photometry, we identify a new generation of stars forming within this structure.

``Making the Molecular Movie'': First Frames

Science.gov (United States)

Miller, R. J. Dwayne

2011-03-01

cooperativity has also been discovered in recent studies of molecular crystals. These new developments will be discussed in the context of developing the necessary technology to directly observe the structure-function correlation in biomolecules--the fundamental molecular basis of biological systems.

Colloquium on Atomic, Molecular and Optical Physics of the French Physics Society. Days of Molecular Spectroscopy, Lille, 7-10 July 2008

International Nuclear Information System (INIS)

Balcou, Philippe; Aspect, Alain; Merkt, Frederic; Haroche, Serge; Hendecourt, Louis d'; Dereux, Alain; Bloch, Daniel; Courty, Jean-Michel; Demaison, Jean; Hynes, James T.; Lievin, Jacky; Billy, J.; Josse, V.; Zuo, Z.; Bernard, A.; Hambrecht, B.; Lugan, P.; Clement, D.; Sanchez-Palencia, L.; Bouyer, P.; Aspect, A.; Garreau, Jean-Claude; Chabe, Julien; Szriftgiser, Pascal; Lemarie, Gabriel; Gremaud, Benoit; Delande, Dominique; Simoni, Andrea; Browaeys, Antoine; Kasparian, Jerome; Boutou, Veronique; Guyon, Laurent; Courvoisier, Francois; Roth, Matthias; Roslund, Jon; Rabitz, Herschel; Bonacina, Luigi; Rondi, Ariana; Extermann, Jerome; Wolf, Jean-Pierre; Maitre, Philippe; Zehnacker, Anne; Le Barbu-Debus, Katia; Sidis, Victor; Aguillon, Francois; Sizun, Muriel; Rougeau, Nathalie; Teillet-Billy, Dominique; Bachellerie, Damien; Jeloaica, Leonard; Morisset, Sabine; Picaud, Sylvain; Cacciani, Patrice; Grosliere, Marie-Christine; Joly, Gilles; Joly, Nicolas; Kudlinsky, Alexandre; Martinelli, Gilbert; Buchard, Virginie; Tudorie, Marcela; Khelkhal, Mohamed; Cosleou, Jean; Hennequin, Daniel; Beaugeois, Maxime; Lebrun, Nathalie; Droz, Daniel; El Aydam, Mohamed; Gama, Marie-Jose; Ferri, Sandrine; Schyns, Bernadette; Courty, Jean Michel

2008-07-01

This colloquium of the French Physics Society on atomic, molecular and optical physics (and more particularly on molecular spectroscopy) comprised several mini-colloquia: methane and its applications in planetology, moving mirrors and Casimir, atoms and molecules in interaction with surfaces, electronic properties of small molecules, molecular spectroscopy for atmospheric applications, quantum memories in atomic sets, methods and applications of reaction dynamics, dynamics of super-excited molecular statuses, mass spectrometry, quantum spectroscopy and chemistry, spectroscopy and reactivity of of confined molecules, electronic and molecular dynamics, dipolar quantum gases. It also comprised plenary sessions: atto-second optics, the atomic Hanbury-Brown-Twiss effect with fermions and bosons, atom and molecule slowing down by Zeeman effect and by Stark effect on Rydberg levels, non destructive counting of photons trapped in a cavity, interstellar chemistry, atom-surface van der Waals interaction noticed in the exotic regime of short distances, communication, vulgarisation and education (the multiple lives of a scientific result), the actual precision of molecular parameters, towards the formation of an amine acid precursor in the interstellar medium via proton transfer, prediction of the ionized and excited molecular electronic structure by Quantum Chemistry (from bi-atomic to bio-molecules), direct observation of Anderson location of matter waves in a controlled disordered potential, experimental observation of the Anderson transition of cold atoms, ultra-cold collisions as a key towards the quantum world, Quantum physics with a single atom, Teramobile or plasma filaments to study the atmosphere, optimal control or how to discriminate two almost identical bio-molecules, infrared spectroscopy as a new dimension for mass spectrometry, chiral recognition in gaseous phase, interactions and reactions between H atoms and graphite surfaces, modelling of gas

Discovering new information in bibliographic databases

Directory of Open Access Journals (Sweden)

Emil Hudomalj

2005-01-01

Full Text Available Databases contain information that can usually not be revealed by standard query systems. For that purpose, the methods for knowledge discovery from databases can be applied, which enable the user to browse aggregated data, discover trends, produce online reports, explore possible new associations within the data etc. Such methods are successfully employed in various fields, such as banking, insurance and telecommunications, while they are seldom used in libraries. The article reviews the development of query systems for bibliographic databases, including some early attempts to apply modern knowledge discovery methods. Analytical databases are described in more detail, since they usually serve as the basis for knowledge discovery. Data mining approaches are presented, since they are a central step in the knowledge discovery process. The key role of librarians who can play a key part in developing systems for finding new information in existing bibliographic databases is stressed.

Extensive molecular differences between anterior- and posterior-half-sclerotomes underlie somite polarity and spinal nerve segmentation

Directory of Open Access Journals (Sweden)

Keynes Roger J

2009-05-01

Full Text Available Abstract Background The polarization of somite-derived sclerotomes into anterior and posterior halves underlies vertebral morphogenesis and spinal nerve segmentation. To characterize the full extent of molecular differences that underlie this polarity, we have undertaken a systematic comparison of gene expression between the two sclerotome halves in the mouse embryo. Results Several hundred genes are differentially-expressed between the two sclerotome halves, showing that a marked degree of molecular heterogeneity underpins the development of somite polarity. Conclusion We have identified a set of genes that warrant further investigation as regulators of somite polarity and vertebral morphogenesis, as well as repellents of spinal axon growth. Moreover the results indicate that, unlike the posterior half-sclerotome, the central region of the anterior-half-sclerotome does not contribute bone and cartilage to the vertebral column, being associated instead with the development of the segmented spinal nerves.

Discovering biological progression underlying microarray samples.

Directory of Open Access Journals (Sweden)

Peng Qiu

2011-04-01

Full Text Available In biological systems that undergo processes such as differentiation, a clear concept of progression exists. We present a novel computational approach, called Sample Progression Discovery (SPD, to discover patterns of biological progression underlying microarray gene expression data. SPD assumes that individual samples of a microarray dataset are related by an unknown biological process (i.e., differentiation, development, cell cycle, disease progression, and that each sample represents one unknown point along the progression of that process. SPD aims to organize the samples in a manner that reveals the underlying progression and to simultaneously identify subsets of genes that are responsible for that progression. We demonstrate the performance of SPD on a variety of microarray datasets that were generated by sampling a biological process at different points along its progression, without providing SPD any information of the underlying process. When applied to a cell cycle time series microarray dataset, SPD was not provided any prior knowledge of samples' time order or of which genes are cell-cycle regulated, yet SPD recovered the correct time order and identified many genes that have been associated with the cell cycle. When applied to B-cell differentiation data, SPD recovered the correct order of stages of normal B-cell differentiation and the linkage between preB-ALL tumor cells with their cell origin preB. When applied to mouse embryonic stem cell differentiation data, SPD uncovered a landscape of ESC differentiation into various lineages and genes that represent both generic and lineage specific processes. When applied to a prostate cancer microarray dataset, SPD identified gene modules that reflect a progression consistent with disease stages. SPD may be best viewed as a novel tool for synthesizing biological hypotheses because it provides a likely biological progression underlying a microarray dataset and, perhaps more importantly, the

The Emerging Role of Complement Lectin Pathway in Trypanosomatids: Molecular Bases in Activation, Genetic Deficiencies, Susceptibility to Infection, and Complement System-Based Therapeutics

Directory of Open Access Journals (Sweden)

Ingrid Evans-Osses

2013-01-01

Full Text Available The innate immune system is evolutionary and ancient and is the pivotal line of the host defense system to protect against invading pathogens and abnormal self-derived components. Cellular and molecular components are involved in recognition and effector mechanisms for a successful innate immune response. The complement lectin pathway (CLP was discovered in 1990. These new components at the complement world are very efficient. Mannan-binding lectin (MBL and ficolin not only recognize many molecular patterns of pathogens rapidly to activate complement but also display several strategies to evade innate immunity. Many studies have shown a relation between the deficit of complement factors and susceptibility to infection. The recently discovered CLP was shown to be important in host defense against protozoan microbes. Although the recognition of pathogen-associated molecular patterns by MBL and Ficolins reveal efficient complement activations, an increase in deficiency of complement factors and diversity of parasite strategies of immune evasion demonstrate the unsuccessful effort to control the infection. In the present paper, we will discuss basic aspects of complement activation, the structure of the lectin pathway components, genetic deficiency of complement factors, and new therapeutic opportunities to target the complement system to control infection.

Regulation of assimilate import into sink organs: Update on molecular drivers of sink strength

Directory of Open Access Journals (Sweden)

Saadia eBihmidine

2013-06-01

Full Text Available Recent developments have altered our view of molecular mechanisms that determine sink strength, defined here as the capacity of non-photosynthetic structures to compete for import of photoassimilates. We review new findings from diverse systems, including stems, seeds, flowers, and fruits. An important advance has been the identification of new transporters and facilitators with major roles in the accumulation and equilibration of sugars at a cellular level. Exactly where each exerts its effect varies among systems. Sugarcane and sweet sorghum stems, for example, both accumulate high levels of sucrose, but may do so via different paths. The distinction is central to strategies for targeted manipulation of sink strength using transporter genes, and shows the importance of system-specific analyses. Another major advance has been the identification of deep hypoxia as a feature of normal grain development. This means that molecular drivers of sink strength in endosperm operate in very low oxygen levels, and under metabolic conditions quite different than previously assumed. Successful enhancement of sink strength has nonetheless been achieved in grains by up-regulating genes for starch biosynthesis. Additionally, our understanding of sink strength is enhanced by awareness of the dual roles played by invertases (INV, not only in sucrose metabolism, but also in production of the hexose sugar signals that regulate cell-cycle and cell-division programs. These contributions of INV to cell expansion and division prove to be vital for establishment of young sinks ranging from flowers to fruit. Since INV genes are themselves sugar-responsive feast genes, they can mediate a feed-forward enhancement of sink strength when assimilates are abundant. Greater overall productivity and yield have thus been attained in key instances, indicating that even broader enhancements may be achievable as we discover the detailed molecular mechanisms that drive sink strength

Molecular genetic studies of bacteroides fragilis

International Nuclear Information System (INIS)

Southern, J.A.

1986-03-01

This study aimed at providing a means for probing the molecular genetic organization of B.fragilis, particularly those strains where the DNA repair mechanisms had been described. The following routes of investigation were followed: the bacteriocin of B.fragilis BF-1; the investigation of any plasmids which might be discovered, with the aim of constructing a hybrid plasmid which might replicate in both E.coli and B.fragilis; and the preparation of a genetic library which could be screened for Bacteroides genes which might function in E.coli. Should any genes be isolated by screening the library they were to be studied with regard to their expression and regulation in E.coli. The above assays make use of radioactive markers such as 14 C, 35 S, 32 P, and 3 H in the labelling of RNA, plasmids and probes

Very Bright CV discovered by MASTER-ICATE (Argentina)

Science.gov (United States)

Saffe, C.; Levato, H.; Mallamaci, C.; Lopez, C.; Lipunov, F. Podest V.; Denisenko, D.; Gorbovskoy, E.; Tiurina, N.; Balanutsa, P.; Kornilov, V.; Belinski, A.; Shatskiy, N.; Chazov, V.; Kuznetsov, A.; Yecheistov, V.; Yurkov, V.; Sergienko, Y.; Varda, D.; Sinyakov, E.; Gabovich, A.; Ivanov, K.; Yazev, S.; Budnev, N.; Konstantinov, E.; Chuvalaev, O.; Poleshchuk, V.; Gress, O.; Frolova, A.; Krushinsky, V.; Zalozhnih, I.; Popov, A.; Bourdanov, A.; Parkhomenko, A.; Tlatov, A.; Dormidontov, D.; Senik, V.; Podvorotny, P.; Shumkov, V.; Shurpakov, S.

2013-06-01

MASTER-ICATE very wide-field camera (d=72mm f/1.2 lens + 11 Mpix CCD) located near San Juan, Argentina has discovered OT source at (RA, Dec) = 14h 20m 23.5s -48d 55m 40s on the combined image (exposure 275 sec) taken on 2013-06-08.048 UT. The OT unfiltered magnitude is 12.1m (limit 13.1m). There is no minor planet at this place. The OT is seen in more than 10 images starting from 2013-06-02.967 UT (275 sec exposure) when it was first detected at 12.4m.

Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening.

Science.gov (United States)

Yu, Miao; Gu, Qiong; Xu, Jun

2018-02-01

PI3Kα is a promising drug target for cancer chemotherapy. In this paper, we report a strategy of combing ligand-based and structure-based virtual screening to identify new PI3Kα inhibitors. First, naïve Bayesian (NB) learning models and a 3D-QSAR pharmacophore model were built based upon known PI3Kα inhibitors. Then, the SPECS library was screened by the best NB model. This resulted in virtual hits, which were validated by matching the structures against the pharmacophore models. The pharmacophore matched hits were then docked into PI3Kα crystal structures to form ligand-receptor complexes, which are further validated by the Glide-XP program to result in structural validated hits. The structural validated hits were examined by PI3Kα inhibitory assay. With this screening protocol, ten PI3Kα inhibitors with new scaffolds were discovered with IC 50 values ranging 0.44-31.25 μM. The binding affinities for the most active compounds 33 and 74 were estimated through molecular dynamics simulations and MM-PBSA analyses.

Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening

Science.gov (United States)

Yu, Miao; Gu, Qiong; Xu, Jun

2018-02-01

PI3Kα is a promising drug target for cancer chemotherapy. In this paper, we report a strategy of combing ligand-based and structure-based virtual screening to identify new PI3Kα inhibitors. First, naïve Bayesian (NB) learning models and a 3D-QSAR pharmacophore model were built based upon known PI3Kα inhibitors. Then, the SPECS library was screened by the best NB model. This resulted in virtual hits, which were validated by matching the structures against the pharmacophore models. The pharmacophore matched hits were then docked into PI3Kα crystal structures to form ligand-receptor complexes, which are further validated by the Glide-XP program to result in structural validated hits. The structural validated hits were examined by PI3Kα inhibitory assay. With this screening protocol, ten PI3Kα inhibitors with new scaffolds were discovered with IC50 values ranging 0.44-31.25 μM. The binding affinities for the most active compounds 33 and 74 were estimated through molecular dynamics simulations and MM-PBSA analyses.

Electrical properties of molecular crystals

International Nuclear Information System (INIS)

Barraud, A.

1968-01-01

This literature survey summarizes the electrical properties of molecular crystals: molecular crystal structure, transport and excitation mechanisms of charge-carriers, and differences compared to inorganic semi-conductors. The main results concerning the electrical conductivity of the most-studied molecular crystals are presented, together with the optical and photo-electrical properties of these crystals. Finally the different types of electrical measurements used are reviewed, as well as the limits of each method. (author) [fr

Liquid-Phase Exfoliation of Phosphorene: Design Rules from Molecular Dynamics Simulations.

Science.gov (United States)

Sresht, Vishnu; Pádua, Agílio A H; Blankschtein, Daniel

2015-08-25

The liquid-phase exfoliation of phosphorene, the two-dimensional derivative of black phosphorus, in the solvents dimethyl sulfoxide (DMSO), dimethylformamide (DMF), isopropyl alcohol, N-methyl-2-pyrrolidone, and N-cyclohexyl-2-pyrrolidone is investigated using three molecular-scale "computer experiments". We modeled solvent-phosphorene interactions using an atomistic force field, based on ab initio calculations and lattice dynamics, that accurately reproduces experimental mechanical properties. We probed solvent molecule ordering at phosphorene/solvent interfaces and discovered that planar molecules such as N-methyl-2-pyrrolidone preferentially orient parallel to the interface. We subsequently measured the energy required to peel a single phosphorene monolayer from a stack of black phosphorus and analyzed the role of "wedges" of solvent molecules intercalating between phosphorene sheets in initiating exfoliation. The exfoliation efficacy of a solvent is enhanced when either molecular planarity "sharpens" this molecular wedge or strong phosphorene-solvent adhesion stabilizes the newly exposed phosphorene surfaces. Finally, we examined the colloidal stability of exfoliated flakes by simulating their aggregation and showed that dispersion is favored when the cohesive energy between the molecules in the solvent monolayer confined between the phosphorene sheets is high (as with DMSO) and is hindered when the adhesion between these molecules and phosphorene is strong; the molecular planarity in solvents like DMF enhances the cohesive energy. Our results are consistent with, and provide a molecular context for, experimental exfoliation studies of phosphorene and other layered solids, and our molecular insights into the significant role of solvent molecular geometry and ordering should complement prevalent solubility-parameter-based approaches in establishing design rules for effective nanomaterial exfoliation media.

SUB-KILOPARSEC IMAGING OF COOL MOLECULAR GAS IN TWO STRONGLY LENSED DUSTY, STAR-FORMING GALAXIES

Energy Technology Data Exchange (ETDEWEB)

Spilker, J. S.; Marrone, D. P. [Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721 (United States); Aravena, M. [Núcleo de Astronomía, Facultad de Ingeniería, Universidad Diego Portales, Av. Ejército 441, Santiago (Chile); Béthermin, M.; Breuck, C. de [European Southern Observatory, Karl Schwarzschild Straße 2, D-85748 Garching (Germany); Bothwell, M. S. [Cavendish Laboratory, University of Cambridge, JJ Thompson Ave, Cambridge CB3 0HA (United Kingdom); Carlstrom, J. E. [Kavli Institute for Cosmological Physics, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 (United States); Chapman, S. C.; Rotermund, K. M. [Dalhousie University, Halifax, Nova Scotia (Canada); Collier, J. D.; Galvin, T.; Grieve, K.; O’Brien, A. [University of Western Sydney, Locked Bag 1797, Penrith, NSW 2751 (Australia); Fassnacht, C. D. [Department of Physics, University of California, One Shields Avenue, Davis, CA 95616 (United States); Gonzalez, A. H.; Ma, J. [Department of Astronomy, University of Florida, Gainesville, FL 32611 (United States); González-López, J. [Instituto de Astrofísica, Facultad de Física, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, 782-0436 Macul, Santiago (Chile); Hezaveh, Y. [Kavli Institute for Particle Astrophysics and Cosmology, Stanford University, Stanford, CA 94305 (United States); Malkan, M., E-mail: jspilker@as.arizona.edu [Department of Physics and Astronomy, University of California, Los Angeles, CA 90095-1547 (United States); and others

2015-10-01

We present spatially resolved imaging obtained with the Australia Telescope Compact Array (ATCA) of three CO lines in two high-redshift gravitationally lensed dusty star-forming galaxies, discovered by the South Pole Telescope. Strong lensing allows us to probe the structure and dynamics of the molecular gas in these two objects, at z = 2.78 and z = 5.66, with effective source-plane resolution of less than 1 kpc. We model the lensed emission from multiple CO transitions and the dust continuum in a consistent manner, finding that the cold molecular gas as traced by low-J CO always has a larger half-light radius than the 870 μm dust continuum emission. This size difference leads to up to 50% differences in the magnification factor for the cold gas compared to dust. In the z = 2.78 galaxy, these CO observations confirm that the background source is undergoing a major merger, while the velocity field of the other source is more complex. We use the ATCA CO observations and comparable resolution Atacama Large Millimeter/submillimeter Array dust continuum imaging of the same objects to constrain the CO–H{sub 2} conversion factor with three different procedures, finding good agreement between the methods and values consistent with those found for rapidly star-forming systems. We discuss these galaxies in the context of the star formation—gas mass surface density relation, noting that the change in emitting area with observed CO transition must be accounted for when comparing high-redshift galaxies to their lower redshift counterparts.

Metabolome analysis for discovering biomarkers of gastroenterological cancer.

Science.gov (United States)

Suzuki, Makoto; Nishiumi, Shin; Matsubara, Atsuki; Azuma, Takeshi; Yoshida, Masaru

2014-09-01

Improvements in analytical technologies have made it possible to rapidly determine the concentrations of thousands of metabolites in any biological sample, which has resulted in metabolome analysis being applied to various types of research, such as clinical, cell biology, and plant/food science studies. The metabolome represents all of the end products and by-products of the numerous complex metabolic pathways operating in a biological system. Thus, metabolome analysis allows one to survey the global changes in an organism's metabolic profile and gain a holistic understanding of the changes that occur in organisms during various biological processes, e.g., during disease development. In clinical metabolomic studies, there is a strong possibility that differences in the metabolic profiles of human specimens reflect disease-specific states. Recently, metabolome analysis of biofluids, e.g., blood, urine, or saliva, has been increasingly used for biomarker discovery and disease diagnosis. Mass spectrometry-based techniques have been extensively used for metabolome analysis because they exhibit high selectivity and sensitivity during the identification and quantification of metabolites. Here, we describe metabolome analysis using liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, and capillary electrophoresis-mass spectrometry. Furthermore, the findings of studies that attempted to discover biomarkers of gastroenterological cancer are also outlined. Finally, we discuss metabolome analysis-based disease diagnosis. Copyright © 2014 Elsevier B.V. All rights reserved.

Dealing with Wormhole Attacks in Wireless Sensor Networks Through Discovering Separate Routes Between Nodes

Directory of Open Access Journals (Sweden)

F. Rezaei

2017-08-01

Full Text Available One of the most common attacks against Wireless Sensor Networks is the wormhole attack. In this attack, the enemy deploys two malicious nodes in two different areas of the network and establishes a high-speed dedicated channel between these two. This will cause the normal nodes in two different areas wrongly think that they are two-hop neighbors. Therefore, this attack will greatly affect the routing algorithms. In this paper, a new distributed algorithm is provided to deal with the wormhole attack. The main idea of the proposed algorithm is to discover separate routes between pairs of two-hop neighboring nodes. The proposed algorithm was implemented and evaluated in terms of true and false detection rate by performing a series of experiments and the results were compared with the base algorithm. The test results showed that the proposed algorithm has desirable efficacy.

Theoretical study of the electronic structure of different states of the KRb+ molecular ion

International Nuclear Information System (INIS)

Korek, M.; Younis, G.

2000-01-01

Full text.The molecular activities in ultra-cold alkali atom trapping stimulate theoretical developments to compute relevant adiabatic potential curves, especially in the framework of the pseudopotential methods. For these methods the molecular ion KRb+ is treated as system with one active electron moving in a field of two ionic cores, where core valence electron interactions are presented by an effective potential. Potential energies have been calculated over a wide range of internuclear distance (5.0-60a o ) for the lowest states of symmetry 2 Σ, 2 Π, 2 Δ and Ω for the molecular ion KRb+. To avoid an over estimation of the dissociation energy the perturbative treatment is replaced by an l-dependent core-polarization potential of the Foucrault et al. For the one valence electron of the two considered atoms, we recalculated the polarization potential cut-off parameters r k l , and r R b l by taking l=0,1,2 and r i 2 =r i 3 . Molecular orbital for the molecular ion KRb+ were derived from Self Consistent Field calculations (SCF), and full valence Configuration Interaction (IC) calculations were performed. Extensive tables of energy values versus internuclear distance are displayed and molecular spectroscopic constants have been derived, for the first time, for the bound states with regular shape

Molecular Electronics

DEFF Research Database (Denmark)

Jennum, Karsten Stein

This thesis includes the synthesis and characterisation of organic compounds designed for molecular electronics. The synthesised organic molecules are mainly based on two motifs, the obigo(phenyleneethynylenes) (OPE)s and tetrathiafulvalene (TTF) as shown below. These two scaffolds (OPE and TTF......) are chemically merged together to form cruciform-like structures that are an essential part of the thesis. The cruciform molecules were subjected to molecular conductance measurements to explore their capability towards single-crystal field-effect transistors (Part 1), molecular wires, and single electron......, however, was obtained by a study of a single molecular transistor. The investigated OPE5-TTF compound was captured in a three-terminal experiment, whereby manipulation of the molecule’s electronic spin was possible in different charge states. Thus, we demonstrated how the cruciform molecules could...

Decision Tree Approach to Discovering Fraud in Leasing Agreements

OpenAIRE

Horvat Ivan; Pejić Bach Mirjana; Merkač Skok Marjana

2014-01-01

Background: Fraud attempts create large losses for financing subjects in modern economies. At the same time, leasing agreements have become more and more popular as a means of financing objects such as machinery and vehicles, but are more vulnerable to fraud attempts. Objectives: The goal of the paper is to estimate the usability of the data mining approach in discovering fraud in leasing agreements. Methods/Approach: Real-world data from one Croatian leasing firm was used for creating tow mo...

Genomic DNA Enrichment Using Sequence Capture Microarrays: a Novel Approach to Discover Sequence Nucleotide Polymorphisms (SNP) in Brassica napus L

Science.gov (United States)

Clarke, Wayne E.; Parkin, Isobel A.; Gajardo, Humberto A.; Gerhardt, Daniel J.; Higgins, Erin; Sidebottom, Christine; Sharpe, Andrew G.; Snowdon, Rod J.; Federico, Maria L.; Iniguez-Luy, Federico L.

2013-01-01

Targeted genomic selection methodologies, or sequence capture, allow for DNA enrichment and large-scale resequencing and characterization of natural genetic variation in species with complex genomes, such as rapeseed canola (Brassica napus L., AACC, 2n=38). The main goal of this project was to combine sequence capture with next generation sequencing (NGS) to discover single nucleotide polymorphisms (SNPs) in specific areas of the B. napus genome historically associated (via quantitative trait loci –QTL– analysis) to traits of agronomical and nutritional importance. A 2.1 million feature sequence capture platform was designed to interrogate DNA sequence variation across 47 specific genomic regions, representing 51.2 Mb of the Brassica A and C genomes, in ten diverse rapeseed genotypes. All ten genotypes were sequenced using the 454 Life Sciences chemistry and to assess the effect of increased sequence depth, two genotypes were also sequenced using Illumina HiSeq chemistry. As a result, 589,367 potentially useful SNPs were identified. Analysis of sequence coverage indicated a four-fold increased representation of target regions, with 57% of the filtered SNPs falling within these regions. Sixty percent of discovered SNPs corresponded to transitions while 40% were transversions. Interestingly, fifty eight percent of the SNPs were found in genic regions while 42% were found in intergenic regions. Further, a high percentage of genic SNPs was found in exons (65% and 64% for the A and C genomes, respectively). Two different genotyping assays were used to validate the discovered SNPs. Validation rates ranged from 61.5% to 84% of tested SNPs, underpinning the effectiveness of this SNP discovery approach. Most importantly, the discovered SNPs were associated with agronomically important regions of the B. napus genome generating a novel data resource for research and breeding this crop species. PMID:24312619

Yield, Esterification Degree and Molecular Weight Evaluation of Pectins Isolated from Orange and Grapefruit Peels under Different Conditions

Science.gov (United States)

Sayah, Mohamed Yassine; Chabir, Rachida; Benyahia, Hamid; Rodi Kandri, Youssef; Ouazzani Chahdi, Fouad; Touzani, Hanan; Errachidi, Faouzi

2016-01-01

Orange (Citrus sinensis) and grapefruit (Citrus paradise) peels were used as a source of pectin, which was extracted under different conditions. The peels are used under two states: fresh and residual (after essential oil extraction). Organic acid (citric acid) and mineral acid (sulfuric acid) were used in the pectin extraction. The aim of this study is the evaluation the effect of extraction conditions on pectin yield, degree of esterification “DE” and on molecular weight “Mw”. Results showed that the pectin yield was higher using the residual peels. Moreover, both peels allow the obtainment of a high methoxyl pectin with DE >50%. The molecular weight was calculated using Mark-Houwink-Sakurada equation which describes its relationship with intrinsic viscosity. This later was determined using four equations; Huggins equation, kramer, Schulz-Blaschke and Martin equation. The molecular weight varied from 1.538 x1005 to 2.47x1005 g/mol for grapefruit pectin and from 1.639 x1005 to 2.471 x1005 g/mol for orange pectin. PMID:27644093

Preclinical studies of lymphographic applilcation of 99mTc-dextrans of different molecular weight

International Nuclear Information System (INIS)

Lamka, J.; Kvetina, J.; Kafka, P.

1986-01-01

In a preclinical investigation on rabbits the distribution was tested of dextrans of two molecular weights (40,000 and 70,000) with regard to their use as a carrier in indirect lymphography. The tests showed that both 99m Tc-dextrans achieve high ratios of lymph/blood levels. It is suggested that for clinical work it is better to use dextran with a molecular weight of 70,000 than that with a molecular weight of 40,000. (author)

Discovering Pediatric Asthma Phenotypes on the Basis of Response to Controller Medication Using Machine Learning.

Science.gov (United States)

Ross, Mindy K; Yoon, Jinsung; van der Schaar, Auke; van der Schaar, Mihaela

2018-01-01

Pediatric asthma has variable underlying inflammation and symptom control. Approaches to addressing this heterogeneity, such as clustering methods to find phenotypes and predict outcomes, have been investigated. However, clustering based on the relationship between treatment and clinical outcome has not been performed, and machine learning approaches for long-term outcome prediction in pediatric asthma have not been studied in depth. Our objectives were to use our novel machine learning algorithm, predictor pursuit (PP), to discover pediatric asthma phenotypes on the basis of asthma control in response to controller medications, to predict longitudinal asthma control among children with asthma, and to identify features associated with asthma control within each discovered pediatric phenotype. We applied PP to the Childhood Asthma Management Program study data (n = 1,019) to discover phenotypes on the basis of asthma control between assigned controller therapy groups (budesonide vs. nedocromil). We confirmed PP's ability to discover phenotypes using the Asthma Clinical Research Network/Childhood Asthma Research and Education network data. We next predicted children's asthma control over time and compared PP's performance with that of traditional prediction methods. Last, we identified clinical features most correlated with asthma control in the discovered phenotypes. Four phenotypes were discovered in both datasets: allergic not obese (A + /O - ), obese not allergic (A - /O + ), allergic and obese (A + /O + ), and not allergic not obese (A - /O - ). Of the children with well-controlled asthma in the Childhood Asthma Management Program dataset, we found more nonobese children treated with budesonide than with nedocromil (P = 0.015) and more obese children treated with nedocromil than with budesonide (P = 0.008). Within the obese group, more A + /O + children's asthma was well controlled with nedocromil than with budesonide (P = 0.022) or with placebo

Association Between Imaging Characteristics and Different Molecular Subtypes of Breast Cancer.

