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Sample records for fms homology specifies

  1. New acute transforming feline retovirus with fms homology specifies a C-terminally truncated version of the c-fms protein that is different from SM-feline sarcoma virus v-fms protein

    International Nuclear Information System (INIS)

    Besmer, P.; Lader, E.; George, P.C.; Bergold, P.J.; Qui, F.; Zuckerman, E.E.; Hardy, W.D.

    1986-01-01

    The HZ5-feline sarcoma virus (FeSV) is a new acute transforming feline retrovirus which was isolated from a multicentric fibrosarcoma of a domestic cat. The HZ5-FeSV transforms fibroblasts in vitro and is replication defective. A biologically active integrated HZ5-FeSV provirus was molecularly cloned from cellular DNA of HZ5-FeSV-infected FRE-3A rat cells. The HZ5-FeSV has oncogene homology with the fms sequences of the SM-FeSV. The genome organization of the 8.6-kilobase HZ5-FeSV provirus is 5' Δgag-fms-Δpol-Δenv 3'. The HZ5- and SM-FeSVs display indistinguishable in vitro transformation characteristics, and the structures of the gag-fms transforming genes in the two viruses are very similar. In the HZ5-FeSV and the SM-FeSV, identical c-fms and feline leukemia virus p10 sequences form the 5' gag-fms junction. With regard to v-fms the two viruses are homologous up to 11 amino acids before the C terminus of the SM-FeSV v-fms protein. In HZ5-FeSV a segment of 362 nucleotides then follows before the 3' recombination site with feline leukemia virus pol. The new 3' v-fms sequence encodes 27 amino acids before reaching a TGA termination signal. The relationship of this sequence with the recently characterized human c-fms sequence has been examined. The 3' HZ5-FeSV v-fms sequence is homologous with 3' c-fms sequences. A frameshift mutation (11-base-pair deletion) was found in the C-terminal fms coding sequence of the HZ5-FeSV. As a result, the HZ5-FeSV v-fms protein is predicted to be a C-terminally truncated version of c-fms. This frameshift mutation may determine the oncogenic properties of v-fms in the HZ5-FeSV

  2. New acute transforming feline retovirus with fms homology specifies a C-terminally truncated version of the c-fms protein that is different from SM-feline sarcoma virus v-fms protein

    Energy Technology Data Exchange (ETDEWEB)

    Besmer, P.; Lader, E.; George, P.C.; Bergold, P.J.; Qui, F.; Zuckerman, E.E.; Hardy, W.D.

    1986-10-01

    The HZ5-feline sarcoma virus (FeSV) is a new acute transforming feline retrovirus which was isolated from a multicentric fibrosarcoma of a domestic cat. The HZ5-FeSV transforms fibroblasts in vitro and is replication defective. A biologically active integrated HZ5-FeSV provirus was molecularly cloned from cellular DNA of HZ5-FeSV-infected FRE-3A rat cells. The HZ5-FeSV has oncogene homology with the fms sequences of the SM-FeSV. The genome organization of the 8.6-kilobase HZ5-FeSV provirus is 5' ..delta..gag-fms-..delta..pol-..delta..env 3'. The HZ5- and SM-FeSVs display indistinguishable in vitro transformation characteristics, and the structures of the gag-fms transforming genes in the two viruses are very similar. In the HZ5-FeSV and the SM-FeSV, identical c-fms and feline leukemia virus p10 sequences form the 5' gag-fms junction. With regard to v-fms the two viruses are homologous up to 11 amino acids before the C terminus of the SM-FeSV v-fms protein. In HZ5-FeSV a segment of 362 nucleotides then follows before the 3' recombination site with feline leukemia virus pol. The new 3' v-fms sequence encodes 27 amino acids before reaching a TGA termination signal. The relationship of this sequence with the recently characterized human c-fms sequence has been examined. The 3' HZ5-FeSV v-fms sequence is homologous with 3' c-fms sequences. A frameshift mutation (11-base-pair deletion) was found in the C-terminal fms coding sequence of the HZ5-FeSV. As a result, the HZ5-FeSV v-fms protein is predicted to be a C-terminally truncated version of c-fms. This frameshift mutation may determine the oncogenic properties of v-fms in the HZ5-FeSV.

  3. FMS Implementation Management: Promise and Performance

    DEFF Research Database (Denmark)

    Boer, Harry; Hill, Malcolm; Krabbendam, Koos

    1990-01-01

    At the present time, industry is confronted with ever-increasing customer demand for a wider diversity of products, faster product innovation, shorter delivery times and higher delivery reliability. Flexible Manufacturing Systems (FMS) are widely regarded as a major technological response...... to this need for increased flexibility. Since the development of the first FMS in 1962, a few hundred FMS have been installed worldwide. The number of companies that have experience in operating an FMS over a long period is very much smaller, so it is hardly known whether, and under what circumstances...

  4. Planning and scheduling in an FMS

    NARCIS (Netherlands)

    Aanen, E.; Gaalman, G.J.; Nawijn, W.M.

    1989-01-01

    The Dutch institute of applied physics of TNO and the Institute of Metals TNO (Apeldoorn) have installed a flexible manufacturing system (FMS). The main components of this FMS are a turret lathe, a machining centre and a transport system. One of the objectives of this system is to produce a wide

  5. Expression of a fms-related oncogene in carcinogen-induced neoplastic epithelial cells

    International Nuclear Information System (INIS)

    Walker, C.; Nettesheim, P.; Barrett, J.C.; Gilmer, T.M.

    1987-01-01

    Following carcinogen exposure in vitro, normal rat tracheal epithelial cells are transformed in a multistage process in which the cultured cells become immortal and ultimately, neoplastic. Five cell lines derived from tumors produced by neoplastically transformed rat tracheal epithelial cells were examined for the expression of 11 cellular oncogenes previously implicated in pulmonary or epithelial carcinogenesis. RNA homologous to fms was expressed at a level 5-19 times higher than normal tracheal epithelial cells in three of five of the tumor-derived lines. All three lines expressing high levels of fms-related RNA gave rise to invasive tumors of epithelial origin when injected into nude mice. Increased expression of the fms-related mRNA was not due to gene amplification, and no gene rearrangement was detected by Southern analyses. RNA blot analysis using a 3' v-fms probe detected a 9.5-kilobase message in the three tumor-derived lines, whereas both normal rat aveolar macrophages and the human choriocarcinoma line BeWo expressed a fms transcript of ≅ 4 kilobases. The authors conclude from these data that the gene expressed as a 9.5-kilobase transcript in these neoplastic epithelial cells is a member of a fms-related gene family but may be distinct from the gene that encodes the macrophage colony-stimulating factor (CSF-1) receptor

  6. 48 CFR 225.7304 - FMS customer involvement.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false FMS customer involvement... Military Sales 225.7304 FMS customer involvement. (a) FMS customers may request that a defense article or... contract without full and open competition. The FMS customer may also request that a subcontract be placed...

  7. Specifying Specification.

    Science.gov (United States)

    Paulo, Norbert

    2016-03-01

    This paper tackles the accusation that applied ethics is no serious academic enterprise because it lacks theoretical bracing. It does so in two steps. In the first step I introduce and discuss a highly acclaimed method to guarantee stability in ethical theories: Henry Richardson's specification. The discussion shows how seriously ethicists take the stability of the connection between the foundational parts of their theories and their further development as well as their "application" to particular problems or cases. A detailed scrutiny of specification leads to the second step, where I use insights from legal theory to inform the debate around stability from that point of view. This view reveals some of specification's limitations. I suggest that, once specification is sufficiently specified, it appears astonishingly similar to deduction as used in legal theory. Legal theory also provides valuable insight into the functional range of deduction and its relation to other forms of reasoning. This leads to a richer understanding of stability in normative theories and to a smart division of labor between deduction and other forms of reasoning. The comparison to legal theory thereby provides a framework for how different methods such as specification, deduction, balancing, and analogy relate to one another.

  8. Construct Validation of the FMS: Relationship between a Jump-Landing Task and FMS Items.

    Science.gov (United States)

    Kraus, Kornelius; Schütz, Elisabeth; Doyscher, Ralf

    2017-08-29

    Sports injuries and athletic performance are complex areas, which are characterized by manifold interdependencies. The landing error scoring system (LESS) is a valid screening tool to examine bilateral jump-landing mechanics. Whereas, the Functional Movement Screen (FMS) items are thought to operationalize flexibility and motor behaviour during low intense bodyweight patterns. The aim of the study was to explore possible interdependency of the diagnostic information of these screening tools. 53 athletes (age 23.3±2.1 yrs.) were tested in a sport scientific lab. In detail, 31 professional soccer players (3 Division) and 22 collegiate athletes were studied. Linear, partial correlational and cluster analysis were performed to examine possible trends. Generally, the sportsmen achieved a LESS score of 6.6±2 and a jumping height of 37±7.8cm. Partial correlational analysis indicates that trunk control (r=0.4; p<0.01) is moderately related to landing mechanics, which in turn was negatively related on LESS height (r=-0.67, p<0.01). In addition, clustering showed by trend, that a higher active straight leg raise (ASLR) score is related to better landing mechanics (ASLR score 1: LESS 6.9±1.8; n=15 vs. ASLR score 3: LESS 5.6±2.1; n=10). On the task-specific level, jump-landing mechanics were directly related to jumping performance in this cohort with poor mechanics. On unspecific analysis level, kinetic chain length (ASLR) and trunk control has been identified as potential moderator variables for landing mechanics, indicating that these parameter can limit landing mechanics and ought to be optimized within the individual´s context. A potential cognitive strategy shift from internal (FMS) to external focus (LESS) as well as different muscle recruitment patterns are potential explanations for the non-significant linear relationship between the FMS and LESS data.

  9. Metasystem approach to increase the load factor FMS

    Directory of Open Access Journals (Sweden)

    Pishchukhin Alexandr

    2017-01-01

    Full Text Available The work is devoted to increasing the efficiency of using flexible manufacture systems (FMS by increasing the load factor. Unlike the well-known multi-agent approach to production management, we are investigating the addition of a metasystem level allowing flexible combination of the decentralized control method with centralization. The metasystem approach allows to reduce management to flexible switching of functioning technologies on the basis of the replacement rule, while describing FMS as a metasystem consisting of classification of the system analyst J. Klir from structured data systems. Production events are simulated in virtual space with the help of a multi-agent approach. At the same time, the number of requests from the waiting queue is chosen such that it becomes possible to optimize the loading of the FMS in the simplest case by the full-scan method, if the queue is not available, then the initiative of choice is provided to communications of agents-technologies and agents-equipments. Experimental studies were carried out on the FMS model including six pieces of equipment divided into three groups with a stream of six applications, each of which has a technological route of six operations each‥ The experimental results showed the consistency of the developed approach by increasing the load factor of the FMS.

  10. Functional Movement Screen (FMS - kompleksowy system oceny funkcjonalnej pacjenta = Functional Movement Screen (FMS - a comprehensive system for the functional evaluation of the patient

    Directory of Open Access Journals (Sweden)

    Bartosz Kochański

    2015-04-01

    4 Wydział Kultury Fizycznej, Zdrowia i Turystyki, Uniwersytet Kazimierza Wielkiego w Bydgoszczy, Polska   Streszczenie   System oceny funkcjonalnej - Functional Movement Screen (FMS został stworzony przez Graya Cooka oraz Lee Burtona w 1995 roku. FMS jest koncepcją, która umożliwia kompleksową analizę jakości podstawowych wzorców ruchowych, ocenę ryzyka kontuzji oraz stwierdzenie istnienia ograniczeń i asymetrii. Test FMS złożony jest z 7 prób (głęboki przysiad, przeniesienie kończyny dolnej nad płotkiem, przysiad w wykroku, ruchomość obręczy barkowej, aktywne uniesienie wyprostowanej kończyny dolnej, ugięcie ramion w podporze, stabilność rotacyjna tułowia. W pracy zaprezentowano test Functional Movement Screen, jako kompleksowy system oceny funkcjonalnej pacjenta.   Słowa kluczowe: Functional Movement Screen, FMS, ocena funkcjonalna, rehabilitacja.   Abstract   Functional Movement Screen (FMS was created by Gray Cook and Lee Burton in 1995. FMS is a concept that allows comprehensive analysis of the quality of basic movement patterns, risk assessment and finding of injury to the limitations and asymmetries. FMS test consists of 7 samples (deep squat, hurdle step, in-line lunge, shoulder mobility, active straight leg raise, trunk stability push up, rotational stability. The paper presents the Functional Movement Screen test, as a comprehensive system of functional assessment of the patient.   Key words: Functional Movement Screen, FMS, functional assessment, rehabilitation.

  11. 31 CFR 256.52 - How does FMS issue a payment?

    Science.gov (United States)

    2010-07-01

    ... requirement for payment by EFT is appropriate, FMS will issue a payment by check. The Voucher for Payment must... 31 Money and Finance: Treasury 2 2010-07-01 2010-07-01 false How does FMS issue a payment? 256.52... SERVICE, DEPARTMENT OF THE TREASURY FINANCIAL MANAGEMENT SERVICE OBTAINING PAYMENTS FROM THE JUDGMENT FUND...

  12. Teachers' Perceptions of a Fundamental Movement Skill (FMS) Assessment Battery in a School Setting

    Science.gov (United States)

    Lander, Natalie; Morgan, Philip J.; Salmon, Jo; Barnett, Lisa M.

    2016-01-01

    Fundamental movement skills (FMS) competence is low in adolescent girls. An assessment tool for teachers is needed to monitor FMS in this demographic. The present study explored whether the Canadian Agility and Movement Skill Assessment (CAMSA) is feasible for use by physical education (PE) teachers of Australian Year 7 girls in a school setting.…

  13. A Post Shower detector for the FMS to study Drell Yan and Direct Photons

    Science.gov (United States)

    Kapukchyan, David; STAR Collaboration

    2017-09-01

    One of the goals of the 2017 run at STAR was to measure the direct photon and Drell Yan electrons in polarized pp collisions in order to understand the Sivers and Collins effects. To make such a measurement a postshower detector (FPOST) for the Forward Meson spectrometer (FMS) was commissioned and installed for the 2017 run. The FMS together with its preshower (FPS) detector and the new FPOST cover 2 FPS the FPOST is a scintillator hodoscope with a channel size that matches that of the FMS. Its purpose is to discriminate the hadrons that punch through and the partially contained showers that leak out of the FMS. This talk will discuss the design requirements and performance of the FPOST during the 2017 run. Funding by DOE Award No. DE-FG02-04ER41325.

  14. Generic FMS Platform for Evaluation of Autonomous Trajectory-Based Operation Concepts, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The objective of this research is to create a generic advanced Flight Management System (FMS) platform that could be used for evaluation of autonomous...

  15. Generic FMS Platform for Evaluation of Autonomous Trajectory-Based Operation Concepts, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — The objective of the Phase II work is to develop a generic, advanced Flight Management System (FMS) for the evaluation of autonomous 4D-trajectory based operations...

  16. Control of nuclear material specified equipment and specified material

    International Nuclear Information System (INIS)

    1982-04-01

    The goal and application field of NE 2.02 regulatory guide of CNEN (Comissao Nacional de Energia Nuclear), are described. This regulatory guide is about nuclear material management, specified equipment and specified material. (E.G.) [pt

  17. FMS Scores Change With Performers' Knowledge of the Grading Criteria-Are General Whole-Body Movement Screens Capturing "Dysfunction"?

    Science.gov (United States)

    Frost, David M; Beach, Tyson A C; Callaghan, Jack P; McGill, Stuart M

    2015-11-01

    Deficits in joint mobility and stability could certainly impact individuals' Functional Movement Screen (FMS) scores; however, it is also plausible that the movement patterns observed are influenced by the performers' knowledge of the grading criteria. Twenty-one firefighters volunteered to participate, and their FMS scores were graded before and immediately after receiving knowledge of the movement patterns required to achieve a perfect score on the FMS. Standardized verbal instructions were used to administer both screens, and the participants were not provided with any coaching or feedback. Time-synchronized sagittal and frontal plane videos were used to grade the FMS. The firefighters significantly (p injury risk.

  18. Pure homology of algebraic varieties

    OpenAIRE

    Weber, Andrzej

    2003-01-01

    We show that for a complete complex algebraic variety the pure component of homology coincides with the image of intersection homology. Therefore pure homology is topologically invariant. To obtain slightly more general results we introduce "image homology" for noncomplete varieties.

  19. Experience on the FMS Communication module Development for an Application to Safety- Critical Communication Network

    Energy Technology Data Exchange (ETDEWEB)

    Son, Kwang Seop; Lee, Jang Soo; Kim, Jung Heon [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2009-05-15

    The field bus has been developed for a network system which supports the real-time communication of various controls and automation equipment. It is known for Profibus in the field of a production automation environment. The Profibus standard uses open communication based on the ISO/OSI model. The Probibus standard uses layer 1, layer 2, layer 7. Layer 7 of Probibus FMS(Fieldbus Message Specification) provides a information and the user of a station. The high-level communication of the safety-grade PLC (POSAFE-Q) developed through the KNICS(Korea Nuclear I and C System) project is the FMS This paper describes the design, the configuration, and the test method of the FMS communication module.

  20. Experience on the FMS Communication module Development for an Application to Safety- Critical Communication Network

    International Nuclear Information System (INIS)

    Son, Kwang Seop; Lee, Jang Soo; Kim, Jung Heon

    2009-01-01

    The field bus has been developed for a network system which supports the real-time communication of various controls and automation equipment. It is known for Profibus in the field of a production automation environment. The Profibus standard uses open communication based on the ISO/OSI model. The Probibus standard uses layer 1, layer 2, layer 7. Layer 7 of Probibus FMS(Fieldbus Message Specification) provides a information and the user of a station. The high-level communication of the safety-grade PLC (POSAFE-Q) developed through the KNICS(Korea Nuclear I and C System) project is the FMS This paper describes the design, the configuration, and the test method of the FMS communication module

  1. Lectures on functor homology

    CERN Document Server

    Touzé, Antoine

    2015-01-01

    This book features a series of lectures that explores three different fields in which functor homology (short for homological algebra in functor categories) has recently played a significant role. For each of these applications, the functor viewpoint provides both essential insights and new methods for tackling difficult mathematical problems. In the lectures by Aurélien Djament, polynomial functors appear as coefficients in the homology of infinite families of classical groups, e.g. general linear groups or symplectic groups, and their stabilization. Djament’s theorem states that this stable homology can be computed using only the homology with trivial coefficients and the manageable functor homology. The series includes an intriguing development of Scorichenko’s unpublished results. The lectures by Wilberd van der Kallen lead to the solution of the general cohomological finite generation problem, extending Hilbert’s fourteenth problem and its solution to the context of cohomology. The focus here is o...