Science.gov (United States)

Wu, Mingxiang; Ma, Jie

2017-04-01

Breast cancer can be divided into four major molecular subtypes based on the expression of hormone receptor (estrogen receptor and progesterone receptor), human epidermal growth factor receptor 2, HER2 status, and molecular proliferation rate (Ki67). In this study, we sought to investigate the association between breast cancer subtype and radiological findings in the Chinese population. Medical records of 300 consecutive invasive breast cancer patients were reviewed from the database: the Breast Imaging Reporting and Data System. The imaging characteristics of the lesions were evaluated. The molecular subtypes of breast cancer were classified into four types: luminal A, luminal B, HER2 overexpressed (HER2), and basal-like breast cancer (BLBC). Univariate and multivariate logistic regression analyses were performed to assess the association between the subtype (dependent variable) and mammography or 15 magnetic resonance imaging (MRI) indicators (independent variables). Luminal A and B subtypes were commonly associated with "clustered calcification distribution," "nipple invasion," or "skin invasion" (P cancers showed association with persistent enhancement in the delayed phase on MRI and "clustered calcification distribution" on mammography (P breast tumor, which are potentially useful tools in the diagnosis and subtyping of breast cancer. Copyright © 2017 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

Molecular analyses of 6 different types of uterine smooth muscle tumors: Emphasis in atypical leiomyoma.

Science.gov (United States)

Zhang, Qing; Ubago, Julianne; Li, Li; Guo, Haiyang; Liu, Yugang; Qiang, Wenan; Kim, J Julie; Kong, Beihua; Wei, Jian-Jun

2014-10-15

Uterine smooth muscle tumors (USMTs) constitute a group of histologic, genetic, and clinical heterogeneous tumors that include at least 6 major histologically defined tumor types: leiomyoma (ULM), mitotically active leiomyoma (MALM), cellular leiomyoma (CLM), atypical leiomyoma (ALM), uncertain malignant potential (STUMP), and leiomyosarcoma (LMS). Apart from ULM and LMS, the nature of these variants is not well defined. A total of 167 cases of different USMT variants were collected, reviewed, and diagnostically confirmed based on the World Health Organization and Stanford schemes. These included 38 cases of LMS, 18 cases of STUMP, 42 cases of ALM, 22 cases of CLM, 7 cases of MALM, and 40 cases of ULM. Molecular analysis included selected microRNAs (miRNAs), oncogenes, and tumor suppressors that are highly relevant to USMT. Overall, 49% (17/35) of LMS cases and 7% (1/14) of STUMP cases died due to their USMT, but no deaths were attributed to ALM. miRNA profiling revealed that ALM and LMS shared similar miRNA signatures. P53 mutations and PTEN deletions were significantly higher in LMS, ALM, and STUMP compared with other USMT variants (P 74%) but were significantly less common (< 15%) in CLM, ALM, STUMP, and LMS (P < .01). Six types of USMT have different gene mutation fingerprints. ALM shares many molecular alterations with LMS. Our findings suggest that ALM may be a precursor lesion of LMS or have similar genetic changes during its early stage. © 2014 American Cancer Society.

Discovering, Indexing and Interlinking Information Resources.

Science.gov (United States)

Celli, Fabrizio; Keizer, Johannes; Jaques, Yves; Konstantopoulos, Stasinos; Vudragović, Dušan

2015-01-01

The social media revolution is having a dramatic effect on the world of scientific publication. Scientists now publish their research interests, theories and outcomes across numerous channels, including personal blogs and other thematic web spaces where ideas, activities and partial results are discussed. Accordingly, information systems that facilitate access to scientific literature must learn to cope with this valuable and varied data, evolving to make this research easily discoverable and available to end users. In this paper we describe the incremental process of discovering web resources in the domain of agricultural science and technology. Making use of Linked Open Data methodologies, we interlink a wide array of custom-crawled resources with the AGRIS bibliographic database in order to enrich the user experience of the AGRIS website. We also discuss the SemaGrow Stack, a query federation and data integration infrastructure used to estimate the semantic distance between crawled web resources and AGRIS.

Michael Maier--nine newly discovered letters.

Science.gov (United States)

Lenke, Nils; Roudet, Nicolas; Tilton, Hereward

2014-02-01

The authors provide a transcription, translation, and evaluation of nine newly discovered letters from the alchemist Michael Maier (1568-1622) to Gebhardt Johann von Alvensleben (1576-1631), a noble landholder in the vicinity of Magdeburg. Stemming from the final year of his life, this correspondence casts new light on Maier's biography, detailing his efforts to secure patronage amid the financial crisis of the early Thirty Years' War. While his ill-fated quest to perfect potable gold continued to form the central focus of his patronage suits, Maier also offered his services in several arts that he had condemned in his printed works, namely astrology and "supernatural" magic. Remarks concerning his previously unknown acquaintance with Heinrich Khunrath call for a re-evaluation of Maier's negotiation of the discursive boundaries between Lutheran orthodoxy and Paracelsianism. The letters also reveal Maier's substantial contribution to a work previously ascribed solely to the English alchemist Francis Anthony.

Molecular Nevogenesis

Directory of Open Access Journals (Sweden)

Andrew L. Ross

2011-01-01

Full Text Available Despite recent advances, the biology underlying nevogenesis remains unclear. Activating mutations in NRAS, HRAS, BRAF, and GNAQ have been identified in benign nevi. Their presence roughly correlates with congenital, Spitz, acquired, and blue nevi, respectively. These mutations are likely to play a critical role in driving nevogenesis. While each mutation is able to activate the MAP kinase pathway, they also interact with a host of different proteins in other pathways. The different melanocytic developmental pathways activated by each mutation cause the cells to migrate, proliferate, and differentiate to different extents within the skin. This causes each mutation to give rise to a characteristic growth pattern. The exact location and differentiation state of the cell of origin for benign moles remains to be discovered. Further research is necessary to fully understand nevus development given that most of the same developmental pathways are also present in melanoma.

Improving the Interpretability of Classification Rules Discovered by an Ant Colony Algorithm: Extended Results.

Science.gov (United States)

Otero, Fernando E B; Freitas, Alex A

2016-01-01

Most ant colony optimization (ACO) algorithms for inducing classification rules use a ACO-based procedure to create a rule in a one-at-a-time fashion. An improved search strategy has been proposed in the cAnt-Miner[Formula: see text] algorithm, where an ACO-based procedure is used to create a complete list of rules (ordered rules), i.e., the ACO search is guided by the quality of a list of rules instead of an individual rule. In this paper we propose an extension of the cAnt-Miner[Formula: see text] algorithm to discover a set of rules (unordered rules). The main motivations for this work are to improve the interpretation of individual rules by discovering a set of rules and to evaluate the impact on the predictive accuracy of the algorithm. We also propose a new measure to evaluate the interpretability of the discovered rules to mitigate the fact that the commonly used model size measure ignores how the rules are used to make a class prediction. Comparisons with state-of-the-art rule induction algorithms, support vector machines, and the cAnt-Miner[Formula: see text] producing ordered rules are also presented.

Different routes, same pathways: Molecular mechanisms under silver ion and nanoparticle exposures in the soil sentinel Eisenia fetida

International Nuclear Information System (INIS)

Novo, Marta; Lahive, Elma; Díez-Ortiz, María; Matzke, Marianne; Morgan, Andrew J.; Spurgeon, David J.; Svendsen, Claus; Kille, Peter

2015-01-01

Use of nanotechnology products is increasing; with silver (Ag) nanoparticles particularly widely used. A key uncertainty surrounding the risk assessment of AgNPs is whether their effects are driven through the same mechanism of action that underlies the toxic effects of Ag ions. We present the first full transcriptome study of the effects of Ag ions and NPs in an ecotoxicological model soil invertebrate, the earthworm Eisenia fetida. Gene expression analyses indicated similar mechanisms for both silver forms with toxicity being exerted through pathways related to ribosome function, sugar and protein metabolism, molecular stress, disruption of energy production and histones. The main difference seen between Ag ions and NPs was associated with potential toxicokinetic effects related to cellular internalisation and communication, with pathways related to endocytosis and cilia being significantly enriched. These results point to a common final toxicodynamic response, but initial internalisation driven by different exposure routes and toxicokinetic mechanisms. - Highlights: • Molecular effects underlying Ag ions and NPs exposure were studied in Eisenia fetida. • Full transcriptomic study of a genetically characterised lineage. • NPs and ions presented a similar toxicodynamic response. • Internalisation of the two Ag forms by different toxicokinetic mechanisms. - Transcriptomic analyses after exposure of earthworms to silver NPs or ions showed a final common toxicodynamic response, but internalisation by different toxicokinetic mechanisms

Discovering significant evolution patterns from satellite image time series.

Science.gov (United States)

Petitjean, François; Masseglia, Florent; Gançarski, Pierre; Forestier, Germain

2011-12-01

Satellite Image Time Series (SITS) provide us with precious information on land cover evolution. By studying these series of images we can both understand the changes of specific areas and discover global phenomena that spread over larger areas. Changes that can occur throughout the sensing time can spread over very long periods and may have different start time and end time depending on the location, which complicates the mining and the analysis of series of images. This work focuses on frequent sequential pattern mining (FSPM) methods, since this family of methods fits the above-mentioned issues. This family of methods consists of finding the most frequent evolution behaviors, and is actually able to extract long-term changes as well as short term ones, whenever the change may start and end. However, applying FSPM methods to SITS implies confronting two main challenges, related to the characteristics of SITS and the domain's constraints. First, satellite images associate multiple measures with a single pixel (the radiometric levels of different wavelengths corresponding to infra-red, red, etc.), which makes the search space multi-dimensional and thus requires specific mining algorithms. Furthermore, the non evolving regions, which are the vast majority and overwhelm the evolving ones, challenge the discovery of these patterns. We propose a SITS mining framework that enables discovery of these patterns despite these constraints and characteristics. Our proposal is inspired from FSPM and provides a relevant visualization principle. Experiments carried out on 35 images sensed over 20 years show the proposed approach makes it possible to extract relevant evolution behaviors.

Endocrine-disrupting Chemicals: Review of Toxicological Mechanisms Using Molecular Pathway Analysis

Science.gov (United States)

Yang, Oneyeol; Kim, Hye Lim; Weon, Jong-Il; Seo, Young Rok

2015-01-01

Endocrine disruptors are known to cause harmful effects to human through various exposure routes. These chemicals mainly appear to interfere with the endocrine or hormone systems. As importantly, numerous studies have demonstrated that the accumulation of endocrine disruptors can induce fatal disorders including obesity and cancer. Using diverse biological tools, the potential molecular mechanisms related with these diseases by exposure of endocrine disruptors. Recently, pathway analysis, a bioinformatics tool, is being widely used to predict the potential mechanism or biological network of certain chemicals. In this review, we initially summarize the major molecular mechanisms involved in the induction of the above mentioned diseases by endocrine disruptors. Additionally, we provide the potential markers and signaling mechanisms discovered via pathway analysis under exposure to representative endocrine disruptors, bisphenol, diethylhexylphthalate, and nonylphenol. The review emphasizes the importance of pathway analysis using bioinformatics to finding the specific mechanisms of toxic chemicals, including endocrine disruptors. PMID:25853100

Synthesis of Molecularly Imprinted Polymers for Amino Acid Derivates by Using Different Functional Monomers

Directory of Open Access Journals (Sweden)

Sonia Scorrano

2011-03-01

Full Text Available Fmoc-3-nitrotyrosine (Fmoc-3-NT molecularly imprinted polymers (MIPs were synthesized to understand the influence of several functional monomers on the efficiency of the molecular imprinting process. Acidic, neutral and basic functional monomers, such as acrylic acid (AA, methacrylic acid (MAA, methacrylamide (MAM, 2-vinylpyridine (2-VP, 4-vinylpyridine (4-VP, have been used to synthesize five different polymers. In this study, the MIPs were tested in batch experiments by UV-visible spectroscopy in order to evaluate their binding properties. The MIP prepared with 2-VP exhibited the highest binding affinity for Fmoc-3NT, for which Scatchard analysis the highest association constant (2.49 × 104 M−1 was obtained. Furthermore, titration experiments of Fmoc-3NT into acetonitrile solutions of 2-VP revealed a stronger bond to the template, such that a total interaction is observed. Non-imprinted polymers as control were prepared and showed no binding affinities for Fmoc-3NT. The results are indicative of the importance of ionic bonds formed between the –OH residues of the template molecule and the pyridinyl groups of the polymer matrix. In conclusion, 2-VP assists to create a cavity which allows better access to the analytes.

Fabrication and Molecular Transport Studies of Highly c-Oriented AFI Membranes

KAUST Repository

Liu, Yang

2017-01-10

The AFI membrane with one-dimensional straight channels is an ideal platform for various applications. In this work, we report the fabrication of a highly c-oriented, compact and stable AFI membrane by epitaxial growth from an almost close-packed and c-oriented monolayer of plate-like seeds that is manually assembled on a porous alumina support. The straight channels in the membrane are not only aligned vertically along the membrane depth, but are also continuous without disruption. The transport resistance is thus minimized and as a result, the membrane shows almost two orders of magnitude greater permeance in pervaporation of hydrocarbons compared to reported values in the literature. The selectivity of p-xylene to 1,3,5-triisopropylbenzene (TIPB) is approximately 850. In addition, through gas permeation studies on a number of gas and liquid molecules, different transport mechanisms including activated Knudsen diffusion, surface diffusion and molecular sieving were discovered for different diffusion species. The ratio of kinetic diameter to channel diameter, dm/dc, and the ratio of the Lennard-Jones length constant to channel diameter, σm/dc, are found very useful in explaining the different transport behaviors. These results should be useful not only for potential industrial applications of the AFI membranes but also for the fundamental understanding of transport in nanoporous structures.

Knots and surfaces a guide to discovering mathematics

CERN Document Server

Farmer, David W

1995-01-01

In most mathematics textbooks, the most exciting part of mathematics-the process of invention and discovery-is completely hidden from the reader. The aim of Knots and Surfaces is to change all that. By means of a series of carefully selected tasks, this book leads readers to discover some real mathematics. There are no formulas to memorize; no procedures to follow. The book is a guide: its job is to start you in the right direction and to bring you back if you stray too far. Discovery is left to you. Suitable for a one-semester course at the beginning undergraduate level, there are no prerequi

Discovering cancer vulnerabilities using high-throughput micro-RNA screening.

Science.gov (United States)

Nikolic, Iva; Elsworth, Benjamin; Dodson, Eoin; Wu, Sunny Z; Gould, Cathryn M; Mestdagh, Pieter; Marshall, Glenn M; Horvath, Lisa G; Simpson, Kaylene J; Swarbrick, Alexander

2017-12-15

Micro-RNAs (miRNAs) are potent regulators of gene expression and cellular phenotype. Each miRNA has the potential to target hundreds of transcripts within the cell thus controlling fundamental cellular processes such as survival and proliferation. Here, we exploit this important feature of miRNA networks to discover vulnerabilities in cancer phenotype, and map miRNA-target relationships across different cancer types. More specifically, we report the results of a functional genomics screen of 1280 miRNA mimics and inhibitors in eight cancer cell lines, and its presentation in a sophisticated interactive data portal. This resource represents the most comprehensive survey of miRNA function in oncology, incorporating breast cancer, prostate cancer and neuroblastoma. A user-friendly web portal couples this experimental data with multiple tools for miRNA target prediction, pathway enrichment analysis and visualization. In addition, the database integrates publicly available gene expression and perturbation data enabling tailored and context-specific analysis of miRNA function in a particular disease. As a proof-of-principle, we use the database and its innovative features to uncover novel determinants of the neuroblastoma malignant phenotype. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Prediction of Human Activity by Discovering Temporal Sequence Patterns.

Science.gov (United States)

Li, Kang; Fu, Yun

2014-08-01

Early prediction of ongoing human activity has become more valuable in a large variety of time-critical applications. To build an effective representation for prediction, human activities can be characterized by a complex temporal composition of constituent simple actions and interacting objects. Different from early detection on short-duration simple actions, we propose a novel framework for long -duration complex activity prediction by discovering three key aspects of activity: Causality, Context-cue, and Predictability. The major contributions of our work include: (1) a general framework is proposed to systematically address the problem of complex activity prediction by mining temporal sequence patterns; (2) probabilistic suffix tree (PST) is introduced to model causal relationships between constituent actions, where both large and small order Markov dependencies between action units are captured; (3) the context-cue, especially interactive objects information, is modeled through sequential pattern mining (SPM), where a series of action and object co-occurrence are encoded as a complex symbolic sequence; (4) we also present a predictive accumulative function (PAF) to depict the predictability of each kind of activity. The effectiveness of our approach is evaluated on two experimental scenarios with two data sets for each: action-only prediction and context-aware prediction. Our method achieves superior performance for predicting global activity classes and local action units.

Discretization of Gene Expression Data Unmasks Molecular Subgroups Recurring in Different Human Cancer Types.

Directory of Open Access Journals (Sweden)

Manfred Beleut

Full Text Available Despite the individually different molecular alterations in tumors, the malignancy associated biological traits are strikingly similar. Results of a previous study using renal cell carcinoma (RCC as a model pointed towards cancer-related features, which could be visualized as three groups by microarray based gene expression analysis. In this study, we used a mathematic model to verify the presence of these groups in RCC as well as in other cancer types. We developed an algorithm for gene-expression deviation profiling for analyzing gene expression data of a total of 8397 patients with 13 different cancer types and normal tissues. We revealed three common Cancer Transcriptomic Profiles (CTPs which recurred in all investigated tumors. Additionally, CTPs remained robust regardless of the functions or numbers of genes analyzed. CTPs may represent common genetic fingerprints, which potentially reflect the closely related biological traits of human cancers.

Molecular fingerprinting reflects different histotypes and brain region in low grade gliomas

International Nuclear Information System (INIS)

Mascelli, Samantha; Fasulo, Daniel; Noy, Karin; Wittemberg, Gayle; Pignatelli, Sara; Piatelli, Gianluca; Cama, Armando; Garré, Maria Luisa; Capra, Valeria; Verri, Alessandro; Barla, Annalisa; Raso, Alessandro; Mosci, Sofia; Nozza, Paolo; Biassoni, Roberto; Morana, Giovanni; Huber, Martin; Mircean, Cristian

2013-01-01

Paediatric low-grade gliomas (LGGs) encompass a heterogeneous set of tumours of different histologies, site of lesion, age and gender distribution, growth potential, morphological features, tendency to progression and clinical course. Among LGGs, Pilocytic astrocytomas (PAs) are the most common central nervous system (CNS) tumours in children. They are typically well-circumscribed, classified as grade I by the World Health Organization (WHO), but recurrence or progressive disease occurs in about 10-20% of cases. Despite radiological and neuropathological features deemed as classic are acknowledged, PA may present a bewildering variety of microscopic features. Indeed, tumours containing both neoplastic ganglion and astrocytic cells occur at a lower frequency. Gene expression profiling on 40 primary LGGs including PAs and mixed glial-neuronal tumours comprising gangliogliomas (GG) and desmoplastic infantile gangliogliomas (DIG) using Affymetrix array platform was performed. A biologically validated machine learning workflow for the identification of microarray-based gene signatures was devised. The method is based on a sparsity inducing regularization algorithm l 1 l 2 that selects relevant variables and takes into account their correlation. The most significant genetic signatures emerging from gene-chip analysis were confirmed and validated by qPCR. We identified an expression signature composed by a biologically validated list of 15 genes, able to distinguish infratentorial from supratentorial LGGs. In addition, a specific molecular fingerprinting distinguishes the supratentorial PAs from those originating in the posterior fossa. Lastly, within supratentorial tumours, we also identified a gene expression pattern composed by neurogenesis, cell motility and cell growth genes which dichotomize mixed glial-neuronal tumours versus PAs. Our results reinforce previous observations about aberrant activation of the mitogen-activated protein kinase (MAPK) pathway in LGGs

Apoptosis-related molecular differences for response to tyrosin kinase inhibitors in drug-sensitive and drug-resistant human bladder cancer cells

Directory of Open Access Journals (Sweden)

Jixia Li

2013-01-01

Full Text Available Context: The epidermal growth factor receptor (EGFR family is reportedly overexpressed in bladder cancer, and tyrosine kinaseinhibitors (TKIs have been suggested as treatment. Gefitinib is a selective inhibitor of the EGFR and lapatinib is a dual inhibitor of both the EGFR and HER2 (human EGFR type 2 receptor. Both compounds compete with the binding of adenosine triphosphate (ATP to the tyrosine kinase domain of the respective receptors to inhibit receptor autophosphorylation causing suppression of signal transduction. Unfortunately, resistance to these inhibitors is a major clinical problem. Aims: To compare the apoptosis signaling pathway(s induced by gefitinib and lapatinib, in UM-UC-5 (drug-sensitive and UM-UC-14 (drug-resistant bladder cancer cells and to identify molecular differences that might be useful predictors of their efficacy. Materials and Methods: Cell proliferation, cell cycle and apoptosis assay were used to detect the effect of TKIs on UM-UC-5 and UM-UC-14 cells. Molecular differences for response to TKIs were examined by protein array. Results: TKIs strongly inhibited cell proliferation and induced cell cycle G1 arrest and apoptosis in UM-UC-5 cells. Most notable apoptosis molecular differences included decreased claspin, trail, and survivin by TKIs in the sensitive cells. In contrast, TKIs had no effect on resistant cells. Conclusions: Claspin, trail, and survivin might be used to determine the sensitivity of bladder cancers to TKIs.

A tunable pH-sensing system based on Ag nanoclusters capped by hyperbranched polyethyleneimine with different molecular weights.

Science.gov (United States)

Qu, Fei; Zou, Xuan; Kong, Rongmei; You, Jinmao

2016-01-01

In this assay, a tunable pH sensing system was developed based on Ag nanoclusters (Ag NCs) capped by hyperbranched polyethyleneimine (PEI) with different molecular weights (abbreviated as Ag NC-PEIs). For instance, when the molecular weight of PEI was 600 or 1800, the fluorescence intensities of Ag NCs exhibited a linear fashion over the pH range 4.10-7.96; when the molecular weight of PEI was 25,000, the pH linear range was from 4.78 to 7.96; when the molecular weight of PEI was 70,000, the pH linear range was 6.09-8.95. According to the molecular weight of PEI 600/1800, 25,000, and 70,000, the color change point was pH 4.10-4.78, 5.33-6.09, and 6.09-6.80, respectively. Therefore, Ag NC-PEI 600 and 1800 were proper to acid conditions; Ag NC-PEI 25,000 was sensitive to weak acid media; while Ag NC-PEI 70,000 was adapted to neutral solution. The tunable and selective color change points brought an excellent feature of Ag NC-PEIs as visual pH indicators, which was flexible and applicable to a variety of environments. Besides, the ratios of absorbance at 415 nm and 268 nm of Ag NCs also showed linear relationships with pH variations. Therefore, there were three ways of this system for sensing pH values, including fluorescence assay, ultraviolet-visible measurement, and visual detection, suggesting that this tunable pH-sensing platform was more feasible, reliable, and accurate. Copyright © 2015 Elsevier B.V. All rights reserved.

Tuppiap Qeqertaa (Tobias Island): a newly discovered island off northeast Greenland

DEFF Research Database (Denmark)

Bennike, O.; Mikkelsen, N.; Forsberg, René

2006-01-01

The small island of Tuppiap Qeqertaa, formerly known as Tobias circle divide or Tobias Island, is situated 80 km off the northeast Greenland coast. The island was discovered in 1993 and is approximately 2 km long and 1.5 km wide. Most of the island is covered by an ice cap that rises to 35 in abo...

Discovering the Art of Mathematics: Using String Art to Investigate Calculus

Science.gov (United States)

von Renesse, Christine; Ecke, Volker

2016-01-01

One goal of our Discovering the Art of Mathematics project is to empower students in the liberal arts to become confident creators of art and imaginative creators of mathematics. In this paper, we describe our experience with using string art to guide liberal arts students in exploring ideas of calculus. We provide excerpts from our inquiry-based…

Novel Transrotational Solid State Order Discovered by TEM in Crystallizing Amorphous Films

Science.gov (United States)

Kolosov, Vladimir

Exotic thin crystals with unexpected transrotational microstructures have been discovered by transmission electron microscopy (TEM) for crystal growth in thin (10-100 nm) amorphous films of different chemical nature (oxides, chalcogenides, metals and alloys) prepared by various methods. Primarily we use our TEM bend contour technique. The unusual phenomenon can be traced in situ in TEM column: dislocation independent regular internal bending of crystal lattice planes in a growing crystal. Such transrotation (unit cell trans lation is complicated by small rotationrealized round an axis lying in the film plane) can result in strong regular lattice orientation gradients (up to 300 degrees per micrometer) of different geometries: cylindrical, ellipsoidal, toroidal, saddle, etc. Transrotation is increasing as the film gets thinner. Transrotational crystal resembles ideal single crystal enclosed in a curved space. Transrotational micro crystals have been eventually recognized by other authors in some vital thin film materials, i.e. PCMs for memory, silicides, SrTiO3. Atomic model and possible mechanisms of the phenomenon are discussed. New transrotational nanocrystalline model of amorphous state is also proposed Support of RF Ministry of Education and Science is acknowledged.

Different Achilles Tendon Pathologies Show Distinct Histological and Molecular Characteristics

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Franka Klatte-Schulz

2018-01-01

Full Text Available Reasons for the development of chronic tendon pathologies are still under debate and more basic knowledge is needed about the different diseases. The aim of the present study was therefore to characterize different acute and chronic Achilles tendon disorders. Achilles tendon samples from patients with chronic tendinopathy (n = 7, chronic ruptures (n = 6, acute ruptures (n = 13, and intact tendons (n = 4 were analyzed. The histological score investigating pathological changes was significantly increased in tendinopathy and chronic ruptures compared to acute ruptures. Inflammatory infiltration was detected by immunohistochemistry in all tendon pathology groups, but was significantly lower in tendinopathy compared to chronic ruptures. Quantitative real-time PCR (qRT-PCR analysis revealed significantly altered expression of genes related to collagens and matrix modeling/remodeling (matrix metalloproteinases, tissue inhibitors of metalloproteinases in tendinopathy and chronic ruptures compared to intact tendons and/or acute ruptures. In all three tendon pathology groups markers of inflammation (interleukin (IL 1β, tumor necrosis factor α, IL6, IL10, IL33, soluble ST2, transforming growth factor β1, cyclooxygenase 2, inflammatory cells (cluster of differentaition (CD 3, CD68, CD80, CD206, fat metabolism (fatty acid binding protein 4, peroxisome proliferator-activated receptor γ, CCAAT/enhancer-binding protein α, adiponectin, and innervation (protein gene product 9.5, growth associated protein 43, macrophage migration inhibitory factor were detectable, but only in acute ruptures significantly regulated compared to intact tendons. The study gives an insight into structural and molecular changes of pathological processes in tendons and might be used to identify targets for future therapy of tendon pathologies.

Discovering time-lagged rules from microarray data using gene profile classifiers

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Ponzoni Ignacio

2011-04-01

Full Text Available Abstract Background Gene regulatory networks have an essential role in every process of life. In this regard, the amount of genome-wide time series data is becoming increasingly available, providing the opportunity to discover the time-delayed gene regulatory networks that govern the majority of these molecular processes. Results This paper aims at reconstructing gene regulatory networks from multiple genome-wide microarray time series datasets. In this sense, a new model-free algorithm called GRNCOP2 (Gene Regulatory Network inference by Combinatorial OPtimization 2, which is a significant evolution of the GRNCOP algorithm, was developed using combinatorial optimization of gene profile classifiers. The method is capable of inferring potential time-delay relationships with any span of time between genes from various time series datasets given as input. The proposed algorithm was applied to time series data composed of twenty yeast genes that are highly relevant for the cell-cycle study, and the results were compared against several related approaches. The outcomes have shown that GRNCOP2 outperforms the contrasted methods in terms of the proposed metrics, and that the results are consistent with previous biological knowledge. Additionally, a genome-wide study on multiple publicly available time series data was performed. In this case, the experimentation has exhibited the soundness and scalability of the new method which inferred highly-related statistically-significant gene associations. Conclusions A novel method for inferring time-delayed gene regulatory networks from genome-wide time series datasets is proposed in this paper. The method was carefully validated with several publicly available data sets. The results have demonstrated that the algorithm constitutes a usable model-free approach capable of predicting meaningful relationships between genes, revealing the time-trends of gene regulation.

IC 751: A New Changing Look AGN Discovered by NuSTAR

Science.gov (United States)

Ricci, C.; Bauer, F. E.; Arevalo, P.; Boggs, S.; Brandt, W. N.; Christensen, F. E.; Craig, W. W.; Ghandi, P.; Hailey, C. J.; Harrison, F. A.;

Discovering and explaining work-family strategies of parents in Luxembourg

OpenAIRE

Zhelyazkova, Nevena

2014-01-01

The presented analysis discovers and explains typical patterns of work-family reconciliation for parents who had a child in the same period (2003) and in the same country (Luxembourg), thus facing the same macroeconomic and institutional conditions. Work-family trajectories are reconstructed as sequences of states using administrative records, so that working hours and use of leave provisions or other social security benefits are taken into account. Next, a clustering algorithm is applied to ...

Discovering Social Circles in Ego Networks (Author’s Manuscript)

Science.gov (United States)

2013-01-10

refer to as social cir- cles. Practically all major social networks provide such functionality, for example, ‘circles’ on Google+, and ‘lists’ on Facebook ...Discovering Social Circles in Ego Networks Julian McAuley and Jure Leskovec Stanford jmcauley@cs.stanford.edu, jure@cs.stanford.edu January 11, 2013...Abstract People’s personal social networks are big and cluttered, and currently there is no good way to automatically organize them. Social networking

On the structural affinity of macromolecules with different biological properties: Molecular dynamics simulations of a series of TEM-1 mutants

Energy Technology Data Exchange (ETDEWEB)

Giampaolo, Alessia Di [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Mazza, Fernando [Department of Health Sciences, Univ. of L’Aquila, 67010 L’Aquila (Italy); Daidone, Isabella [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Amicosante, Gianfranco; Perilli, Mariagrazia [Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Aschi, Massimiliano, E-mail: massimiliano.aschi@univaq.it [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy)

2013-07-12

Highlights: •We have performed molecular dynamics simulations of TEM-1 mutants. •Mutations effects on the mechanical properties are considered. •Mutants do not significantly alter the average enzymes structure. •Mutants produce sharp alterations in enzyme conformational repertoire. •Mutants also produce changes in the active site volume. -- Abstract: Molecular Dynamics simulations have been carried out in order to provide a molecular rationalization of the biological and thermodynamic differences observed for a class of TEM β-lactamases. In particular we have considered the TEM-1(wt), the single point mutants TEM-40 and TEM-19 representative of IRT and ESBL classes respectively, and TEM-1 mutant M182T, TEM-32 and TEM-20 which differ from the first three for the additional of M182T mutation. Results indicate that most of the thermodynamic, and probably biological behaviour of these systems arise from subtle effects which, starting from the alterations of the local interactions, produce drastic modifications of the conformational space spanned by the enzymes. The present study suggests that systems showing essentially the same secondary and tertiary structure may differentiate their chemical–biological activity essentially (and probably exclusively) on the basis of the thermal fluctuations occurring in their physiological environment.

On the structural affinity of macromolecules with different biological properties: Molecular dynamics simulations of a series of TEM-1 mutants

International Nuclear Information System (INIS)

Giampaolo, Alessia Di; Mazza, Fernando; Daidone, Isabella; Amicosante, Gianfranco; Perilli, Mariagrazia; Aschi, Massimiliano

2013-01-01

Highlights: •We have performed molecular dynamics simulations of TEM-1 mutants. •Mutations effects on the mechanical properties are considered. •Mutants do not significantly alter the average enzymes structure. •Mutants produce sharp alterations in enzyme conformational repertoire. •Mutants also produce changes in the active site volume. -- Abstract: Molecular Dynamics simulations have been carried out in order to provide a molecular rationalization of the biological and thermodynamic differences observed for a class of TEM β-lactamases. In particular we have considered the TEM-1(wt), the single point mutants TEM-40 and TEM-19 representative of IRT and ESBL classes respectively, and TEM-1 mutant M182T, TEM-32 and TEM-20 which differ from the first three for the additional of M182T mutation. Results indicate that most of the thermodynamic, and probably biological behaviour of these systems arise from subtle effects which, starting from the alterations of the local interactions, produce drastic modifications of the conformational space spanned by the enzymes. The present study suggests that systems showing essentially the same secondary and tertiary structure may differentiate their chemical–biological activity essentially (and probably exclusively) on the basis of the thermal fluctuations occurring in their physiological environment

Signal Transduction and Molecular Targets of Selected Flavonoids

Science.gov (United States)

Bode, Ann M.

2013-01-01

Abstract Significance: Diet exerts a major influence on the risk for developing cancer and heart disease. Food factors such as flavonoids are alleged to protect cells from premature aging and disease by shielding DNA, proteins, and lipids from oxidative damage. Recent Advances: Our work has focused on clarifying the effects of dietary components on cancer cell proliferation and tumor growth, discovering mechanisms to explain the effects, and identifying the specific molecular targets of these compounds. Our strategy for identifying specific molecular targets of phytochemicals involves the use of supercomputer technology combined with protein crystallography, molecular biology, and experimental laboratory verification. Critical Issues: One of the greatest challenges for scientists is to reduce the accumulation of distortion and half truths reported in the popular media regarding the health benefits of certain foods or food supplements. The use of these is not new, but interest has increased dramatically because of perceived health benefits that are presumably acquired without unpleasant side effects. Flavonoids are touted to exert many beneficial effects in vitro. However, whether they can produce these effects in vivo is disputed. Future Directions: The World Health Organization indicates that one third of all cancer deaths are preventable and that diet is closely linked to prevention. Based on this idea and epidemiological findings, attention has centered on dietary phytochemicals as an effective intervention in cancer development. However, an unequivocal link between diet and cancer has not been established. Thus, identifying cancer preventive dietary agents with specific molecular targets is essential to move forward toward successful cancer prevention. Antioxid. Redox Signal. 19, 163–180. PMID:23458437

A Topic Space Oriented User Group Discovering Scheme in Social Network: A Trust Chain Based Interest Measuring Perspective

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Wang Dong

2016-01-01

Full Text Available Currently, user group has become an effective platform for information sharing and communicating among users in social network sites. In present work, we propose a single topic user group discovering scheme, which includes three phases: topic impact evaluation, interest degree measurement, and trust chain based discovering, to enable selecting influential topic and discovering users into a topic oriented group. Our main works include (1 an overview of proposed scheme and its related definitions; (2 topic space construction method based on topic relatedness clustering and its impact (influence degree and popularity degree evaluation; (3 a trust chain model to take user relation network topological information into account with a strength classification perspective; (4 an interest degree (user explicit and implicit interest degree evaluation method based on trust chain among users; and (5 a topic space oriented user group discovering method to group core users according to their explicit interest degrees and to predict ordinary users under implicit interest and user trust chain. Finally, experimental results are given to explain effectiveness and feasibility of our scheme.

Using Appreciative Inquiry to Discover and Deliver Change for Surgical Technology Students

Science.gov (United States)

Cabai, Katherine A.

2012-01-01

The purpose of this study was to examine efficacious teaching-learning strategies that community college stakeholders employ that enhance surgical technology student outcomes. Knowles's adult learning theory, constructivist theory, and appreciative inquiry served as the theoretical foundation for this study. Discovering effective aspects and…

M(o)TOR of aging: MTOR as a universal molecular hypothalamus.

Science.gov (United States)

Blagosklonny, Mikhail V

2013-07-01

A recent ground-breaking publication described hypothalamus-driven programmatic aging. As a Russian proverb goes "everything new is well-forgotten old". In 1958, Dilman proposed that aging and its related diseases are programmed by the hypothalamus. This theory, supported by beautiful experiments, remained unnoticed just to be re-discovered recently. Yet, it does not explain all manifestations of aging. And would organism age without hypothalamus? Do sensing pathways such as MTOR (mechanistic Target of Rapamycin) and IKK-beta play a role of a "molecular hypothalamus" in every cell? Are hypothalamus-driven alterations simply a part of quasi-programmed aging manifested by hyperfunction and secondary signal-resistance? Here are some answers.

Prospects for Ground-Based Detection and Follow-up of TESS-Discovered Exoplanets

Science.gov (United States)

Varakian, Matthew; Deming, Drake

2018-01-01

The Transiting Exoplanet Survey Satellite (TESS) will monitor over 200,000 main sequence dwarf stars for exoplanetary transits, with the goal of discovering small planets orbiting stars that are bright enough for follow-up observations. We here evaluate the prospects for ground-based transit detection and follow-up of the TESS-discovered planets. We focus particularly on the TESS planets that only transit once during each 27.4 day TESS observing window per region, and we calculate to what extent ground-based recovery of additional transits will be possible. Using simulated exoplanet systems from Sullivan et al. and assuming the use of a 60-cm telescope at a high quality observing site, we project the S/N ratios for transits of such planets. We use Phoenix stellar models for stars with surface temperatures from 2500K to 12000K, and we account for limb darkening, red atmospheric noise, and missed transits due to the day-night cycle and poor weather.

Characterization of Adelphocoris suturalis (Hemiptera: Miridae) Transcriptome from Different Developmental Stages

Science.gov (United States)

Tian, Caihong; Tek Tay, Wee; Feng, Hongqiang; Wang, Ying; Hu, Yongmin; Li, Guoping

2015-06-01

Adelphocoris suturalis is one of the most serious pest insects of Bt cotton in China, however its molecular genetics, biochemistry and physiology are poorly understood. We used high throughput sequencing platform to perform de novo transcriptome assembly and gene expression analyses across different developmental stages (eggs, 2nd and 5th instar nymphs, female and male adults). We obtained 20 GB of clean data and revealed 88,614 unigenes, including 23,830 clusters and 64,784 singletons. These unigene sequences were annotated and classified by Gene Ontology, Clusters of Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes databases. A large number of differentially expressed genes were discovered through pairwise comparisons between these developmental stages. Gene expression profiles were dramatically different between life stage transitions, with some of these most differentially expressed genes being associated with sex difference, metabolism and development. Quantitative real-time PCR results confirm deep-sequencing findings based on relative expression levels of nine randomly selected genes. Furthermore, over 791,390 single nucleotide polymorphisms and 2,682 potential simple sequence repeats were identified. Our study provided comprehensive transcriptional gene expression information for A. suturalis that will form the basis to better understanding of development pathways, hormone biosynthesis, sex differences and wing formation in mirid bugs.

Discovering Land Cover Web Map Services from the Deep Web with JavaScript Invocation Rules

Directory of Open Access Journals (Sweden)

Dongyang Hou

2016-06-01

Full Text Available Automatic discovery of isolated land cover web map services (LCWMSs can potentially help in sharing land cover data. Currently, various search engine-based and crawler-based approaches have been developed for finding services dispersed throughout the surface web. In fact, with the prevalence of geospatial web applications, a considerable number of LCWMSs are hidden in JavaScript code, which belongs to the deep web. However, discovering LCWMSs from JavaScript code remains an open challenge. This paper aims to solve this challenge by proposing a focused deep web crawler for finding more LCWMSs from deep web JavaScript code and the surface web. First, the names of a group of JavaScript links are abstracted as initial judgements. Through name matching, these judgements are utilized to judge whether or not the fetched webpages contain predefined JavaScript links that may prompt JavaScript code to invoke WMSs. Secondly, some JavaScript invocation functions and URL formats for WMS are summarized as JavaScript invocation rules from prior knowledge of how WMSs are employed and coded in JavaScript. These invocation rules are used to identify the JavaScript code for extracting candidate WMSs through rule matching. The above two operations are incorporated into a traditional focused crawling strategy situated between the tasks of fetching webpages and parsing webpages. Thirdly, LCWMSs are selected by matching services with a set of land cover keywords. Moreover, a search engine for LCWMSs is implemented that uses the focused deep web crawler to retrieve and integrate the LCWMSs it discovers. In the first experiment, eight online geospatial web applications serve as seed URLs (Uniform Resource Locators and crawling scopes; the proposed crawler addresses only the JavaScript code in these eight applications. All 32 available WMSs hidden in JavaScript code were found using the proposed crawler, while not one WMS was discovered through the focused crawler

Molecular and morphological diversity of pezizalean ectomycorrhiza

DEFF Research Database (Denmark)

Tedersoo, Leho; Hansen, Karen; Perry, Brian A

2006-01-01

A growing body of molecular research is discovering a high diversity of pezizalean ectomycorrhiza (EcM), yet most remain unidentified at the genus or species level. This study describes EcM-forming taxa within the Pezizales. EcM-forming Pezizales were revealed by morphotyping and sequencing of EcM...... root tips from forests in Estonia and Denmark. The taxa on EcM root tips were identified using phylogenetic analyses of large-subunit rDNA sequences derived from sporocarps of 301 pezizalean species, and comparisons with internal transcribed spacer rDNA sequences. Thirty-three species are suggested...... as EcM symbionts, representing all three major clades of Pezizales, the genera Genea, Geopora, Humaria, Tarzetta, Trichophaea, Wilcoxina, Helvella, Hydnotrya, Tuber, Pachyphloeus, Peziza and Sarcosphaera, and two Pezizaceae anamorphs. EcM of Pezizales species are easily distinguished by their anatomy...

Milestone in the NTB phase investigation and beyond: direct insight into molecular self-assembly.

Science.gov (United States)

Ivšić, Trpimir; Vinković, Marijana; Baumeister, Ute; Mikleušević, Ana; Lesac, Andreja

2014-12-14

Although liquid-crystalline materials are most widely exploited for flat-panel displays, their ability to self-organize into periodically ordered nanostructures gives rise to a broad variety of additional applications. The recently discovered low-temperature nematic phase (N(TB)) with unusual characteristics generated considerable attention within the scientific community: despite the fact that the molecules from which the phase is composed are not chiral, the helicoidal structure of the phase is strongly implicated. Here we report on combined experimental, computational and spectroscopic studies of the structural aspects influencing formation of the N(TB) phase as well as on the molecular organization within the phase. In an extensive DFT study, the structure-property prerequisite was traced to a "bent-propeller" shape of the molecule. We also demonstrate the first utilization of liquid state NMR for direct analysis of intermolecular interactions within thermotropic liquid-crystalline phases, providing new insight into molecular packing that can lead towards design of novel chiral functional materials. The synergy of experimental, computational and NMR studies suggests a syn-parallel helical molecular organization within the N(TB) phase.

Leishmania infections: Molecular targets and diagnosis.

Science.gov (United States)

Akhoundi, Mohammad; Downing, Tim; Votýpka, Jan; Kuhls, Katrin; Lukeš, Julius; Cannet, Arnaud; Ravel, Christophe; Marty, Pierre; Delaunay, Pascal; Kasbari, Mohamed; Granouillac, Bruno; Gradoni, Luigi; Sereno, Denis

2017-10-01

Progress in the diagnosis of leishmaniases depends on the development of effective methods and the discovery of suitable biomarkers. We propose firstly an update classification of Leishmania species and their synonymies. We demonstrate a global map highlighting the geography of known endemic Leishmania species pathogenic to humans. We summarize a complete list of techniques currently in use and discuss their advantages and limitations. The available data highlights the benefits of molecular markers in terms of their sensitivity and specificity to quantify variation from the subgeneric level to species complexes, (sub) species within complexes, and individual populations and infection foci. Each DNA-based detection method is supplied with a comprehensive description of markers and primers and proposal for a classification based on the role of each target and primer in the detection, identification and quantification of leishmaniasis infection. We outline a genome-wide map of genes informative for diagnosis that have been used for Leishmania genotyping. Furthermore, we propose a classification method based on the suitability of well-studied molecular markers for typing the 21 known Leishmania species pathogenic to humans. This can be applied to newly discovered species and to hybrid strains originating from inter-species crosses. Developing more effective and sensitive diagnostic methods and biomarkers is vital for enhancing Leishmania infection control programs. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Docosahexaenoate-containing molecular species of glycerophospholipids from frog retinal rod outer segments show different rates of biosynthesis and turnover

International Nuclear Information System (INIS)

Louie, K.; Wiegand, R.D.; Anderson, R.E.

1988-01-01

The authors have studied the de novo synthesis and subsequent turnover of major docosahexaenoate-containing molecular species in frog rod outer segment (ROS) phospholipids following intravitreal injection of [2- 3 H]glycerol. On selected days after injection, ROS were prepared and phospholipids extracted. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS) were isolated and converted to diradylglycerols with phospholipase C. Diradylglycerols were derivatized with benzoic anhydride and resolve into diacylglycerobenzoates and ether-linked glycerobenzoates. The diacylglycerobenzoates were fractionated into molecular species by HPLC, quantitated, and counted for radioactivity. Label was incorporated into ROS phospholipids by day 1 and was followed up through the eighth day. The dipolyenoic species 22:6-22:6 from PC showed 1 3-5 times higher radiospecific activity than the same species from either PE or PS. The rate of decline was determined by calculating the half-life of each molecular species, which was used as a measure of the turnover of the species. The percent distribution of radioactivity in the molecular species of PC and PE was quite different from the relative mass distribution at day 1. However, percent dpm approached the mole percent by 31 days. In PS, percent dpm and mole percent were the same at all time points. These results indicate that the molecular species composition of PC and PE in frog retinal ROS is determined by a combination of factors, which include rate of synthesis, rate of degradation, and selective interconversions. In contrast, PS composition appears to be determined at the time of synthesis

Organic-based molecular switches for molecular electronics.

Science.gov (United States)

Fuentes, Noelia; Martín-Lasanta, Ana; Alvarez de Cienfuegos, Luis; Ribagorda, Maria; Parra, Andres; Cuerva, Juan M

2011-10-05

In a general sense, molecular electronics (ME) is the branch of nanotechnology which studies the application of molecular building blocks for the fabrication of electronic components. Among the different types of molecules, organic compounds have been revealed as promising candidates for ME, due to the easy access, great structural diversity and suitable electronic and mechanical properties. Thanks to these useful capabilities, organic molecules have been used to emulate electronic devices at the nanoscopic scale. In this feature article, we present the diverse strategies used to develop organic switches towards ME with special attention to non-volatile systems.

Molecular differences between deuterated and protonated polystyrenes using reversed-phase high-performance liquid chromatography.

Science.gov (United States)

Kayillo, Sindy; Gray, Michael J; Shalliker, R Andrew; Dennis, Gary R

2005-05-06

Isotopic substitution is a technique used to highlight particular bonds within a molecule for kinetic, spectroscopic and structure analysis. It is presumed that although some properties such as stretching frequencies will not be the same for substituted analogues, the chemical interactions will not vary appreciably as a function of labelling. Reversed-phase liquid chromatography has been used to demonstrate that there are significant differences between the chromatographic behaviour of a sequence of deuterated and protonated oligomeric polystyrenes. Two-dimensional reversed-phase liquid chromatography was used to show that even the diasteromers of the oligomers (n = 5) have retention mechanisms that are dependent on the subtle changes to the molecular conformation and electronic structure, which are a consequence of deuteration.

Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems.

Science.gov (United States)

Hudson, Phillip S; Woodcock, H Lee; Boresch, Stefan

2015-12-03

Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on using "indirect" thermodynamic cycles to connect "low level" simulation results to "high level" free energies. The main obstacle to computing converged free energy results between molecular mechanical (MM) and QM (ΔA(MM→QM)), as recently demonstrated by us and others, is differences in the so-called "stiff" degrees of freedom (e.g., bond stretching) between the respective energy surfaces. Herein, we demonstrate that this problem can be efficiently circumvented using nonequilibrium work (NEW) techniques, i.e., Jarzynski's and Crooks' equations. Initial applications of computing ΔA(NEW)(MM→QM), for blocked amino acids alanine and serine as well as to generate butane's potentials of mean force via the indirect QM/MM FES method, showed marked improvement over traditional FES approaches.

Function and application of a non-ester-hydrolyzing carboxylesterase discovered in tulip.

Science.gov (United States)

Nomura, Taiji

2017-01-01

Plants have evolved secondary metabolite biosynthetic pathways of immense rich diversity. The genes encoding enzymes for secondary metabolite biosynthesis have evolved through gene duplication followed by neofunctionalization, thereby generating functional diversity. Emerging evidence demonstrates that some of those enzymes catalyze reactions entirely different from those usually catalyzed by other members of the same family; e.g. transacylation catalyzed by an enzyme similar to a hydrolytic enzyme. Tuliposide-converting enzyme (TCE), which we recently discovered from tulip, catalyzes the conversion of major defensive secondary metabolites, tuliposides, to antimicrobial tulipalins. The TCEs belong to the carboxylesterase family in the α/β-hydrolase fold superfamily, and specifically catalyze intramolecular transesterification, but not hydrolysis. This non-ester-hydrolyzing carboxylesterase is an example of an enzyme showing catalytic properties that are unpredictable from its primary structure. This review describes the biochemical and physiological aspects of tulipalin biogenesis, and the diverse functions of plant carboxylesterases in the α/β-hydrolase fold superfamily.

Molecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers

KAUST Repository

Kandeel, Mahmoud

2018-05-17

Structural studies related to Middle East Respiratory Syndrome Coronavirus (MERS CoV) infection process are so limited. In this study, molecular dynamics (MD) simulation was carried out to unravel changes in the MERS CoV heptad repeat domains (HRs) and factors affecting fusion state HR stability. Results indicated that HR trimer is more rapidly stabilized, having stable system energy and lowest root mean square deviations (RMSDs). While trimers were the predominant active form of CoVs HR, monomers were also discovered in both of viral and cellular membranes. In order to find the differences between S2 monomer and trimer molecular dynamics, S2 monomer were modelled and subjected to MD simulation. In contrast to S2 trimer, S2 monomer was unstable, having high RMSDs with major drifts above 8 Å. Fluctuation of HR residue positions revealed major changes in the C-terminal of HR2 and the linker coil between HR1 and HR2 in both monomer and trimer. Hydrophobic residues at the “a” and “d” positions of HR helices stabilize the whole system, having minimal changes in RMSD. The global distance test and contact area difference scores support instability of MERS CoV S2 monomer. Analysis of HR1-HR2 inter-residue contacts and interaction energy revealed three different energy scales along HR helices. Two strong interaction energies were identified at the start of the HR2 helix and at the C-terminal of HR2. The identified critical residues by MD simulation and residues at a and d position of HR helix were strong stabilizers of HRs recognition.

Incidentally found and unexpected tumors discovered by MRI examination for temporomandibular joint arthrosis

International Nuclear Information System (INIS)

Yanagi, Yoshinobu; Asaumi, Jun-ichi; Maki, Yuu; Murakami, Jun; Hisatomi, Miki; Matsuzaki, Hidenobu; Konouchi, Hironobu; Honda, Yosutoshi; Kishi, Kanji

2003-01-01

We examined the frequency of incidentally found or unexpected tumors discovered at the time of magnetic resonance imaging (MRI) examinations in the temporomandibular joint (TMJ) region for patients with suspicion of TMJ arthrosis. Five MR images (T1-weighted transverse scout image and proton density and T2-weighted oblique sagittal images at the open and closed mouth) were acquired. In 2776 MRI examinations of TMJ arthrosis, two tumors were discovered. They consisted of an adenoid cystic carcinoma in the deep portion of the parotid gland, and a malignant tumor extending from the infratemporal fossa to the parapharyngeal space. The rate of incidentally founded or unexpected tumors in TMJ examinations was low (0.072%), but the two tumors found were malignant tumors, and therefore, scout image should be carefully examined, not only used for positing the slice

Incidentally found and unexpected tumors discovered by MRI examination for temporomandibular joint arthrosis

Energy Technology Data Exchange (ETDEWEB)

Yanagi, Yoshinobu; Asaumi, Jun-ichi E-mail: asaumi@md.okayama-u.ac.jp; Maki, Yuu; Murakami, Jun; Hisatomi, Miki; Matsuzaki, Hidenobu; Konouchi, Hironobu; Honda, Yosutoshi; Kishi, Kanji

2003-07-01

We examined the frequency of incidentally found or unexpected tumors discovered at the time of magnetic resonance imaging (MRI) examinations in the temporomandibular joint (TMJ) region for patients with suspicion of TMJ arthrosis. Five MR images (T1-weighted transverse scout image and proton density and T2-weighted oblique sagittal images at the open and closed mouth) were acquired. In 2776 MRI examinations of TMJ arthrosis, two tumors were discovered. They consisted of an adenoid cystic carcinoma in the deep portion of the parotid gland, and a malignant tumor extending from the infratemporal fossa to the parapharyngeal space. The rate of incidentally founded or unexpected tumors in TMJ examinations was low (0.072%), but the two tumors found were malignant tumors, and therefore, scout image should be carefully examined, not only used for positing the slice.

Molecular biology of the blood-brain and the blood-cerebrospinal fluid barriers: similarities and differences

Directory of Open Access Journals (Sweden)

Redzic Zoran

2011-01-01

differences in their expression between the two barriers. Also, many blood-borne molecules and xenobiotics can diffuse into brain ISF and then into neuronal membranes due to their physicochemical properties. Entry of these compounds could be detrimental for neural transmission and signalling. Thus, BBB and BCSFB express transport proteins that actively restrict entry of lipophilic and amphipathic substances from blood and/or remove those molecules from the brain extracellular fluids. The third part of this review concentrates on the molecular biology of ATP-binding cassette (ABC-transporters and those SLC transporters that are involved in efflux transport of xenobiotics, their expression at the BBB and BCSFB and differences in expression in the two major blood-brain interfaces. In addition, transport and diffusion of ions by the BBB and CP epithelium are involved in the formation of fluid, the ISF and CSF, respectively, so the last part of this review discusses molecular biology of ion transporters/exchangers and ion channels in the brain endothelial and CP epithelial cells.

Discover Earth: An earth system science program for libraries and their communities

Science.gov (United States)

Curtis, L.; Dusenbery, P.

2010-12-01

The view from space has deepened our understanding of Earth as a global, dynamic system. Instruments on satellites and spacecraft, coupled with advances in ground-based research, have provided us with astonishing new perspectives of our planet. Now more than ever, enhancing the public’s understanding of Earth’s physical and biological systems is vital to helping citizens make informed policy decisions especially when they are faced with the consequences of global climate change. In spite of this relevance, there are many obstacles to achieving broad public understanding of key earth system science (ESS) concepts. Strategies for addressing climate change can only succeed with the full engagement of the general public. As reported by U.S. News and World Report in 2010, small towns in rural America are emerging as the front line in the climate change debate in the country. The Space Science Institute’s National Center for Interactive Learning (NCIL) in partnership with the American Library Association (ALA), the Lunar and Planetary Institute (LPI), and the National Girls Collaborative Project (NGCP) have received funding from NSF to develop a national project called the STAR Library Education Network: a hands-on learning program for libraries and their communities (or STAR-Net for short). STAR stands for Science-Technology, Activities and Resources. There are two distinct components of STAR-Net: Discover Earth and Discover Tech. While the focus for education reform is on school improvement, there is considerable research that supports the role that out-of-school experiences can play in student achievement. Libraries provide an untapped resource for engaging underserved youth and their families in fostering an appreciation and deeper understanding of science and technology topics. The overarching goal of the project is to reach underserved youth and their families with informal STEM learning experiences. The Discover Earth part of STAR_Net will produce ESS

Discovering beaten paths in collaborative ontology-engineering projects using Markov chains.

Science.gov (United States)

Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A; Noy, Natalya F

2014-10-01

Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50,000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology

Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains

Science.gov (United States)

Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A.; Noy, Natalya F.

2014-01-01

Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50, 000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology

Caracterização molecular de populações do nematóide-de-cisto-da-soja com diferentes índices de parasitismo na cultivar Hartwig Molecular characterization of soybean cyst nematode populations with different parasitism index to the Hartwig cultivar

Directory of Open Access Journals (Sweden)

Ricardo Vilela Abdelnoor

2001-02-01

Full Text Available Recentemente, foi descoberta uma raça do nematóide-de-cisto-da-soja (NCS; Heterodera glycines que apresentou a capacidade de quebrar a resistência da cultivar Hartwig, até então considerada resistente a todas as raças conhecidas do nematóide. Essa população foi coletada no Município de Sorriso, Estado do Mato Grosso, e foi caracterizada como raça 4. Para verificar a diversidade genética entre esta e outras populações pertencentes às raças 4 e 9, foi feita uma caracterização molecular pela técnica de marcadores moleculares RAPD. Foram utilizadas nove populações do NCS, das quais quatro apresentavam a capacidade de parasitar 'Hartwig'. Foi verificado que as populações capazes de parasitar 'Hartwig' foram bastante diferentes das demais. Por meio de análise de agrupamento, com base nas distâncias genéticas encontradas, foram obtidos três grupos: o primeiro, constituído por indivíduos classificados como raça 4, mas que não parasitam 'Hartwig'; o segundo, constituído por quatro populações capazes de parasitar 'Hartwig', e o terceiro, por apenas uma população, classificado como raça 9, e que também não parasita 'Hartwig'. Este estudo confirmou que a população de NCS, encontrada em Sorriso, é geneticamente distinta das demais populações da raça 4 encontradas e constitui uma nova raça, denominada 4+.Recently, a new race of soybean cyst nematode (SCN (Heterodera glycines was discovered, which breaks the resistance of cultivar Hartwig, resistant to all known races of SCN. This population was obtained from soybean plants collected in the Sorriso county, state of Mato Grosso, Brazil, and is characterized as race 4. To verify if this isolate was different from others classified as races 4 and 9, their genetic diversity was analyzed by using the RAPD technique. Nine populations of SCN were analyzed, and only four populations were able to parasitize soybean plants cultivar Hartwig. Based on this study, it was

'Ogura'-based 'CMS' lines with different nuclear backgrounds of cabbage revealed substantial diversity at morphological and molecular levels.

Science.gov (United States)

Parkash, Chander; Kumar, Sandeep; Singh, Rajender; Kumar, Ajay; Kumar, Satish; Dey, Shyam Sundar; Bhatia, Reeta; Kumar, Raj

2018-01-01

A comprehensive study on characterization and genetic diversity analysis was carried out in 16 'Ogura'-based 'CMS' lines of cabbage using 14 agro-morphological traits and 29 SSR markers. Agro-morphological characterization depicted considerable variations for different horticultural traits studied. The genotype, ZHA-2, performed better for most of the economically important quantitative traits. Further, gross head weight (0.76), head length (0.60) and head width (0.83) revealed significant positive correlation with net head weight. Dendrogram based on 10 quantitative traits exhibited considerable diversity among different CMS lines and principle component analysis (PCA) indicated that net and gross head weight, and head length and width are the main components of divergence between 16 CMS lines of cabbage. In molecular study, a total of 58 alleles were amplified by 29 SSR primers, averaging to 2.0 alleles in each locus. High mean values of Shannon's Information index (0.62), expected (0.45) and observed (0.32) heterozygosity and polymorphic information content (0.35) depicted substantial polymorphism. Dendrogram based on Jaccard's similarity coefficient constructed two major groups and eight sub-groups, which revealed substantial diversity among different CMS lines. In overall, based on agro-morphological and molecular studies genotype RRMA, ZHA-2 and RCA were found most divergent. Hence, they have immense potential in future breeding programs for the high-yielding hybrid development in cabbage.