  2. Material physical properties of 11Cr-ferritic/martensitic steel (PNC-FMS) wrapper tube materials

    International Nuclear Information System (INIS)

    Yano, Yasuhide; Kaito, Takeji; Ohtsuka, Satoshi; Tanno, Takashi; Uwaba, Tomoyuki; Koyama, Shinichi

    2012-09-01

    It is necessary to develop core materials for fast reactors in order to achieve high-burnup. Ferritic steels are expected to be good candidate core materials to achieve this objective because of their excellent void swelling resistance. Therefore, oxide dispersion strengthened (ODS) ferritic steel and 11Cr-ferritic/martensitic steel (PNC-FMS) have been respectively developed for cladding and wrapper tube materials in Japan Atomic Energy Agency. In this study, various physical properties of PNC-FMS wrapper materials were measured and equations and future standard measurement technique of physical properties for the design and evaluation were conducted. (author)

  3. Evolution of Flux Mapping System (FMS) from 540 MWe to 700 MWe Indian PHWR: design perspective

    International Nuclear Information System (INIS)

    Sonavani, Manojkumar; Kelkar, M.G.; Singhvi, P.K.; Roy, S.; Ingle, V.J.

    2013-01-01

    The Flux Mapping System (FMS) of 700 MWe PHWR computes a detailed flux/power distribution of the reactor core using modal synthesis method and is also generate setback on different parameters by monitoring thermal neutron flux at more than 100 points inside the reactor core. These types of setbacks are introduced first time in Indian PHWRs. The paper brings out the Evolution of Flux Mapping System (FMS) from 540 MWe to 700 MWe and the overall design philosophy. The paper emphasizes on comparisons between 540 MWe and 700 MWe design, considerations for architectural design and setbacks for 700 MWe. (author)

  4. Homological stabilizer codes

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Jonas T., E-mail: jonastyleranderson@gmail.com

    2013-03-15

    In this paper we define homological stabilizer codes on qubits which encompass codes such as Kitaev's toric code and the topological color codes. These codes are defined solely by the graphs they reside on. This feature allows us to use properties of topological graph theory to determine the graphs which are suitable as homological stabilizer codes. We then show that all toric codes are equivalent to homological stabilizer codes on 4-valent graphs. We show that the topological color codes and toric codes correspond to two distinct classes of graphs. We define the notion of label set equivalencies and show that under a small set of constraints the only homological stabilizer codes without local logical operators are equivalent to Kitaev's toric code or to the topological color codes. - Highlights: Black-Right-Pointing-Pointer We show that Kitaev's toric codes are equivalent to homological stabilizer codes on 4-valent graphs. Black-Right-Pointing-Pointer We show that toric codes and color codes correspond to homological stabilizer codes on distinct graphs. Black-Right-Pointing-Pointer We find and classify all 2D homological stabilizer codes. Black-Right-Pointing-Pointer We find optimal codes among the homological stabilizer codes.

  5. c-Fms signaling mediates neurofibromatosis Type-1 osteoclast gain-in-functions.

    Directory of Open Access Journals (Sweden)

    Yongzheng He

    Full Text Available Skeletal abnormalities including osteoporosis and osteopenia occur frequently in both pediatric and adult neurofibromatosis type 1 (NF1 patients. NF1 (Nf1 haploinsufficient osteoclasts and osteoclast progenitors derived from both NF1 patients and Nf1(+/- mice exhibit increased differentiation, migration, and bone resorptive capacity in vitro, mediated by hyperactivation of p21(Ras in response to limiting concentrations of macrophage-colony stimulating factor (M-CSF. Here, we show that M-CSF binding to its receptor, c-Fms, results in increased c-Fms activation in Nf1(+/ (- osteoclast progenitors, mediating multiple gain-in-functions through the downstream effectors Erk1/2 and p90RSK. PLX3397, a potent and selective c-Fms inhibitor, attenuated M-CSF mediated Nf1(+/- osteoclast migration by 50%, adhesion by 70%, and pit formation by 60%. In vivo, we administered PLX3397 to Nf1(+/- osteoporotic mice induced by ovariectomy (OVX and evaluated changes in bone mass and skeletal architecture. We found that PLX3397 prevented bone loss in Nf1(+/--OVX mice by reducing osteoclast differentiation and bone resorptive activity in vivo. Collectively, these results implicate the M-CSF/c-Fms signaling axis as a critical pathway underlying the aberrant functioning of Nf1 haploinsufficient osteoclasts and may provide a potential therapeutic target for treating NF1 associated osteoporosis and osteopenia.

  6. Physical Education Teachers' Perspectives and Experiences When Teaching FMS to Early Adolescent Girls

    Science.gov (United States)

    Lander, Natalie J.; Hanna, Lisa; Brown, Helen; Telford, Amanda; Morgan, Philip J.; Salmon, Jo; Barnett, Lisa M.

    2017-01-01

    Purpose: Competence in fundamental movement skills (FMSs) is positively associated with physical activity, fitness, and healthy weight status. However, adolescent girls exhibit very low levels of fundamental movement skill (FMS) proficiency. Method: In the current study, interviews were carried out with physical education teachers to investigate…

  7. Equivariant ordinary homology and cohomology

    CERN Document Server

    Costenoble, Steven R

    2016-01-01

    Filling a gap in the literature, this book takes the reader to the frontiers of equivariant topology, the study of objects with specified symmetries. The discussion is motivated by reference to a list of instructive “toy” examples and calculations in what is a relatively unexplored field. The authors also provide a reading path for the first-time reader less interested in working through sophisticated machinery but still desiring a rigorous understanding of the main concepts. The subject’s classical counterparts, ordinary homology and cohomology, dating back to the work of Henri Poincaré in topology, are calculational and theoretical tools which are important in many parts of mathematics and theoretical physics, particularly in the study of manifolds. Similarly powerful tools have been lacking, however, in the context of equivariant topology. Aimed at advanced graduate students and researchers in algebraic topology and related fields, the book assumes knowledge of basic algebraic topology and group act...

  8. Geometric homology revisited

    OpenAIRE

    Ruffino, Fabio Ferrari

    2013-01-01

    Given a cohomology theory, there is a well-known abstract way to define the dual homology theory using the theory of spectra. In [4] the author provides a more geometric construction of the homology theory, using a generalization of the bordism groups. Such a generalization involves in its definition the vector bundle modification, which is a particular case of the Gysin map. In this paper we provide a more natural variant of that construction, which replaces the vector bundle modification wi...

  9. FMS: A Format Manipulation System for Automatic Production of Natural Language Documents, Second Edition. Final Report.

    Science.gov (United States)

    Silver, Steven S.

    FMS/3 is a system for producing hard copy documentation at high speed from free format text and command input. The system was originally written in assembler language for a 12K IBM 360 model 20 using a high speed 1403 printer with the UCS-TN chain option (upper and lower case). Input was from an IBM 2560 Multi-function Card Machine. The model 20…

  10. Evaluation of creep rupture property of high strength ferritic/martensitic steel (PNC-FMS)

    International Nuclear Information System (INIS)

    Uehira, Akihiro; Mizuno, Tomoyasu; Ukai, Shigeharu; Yoshida, Eiichi

    1999-04-01

    High Strength Ferritic/Martensitic Steel (PNC-FMS : 11Cr-0.5Mo-2W,Nb,V), developed by JNC, is one of the candidate materials for the long-life core of large-scale fast breeder reactor. The material design base standard (tentative) of PNC-FMS was established and the creep rupture strength reduction factor in the standard was determined in 1992. This factor was based on only evaluation of decarburization effect on tensile strength after sodium exposure. In this study, creep rupture properties of PNC-FMS under out of pile sodium exposure and in pile were evaluated, using recent test results as well as previous ones. The evaluation results are summarized as follows : a. Decarburization rate constant of pressurized tubes under sodium exposure is identical with stress free specimens. b. In case of the same decarburization content under out of pile sodium exposure, creep strength tends to decrease more significantly than tensile strength. c. Creep strength under out of pile sodium exposure showed significant decrease in high temperature and long exposure time, but in pile (MOTA) creep strength showed little decrease. A new creep rupture strength reduction factor, which is the ratio of creep rupture strength under sodium exposure or in pile to in air, was made by correlating the creep rupture strength. This new method directly using the ratio of creep rupture strength was evaluated and discussed from the viewpoint of design applicability, compared with the conventional method based on decarburization effect on tensile strength. (author)

  11. Targeting cFMS signaling to restore immune function and eradicate HIV reservoirs

    Science.gov (United States)

    Gerngross, Lindsey

    While combination anti-retroviral therapy (cART) has improved the length and quality of life of individuals living with HIV-1 infection, the prevalence of HIV-associated neurocognitive disorders (HAND) has increased and remains a significant clinical concern. The neuropathogenesis of HAND is not completely understood, however, latent HIV infection in the central nervous system (CNS) and chronic neuroinflammation are believed to play a prominent role. CNS-associated macrophages and resident microglia are significant contributors to CNS inflammation and constitute the chief reservoir of HIV-1 infection in the CNS. Previous studies from our lab suggest monocyte/macrophage invasion of the CNS in HIV may be driven by altered monocyte/macrophage homeostasis. We have reported expansion of a monocyte subset (CD14+CD16 +CD163+) in peripheral blood of HIV+ patients that is phenotypically similar to macrophages/microglia that accumulate in the CNS as seen in post-mortem tissue. The factors driving the expansion of this monocyte subset are unknown, however, signaling through cFMS, a type III receptor tyrosine kinase (RTK), may play a role. Macrophage-colony stimulating factor (M-CSF), a ligand of cFMS, has been shown to be elevated in the cerebral spinal fluid (CSF) of individuals with the most severe form of HAND, HIV-associated dementia (HAD). M-CSF promotes a Macrophage-2-like phenotype and increases CD16 and CD163 expression in cultured monocytes. M-CSF has also been shown to increase the susceptibility of macrophages to HIV infection and enhance virus production. These findings, in addition to the known function of M-CSF in promoting macrophage survival, supports a role for M-CSF in the development and maintenance of macrophage viral reservoirs in tissues where these cells accumulate, including the CNS. Interestingly, a second ligand for cFMS, IL-34, was recently identified and reported to share some functions with M-CSF, suggesting that both ligands may contribute to HIV

  12. Amino-terminal domain of the v-fms oncogene product includes a functional signal peptide that directs synthesis of a transforming glycoprotein in the absence of feline leukemia virus gag sequences

    International Nuclear Information System (INIS)

    Wheeler, E.F.; Roussel, M.F.; Hampe, A.; Walker, M.H.; Fried, V.A.; Look, A.T.; Rettenmier, C.W.; Sherr, C.J.

    1986-01-01

    The nucleotide sequence of a 5' segment of the human genomic c-fms proto-oncogene suggested that recombination between feline leukemia virus and feline c-fms sequences might have occurred in a region encoding the 5' untranslated portion of c-fms mRNA. The polyprotein precursor gP180/sup gag-fms/ encoded by the McDonough strain of feline sarcoma virus was therefore predicted to contain 34 v-fms-coded amino acids derived from sequences of the c-fms gene that are not ordinarily translated from the proto-oncogene mRNA. The (gP180/sup gag-fms/) polyprotein was cotranslationally cleaved near the gag-fms junction to remove its gag gene-coded portion. Determination of the amino-terminal sequence of the resulting v-fms-coded glycoprotein, gp120/sup v-fms/, showed that the site of proteolysis corresponded to a predicted signal peptidase cleavage site within the c-fms gene product. Together, these analyses suggested that the linked gag sequences may not be necessary for expression of a biologically active v-fms gene product. The gag-fms sequences of feline sarcoma virus strain McDonough and the v-fms sequences alone were inserted into a murine retroviral vector containing a neomycin resistance gene. The authors conclude that a cryptic hydrophobic signal peptide sequence in v-fms was unmasked by gag deletion, thereby allowing the correct orientation and transport of the v-fms was unmasked by gag deletion, thereby allowing the correct orientation and transport of the v-fms gene product within membranous organelles. It seems likely that the proteolytic cleavage of gP180/gag-fms/ is mediated by signal peptidase and that the amino termini of gp140/sup v-fms/ and the c-fms gene product are identical

  13. Amino-terminal domain of the v-fms oncogene product includes a functional signal peptide that directs synthesis of a transforming glycoprotein in the absence of feline leukemia virus gag sequences

    Energy Technology Data Exchange (ETDEWEB)

    Wheeler, E.F.; Roussel, M.F.; Hampe, A.; Walker, M.H.; Fried, V.A.; Look, A.T.; Rettenmier, C.W.; Sherr, C.J.

    1986-08-01

    The nucleotide sequence of a 5' segment of the human genomic c-fms proto-oncogene suggested that recombination between feline leukemia virus and feline c-fms sequences might have occurred in a region encoding the 5' untranslated portion of c-fms mRNA. The polyprotein precursor gP180/sup gag-fms/ encoded by the McDonough strain of feline sarcoma virus was therefore predicted to contain 34 v-fms-coded amino acids derived from sequences of the c-fms gene that are not ordinarily translated from the proto-oncogene mRNA. The (gP180/sup gag-fms/) polyprotein was cotranslationally cleaved near the gag-fms junction to remove its gag gene-coded portion. Determination of the amino-terminal sequence of the resulting v-fms-coded glycoprotein, gp120/sup v-fms/, showed that the site of proteolysis corresponded to a predicted signal peptidase cleavage site within the c-fms gene product. Together, these analyses suggested that the linked gag sequences may not be necessary for expression of a biologically active v-fms gene product. The gag-fms sequences of feline sarcoma virus strain McDonough and the v-fms sequences alone were inserted into a murine retroviral vector containing a neomycin resistance gene. The authors conclude that a cryptic hydrophobic signal peptide sequence in v-fms was unmasked by gag deletion, thereby allowing the correct orientation and transport of the v-fms was unmasked by gag deletion, thereby allowing the correct orientation and transport of the v-fms gene product within membranous organelles. It seems likely that the proteolytic cleavage of gP180/gag-fms/ is mediated by signal peptidase and that the amino termini of gp140/sup v-fms/ and the c-fms gene product are identical.

  14. Flexible maintenance system (FMS). Background, concept, and results of technical development

    International Nuclear Information System (INIS)

    Yoshikawa, Hidekazu; Watanabe, Osami; Takizawa, Yoji; Ohga, Yukiharu; Ohi, Tadashi

    2006-01-01

    Maintenance works of nuclear power plants have been involved with various people and organizations. Thus human errors are apt to be made. Since 2000, the project on development of flexible maintenance system (FMS) has been conducted for five years in order to make maintenance works more rational and reduce human errors probability. Background, concept and results of technical development to upgrade maintenance works and training are reviewed. Advanced technology such as optical viewing equipments, laser holography inspection systems and neural networks shall be applied to maintenance works. (T. Tanaka)

  15. Experience on the COTS Software Dedication of the PROFIBUS FMS-Driver

    International Nuclear Information System (INIS)

    Kim, Jang Yeol; Lee, Young Jun; Cha, Kyung Ho; Cheon, Se Woo; Lee, Jang Soo; Kwon, Kee Choon

    2007-01-01

    From the middle of the 1980's, the field bus has been developed for the network system which supports the real-time communication of various controls and automation equipment. It is known for PROFIBUS in the field of a production automation environment. The PROFIBUS architecture uses open communication (ISO 7498) based on the ISO/OSI model. The PROFIBUS standard uses layer 1 (physical layer : PHY), layer 2, (data link : FDL) and layer 7 (application). Layer 7 of PROFIBUS FMS(Fieldbus Message Specification) provides a information level communication service to a communication and the user of a station

  16. Experience on the COTS Software Dedication of the PROFIBUS FMS-Driver

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jang Yeol; Lee, Young Jun; Cha, Kyung Ho; Cheon, Se Woo; Lee, Jang Soo; Kwon, Kee Choon [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2007-07-01

    From the middle of the 1980's, the field bus has been developed for the network system which supports the real-time communication of various controls and automation equipment. It is known for PROFIBUS in the field of a production automation environment. The PROFIBUS architecture uses open communication (ISO 7498) based on the ISO/OSI model. The PROFIBUS standard uses layer 1 (physical layer : PHY), layer 2, (data link : FDL) and layer 7 (application). Layer 7 of PROFIBUS FMS(Fieldbus Message Specification) provides a information level communication service to a communication and the user of a station.

  17. Fuel element thermo-mechanical analysis during transient events using the FMS and FETMA codes

    International Nuclear Information System (INIS)

    Hernandez Lopez Hector; Hernandez Martinez Jose Luis; Ortiz Villafuerte Javier

    2005-01-01

    In the Instituto Nacional de Investigaciones Nucleares of Mexico, the Fuel Management System (FMS) software package has been used for long time to simulate the operation of a BWR nuclear power plant in steady state, as well as in transient events. To evaluate the fuel element thermo-mechanical performance during transient events, an interface between the FMS codes and our own Fuel Element Thermo Mechanical Analysis (FETMA) code is currently being developed and implemented. In this work, the results of the thermo-mechanical behavior of fuel rods in the hot channel during the simulation of transient events of a BWR nuclear power plant are shown. The transient events considered for this work are a load rejection and a feedwater control failure, which among the most important events that can occur in a BWR. The results showed that conditions leading to fuel rod failure at no time appeared for both events. Also, it is shown that a transient due load rejection is more demanding on terms of safety that the failure of a controller of the feedwater. (authors)

  18. An FMS Dynamic Production Scheduling Algorithm Considering Cutting Tool Failure and Cutting Tool Life

    International Nuclear Information System (INIS)

    Setiawan, A; Wangsaputra, R; Halim, A H; Martawirya, Y Y

    2016-01-01

    This paper deals with Flexible Manufacturing System (FMS) production rescheduling due to unavailability of cutting tools caused either of cutting tool failure or life time limit. The FMS consists of parallel identical machines integrated with an automatic material handling system and it runs fully automatically. Each machine has a same cutting tool configuration that consists of different geometrical cutting tool types on each tool magazine. The job usually takes two stages. Each stage has sequential operations allocated to machines considering the cutting tool life. In the real situation, the cutting tool can fail before the cutting tool life is reached. The objective in this paper is to develop a dynamic scheduling algorithm when a cutting tool is broken during unmanned and a rescheduling needed. The algorithm consists of four steps. The first step is generating initial schedule, the second step is determination the cutting tool failure time, the third step is determination of system status at cutting tool failure time and the fourth step is the rescheduling for unfinished jobs. The approaches to solve the problem are complete-reactive scheduling and robust-proactive scheduling. The new schedules result differences starting time and completion time of each operations from the initial schedule. (paper)

  19. Specified assurance level sampling procedure

    International Nuclear Information System (INIS)

    Willner, O.