Molecular Stirrers in Action

NARCIS (Netherlands)

Chen, Jiawen; Kistemaker, Jos C. M.; Robertus, Jort; Feringa, Ben L.

2014-01-01

A series of first-generation light-driven molecular motors with rigid substituents of varying length was synthesized to act as "molecular stirrers". Their rotary motion was studied by H-1 NMR and UV-vis absorption spectroscopy in a variety of solvents with different polarity and viscosity.

Aux/IAA Gene Family in Plants: Molecular Structure, Regulation, and Function

Directory of Open Access Journals (Sweden)

Jie Luo

2018-01-01

Full Text Available Auxin plays a crucial role in the diverse cellular and developmental responses of plants across their lifespan. Plants can quickly sense and respond to changes in auxin levels, and these responses involve several major classes of auxin-responsive genes, including the Auxin/Indole-3-Acetic Acid (Aux/IAA family, the auxin response factor (ARF family, small auxin upregulated RNA (SAUR, and the auxin-responsive Gretchen Hagen3 (GH3 family. Aux/IAA proteins are short-lived nuclear proteins comprising several highly conserved domains that are encoded by the auxin early response gene family. These proteins have specific domains that interact with ARFs and inhibit the transcription of genes activated by ARFs. Molecular studies have revealed that Aux/IAA family members can form diverse dimers with ARFs to regulate genes in various ways. Functional analyses of Aux/IAA family members have indicated that they have various roles in plant development, such as root development, shoot growth, and fruit ripening. In this review, recently discovered details regarding the molecular characteristics, regulation, and protein–protein interactions of the Aux/IAA proteins are discussed. These details provide new insights into the molecular basis of the Aux/IAA protein functions in plant developmental processes.

Chemical Abundance Measurements of Ultra-Faint Dwarf Galaxies Discovered by the Dark Energy Survey

Science.gov (United States)

Nagasawa, Daniel; Marshall, Jennifer L.; Simon, Joshua D.; Hansen, Terese; Li, Ting; Bernstein, Rebecca; Balbinot, Eduardo; Drlica-Wagner, Alex; Pace, Andrew; Strigari, Louis; Pellegrino, Craig; DePoy, Darren L.; Suntzeff, Nicholas; Bechtol, Keith; Dark Energy Suvey

2018-01-01

We present chemical abundance analysis results derived from high-resolution spectroscopy of ultra-faint dwarfs discovered by the Dark Energy Survey. Ultra-faint dwarf galaxies preserve a fossil record of the chemical abundance patterns imprinted by the first stars in the Universe. High-resolution spectroscopic observations of member stars in several recently discovered Milky Way satellites reveal a range of abundance patterns among ultra-faint dwarfs suggesting that star formation processes in the early Universe were quite diverse. The chemical content provides a glimpse not only of the varied nucleosynthetic processes and chemical history of the dwarfs themselves, but also the environment in which they were formed. We present the chemical abundance analysis of these objects and discuss possible explanations for the observed abundance patterns.

Molecular ultrasound imaging: current status and future directions

International Nuclear Information System (INIS)

Deshpande, N.; Needles, A.; Willmann, J.K.

2010-01-01

Targeted contrast-enhanced ultrasound (molecular ultrasound) is an emerging imaging strategy that combines ultrasound technology with novel molecularly-targeted ultrasound contrast agents for assessing biological processes at the molecular level. Molecular ultrasound contrast agents are nano- or micro-sized particles that are targeted to specific molecular markers by adding high-affinity binding ligands onto the surface of the particles. Following intravenous administration, these targeted ultrasound contrast agents accumulate at tissue sites overexpressing specific molecular markers, thereby enhancing the ultrasound imaging signal. High spatial and temporal resolution, real-time imaging, non-invasiveness, relatively low costs, lack of ionising irradiation and wide availability of ultrasound systems are advantages compared to other molecular imaging modalities. In this article we review current concepts and future directions of molecular ultrasound imaging, including different classes of molecular ultrasound contrast agents, ongoing technical developments of pre-clinical and clinical ultrasound systems, the potential of molecular ultrasound for imaging different diseases at the molecular level, and the translation of molecular ultrasound into the clinic.

The intellectual capacity of patients with Laron syndrome (LS) differs with various molecular defects of the growth hormone receptor gene. Correlation with CNS abnormalities.

Science.gov (United States)

Shevah, O; Kornreich, L; Galatzer, A; Laron, Z

2005-12-01

The correlation between the molecular defects of the GH receptor (R), psychosocial development and brain abnormalities were evaluated in 10 patients with Laron syndrome (LS), in whom all data were available. The findings revealed that the intelligence quotient (IQ) and abnormalities in the brain of the patients with LS differ with various molecular defects of the GH-receptor. The most severe mental deficits and brain pathology occurred in patients with 3, 5, 6 exon deletion. Patients with point mutations in exons 2, 4 and 7 presented various degrees of medium to mild CNS abnormalities that correlated with the IQ. Notably, the patient with the E180 splice mutation in exon 6 had a normal IQ, which fits the report on normal IQ in a large Ecuadorian cohort with the same mutation. This is the first report to support a correlation between IQ, brain abnormalities and localization of the molecular defects in the GH-R gene. As all patients with LS are IGF-I-deficient, it must be assumed that other as yet unknown factors related to the molecular defects in the GH-R are the major cause of the differences in intellect and brain abnormalities.

Inner solar system material discovered in the Oort cloud.

Science.gov (United States)

Meech, Karen J; Yang, Bin; Kleyna, Jan; Hainaut, Olivier R; Berdyugina, Svetlana; Keane, Jacqueline V; Micheli, Marco; Morbidelli, Alessandro; Wainscoat, Richard J

2016-04-01

We have observed C/2014 S3 (PANSTARRS), a recently discovered object on a cometary orbit coming from the Oort cloud that is physically similar to an inner main belt rocky S-type asteroid. Recent dynamical models successfully reproduce the key characteristics of our current solar system; some of these models require significant migration of the giant planets, whereas others do not. These models provide different predictions on the presence of rocky material expelled from the inner solar system in the Oort cloud. C/2014 S3 could be the key to verifying these predictions of the migration-based dynamical models. Furthermore, this object displays a very faint, weak level of comet-like activity, five to six orders of magnitude less than that of typical ice-rich comets on similar Orbits coming from the Oort cloud. For the nearly tailless appearance, we are calling C/2014 S3 a Manx object. Various arguments convince us that this activity is produced by sublimation of volatile ice, that is, normal cometary activity. The activity implies that C/2014 S3 has retained a tiny fraction of the water that is expected to be present at its formation distance in the inner solar system. We may be looking at fresh inner solar system Earth-forming material that was ejected from the inner solar system and preserved for billions of years in the Oort cloud.

Unified Photo Enhancement by Discovering Aesthetic Communities From Flickr.

Science.gov (United States)

Hong, Richang; Zhang, Luming; Tao, Dacheng

2016-03-01

Photo enhancement refers to the process of increasing the aesthetic appeal of a photo, such as changing the photo aspect ratio and spatial recomposition. It is a widely used technique in the printing industry, graphic design, and cinematography. In this paper, we propose a unified and socially aware photo enhancement framework which can leverage the experience of photographers with various aesthetic topics (e.g., portrait and landscape). We focus on photos from the image hosting site Flickr, which has 87 million users and to which more than 3.5 million photos are uploaded daily. First, a tagwise regularized topic model is proposed to describe the aesthetic topic of each Flickr user, and coherent and interpretable topics are discovered by leveraging both the visual features and tags of photos. Next, a graph is constructed to describe the similarities in aesthetic topics between the users. Noticeably, densely connected users have similar aesthetic topics, which are categorized into different communities by a dense subgraph mining algorithm. Finally, a probabilistic model is exploited to enhance the aesthetic attractiveness of a test photo by leveraging the photographic experiences of Flickr users from the corresponding communities of that photo. Paired-comparison-based user studies show that our method performs competitively on photo retargeting and recomposition. Moreover, our approach accurately detects aesthetic communities in a photo set crawled from nearly 100000 Flickr users.

Use of the Culture Care Theory and ethnonursing method to discover how nursing faculty teach culture care.

Science.gov (United States)

Mixer, Sandra J

2008-04-01

As the world becomes increasingly multicultural, transcultural nursing education is critical to ensuring a culturally competent workforce. This paper presents a comprehensive review of literature and results of an ethnonursing pilot study using the Culture Care Theory (CCT) to discover how nursing faculty teach culture care. The literature revealed that despite 50 years of transcultural nursing knowledge development through theory, research and practice, there remains a lack of formal, integrated culture education in nursing. The importance of faculty providing generic and professional care to nursing students and using an organising framework to teach culture care was discovered. Additionally, care was essential for faculty health and well-being to enable faculty to teach culture care. This unique use of the theory and method demonstrates its usefulness in discovering and describing the complex nature of teaching culture care. Larger scale studies are predicted to further substantiate the CCT, building the discipline of nursing.

Cultural diversity in heart failure management: findings from the DISCOVER study (Part 2).

Science.gov (United States)

Davidson, Patricia M; Macdonald, Peter; Moser, Debra K; Ang, Esther; Paull, Glenn; Choucair, Sam; Daly, John; Gholizadeh, Leila; Dracup, Kathleen

2007-01-01

Self-management is a critical dimension in managing chronic conditions, particularly in heart failure (HF). Knowledge, attitudes and beliefs, relating to both illness and wellness, are strongly influenced by culture and ethnicity, impacting upon an individual's capacity to engage in self-care behaviours. Effective management of HF is largely dependent on facilitation of culturally informed, self-care behaviours to increase adherence to both pharmacological and non-pharmacological strategies. The Understanding the cultural experiences of individuals with chronic heart failure (CHF) in South East Health (DISCOVER) study is an exploratory, observational study investigating health patterns, information needs and the adjustment process for overseas-born people with HF living in Australia. An integrative literature review was augmented by qualitative data derived from key informant interviews, focus groups and individual interviews. A key finding of this study is that culture provides an important context to aid interpretations of attitudes, values, beliefs and behaviours, not only in illness but in health. While individual differences in attitudes and beliefs were observed among participants, common themes and issues were identified across cultural groups. Data from the DISCOVER study revealed the primacy of family and kinship ties. These relationships were important in making decisions about treatment choices and care plans. Participants also revealed the critical role of the 'family doctor' in assisting people and their families in brokering the health care system. In this study, heart disease was considered to be a significant condition but cancer was the condition that people both feared and dreaded the most, despite the high mortality rates of HF. This sample reported that religious and traditional beliefs became more important as people aged and considered their mortality. As HF is predominately a condition of ageing, the information derived from this study will

MOLECULAR OXYGEN IN OORT CLOUD COMET 1P/HALLEY

Energy Technology Data Exchange (ETDEWEB)

Rubin, M.; Altwegg, K. [Physikalisches Institut, University of Bern, Sidlerstrasse 5, CH-3012 Bern (Switzerland); Dishoeck, E. F. van [Leiden Observatory, Leiden University, P.O. Box 9513, 2300 RA Leiden (Netherlands); Schwehm, G. [ESA (retired) Science Operations Department, ESTEC, Keplerlaan 1, 2201 AZ Noordwijk (Netherlands)

2015-12-10

Recently, the ROSINA mass spectrometer suite on board the European Space Agency's Rosetta spacecraft discovered an abundant amount of molecular oxygen, O{sub 2}, in the coma of Jupiter family comet 67P/Churyumov–Gerasimenko of O{sub 2}/H{sub 2}O = 3.80 ± 0.85%. It could be shown that O{sub 2} is indeed a parent species and that the derived abundances point to a primordial origin. Crucial questions are whether the O{sub 2} abundance is peculiar to comet 67P/Churyumov–Gerasimenko or Jupiter family comets in general, and also whether Oort cloud comets such as comet 1P/Halley contain similar amounts of molecular oxygen. We investigated mass spectra obtained by the Neutral Mass Spectrometer instrument during the flyby by the European Space Agency's Giotto probe of comet 1P/Halley. Our investigation indicates that a production rate of O{sub 2} of 3.7 ± 1.7% with respect to water is indeed compatible with the obtained Halley data and therefore that O{sub 2} might be a rather common and abundant parent species.

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

NARCIS (Netherlands)

Dutilh, Bas E; Cassman, Noriko; McNair, Katelyn; Sanchez, Savannah E; Silva, Genivaldo G Z; Boling, Lance; Barr, Jeremy J; Speth, Daan R; Seguritan, Victor; Aziz, Ramy K; Felts, Ben; Dinsdale, Elizabeth A; Mokili, John L; Edwards, Robert A

2014-01-01

Metagenomics, or sequencing of the genetic material from a complete microbial community, is a promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many unknown sequences. Here we describe the discovery of a previously unidentified bacteriophage present in the

Risk Differences Between Prediabetes And Diabetes According To Breast Cancer Molecular Subtypes.

Science.gov (United States)

Crispo, A; Augustin, L S A; Grimaldi, M; Nocerino, F; Giudice, A; Cavalcanti, E; Di Bonito, M; Botti, G; De Laurentiis, M; Rinaldo, M; Esposito, E; Riccardi, G; Amore, A; Libra, M; Ciliberto, G; Jenkins, D J A; Montella, M

2017-05-01

Hyperglycemia and hyperinsulinemia may play a role in breast carcinogenesis and prediabetes and diabetes have been associated with increased breast cancer (BC) risk. However, whether BC molecular subtypes may modify these associations is less clear. We therefore investigated these associations in all cases and by BC molecular subtypes among women living in Southern Italy. Cases were 557 patients with non-metastatic incident BC and controls were 592 outpatients enrolled during the same period as cases and in the same hospital for skin-related non-malignant conditions. Adjusted multivariate logistic regression models were built to assess the risks of developing BC in the presence of prediabetes or diabetes. The analyses were repeated by strata of BC molecular subtypes: Luminal A, Luminal B, HER2+, and Triple Negative (TN). Prediabetes and diabetes were significantly associated with higher BC incidence after controlling for known risk factors (OR = 1.94, 95% CI 1.32-2.87 and OR = 2.46, 95% CI 1.38-4.37, respectively). Similar results were seen in Luminal A and B while in the TN subtype only prediabetes was associated with BC (OR = 2.43, 95% CI 1.11-5.32). Among HER2+ patients, only diabetes was significantly associated with BC risk (OR = 3.04, 95% CI 1.24-7.47). Furthermore, when postmenopausal HER2+ was split into hormone receptor positive versus negative, the association with diabetes remained significant only in the former (OR = 5.13, 95% CI 1.53-17.22). These results suggest that prediabetes and diabetes are strongly associated with BC incidence and that these metabolic conditions may be more relevant in the presence of breast cancer molecular subtypes with positive hormone receptors. J. Cell. Physiol. 232: 1144-1150, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Agent-Based Modeling in Molecular Systems Biology.

Science.gov (United States)

Soheilypour, Mohammad; Mofrad, Mohammad R K

2018-06-08

Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

How Secondary and Tertiary Amide Moieties are Molecular Stations for Dibenzo-24-crown-8 in [2]Rotaxane Molecular Shuttles?

Science.gov (United States)

Riss-Yaw, Benjamin; Morin, Justine; Clavel, Caroline; Coutrot, Frédéric

2017-11-21

Interlocked molecular machines like [2]rotaxanes are intriguing aesthetic molecules. The control of the localization of the macrocycle, which surrounds a molecular axle, along the thread leads to translational isomers of very different properties. Although many moieties have been used as sites of interactions for crown ethers, the very straightforwardly obtained amide motif has more rarely been envisaged as molecular station. In this article, we report the use of secondary and tertiary amide moieties as efficient secondary molecular station in pH-sensitive molecular shuttles. Depending on the N -substitution of the amide station, and on deprotonation or deprotonation-carbamoylation, the actuation of the molecular machinery differs accordingly to very distinct interactions between the axle and the DB24C8.

In vitro studies of PEG thin films with different molecular weights deposited by MAPLE

DEFF Research Database (Denmark)

Paun, Irina Alexandra; Ion, Valentin; Luculescu, Catalin-Romeo

2012-01-01

and their behavior in vitro. Thus, immersion in PBS induced swelling of the PEG films, which was more pronounced for PEG polymers of higher molecular weight. Prior to immersion in PBS, the PEG films of higher molecular weight were more hydrophilic, the water contact angles decreasing from ∼66 grd for PEG400 to ∼41...

TBX3 regulates splicing in vivo: a novel molecular mechanism for Ulnar-mammary syndrome.

Directory of Open Access Journals (Sweden)

Pavan Kumar P

2014-03-01

Full Text Available TBX3 is a member of the T-box family of transcription factors with critical roles in development, oncogenesis, cell fate, and tissue homeostasis. TBX3 mutations in humans cause complex congenital malformations and Ulnar-mammary syndrome. Previous investigations into TBX3 function focused on its activity as a transcriptional repressor. We used an unbiased proteomic approach to identify TBX3 interacting proteins in vivo and discovered that TBX3 interacts with multiple mRNA splicing factors and RNA metabolic proteins. We discovered that TBX3 regulates alternative splicing in vivo and can promote or inhibit splicing depending on context and transcript. TBX3 associates with alternatively spliced mRNAs and binds RNA directly. TBX3 binds RNAs containing TBX binding motifs, and these motifs are required for regulation of splicing. Our study reveals that TBX3 mutations seen in humans with UMS disrupt its splicing regulatory function. The pleiotropic effects of TBX3 mutations in humans and mice likely result from disrupting at least two molecular functions of this protein: transcriptional regulation and pre-mRNA splicing.

TBX3 regulates splicing in vivo: a novel molecular mechanism for Ulnar-mammary syndrome.

Science.gov (United States)

Kumar P, Pavan; Franklin, Sarah; Emechebe, Uchenna; Hu, Hao; Moore, Barry; Lehman, Chris; Yandell, Mark; Moon, Anne M

2014-03-01

TBX3 is a member of the T-box family of transcription factors with critical roles in development, oncogenesis, cell fate, and tissue homeostasis. TBX3 mutations in humans cause complex congenital malformations and Ulnar-mammary syndrome. Previous investigations into TBX3 function focused on its activity as a transcriptional repressor. We used an unbiased proteomic approach to identify TBX3 interacting proteins in vivo and discovered that TBX3 interacts with multiple mRNA splicing factors and RNA metabolic proteins. We discovered that TBX3 regulates alternative splicing in vivo and can promote or inhibit splicing depending on context and transcript. TBX3 associates with alternatively spliced mRNAs and binds RNA directly. TBX3 binds RNAs containing TBX binding motifs, and these motifs are required for regulation of splicing. Our study reveals that TBX3 mutations seen in humans with UMS disrupt its splicing regulatory function. The pleiotropic effects of TBX3 mutations in humans and mice likely result from disrupting at least two molecular functions of this protein: transcriptional regulation and pre-mRNA splicing.

Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6

Directory of Open Access Journals (Sweden)

Eberlein Annett

2009-04-01

Full Text Available Abstract Background Linkage analyses strongly suggest a number of QTL for production, health and conformation traits in the middle part of bovine chromosome 6 (BTA6. The identification of the molecular background underlying the genetic variation at the QTL and subsequent functional studies require a well-annotated gene sequence map of the critical QTL intervals. To complete the sequence map of the defined subchromosomal regions on BTA6 poorly covered with comparative gene information, we focused on targeted isolation of transcribed sequences from bovine bacterial artificial chromosome (BAC clones mapped to the QTL intervals. Results Using the method of exon trapping, 92 unique exon trapping sequences (ETS were discovered in a chromosomal region of poor gene coverage. Sequence identity to the current NCBI sequence assembly for BTA6 was detected for 91% of unique ETS. Comparative sequence similarity search revealed that 11% of the isolated ETS displayed high similarity to genomic sequences located on the syntenic chromosomes of the human and mouse reference genome assemblies. Nearly a third of the ETS identified similar equivalent sequences in genomic sequence scaffolds from the alternative Celera-based sequence assembly of the human genome. Screening gene, EST, and protein databases detected 17% of ETS with identity to known transcribed sequences. Expression analysis of a subset of the ETS showed that most ETS (84% displayed a distinctive expression pattern in a multi-tissue panel of a lactating cow verifying their existence in the bovine transcriptome. Conclusion The results of our study demonstrate that the exon trapping method based on region-specific BAC clones is very useful for targeted screening for novel transcripts located within a defined chromosomal region being deficiently endowed with annotated gene information. The majority of identified ETS represents unknown noncoding sequences in intergenic regions on BTA6 displaying a

Molecular markers for use in plant molecular breeding and germplasm evaluation

International Nuclear Information System (INIS)

Edwards, J.D.; McCouch, S.R.

2007-01-01

A number of molecular marker technologies exist, each with different advantages and disadvantages. When available, genome sequence allows for the development of greater numbers and higher quality molecular markers. When genome sequence is limited in the organism of interest, related species may serve as sources of molecular markers. Some molecular marker technologies combine the discovery and assay of DNA sequence variations, and therefore can be used in species without the need for prior sequence information and up-front investment in marker development. As a prerequisite for marker-assisted selection (MAS), there must be a known association between genetic markers and genes affecting the phenotype to be modified. Comparative databases can facilitate the transfer of knowledge of genetic marker-phenotype association across species so that discoveries in one species may be applied to many others. Further genomics research and reductions in the costs associated with molecular markers will continue to provide new opportunities to employ MAS. (author)

Nematode consumption by mite communities varies in different forest microhabitats as indicated by molecular gut content analysis.

Science.gov (United States)

Heidemann, Kerstin; Ruess, Liliane; Scheu, Stefan; Maraun, Mark

2014-01-01

Soil animals live in complex and heterogeneous habitats including litter of various types but also microhabitats such as mosses, fungal mats and grass patches. Soil food webs have been separated into a slow fungal and a fast bacterial energy channel. Bacterial-feeding nematodes are an important component of the bacterial energy channel by consuming bacteria and forming prey for higher trophic levels such as soil microarthropods. Investigating the role of nematodes as prey for higher trophic level consumers has been hampered by methodological problems related to their small body size and lack in skeletal structures which can be traced in the gut of consumers. Recent studies using molecular gut content analyses suggest that nematodes form major prey of soil microarthropods including those previously assumed to live as detritivores. Using molecular markers we traced nematode prey in fourteen abundant soil microarthropod taxa of Mesostigmata and Oribatida (both Acari) from three different microhabitats (litter, grass and moss). Consumption of nematodes varied between mite species indicating that trophic niche variation contributes to the high diversity of microarthropods in deciduous forests. Further, consumption of nematodes by Mesostigmata (but not Oribatida) differed between microhabitats indicating that trophic niches vary with habitat characteristics. Overall, the results suggest that free-living bacterial-feeding nematodes form important prey for soil microarthropods including those previously assumed to live as detritivores.

NLRC5: a newly discovered MHC class I transactivator (CITA)

OpenAIRE

Meissner, Torsten B.; Li, Amy; Kobayashi, Koichi S.

2011-01-01

Major histocompatibility complex (MHC) class I and class II are crucial for the function of the human adaptive immune system. An NLR protein, CIITA (MHC class II transactivator), is a master regulator of MHC class II gene expression as well as of some of the genes involved in MHC class II antigen presentation. It has recently been discovered that another member of the NLR protein family, NLRC5, transcriptionally activates MHC class I genes, and thus acts as “CITA” (MHC class I transactivator)...

Repair Effect of Seaweed Polysaccharides with Different Contents of Sulfate Group and Molecular Weights on Damaged HK-2 Cells

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Poonam Bhadja

2016-05-01

Full Text Available The structure–activity relationships and repair mechanism of six low-molecular-weight seaweed polysaccharides (SPSs on oxalate-induced damaged human kidney proximal tubular epithelial cells (HK-2 were investigated. These SPSs included Laminaria japonica polysaccharide, degraded Porphyra yezoensis polysaccharide, degraded Gracilaria lemaneiformis polysaccharide, degraded Sargassum fusiforme polysaccharide, Eucheuma gelatinae polysaccharide, and degraded Undaria pinnatifida polysaccharide. These SPSs have a narrow difference of molecular weight (from 1968 to 4020 Da after degradation by controlling H2O2 concentration. The sulfate group (–SO3H content of the six SPSs was 21.7%, 17.9%, 13.3%, 8.2%, 7.0%, and 5.5%, respectively, and the –COOH contents varied between 1.0% to 1.7%. After degradation, no significant difference was observed in the contents of characteristic –SO3H and –COOH groups of polysaccharides. The repair effect of polysaccharides was determined using cell-viability test by CCK-8 assay and cell-morphology test by hematoxylin-eosin staining. The results revealed that these SPSs within 0.1–100 μg/mL did not express cytotoxicity in HK-2 cells, and each polysaccharide had a repair effect on oxalate-induced damaged HK-2 cells. Simultaneously, the content of polysaccharide –SO3H was positively correlated with repair ability. Furthermore, the low-molecular-weight degraded polysaccharides showed better repair activity on damaged HK-2 cells than their undegraded counterpart. Our results can provide reference for inhibiting the formation of kidney stones and for developing original anti-stone polysaccharide drugs.

Molecular modeling and molecular dynamics simulation study of archaeal leucyl-tRNA synthetase in complex with different mischarged tRNA in editing conformation.

Science.gov (United States)

Rayevsky, A V; Sharifi, M; Tukalo, M A

2017-09-01

Aminoacyl-tRNA synthetases (aaRSs) play important roles in maintaining the accuracy of protein synthesis. Some aaRSs accomplish this via editing mechanisms, among which leucyl-tRNA synthetase (LeuRS) edits non-cognate amino acid norvaline mainly by post-transfer editing. However, the molecular basis for this pathway for eukaryotic and archaeal LeuRS remain unclear. In this study, a complex of archaeal P. horikoshii LeuRS (PhLeuRS) with misacylated tRNA Leu was modeled wherever tRNA's acceptor stem was oriented directly into the editing site. To understand the distinctive features of organization we reconstructed a complex of PhLeuRS with tRNA and visualize post-transfer editing interactions mode by performing molecular dynamics (MD) simulation studies. To study molecular basis for substrate selectivity by PhLeuRS's editing site we utilized MD simulation of the entire LeuRS complexes using a diverse charged form of tRNAs, namely norvalyl-tRNA Leu and isoleucyl-tRNA Leu . In general, the editing site organization of LeuRS from P.horikoshii has much in common with bacterial LeuRS. The MD simulation results revealed that the post-transfer editing substrate norvalyl-A76, binds more strongly than isoleucyl-A76. Moreover, the branched side chain of isoleucine prevents water molecules from being closer and hence the hydrolysis reaction slows significantly. To investigate a possible mechanism of the post-transfer editing reaction, by PhLeuRS we have determined that two water molecules (the attacking and assisting water molecules) are localized near the carbonyl group of the amino acid to be cleaved off. These water molecules approach the substrate from the opposite side to that observed for Thermus thermophilus LeuRS (TtLeuRS). Based on the results obtained, it was suggested that the post-transfer editing mechanism of PhLeuRS differs from that of prokaryotic TtLeuRS. Copyright © 2017 Elsevier Inc. All rights reserved.

Discovering rules for protein-ligand specificity using support vector inductive logic programming.

Science.gov (United States)

Kelley, Lawrence A; Shrimpton, Paul J; Muggleton, Stephen H; Sternberg, Michael J E

2009-09-01

Structural genomics initiatives are rapidly generating vast numbers of protein structures. Comparative modelling is also capable of producing accurate structural models for many protein sequences. However, for many of the known structures, functions are not yet determined, and in many modelling tasks, an accurate structural model does not necessarily tell us about function. Thus, there is a pressing need for high-throughput methods for determining function from structure. The spatial arrangement of key amino acids in a folded protein, on the surface or buried in clefts, is often the determinants of its biological function. A central aim of molecular biology is to understand the relationship between such substructures or surfaces and biological function, leading both to function prediction and to function design. We present a new general method for discovering the features of binding pockets that confer specificity for particular ligands. Using a recently developed machine-learning technique which couples the rule-discovery approach of inductive logic programming with the statistical learning power of support vector machines, we are able to discriminate, with high precision (90%) and recall (86%) between pockets that bind FAD and those that bind NAD on a large benchmark set given only the geometry and composition of the backbone of the binding pocket without the use of docking. In addition, we learn rules governing this specificity which can feed into protein functional design protocols. An analysis of the rules found suggests that key features of the binding pocket may be tied to conformational freedom in the ligand. The representation is sufficiently general to be applicable to any discriminatory binding problem. All programs and data sets are freely available to non-commercial users at http://www.sbg.bio.ic.ac.uk/svilp_ligand/.

A Pan-GTPase Inhibitor as a Molecular Probe.

Directory of Open Access Journals (Sweden)

Lin Hong

Full Text Available Overactive GTPases have often been linked to human diseases. The available inhibitors are limited and have not progressed far in clinical trials. We report here a first-in-class small molecule pan-GTPase inhibitor discovered from a high throughput screening campaign. The compound CID1067700 inhibits multiple GTPases in biochemical, cellular protein and protein interaction, as well as cellular functional assays. In the biochemical and protein interaction assays, representative GTPases from Rho, Ras, and Rab, the three most generic subfamilies of the GTPases, were probed, while in the functional assays, physiological processes regulated by each of the three subfamilies of the GTPases were examined. The chemical functionalities essential for the activity of the compound were identified through structural derivatization. The compound is validated as a useful molecular probe upon which GTPase-targeting inhibitors with drug potentials might be developed.

The agony of choice in dermatophyte diagnostics-performance of different molecular tests and culture in the detection of Trichophyton rubrum and Trichophyton interdigitale.

Science.gov (United States)

Kupsch, C; Ohst, T; Pankewitz, F; Nenoff, P; Uhrlaß, S; Winter, I; Gräser, Y

2016-08-01

Dermatophytosis caused by dermatophytes of the genera Trichophyton and Microsporum belong to the most frequent mycoses worldwide. Molecular detection methods proved to be highly sensitive and enable rapid and accurate detection of dermatophyte species from clinical specimens. For the first time, we compare the performance of different molecular methods with each other and with conventional diagnostics in the detection of dermatophytoses caused by Trichophyton rubrum and Trichophyton interdigitale in clinical specimens (nail, skin and hair). The compared molecular methods comprise two already published PCR-ELISAs, a published quantitative RT-PCR as well as a newly developed PCR-ELISA targeting the internal transcribed spacer region. We investigated the sensitivity of the assays by analysing 375 clinical samples. In 148 specimens (39.5%) a positive result was gained in at least one of the four molecular tests or by culture, but the number of detected agents differed significantly between some of the assays. The most sensitive assay, a PCR-ELISA targeting a microsatellite region, detected 81 T. rubrum infections followed by an internal transcribed spacer PCR-ELISA (60), quantitative RT-PCR (52) and a topoisomerase II PCR-ELISA (51), whereas cultivation resulted in T. rubrum identification in 37 samples. The pros and cons of all four tests in routine diagnostics are discussed. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Stability optimisation of molecular electronic devices based on  nanoelectrode–nanoparticle bridge platform in air and different storage liquids

International Nuclear Information System (INIS)

Jafri, S. H. M.; Blom, T.; Wallner, A.; Ottosson, H.; Leifer, K.

2014-01-01

The long-term stability of metal nanoparticle–molecule junctions in molecular electronic devices based on nanoelectrodes (NEL) is a major challenge in the effort to bring related molecular electronic devices to application. To optimize the reproducibility of molecular electronic nanodevices, the time-dependent modification of such junctions as exposed to different media needs to be known. Here, we have studied (1) the stability of Au-NEL and (2) the electrical stability of molecule–Au nanoparticle (AuNP) junctions themselves with the molecule being  1,8-octanedithiol (ODT). Both the NELs only and the junctions were exposed to air and liquids such as deionized water, tetrahydrofuran, toluene and tetramethylethylenediamine (TMEDA) over a period of 1 month. The nanogaps remained stable in width when stored in either deionized water or toluene, whereas the current through 1,8-octanedithiol–NP junctions remained most stable when stored in TMEDA as compared to other solvents. Although it is difficult to follow the chemical processes in such devices in the 10-nm range with analytical methods, the behavior can be interpreted from known interactions of solvent molecules with electrodes and ODT

Strategic Sustainability Performance Plan. Discovering Sustainable Solutions to Power and Secure America’s Future

Energy Technology Data Exchange (ETDEWEB)

None, None

2010-09-01

Sustainability is fundamental to the Department of Energy’s research mission and operations as reflected in the Department’s Strategic Plan. Our overarching mission is to discover the solutions to power and secure America’s future.

Letting students discover the power, and the limits, of simple models: Coulomb's law

Science.gov (United States)

Bohacek, Peter; Vonk, Matthew; Dill, Joseph; Boehm, Emma

2017-09-01

The inverse-square law pops up all over. It's a simplified model of reality that describes light, sound, gravity, and static electricity. But when it's brought up in class, students are often just handed the equations. They rarely have an opportunity to discover Coulomb's law or Newton's law of gravitation for themselves. It's not hard to understand why. A quantitative demonstration of Coulomb's law can be difficult. The forces are smaller than many force sensors can measure and static electricity tends to be finicky. In addition, off-the-shelf units are expensive or difficult to use. As a result, many instructors skip this lab in favor of qualitative demonstrations or simulations. Adolf Cortel sought to remedy this by designing a straightforward experiment for measuring Coulomb's law using charged metalized-glass spheres (Christmas ornaments) and an electronic balance. Building on Cortel's design, we've made a series of video-based experiments that students can use to discover the relationships that underlie electric force.

Biogenic isoprene emissions driven by regional weather predictions using different initialization methods: case studies during the SEAC4RS and DISCOVER-AQ airborne campaigns

Science.gov (United States)

Huang, Min; Carmichael, Gregory R.; Crawford, James H.; Wisthaler, Armin; Zhan, Xiwu; Hain, Christopher R.; Lee, Pius; Guenther, Alex B.

2017-08-01

Land and atmospheric initial conditions of the Weather Research and Forecasting (WRF) model are often interpolated from a different model output. We perform case studies during NASA's SEAC4RS and DISCOVER-AQ Houston airborne campaigns, demonstrating that using land initial conditions directly downscaled from a coarser resolution dataset led to significant positive biases in the coupled NASA-Unified WRF (NUWRF, version 7) surface and near-surface air temperature and planetary boundary layer height (PBLH) around the Missouri Ozarks and Houston, Texas, as well as poorly partitioned latent and sensible heat fluxes. Replacing land initial conditions with the output from a long-term offline Land Information System (LIS) simulation can effectively reduce the positive biases in NUWRF surface air temperature by ˜ 2 °C. We also show that the LIS land initialization can modify surface air temperature errors almost 10 times as effectively as applying a different atmospheric initialization method. The LIS-NUWRF-based isoprene emission calculations by the Model of Emissions of Gases and Aerosols from Nature (MEGAN, version 2.1) are at least 20 % lower than those computed using the coarser resolution data-initialized NUWRF run, and are closer to aircraft-observation-derived emissions. Higher resolution MEGAN calculations are prone to amplified discrepancies with aircraft-observation-derived emissions on small scales. This is possibly a result of some limitations of MEGAN's parameterization and uncertainty in its inputs on small scales, as well as the representation error and the neglect of horizontal transport in deriving emissions from aircraft data. This study emphasizes the importance of proper land initialization to the coupled atmospheric weather modeling and the follow-on emission modeling. We anticipate it to also be critical to accurately representing other processes included in air quality modeling and chemical data assimilation. Having more confidence in the weather

A comparison study between different molecular weight polysaccharides derived from Lentinus edodes and their antioxidant activities in vivo.

Science.gov (United States)

You, Ruxu; Wang, Kaiping; Liu, Jinyu; Liu, Maochang; Luo, Li; Zhang, Yu

2011-12-01

Polysaccharide purified Lentinus edodes (Berk.) Sing (Tricholomataceae) has been reported to attenuate oxidative stress in vitro. This study investigated whether polysaccharides from L. edodes with different molecular weight have protective effects against oxidative stress induced by D-galactose (D-gal) in vivo, and determined the specific relationship between molecular weight and antioxidant activity. In the present study, we successfully obtained three purified polysaccharides, coded as LT1, LT2, and LT3, and their molecular weights were 25.5, 306.2, and 605.4 kDa, respectively. The D-gal-treated mice received three polysaccharides once daily for 60 days. The activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px), the content of malondialdehyde (MDA), and erythrocyte membrane fluidity were measured to evaluate the changes of the antioxidant ability. It was demonstrated that the administration of LT1, LT2, and LT3 could improve the antioxidant status to different levels. Furthermore, LT2 exhibited the highest antioxidant ability among these samples in vivo. Indeed, LT2 significantly decreased the content of MDA in liver (15.91 ± 0.31 versus 23.79 ± 1.18 nmol/mg protein for the model group, p < 0.05), enhanced the fluidity of erythrocyte membrane (2.458 ± 0.023 versus 2.167 ± 0.024 for the model group, p < 0.05), and increased the activities of SOD (147.19 ± 4.90 versus 82.26 ± 5.55 units/mg protein for the model group, p < 0.05) and GSH-Px (310.91 ± 6.24 versus 243.64 ± 6.77 units/mg protein for the model group, p < 0.05) in liver. The LT2 had a potential to be used as a novel natural antioxidant.

Molecular identification of Trichuris vulpis and Trichuris suis isolated from different hosts.

Science.gov (United States)

Cutillas, Cristina; de Rojas, Manuel; Ariza, Concepción; Ubeda, José Manuel; Guevara, Diego

2007-01-01

Trichuris suis was isolated from the cecum of two different hosts (Sus scrofa domestica -- swine and Sus scrofa scrofa -- wild boar) and Trichuris vulpis from dogs in Sevilla, Spain. Genomic DNA was isolated and internal transcribed spacers (ITS)1-5.8S-ITS2 segment from the ribosomal DNA (rDNA) was amplified and sequenced using polymerase chain reaction techniques. The sequence of T. suis from both hosts was 1,396 bp in length while that of T. vulpis was 1,044 bp. ITS1 of both populations isolated of T. suis was 661 nucleotides in length, while the ITS2 was 534 nucleotides in length. Furthermore, the ITS1 of T. vulpis was 410 nucleotides in length, while the ITS2 was 433 nucleotides in length. One hundred fifty-four nucleotides were observed along the 5.8S gene of T. suis and T. vulpis. Intraindividual and intraspecific variations were detected in the rDNA of both species. The presence of microsatellites was observed in all the individuals assayed. Sequence analysis of the ITSs and the 5.8S gene has demonstrated no sequence differences between T. suis isolated from both hosts (S. scrofa domestica -- swine and S. scrofa scrofa -- wild boar). Nevertheless, clear differences were detected between the ITS1 and ITS2 of T. suis and T. vulpis. Furthermore, a comparative molecular analysis between both species and the previously published ITS1-5.8S-ITS2 sequence data of Trichuris ovis, Trichuris leporis, Trichuris muris, Trichuris arvicolae, and Trichuris skrjabini was carried out. A common homology zone was detected in the ITS1 sequence of all species of trichurids.

Fish allergy in patients with parvalbumin-specific immunoglobulin E depends on parvalbumin content rather than molecular differences in the protein among fish species.

Science.gov (United States)

Kobayashi, Ayako; Kobayashi, Yukihiro; Shiomi, Kazuo

2016-10-01

Allergenic characteristics of purified parvalbumins from different fish species have not been thoroughly investigated. We revealed that purified parvalbumins from nine different fish species have identical IgE-reactivities and high cross-reactivities. We also showed that fish allergenicity is associated with the parvalbumin content of the fish species, rather than species-specific differences in the molecular characteristics of the individual parvalbumin proteins.

Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers

Science.gov (United States)

Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

2016-01-01

The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8–27.6% and 9.5–23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5–26.5% and 7.5%–15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48–49% and 30.5–45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321–0.854 and 0.299–0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil. PMID:26808306

Corrected placement of Mus-Rattus fossil calibration forces precision in the molecular tree of rodents.

Science.gov (United States)

Kimura, Yuri; Hawkins, Melissa T R; McDonough, Molly M; Jacobs, Louis L; Flynn, Lawrence J

2015-09-28

Time calibration derived from the fossil record is essential for molecular phylogenetic and evolutionary studies. Fossil mice and rats, discovered in the Siwalik Group of Pakistan, have served as one of the best-known fossil calibration points in molecular phylogenic studies. Although these fossils have been widely used as the 12 Ma date for the Mus/Rattus split or a more basal split, conclusive paleontological evidence for the nodal assignments has been absent. This study analyzes newly recognized characters that demonstrate lineage separation in the fossil record of Siwalik murines and examines the most reasonable nodal placement of the diverging lineages in a molecular phylogenetic tree by ancestral state reconstruction. Our specimen-based approach strongly indicates that Siwalik murines of the Karnimata clade are fossil members of the Arvicanthini-Otomyini-Millardini clade, which excludes Rattus and its relatives. Combining the new interpretation with the widely accepted hypothesis that the Progonomys clade includes Mus, the lineage separation event in the Siwalik fossil record represents the Mus/Arvicanthis split. Our test analysis on Bayesian age estimates shows that this new calibration point provides more accurate estimates of murine divergence than previous applications. Thus, we define this fossil calibration point and refine two other fossil-based points for molecular dating.

Expression of zinc and cadmium responsive genes in leaves of willow (Salix caprea L.) genotypes with different accumulation characteristics

International Nuclear Information System (INIS)

Konlechner, Cornelia; Türktaş, Mine; Langer, Ingrid; Vaculík, Marek; Wenzel, Walter W.; Puschenreiter, Markus; Hauser, Marie-Theres

2013-01-01

Salix caprea is well suited for phytoextraction strategies. In a previous survey we showed that genetically distinct S. caprea plants isolated from metal-polluted and unpolluted sites differed in their zinc (Zn) and cadmium (Cd) tolerance and accumulation abilities. To determine the molecular basis of this difference we examined putative homologues of genes involved in heavy metal responses and identified over 200 new candidates with a suppression subtractive hybridization (SSH) screen. Quantitative expression analyses of 20 genes in leaves revealed that some metallothioneins and cell wall modifying genes were induced irrespective of the genotype's origin and metal uptake capacity while a cysteine biosynthesis gene was expressed constitutively higher in the metallicolous genotype. The third and largest group of genes was only induced in the metallicolous genotype. These data demonstrate that naturally adapted woody non-model species can help to discover potential novel molecular mechanisms for metal accumulation and tolerance. -- Highlights: ► The transcriptional Zn/Cd response of the willow Salix caprea was quantified. ► Two genotypes from a highly contaminated and a control environment were compared. ► In addition to candidate genes an SSH library revealed over 200 metal induced genes. ► Constitutive upregulation and isolate-specific induction of genes were revealed. ► Willows adapt to environmental Zn/Cd contamination on the transcriptional level. -- Expression analyzes reveal different responses to Cd and Zn exposure of S. caprea genotypes with different heavy metal accumulation abilities

Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins.

Science.gov (United States)

Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

2016-03-05

The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm(-1) and 1545 cm(-1), respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties. Copyright © 2015 Elsevier B.V. All rights reserved.

Discovering Inexpensive, Effective Catalysts for Solar Energy Conversion: An Authentic Research Laboratory Experience

Science.gov (United States)

Shaner, Sarah E.; Hooker, Paul D.; Nickel, Anne-Marie; Leichtfuss, Amanda R.; Adams, Carissa S.; de la Cerda, Dionisia; She, Yuqi; Gerken, James B.; Pokhrel, Ravi; Ambrose, Nicholas J.; Khaliqi, David; Stahl, Shannon S.; Schuttlefield Christus, Jennifer D.

2016-01-01

Electrochemical water oxidation is a major focus of solar energy conversion efforts. A new laboratory experiment has been developed that utilizes real-time, hands-on research to discover catalysts for solar energy conversion. The HARPOON, or Heterogeneous Anodes Rapidly Perused for Oxygen Overpotential Neutralization, experiment allows an array of…

EDITORIAL: Molecular switches at surfaces Molecular switches at surfaces

Science.gov (United States)

Weinelt, Martin; von Oppen, Felix

2012-10-01

In nature, molecules exploit interaction with their environment to realize complex functionalities on the nanometer length scale. Physical, chemical and/or biological specificity is frequently achieved by the switching of molecules between microscopically different states. Paradigmatic examples are the energy production in proton pumps of bacteria or the signal conversion in human vision, which rely on switching molecules between different configurations or conformations by external stimuli. The remarkable reproducibility and unparalleled fatigue resistance of these natural processes makes it highly desirable to emulate nature and develop artificial systems with molecular functionalities. A promising avenue towards this goal is to anchor the molecular switches at surfaces, offering new pathways to control their functional properties, to apply electrical contacts, or to integrate switches into larger systems. Anchoring at surfaces allows one to access the full range from individual molecular switches to self-assembled monolayers of well-defined geometry and to customize the coupling between molecules and substrate or between adsorbed molecules. Progress in this field requires both synthesis and preparation of appropriate molecular systems and control over suitable external stimuli, such as light, heat, or electrical currents. To optimize switching and generate function, it is essential to unravel the geometric structure, the electronic properties and the dynamic interactions of the molecular switches on surfaces. This special section, Molecular Switches at Surfaces, collects 17 contributions describing different aspects of this research field. They analyze elementary processes, both in single molecules and in ensembles of molecules, which involve molecular switching and concomitant changes of optical, electronic, or magnetic properties. Two topical reviews summarize the current status, including both challenges and achievements in the field of molecular switches on

Molecular evolution and the latitudinal biodiversity gradient.

Science.gov (United States)

Dowle, E J; Morgan-Richards, M; Trewick, S A

2013-06-01

Species density is higher in the tropics (low latitude) than in temperate regions (high latitude) resulting in a latitudinal biodiversity gradient (LBG). The LBG must be generated by differential rates of speciation and/or extinction and/or immigration among regions, but the role of each of these processes is still unclear. Recent studies examining differences in rates of molecular evolution have inferred a direct link between rate of molecular evolution and rate of speciation, and postulated these as important drivers of the LBG. Here we review the molecular genetic evidence and examine the factors that might be responsible for differences in rates of molecular evolution. Critical to this is the directionality of the relationship between speciation rates and rates of molecular evolution.

Clustering the Orion B giant molecular cloud based on its molecular emission.

Science.gov (United States)

Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

2018-02-01

Previous attempts at segmenting molecular line maps of molecular clouds have focused on using position-position-velocity data cubes of a single molecular line to separate the spatial components of the cloud. In contrast, wide field spectral imaging over a large spectral bandwidth in the (sub)mm domain now allows one to combine multiple molecular tracers to understand the different physical and chemical phases that constitute giant molecular clouds (GMCs). We aim at using multiple tracers (sensitive to different physical processes and conditions) to segment a molecular cloud into physically/chemically similar regions (rather than spatially connected components), thus disentangling the different physical/chemical phases present in the cloud. We use a machine learning clustering method, namely the Meanshift algorithm, to cluster pixels with similar molecular emission, ignoring spatial information. Clusters are defined around each maximum of the multidimensional Probability Density Function (PDF) of the line integrated intensities. Simple radiative transfer models were used to interpret the astrophysical information uncovered by the clustering analysis. A clustering analysis based only on the J = 1 - 0 lines of three isotopologues of CO proves suffcient to reveal distinct density/column density regimes ( n H ~ 100 cm -3 , ~ 500 cm -3 , and > 1000 cm -3 ), closely related to the usual definitions of diffuse, translucent and high-column-density regions. Adding two UV-sensitive tracers, the J = 1 - 0 line of HCO + and the N = 1 - 0 line of CN, allows us to distinguish two clearly distinct chemical regimes, characteristic of UV-illuminated and UV-shielded gas. The UV-illuminated regime shows overbright HCO + and CN emission, which we relate to a photochemical enrichment effect. We also find a tail of high CN/HCO + intensity ratio in UV-illuminated regions. Finer distinctions in density classes ( n H ~ 7 × 10 3 cm -3 ~ 4 × 10 4 cm -3 ) for the densest regions are also

Molecular Population Genetics.

Science.gov (United States)

Casillas, Sònia; Barbadilla, Antonio

2017-03-01

Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. Copyright © 2017 Casillas and Barbadilla.

Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl-Cytosine

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Mahdi Bagherpoor Helabad

2014-07-01

Full Text Available Distortions in the DNA sequence, such as damage or mispairs, are specifically recognized and processed by DNA repair enzymes. Many repair proteins and, in particular, glycosylases flip the target base out of the DNA helix into the enzyme’s active site. Our molecular dynamics simulations of DNA with intact and damaged (oxidized methyl-cytosine show that the probability of being flipped is similar for damaged and intact methyl-cytosine. However, the accessibility of the different 5-methyl groups allows direct discrimination of the oxidized forms. Hydrogen-bonded patterns that vary between methyl-cytosine forms carrying a carbonyl oxygen atom are likely to be detected by the repair enzymes and may thus help target site recognition.

TOLNet ozone lidar intercomparison during the discover-aq and frappé campaigns

Science.gov (United States)

Newchurch, Michael J.; Alvarez, Raul J.; Berkoff, Timothy A.; Carrion, William; DeYoung, Russell J.; Ganoe, Rene; Gronoff, Guillaume; Kirgis, Guillaume; Kuang, Shi; Langford, Andy O.; Leblanc, Thierry; McGee, Thomas J.; Pliutau, Denis; Senff, Christoph; Sullivan, John T.; Sumnicht, Grant; Twigg, Laurence W.; Wang, Lihua

2018-04-01

The Tropospheric Ozone Lidar Network (TOLNet) is a unique network of lidar systems that measure atmospheric profiles of ozone and aerosols, to contribute to air-quality studies, atmospheric modeling, and satellite validation efforts. The accurate characterization of these lidars is of critical interest, and is necessary to determine cross-instrument calibration uniformity. From July to August 2014, three lidars, the TROPospheric OZone (TROPOZ) lidar, the Tunable Optical Profiler for Aerosol and oZone (TOPAZ) lidar, and the Langley Mobile Ozone Lidar (LMOL), of TOLNet participated in the "Deriving Information on Surface conditions from Column and Vertically Resolved Observations Relevant to Air Quality" (DISCOVER-AQ) mission and the "Front Range Air Pollution and Photochemistry Éxperiment" (FRAPPÉ) to measure sub-hourly ozone variations from near the surface to the top of the troposphere. Although large differences occur at few individual altitudes in the near field and far field range, the TOLNet lidars agree with each other within ±4%. These results indicate excellent measurement accuracy for the TOLNet lidars that is suitable for use in air-quality and ozone modeling efforts.

Incorporating Topic Assignment Constraint and Topic Correlation Limitation into Clinical Goal Discovering for Clinical Pathway Mining

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Xiao Xu

2017-01-01

Full Text Available Clinical pathways are widely used around the world for providing quality medical treatment and controlling healthcare cost. However, the expert-designed clinical pathways can hardly deal with the variances among hospitals and patients. It calls for more dynamic and adaptive process, which is derived from various clinical data. Topic-based clinical pathway mining is an effective approach to discover a concise process model. Through this approach, the latent topics found by latent Dirichlet allocation (LDA represent the clinical goals. And process mining methods are used to extract the temporal relations between these topics. However, the topic quality is usually not desirable due to the low performance of the LDA in clinical data. In this paper, we incorporate topic assignment constraint and topic correlation limitation into the LDA to enhance the ability of discovering high-quality topics. Two real-world datasets are used to evaluate the proposed method. The results show that the topics discovered by our method are with higher coherence, informativeness, and coverage than the original LDA. These quality topics are suitable to represent the clinical goals. Also, we illustrate that our method is effective in generating a comprehensive topic-based clinical pathway model.

Defining behavioral and molecular differences between summer and migratory monarch butterflies

Science.gov (United States)

Zhu, Haisun; Gegear, Robert J; Casselman, Amy; Kanginakudru, Sriramana; Reppert, Steven M

2009-01-01

Background In the fall, Eastern North American monarch butterflies (Danaus plexippus) undergo a magnificent long-range migration. In contrast to spring and summer butterflies, fall migrants are juvenile hormone deficient, which leads to reproductive arrest and increased longevity. Migrants also use a time-compensated sun compass to help them navigate in the south/southwesterly direction en route for Mexico. Central issues in this area are defining the relationship between juvenile hormone status and oriented flight, critical features that differentiate summer monarchs from fall migrants, and identifying molecular correlates of behavioral state. Results Here we show that increasing juvenile hormone activity to induce summer-like reproductive development in fall migrants does not alter directional flight behavior or its time-compensated orientation, as monitored in a flight simulator. Reproductive summer butterflies, in contrast, uniformly fail to exhibit directional, oriented flight. To define molecular correlates of behavioral state, we used microarray analysis of 9417 unique cDNA sequences. Gene expression profiles reveal a suite of 40 genes whose differential expression in brain correlates with oriented flight behavior in individual migrants, independent of juvenile hormone activity, thereby molecularly separating fall migrants from summer butterflies. Intriguing genes that are differentially regulated include the clock gene vrille and the locomotion-relevant tyramine beta hydroxylase gene. In addition, several differentially regulated genes (37.5% of total) are not annotated. We also identified 23 juvenile hormone-dependent genes in brain, which separate reproductive from non-reproductive monarchs; genes involved in longevity, fatty acid metabolism, and innate immunity are upregulated in non-reproductive (juvenile-hormone deficient) migrants. Conclusion The results link key behavioral traits with gene expression profiles in brain that differentiate migratory

Mechanism of microRNA-target interaction: molecular dynamics simulations and thermodynamics analysis.

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Yonghua Wang

Full Text Available MicroRNAs (miRNAs are endogenously produced approximately 21-nt riboregulators that associate with Argonaute (Ago proteins to direct mRNA cleavage or repress the translation of complementary RNAs. Capturing the molecular mechanisms of miRNA interacting with its target will not only reinforce the understanding of underlying RNA interference but also fuel the design of more effective small-interfering RNA strands. To address this, in the present work the RNA-bound (Ago-miRNA, Ago-miRNA-target and RNA-free Ago forms were analyzed by performing both molecular dynamics simulations and thermodynamic analysis. Based on the principal component analysis results of the simulation trajectories as well as the correlation analysis in fluctuations of residues, we discover that: 1 three important (PAZ, Mid and PIWI domains exist in Argonaute which define the global dynamics of the protein; 2 the interdomain correlated movements are so crucial for the interaction of Ago-RNAs that they not only facilitate the relaxation of the interactions between residues surrounding the RNA binding channel but also induce certain conformational changes; and 3 it is just these conformational changes that expand the cavity of the active site and open putative pathways for both the substrate uptake and product release. In addition, by thermodynamic analysis we also discover that for both the guide RNA 5'-end recognition and the facilitated site-specific cleavage of the target, the presence of two metal ions (of Mg(2+ plays a predominant role, and this conclusion is consistent with the observed enzyme catalytic cleavage activity in the ternary complex (Ago-miRNA-mRNA. Our results find that it is the set of arginine amino acids concentrated in the nucleotide-binding channel in Ago, instead of the conventionally-deemed seed base-paring, that makes greater contributions in stabilizing the binding of the nucleic acids to Ago.

Mechanism of microRNA-target interaction: molecular dynamics simulations and thermodynamics analysis.

Science.gov (United States)

Wang, Yonghua; Li, Yan; Ma, Zhi; Yang, Wei; Ai, Chunzhi

2010-07-29

MicroRNAs (miRNAs) are endogenously produced approximately 21-nt riboregulators that associate with Argonaute (Ago) proteins to direct mRNA cleavage or repress the translation of complementary RNAs. Capturing the molecular mechanisms of miRNA interacting with its target will not only reinforce the understanding of underlying RNA interference but also fuel the design of more effective small-interfering RNA strands. To address this, in the present work the RNA-bound (Ago-miRNA, Ago-miRNA-target) and RNA-free Ago forms were analyzed by performing both molecular dynamics simulations and thermodynamic analysis. Based on the principal component analysis results of the simulation trajectories as well as the correlation analysis in fluctuations of residues, we discover that: 1) three important (PAZ, Mid and PIWI) domains exist in Argonaute which define the global dynamics of the protein; 2) the interdomain correlated movements are so crucial for the interaction of Ago-RNAs that they not only facilitate the relaxation of the interactions between residues surrounding the RNA binding channel but also induce certain conformational changes; and 3) it is just these conformational changes that expand the cavity of the active site and open putative pathways for both the substrate uptake and product release. In addition, by thermodynamic analysis we also discover that for both the guide RNA 5'-end recognition and the facilitated site-specific cleavage of the target, the presence of two metal ions (of Mg(2+)) plays a predominant role, and this conclusion is consistent with the observed enzyme catalytic cleavage activity in the ternary complex (Ago-miRNA-mRNA). Our results find that it is the set of arginine amino acids concentrated in the nucleotide-binding channel in Ago, instead of the conventionally-deemed seed base-paring, that makes greater contributions in stabilizing the binding of the nucleic acids to Ago.

Risk of appendicitis in patients with incidentally discovered appendicoliths.

Science.gov (United States)

Khan, Muhammad Sohaib; Chaudhry, Mustafa Belal Hafeez; Shahzad, Noman; Tariq, Marvi; Memon, Wasim Ahmed; Alvi, Abdul Rehman

2018-01-01

An appendicolith-related appendiceal obstruction leading to appendicitis is a commonly encountered surgical emergency that has clear evidence-based management plans. However, there is no consensus on management of asymptomatic patients when appendicoliths are found incidentally. The objective of this study was to determine the risk of appendicitis in patients with an incidental finding of the appendicolith. A retrospective matched cohort study of patients with appendicolith discovered incidentally on computed tomographic scan from January 2008 to December 2014 at our institution was completed. The size and position of the appendicolith were ascertained. The study group was matched by age and gender to a control group. Both groups were contacted and interviewed regarding development of appendicitis. In total, 111 patients with appendicolith were successfully contacted and included in the study. Mean age was found to be 38 ± 15 y with 36 (32%) of the study population being females. Mean length of appendix was 66 ± 16 mm, and mean width was 5.8 ± 0.9 mm. Mean size of the appendicolith was 3.6 ± 1.1 mm (1.4-7.8 mm). Fifty-eight percent of appendicoliths was located at the proximal end or whole of appendix, 31% at mid area, and 11% at the distal end of appendix. All patients of the study and control groups were contacted, and at a mean follow-up of 4.0 ± 1.7 y, there was no occurrence of acute appendicitis in either group. Patients with incidentally discovered appendicolith on radiological imaging did not develop appendicitis. Hence, the risk of developing acute appendicitis for these patients does not seem higher than the general population. Copyright © 2017 Elsevier Inc. All rights reserved.

Feature-based morphometry: discovering group-related anatomical patterns.