    1980-11-01

    In the nuclear industry design specifications for certain quality characteristics require that the final product be inspected by a sampling plan which can demonstrate product conformance to stated assurance levels. The Specified Assurance Level (SAL) Sampling Procedure has been developed to permit the direct selection of attribute sampling plans which can meet commonly used assurance levels. The SAL procedure contains sampling plans which yield the minimum sample size at stated assurance levels. The SAL procedure also provides sampling plans with acceptance numbers ranging from 0 to 10, thus, making available to the user a wide choice of plans all designed to comply with a stated assurance level

  20. Anomaly-specified virtual dimensionality

    Science.gov (United States)

    Chen, Shih-Yu; Paylor, Drew; Chang, Chein-I.

    2013-09-01

    Virtual dimensionality (VD) has received considerable interest where VD is used to estimate the number of spectral distinct signatures, denoted by p. Unfortunately, no specific definition is provided by VD for what a spectrally distinct signature is. As a result, various types of spectral distinct signatures determine different values of VD. There is no one value-fit-all for VD. In order to address this issue this paper presents a new concept, referred to as anomaly-specified VD (AS-VD) which determines the number of anomalies of interest present in the data. Specifically, two types of anomaly detection algorithms are of particular interest, sample covariance matrix K-based anomaly detector developed by Reed and Yu, referred to as K-RXD and sample correlation matrix R-based RXD, referred to as R-RXD. Since K-RXD is only determined by 2nd order statistics compared to R-RXD which is specified by statistics of the first two orders including sample mean as the first order statistics, the values determined by K-RXD and R-RXD will be different. Experiments are conducted in comparison with widely used eigen-based approaches.

  1. PENDEKATAN ACTIVITY-BASED COSTING DAN METODE PENCARIAN HEURISTIC UNTUK MENYELESAIKAN PROBLEM PEMILIHAN PERALATAN PADA FLEXIBLE MANUFACTURING SYSTEMS (FMS

    Directory of Open Access Journals (Sweden)

    Gregorius Satia Budhi

    2002-01-01

    Full Text Available The application of Activity Based Costing (ABC approach to select the set-machine that is used in the production of Flexible Manufacture System (FMS based on technical and economical criteria can be useful for producers to design FMS by considering the minimum production cost. In the other hand, Heuristic Search is known to have a short searching time. Algorithm Heuristic that using ABC approach as the weight in finding the solution to shorten the equipment selection time during the design / redesign process of the FMS in less than exponential time was designed in this research. The increasing speed is useful because with the faster time in design / redesign process, therefore the flexibility level of part variety that can be processed will become better. Theoretical and empirical analysis in Algorithm Heuristic shows that time searching to get appropriate set of equipment is not too long, so that we can assume that the designed Algorithm Heuristic can be implemented in the real world. By comparing the empirical result of Algorithm Heuristic to the Algorithm Exhaustive, we can also assume that Algorithm Heuristic that using ABC method as the weight for finding solution can optimise the equipment selection problem of FMS based on economical criteria too. Abstract in Bahasa Indonesia : Penggunaan pendekatan Activity Based Costing (ABC untuk memilih set mesin yang digunakan dalam produksi pada Flexible Manufacture Systems (FMS berdasar atas kriteria teknis dan ekonomis, dapat membantu pelaku produksi untuk mendisain FMS dengan pertimbangan minimalisasi biaya produksi. Sementara itu, Heuristic Search dikenal memiliki waktu pencarian yang singkat. Pada riset ini didisain sebuah Algoritma Heuristic yang menggunakan pendekatan ABC sebagai bobot dalam pencarian solusi, untuk mempersingkat waktu pemilihan peralatan saat desain/redisain FMS dalam waktu kurang dari waktu Eksponensial. Peningkatan kecepatan ini bermanfaat, karena dengan cepatnya waktu

  2. Specifying pancreatic endocrine cell fates.

    Science.gov (United States)

    Collombat, Patrick; Hecksher-Sørensen, Jacob; Serup, Palle; Mansouri, Ahmed

    2006-07-01

    Cell replacement therapy could represent an attractive alternative to insulin injections for the treatment of diabetes. However, this approach requires a thorough understanding of the molecular switches controlling the specification of the different pancreatic cell-types in vivo. These are derived from an apparently identical pool of cells originating from the early gut endoderm, which are successively specified towards the pancreatic, endocrine, and hormone-expressing cell lineages. Numerous studies have outlined the crucial roles exerted by transcription factors in promoting the cell destiny, defining the cell identity and maintaining a particular cell fate. This review focuses on the mechanisms regulating the morphogenesis of the pancreas with particular emphasis on recent findings concerning the transcription factor hierarchy orchestrating endocrine cell fate allocation.

  3. Formation MicroScanner (FMS) data and orbital cycle records: preliminary interpretation from the Asian Monsoon IODP Expedition 346

    Science.gov (United States)

    Johanna, Lofi; Grizel, Jimenez Soto; Ryuji, Tada; Murray Richard, W.; Alvarez Zarikian Carlos, A.; Martin, Ziegler

    2015-04-01

    Recently, IODP Expedition 346 (29 July-27 September 2013) drilled seven sites in in the marginal sea bordered by the Eurasian continent, the Korean Peninsula, and the Japanese Islands, as well as two closely spaced sites in the East China Sea. Expedition 346 was the first scientific drilling expedition ever to focus exclusively on the climate system in this region. During the expedition, the Formation MicroScanner (FMS) downhole logging tool was deployed, providing high-resolution electrical resistivity-based images of borehole walls. Features such as bedding, slump folding and bioturbation can be resolved. Here we analyze FMS image resistivity data collected at Site U1425 that extend back to the Miocene. Analysis allowed the recognition of several FMS intervals, with vertical extension ranging from several tens of centimeters to a few meters, with an apparent cyclicity. These FMS intervals correlate well with other downhole logs (Total Gamma Ray, Uranium, Thorium, Potassium and density). Conductive intervals generally correlate with low gamma ray and low density log values. Conversely, more resistive intervals generally correlate with higher values in the gamma ray and bulk density logs. This relationship can be interpreted in terms of the relative abundance of terrigenous clay/diatoms in the sediment. Clay has high K and Th contents and relatively higher density and lower porosity than higher diatom-rich sediment. Consequently, with the exception of sporadic ash and dolomite layers, conductive intervals in the FMS images tend to reflect intervals enriched in diatoms, whereas resistive intervals reflect relative high-terrigenous clay content. An apparent cyclic nature, with several orders of cycles on the FMS images, is locally clearly observed. The cyclic pattern consists of ~4-8 m thick resistive intervals alternating with conductive intervals, generally correlating in core with laminated (diatomite or carbonate rich) intervals. These conductive intervals often

  4. Fuel management inside the reactor. Impact of the substitution of the basic libraries of the Eclipse and Record codes of the FMS system of fuel management

    International Nuclear Information System (INIS)

    Alonso V, G.; Hernandez L, H.

    1992-12-01

    The present work is given to know the repercussions in the obtained results by the ECLIPSE-RECORD system of the package of fuel management FMS of SCANDPOWER, with the use of the libraries of effective sections of neutrons, for both codes, generated starting from the ENDF-B/IV database. Inside of the Institute it doesn't have any version of the ECLIPSE code it which drove us to make use of the versions of the THERMOS and GADPOL codes. The obtained results with the libraries generated were compared against those that are obtained making use of the libraries that it possesses the code, generated starting from the ENDF-B/III database, and the data that General Electric Co. reports for the cells that were used for this work. The calculations with the THERMOS-GADPOL-RECORD system, installed in 830 CDC machine of the Institute, its were carried out following the calculation sequence that it is continued during the generation of nuclear databases proposed by CFE only for the series 1 and 2. The obtained results are reported in the Appendixes B and C as well as some of the enter files for the codes used in the Appendix D, which are specified for those installed versions. (Author)

  5. 31 CFR 256.12 - What supporting documentation must agencies submit to FMS when requesting a payment from the...

    Science.gov (United States)

    2010-07-01

    ... 31 Money and Finance: Treasury 2 2010-07-01 2010-07-01 false What supporting documentation must... BILLS Requesting Payments § 256.12 What supporting documentation must agencies submit to FMS when... guardian. Agencies must list the appropriate controlling state law citation on the payment request forms...

  6. Do Functional Movement Screen (FMS) composite scores predict subsequent injury? A systematic review with meta-analysis.

    Science.gov (United States)

    Moran, Robert W; Schneiders, Anthony G; Mason, Jesse; Sullivan, S John

    2017-12-01

    This paper aims to systematically review studies investigating the strength of association between FMS composite scores and subsequent risk of injury, taking into account both methodological quality and clinical and methodological diversity. Systematic review with meta-analysis. A systematic search of electronic databases was conducted for the period between their inception and 3 March 2016 using PubMed, Medline, Google Scholar, Scopus, Academic Search Complete, AMED (Allied and Complementary Medicine Database), CINAHL (Cumulative Index to Nursing and Allied Health Literature), Health Source and SPORTDiscus. Inclusion criteria: (1) English language, (2) observational prospective cohort design, (3) original and peer-reviewed data, (4) composite FMS score, used to define exposure and non-exposure groups and (5) musculoskeletal injury, reported as the outcome. (1) data reported in conference abstracts or non-peer-reviewed literature, including theses, and (2) studies employing cross-sectional or retrospective study designs. 24 studies were appraised using the Quality of Cohort Studies assessment tool. In male military personnel, there was 'strong' evidence that the strength of association between FMS composite score (cut-point ≤14/21) and subsequent injury was 'small' (pooled risk ratio=1.47, 95% CI 1.22 to 1.77, p<0.0001, I 2 =57%). There was 'moderate' evidence to recommend against the use of FMS composite score as an injury prediction test in football (soccer). For other populations (including American football, college athletes, basketball, ice hockey, running, police and firefighters), the evidence was 'limited' or 'conflicting'. The strength of association between FMS composite scores and subsequent injury does not support its use as an injury prediction tool. PROSPERO registration number CRD42015025575. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted

  7. Chemical shift homology in proteins

    International Nuclear Information System (INIS)

    Potts, Barbara C.M.; Chazin, Walter J.

    1998-01-01

    The degree of chemical shift similarity for homologous proteins has been determined from a chemical shift database of over 50 proteins representing a variety of families and folds, and spanning a wide range of sequence homologies. After sequence alignment, the similarity of the secondary chemical shifts of C α protons was examined as a function of amino acid sequence identity for 37 pairs of structurally homologous proteins. A correlation between sequence identity and secondary chemical shift rmsd was observed. Important insights are provided by examining the sequence identity of homologous proteins versus percentage of secondary chemical shifts that fall within 0.1 and 0.3 ppm thresholds. These results begin to establish practical guidelines for the extent of chemical shift similarity to expect among structurally homologous proteins

  8. Mod two homology and cohomology

    CERN Document Server

    Hausmann, Jean-Claude

    2014-01-01

    Cohomology and homology modulo 2 helps the reader grasp more readily the basics of a major tool in algebraic topology. Compared to a more general approach to (co)homology this refreshing approach has many pedagogical advantages: It leads more quickly to the essentials of the subject, An absence of signs and orientation considerations simplifies the theory, Computations and advanced applications can be presented at an earlier stage, Simple geometrical interpretations of (co)chains. Mod 2 (co)homology was developed in the first quarter of the twentieth century as an alternative to integral homology, before both became particular cases of (co)homology with arbitrary coefficients. The first chapters of this book may serve as a basis for a graduate-level introductory course to (co)homology. Simplicial and singular mod 2 (co)homology are introduced, with their products and Steenrod squares, as well as equivariant cohomology. Classical applications include Brouwer's fixed point theorem, Poincaré duality, Borsuk-Ula...

  9. Mechanistic and structural analyses of the role of His67 in the yeast polyamine oxidase Fms1.

    Science.gov (United States)

    Adachi, Mariya S; Taylor, Alexander B; Hart, P John; Fitzpatrick, Paul F

    2012-06-19

    The flavoprotein oxidase Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine and N(1)-acetylspermine to spermidine and 3-aminopropanal or N-acetyl-3-aminopropanal. Within the active site of Fms1, His67 is positioned to form hydrogen bonds with the polyamine substrate. This residue is also conserved in other polyamine oxidases. The catalytic properties of H67Q, H67N, and H67A Fms1 have been characterized to evaluate the role of this residue in catalysis. With both spermine and N(1)-acetylspermine as the amine substrate, the value of the first-order rate constant for flavin reduction decreases 2-3 orders of magnitude, with the H67Q mutation having the smallest effect and H67N the largest. The k(cat)/K(O2) value changes very little upon mutation with N(1)-acetylspermine as the amine substrate and decreases only an order of magnitude with spermine. The k(cat)/K(M)-pH profiles with N(1)-acetylspermine are bell-shaped for all the mutants; the similarity to the profile of the wild-type enzyme rules out His67 as being responsible for either of the pK(a) values. The pH profiles for the rate constant for flavin reduction for all the mutant enzymes similarly show the same pK(a) as wild-type Fms1, about ∼7.4; this pK(a) is assigned to the substrate N4. The k(cat)/K(O2)-pH profiles for wild-type Fms1 and the H67A enzyme both show a pK(a) of about ∼6.9; this suggests His67 is not responsible for this pH behavior. With the H67Q, H67N, and H67A enzymes the k(cat) value decreases when a single residue is protonated, as is the case with the wild-type enzyme. The structure of H67Q Fms1 has been determined at a resolution of 2.4 Å. The structure shows that the mutation disrupts a hydrogen bond network in the active site, suggesting that His67 is important both for direct interactions with the substrate and to maintain the overall active site structure.

  10. Compositional Homology and Creative Thinking

    Directory of Open Access Journals (Sweden)

    Salvatore Tedesco

    2015-05-01

    Full Text Available The concept of homology is the most solid theoretical basis elaborated by the morphological thinking during its history. The enucleation of some general criteria for the interpretation of homology is today a fundamental tool for life sciences, and for restoring their own opening to the question of qualitative innovation that arose so powerfully in the original Darwinian project. The aim of this paper is to verify the possible uses of the concept of compositional homology in order to provide of an adequate understanding of the dynamics of creative thinking.

  11. Fuel management inside the reactor. Impact of the substitution of the basic libraries of the Eclipse and Record codes of the FMS system of fuel management; Administracion de combustible dentro del reactor. Impacto de la sustitucion de las bibliotecas basicas de los codigos Eclipse y Record del sistema FMS de administracion de combustible

    Energy Technology Data Exchange (ETDEWEB)

    Alonso V, G.; Hernandez L, H. [ININ, 52045 Ocoyoacac, Estado de Mexico (Mexico)

    1992-12-15

    The present work is given to know the repercussions in the obtained results by the ECLIPSE-RECORD system of the package of fuel management FMS of SCANDPOWER, with the use of the libraries of effective sections of neutrons, for both codes, generated starting from the ENDF-B/IV database. Inside of the Institute it doesn't have any version of the ECLIPSE code it which drove us to make use of the versions of the THERMOS and GADPOL codes. The obtained results with the libraries generated were compared against those that are obtained making use of the libraries that it possesses the code, generated starting from the ENDF-B/III database, and the data that General Electric Co. reports for the cells that were used for this work. The calculations with the THERMOS-GADPOL-RECORD system, installed in 830 CDC machine of the Institute, its were carried out following the calculation sequence that it is continued during the generation of nuclear databases proposed by CFE only for the series 1 and 2. The obtained results are reported in the Appendixes B and C as well as some of the enter files for the codes used in the Appendix D, which are specified for those installed versions. (Author)

  12. Fuel management inside the reactor. Impact of the substitution of the basic libraries of the Eclipse and Record codes of the FMS system of fuel management; Administracion de combustible dentro del reactor. Impacto de la sustitucion de las bibliotecas basicas de los codigos Eclipse y Record del sistema FMS de administracion de combustible

    Energy Technology Data Exchange (ETDEWEB)

    Alonso V, G; Hernandez L, H [ININ, 52045 Ocoyoacac, Estado de Mexico (Mexico)

    1992-12-15

    The present work is given to know the repercussions in the obtained results by the ECLIPSE-RECORD system of the package of fuel management FMS of SCANDPOWER, with the use of the libraries of effective sections of neutrons, for both codes, generated starting from the ENDF-B/IV database. Inside of the Institute it doesn't have any version of the ECLIPSE code it which drove us to make use of the versions of the THERMOS and GADPOL codes. The obtained results with the libraries generated were compared against those that are obtained making use of the libraries that it possesses the code, generated starting from the ENDF-B/III database, and the data that General Electric Co. reports for the cells that were used for this work. The calculations with the THERMOS-GADPOL-RECORD system, installed in 830 CDC machine of the Institute, its were carried out following the calculation sequence that it is continued during the generation of nuclear databases proposed by CFE only for the series 1 and 2. The obtained results are reported in the Appendixes B and C as well as some of the enter files for the codes used in the Appendix D, which are specified for those installed versions. (Author)

  13. Analyzing and Specifying Reusable Security Requirements

    Science.gov (United States)

    2003-09-01

    avionics applications and ecommerce applications need to specify levels of identification, authentication, authorization, integrity, privacy , etc. At...sections specifying functional requirements. Thus, the functional requirements for an embedded avionics application and an ecommerce website may have... Privacy (a.k.a., confidentiality), which is the degree to which sensitive data and communications are kept private from unauthorized individuals and

  14. Electrochemical Impedance Response of the surface treated FMS in Liquid Sodium Environment

    International Nuclear Information System (INIS)

    Lee, Jeong Hyeon; Shin, Sang Hun; Kim, Ji Hyun

    2014-01-01

    HT9 and Gr.92 are known as compatible in sodium environment because the usual refueling time of SFRs is designed about 54 months. It is very important to investigate the corrosion-related behavior such as surface corrosion rate, carburization, decarburization and mechanical properties for its operation time. SiC and Si 3 N 4 CVD coating for decarburization barrier on the surface of FMS is considered in this study. The decarburization process where dissolved carbon near the specimen surface disused in to the liquid sodium. This process can originate from the difference between dissolved carbon in the material and liquid sodium. A compatibility test the cladding tube revealed that a decrease of the mechanical property instigated by the aging proves governed the whole mechanical property. To monitor the corrosion behavior of these candidate materials in sodium environment, Electrochemical Impedance Spectroscopy (EIS) method is first introduced and investigated in this study. The compatibility of cladding and structural materials with sodium has to be carefully investigated, as sodium could promote corrosion of cladding and structural materials in two ways. One is produced by the dissolution of alloy constituents into the sodium, and the other is produced through a chemical reaction with impurities (especially oxygen and carbon) in the sodium environment. EIS test with pre-oxidized Gr. 92 specimen in 200 .deg. C liquid sodium environment was carried out in this study. A clear Nyquist and Bode plots were obtained in liquid metal environment and the resistance of sodium and the oxide, and the capacitance of the oxide were measured from this result

  15. Persistent homology of complex networks

    International Nuclear Information System (INIS)

    Horak, Danijela; Maletić, Slobodan; Rajković, Milan

    2009-01-01

    Long-lived topological features are distinguished from short-lived ones (considered as topological noise) in simplicial complexes constructed from complex networks. A new topological invariant, persistent homology, is determined and presented as a parameterized version of a Betti number. Complex networks with distinct degree distributions exhibit distinct persistent topological features. Persistent topological attributes, shown to be related to the robust quality of networks, also reflect the deficiency in certain connectivity properties of networks. Random networks, networks with exponential connectivity distribution and scale-free networks were considered for homological persistency analysis

  16. Specifying Functional Requirements Dependency in the REWiki

    OpenAIRE

    ZHANG, ZHANG

    2013-01-01

    Most of the individual requirements cannot be treated in isolation. Requirements may affect each other in various ways. The dependency between requirements impacts a number of software development aspects and activities. How to classify and specify requirements dependency remains a classic research topic. This research aims at providing an approach of specifying functional requirements dependency. In this thesis we generalize a classification of functional requirements dependency. We also pro...