Science.gov (United States)

Toews, Matthew; Wells, William; Collins, D Louis; Arbel, Tal

2010-02-01

This paper presents feature-based morphometry (FBM), a new fully data-driven technique for discovering patterns of group-related anatomical structure in volumetric imagery. In contrast to most morphometry methods which assume one-to-one correspondence between subjects, FBM explicitly aims to identify distinctive anatomical patterns that may only be present in subsets of subjects, due to disease or anatomical variability. The image is modeled as a collage of generic, localized image features that need not be present in all subjects. Scale-space theory is applied to analyze image features at the characteristic scale of underlying anatomical structures, instead of at arbitrary scales such as global or voxel-level. A probabilistic model describes features in terms of their appearance, geometry, and relationship to subject groups, and is automatically learned from a set of subject images and group labels. Features resulting from learning correspond to group-related anatomical structures that can potentially be used as image biomarkers of disease or as a basis for computer-aided diagnosis. The relationship between features and groups is quantified by the likelihood of feature occurrence within a specific group vs. the rest of the population, and feature significance is quantified in terms of the false discovery rate. Experiments validate FBM clinically in the analysis of normal (NC) and Alzheimer's (AD) brain images using the freely available OASIS database. FBM automatically identifies known structural differences between NC and AD subjects in a fully data-driven fashion, and an equal error classification rate of 0.80 is achieved for subjects aged 60-80 years exhibiting mild AD (CDR=1). Copyright (c) 2009 Elsevier Inc. All rights reserved.

OH+ IN DIFFUSE MOLECULAR CLOUDS

International Nuclear Information System (INIS)

Porras, A. J.; Federman, S. R.; Welty, D. E.; Ritchey, A. M.

2014-01-01

Near ultraviolet observations of OH + and OH in diffuse molecular clouds reveal a preference for different environments. The dominant absorption feature in OH + arises from a main component seen in CH + (that with the highest CH + /CH column density ratio), while OH follows CN absorption. This distinction provides new constraints on OH chemistry in these clouds. Since CH + detections favor low-density gas with small fractions of molecular hydrogen, this must be true for OH + as well, confirming OH + and H 2 O + observations with the Herschel Space Telescope. Our observed correspondence indicates that the cosmic ray ionization rate derived from these measurements pertains to mainly atomic gas. The association of OH absorption with gas rich in CN is attributed to the need for a high enough density and molecular fraction before detectable amounts are seen. Thus, while OH + leads to OH production, chemical arguments suggest that their abundances are controlled by different sets of conditions and that they coexist with different sets of observed species. Of particular note is that non-thermal chemistry appears to play a limited role in the synthesis of OH in diffuse molecular clouds

The CUAHSI Water Data Center: Empowering scientists to discover, use, store, and share water data

Science.gov (United States)

Couch, A. L.; Hooper, R. P.; Arrigo, J. S.

2012-12-01

control. The WDC enables this by making both kinds of sources available in the same search interface. c. Data provenance: the appropriateness of data for use in a specific model or analysis often depends upon the exact details of how data was gathered and processed. The WDC will aid this by curating standards for metadata that are as descriptive as practical of the collection procedures. "Plug and play" sensor interfaces will fill in metadata appropriate to each sensor without human intervention. d. Contextual search: discovering data based upon geological (e.g. aquifer) or geographic (e.g., location in a stream network) features external to metadata. e. Data-driven search: discovering data that exhibit quality factors that are not described by the metadata. The WDC will partner with researchers desiring contextual and data driven search, and make results available to all. Many major data providers (e.g. federal agencies) are not mandated to provide access to data other than those they collect. The HIS project assembled data from over 90 different sources, thus demonstrating the promise of this approach. Meeting the grand challenges listed above will greatly enhance scientists' ability to discover, interpret, access, and analyze water data from across domains and sources to test Earth system hypotheses.

Molecular Electronic Shift Registers

Science.gov (United States)

Beratan, David N.; Onuchic, Jose N.

1990-01-01

Molecular-scale shift registers eventually constructed as parts of high-density integrated memory circuits. In principle, variety of organic molecules makes possible large number of different configurations and modes of operation for such shift-register devices. Several classes of devices and implementations in some specific types of molecules proposed. All based on transfer of electrons or holes along chains of repeating molecular units.

Redox-Triggered Bonding-Induced Emission of Thiol-Functionalized Gold Nanoclusters for Luminescence Turn-On Detection of Molecular Oxygen.

Science.gov (United States)

Ao, Hang; Feng, Hui; Zhao, Mengting; Zhao, Meizhi; Chen, Jianrong; Qian, Zhaosheng

2017-11-22

Most optical sensors for molecular oxygen were developed based on the quenching effect of the luminescence of oxygen-sensitive probes; however, the signal turn-off mode of these probes is undesirable to quantify and visualize molecular oxygen. Herein, we report a novel luminescence turn-on detection strategy for molecular oxygen via the specific oxygen-triggered bonding-induced emission of thiol-functionalized gold nanoclusters. Thiol-functionalized gold nanoclusters were prepared by a facile one-step synthesis, and as-prepared gold nanoclusters possess significant aggregation-induced emission (AIE) property. It is the first time to discover the oxygen-triggered bonding-induced emission (BIE) behavior of gold nanoclusters, which results in disulfide-linked covalent bonding assemblies with intensely red luminescence. This specific redox-triggered BIE is capable of quantitatively detecting dissolved oxygen in aqueous solution in a light-up manner, and trace amount of dissolved oxygen at ppb level is achieved based on this detection method. A facile and convenient test strip for oxygen detection was also developed to monitor molecular oxygen in a gas matrix. Covalent bonding-induced emission is proven to be a more efficient way to attain high brightness of AIEgens than a physical aggregation-induced emission process, and provides a more convenient and desirable detection method for molecular oxygen than the previous sensors.

Examining Pre-K Professional Development Programs: Discovering the Road to Exceptional Instructional Practices

Science.gov (United States)

Williams, Sheila D.

2016-01-01

The purpose of this qualitative research study was to discover and interpret the experiences of pre-k teachers in an urban school district located in a Northeastern region of the United States. Using a basic qualitative research design, fifteen participants were recruited by a purposeful sampling method to be interviewed after the implementation…

Energy harvesting through gas dynamics in the free molecular flow regime between structured surfaces at different temperatures

DEFF Research Database (Denmark)

Baier, Tobias; Dölger, Julia; Hardt, Steffen

2014-01-01

For a gas confined between surfaces held at different temperatures the velocity distribution shows a significant deviation from the Maxwell distribution when the mean free path of the molecules is comparable to or larger than the channel dimensions. If one of the surfaces is suitably structured...... from the thermal creep flow that has gained more attention so far. This situation is studied in the limit of free-molecular flow for the case that an unstructured surface is allowed to move tangentially with respect to a structured surface. Parameter studies are conducted, and configurations...

Epoxy/anhydride thermosets modified with end-capped star polymers with poly(ethyleneimine cores of different molecular weight and poly(ε–caprolactone arms

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C. Acebo

2015-09-01

Full Text Available Multiarm star polymers, with a hyperbranched poly(ethyleneimine (PEI core and poly(ε-caprolactone (PCL arms end-capped with acetyl groups were synthesized by ring-opening polymerization of ε-caprolactone from PEI cores of different molecular weight. These star polymers were used as toughening agents for epoxy/anhydride thermosets. The curing process was studied by calorimetry, thermomechanical analysis and infrared spectroscopy. The final properties of the resulting materials were determined by thermal and mechanical tests. The addition of the star polymers led to an improvement up to 130% on impact strength and a reduction in the thermal stresses up to 55%. The structure and molecular weight of the modifier used affected the morphology of the resulting materials. Electron microscopy showed phase-separated morphologies with nano-sized fine particles well adhered to the epoxy/anhydride matrix when the higher molecular weight modifier was used.

Site-discrimination by molecular imposters at dissymmetric molecular crystal surfaces

Science.gov (United States)

Poloni, Laura N.

The organization of atoms and molecules into crystalline forms is ubiquitous in nature and has been critical to the development of many technologies on which modern society relies. Classical crystal growth theory can describe atomic crystal growth, however, a description of molecular crystal growth is lacking. Molecular crystals are often characterized by anisotropic intermolecular interactions and dissymmetric crystal surfaces with anisotropic growth rates along different crystallographic directions. This thesis describes combination of experimental and computational techniques to relate crystal structure to surface structure and observed growth rates. Molecular imposters, also known as tailor-made impurities, can be used to control crystal growth for practical applications such as inhibition of pathological crystals, but can also be used to understand site specificity at crystal growth surfaces. The first part of this thesis builds on previous real-time in situ atomic force microscopy (AFM) observations of dislocation-actuated growth on the morphologically significant face of hexagonal L-cystine crystals, which aggregate in vivo to form kidney stones in patients suffering from cystinuria. The inhibitory effect of various L-cystine structural mimics (a.k.a. molecular imposters) was investigated through experimental and computational methods to identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal surface sites. The investigation of L-cystine crystal growth in the presence of molecular imposters through a combination of kinetic analysis using in situ AFM, morphology analysis and birefringence measurements of bulk crystals, and molecular modeling of imposter binding to energetically inequivalent surface sites revealed that different molecular imposters inhibited crystal growth by a Cabrera-Vermilyea pinning mechanism and that imposters bind to a single binding site on the dissymmetric {1000} L

Molecular heterogeneity in a patient-derived glioblastoma xenoline is regulated by different cancer stem cell populations.

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Jo Meagan Garner

Full Text Available Malignant glioblastoma (GBM is a highly aggressive brain tumor with a dismal prognosis and limited therapeutic options. Genomic profiling of GBM samples has identified four molecular subtypes (Proneural, Neural, Classical and Mesenchymal, which may arise from different glioblastoma stem-like cell (GSC populations. We previously showed that adherent cultures of GSCs grown on laminin-coated plates (Ad-GSCs and spheroid cultures of GSCs (Sp-GSCs had high expression of stem cell markers (CD133, Sox2 and Nestin, but low expression of differentiation markers (βIII-tubulin and glial fibrillary acid protein. In the present study, we characterized GBM tumors produced by subcutaneous and intracranial injection of Ad-GSCs and Sp-GSCs isolated from a patient-derived xenoline. Although they formed tumors with identical histological features, gene expression analysis revealed that xenografts of Sp-GSCs had a Classical molecular subtype similar to that of bulk tumor cells. In contrast xenografts of Ad-GSCs expressed a Mesenchymal gene signature. Adherent GSC-derived xenografts had high STAT3 and ANGPTL4 expression, and enrichment for stem cell markers, transcriptional networks and pro-angiogenic markers characteristic of the Mesenchymal subtype. Examination of clinical samples from GBM patients showed that STAT3 expression was directly correlated with ANGPTL4 expression, and that increased expression of these genes correlated with poor patient survival and performance. A pharmacological STAT3 inhibitor abrogated STAT3 binding to the ANGPTL4 promoter and exhibited anticancer activity in vivo. Therefore, Ad-GSCs and Sp-GSCs produced histologically identical tumors with different gene expression patterns, and a STAT3/ANGPTL4 pathway is identified in glioblastoma that may serve as a target for therapeutic intervention.

Noncovalent Molecular Electronics.

Science.gov (United States)

Gryn'ova, G; Corminboeuf, C

2018-05-03

Molecular electronics covers several distinctly different conducting architectures, including organic semiconductors and single-molecule junctions. The noncovalent interactions, abundant in the former, are also often found in the latter, i.e., the dimer junctions. In the present work, we draw the parallel between the two types of noncovalent molecular electronics for a range of π-conjugated heteroaromatic molecules. In silico modeling allows us to distill the factors that arise from the chemical nature of their building blocks and from their mutual arrangement. We find that the same compounds are consistently the worst and the best performers in the two types of electronic assemblies, emphasizing the universal imprint of the underlying chemistry of the molecular cores on their diverse charge transport characteristics. The interplay between molecular and intermolecular factors creates a spectrum of noncovalent conductive architectures, which can be manipulated using the design strategies based upon the established relationships between chemistry and transport.

A Systems Biology Approach Reveals Converging Molecular Mechanisms that Link Different POPs to Common Metabolic Diseases.

Science.gov (United States)

Ruiz, Patricia; Perlina, Ally; Mumtaz, Moiz; Fowler, Bruce A

2016-07-01

A number of epidemiological studies have identified statistical associations between persistent organic pollutants (POPs) and metabolic diseases, but testable hypotheses regarding underlying molecular mechanisms to explain these linkages have not been published. We assessed the underlying mechanisms of POPs that have been associated with metabolic diseases; three well-known POPs [2,3,7,8-tetrachlorodibenzodioxin (TCDD), 2,2´,4,4´,5,5´-hexachlorobiphenyl (PCB 153), and 4,4´-dichlorodiphenyldichloroethylene (p,p´-DDE)] were studied. We used advanced database search tools to delineate testable hypotheses and to guide laboratory-based research studies into underlying mechanisms by which this POP mixture could produce or exacerbate metabolic diseases. For our searches, we used proprietary systems biology software (MetaCore™/MetaDrug™) to conduct advanced search queries for the underlying interactions database, followed by directional network construction to identify common mechanisms for these POPs within two or fewer interaction steps downstream of their primary targets. These common downstream pathways belong to various cytokine and chemokine families with experimentally well-documented causal associations with type 2 diabetes. Our systems biology approach allowed identification of converging pathways leading to activation of common downstream targets. To our knowledge, this is the first study to propose an integrated global set of step-by-step molecular mechanisms for a combination of three common POPs using a systems biology approach, which may link POP exposure to diseases. Experimental evaluation of the proposed pathways may lead to development of predictive biomarkers of the effects of POPs, which could translate into disease prevention and effective clinical treatment strategies. Ruiz P, Perlina A, Mumtaz M, Fowler BA. 2016. A systems biology approach reveals converging molecular mechanisms that link different POPs to common metabolic diseases. Environ

Barriers to early presentation of self-discovered breast cancer in Singapore and Malaysia: a qualitative multicentre study.

Science.gov (United States)

Lim, Jennifer N W; Potrata, Barbara; Simonella, Leonardo; Ng, Celene W Q; Aw, Tar-Ching; Dahlui, Maznah; Hartman, Mikael; Mazlan, Rifhan; Taib, Nur Aishah

2015-12-21

To explore and compare barriers to early presentation of self-discovered breast cancer in Singapore and Malaysia. A qualitative interview study with thematic analysis of transcripts. 67 patients with self-discovered breast symptoms were included in the analysis. Of these, 36% were of Malay ethnicity, 39% were Chinese and 25% Indian, with an average age of 58 years (range 24-82 years). The number of women diagnosed at early stages of cancer almost equalled those at advanced stages. Approximately three-quarters presented with a painless lump, one-quarter experienced a painful lump and 10% had atypical symptoms. University hospital setting in Singapore and Malaysia. Patients revealed barriers to early presentation not previously reported: the poor quality of online website information about breast symptoms, financial issues and the negative influence of relatives in both countries, while perceived poor quality of care and services in state-run hospitals and misdiagnosis by healthcare professionals were reported in Malaysia. The pattern of presentation by ethnicity remained unchanged where more Malay delayed help-seeking and had more advanced cancer compared to Chinese and Indian patients. There are few differences in the pattern of presentation and in the reported barriers to seek medical care after symptom discovery between Singapore and Malaysia despite their differing economic status. Strategies to reduce delayed presentation are: a need to improve knowledge of disease, symptoms and causes, quality of care and services, and quality of online information; and addressing fear of diagnosis, treatment and hospitalisation, with more effort focused on the Malay ethnic group. Training is needed to avoid missed diagnoses and other factors contributing to delay among health professionals. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Stereodivergent synthesis with a programmable molecular machine

Science.gov (United States)

Kassem, Salma; Lee, Alan T. L.; Leigh, David A.; Marcos, Vanesa; Palmer, Leoni I.; Pisano, Simone

2017-09-01

It has been convincingly argued that molecular machines that manipulate individual atoms, or highly reactive clusters of atoms, with Ångström precision are unlikely to be realized. However, biological molecular machines routinely position rather less reactive substrates in order to direct chemical reaction sequences, from sequence-specific synthesis by the ribosome to polyketide synthases, where tethered molecules are passed from active site to active site in multi-enzyme complexes. Artificial molecular machines have been developed for tasks that include sequence-specific oligomer synthesis and the switching of product chirality, a photo-responsive host molecule has been described that is able to mechanically twist a bound molecular guest, and molecular fragments have been selectively transported in either direction between sites on a molecular platform through a ratchet mechanism. Here we detail an artificial molecular machine that moves a substrate between different activating sites to achieve different product outcomes from chemical synthesis. This molecular robot can be programmed to stereoselectively produce, in a sequential one-pot operation, an excess of any one of four possible diastereoisomers from the addition of a thiol and an alkene to an α,β-unsaturated aldehyde in a tandem reaction process. The stereodivergent synthesis includes diastereoisomers that cannot be selectively synthesized through conventional iminium-enamine organocatalysis. We anticipate that future generations of programmable molecular machines may have significant roles in chemical synthesis and molecular manufacturing.

Utilizing NASA DISCOVER-AQ Data to Examine Spatial Gradients in Complex Emission Environments

Science.gov (United States)

Buzanowicz, M. E.; Moore, W.; Crawford, J. H.; Schroeder, J.

2017-12-01

Although many regulations have been enacted with the goal of improving air quality, many parts of the US are still classified as `non-attainment areas' because they frequently violate federal air quality standards. Adequately monitoring the spatial distribution of pollutants both within and outside of non-attainment areas has been an ongoing challenge for regulators. Observations of near-surface pollution from space-based platforms would provide an unprecedented view of the spatial distribution of pollution, but this goal has not yet been realized due to fundamental limitations of satellites, specifically because the footprint size of satellite measurements may not be sufficiently small enough to capture true gradients in pollution, and rather represents an average over a large area. NASA's DISCOVER-AQ was a multi-year field campaign aimed at improving our understanding of the role that remote sensing, including satellite-based remote sensing, could play in air quality monitoring systems. DISCOVER-AQ data will be utilized to create a metric to examine spatial gradients and how satellites can capture those gradients in areas with complex emission environments. Examining horizontal variability within a vertical column is critical to understanding mixing within the atmosphere. Aircraft spirals conducted during DISCOVER-AQ were divided into octants, and averages of a given a species were calculated, with certain points receiving a flag. These flags were determined by calculating gradients between subsequent octants. Initial calculations have shown that over areas with large point source emissions, such as Platteville and Denver-La Casa in Colorado, and Essex, Maryland, satellite retrievals may not adequately capture spatial variability in the atmosphere, thus complicating satellite inversion techniques and limiting our ability to understand human exposure on sub-grid scales. Further calculations at other locations and for other trace gases are necessary to determine

Caffeine and sulfadiazine interact differently with human serum albumin: A combined fluorescence and molecular docking study

Science.gov (United States)

Islam, Mullah Muhaiminul; Sonu, Vikash K.; Gashnga, Pynsakhiat Miki; Moyon, N. Shaemningwar; Mitra, Sivaprasad

2016-01-01

The interaction and binding behavior of the well-known drug sulfadiazine (SDZ) and psychoactive stimulant caffeine (CAF) with human serum albumin (HSA) was monitored by in vitro fluorescence titration and molecular docking calculations under physiological condition. The quenching of protein fluorescence on addition of CAF is due to the formation of protein-drug complex in the ground state; whereas in case of SDZ, the experimental results were explained on the basis of sphere of action model. Although both these compounds bind preferentially in Sudlow's site 1 of the protein, the association constant is approximately two fold higher in case of SDZ (∼4.0 × 104 M-1) in comparison with CAF (∼9.3 × 102 M-1) and correlates well with physico-chemical properties like pKa and lipophilicity of the drugs. Temperature dependent fluorescence study reveals that both SDZ and CAF bind spontaneously with HSA. However, the binding of SDZ with the protein is mainly governed by the hydrophobic forces in contrast with that of CAF; where, the interaction is best explained in terms of electrostatic mechanism. Molecular docking calculation predicts the binding of these drugs in different location of sub-domain IIA in the protein structure.

Elucidation of molecular mechanisms of physiological variations between bovine subcutaneous and visceral fat depots under different nutritional regimes.

Science.gov (United States)

Romao, Josue Moura; Jin, Weiwu; He, Maolong; McAllister, Tim; Guan, Le Luo

2013-01-01

Adipose tissue plays a critical role in energy homeostasis and metabolism. There is sparse understanding of the molecular regulation at the protein level of bovine adipose tissues, especially within different fat depots under different nutritional regimes. The objective of this study was to analyze the differences in protein expression between bovine subcutaneous and visceral fat depots in steers fed different diets and to identify the potential regulatory molecular mechanisms of protein expression. Subcutaneous and visceral fat tissues were collected from 16 British-continental steers (15.5 month old) fed a high-fat diet (7.1% fat, n=8) or a control diet (2.7% fat, n=8). Protein expression was profiled using label free quantification LC-MS/MS and expression of selected transcripts was evaluated using qRT-PCR. A total of 682 proteins were characterized and quantified with fat depot having more impact on protein expression, altering the level of 51.0% of the detected proteins, whereas diet affected only 5.3%. Functional analysis revealed that energy production and lipid metabolism were among the main functions associated with differentially expressed proteins between fat depots, with visceral fat being more metabolically active than subcutaneous fat as proteins associated with lipid and energy metabolism were upregulated. The expression of several proteins was significantly correlated to subcutaneous fat thickness and adipocyte size, indicating their potential as adiposity markers. A poor correlation (r=0.245) was observed between mRNA and protein levels for 9 genes, indicating that many proteins may be subjected to post-transcriptional regulation. A total of 8 miRNAs were predicted to regulate more than 20% of lipid metabolism proteins differentially expressed between fat depots, suggesting that miRNAs play a role in adipose tissue regulation. Our results show that proteomic changes support the distinct metabolic and physiological characteristics observed between

The Role of Antisymmetric Exchange on the Quantum Interference between States of Different Spin Length in a dimeric Molecular Nanomagnet.

Science.gov (United States)

Del Barco, Enrique

2009-03-01

We report direct evidence of quantum oscillations of the total spin length of a dimeric molecular nanomagnet through the observation of quantum interference associated with tunneling trajectories between states having different spin quantum numbers. As we outline, this is a consequence of the unique characteristics of a molecular Mn12 wheel which behaves as a (weak) ferromagnetic exchange-coupled molecular dimer: each half of the molecule acts as a single-molecule magnet (SMM), while the weak coupling between the two halves gives rise to an additional internal spin degree of freedom within the molecule, namely that its total spin may fluctuate. This extra degree of freedom accounts for several magnetization tunneling resonances that cannot be explained within the usual giant spin approximation. More importantly, the observation of quantum interference provides unambiguous evidence for the quantum mechanical superposition involving entangled states of both halves of the wheel. Magnetization results obtained in two other versions of this compound, in which the ligands have been modified, show that slight variations of the relative distance between the Mn ions determine whether the molecule behaves as a rigid magnetic unit of spin S = 7 or as two exchange-coupled halves of spin S = 7/2. We analyze the effect of the Dzyaloshinskii-Moriya antisymmetric exchange interaction in a molecule with a centre of inversion symmetry and propose a formal model to account for the observed broken degeneracy that preserves the molecular inversion symmetry.

Combined Ligand/Structure-Based Virtual Screening and Molecular Dynamics Simulations of Steroidal Androgen Receptor Antagonists

Directory of Open Access Journals (Sweden)

Yuwei Wang

2017-01-01

Full Text Available The antiandrogens, such as bicalutamide, targeting the androgen receptor (AR, are the main endocrine therapies for prostate cancer (PCa. But as drug resistance to antiandrogens emerges in advanced PCa, there presents a high medical need for exploitation of novel AR antagonists. In this work, the relationships between the molecular structures and antiandrogenic activities of a series of 7α-substituted dihydrotestosterone derivatives were investigated. The proposed MLR model obtained high predictive ability. The thoroughly validated QSAR model was used to virtually screen new dihydrotestosterones derivatives taken from PubChem, resulting in the finding of novel compounds CID_70128824, CID_70127147, and CID_70126881, whose in silico bioactivities are much higher than the published best one, even higher than bicalutamide. In addition, molecular docking, molecular dynamics (MD simulations, and MM/GBSA have been employed to analyze and compare the binding modes between the novel compounds and AR. Through the analysis of the binding free energy and residue energy decomposition, we concluded that the newly discovered chemicals can in silico bind to AR with similar position and mechanism to the reported active compound and the van der Waals interaction is the main driving force during the binding process.

Safety assessment of nanoparamagnetic contrast agents with different coatings for molecular MRI

Science.gov (United States)

Azizian, Gholamreza; Riyahi-Alam, Nader; Haghgoo, Soheila; Saffari, Mojtaba; Zohdiaghdam, Reza; Gorji, Ensieh

2013-04-01

Despite the wide application of gadolinium as a contrast agent for magnetic resonance imaging (MRI), there is a serious lack of information on its toxicity. Gadolinium and gadolinium oxide (Gd-oxide) are used as contrast agents for magnetic resonance imaging (MRI). There are methods for reducing toxicity of these materials, such as core nanoparticles coating or conjugating. Therefore, for toxicity evaluation, we compared the viability of commercial contrast agents in MRI (Gd-DTPA) and three nanoparticles with the same core Gd2O3 and small particulate gadolinium oxide or SPGO (DTPA. The MTT and LDH assay results showed that Gd2O3-DEG nanoparticles were more toxic than Gd-DTPA and other nanoparticles. Also, SPGO-mPEG-silane2000 was more biocompatible than other nanoparticles. The obtained results did not show any significant increase in cytotoxicity of the nanoparticles and Gd-DTPA, neither dose-dependent nor time-dependent. Therefore, DEG and PEG, due to their considerable properties and irregular sizes (different molecular weights), were selected as the useful surface covering materials of nanomagnetic particles that could reveal noticeable relaxivity and biocompatibility characteristics.

Evaluation and application of summary statistic imputation to discover new height-associated loci.

Science.gov (United States)

Rüeger, Sina; McDaid, Aaron; Kutalik, Zoltán

2018-05-01

As most of the heritability of complex traits is attributed to common and low frequency genetic variants, imputing them by combining genotyping chips and large sequenced reference panels is the most cost-effective approach to discover the genetic basis of these traits. Association summary statistics from genome-wide meta-analyses are available for hundreds of traits. Updating these to ever-increasing reference panels is very cumbersome as it requires reimputation of the genetic data, rerunning the association scan, and meta-analysing the results. A much more efficient method is to directly impute the summary statistics, termed as summary statistics imputation, which we improved to accommodate variable sample size across SNVs. Its performance relative to genotype imputation and practical utility has not yet been fully investigated. To this end, we compared the two approaches on real (genotyped and imputed) data from 120K samples from the UK Biobank and show that, genotype imputation boasts a 3- to 5-fold lower root-mean-square error, and better distinguishes true associations from null ones: We observed the largest differences in power for variants with low minor allele frequency and low imputation quality. For fixed false positive rates of 0.001, 0.01, 0.05, using summary statistics imputation yielded a decrease in statistical power by 9, 43 and 35%, respectively. To test its capacity to discover novel associations, we applied summary statistics imputation to the GIANT height meta-analysis summary statistics covering HapMap variants, and identified 34 novel loci, 19 of which replicated using data in the UK Biobank. Additionally, we successfully replicated 55 out of the 111 variants published in an exome chip study. Our study demonstrates that summary statistics imputation is a very efficient and cost-effective way to identify and fine-map trait-associated loci. Moreover, the ability to impute summary statistics is important for follow-up analyses, such as Mendelian

A tight-binding model of the transmission probability through a molecular junction; a single molecule vs. a molecular layer

International Nuclear Information System (INIS)

Landau, A.; Nitzan, A.

2006-01-01

Full Text: Molecular electronics, one of the major fields of the current effort in nano-science, may be de ed as the study of electronic behaviors, devices and applications that depend on the properties of matter at the molecular scale. If the miniaturization trend of microelectronic devices is to continue, elements such as transistors and contacts will soon shrink to single molecules. The promise of these new technological breakthroughs has been major driving force in this ld. Moreover, the consideration of molecular systems as electronic devices has raised new fundamental questions. In particular, while traditional quantum chemistry deals with electronically closed systems, we now face problems involving molecular systems that are open to their electronic environment, moreover, function in far from equilibrium situations. A generic molecular junction is made of two electrodes connected by a molecular spacer that takes the form of a molecular chain of varying length or a molecular layer of varying thickness. We use a simple nearest-neighbors tight-biding model with the non-equilibrium Green's function (NEGF) method to investigate and compare between a self-assembled monolayer (SAM), finite molecular layer (FML), and single molecule (SM) chemisorption to a surface of a metal substrate. In addition, we examine the difference in the transmission probability through a SAM, FML and SM sandwiched between two metallic electrodes. Dramatic differences are observed between the SM, FML and SAM density of electronic states and transmission functions. In addition, we analyze the effects of changing different physical parameters such as molecule-substrate interaction, molecule-molecule interactions, etc; interesting effects that pertain to the conduction properties of single molecules and molecular layers are observed. Intriguing results are attained when we investigate the commensurability of the SAM with the metallic surface

Microscopic mechanism of amino silicone oil modification and modification effect with different amino group contents based on molecular dynamics simulation

Science.gov (United States)

He, Liping; Li, Wenjun; Chen, Dachuan; Yuan, Jianmin; Lu, Gang; Zhou, Dianwu

2018-05-01

The microscopic mechanism of amino silicone oil (ASO) modification of natural fiber was investigated for the first time using molecular dynamics (MD) simulation at the atomic and molecular levels. The MD simulation results indicated that the ASO molecular interacted with the cellulose molecular within the natural fiber, mainly by intermolecular forces of Nsbnd Hsbnd O and Osbnd Hsbnd N hydrogen bonds and the molecular chain of ASO absorbed onto the natural fiber in a selective orientation, i.e., the hydrophobic alkyl groups (sbnd CnH2n+1) project outward and the polar amino groups (sbnd NH2) point to the surface of natural fiber. Consequently, the ASO modification changed the surface characteristic of natural fiber from hydrophilic to hydrophobic. Furthermore, the modification effects of the ASO modification layer with different amino group contents (m:n ratio) were also evaluated in this study by calculating the binding energy between the ASO modifier and natural fiber, and the cohesive energy density and free volume of the ASO modification layer. The results showed that the binding energy reached a maximum when the m:n ratio of ASO was of 8:4, suggesting that a good bonding strength was achieved at this m:n ratio. It was also found that the cohesive energy density enhanced with the increase in the amino group content, and the higher the cohesive energy density, the easier the formation of the ASO modification layer. However, the fraction free volume decreased with the increase in the amino group content. This is good for improving the water-proof property of natural fiber. The present work can provide an effective method for predicting the modification effects and designing the optimized m:n ratio of ASO modification.

Exposure of honey bees (Apis mellifera) to different classes of insecticides exhibit distinct molecular effect patterns at concentrations that mimic environmental contamination.

Science.gov (United States)

Christen, Verena; Fent, Karl

2017-07-01

Pesticides are implicated in the decline of honey bee populations. Many insecticides are neurotoxic and act by different modes of actions. Although a link between insecticide exposure and changed behaviour has been made, molecular effects underlying these effects are poorly understood. Here we elucidated molecular effects at environmental realistic concentrations of two organophosphates, chlorpyrifos and malathion, the pyrethroid cypermethrin, and the ryanodine receptor activator, chlorantraniliprole. We assessed transcriptional alterations of selected genes at three exposure times (24 h, 48 h, 72 h) in caged honey bees exposed to different concentrations of these compounds. Our targeted gene expression concept focused on several transcripts, including nicotinic acetylcholine receptor α 1 and α 2 (nAChRα1, nAChRα2) subunits, the multifunctional gene vitellogenin, immune system related genes of three immune system pathways, genes belonging to the detoxification system and ER stress genes. Our data indicate a dynamic pattern of expressional changes at different exposure times. All four insecticides induced strong alterations in the expression of immune system related genes suggesting negative implications for honey bee health, as well as cytochrome P450 enzyme transcripts suggesting an interference with metabolism. Exposure to neurotoxic chlorpyrifos, malathion and cypermethrin resulted in up-regulation of nAChRα1 and nAChRα2. Moreover, alterations in the expression of vitellogenin occurred, which suggests implications on foraging activity. Chlorantraniliprole induced ER stress which may be related to toxicity. The comparison of all transcriptional changes indicated that the expression pattern is rather compound-specific and related to its mode of action, but clusters of common transcriptional changes between different compounds occurred. As transcriptional alterations occurred at environmental concentrations our data provide a molecular basis for observed

Quantification of the N-terminal propeptide of human procollagen type I (PINP): comparison of ELISA and RIA with respect to different molecular forms

DEFF Research Database (Denmark)

Jensen, Charlotte Harken; Hansen, M; Brandt, J

1998-01-01

This paper compares the results of procollagen type I N-terminal propeptide (PINP) quantification by radioimmunoassay (RIA) and enzyme linked immunosorbent assay (ELISA). PINP in serum from a patient with uremic hyperparathyroidism was measured in RIA and ELISA to 20 micrograms l-1 and 116...... of PINP when analysed in a direct ELISA. It is concluded that the major difference in the ELISA and RIA results is due to assay efficacy with respect to the low molecular weight form of PINP. Udgivelsesdato: 1998-Jan-12......-PAGE). Analysis of fractions from size separated amniotic fluid, serum and dialysis fluid demonstrated that the RIA failed to measure the low molecular weight form of PINP. However, the anti-PINP supplied with the RIA-kit and the anti-PINP applied in the ELISA reacted equally well with both molecular forms...

Imagenología molecular: Un nuevo paradigma en Radiología Molecular Imagenología: A new paradigm in Radiology

Directory of Open Access Journals (Sweden)

Héctor Pereira Recio

2006-12-01

Full Text Available Desde la antigüedad el hombre mostró interés por conocer los secretos del interior del cuerpo humano, pero solo hasta finales del siglo XIX al descubrirse los Rayos X es que los médicos pudieron observarlo en pacientes vivos. En este trabajo hacemos un análisis de la evolución de la imagenología médica y su interrelación con importantes avances de las ciencias moleculares y genéticas que han ayudado al surgimiento y desarrollo de la imagenología molecular, sus herramientas y sus aplicaciones tanto para la detección precoz de las enfermedades como el monitoreo de la efectividad terapéutica, también analizamos sus implicaciones bioéticas pues como toda actividad humana ocurre en un contexto socioeconómico caracterizado por la desigualdad, además de los peligros potenciales que entraña para la humanidad por lo que se requiere de la educación tanto de los proveedores de servicios de salud como de pacientes y público, siendo esto nuestro principal objetivoSince ancient times men showed interest in knowing about the secrets of the inside of the human body, but only at the end of the XIX Century, when X-rays were discovered, doctors could observe it in alive patients. Trough the work we make an analysis of the evolution of the medical imaginology and its interrelation with important advances of the molecular and genetic sciences that have helped so much in the coming forth and development of the molecular imaginology, its tools and applications as much for the precocious illnesses detection as to monitor of the therapeutic effectiveness, we also analyse this bioethics implications since, as well as all human activity, occurs in a socio-economic context characterized by inequality, besides the potential risks that it involves for humanity, that is why the education of suppliers of health services, patients and public is required, being this our main objective.

A Phenomenological Study to Discover Low-Income Adults' Perceptions and Expectations Regarding Financial Literacy

Science.gov (United States)

Schaffer, Brigid Ann

2013-01-01

This phenomenological study explored the perceptions and expectations of low income adults regarding financial literacy to discover ways to increase attendance in financial literacy programs designs for this cohort. The study utilized interviews with closed-ended questions to establish the participants' backgrounds, then opened-ended questions to…

Development of RAPD-SCAR markers for different Ganoderma species authentication by improved RAPD amplification and molecular cloning.

Science.gov (United States)

Fu, J J; Mei, Z Q; Tania, M; Yang, L Q; Cheng, J L; Khan, M A

2015-05-25

The sequence-characterized amplified region (SCAR) is a valuable molecular technique for the genetic identification of any species. This method is mainly derived from the molecular cloning of the amplified DNA fragments achieved from the random amplified polymorphic DNA (RAPD). In this study, we collected DNA from 10 species of Ganoderma mushroom and amplified the DNA using an improved RAPD technique. The amplified fragments were then cloned into a T-vector, and positive clones were screened, indentified, and sequenced for the development of SCAR markers. After designing PCR primers and optimizing PCR conditions, 4 SCAR markers, named LZ1-4, LZ2-2, LZ8-2, and LZ9-15, were developed, which were specific to Ganoderma gibbosum (LZ1-4 and LZ8-2), Ganoderma sinense (LZ2-2 and LZ8-2), Ganoderma tropicum (LZ8-2), and Ganoderma lucidum HG (LZ9-15). These 4 novel SCAR markers were deposited into GenBank with the accession Nos. KM391935, KM391936, KM391937, and KM391938, respectively. Thus, in this study we developed specific SCAR markers for the identification and authentication of different Ganoderma species.

Synthesis and characterization of Co (Ni or Cu)-MCM-41 mesoporous molecular sieves with different amount of metal obtained by using microwave irradiation method

International Nuclear Information System (INIS)

Jiang Tingshun; Zhao Qian; Chen Kangmin; Tang Yajing; Yu Longbao; Yin Hengbo

2008-01-01

Co (Ni or Cu)-MCM-41 mesoporous molecular sieves with different amount of metal were synthesized by using cetyltrimethyl ammonium bromide as a template and by a novel microwave irradiation method. These samples were characterized by powder X-ray diffraction (XRD), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR) and N 2 physical adsorption. The experimental results show that Co (Ni or Cu)-MCM-41 mesoporous molecular sieves were successfully synthesized. When the as-synthesized samples were calcined at 550 deg. C for 10 h, the template was effectively removed. Under microwave irradiation condition, Co-MCM-41 mesoporous molecular sieves have specific surface areas in a range of 745.7-1188.8 m 2 /g and average pore sizes in a range of 2.46-2.75 nm; Ni-MCM-41 mesoporous molecular sieves have specific surface areas in a range of 625.8-1161.3 m 2 /g and average pore sizes of ca. 2.7 nm; Cu-MCM-41 mesoporous molecular sieves have specific surface areas in a range of 601.6-1142.9 m 2 /g and average pore sizes in a range of 2.46-2.76 nm. On the other hand, with increasing the introduced metal amount, the specific surface area and pore volume of the synthesized Co (Ni or Cu)-MCM-41 mesoporous molecular sieves became small, and the mesoporous ordering of the samples became poor. Under the comparable synthesis conditions, the synthesized Co-MCM-41 mesoporous molecular sieve has a bigger specific surface area and a more uniform pore distribution as compared with the synthesized Ni-MCM-41and Cu-MCM-41 mesoporous molecular sieves

A new hard X-ray transient discovered by INTEGRAL

DEFF Research Database (Denmark)

Gibaud, L.; Bazzano, A.; Bozzo, E.

2011-01-01

INTEGRAL discovered a new hard X-ray transient, IGR J17498-2921, during the observations performed from 2011-08-11 22:45 to 2011-08-12 05:54 UTC. The source is detected in the IBIS/ISGRI mosaic at a preliminary significance level of 11 and 9 sigma in the 20-40 keV and 40-80 keV energy bands......, respectively. The corresponding fluxes are 19+/-2 and 23+/-3 mCrab (68% c.l., only statistical). The best determined source position is at RA=17:49:49; DEC=-29:21:14 (J2000) with a 90% confinement radius of 2.3 arcmin. The IBIS/ISGRI spectrum (exposure time 15.9 ks) can be well described by a a power...

Structure homology and interaction redundancy for discovering virus–host protein interactions

Science.gov (United States)

de Chassey, Benoît; Meyniel-Schicklin, Laurène; Aublin-Gex, Anne; Navratil, Vincent; Chantier, Thibaut; André, Patrice; Lotteau, Vincent

2013-01-01

Virus–host interactomes are instrumental to understand global perturbations of cellular functions induced by infection and discover new therapies. The construction of such interactomes is, however, technically challenging and time consuming. Here we describe an original method for the prediction of high-confidence interactions between viral and human proteins through a combination of structure and high-quality interactome data. Validation was performed for the NS1 protein of the influenza virus, which led to the identification of new host factors that control viral replication. PMID:24008843

Structure homology and interaction redundancy for discovering virus-host protein interactions.

Science.gov (United States)

de Chassey, Benoît; Meyniel-Schicklin, Laurène; Aublin-Gex, Anne; Navratil, Vincent; Chantier, Thibaut; André, Patrice; Lotteau, Vincent

2013-10-01

Virus-host interactomes are instrumental to understand global perturbations of cellular functions induced by infection and discover new therapies. The construction of such interactomes is, however, technically challenging and time consuming. Here we describe an original method for the prediction of high-confidence interactions between viral and human proteins through a combination of structure and high-quality interactome data. Validation was performed for the NS1 protein of the influenza virus, which led to the identification of new host factors that control viral replication.

Molecular epidemiology of human rhinoviruses

OpenAIRE

Savolainen-Kopra, Carita

2006-01-01

The first part of this work investigates the molecular epidemiology of a human enterovirus (HEV), echovirus 30 (E-30). This project is part of a series of studies performed in our research team analyzing the molecular epidemiology of HEV-B viruses. A total of 129 virus strains had been isolated in different parts of Europe. The sequence analysis was performed in three different genomic regions: 420 nucleotides (nt) in the VP4/VP2 capsid protein coding region, the entire VP1 capsid protein cod...

Molecular dewetting on insulators

International Nuclear Information System (INIS)

Burke, S A; Topple, J M; Gruetter, P

2009-01-01

Recent attention given to the growth and morphology of organic thin films with regard to organic electronics has led to the observation of dewetting (a transition from layer(s) to islands) of molecular deposits in many of these systems. Dewetting is a much studied phenomenon in the formation of polymer and liquid films, but its observation in thin films of the 'small' molecules typical of organic electronics requires additional consideration of the structure of the interface between the molecular film and the substrate. This review covers some key concepts related to dewetting and molecular film growth. In particular, the origins of different growth modes and the thickness dependent interactions which give rise to dewetting are discussed in terms of surface energies and the disjoining pressure. Characteristics of molecular systems which may lead to these conditions, including the formation of metastable interface structures and commensurate-incommensurate phase transitions, are also discussed. Brief descriptions of some experimental techniques which have been used to study molecular dewetting are given as well. Examples of molecule-on-insulator systems which undergo dewetting are described in some detail, specifically perylene derivatives on alkali halides, C 60 on alkali halides, and the technologically important system of pentacene on SiO 2 . These examples point to some possible predicting factors for the occurrence of dewetting, most importantly the formation of an interface layer which differs from the bulk crystal structure. (topical review)

Molecular dewetting on insulators.

Science.gov (United States)

Burke, S A; Topple, J M; Grütter, P

2009-10-21

Recent attention given to the growth and morphology of organic thin films with regard to organic electronics has led to the observation of dewetting (a transition from layer(s) to islands) of molecular deposits in many of these systems. Dewetting is a much studied phenomenon in the formation of polymer and liquid films, but its observation in thin films of the 'small' molecules typical of organic electronics requires additional consideration of the structure of the interface between the molecular film and the substrate. This review covers some key concepts related to dewetting and molecular film growth. In particular, the origins of different growth modes and the thickness dependent interactions which give rise to dewetting are discussed in terms of surface energies and the disjoining pressure. Characteristics of molecular systems which may lead to these conditions, including the formation of metastable interface structures and commensurate-incommensurate phase transitions, are also discussed. Brief descriptions of some experimental techniques which have been used to study molecular dewetting are given as well. Examples of molecule-on-insulator systems which undergo dewetting are described in some detail, specifically perylene derivatives on alkali halides, C(60) on alkali halides, and the technologically important system of pentacene on SiO(2). These examples point to some possible predicting factors for the occurrence of dewetting, most importantly the formation of an interface layer which differs from the bulk crystal structure.

The Challenges of Recombinant Endostatin in Clinical Application: Focus on the Different Expression Systems and Molecular Bioengineering

Directory of Open Access Journals (Sweden)

Abbas Mohajeri

2017-04-01

Full Text Available Angiogenesis plays an essential role in rapid growing and metastasis of the tumors. Inhibition of angiogenesis is a putative strategy for cancer therapy. Endostatin (Es is an attractive anti-angiogenesis protein with some clinical application challenges including; short half-life, instability in serum and requirement to high dosage. Therefore, production of recombinant endostatin (rEs is necessary in large scale. The production of rEs is difficult because of its structural properties and is high-cost. Therefore, this review focused on the different expression systems that involved in rEs production including; mammalian, baculovirus, yeast, and Escherichia coli (E. coli expression systems. The evaluating of the results of different expression systems declared that none of the mentioned systems can be considered to be generally superior to the other. Meanwhile with considering the advantages and disadvantage of E. coli expression system compared with other systems beside the molecular properties of Es, E. coli expression system can be a preferred expression system for expressing of the Es in large scale. Also, the molecular bioengineering and sustained release formulations that lead to improving of its stability and bioactivity will be discussed. Point mutation (P125A of Es, addition of RGD moiety or an additional zinc biding site to N-terminal of Es , fusing of Es to anti-HER2 IgG or heavy-chain of IgG, and finally loading of the endostar by PLGA and PEG- PLGA nanoparticles and gold nano-shell particles are the effective bioengineering methods to overcome to clinical changes of endostatin.

Inside a plant nucleus: discovering the proteins

Czech Academy of Sciences Publication Activity Database

Petrovská, Beáta; Šebela, M.; Doležel, Jaroslav

2015-01-01

Roč. 66, č. 6 (2015), s. 1627-1640 ISSN 0022-0957 R&D Projects: GA ČR(CZ) GA14-28443S; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Cell nucleus * chromatin * genome function Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.677, year: 2015

Unraveling molecular mechanistic differences in liver metabolism between lean and fat lines of Pekin duck (Anas platyrhynchos domestica): a proteomic study.

Science.gov (United States)

Zheng, Aijuan; Chang, Wenhuan; Hou, Shuisheng; Zhang, Shu; Cai, Huiyi; Chen, Guilan; Lou, Ruiying; Liu, Guohua

2014-02-26

Duck is one of the major poultry meat sources for human consumption. To satisfy different eating habits, lean and fat strains of Pekin ducks have been developed. The objective of this study was to determine the molecular mechanistic differences in liver metabolism between two duck strains. The liver proteome of the Pekin duck lines was compared on days 1, 14, 28, and 42 posthatching using 2-DE based proteomics. There was a different abundance of 76 proteins in the livers of the two duck lines. Fat ducks strongly expressed proteins related to pathways of glycolysis, ATP synthesis, and protein catabolism, suggesting enhanced fat deposition rather than protein retention. In contrast, highly expressed proteins in lean ducks improved protein anabolism and reduced protein catabolism, resulting in an enhancement of lean meat deposition. Along with the decrease in fat deposition, the immune system of the lean duck strain may be enhanced by enhanced expression of proteins involved in stress response, immune defense, and antioxidant functions. These results indicate that selection pressure has shaped the two duck lines differently resulting in different liver metabolic capacities. These observed variations between the two strains at the molecular level are matched with physiological changes in growth performance and meat production. This information may have beneficial impacts in areas such as genetic modification through the manipulation of target proteins or genes in specific pathways to improve the efficiency of duck meat production. The objective of this study was to unravel molecular mechanistic differences in liver metabolism between lean and fat Pekin duck (Anas platyrhynchos domestica) strains. There was a different abundance of 76 proteins in the livers of the two duck lines. Enhanced protein expression in the fat ducks related to pathways of glycolysis, ATP synthesis and protein catabolism suggesting increased fat deposition rather than protein retention. In

Molecular beam epitaxy of Cd3As2 on a III-V substrate

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Timo Schumann

2016-12-01

Full Text Available Epitaxial, strain-engineered Dirac semimetal heterostructures promise tuning of the unique properties of these materials. In this study, we investigate the growth of thin films of the recently discovered Dirac semimetal Cd3As2 by molecular beam epitaxy. We show that epitaxial Cd3As2 layers can be grown at low temperatures (110 °C–220 °C, in situ, on (111 GaSb buffer layers deposited on (111 GaAs substrates. The orientation relationship is described by ( 112 Cd 3 As 2 || (111 GaSb and [ 1 1 ¯ 0 ] Cd 3 As 2 || [ 1 ¯ 01 ] GaSb . The films are shown to grow in the low-temperature, vacancy ordered, tetragonal Dirac semimetal phase. They exhibit high room temperature mobilities of up to 19300 cm2/Vs, despite a three-dimensional surface morphology indicative of island growth and the presence of twin variants. The results indicate that epitaxial growth on more closely lattice matched buffer layers, such as InGaSb or InAlSb, which allow for imposing different degrees of epitaxial coherency strains, should be possible.

Molecular dynamics simulation of carbon molecular sieve preparation for air separation

International Nuclear Information System (INIS)

Yaghoobpour, Elham; Ahmadpour, Ali; Farhadian, Nafiseh; Shariaty-Niassar, Mojtaba

2015-01-01

Carbon deposition process on activated carbon (AC) in order to produce carbon molecular sieve (CMS) was simulated using molecular dynamics simulation. The proposed activated carbon for simulation includes micropores with different characteristic diameters and lengths. Three different temperatures of 773 K, 973 K, and 1,273 K were selected to investigate the optimum deposition temperature. Simulation results show that the carbon deposition process at 973 K creates the best adsorbent structure. While at lower temperature some micropore openings are blocked with carbon atoms, at higher temperature the number of deposited carbons on the micropores does not change significantly. Also, carbon deposition process confirms the pseudo-second-order kinetic model with an endothermic behavior. To evaluate the sieving property of adsorbent products, nitrogen and oxygen adsorption on the initial and final adsorbent products are examined. Results show that there is not any considerable difference between the equilibrium adsorption amounts of nitrogen and oxygen on the initial and final adsorbents especially at low pressure (P<10 atm). Although, adsorption kinetics curves of these gases change significantly after the carbon deposition process in comparison with the initial sample. These observations indicate that the final adsorbent has high selectivity towards oxygen compared with the nitrogen, so it can be called a carbon molecular sieve. All simulated results are in good agreement with experiments

Molecular dynamics simulation of carbon molecular sieve preparation for air separation

Energy Technology Data Exchange (ETDEWEB)

Yaghoobpour, Elham; Ahmadpour, Ali; Farhadian, Nafiseh [Ferdowsi University of Mashhad, Mashhad (Iran, Islamic Republic of); Shariaty-Niassar, Mojtaba [University of Tehran, Tehran(Iran, Islamic Republic of)

2015-03-15

Carbon deposition process on activated carbon (AC) in order to produce carbon molecular sieve (CMS) was simulated using molecular dynamics simulation. The proposed activated carbon for simulation includes micropores with different characteristic diameters and lengths. Three different temperatures of 773 K, 973 K, and 1,273 K were selected to investigate the optimum deposition temperature. Simulation results show that the carbon deposition process at 973 K creates the best adsorbent structure. While at lower temperature some micropore openings are blocked with carbon atoms, at higher temperature the number of deposited carbons on the micropores does not change significantly. Also, carbon deposition process confirms the pseudo-second-order kinetic model with an endothermic behavior. To evaluate the sieving property of adsorbent products, nitrogen and oxygen adsorption on the initial and final adsorbent products are examined. Results show that there is not any considerable difference between the equilibrium adsorption amounts of nitrogen and oxygen on the initial and final adsorbents especially at low pressure (P<10 atm). Although, adsorption kinetics curves of these gases change significantly after the carbon deposition process in comparison with the initial sample. These observations indicate that the final adsorbent has high selectivity towards oxygen compared with the nitrogen, so it can be called a carbon molecular sieve. All simulated results are in good agreement with experiments.

Discovering governing equations from data by sparse identification of nonlinear dynamics

Science.gov (United States)

Brunton, Steven

The ability to discover physical laws and governing equations from data is one of humankind's greatest intellectual achievements. A quantitative understanding of dynamic constraints and balances in nature has facilitated rapid development of knowledge and enabled advanced technology, including aircraft, combustion engines, satellites, and electrical power. There are many more critical data-driven problems, such as understanding cognition from neural recordings, inferring patterns in climate, determining stability of financial markets, predicting and suppressing the spread of disease, and controlling turbulence for greener transportation and energy. With abundant data and elusive laws, data-driven discovery of dynamics will continue to play an increasingly important role in these efforts. This work develops a general framework to discover the governing equations underlying a dynamical system simply from data measurements, leveraging advances in sparsity-promoting techniques and machine learning. The resulting models are parsimonious, balancing model complexity with descriptive ability while avoiding overfitting. The only assumption about the structure of the model is that there are only a few important terms that govern the dynamics, so that the equations are sparse in the space of possible functions. This perspective, combining dynamical systems with machine learning and sparse sensing, is explored with the overarching goal of real-time closed-loop feedback control of complex systems. This is joint work with Joshua L. Proctor and J. Nathan Kutz. Video Abstract: https://www.youtube.com/watch?v=gSCa78TIldg

Molecular detection and identification of Rickettsiales pathogens in dog ticks from Costa Rica.

Science.gov (United States)

Campos-Calderón, Liliana; Ábrego-Sánchez, Leyda; Solórzano-Morales, Antony; Alberti, Alberto; Tore, Gessica; Zobba, Rosanna; Jiménez-Rocha, Ana E; Dolz, Gaby

2016-10-01

Although vector-borne diseases are globally widespread with considerable impact on animal production and on public health, few reports document their presence in Central America. This study focuses on the detection and molecular identification of species belonging to selected bacterial genera (Ehrlichia, Anaplasma and Rickettsia) in ticks sampled from dogs in Costa Rica by targeting several genes: 16S rRNA/dsb genes for Ehrlichia; 16S rRNA/groEL genes for Anaplasma, and ompA/gltA/groEL genes for Rickettsia. PCR and sequence analyses provides evidences of Ehrlichia canis, Anaplasma platys, and Anaplasma phagocytophilum infection in Rhipicephalus sanguineus s.l ticks, and allow establishing the presence of Rickettsia monacensis in Ixodes boliviensis. Furthermore, the presence of recently discovered Mediterranean A. platys-like strains is reported for the first time in Central America. Results provide new background on geographical distribution of selected tick-transmitted bacterial pathogens in Costa Rica and on their molecular epidemiology, and are pivotal to the development of effective and reliable diagnostic tools in Central America. Copyright © 2016 Elsevier GmbH. All rights reserved.

Description of a newly discovered Triatoma infestans (Hemiptera: Reduviidae Foci in Ibipeba, State of Bahia, Brazil

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Renato Freitas Araújo

2014-07-01

Full Text Available Introduction Chagas disease transmitted by the Triatoma infestans was eradicated from Brazil in 2006. However, reports of triatomine foci threaten the control of Chagas disease. The goal of this study was to determine T. infestans foci in the City of Ibipeba, State of Bahia. Methods Triatominae specimens were collected in Ibipeba and entomologic indicators were calculated using indices of domiciliary infestation, density, and colonization. Results T. infestans foci was discovery in Ibipeba, State of Bahia. Approximately 95% of the specimens were discovered inside dwellings, of which 34% were T. infestans. This species was also discovered forming a colony in tree bark in the peridomicile. Conclusions Triatoma infestans foci in peridomestic ecotopes in Ibipeba, BA, indicate increased the risk of transmission Chagas disease.

Structural differences between native Hen egg white lysozyme and its fibrils under different environmental conditions

Science.gov (United States)

Bhattacharya, Susmita; Ghosh, Sudeshna; Dasgupta, Swagata; Roy, Anushree

2013-10-01

The difference in molecular structure of native HEWL and its fibrils, grown at a pH value near physiological pH 7.4 and at a pH value just above the pI, 10.7 in presence and absence of Cu(II) ions, is discussed. We focus on differences between the molecular structure of the native protein and fibrils using principal component analysis of their Raman spectra. The overlap areas of the scores of each species are used to quantify the difference in the structure of the native HEWL and fibrils in different environments. The overall molecular structures are significantly different for fibrils grown at two pH values. However, in presence of Cu(II) ions, the fibrils have similarities in their molecular structures at these pH environments. Spectral variation within each species, as obtained from the standard deviations of the scores in PCA plots, reveals the variability in the structure within a particular species.

Chapare virus, a newly discovered arenavirus isolated from a fatal hemorrhagic fever case in Bolivia.

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Simon Delgado

2008-04-01

Full Text Available A small focus of hemorrhagic fever (HF cases occurred near Cochabamba, Bolivia, in December 2003 and January 2004. Specimens were available from only one fatal case, which had a clinical course that included fever, headache, arthralgia, myalgia, and vomiting with subsequent deterioration and multiple hemorrhagic signs. A non-cytopathic virus was isolated from two of the patient serum samples, and identified as an arenavirus by IFA staining with a rabbit polyvalent antiserum raised against South American arenaviruses known to be associated with HF (Guanarito, Machupo, and Sabiá. RT-PCR analysis and subsequent analysis of the complete virus S and L RNA segment sequences identified the virus as a member of the New World Clade B arenaviruses, which includes all the pathogenic South American arenaviruses. The virus was shown to be most closely related to Sabiá virus, but with 26% and 30% nucleotide difference in the S and L segments, and 26%, 28%, 15% and 22% amino acid differences for the L, Z, N, and GP proteins, respectively, indicating the virus represents a newly discovered arenavirus, for which we propose the name Chapare virus. In conclusion, two different arenaviruses, Machupo and Chapare, can be associated with severe HF cases in Bolivia.

Discovering a Reliable Heat-Shock Factor-1 Inhibitor to Treat Human Cancers: Potential Opportunity for Phytochemists

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Murugesan Velayutham

2018-04-01

Full Text Available Heat-shock factor-1 (HSF-1 is an important transcription factor that regulates pathogenesis of many human diseases through its extensive transcriptional regulation. Especially, it shows pleiotropic effects in human cancer, and hence it has recently received increased attention of cancer researchers. After myriad investigations on HSF-1, the field has advanced to the phase where there is consensus that finding a potent and selective pharmacological inhibitor for this transcription factor will be a major break-through in the treatment of various human cancers. Presently, all reported inhibitors have their limitations, made evident at different stages of clinical trials. This brief account summarizes the advances with tested natural products as HSF-1 inhibitors and highlights the necessity of phytochemistry in this endeavor of discovering a potent pharmacological HSF-1 inhibitor.

Evolution of cell cycle control: same molecular machines, different regulation

DEFF Research Database (Denmark)

de Lichtenberg, Ulrik; Jensen, Thomas Skøt; Brunak, Søren

2007-01-01

Decades of research has together with the availability of whole genomes made it clear that many of the core components involved in the cell cycle are conserved across eukaryotes, both functionally and structurally. These proteins are organized in complexes and modules that are activated or deacti......Decades of research has together with the availability of whole genomes made it clear that many of the core components involved in the cell cycle are conserved across eukaryotes, both functionally and structurally. These proteins are organized in complexes and modules that are activated...... for assembling the same molecular machines just in time for action....

Stereoselective Degradation and Molecular Ecological Mechanism of Chiral Pesticides Beta-Cypermethrin in Soils with Different pH Values.

Science.gov (United States)

Yang, Zhong-Hua; Ji, Guo-Dong

2015-12-15

For decades, pesticides have been widely used for agricultural activities around the world, and the environmental problems caused by these compounds have raised widespread concern. However, the different enantioselective behaviors of chiral pesticide enantiomers are often ignored. Here, the selective degradation patterns and mechanisms of chiral pesticide enantiomers were successfully investigated for the first time in the soils of three cultivation areas with different pH values. Beta-cypermethrin was chosen as the target analyte. We found that the degradation rates of the four isomers of beta-cypermethrin were different. We used stepwise regression equations between degradation rates and functional genes to quantitatively study their relationships. Quantitative response analysis revealed that different isomers have different equations even under identical conditions. The results of path analysis showed that a single functional gene can make different direct and indirect contributions to the degradation of different isomers. Finally, the high-throughput technology was used to analysis the genome of the three tested soils and then compared the main microbial communities in them. We have successfully devised a method to investigate the molecular biological mechanisms of the selective degradation behavior of chiral compounds, thus enabling us to better understand these mechanisms.