  17. Homological stability of diffeomorphism groups

    DEFF Research Database (Denmark)

    Berglund, Alexander; Madsen, Ib Henning

    2013-01-01

    In this paper we prove a stability theorem for block diffeomorphisms of 2d -dimensional manifolds that are connected sums of S d ×S d . Combining this with a recent theorem of S. Galatius and O. Randal-Williams and Morlet’s lemma of disjunction, we determine the homology of the classifying space ...

  18. Inhibition of colony-stimulating-factor-1 signaling in vivo with the orally bioavailable cFMS kinase inhibitor GW2580.

    Science.gov (United States)

    Conway, James G; McDonald, Brad; Parham, Janet; Keith, Barry; Rusnak, David W; Shaw, Eva; Jansen, Marilyn; Lin, Peiyuan; Payne, Alan; Crosby, Renae M; Johnson, Jennifer H; Frick, Lloyd; Lin, Min-Hwa Jasmine; Depee, Scott; Tadepalli, Sarva; Votta, Bart; James, Ian; Fuller, Karen; Chambers, Timothy J; Kull, Frederick C; Chamberlain, Stanley D; Hutchins, Jeff T

    2005-11-01

    Colony-stimulating-factor-1 (CSF-1) signaling through cFMS receptor kinase is increased in several diseases. To help investigate the role of cFMS kinase in disease, we identified GW2580, an orally bioavailable inhibitor of cFMS kinase. GW2580 completely inhibited human cFMS kinase in vitro at 0.06 microM and was inactive against 26 other kinases. GW2580 at 1 microM completely inhibited CSF-1-induced growth of mouse M-NFS-60 myeloid cells and human monocytes and completely inhibited bone degradation in cultures of human osteoclasts, rat calvaria, and rat fetal long bone. In contrast, GW2580 did not affect the growth of mouse NS0 lymphoblastoid cells, human endothelial cells, human fibroblasts, or five human tumor cell lines. GW2580 also did not affect lipopolysaccharide (LPS)-induced TNF, IL-6, and prostaglandin E2 production in freshly isolated human monocytes and mouse macrophages. After oral administration, GW2580 blocked the ability of exogenous CSF-1 to increase LPS-induced IL-6 production in mice, inhibited the growth of CSF-1-dependent M-NFS-60 tumor cells in the peritoneal cavity, and diminished the accumulation of macrophages in the peritoneal cavity after thioglycolate injection. Unexpectedly, GW2580 inhibited LPS-induced TNF production in mice, in contrast to effects on monocytes and macrophages in vitro. In conclusion, GW2580's selective inhibition of monocyte growth and bone degradation is consistent with cFMS kinase inhibition. The ability of GW2580 to chronically inhibit CSF-1 signaling through cFMS kinase in normal and tumor cells in vivo makes GW2580 a useful tool in assessing the role of cFMS kinase in normal and disease processes.

  19. Metformin as a prevention and treatment for preeclampsia: effects on soluble fms-like tyrosine kinase 1 and soluble endoglin secretion and endothelial dysfunction.

    Science.gov (United States)

    Brownfoot, Fiona C; Hastie, Roxanne; Hannan, Natalie J; Cannon, Ping; Tuohey, Laura; Parry, Laura J; Senadheera, Sevvandi; Illanes, Sebastian E; Kaitu'u-Lino, Tu'uhevaha J; Tong, Stephen

    2016-03-01

    Preeclampsia is associated with placental ischemia/hypoxia and secretion of soluble fms-like tyrosine kinase 1 and soluble endoglin into the maternal circulation. This causes widespread endothelial dysfunction that manifests clinically as hypertension and multisystem organ injury. Recently, small molecule inhibitors of hypoxic inducible factor 1α have been found to reduce soluble fms-like tyrosine kinase 1 and soluble endoglin secretion. However, their safety profile in pregnancy is unknown. Metformin is safe in pregnancy and is also reported to inhibit hypoxic inducible factor 1α by reducing mitochondrial electron transport chain activity. The purposes of this study were to determine (1) the effects of metformin on placental soluble fms-like tyrosine kinase 1 and soluble endoglin secretion, (2) to investigate whether the effects of metformin on soluble fms-like tyrosine kinase 1 and soluble endoglin secretion are regulated through the mitochondrial electron transport chain, and (3) to examine its effects on endothelial dysfunction, maternal blood vessel vasodilation, and angiogenesis. We performed functional (in vitro and ex vivo) experiments using primary human tissues to examine the effects of metformin on soluble fms-like tyrosine kinase 1 and soluble endoglin secretion from placenta, endothelial cells, and placental villous explants. We used succinate, mitochondrial complex II substrate, to examine whether the effects of metformin on soluble fms-like tyrosine kinase 1 and soluble endoglin secretion were mediated through the mitochondria. We also isolated mitochondria from preterm preeclamptic placentas and gestationally matched control subjects and measured mitochondrial electron transport chain activity using kinetic spectrophotometric assays. Endothelial cells or whole maternal vessels were incubated with metformin to determine whether it rescued endothelial dysfunction induced by either tumor necrosis factor-α (to endothelial cells) or placenta villous

  20. Simultaneous Scheduling of Jobs, AGVs and Tools Considering Tool Transfer Times in Multi Machine FMS By SOS Algorithm

    Science.gov (United States)

    Sivarami Reddy, N.; Ramamurthy, D. V., Dr.; Prahlada Rao, K., Dr.

    2017-08-01

    This article addresses simultaneous scheduling of machines, AGVs and tools where machines are allowed to share the tools considering transfer times of jobs and tools between machines, to generate best optimal sequences that minimize makespan in a multi-machine Flexible Manufacturing System (FMS). Performance of FMS is expected to improve by effective utilization of its resources, by proper integration and synchronization of their scheduling. Symbiotic Organisms Search (SOS) algorithm is a potent tool which is a better alternative for solving optimization problems like scheduling and proven itself. The proposed SOS algorithm is tested on 22 job sets with makespan as objective for scheduling of machines and tools where machines are allowed to share tools without considering transfer times of jobs and tools and the results are compared with the results of existing methods. The results show that the SOS has outperformed. The same SOS algorithm is used for simultaneous scheduling of machines, AGVs and tools where machines are allowed to share tools considering transfer times of jobs and tools to determine the best optimal sequences that minimize makespan.

  1. Multi-objective AGV scheduling in an FMS using a hybrid of genetic algorithm and particle swarm optimization.

    Directory of Open Access Journals (Sweden)

    Maryam Mousavi

    Full Text Available Flexible manufacturing system (FMS enhances the firm's flexibility and responsiveness to the ever-changing customer demand by providing a fast product diversification capability. Performance of an FMS is highly dependent upon the accuracy of scheduling policy for the components of the system, such as automated guided vehicles (AGVs. An AGV as a mobile robot provides remarkable industrial capabilities for material and goods transportation within a manufacturing facility or a warehouse. Allocating AGVs to tasks, while considering the cost and time of operations, defines the AGV scheduling process. Multi-objective scheduling of AGVs, unlike single objective practices, is a complex and combinatorial process. In the main draw of the research, a mathematical model was developed and integrated with evolutionary algorithms (genetic algorithm (GA, particle swarm optimization (PSO, and hybrid GA-PSO to optimize the task scheduling of AGVs with the objectives of minimizing makespan and number of AGVs while considering the AGVs' battery charge. Assessment of the numerical examples' scheduling before and after the optimization proved the applicability of all the three algorithms in decreasing the makespan and AGV numbers. The hybrid GA-PSO produced the optimum result and outperformed the other two algorithms, in which the mean of AGVs operation efficiency was found to be 69.4, 74, and 79.8 percent in PSO, GA, and hybrid GA-PSO, respectively. Evaluation and validation of the model was performed by simulation via Flexsim software.

  2. S-27: Hentbol Sporcularının Fonksiyonel Hareket Analizi (FMS Sonuçları

    Directory of Open Access Journals (Sweden)

    Emre Serdar Vayvay

    2017-03-01

    Full Text Available GİRİŞ-AMAÇ: Uluslararası Olimpiyat Komitesine (IOC göre hentbol, yüksek yaralanma riskine sahip bir olimpik spordur. Bu oyun yüksek tempo, seri hareket değişiklikleri, yere sert inmeyle sonlanan sıçramalar, sporcular arasında sık sık gerçekleşen temas, tekrarlayan diz ve omuz stresi ile karakterizedir. Yaralanmaların önlenmesi her sporda, fizyoterapistlerin birincil sorumluluklarındandır. Bu da ancak detaylı ve bütüncül bir analiz ile mümkün olmaktadır. Fonksiyonel Hareket Analizi (FMS yüksek seviye fonksiyonlarda yer alabilmek için gerekli olan yetenekleri değerlendirmek için tasarlanmıştır. FMS, üç hareket düzleminde de hareket edebilme kabiliyetini değerlendirir. Deep squat, yüksek adımlama, tek çizgide hamle, omuz mobilitesi, aktif düz bacak kaldırma, gövde stabilite şınavı ve rotasyon stabilitesi testlerinden oluşur. Her test için 0-3 arasında bir skor verilir. Düşük skor(<14 ya da asimetrilerin varlığı literatürde yüksek yaralanma riski ile ilişkilendirilmiştir. Birçok spor dalı, meslek ya da aktivite düzeyi için FMS değerlendirme sistemini kullanmış çalışma mevcuttur ancak hentbol sporu için FMS skor normlarını oluşturabilecek bir çalışma bulunmamaktadır.Bu çalışmanın amacı, Hentbol süper ligi ve 1. Lig A takım sporcularında fonksiyonel hareket analizi skorlarını ortaya koymaktır.MATERYAL-METOD: Bu çalışmaya Hentbol Süper Lig ve 1. Ligde oynayan 51 hentbol sporcusu dahil edildi. Sporcuların demografik verileri, spor geçmişleri ile ilişkili bilgiler kaydedildikten sonra hafif ısınma yapmaları istendi. Sonrasında FMS analizleri yapıldı. En fazla üçer tekrar ile fizyoterapistin gözlem sonucu verdiği değerlendirme notu kaydedildi.BULGULAR: Çalışmaya 37 kadın, 14 erkek sporcu dahil edildi. Sporcuların yaş ort. 21± 4,50, Vücut Kitle İndeksleri ort. 22,1 ± 2,18, spor yaşı 10,25± 4,86 olarak bulundu. Mevki dağılımı; Kaleci

  3. Multi-objective AGV scheduling in an FMS using a hybrid of genetic algorithm and particle swarm optimization.

    Science.gov (United States)

    Mousavi, Maryam; Yap, Hwa Jen; Musa, Siti Nurmaya; Tahriri, Farzad; Md Dawal, Siti Zawiah

    2017-01-01

    Flexible manufacturing system (FMS) enhances the firm's flexibility and responsiveness to the ever-changing customer demand by providing a fast product diversification capability. Performance of an FMS is highly dependent upon the accuracy of scheduling policy for the components of the system, such as automated guided vehicles (AGVs). An AGV as a mobile robot provides remarkable industrial capabilities for material and goods transportation within a manufacturing facility or a warehouse. Allocating AGVs to tasks, while considering the cost and time of operations, defines the AGV scheduling process. Multi-objective scheduling of AGVs, unlike single objective practices, is a complex and combinatorial process. In the main draw of the research, a mathematical model was developed and integrated with evolutionary algorithms (genetic algorithm (GA), particle swarm optimization (PSO), and hybrid GA-PSO) to optimize the task scheduling of AGVs with the objectives of minimizing makespan and number of AGVs while considering the AGVs' battery charge. Assessment of the numerical examples' scheduling before and after the optimization proved the applicability of all the three algorithms in decreasing the makespan and AGV numbers. The hybrid GA-PSO produced the optimum result and outperformed the other two algorithms, in which the mean of AGVs operation efficiency was found to be 69.4, 74, and 79.8 percent in PSO, GA, and hybrid GA-PSO, respectively. Evaluation and validation of the model was performed by simulation via Flexsim software.

  4. Homological algebra in -abelian categories

    Indian Academy of Sciences (India)

    Deren Luo

    2017-08-16

    Aug 16, 2017 ... Homological algebra in n-abelian categories. 627. We recall the Comparison lemma, together with its dual, plays a central role in the sequel. Lemma 2.1 [13, Comparison lemma 2.1]. Let C be an additive category and X ∈ Ch. ≥0(C) a complex such that for all k ≥ 0the morphism dk+1. X is a weak cokernel ...

  5. A functional language for specifying business reports

    DEFF Research Database (Denmark)

    Bahr, Patrick

    2011-01-01

    We describe our work on developing a functional domain specificlanguage for specifying business reports. The report specificationlanguage is part of a novel enterprise resource planing system basedon the idea of a providing a lean core system that is highlycustomisable via a variety of domain...... specific languages....

  6. A Functional Language for Specifying Business Reports

    DEFF Research Database (Denmark)

    Bahr, Patrick

    2011-01-01

    We describe our work on developing a functional domain specific language for specifying business reports. The report specification language is part of a novel enterprise resource planing system based on the idea of a providing a lean core system that is highly customisable via a variety of domain...

  7. 50 CFR 216.211 - Specified activity and specified geographical region.

    Science.gov (United States)

    2010-10-01

    ... OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS Taking of Marine Mammals Incidental to Explosive Severance.... Gulf of Mexico § 216.211 Specified activity and specified geographical region. (a) Regulations in this...

  8. 50 CFR 216.250 - Specified activity and specified geographical region.

    Science.gov (United States)

    2010-10-01

    ... OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS Taking Marine Mammals Incidental to Conducting Precision Strike Weapon Missions in the Gulf of Mexico § 216.250 Specified activity and specified geographical region. (a...

  9. Rational Homological Stability for Automorphisms of Manifolds

    DEFF Research Database (Denmark)

    Grey, Matthias

    In this thesis we prove rational homological stability for the classifying spaces of the homotopy automorphisms and block di↵eomorphisms of iterated connected sums of products of spheres of a certain connectivity.The results in particular apply to the manifolds       Npg,q  = (#g(Sp x Sq)) - int...... with coefficients in the homology of the universal covering, which is studied using rational homology theory. The result for the block di↵eomorphisms is deduced from the homological stability for the homotopy automorphisms upon using Surgery theory. Themain theorems of this thesis extend the homological stability...

  10. Kuranishi homology and Kuranishi cohomology

    OpenAIRE

    Joyce, Dominic

    2007-01-01

    A Kuranishi space is a topological space with a Kuranishi structure, defined by Fukaya and Ono. Kuranishi structures occur naturally on moduli spaces of J-holomorphic curves in symplectic geometry. Let Y be an orbifold and R a commutative ring or Q-algebra. We define two kinds of Kuranishi homology KH_*(Y;R). The chain complex KC_*(Y;R) defining KH_*(Y;R) is spanned over R by [X,f,G], for X a compact oriented Kuranishi space with corners, f : X --> Y smooth, and G "gauge-fixing data" which ma...

  11. Computational Homology for Software Validation

    Science.gov (United States)

    2015-03-01

    involving compound data-types. 15. SUBJECT TERMS Abstract datatypes , convergence structure, topological methods, specification logics, hybrid software...composite datatype values are networks strewn through the device’s memory; think of a variable whose type is an array of balanced trees. Some means...structural in nature, is required to rigorously specify the evolution of composite states involving non-numerical, non-metric components. Composite datatypes

  12. Specifying semantic information on functional requirements

    OpenAIRE

    YAO, WUPING

    2012-01-01

    Requirements engineering is a challenging process in software development projects. Requirements, in general, are documented in natural language. They often have issues related to ambiguity, completeness and consistency. How to improve the quality of requirements documentation remains a classic research topic. This research aims at improving the way of editing and documenting functional requirements. We propose a meta-model to specify the semantic information of functional requirements, and d...

  13. Specified radioactive waste final disposal act

    International Nuclear Information System (INIS)

    Yasui, Masaya

    2001-01-01

    Radioactive wastes must be finally and safely disposed far from human activities. Disposal act is a long-range task and needs to be understood and accepted by public for site selection. This paper explains basic policy of Japanese Government for final disposal act of specified radioactive wastes, examination for site selection guidelines to promote residential understanding, general concept of multi-barrier system for isolating the specific radioactive wastes, and research and technical development for radioactive waste management. (S. Ohno)

  14. Clonal evolution of AML on novel FMS-like tyrosine kinase-3 (FLT3 inhibitor therapy with evolving actionable targets

    Directory of Open Access Journals (Sweden)

    Pashtoon M. Kasi

    2016-01-01

    Full Text Available For acute myeloid leukemia (AML, identification of activating mutations in the FMS-like tyrosine kinase-3 (FLT3 has led to the development of several FLT3-inhibitors. Here we present clinical and next generation sequencing data at the time of progression of a patient on a novel FLT3-inhibitor clinical trial (ASP2215 to show that employing therapeutic interventions with these novel targeted therapies can lead to consequences secondary to selective pressure and clonal evolution of cancer. We describe novel findings alongside data on treatment directed towards actionable aberrations acquired during the process. (Clinical Trial: NCT02014558; registered at: 〈https://clinicaltrials.gov/ct2/show/NCT02014558〉

  15. Relation between circulating angiotensin II type 1 receptor agonistic autoantibodies and soluble fms-like tyrosine kinase 1 in the pathogenesis of preeclampsia

    NARCIS (Netherlands)

    H. Stepan (Holger); R. Faber (Renaldo); N. Wessel; G. Wallukat (Gerd); H.P. Schultheiss (Heinz-Peter); T. Walther (Thomas)

    2006-01-01

    textabstractContext: Placental and circulatory soluble fms-like tyrosine kinase 1 (sFlt1) has proven to be elevated in pregnant women with preeclampsia, a disease characterized by hypertension, proteinuria, and endothelial dysfunction. Recent studies also demonstrated an autoantibody against the

  16. High Level of Soluble FMS-Like Tyrosine Kinase-1 (sFlt-1 Serum in Pregnancy as a Risk Factor of Preeclampsia

    Directory of Open Access Journals (Sweden)

    I Gede Mega Putra

    2016-07-01

    Full Text Available Background: Recently, etiology and pathogenesis of preeclampsia remain unknown. One of the theory indicating that hypoxia and ischemic placenta caused by abnormal cytotrophoblast invasion in preeclampsia. Soluble Fms-like tyrosine kinase-1 (sFlt-1 serum as a laboratory marker of hypoxia condition that contributes to the occurrence of endothelial damage and clinical manifestations in preeclampsia. Objective: This study was aimed at proving that high level of soluble Fms-like tyrosine kinase-1 (sFlt-1 serum in pregnancy as a risk factor for preeclampsia. Methods: This study was a case control. Among 58 pregnant women studied, 29 women with preeclampsia as a case group and 29 women with normal pregnancy as a control group. Soluble Fms-like tyrosine kinase-1 (sFlt-1 serum was analyzed in the Prodia Laboratory. Collected data were tested for normality using Kolmogorov-Smirnov, then analyzed with independent sample test. Chi-Square test used to determine soluble Fms-like tyrosine kinase-1 (sFlt-1 serum level in preeclampsia. Results: This research concluded that the average level of soluble Fms-like tyrosine kinase-1 (sFlt-1 serum in preeclampsia were 11231.00 ± 8390.3 pg/mL and 3981.62 ± 4921.5 pg/mL in normal pregnancy. Analysis of significance with independent t-test concluded that the value of t = 4.01 and p = 0.001. This mean the average levels of soluble Fms-like tyrosine kinase-1 (sFlt-1serum levels in both groups were difference significantly (p <0.05. Based on the cut-off point of sFlt-1 serum levels was 4505.50 pg/mL with 79.3% sensitivity and 82.8% specificity, the relative risk of preeclampsia was 18 times (OR = 18.40, IK 95% = 4.93 to 68.70, p = 0.001. Conclusion:  Based on this research, high levels of soluble Fms-like tyrosine kinase-1 (sFlt-1 in pregnancy was proved as a risk factor for preeclampsia.

  17. Persistent homology and string vacua

    Energy Technology Data Exchange (ETDEWEB)

    Cirafici, Michele [Center for Mathematical Analysis, Geometry and Dynamical Systems,Instituto Superior Técnico, Universidade de Lisboa,Av. Rovisco Pais, 1049-001 Lisboa (Portugal); Institut des Hautes Études Scientifiques,Le Bois-Marie, 35 route de Chartres, F-91440 Bures-sur-Yvette (France)

    2016-03-08

    We use methods from topological data analysis to study the topological features of certain distributions of string vacua. Topological data analysis is a multi-scale approach used to analyze the topological features of a dataset by identifying which homological characteristics persist over a long range of scales. We apply these techniques in several contexts. We analyze N=2 vacua by focusing on certain distributions of Calabi-Yau varieties and Landau-Ginzburg models. We then turn to flux compactifications and discuss how we can use topological data analysis to extract physical information. Finally we apply these techniques to certain phenomenologically realistic heterotic models. We discuss the possibility of characterizing string vacua using the topological properties of their distributions.

  18. Peripheral T cell lymphoma: Not otherwise specified

    Directory of Open Access Journals (Sweden)

    Anusha H Pai

    2015-01-01

    Full Text Available Peripheral T cell lymphoma (PTCL is a heterogeneous group of hematological tumors originating from mature T cells, which constitutes less than 15% of all non-Hodgkins lymphomas in adults. Primary cutaneous PTCL-not otherwise specified (NOS represent a subgroup of PTCLs with no consistent immunophenotypic, genetic or clinical features. PTCL-NOS frequently has an aggressive course with a tendency for systemic involvement, however, a well-defined therapeutic and prognostic approach has not been outlined yet. We report a case of PTCL-NOS with multiple cutaneous lesions in a young adult male with an emphasis on the treatment modality used.

  19. Logic for specifying partially observable stochastic domains

    CSIR Research Space (South Africa)

    Rens, G

    2011-07-01

    Full Text Available to place it back on the floor. In situations where the oil-can is full, the robot gets 5 units of reward for grabbing the can, and it gets 10 units for a drink action. Otherwise, the robot gets no rewards. Rewards motivate an agent to behave as desired... with notions of probability. It will be shown how stochastic domains can be specified, including new kinds of axioms dealing with perception and a frame solution for the proposed logic. 1 Introduction and Motivation In the physical real world...

  20. The effect of microstructural change on the Charpy impact properties of the high-strength ferritic/martensitic steel (PNC-FMS) irradiated in JOYO/MARICO-1

    International Nuclear Information System (INIS)

    Yano, Yasuhide; Akasaka, Naoaki; Yoshitake, Tsunemitsu; Abe, Yasuhiro

    2004-03-01

    It is well known that the irradiation embrittlement is one of the most important issues to apply ferritic steels for FBR core materials, although ferritic steels have been considered to be candidate core materials of the commercialized FBR core material because of their superior swelling resistance. In order to evaluate the effects of microstructural changes during irradiation on the Charpy impact properties of the high-strength ferritic/martensitic steel (PNC-FMS), microstructural observations were performed with transmission electron microscopy on ruptured halves of the half-sized Charpy specimens of PNC-FMS irradiated in the JOYO/MARICO-1. The results obtained in this study are as follows: (1) There was remarkable disappearance of the lath of martensite in the samples irradiated at 650degC, although there was no significant change in microstructures, especially the lath of martensite between the samples irradiated at 500degC and unirradiated. The disappearance of martensitic lath in the samples irradiated at 650degC was larger than that of the samples thermally aged at 650degC. (2) The ductile-brittle transition temperature (DBTT) of irradiated PNC-FMS is judged to increase with the disappearance of martensitic lath and to decrease with the recovery in dislocations. (3) The decrease in the upper shelf energy (USE) of irradiated PNC-FMS is significantly accompanied by the change of precipitation behavior. (4) The Charpy impact properties and microstructures of PNC-FMS irradiated at 500degC were superior under these irradiation conditions. In future, it is necessary to establish how to evaluate Charpy impact properties in a high fluence region, based on theoretical methods introduced from the data gained in low fluence experiments, in addition to expanding the data area widely. (author)

  1. Homology in Electromagnetic Boundary Value Problems

    Directory of Open Access Journals (Sweden)

    Pellikka Matti

    2010-01-01

    Full Text Available We discuss how homology computation can be exploited in computational electromagnetism. We represent various cellular mesh reduction techniques, which enable the computation of generators of homology spaces in an acceptable time. Furthermore, we show how the generators can be used for setting up and analysis of an electromagnetic boundary value problem. The aim is to provide a rationale for homology computation in electromagnetic modeling software.

  2. OPTIMAL AIRCRAFT TRAJECTORIES FOR SPECIFIED RANGE

    Science.gov (United States)

    Lee, H.

    1994-01-01

    For an aircraft operating over a fixed range, the operating costs are basically a sum of fuel cost and time cost. While minimum fuel and minimum time trajectories are relatively easy to calculate, the determination of a minimum cost trajectory can be a complex undertaking. This computer program was developed to optimize trajectories with respect to a cost function based on a weighted sum of fuel cost and time cost. As a research tool, the program could be used to study various characteristics of optimum trajectories and their comparison to standard trajectories. It might also be used to generate a model for the development of an airborne trajectory optimization system. The program could be incorporated into an airline flight planning system, with optimum flight plans determined at takeoff time for the prevailing flight conditions. The use of trajectory optimization could significantly reduce the cost for a given aircraft mission. The algorithm incorporated in the program assumes that a trajectory consists of climb, cruise, and descent segments. The optimization of each segment is not done independently, as in classical procedures, but is performed in a manner which accounts for interaction between the segments. This is accomplished by the application of optimal control theory. The climb and descent profiles are generated by integrating a set of kinematic and dynamic equations, where the total energy of the aircraft is the independent variable. At each energy level of the climb and descent profiles, the air speed and power setting necessary for an optimal trajectory are determined. The variational Hamiltonian of the problem consists of the rate of change of cost with respect to total energy and a term dependent on the adjoint variable, which is identical to the optimum cruise cost at a specified altitude. This variable uniquely specifies the optimal cruise energy, cruise altitude, cruise Mach number, and, indirectly, the climb and descent profiles. If the optimum

  3. Homotopic Chain Maps Have Equal s-Homology and d-Homology

    Directory of Open Access Journals (Sweden)

    M. Z. Kazemi-Baneh

    2016-01-01

    Full Text Available The homotopy of chain maps on preabelian categories is investigated and the equality of standard homologies and d-homologies of homotopic chain maps is established. As a special case, if X and Y are the same homotopy type, then their nth d-homology R-modules are isomorphic, and if X is a contractible space, then its nth d-homology R-modules for n≠0 are trivial.

  4. Mechanistic Studies of the Yeast Polyamine Oxidase Fms1: Kinetic Mechanism, Substrate Specificity, and pH Dependence†

    Science.gov (United States)

    Adachi, Mariya S.; Torres, Jason M.; Fitzpatrick, Paul F.

    2010-01-01

    The flavoprotein oxidase Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine and N1-acetylspermine to yield spermidine and 3-aminopropanal or N-acetyl-3-aminopropanal. The kinetic mechanism of the enzyme has been determined with both substrates. The initial velocity patterns are ping-pong, consistent with reduction being kinetically irreversible. Reduction of Fms1 by either substrate is biphasic. The rate constant for the rapid phase varies with the substrate concentration, with limiting rates for reduction of the enzyme of 126 and 1410 s−1 and apparent Kd values of 24.3 and 484 μM for spermine and N1-acetylspermine, respectively. The rapid phase is followed by a concentration-independent phase that is slower than turnover. The reaction of the reduced enzyme with oxygen is monophasic, with a rate constant of 402 mM−1 s−1 with spermine at 25 °C, and 204 mM−1 s−1 with N1-acetylspermine at 4 °C, pH 9.0. This step is followed by rate-limiting product dissociation. The kcat/Kamine-pH profiles are bell-shaped, with an average pKa value of 9.3 with spermine and pKa values of 8.3 and 9.6 with N1-acetylspermine. Both profiles are consistent with the active forms of substrates having two charged nitrogens. The pH profiles for the rate constant for flavin reduction show pKa values of 8.3 and 7.2 for spermine and N1-acetylspermine, respectively, for groups that must be unprotonated; these pKa values are assigned to the substrate N4. The kcat/KO2-pH profiles show pKa values of 7.5 for spermine and 6.8 for N1-acetylspermine. With both substrates, the kcat value decreases when a single residue is protonated. PMID:21067138

  5. Relative K-homology and normal operators

    DEFF Research Database (Denmark)

    Manuilov, Vladimir; Thomsen, Klaus

    2009-01-01

    -term exact sequence which generalizes the excision six-term exact sequence in the first variable of KK-theory. Subsequently we investigate the relative K-homology which arises from the group of relative extensions by specializing to abelian $C^*$-algebras. It turns out that this relative K-homology carries...

  6. Lectures on homology with internal symmetries

    International Nuclear Information System (INIS)

    Solovyov, Yu.

    1993-09-01

    Homology with internal symmetries is a natural generalization of cyclic homology introduced, independently, by Connes and Tsygan, which has turned out to be a very useful tool in a number of problems of algebra, geometry topology, analysis and mathematical physics. It suffices to say cycling homology and cohomology are successfully applied in the index theory of elliptic operators on foliations, in the description of the homotopy type of pseudoisotopy spaces, in the theory of characteristic classes in algebraic K-theory. They are also applied in noncommutative differential geometry and in the cohomology of Lie algebras, the branches of mathematics which brought them to life in the first place. Essentially, we consider dihedral homology, which was successfully applied for the description of the homology type of groups of homeomorphisms and diffeomorphisms of simply connected manifolds. (author). 27 refs

  7. Serum Soluble Fms-Like Tyrosine Kinase 1 (sFlt-1 Predicts the Severity of Acute Pancreatitis

    Directory of Open Access Journals (Sweden)

    Paulina Dumnicka

    2016-12-01

    Full Text Available Organ failure is the most important determinant of the severity of acute pancreatitis (AP. Soluble fms-like tyrosine kinase 1 (sFlt-1 is positively associated with organ failure in sepsis. Our aim was to evaluate the diagnostic utility of automated sFlt-1 measurements for early prediction of AP severity. Adult patients (66 with AP were recruited, including 46 with mild (MAP, 15 with moderately-severe (MSAP and 5 with severe AP (SAP. Serum and urine samples were collected twice. Serum sFlt-1 was measured with automated electrochemiluminescence immunoassay. Serum concentrations of sFlt-1 were significantly higher in patients with MSAP and SAP as compared to MAP. SAP patients had the highest concentrations. At 24 and 48 h, sFlt-1 positively correlated with inflammatory markers (leukocyte count, C-reactive protein, kidney function (creatinine, urea, cystatin C, serum and urine neutrophil gelatinase-associated lipocalin, urine albumin/creatinine ratio, D-dimer and angiopoietin-2. sFlt-1 positively correlated with the bedside index of severity in AP (BISAP score and the duration of hospital stay. Serum sFlt-1 above 139 pg/mL predicted more severe AP (MSAP + SAP. In the early phase of AP, sFlt-1 is positively associated with the severity of AP and predicts organ failure, in particular kidney failure. Serum sFlt-1 may be a practical way to improve early assessment of AP severity.

  8. Focal glomerulosclerosis in proviral and c-fms transgenic mice links Vpr expression to HIV-associated nephropathy

    International Nuclear Information System (INIS)

    Dickie, Peter; Roberts, Amanda; Uwiera, Richard; Witmer, Jennifer; Sharma, Kirti; Kopp, Jeffrey B.

    2004-01-01

    Clinical and morphologic features of human immunodeficiency virus (HIV)-associated nephropathy (HIVAN), such as proteinuria, sclerosing glomerulopathy, tubular degeneration, and interstitial disease, have been modeled in mice bearing an HIV proviral transgene rendered noninfectious through a deletion in gag/pol. Exploring the genetic basis of HIVAN, HIV transgenic mice bearing mutations in either or both of the accessory genes nef and vpr were created. Proteinuria and focal glomerulosclerosis (FGS) only developed in mice with an intact vpr gene. Transgenic mice bearing a simplified proviral DNA (encoding only Tat and Vpr) developed renal disease characterized by FGS in which Vpr protein was localized to glomerular and tubular epithelia by immunohistochemistry. The dual transgenic progeny of HIV[Tat/Vpr] mice bred to HIV[ΔVpr] proviral transgenic mice displayed a more severe nephropathy with no apparent increase in Vpr expression, implying that multiple viral genes contribute to HIVAN. However, the unique contribution of macrophage-specific Vpr expression in the development of glomerular disease was underscored by the induction of FGS in multiple murine lines bearing a c-fms/vpr transgene

  9. The Effect of Maternal Soluble FMS-like Tyrosine Kinase 1 during Pregnancy on Risk of Preterm Delivery

    Science.gov (United States)

    Straughen, Jennifer K.; Kumar, Pawan; Misra, Vinod K.

    2013-01-01

    Objective Soluble fms-like tyrosine kinase 1 (sFlt1) is an antiangiogenic protein that is associated with a number of disorders of placental angiogenesis. It has been hypothesized that disruption of placental angiogenesis may contribute to the pathophysiology of preterm delivery (PTD). However, the relationship of PTD risk to variation in sFlt1 levels is not well known. We investigate the relationship between longitudinal variation in maternal serum concentrations of sFlt1 and risk of PTD. Methods Data were collected in a longitudinal cohort study involving 278 pregnant women. Maternal serum sFlt1 concentrations were measured at 6–10, 10–14, 16–20, 22–26, and 32–36 weeks gestation. Data analyses used longitudinal regression models using repeated measures that allow robust inferences from our modest sample size. The outcome was birth prior to 37 weeks gestation. Results sFlt1 concentrations were higher in first trimester for preterm compared to term deliveries. This relationship reversed in second trimester because sFlt1 concentrations increased more rapidly across gestation for term deliveries. In Cox proportional hazards analyses, a 2 ng higher sFlt1 concentration across gestation was associated with a hazard ratio of 1.3 (95% CI: 1.1, 1.5) for PTD suggesting the importance of levels in early pregnancy. Conclusion Elevated maternal serum sFlt1 concentration during pregnancy is associated with increased risk of PTD. PMID:22348624

  10. Note on specifying and verifying concurrent processes

    Energy Technology Data Exchange (ETDEWEB)

    Holenderski, L.