Dynamics and Thermodynamics of Molecular Machines

DEFF Research Database (Denmark)

Golubeva, Natalia

2014-01-01

to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...

Lung eQTLs to help reveal the molecular underpinnings of asthma.

Directory of Open Access Journals (Sweden)

Ke Hao

Full Text Available Genome-wide association studies (GWAS have identified loci reproducibly associated with pulmonary diseases; however, the molecular mechanism underlying these associations are largely unknown. The objectives of this study were to discover genetic variants affecting gene expression in human lung tissue, to refine susceptibility loci for asthma identified in GWAS studies, and to use the genetics of gene expression and network analyses to find key molecular drivers of asthma. We performed a genome-wide search for expression quantitative trait loci (eQTL in 1,111 human lung samples. The lung eQTL dataset was then used to inform asthma genetic studies reported in the literature. The top ranked lung eQTLs were integrated with the GWAS on asthma reported by the GABRIEL consortium to generate a Bayesian gene expression network for discovery of novel molecular pathways underpinning asthma. We detected 17,178 cis- and 593 trans- lung eQTLs, which can be used to explore the functional consequences of loci associated with lung diseases and traits. Some strong eQTLs are also asthma susceptibility loci. For example, rs3859192 on chr17q21 is robustly associated with the mRNA levels of GSDMA (P = 3.55 × 10(-151. The genetic-gene expression network identified the SOCS3 pathway as one of the key drivers of asthma. The eQTLs and gene networks identified in this study are powerful tools for elucidating the causal mechanisms underlying pulmonary disease. This data resource offers much-needed support to pinpoint the causal genes and characterize the molecular function of gene variants associated with lung diseases.

Molecular thermodynamics of nonideal fluids

CERN Document Server

Lee, Lloyd L

2013-01-01

Molecular Thermodynamics of Nonideal Fluids serves as an introductory presentation for engineers to the concepts and principles behind and the advances in molecular thermodynamics of nonideal fluids. The book covers related topics such as the laws of thermodynamics; entropy; its ensembles; the different properties of the ideal gas; and the structure of liquids. Also covered in the book are topics such as integral equation theories; theories for polar fluids; solution thermodynamics; and molecular dynamics. The text is recommended for engineers who would like to be familiarized with the concept

Discover Health Services Near You! The North Dakota Story: Part II

OpenAIRE

Safratowich, Michael; Markland, Mary J.; Rieke, Judith L.

2009-01-01

Since the 2003 launch of NC Health Info, the National Library of Medicine has encouraged the development of Go Local databases. A team of Go Local enthusiasts at North Dakota’s only medical school library wanted to obtain NLM funding and build a resource for their rural state. Although short on staff, money, and time, the team found a way to realize a Go Local database that serves the state’s residents and helps them “Discover Health Services Near You!” A team approach and collaboration with ...

Discover Health Services Near You! The North Dakota Story: Part I

OpenAIRE

Rieke, Judith L.; Safratowich, Michael; Markland, Mary J.

2009-01-01

Since the 2003 launch of NC Health Info, the National Library of Medicine has encouraged the development of Go Local databases. A team of Go Local enthusiasts at North Dakota’s only medical school library wanted to obtain NLM funding and build a resource for their rural state. Although short on staff, money, and time, the team found a way to realize a Go Local database that serves the state’s residents and helps them “Discover Health Services Near You!” A team approach and collaboration with ...

Communication between the right and circumflex coronary arteries discovered incidentally by multidetector computed tomography

Energy Technology Data Exchange (ETDEWEB)

Kwon, Se Hwan; Kim, Eui Jong; Woo, Jong Shin; Kim, Soo Joong; Youn, Hyo Chul; Oh, Joo Hyeong [College of Medicine, Kyung Hee University, Seoul (Korea, Republic of)

2016-09-15

Intercoronary communication is a rare congenital coronary anomaly. We present a case of a 48-year-old man with an incidentally discovered communication between the right and circumflex coronary arteries, who was admitted with chest tightness and exertional dyspnea. The initial diagnosis was made using electrocardiogram-gated multidetector computed tomography.

Morphological, molecular and functional differences of adult bone marrow- and adipose-derived stem cells isolated from rats of different ages

International Nuclear Information System (INIS)

Mantovani, Cristina; Raimondo, Stefania; Haneef, Maryam S.; Geuna, Stefano; Terenghi, Giorgio; Shawcross, Susan G.; Wiberg, Mikael

2012-01-01

Adult mesenchymal stem cells have self-renewal and multiple differentiation potentials, and play important roles in regenerative medicine. However, their use may be limited by senescence or age of the donor, leading to changes in stem cell functionality. We investigated morphological, molecular and functional differences between bone marrow-derived (MSC) and adipose-derived (ASC) stem cells isolated from neonatal, young and old rats compared to Schwann cells from the same animals. Immunocytochemistry, RT-PCR, proliferation assays, western blotting and transmission electron microscopy were used to investigate expression of senescence markers. Undifferentiated and differentiated ASC and MSC from animals of different ages expressed Notch-2 at similar levels; protein-38 and protein-53 were present in all groups of cells with a trend towards increased levels in cells from older animals compared to those from neonatal and young rats. Following co-culture with adult neuronal cells, dMSC and dASC from animals of all ages elicited robust neurite outgrowth. Mitotracker ® staining was consistent with ultrastructural changes seen in the mitochondria of cells from old rats, indicative of senescence. In conclusion, this study showed that although the cells from aged animals expressed markers of senescence, aged MSC and ASC differentiated into SC-like cells still retain potential to support axon regeneration. -- Highlights: ► Aged MSC and ASC differentiated into Schwann-like cells support axon regeneration. ► p53 expression does not appreciably influence the biology of Schwann or stem cells. ► Notch 2 expression was similar in cells derived from animals of different ages. ► Proliferation rates of dMSC varied little over time or with animal age.

Molecular Evolution of Slow and Quick Anion Channels (SLACs and QUACs/ALMTs).

Science.gov (United States)

Dreyer, Ingo; Gomez-Porras, Judith Lucia; Riaño-Pachón, Diego Mauricio; Hedrich, Rainer; Geiger, Dietmar

2012-01-01

Electrophysiological analyses conducted about 25 years ago detected two types of anion channels in the plasma membrane of guard cells. One type of channel responds slowly to changes in membrane voltage while the other responds quickly. Consequently, they were named SLAC, for SLow Anion Channel, and QUAC, for QUick Anion Channel. Recently, genes SLAC1 and QUAC1/ALMT12, underlying the two different anion current components, could be identified in the model plant Arabidopsis thaliana. Expression of the gene products in Xenopus oocytes confirmed the quick and slow current kinetics. In this study we provide an overview on our current knowledge on slow and quick anion channels in plants and analyze the molecular evolution of ALMT/QUAC-like and SLAC-like channels. We discovered fingerprints that allow screening databases for these channel types and were able to identify 192 (177 non-redundant) SLAC-like and 422 (402 non-redundant) ALMT/QUAC-like proteins in the fully sequenced genomes of 32 plant species. Phylogenetic analyses provided new insights into the molecular evolution of these channel types. We also combined sequence alignment and clustering with predictions of protein features, leading to the identification of known conserved phosphorylation sites in SLAC1-like channels along with potential sites that have not been yet experimentally confirmed. Using a similar strategy to analyze the hydropathicity of ALMT/QUAC-like channels, we propose a modified topology with additional transmembrane regions that integrates structure and function of these membrane proteins. Our results suggest that cross-referencing phylogenetic analyses with position-specific protein properties and functional data could be a very powerful tool for genome research approaches in general.

Molecular evolution of slow and quick anion channels (SLACs and QUACs/ALMTs

Directory of Open Access Journals (Sweden)

Ingo eDreyer

2012-11-01

Full Text Available Electrophysiological analyses conducted about 25 years ago detected two types of anion channels in the plasma membrane of guard cells. One type of channel responds slowly to changes in membrane voltage while the other responds quickly. Consequently, they were named SLAC, for SLow Anion Channel, and QUAC, for QUick Anion Channel. Recently, genes SLAC1 and QUAC1/ALMT12, underlying the two different anion current components, could be identified in the model plant Arabidopsis thaliana. Expression of the gene products in Xenopus oocytes confirmed the quick and slow current kinetics. In this study we provide an overview on our current knowledge on slow and quick anion channels in plants and analyze the molecular evolution of ALMT/QUAC-like and SLAC-like channels. We discovered fingerprints that allow screening databases for these channel types and were able to identify 192 (177 non-redundant SLAC-like and 422 (402 non-redundant ALMT/QUAC-like proteins in the fully sequenced genomes of 32 plant species. Phylogenetic analyses provided new insights into the molecular evolution of these channel types. We also combined sequence alignment and clustering with predictions of protein features, leading to the identification of known conserved phosphorylation sites in SLAC1-like channels along with potential sites that have not been yet experimentally confirmed. Using a similar strategy to analyze the hydropathicity of ALMT/QUAC-like channels, we propose a modified topology with additional transmembrane regions that integrates structure and function of these membrane proteins. Our results suggest that cross-referencing phylogenetic analyses with position-specific protein properties and functional data could be a very powerful tool for genome research approaches in general.

Distinct high molecular weight organic compound (HMW-OC) types in aerosol particles collected at a coastal urban site

Science.gov (United States)

Dall'Osto, M.; Healy, R. M.; Wenger, J. C.; O'Dowd, C.; Ovadnevaite, J.; Ceburnis, D.; Harrison, Roy M.; Beddows, D. C. S.

2017-12-01

Organic oligomers were discovered in laboratory-generated atmospheric aerosol over a decade ago. However, evidence for the presence of oligomers in ambient aerosols is scarce and mechanisms for their formation have yet to be fully elucidated. In this work, three unique aerosol particle types internally mixed with High molecular weight organic compounds (HMW-OC) species - likely oligomers - were detected in ambient air using single particle Aerosol Time-Of-Flight Mass Spectrometry (ATOFMS) in Cork (Ireland) during winter 2009. These particle types can be described as follows: (1) HMW-OCs rich in organic nitrogen - possibly containing nitrocatechols and nitroguaiacols - originating from primary emissions of biomass burning particles during evening times; (2) HMW-OCs internally mixed with nitric acid, occurring in stagnant conditions during night time; and (3) HMW-OCs internally mixed with sea salt, likely formed via photochemical reactions during day time. The study exemplifies the power of methodologies capable of monitoring the simultaneous formation of organic and inorganic particle-phase reaction products. Primary emissions and atmospheric aging of different types of HMW-OC contributes to aerosol with a range of acidity, hygroscopic and optical properties, which can have different impacts on climate and health.

Molecular Weight and Structural Properties of Biodegradable PLA Synthesized with Different Catalysts by Direct Melt Polycondensation

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Hyung Woo Lee

2015-09-01

Full Text Available Production of biodegradable polylactic acid (PLA from biomassbased lactic acid is widely studied for substituting petro-based plastics or polymers. This study investigated PLA production from commercial lactic acid in a batch reactor by applying a direct melt polycondensation method with two kinds of catalyst, γ-aluminium(III oxide (γ-Al2O3 or zinc oxide (ZnO, in reduced pressure. The molecular weight of the synthesized PLA was determined by capillary viscometry and its structural properties were analyzed by functional group analysis using FT-IR. The yields of polymer production with respect to the theoretical conversion were 47% for γ-Al2O3 and 35% for ZnO. However, the PLA from ZnO had a higher molecular weight (150,600 g/mol than that from γ-Al2O3 (81,400 g/mol. The IR spectra of the synthesized PLA from both catalysts using polycondensation show the same behavior of absorption peaks at wave numbers from 4,500 cm-1 to 500 cm-1, whereas the PLA produced by two other polymerization methods – polycondensation and ring opening polymerization –showed a significant difference in % transmittance intensity pattern as well as peak area absorption at a wave number of 3,500 cm-1 as –OH vibration peak and at 1,750 cm-1 as –C=O carbonyl vibrational peak.

Molecular genetics of pancreatic neoplasms and their morphologic correlates: an update on recent advances and potential diagnostic applications.

Science.gov (United States)

Reid, Michelle D; Saka, Burcu; Balci, Serdar; Goldblum, Andrew S; Adsay, N Volkan

2014-02-01

To summarize the most clinically and biologically relevant advances in molecular/genetic characteristics of various pancreatic neoplasms, with morphologic correlation. Whole-exome sequencing of numerous benign and malignant pancreatic tumors, along with the plethora of highly sensitive molecular studies now available for analyzing these tumors, provide mounting evidence to support the long-held belief that cancer is essentially a genetic disease. These genetic discoveries have not only helped to confirm the age-old, morphology-based classifications of pancreatic neoplasia but have shed new light on their mechanisms. Many of these molecular discoveries are currently being used in preoperative diagnosis. Mutations in KRAS, P16/CDKN2A, TP53, and SMAD4/DPC4 are commonly seen in ductal neoplasia but not in nonductal tumors; ductal adenocarcinomas with SMAD4/DPC4 loss are associated with widespread metastasis and poor prognosis. GNAS and RNF43 mutations have been discovered in most intraductal pancreatic mucinous neoplasms, providing critical molecular fingerprints for their diagnosis. Mutation in DAXX/ATRX is only seen in pancreatic neuroendocrine tumors, making it a useful potential marker in distinguishing these tumors from mimics. When combined with morphologic observations, molecular studies will increase our understanding of the pathogenesis and morphomolecular signatures associated with specific neoplasms and provide new horizons for precision medicine and targeted therapies.

Glioblastoma: Molecular Pathways, Stem Cells and Therapeutic Targets

International Nuclear Information System (INIS)

Jhanwar-Uniyal, Meena; Labagnara, Michael; Friedman, Marissa; Kwasnicki, Amanda; Murali, Raj

2015-01-01

Glioblastoma (GBM), a WHO-defined Grade IV astrocytoma, is the most common and aggressive CNS malignancy. Despite current treatment modalities, the survival time remains dismal. The main cause of mortality in patients with this disease is reoccurrence of the malignancy, which is attributed to treatment-resistant cancer stem cells within and surrounding the primary tumor. Inclusion of novel therapies, such as immuno- and DNA-based therapy, may provide better means of treating GBM. Furthermore, manipulation of recently discovered non-coding microRNAs, some of which regulate tumor growth through the development and maintenance of GBM stem cells, could provide new prospective therapies. Studies conducted by The Cancer Genome Atlas (TCGA) also demonstrate the role of molecular pathways, specifically the activated PI3K/AKT/mTOR pathway, in GBM tumorigenesis. Inhibition of the aforementioned pathway may provide a more direct and targeted method to GBM treatment. The combination of these treatment modalities may provide an innovative therapeutic approach for the management of GBM

Glioblastoma: Molecular Pathways, Stem Cells and Therapeutic Targets

Energy Technology Data Exchange (ETDEWEB)

Jhanwar-Uniyal, Meena, E-mail: meena_jhanwar@nymc.edu; Labagnara, Michael; Friedman, Marissa; Kwasnicki, Amanda; Murali, Raj [Department of Neurosurgery, New York Medical College, Valhalla, NY 10595 (United States)

2015-03-25

Glioblastoma (GBM), a WHO-defined Grade IV astrocytoma, is the most common and aggressive CNS malignancy. Despite current treatment modalities, the survival time remains dismal. The main cause of mortality in patients with this disease is reoccurrence of the malignancy, which is attributed to treatment-resistant cancer stem cells within and surrounding the primary tumor. Inclusion of novel therapies, such as immuno- and DNA-based therapy, may provide better means of treating GBM. Furthermore, manipulation of recently discovered non-coding microRNAs, some of which regulate tumor growth through the development and maintenance of GBM stem cells, could provide new prospective therapies. Studies conducted by The Cancer Genome Atlas (TCGA) also demonstrate the role of molecular pathways, specifically the activated PI3K/AKT/mTOR pathway, in GBM tumorigenesis. Inhibition of the aforementioned pathway may provide a more direct and targeted method to GBM treatment. The combination of these treatment modalities may provide an innovative therapeutic approach for the management of GBM.

Preparing for TESS: Precision Ground-based Light-curves of Newly Discovered Transiting Exoplanets

Science.gov (United States)

Li, Yiting; Stefansson, Gudmundur; Mahadevan, Suvrath; Monson, Andy; Hebb, Leslie; Wisniewski, John; Huehnerhoff, Joseph

2018-01-01

NASA’s Transiting Exoplanet Survey Satellite (TESS), to be launched in early 2018, is expected to catalog a myriad of transiting exoplanet candidates ranging from Earth-sized to gas giants, orbiting a diverse range of stellar types in the solar neighborhood. In particular, TESS will find small planets orbiting the closest and brightest stars, and will enable detailed atmospheric characterizations of planets with current and future telescopes. In the TESS era, ground-based follow-up resources will play a critical role in validating and confirming the planetary nature of the candidates TESS will discover. Along with confirming the planetary nature of exoplanet transits, high precision ground-based transit observations allow us to put further constraints on exoplanet orbital parameters and transit timing variations. In this talk, we present new observations of transiting exoplanets recently discovered by the K2 mission, using the optical diffuser on the 3.5m ARC Telescope at Apache Point Observatory. These include observations of the mini-Neptunes K2-28b and K2-104b orbiting early-to-mid M-dwarfs. In addition, other recent transit observations performed using the robotic 30cm telescope at Las Campanas Observatory in Chile will be presented.

Plasticization of poly(lactic acid) using different molecular weight of Poly(ethylene glycol)

Science.gov (United States)

Septevani, Athanasia Amanda; Bhakri, Samsul

2017-11-01

Poly (lactic acid) (PLA) has been known as an excellent candidate for developing the future bioplastic due to its biodegradability and competitive price. However, inherent brittleness and low thermal stability of PLA have limited its applications. Considerable studies have been developed to improve the flexibility of PLA, in which blending PLA with various plasticizers has been identified as a cost-effective way to lower glass-transition temperature (Tg) and thus improve its elongation property. In this study, PLA was modified by incorporating poly(ethylene glycol) as a plasticizer with different molecular weights (M¯w 400, 1000, and 6000, called respectively as PEG 400, PEG 1000, and PEG 6000) via a solvent-casting blend method. FTIR was used for analyzing the chemical interaction while TGA and DSC measured the thermal behavior of PLA/PEG. The results indicated that the addition of lower M¯w (PEG 400 and PEG 1000) could reduce the Tg due to the enhancement of chain mobility of PLA with PEG and so driving into a more amorphous states resulted reduction of melting temperature (Tm) compared to the neat PLA. Further, at a higher M¯w of PEG 6000, the longer chain of ethylene glycol, in contrast, resulted a gradual increase in the Tg as well as Tm where the value went back to the point of neat PLA compared to the other lower molecular weight of PLA. This was due to the decrease in polymer miscibility with the increasing of M¯w. In terms of thermal stability, the addition of PEG exhibited two step degradation behavior while the neat PLA only possessed single step degradation. The presence of PEG could act as a protective barrier layer that could hinder the permeability of the volatile compound and product during decomposition reaction and thus could eventually delay and slower the degradation process. It was observed that the addition of PEG at higher M¯w (PEG1000 and PEG 6000) exhibited a higher second degradation temperature up to 380 °C.

SOLAR SYSTEM ANALOGS AROUND IRAS-DISCOVERED DEBRIS DISKS

International Nuclear Information System (INIS)

Chen, Christine H.; Sheehan, Patrick; Watson, Dan M.; Manoj, P.; Najita, Joan R.

2009-01-01

We have rereduced Spitzer IRS spectra and reanalyzed the spectral energy distributions (SEDs) of three nearby debris disks: λ Boo, HD 139664, and HR 8799. We find that the thermal emission from these objects is well modeled using two single temperature black body components. For HR 8799 - with no silicate emission features despite a relatively hot inner dust component (T gr = 150 K) - we infer the presence of an asteroid belt interior to and a Kuiper Belt exterior to the recently discovered orbiting planets. For HD 139664, which has been imaged in scattered light, we infer the presence of strongly forward scattering grains, consistent with porous grains, if the cold, outer disk component generates both the observed scattered light and thermal emission. Finally, careful analysis of the λ Boo SED suggests that this system possesses a central clearing, indicating that selective accretion of solids onto the central star does not occur from a dusty disk.

Molecular Evolution at a Meiosis Gene Mediates Species Differences in the Rate and Patterning of Recombination.

Science.gov (United States)

Brand, Cara L; Cattani, M Victoria; Kingan, Sarah B; Landeen, Emily L; Presgraves, Daven C

2018-04-23

Crossing over between homologous chromosomes during meiosis repairs programmed DNA double-strand breaks, ensures proper segregation at meiosis I [1], shapes the genomic distribution of nucleotide variability in populations, and enhances the efficacy of natural selection among genetically linked sites [2]. Between closely related Drosophila species, large differences exist in the rate and chromosomal distribution of crossing over. Little, however, is known about the molecular genetic changes or population genetic forces that mediate evolved differences in recombination between species [3, 4]. Here, we show that a meiosis gene with a history of rapid evolution acts as a trans-acting modifier of species differences in crossing over. In transgenic flies, the dicistronic gene, mei-217/mei-218, recapitulates a large part of the species differences in the rate and chromosomal distribution of crossing over. These phenotypic differences appear to result from changes in protein sequence not gene expression. Our population genetics analyses show that the protein-coding sequence of mei-218, but not mei-217, has a history of recurrent positive natural selection. By modulating the intensity of centromeric and telomeric suppression of crossing over, evolution at mei-217/-218 has incidentally shaped gross differences in the chromosomal distribution of nucleotide variability between species. We speculate that recurrent bouts of adaptive evolution at mei-217/-218 might reflect a history of coevolution with selfish genetic elements. Copyright © 2018 Elsevier Ltd. All rights reserved.

Clustering the Orion B giant molecular cloud based on its molecular emission

Science.gov (United States)

Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H.; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R.; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

2018-02-01

Context. Previous attempts at segmenting molecular line maps of molecular clouds have focused on using position-position-velocity data cubes of a single molecular line to separate the spatial components of the cloud. In contrast, wide field spectral imaging over a large spectral bandwidth in the (sub)mm domain now allows one to combine multiple molecular tracers to understand the different physical and chemical phases that constitute giant molecular clouds (GMCs). Aims: We aim at using multiple tracers (sensitive to different physical processes and conditions) to segment a molecular cloud into physically/chemically similar regions (rather than spatially connected components), thus disentangling the different physical/chemical phases present in the cloud. Methods: We use a machine learning clustering method, namely the Meanshift algorithm, to cluster pixels with similar molecular emission, ignoring spatial information. Clusters are defined around each maximum of the multidimensional probability density function (PDF) of the line integrated intensities. Simple radiative transfer models were used to interpret the astrophysical information uncovered by the clustering analysis. Results: A clustering analysis based only on the J = 1-0 lines of three isotopologues of CO proves sufficient to reveal distinct density/column density regimes (nH 100 cm-3, 500 cm-3, and >1000 cm-3), closely related to the usual definitions of diffuse, translucent and high-column-density regions. Adding two UV-sensitive tracers, the J = 1-0 line of HCO+ and the N = 1-0 line of CN, allows us to distinguish two clearly distinct chemical regimes, characteristic of UV-illuminated and UV-shielded gas. The UV-illuminated regime shows overbright HCO+ and CN emission, which we relate to a photochemical enrichment effect. We also find a tail of high CN/HCO+ intensity ratio in UV-illuminated regions. Finer distinctions in density classes (nH 7 × 103 cm-3, 4 × 104 cm-3) for the densest regions are also

Role of ELA region in auto-activation of mutant KIT receptor: a molecular dynamics simulation insight.

Science.gov (United States)

Purohit, Rituraj

2014-01-01

KIT receptor is the prime target in gastrointestinal stromal tumor (GISTs) therapy. Second generation inhibitor, Sunitinib, binds to an inactivated conformation of KIT receptor and stabilizes it in order to prevent tumor formation. Here, we investigated the dynamic behavior of wild type and mutant D816H KIT receptor, and emphasized the extended A-loop (EAL) region (805-850) by conducting molecular dynamics simulation (∼100 ns). We analyzed different properties such as root mean square cutoff or deviation, root mean square fluctuation, radius of gyration, solvent-accessible surface area, hydrogen bonding network analysis, and essential dynamics. Apart from this, clustering and cross-correlation matrix approach was used to explore the conformational space of the wild type and mutant EAL region of KIT receptor. Molecular dynamics analysis indicated that mutation (D816H) was able to alter intramolecular hydrogen bonding pattern and affected the structural flexibility of EAL region. Moreover, flexible secondary elements, specially, coil and turns were dominated in EAL region of mutant KIT receptor during simulation. This phenomenon increased the movement of EAL region which in turn helped in shifting the equilibrium towards the active kinase conformation. Our atomic investigation of mutant KIT receptor which emphasized on EAL region provided a better insight into the understanding of Sunitinib resistance mechanism of KIT receptor and would help to discover new therapeutics for KIT-based resistant tumor cells in GIST therapy.

Molecular dynamics simulations revealed structural differences among WRKY domain-DNA interaction in barley (Hordeum vulgare).

Science.gov (United States)

Pandey, Bharati; Grover, Abhinav; Sharma, Pradeep

2018-02-12

The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles. So far, the crystal structure of WRKY from barley has not been resolved; moreover, knowledge of the three-dimensional structure of WRKY domain is pre-requisites for exploring the protein-DNA recognition mechanisms. Homology modelling based approach was used to generate structures for WRKY DNA binding domain (DBD) and its variants using AtWRKY1 as a template. Finally, the stability and conformational changes of the generated model in unbound and bound form was examined through atomistic molecular dynamics (MD) simulations for 100 ns time period. In this study, we investigated the comparative binding pattern of WRKY domain and its variants with W-box cis-regulatory element using molecular docking and dynamics (MD) simulations assays. The atomic insight into WRKY domain exhibited significant variation in the intermolecular hydrogen bonding pattern, leading to the structural anomalies in the variant type and differences in the DNA-binding specificities. Based on the MD analysis, residual contribution and interaction contour, wild-type WRKY (HvWRKY46) were found to interact with DNA through highly conserved heptapeptide in the pre- and post-MD simulated complexes, whereas heptapeptide interaction with DNA was missing in variants (I and II) in post-MD complexes. Consequently, through principal component analysis, wild-type WRKY was also found to be more stable by obscuring a reduced conformational space than the variant I (HvWRKY34). Lastly, high binding free energy for wild-type and variant II allowed us to conclude that wild-type WRKY-DNA complex was more stable relative to variants I. The results of our study revealed complete dynamic and structural information

The Cellular and Molecular Mechanisms of Immuno-suppression by Human Type 1 Regulatory T cells

Directory of Open Access Journals (Sweden)

Silvia eGregori

2012-02-01

Full Text Available The immuno-regulatory mechanisms of IL-10-producing type 1 regulatory T (Tr1 cells have been widely studied over the years. However, several recent discoveries have shed new light on the cellular and molecular mechanisms that human Tr1 cells use to control immune responses and induce tolerance. In this review we outline the well-known and newly discovered regulatory properties of human Tr1 cells and provide an in-depth comparison of the known suppressor mechanisms of Tr1 cells with FOXP3+ Treg. We also highlight the role that Tr1 cells play in promoting and maintaining tolerance in autoimmunity, allergy, and transplantation.

Discovering MicroRNAs and Their Targets in Plants

Czech Academy of Sciences Publication Activity Database

Mishra, Ajay Kumar; Duraisamy, Ganesh Selvaraj; Matoušek, Jaroslav

2015-01-01

Roč. 34, č. 6 (2015), s. 553-571 ISSN 0735-2689 Institutional support: RVO:60077344 Keywords : computational methods * degradome * high-throughput approaches Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.810, year: 2015

Understanding Particulate Matter Dynamics in the San Joaquin Valley during DISCOVER-AQ, 2013

Science.gov (United States)

Prabhakar, G.; Zhang, X.; Kim, H.; Parworth, C.; Pusede, S. E.; Wooldridge, P. J.; Cohen, R. C.; Zhang, Q.; Cappa, C. D.

2015-12-01

Air quality in the California San Joaquin Valley (SJV) during winter continues to be the worst in the state, failing EPA's 24-hour standard for particulate matter. Despite our improved understanding of the sources of particulate matter (PM) in the valley, air-quality models are unable to predict PM concentrations accurately. We aim to characterize periods of high particulate matter concentrations in the San Joaquin Valley based on ground and airborne measurements of aerosols and gaseous pollutants, during the DISCOVER-AQ campaign, 2013. A highly instrumented aircraft flew across the SJV making three transects in a repeatable pattern, with vertical spirals over select locations. The aircraft measurements were complemented by ground measurements at these locations, with extensive chemically-speciated measurements at a ground "supersite" at Fresno. Hence, the campaign provided a comprehensive three-dimensional view of the particulate and gaseous pollutants around the valley. The vertical profiles over the different sites indicate significant variability in the concentrations and vertical distribution of PM around the valley, which are most likely driven by differences in the combined effects of emissions, chemistry and boundary layer dynamics at each site. The observations suggest that nighttime PM is dominated by surface emissions of PM from residential fuel combustion, while early morning PM is strongly influenced by mixing of low-level, above-surface, nitrate-rich layers formed from dark chemistry overnight to the surface.

Molecular weight distribution of Athabasca bitumen

Energy Technology Data Exchange (ETDEWEB)

Champagne, P J; Manolakis, E; Ternan, M

1985-03-01

A sample of whole Athabasca bitumen has been fractionated by preparative g.p.c. The weights of the fractions have been determined and their molecular weights measured by several methods. In contras to previously published data, consistent results were obtained using different solvents (THF, benzene/water) and using different techniques (v.p.o., f.p.d. and g.c.-m.s.). This has resulted in a accurate definition of the molecular weight distribution of Athabasca bitumen.