    1984-02-28

    To represent sequential processes, sets of finite sequences of symbols from a finite alphabet are used in this approach, alphabet symbols denote events occurring when a process is being executed, a sequence of symbols is a record of one execution of the process, and a set of such sequences represents the process itself by combining all its possible executions together. Although this model turned out adequate for specifying concurrent processes and allows proving their properties, there are two reasons, at least, why this note takes the same subject up again. First, by analogy to shuffle and its closure, which express parallel combination and parallel iteration of non-interacting processes, there is a need for a similar operation describing the behaviour of interaction processes. A new extension of shuffle is proposed as a generalization. The closure of this operation provides a tool for specification of parallelly iterated processes. Moreover, the closure makes mutually recursive specification unnecessary. Second, when this model was used to prove properties of concurrent computations, only flow-of-control schemes were considered (thus, only some general properties were proved). When applied to concrete programs using variables that have values, such schemes had to be interpreted. In contrast to such a schematic approach, the usefulness of the same method for concrete programs is argued. This is shown using an example of a correctness proof of an implementation of unbounded semaphore by binary semaphores. 8 references.

  11. Eating disorder not otherwise specified in adolescents.

    Science.gov (United States)

    Eddy, Kamryn T; Celio Doyle, Angela; Hoste, Renee Rienecke; Herzog, David B; le Grange, Daniel

    2008-02-01

    To examine the frequency, type, and clinical severity of eating disorder not otherwise specified (EDNOS) in adolescents seeking treatment through an outpatient eating disorders service. Two hundred eighty-one consecutive referrals to an eating disorders program were assessed using the Eating Disorder Examination (EDE) and self-report measures of depression and self-esteem. The majority of adolescents presented with EDNOS (59.1%; n = 166) relative to anorexia nervosa (AN; 20.3%; n = 57) and bulimia nervosa (BN; 20.6%; n = 58). Most EDNOS youths could be described as subthreshold AN (SAN; 27.7%; n = 46), subthreshold BN (SBN; 19.9%; n = 33), EDNOS purging (27.7%; n = 46), or EDNOS bingeing (6.0%; n = 10); yet 31 (18.7%) could not be categorized as such (EDNOS "other"). Overall differences in eating disorder pathology, depressive symptoms, and self-esteem emerged between the EDNOS types, wherein adolescents with EDNOS bulimic variants (SBN, EDNOS purging, and EDNOS bingeing) had more pathology than youths with SAN or EDNOS "other." There were no differences in these variables between AN and SAN; in contrast, compared with BN, youths with EDNOS bulimic variants reported lower EDE scores and higher self-esteem, although there were no between-group differences in depression. As in adults with eating disorders, EDNOS predominates and is heterogeneous with regard to eating disorder pathology and associated features in an adolescent clinical sample. Lack of differences between AN and SAN suggests that the strict criteria for AN could be relaxed; differences between BN and EDNOS bulimic variants do not support their combination.

  12. Report of the generation of the nuclear bank Presto-Hot for the SVEA-96 fuel with the FMS codes

    International Nuclear Information System (INIS)

    Alonso V, G.

    1991-12-01

    In this work it is described in a general way the form in that was generated the database of the SVEA-96 fuel for Laguna Verde. The formation of the bank it was carried out with the ECLIPSE 86-2D, RECORD 89-1A and POLGEN 88-lB codes of the FMS package installed in the VAX system of the offices of the National Commission of Nuclear Safety and Safeguards in Mexico, D.F. The formed bank is denominated 'LlPG9102'. All this was carried out following the '6F3/I/CN029/90/P1' procedure. By means of the MERGE code of the FMS package installed in the VAX system of the offices of the Federal Commission of Electricity in Mexico, D.F., it was annex this information to the contained bank 'LlPG3314' being generated the one bank 'LlPG9701'. This contains the information of the 5 fuel types of the initial load of the unit 1 and of the first reload of Laguna Verde as well as the information corresponding to the SVEA-96 fuel. The results obtained during the formation of the data bank of the fuel as for the behavior of those different cell parameters regarding the burnt of the fuel and the variation of vacuums in the coolant channel is compared with those reported in the documents of fuel design provided by ABB-ATOM. These comparisons, although they are not exhaustive they show the general tendency of the results the which is quite favorable. The generated database contains the enough information in terms of constant in two dependent groups of burnt and instantaneous vacuums, for the different arrangements of present fuel bars in the one assemble as well as those coefficients that take into account the presence of the control bar, the variation in the fuel temperature and the one effect of the 'historical' vacuums. All this included in that is knows as SUPER option of the bank for PRESTO with the options PRCOEF and POLRAM. Also, in the Annex G of this report its were provided for separate the M-Factor, the coefficients of Xenon and the parameters of burnt of the control bar for Presto

  13. Preserved irradiated homologous cartilage for orbital reconstruction

    International Nuclear Information System (INIS)

    Linberg, J.V.; Anderson, R.L.; Edwards, J.J.; Panje, W.R.; Bardach, J.

    1980-01-01

    Human costal cartilage is an excellent implant material for orbital and periorbital reconstruction because of its light weight, strength, homogeneous consistency and the ease with which it can be carved. Its use has been limited by the necessity of a separate surgical procedure to obtain the material. Preserved irradiated homologous cartilage has been shown to have almost all the autogenous cartilage and is convenient to use. Preserved irradiated homologous cartilage transplants do not elicit rejection reactions, resist infection and rarely undergo absorption

  14. Dualities in persistent (co)homology

    International Nuclear Information System (INIS)

    De Silva, Vin; Morozov, Dmitriy; Vejdemo-Johansson, Mikael

    2011-01-01

    We consider sequences of absolute and relative homology and cohomology groups that arise naturally for a filtered cell complex. We establish algebraic relationships between their persistence modules, and show that they contain equivalent information. We explain how one can use the existing algorithm for persistent homology to process any of the four modules, and relate it to a recently introduced persistent cohomology algorithm. We present experimental evidence for the practical efficiency of the latter algorithm

  15. Delineation and analysis of chromosomal regions specifying Yersinia pestis.

    Science.gov (United States)

    Derbise, Anne; Chenal-Francisque, Viviane; Huon, Christèle; Fayolle, Corinne; Demeure, Christian E; Chane-Woon-Ming, Béatrice; Médigue, Claudine; Hinnebusch, B Joseph; Carniel, Elisabeth

    2010-09-01

    Yersinia pestis, the causative agent of plague, has recently diverged from the less virulent enteropathogen Yersinia pseudotuberculosis. Its emergence has been characterized by massive genetic loss and inactivation and limited gene acquisition. The acquired genes include two plasmids, a filamentous phage, and a few chromosomal loci. The aim of this study was to characterize the chromosomal regions acquired by Y. pestis. Following in silico comparative analysis and PCR screening of 98 strains of Y. pseudotuberculosis and Y. pestis, we found that eight chromosomal loci (six regions [R1pe to R6pe] and two coding sequences [CDS1pe and CDS2pe]) specified Y. pestis. Signatures of integration by site specific or homologous recombination were identified for most of them. These acquisitions and the loss of ancestral DNA sequences were concentrated in a chromosomal region opposite to the origin of replication. The specific regions were acquired very early during Y. pestis evolution and were retained during its microevolution, suggesting that they might bring some selective advantages. Only one region (R3pe), predicted to carry a lambdoid prophage, is most likely no longer functional because of mutations. With the exception of R1pe and R2pe, which have the potential to encode a restriction/modification and a sugar transport system, respectively, no functions could be predicted for the other Y. pestis-specific loci. To determine the role of the eight chromosomal loci in the physiology and pathogenicity of the plague bacillus, each of them was individually deleted from the bacterial chromosome. None of the deletants exhibited defects during growth in vitro. Using the Xenopsylla cheopis flea model, all deletants retained the capacity to produce a stable and persistent infection and to block fleas. Similarly, none of the deletants caused any acute flea toxicity. In the mouse model of infection, all deletants were fully virulent upon subcutaneous or aerosol infections. Therefore

  16. Investigating homology between proteins using energetic profiles.

    Science.gov (United States)

    Wrabl, James O; Hilser, Vincent J

    2010-03-26

    Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding) and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved local stability, may

  17. Investigating homology between proteins using energetic profiles.

    Directory of Open Access Journals (Sweden)

    James O Wrabl

    2010-03-01

    Full Text Available Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved

  18. Dinucleotide repeat polymorphism in Fms-like tyrosine kinase-1 (Flt-1 gene is not associated with preeclampsia

    Directory of Open Access Journals (Sweden)

    Park So-Yeon

    2008-07-01

    Full Text Available Abstract Background Preeclampsia is a major cause of maternal and perinatal mortality and morbidity. The etiology of preeclampsia remains unclear. Recently, it was shown that misregulation of fms-like tyrosine kinase-1 (Flt-1 in the peripheral blood mononuclear cells of pregnant women results in over-expression of the soluble splice variant of Flt-1, sFlt-1, producing an additional (extra-placental source of sFlt-1 that can contribute to the etiology of preeclampsia. The aim of this study was to investigate the relationship between preeclampsia and a dinucleotide (threonine-glycine; TGn repeat polymorphism in the 3' non-coding region of the Flt-1 gene. Methods The number of the d(TGn repeats was analyzed in 170 patients with preeclampsia and in 202 normotensive pregnancies. The region containing the dinucleotide repeat polymorphism of the Flt-1 gene was amplified by polymerase chain reaction (PCR from the DNA samples and was analyzed by direct PCR sequencing. Results We found 10 alleles of the dinucleotide repeat polymorphism and designated these as allele*12 (A1 through allele*23 (A12 according to the number of the TG repeats, from 12 to 23. The frequency of the 14-repeat allele (A3 was most abundant (63.82% in preeclampsia and 69.06% in controls, followed by the 21-repeat allele (A10; 28.53% in preeclampsia and 23.76% in controls. There was no significant difference in the allele frequency between patients with preeclampsia and normal controls. The most common genotype in preeclamptic and normotensive pregnancies was heterozygous (TG14/(TG21 (41.76% and homozygous (TG14/(TG14 (45.05%, respectively. However, the genotype frequencies were not significantly different between preeclamptic patients and controls. Conclusion This is the first study to characterize the dinucleotide repeat polymorphism of the Flt-1 gene in patients with preeclampsia. We found no differences in the allele or genotype frequencies between patients with preeclampsia and

  19. Homological methods, representation theory, and cluster algebras

    CERN Document Server

    Trepode, Sonia

    2018-01-01

    This text presents six mini-courses, all devoted to interactions between representation theory of algebras, homological algebra, and the new ever-expanding theory of cluster algebras. The interplay between the topics discussed in this text will continue to grow and this collection of courses stands as a partial testimony to this new development. The courses are useful for any mathematician who would like to learn more about this rapidly developing field; the primary aim is to engage graduate students and young researchers. Prerequisites include knowledge of some noncommutative algebra or homological algebra. Homological algebra has always been considered as one of the main tools in the study of finite-dimensional algebras. The strong relationship with cluster algebras is more recent and has quickly established itself as one of the important highlights of today’s mathematical landscape. This connection has been fruitful to both areas—representation theory provides a categorification of cluster algebras, wh...

  20. A homology theory for smale spaces

    CERN Document Server

    Putnam, Ian F

    2014-01-01

    The author develops a homology theory for Smale spaces, which include the basics sets for an Axiom A diffeomorphism. It is based on two ingredients. The first is an improved version of Bowen's result that every such system is the image of a shift of finite type under a finite-to-one factor map. The second is Krieger's dimension group invariant for shifts of finite type. He proves a Lefschetz formula which relates the number of periodic points of the system for a given period to trace data from the action of the dynamics on the homology groups. The existence of such a theory was proposed by Bowen in the 1970s.

  1. 42 CFR 480.138 - Disclosure for other specified purposes.

    Science.gov (United States)

    2010-10-01

    ...) General requirements for disclosure. Except as specified in paragraph (b) of this section, the following... information is necessary to protect against a substantial risk to the public health. (3) Disclosure to the... 42 Public Health 4 2010-10-01 2010-10-01 false Disclosure for other specified purposes. 480.138...

  2. 31 CFR 129.6 - Penalties specified by law.

    Science.gov (United States)

    2010-07-01

    ... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false Penalties specified by law. 129.6 Section 129.6 Money and Finance: Treasury Regulations Relating to Money and Finance PORTFOLIO INVESTMENT SURVEY REPORTING § 129.6 Penalties specified by law. Reporters are advised that the Act provides the...

  3. 77 FR 9877 - Reporting of Specified Foreign Financial Assets; Correction

    Science.gov (United States)

    2012-02-21

    ... Reporting of Specified Foreign Financial Assets; Correction AGENCY: Internal Revenue Service (IRS). ACTION... the reporting of specified foreign financial assets. FOR FURTHER INFORMATION CONTACT: Joseph S.... List of Subjects in 26 CFR Part 1 Income taxes, Reporting and recordkeeping requirements. PART 1...

  4. 77 FR 10422 - Reporting of Specified Foreign Financial Assets; Correction

    Science.gov (United States)

    2012-02-22

    ... Reporting of Specified Foreign Financial Assets; Correction AGENCY: Internal Revenue Service (IRS). ACTION... to the reporting of specified foreign financial assets. DATES: Effective Date: December 19, 2011. FOR... ``Explanation of Provisions'', paragraph B. 2., line three, the language ``or executor is a bank, financial'' is...

  5. 76 FR 78594 - Reporting of Specified Foreign Financial Assets

    Science.gov (United States)

    2011-12-19

    ... Reporting of Specified Foreign Financial Assets AGENCY: Internal Revenue Service (IRS), Treasury. ACTION... foreign financial assets and the value of those assets is more than the applicable reporting threshold... hold specified foreign financial assets generally will be excepted from reporting such assets under...

  6. 77 FR 9845 - Reporting of Specified Foreign Financial Assets; Correction

    Science.gov (United States)

    2012-02-21

    ... Reporting of Specified Foreign Financial Assets; Correction AGENCY: Internal Revenue Service (IRS), Treasury...), which were published in the Federal Register on Monday, December 19, 2011, relating to the reporting of specified foreign financial assets. DATES: Effective date: This correction is effective February 21, 2012...

  7. Examining the Panic Attack Specifier in Social Anxiety Disorder.

    Science.gov (United States)

    Allan, Nicholas P; Oglesby, Mary E; Short, Nicole A; Schmidt, Norman B

    2016-04-01

    Panic attacks (PAs) are characterized by overwhelming surges of fear and discomfort and are one of the most frequently occurring symptoms in psychiatric populations. The most recent version of the Diagnostic and Statistical Manual of Mental Disorders (i.e. DSM-5) allows for a panic attack (PA) specifier for all disorders, including social anxiety disorder (SAD). However, there is little research examining differences between individuals diagnosed with SAD with the PA specifier versus individuals diagnosed with SAD without the PA specifier. The current study examined social anxiety, mood, anxiety, and anxiety sensitivity social concerns, a risk factor for social anxiety in SAD-diagnosed individuals without (N = 52) and with (N = 14) the PA specifier. The groups differed only in somatic symptoms of anxiety. Result of the current study provides preliminary evidence that the presence of the PA specifier in social anxiety does not result in elevated levels of comorbidity or a more severe presentation of social anxiety.

  8. Homology and cohomology of Rees semigroup algebras

    DEFF Research Database (Denmark)

    Grønbæk, Niels; Gourdeau, Frédéric; White, Michael C.

    2011-01-01

    Let S by a Rees semigroup, and let 1¹(S) be its convolution semigroup algebra. Using Morita equivalence we show that bounded Hochschild homology and cohomology of l¹(S) is isomorphic to those of the underlying discrete group algebra....

  9. Induction of homologous recombination in Saccharomyces cerevisiae.

    Science.gov (United States)

    Simon, J R; Moore, P D

    1988-09-01

    We have investigated the effects of UV irradiation of Saccharomyces cerevisiae in order to distinguish whether UV-induced recombination results from the induction of enzymes required for homologous recombination, or the production of substrate sites for recombination containing regions of DNA damage. We utilized split-dose experiments to investigate the induction of proteins required for survival, gene conversion, and mutation in a diploid strain of S. cerevisiae. We demonstrate that inducing doses of UV irradiation followed by a 6 h period of incubation render the cells resistant to challenge doses of UV irradiation. The effects of inducing and challenge doses of UV irradiation upon interchromosomal gene conversion and mutation are strictly additive. Using the yeast URA3 gene cloned in non-replicating single- and double-stranded plasmid vectors that integrate into chromosomal genes upon transformation, we show that UV irradiation of haploid yeast cells and homologous plasmid DNA sequences each stimulate homologous recombination approximately two-fold, and that these effects are additive. Non-specific DNA damage has little effect on the stimulation of homologous recombination, as shown by studies in which UV-irradiated heterologous DNA was included in transformation/recombination experiments. We further demonstrate that the effect of competing single- and double-stranded heterologous DNA sequences differs in UV-irradiated and unirradiated cells, suggesting an induction of recombinational machinery in UV-irradiated S. cerevisiae cells.

  10. Threading homology through algebra selected patterns

    CERN Document Server

    Boffi, Giandomenico

    2006-01-01

    Aimed at graduate students and researchers in mathematics, this book takes homological themes, such as Koszul complexes and their generalizations, and shows how these can be used to clarify certain problems in selected parts of algebra, as well as their success in solving a number of them.

  11. Cell biology of homologous recombination in yeast

    DEFF Research Database (Denmark)

    Eckert-Boulet, Nadine Valerie; Rothstein, Rodney; Lisby, Michael

    2011-01-01

    Homologous recombination is an important pathway for error-free repair of DNA lesions, such as single- and double-strand breaks, and for rescue of collapsed replication forks. Here, we describe protocols for live cell imaging of single-lesion recombination events in the yeast Saccharomyces...

  12. Polar representation of centrifugal pump homologous curves

    International Nuclear Information System (INIS)

    Veloso, Marcelo Antonio; Mattos, Joao Roberto Loureiro de

    2008-01-01

    Essential for any mathematical model designed to simulate flow transient events caused by pump operations is the pump performance data. The performance of a centrifugal pump is characterized by four basic parameters: the rotational speed, the volumetric flow rate, the dynamic head, and the hydraulic torque. Any one of these quantities can be expressed as a function of any two others. The curves showing the relationships between these four variables are called the pump characteristic curves, also referred to as four-quadrant curves. The characteristic curves are empirically developed by the pump manufacturer and uniquely describe head and torque as functions of volumetric flow rate and rotation speed. Because of comprising a large amount of points, the four-quadrant configuration is not suitable for computational purposes. However, it can be converted to a simpler form by the development of the homologous curves, in which dynamic head and hydraulic torque ratios are expressed as functions of volumetric flow and rotation speed ratios. The numerical use of the complete set of homologous curves requires specification of sixteen partial curves, being eight for the dynamic head and eight for the hydraulic torque. As a consequence, the handling of homologous curves is still somewhat complicated. In solving flow transient problems that require the pump characteristic data for all the operation zones, the polar form appears as the simplest way to represent the homologous curves. In the polar method, the complete characteristics of a pump can be described by only two closed curves, one for the dynamic head and other for the hydraulic torque, both in function of a single angular coordinate defined adequately in terms of the quotient between volumetric flow ratio and rotation speed ratio. The usefulness and advantages of this alternative method are demonstrated through a practical example in which the homologous curves for a pump of the type used in the main coolant loops of a

  13. Parametric representation of centrifugal pump homologous curves

    International Nuclear Information System (INIS)

    Veloso, Marcelo A.; Mattos, Joao R.L. de

    2015-01-01

    Essential for any mathematical model designed to simulate flow transient events caused by pump operations is the pump performance data. The performance of a centrifugal pump is characterized by four basic quantities: the rotational speed, the volumetric flow rate, the dynamic head, and the hydraulic torque. The curves showing the relationships between these four variables are called the pump characteristic curves. The characteristic curves are empirically developed by the pump manufacturer and uniquely describe head and torque as functions of volumetric flow rate and rotation speed. Because of comprising a large amount of points, this configuration is not suitable for computational purposes. However, it can be converted to a simpler form by the development of the homologous curves, in which dynamic head and hydraulic torque ratios are expressed as functions of volumetric flow and rotation speed ratios. The numerical use of the complete set of homologous curves requires specification of sixteen partial curves, being eight for the dynamic head and eight for the hydraulic torque. As a consequence, the handling of homologous curves is still somewhat complicated. In solving flow transient problems that require the pump characteristic data for all the operation zones, the parametric form appears as the simplest way to deal with the homologous curves. In this approach, the complete characteristics of a pump can be described by only two closed curves, one for the dynamic head and other for the hydraulic torque, both in function of a single angular coordinate defined adequately in terms of the quotient between volumetric flow ratio and rotation speed ratio. The usefulness and advantages of this alternative method are demonstrated through a practical example in which the homologous curves for a pump of the type used in the main coolant loops of a pressurized water reactor (PWR) are transformed to the parametric form. (author)

  14. Charts for specifying limits on copper stabilizer damage rate

    International Nuclear Information System (INIS)

    Sawan, M.E.

    1984-01-01

    Charts that simplify the task of specifying the damage rate limit in the copper stabilizer of fusion reactor superconducting magnets are presented. Partial damage recovery with annealing is accounted for. Applications to the MARS magnets are discussed. (orig.)

  15. 42 CFR 8.24 - Specifying who represents the parties.

    Science.gov (United States)

    2010-10-01

    ... CERTIFICATION OF OPIOID TREATMENT PROGRAMS Procedures for Review of Suspension or Proposed Revocation of OTP Certification, and of Adverse Action Regarding Withdrawal of Approval of an Accreditation Body § 8.24 Specifying...

  16. Homologation Reaction of Ketones with Diazo Compounds.

    Science.gov (United States)

    Candeias, Nuno R; Paterna, Roberta; Gois, Pedro M P

    2016-03-09

    This review covers the addition of diazo compounds to ketones to afford homologated ketones, either in the presence or in the absence of promoters or catalysts. Reactions with diazoalkanes, aryldiazomethanes, trimethylsilyldiazomethane, α-diazo esters, and disubstituted diazo compounds are covered, commenting on the complex regiochemistry of the reaction and the nature of the catalysts and promoters. The recent reports on the enantioselective version of ketone homologation reactions are gathered in one section, followed by reports on the use of cyclic ketones ring expansion in total synthesis. Although the first reports of this reaction appeared in the literature almost one century ago, the recent achievements, in particular, for the asymmetric version, forecast the development of new breakthroughs in the synthetically valuable field of diazo chemistry.

  17. Homological mirror symmetry and tropical geometry

    CERN Document Server

    Catanese, Fabrizio; Kontsevich, Maxim; Pantev, Tony; Soibelman, Yan; Zharkov, Ilia

    2014-01-01

    The relationship between Tropical Geometry and Mirror Symmetry goes back to the work of Kontsevich and Y. Soibelman (2000), who applied methods of non-archimedean geometry (in particular, tropical curves) to Homological Mirror Symmetry. In combination with the subsequent work of Mikhalkin on the “tropical” approach to Gromov-Witten theory, and the work of Gross and Siebert, Tropical Geometry has now become a powerful tool. Homological Mirror Symmetry is the area of mathematics concentrated around several categorical equivalences connecting symplectic and holomorphic (or algebraic) geometry. The central ideas first appeared in the work of Maxim Kontsevich (1993). Roughly speaking, the subject can be approached in two ways: either one uses Lagrangian torus fibrations of Calabi-Yau manifolds (the so-called Strominger-Yau-Zaslow picture, further developed by Kontsevich and Soibelman) or one uses Lefschetz fibrations of symplectic manifolds (suggested by Kontsevich and further developed by Seidel). Tropical Ge...

  18. Homological stability for unordered configuration spaces

    DEFF Research Database (Denmark)

    Randal-Williams, Oscar

    2013-01-01

    This paper consists of two related parts. In the first part we give a self-contained proof of homological stability for the spaces C_n(M;X) of configurations of n unordered points in a connected open manifold M with labels in a path-connected space X, with the best possible integral stability range...... of the spaces C_n(M) can be considered stable when M is a closed manifold. In this case there are no stabilisation maps, but one may still ask if the dimensions of the homology groups over some field stabilise with n. We prove that this is true when M is odd-dimensional, or when the field is F_2 or Q...

  19. Regulation of homologous recombination in eukaryotes

    OpenAIRE

    Heyer, Wolf-Dietrich; Ehmsen, Kirk T.; Liu, Jie

    2010-01-01

    Homologous recombination is required for accurate chromosome segregation during the first meiotic division and constitutes a key repair and tolerance pathway for complex DNA damage including DNA double-stranded breaks, interstrand crosslinks, and DNA gaps. In addition, recombination and replication are inextricably linked, as recombination recovers stalled and broken replication forks enabling the evolution of larger genomes/replicons. Defects in recombination lead to genomic instability and ...

  20. Khovanov homology of graph-links

    Energy Technology Data Exchange (ETDEWEB)

    Nikonov, Igor M [M. V. Lomonosov Moscow State University, Faculty of Mechanics and Mathematics, Moscow (Russian Federation)

    2012-08-31

    Graph-links arise as the intersection graphs of turning chord diagrams of links. Speaking informally, graph-links provide a combinatorial description of links up to mutations. Many link invariants can be reformulated in the language of graph-links. Khovanov homology, a well-known and useful knot invariant, is defined for graph-links in this paper (in the case of the ground field of characteristic two). Bibliography: 14 titles.

  1. Improving fundamental movement skills in Hong Kong students through an assessment for learning intervention that emphasizes fun, mastery, and support: the A + FMS randomized controlled trial study protocol.

    Science.gov (United States)

    Chan, Cecilia; Ha, Amy; Ng, Johan Y Y

    2016-01-01

    Assessment for learning has been identified as an effective strategy to help children learn more effectively. Developing children to master basic movement skills in primary school requires formative assessments to inform instruction and learning. This study reports the rationale and methods for an assessment-based intervention that emphasizes fun, mastery and support (A + FMS) designed to improve fundamental movement skill (FMS) proficiency of primary schoolchildren. Utilizing a cluster randomized controlled trial, the A + FMS intervention was designed to improve FMS proficiency of Hong Kong Chinese schoolchildren. A target sample of 282 students or more from 10 Grade 3 classes (from five schools) will be recruited and randomly assigned into an experimental group or a wait-list control group. Competence motivation theory provided a framework for the intervention that emphasizes fun activities to develop basic fundamentals, improving mastery of movement, and providing support for teaching and learning skills. Primary outcome measures are the raw scores of six objectively measured FMS (i.e., jump, hop, skip, dribble, catch, and overhand throw). Secondary outcomes include self-reported measures: enjoyment in physical education, perceived physical competence, perceived skill competence, and perceived social support. Teachers in the experimental group are required to attend a six-h training workshop and integrate 550 min of assessment for learning strategies into their physical education lessons. Resources such as videos, skills checklists, and equipment will also be provided to support children to accumulate extra learning and practice time after school. The rate of changes in primary and secondary outcomes across the experimental and control groups will be compared to determine the effectiveness of the program. The A + FMS is an innovative school-based intervention targeting improvements in movement mastery by supporting physical education teachers in FMS

  2. Quandle and Biquandle Homology Calculation in R

    Directory of Open Access Journals (Sweden)

    Roger Fenn

    2018-01-01

    Full Text Available In knot theory several knot invariants have been found over the last decades. This paper concerns itself with invariants of several of those invariants, namely the Homology of racks, quandles, biracks and biquandles. The software described in this paper calculates the rack, quandle and degenerate homology groups of racks and biracks. It works for any rack/quandle with finite elements where there are homology coefficients in 'Z'k. The up and down actions can be given either as a function of the elements of 'Z'k or provided as a matrix. When calculating a rack, the down action should coincide with the identity map. We have provided actions for both the general dihedral quandle and the group quandle over 'S'3. We also provide a second function to test if a set with a given action (or with both actions gives rise to a quandle or biquandle. The program is provided as an R package and can be found at https://github.com/ansgarwenzel/quhomology.   AMS subject classification: 57M27; 57M25

  3. Several aspects of some techniques avoiding homologous blood transfusions

    NARCIS (Netherlands)

    E.C.S.M. van Woerkens (Liesbeth)

    1998-01-01

    textabstractThe use of homologous blood products during anesthesia and surgery is not without risks. Complications due to homologous blood transfusions include transfusion reactions, isosensitization, transmission of infections (including HIV, hepatitis, CMV) and immunosuppression (resuiting in

  4. Computing Homology Group Generators of Images Using Irregular Graph Pyramids

    OpenAIRE

    Peltier , Samuel; Ion , Adrian; Haxhimusa , Yll; Kropatsch , Walter; Damiand , Guillaume

    2007-01-01

    International audience; We introduce a method for computing homology groups and their generators of a 2D image, using a hierarchical structure i.e. irregular graph pyramid. Starting from an image, a hierarchy of the image is built, by two operations that preserve homology of each region. Instead of computing homology generators in the base where the number of entities (cells) is large, we first reduce the number of cells by a graph pyramid. Then homology generators are computed efficiently on...

  5. Conserved gene regulatory module specifies lateral neural borders across bilaterians.

    Science.gov (United States)

    Li, Yongbin; Zhao, Di; Horie, Takeo; Chen, Geng; Bao, Hongcun; Chen, Siyu; Liu, Weihong; Horie, Ryoko; Liang, Tao; Dong, Biyu; Feng, Qianqian; Tao, Qinghua; Liu, Xiao

    2017-08-01

    The lateral neural plate border (NPB), the neural part of the vertebrate neural border, is composed of central nervous system (CNS) progenitors and peripheral nervous system (PNS) progenitors. In invertebrates, PNS progenitors are also juxtaposed to the lateral boundary of the CNS. Whether there are conserved molecular mechanisms determining vertebrate and invertebrate lateral neural borders remains unclear. Using single-cell-resolution gene-expression profiling and genetic analysis, we present evidence that orthologs of the NPB specification module specify the invertebrate lateral neural border, which is composed of CNS and PNS progenitors. First, like in vertebrates, the conserved neuroectoderm lateral border specifier Msx/vab-15 specifies lateral neuroblasts in Caenorhabditis elegans Second, orthologs of the vertebrate NPB specification module ( Msx/vab-15 , Pax3/7/pax-3 , and Zic/ref-2 ) are significantly enriched in worm lateral neuroblasts. In addition, like in other bilaterians, the expression domain of Msx/vab-15 is more lateral than those of Pax3/7/pax-3 and Zic/ref- 2 in C. elegans Third, we show that Msx/vab-15 regulates the development of mechanosensory neurons derived from lateral neural progenitors in multiple invertebrate species, including C. elegans , Drosophila melanogaster , and Ciona intestinalis We also identify a novel lateral neural border specifier, ZNF703/tlp-1 , which functions synergistically with Msx/vab- 15 in both C. elegans and Xenopus laevis These data suggest a common origin of the molecular mechanism specifying lateral neural borders across bilaterians.

  6. A PHF8 homolog in C. elegans promotes DNA repair via homologous recombination.

    Directory of Open Access Journals (Sweden)

    Changrim Lee

    Full Text Available PHF8 is a JmjC domain-containing histone demethylase, defects in which are associated with X-linked mental retardation. In this study, we examined the roles of two PHF8 homologs, JMJD-1.1 and JMJD-1.2, in the model organism C. elegans in response to DNA damage. A deletion mutation in either of the genes led to hypersensitivity to interstrand DNA crosslinks (ICLs, while only mutation of jmjd-1.1 resulted in hypersensitivity to double-strand DNA breaks (DSBs. In response to ICLs, JMJD-1.1 did not affect the focus formation of FCD-2, a homolog of FANCD2, a key protein in the Fanconi anemia pathway. However, the dynamic behavior of RPA-1 and RAD-51 was affected by the mutation: the accumulations of both proteins at ICLs appeared normal, but their subsequent disappearance was retarded, suggesting that later steps of homologous recombination were defective. Similar changes in the dynamic behavior of RPA-1 and RAD-51 were seen in response to DSBs, supporting a role of JMJD-1.1 in homologous recombination. Such a role was also supported by our finding that the hypersensitivity of jmjd-1.1 worms to ICLs was rescued by knockdown of lig-4, a homolog of Ligase 4 active in nonhomologous end-joining. The hypersensitivity of jmjd-1.1 worms to ICLs was increased by rad-54 knockdown, suggesting that JMJD-1.1 acts in parallel with RAD-54 in modulating chromatin structure. Indeed, the level of histone H3 Lys9 tri-methylation, a marker of heterochromatin, was higher in jmjd-1.1 cells than in wild-type cells. We conclude that the histone demethylase JMJD-1.1 influences homologous recombination either by relaxing heterochromatin structure or by indirectly regulating the expression of multiple genes affecting DNA repair.

  7. Hochschild Homology and Cohomology of Klein Surfaces

    Directory of Open Access Journals (Sweden)

    Frédéric Butin

    2008-09-01

    Full Text Available Within the framework of deformation quantization, a first step towards the study of star-products is the calculation of Hochschild cohomology. The aim of this article is precisely to determine the Hochschild homology and cohomology in two cases of algebraic varieties. On the one hand, we consider singular curves of the plane; here we recover, in a different way, a result proved by Fronsdal and make it more precise. On the other hand, we are interested in Klein surfaces. The use of a complex suggested by Kontsevich and the help of Groebner bases allow us to solve the problem.

  8. Homology in vertebrates bone mineral structure

    International Nuclear Information System (INIS)

    Batdehmbehrehl, G.; Chultehm, D.; Sangaa, D.

    1999-01-01

    Using the neutron diffraction method a domination of low crystal syngonic (sp. gr. P63/m) phase Ca 5 [PO 4 ] 3 (OH, F, Cl) in bull and sheep bones as well as in the fossil dinosaur bone has been established and crystal phases in all the bones have identical structure (homology). The result becomes to be an important contribution to fundamental science such as biological evolution and to be useful in medical practice and solution of radiobiological problems connected with vertebrates and man. (author)

  9. Homological Perturbation Theory for Nonperturbative Integrals

    Science.gov (United States)

    Johnson-Freyd, Theo

    2015-11-01

    We use the homological perturbation lemma to produce explicit formulas computing the class in the twisted de Rham complex represented by an arbitrary polynomial. This is a non-asymptotic version of the method of Feynman diagrams. In particular, we explain that phenomena usually thought of as particular to asymptotic integrals in fact also occur exactly: integrals of the type appearing in quantum field theory can be reduced in a totally algebraic fashion to integrals over an Euler-Lagrange locus, provided this locus is understood in the scheme-theoretic sense, so that imaginary critical points and multiplicities of degenerate critical points contribute.

  10. Specifying design conservatism: Worst case versus probabilistic analysis

    Science.gov (United States)

    Miles, Ralph F., Jr.

    1993-01-01

    Design conservatism is the difference between specified and required performance, and is introduced when uncertainty is present. The classical approach of worst-case analysis for specifying design conservatism is presented, along with the modern approach of probabilistic analysis. The appropriate degree of design conservatism is a tradeoff between the required resources and the probability and consequences of a failure. A probabilistic analysis properly models this tradeoff, while a worst-case analysis reveals nothing about the probability of failure, and can significantly overstate the consequences of failure. Two aerospace examples will be presented that illustrate problems that can arise with a worst-case analysis.

  11. Specifying structural constraints of architectural patterns in the ARCHERY language

    International Nuclear Information System (INIS)

    Sanchez, Alejandro; Barbosa, Luis S.; Riesco, Daniel

    2015-01-01

    ARCHERY is an architectural description language for modelling and reasoning about distributed, heterogeneous and dynamically reconfigurable systems in terms of architectural patterns. The language supports the specification of architectures and their reconfiguration. This paper introduces a language extension for precisely describing the structural design decisions that pattern instances must respect in their (re)configurations. The extension is a propositional modal logic with recursion and nominals referencing components, i.e., a hybrid µ-calculus. Its expressiveness allows specifying safety and liveness constraints, as well as paths and cycles over structures. Refinements of classic architectural patterns are specified

  12. Finding small OBDDs for incompletely specified truth tables is hard

    DEFF Research Database (Denmark)

    Miltersen, Peter Bro; Kristensen, Jesper Torp

    2006-01-01

    We present an efficient reduction mapping undirected graphs G with n = 2^k vertices for integers k to tables of partially specified Boolean functions g: {0,1}^(4k+1) -> {0,1,*} so that for any integer m, G has a vertex colouring using m colours if and only if g has a consistent ordered binary dec...... decision diagram with at most (2m + 2)n^2 + 4n decision nodes. From this it follows that the problem of finding a minimum-sized consistent OBDD for an incompletely specified truth table is NP-hard and also hard to approximate....

  13. Specifying structural constraints of architectural patterns in the ARCHERY language

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez, Alejandro [Departamento de Informática, Universidad Nacional de San Luis, Ejército de los Andes 950, D5700HHW San Luis (Argentina); HASLab INESC TEC and Universidade do Minho, Campus de Gualtar, 4710-057 Braga (Portugal); Barbosa, Luis S. [HASLab INESC TEC and Universidade do Minho, Campus de Gualtar, 4710-057 Braga (Portugal); Riesco, Daniel [Departamento de Informática, Universidad Nacional de San Luis, Ejército de los Andes 950, D5700HHW San Luis (Argentina)

    2015-03-10

    ARCHERY is an architectural description language for modelling and reasoning about distributed, heterogeneous and dynamically reconfigurable systems in terms of architectural patterns. The language supports the specification of architectures and their reconfiguration. This paper introduces a language extension for precisely describing the structural design decisions that pattern instances must respect in their (re)configurations. The extension is a propositional modal logic with recursion and nominals referencing components, i.e., a hybrid µ-calculus. Its expressiveness allows specifying safety and liveness constraints, as well as paths and cycles over structures. Refinements of classic architectural patterns are specified.

  14. SANSparallel: interactive homology search against Uniprot.

    Science.gov (United States)

    Somervuo, Panu; Holm, Liisa

    2015-07-01

    Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi. It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Nitrile-specifier Proteins Involved in Glucosinolate Hydrolysis in Arabidopsis thaliana*S⃞

    Science.gov (United States)

    Kissen, Ralph; Bones, Atle M.

    2009-01-01

    Glucosinolates are plant secondary metabolites present in Brassicaceae plants such as the model plant Arabidopsis thaliana. Intact glucosinolates are believed to be biologically inactive, whereas degradation products after hydrolysis have multiple roles in growth regulation and defense. The degradation of glucosinolates is catalyzed by thioglucosidases called myrosinases and leads by default to the formation of isothiocyanates. The interaction of a protein called epithiospecifier protein (ESP) with myrosinase diverts the reaction toward the production of epithionitriles or nitriles depending on the glucosinolate structure. Here we report the identification of a new group of nitrile-specifier proteins (AtNSPs) in A. thaliana able to generate nitriles in conjunction with myrosinase and a more detailed characterization of one member (AtNSP2). Recombinant AtNSP2 expressed in Escherichia coli was used to test its impact on the outcome of glucosinolate hydrolysis using a gas chromatography-mass spectrometry approach. AtNSP proteins share 30–45% sequence homology with A. thaliana ESP. Although AtESP and AtNSP proteins can switch myrosinase-catalyzed degradation of 2-propenylglucosinolate from isothiocyanate to nitrile, only AtESP generates the corresponding epithionitrile. Using the aromatic benzylglucosinolate, recombinant AtNSP2 is also able to direct product formation to the nitrile. Analysis of glucosinolate hydrolysis profiles of transgenic A. thaliana plants overexpressing AtNSP2 confirms its nitrile-specifier activity in planta. In silico expression analysis reveals distinctive expression patterns of AtNSPs, which supports a biological role for these proteins. In conclusion, we show that AtNSPs belonging to a new family of A. thaliana proteins structurally related to AtESP divert product formation from myrosinase-catalyzed glucosinolate hydrolysis and, thereby, likely affect the biological consequences of glucosinolate degradation. We discuss similarities and

  16. The prevalence of eating disorders not otherwise specified

    NARCIS (Netherlands)

    Machado, Paulo P. P.; Machado, Barbara C.; Goncalves, Sonia; Hoek, Hans W.

    Objective: Eating Disorders Not Otherwise Specified (EDNOS) represent the most common eating disorder diagnosed in specialized treatment settings. The purpose of the current study is to assess the prevalence of EDNOS in a nationwide community sample. Method: Participants were 2,028 female students,

  17. 76 FR 78553 - Reporting of Specified Foreign Financial Assets

    Science.gov (United States)

    2011-12-19

    ... maintained by a foreign financial institution and, to the extent not held in an account at a financial... account, the name and address of the financial institution in which the account is maintained must be... one or more specified foreign financial assets and those assets have an aggregate fair market value...

  18. Homologous Recombination—Experimental Systems, Analysis and Significance

    Science.gov (United States)

    Kuzminov, Andrei

    2014-01-01

    Homologous recombination is the most complex of all recombination events that shape genomes and produce material for evolution. Homologous recombination events are exchanges between DNA molecules in the lengthy regions of shared identity, catalyzed by a group of dedicated enzymes. There is a variety of experimental systems in E. coli and Salmonella to detect homologous recombination events of several different kinds. Genetic analysis of homologous recombination reveals three separate phases of this process: pre-synapsis (the early phase), synapsis (homologous strand exchange) and post-synapsis (the late phase). In E. coli, there are at least two independent pathway of the early phase and at least two independent pathways of the late phase. All this complexity is incongruent with the originally ascribed role of homologous recombination as accelerator of genome evolution: there is simply not enough duplication and repetition in enterobacterial genomes for homologous recombination to have a detectable evolutionary role, and therefore not enough selection to maintain such a complexity. At the same time, the mechanisms of homologous recombination are uniquely suited for repair of complex DNA lesions called chromosomal lesions. In fact, the two major classes of chromosomal lesions are recognized and processed by the two individual pathways at the early phase of homologous recombination. It follows, therefore, that homologous recombination events are occasional reflections of the continual recombinational repair, made possible in cases of natural or artificial genome redundancy. PMID:26442506

  19. Working with Specify in a Paleo-Geological Context

    Science.gov (United States)

    Molineux, A.; Thompson, A. C.; Appleton, L.

    2014-12-01

    For geological collections with limited funding an open source relational database provides an opportunity to digitize specimens and related data. At the Non-vertebrate Paleontology Lab, a large mixed paleo and geological repository on a restricted budget, we opted for one such database, Specify. Initially created at Kansas University for neontological collections and based on a single computer, Specify has moved into the networked scene and will soon be web-based as Specify 7. We currently use the server version of Specify 6, networked to all computers in the lab each running a desktop client, often with six users at any one time. Along with improved access there have been great efforts to broaden the applicability of this database to other disciplines. Current developments are of great importance to us because they focus on the geological aspects of lithostratigraphy and chronostratigaphy and their relationship to other variables. Adoption of this software has required constant change as we move to take advantage of the great improvements. We enjoy the interaction with the developers and their willingness to listen and consider our issues. Here we discuss some of the ways in which we have fashioned Specify into a database that provides us with the flexibility that we need without removing the ability to share our data with other aggregators through accepted protocols. We discuss the customization of forms, the attachment of media and tracking of original media files, our efforts to incorporate geological specimens, and our plans to link the individual specimen record GUIDs to an IGSN numbers and thence to future connections to data derived from our specimens.

  20. Acetylcholine Receptor: Complex of Homologous Subunits

    Science.gov (United States)

    Raftery, Michael A.; Hunkapiller, Michael W.; Strader, Catherine D.; Hood, Leroy E.

    1980-06-01

    The acetylcholine receptor from the electric ray Torpedo californica is composed of five subunits; two are identical and the other three are structurally related to them. Microsequence analysis of the four polypeptides demonstrates amino acid homology among the subunits. Further sequence analysis of both membrane-bound and Triton-solubilized, chromatographically purified receptor gave the stoichiometry of the four subunits (40,000:50,000:60,000:65,000 daltons) as 2:1:1:1, indicating that this protein is a pentameric complex with a molecular weight of 255,000 daltons. Genealogical analysis suggests that divergence from a common ancestral gene occurred early in the evolution of the receptor. This shared ancestry argues that each of the four subunits plays a functional role in the receptor's physiological action.

  1. Regulation of Homologous Recombination by SUMOylation

    DEFF Research Database (Denmark)

    Pinela da Silva, Sonia Cristina

    factors such as the homologous recombination (HR) machinery. HR constitutes the main DSB repair pathway in Saccharomyces cerevisiae and despite being largely considered an error-free process and essential for genome stability, uncontrolled recombination can lead to loss of heterozygosity, translocations......, deletions, and genome rearrangements that can lead to cell death or cancer in humans. The post-translational modification by SUMO (small ubiquitinlike modifier) has proven to be an important regulator of HR and genome integrity, but the molecular mechanisms responsible for these roles are still unclear....... In this study I present new insights for the role of SUMOylation in regulating HR by dissecting the role of SUMO in the interaction between the central HR-mediator protein Rad52 and its paralogue Rad59 and the outcome of recombination. This data provides evidence for the importance of SUMO in promoting protein...

  2. Homological mirror symmetry. New developments and perspectives

    International Nuclear Information System (INIS)

    Kapustin, Anton; Kreuzer, Maximilian; Schlesinger, Karl-Georg

    2009-01-01

    Homological Mirror Symmetry, the study of dualities of certain quantum field theories in a mathematically rigorous form, has developed into a flourishing subject on its own over the past years. The present volume bridges a gap in the literature by providing a set of lectures and reviews that both introduce and representatively review the state-of-the art in the field from different perspectives. With contributions by K. Fukaya, M. Herbst, K. Hori, M. Huang, A. Kapustin, L. Katzarkov, A. Klemm, M. Kontsevich, D. Page, S. Quackenbush, E. Sharpe, P. Seidel, I. Smith and Y. Soibelman, this volume will be a reference on the topic for everyone starting to work or actively working on mathematical aspects of quantum field theory. (orig.)

  3. HOMOLOGOUS CYCLONES IN THE QUIET SUN

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Xinting; Zhang, Jun; Li, Ting; Zhang, Yuzong; Yang, Shuhong, E-mail: yxt27272@mail.ustc.edu.cn, E-mail: zjun@nao.cas.cn, E-mail: liting@nao.cas.cn, E-mail: yuzong@nao.cas.cn, E-mail: shuhongyang@nao.cas.cn [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China)

    2014-02-20

    Through observations with the Solar Dynamics Observatory Atmospheric Imaging Assembly (AIA) and Helioseismic and Magnetic Imager, we tracked one rotating network magnetic field (RNF) near the solar equator. It lasted for more than 100 hr, from 2013 February 23 to 28. During its evolution, three cyclones were found to be rooted in this structure. Each cyclone event lasted for about 8 to 10 hr. While near the polar region, another RNF was investigated. It lasted for a shorter time (∼70 hr), from 2013 July 7 to 9. There were two cyclones rooted in the RNF and each lasted for 8 and 11 hr, respectively. For the two given examples, the cyclones have a similar dynamic evolution, and thus we put forward a new term: homologous cyclones. The detected brightening in AIA 171 Å maps indicates the release of energy, which is potentially available to heat the corona.

  4. Modeling Non-homologous End Joining

    Science.gov (United States)

    Li, Yongfeng

    2013-01-01

    Non-homologous end joining (NHEJ) is the dominant DNA double strand break (DSB) repair pathway and involves several NHEJ proteins such as Ku, DNA-PKcs, XRCC4, Ligase IV and so on. Once DSBs are generated, Ku is first recruited to the DNA end, followed by other NHEJ proteins for DNA end processing and ligation. Because of the direct ligation of break ends without the need for a homologous template, NHEJ turns out to be an error-prone but efficient repair pathway. Some mechanisms have been proposed of how the efficiency of NHEJ repair is affected. The type of DNA damage is an important factor of NHEJ repair. For instance, the length of DNA fragment may determine the recruitment efficiency of NHEJ protein such as Ku [1], or the complexity of the DNA breaks [2] is accounted for the choice of NHEJ proteins and subpathway of NHEJ repair. On the other hand, the chromatin structure also plays a role of the accessibility of NHEJ protein to the DNA damage site. In this talk, some mathematical models of NHEJ, that consist of series of biochemical reactions complying with the laws of chemical reaction (e.g. mass action, etc.), will be introduced. By mathematical and numerical analysis and parameter estimation, the models are able to capture the qualitative biological features and show good agreement with experimental data. As conclusions, from the viewpoint of modeling, how the NHEJ proteins are recruited will be first discussed for connection between the classical sequential model [4] and recently proposed two-phase model [5]. Then how the NHEJ repair pathway is affected, by the length of DNA fragment [6], the complexity of DNA damage [7] and the chromatin structure [8], will be addressed

  5. More on homological supersymmetric quantum mechanics

    Science.gov (United States)

    Behtash, Alireza

    2018-03-01

    In this work, we first solve complex Morse flow equations for the simplest case of a bosonic harmonic oscillator to discuss localization in the context of Picard-Lefschetz theory. We briefly touch on the exact non-BPS solutions of the bosonized supersymmetric quantum mechanics on algebraic geometric grounds and report that their complex phases can be accessed through the cohomology of WKB 1-form of the underlying singular spectral curve subject to necessary cohomological corrections for nonzero genus. Motivated by Picard-Lefschetz theory, we write down a general formula for the index of N =4 quantum mechanics with background R -symmetry gauge fields. We conjecture that certain symmetries of the refined Witten index and singularities of the moduli space may be used to determine the correct intersection coefficients. A few examples, where this conjecture holds, are shown in both linear and closed quivers with rank-one quiver gauge groups. The R -anomaly removal along the "Morsified" relative homology cycles also called "Lefschetz thimbles" is shown to lead to the appearance of Stokes lines. We show that the Fayet-Iliopoulos parameters appear in the intersection coefficients for the relative homology of the quiver quantum mechanics resulting from dimensional reduction of 2 d N =(2 ,2 ) gauge theory on a circle and explicitly calculate integrals along the Lefschetz thimbles in N =4 C Pk -1 model. The Stokes jumping of coefficients and its relation to wall crossing phenomena is briefly discussed. We also find that the notion of "on-the-wall" index is related to the invariant Lefschetz thimbles under Stokes phenomena. An implication of the Lefschetz thimbles in constructing knots from quiver quantum mechanics is indicated.

  6. Clustering evolving proteins into homologous families.

    Science.gov (United States)

    Chan, Cheong Xin; Mahbob, Maisarah; Ragan, Mark A

    2013-04-08

    Clustering sequences into groups of putative homologs (families) is a critical first step in many areas of comparative biology and bioinformatics. The performance of clustering approaches in delineating biologically meaningful families depends strongly on characteristics of the data, including content bias and degree of divergence. New, highly scalable methods have recently been introduced to cluster the very large datasets being generated by next-generation sequencing technologies. However, there has been little systematic investigation of how characteristics of the data impact the performance of these approaches. Using clusters from a manually curated dataset as reference, we examined the performance of a widely used graph-based Markov clustering algorithm (MCL) and a greedy heuristic approach (UCLUST) in delineating protein families coded by three sets of bacterial genomes of different G+C content. Both MCL and UCLUST generated clusters that are comparable to the reference sets at specific parameter settings, although UCLUST tends to under-cluster compositionally biased sequences (G+C content 33% and 66%). Using simulated data, we sought to assess the individual effects of sequence divergence, rate heterogeneity, and underlying G+C content. Performance decreased with increasing sequence divergence, decreasing among-site rate variation, and increasing G+C bias. Two MCL-based methods recovered the simulated families more accurately than did UCLUST. MCL using local alignment distances is more robust across the investigated range of sequence features than are greedy heuristics using distances based on global alignment. Our results demonstrate that sequence divergence, rate heterogeneity and content bias can individually and in combination affect the accuracy with which MCL and UCLUST can recover homologous protein families. For application to data that are more divergent, and exhibit higher among-site rate variation and/or content bias, MCL may often be the better

  7. K-homology and K-cohomology constructions of relations

    International Nuclear Information System (INIS)

    Abd El-Sattar, A. Dabbour; Bayoumy, F.M.

    1990-08-01

    One of the important homology (cohomology) theories, based on systems of covering of the space, is the homology (cohomology) theory of relations. In the present work, by using the idea of K-homology and K-cohomology groups different varieties of the Dowker's theory are introduced and studied. These constructions are defined on the category of pairs of topological spaces and over a pair of coefficient groups. (author). 14 refs

  8. A local homology theory for linearly compact modules

    International Nuclear Information System (INIS)

    Nguyen Tu Cuong; Tran Tuan Nam

    2004-11-01

    We introduce a local homology theory for linearly modules which is in some sense dual to the local cohomology theory of A. Grothendieck. Some basic properties of local homology modules are shown such as: the vanishing and non-vanishing, the noetherianness of local homology modules. By using duality, we extend some well-known results in theory of local cohomology of A. Grothendieck. (author)

  9. On (co)homology of Frobenius Poisson algebras

    OpenAIRE

    Zhu, Can; Van Oystaeyen, Fred; ZHANG, Yinhuo

    2014-01-01

    In this paper, we study Poisson (co)homology of a Frobenius Poisson algebra. More precisely, we show that there exists a duality between Poisson homology and Poisson cohomology of Frobenius Poisson algebras, similar to that between Hochschild homology and Hochschild cohomology of Frobenius algebras. Then we use the non-degenerate bilinear form on a unimodular Frobenius Poisson algebra to construct a Batalin-Vilkovisky structure on the Poisson cohomology ring making it into a Batalin-Vilkovisk...

  10. A geometric model for Hochschild homology of Soergel bimodules

    DEFF Research Database (Denmark)

    Webster, Ben; Williamson, Geordie

    2008-01-01

    An important step in the calculation of the triply graded link homology of Khovanov and Rozansky is the determination of the Hochschild homology of Soergel bimodules for SL(n). We present a geometric model for this Hochschild homology for any simple group G, as B–equivariant intersection cohomology...... on generators whose degree is explicitly determined by the geometry of the orbit closure, and to describe its Hilbert series, proving a conjecture of Jacob Rasmussen....

  11. Heteromorphic Sex Chromosomes: Navigating Meiosis without a Homologous Partner

    OpenAIRE

    Checchi, Paula M.; Engebrecht, JoAnne

    2011-01-01

    Accurate chromosome segregation during meiosis relies on homology between the maternal and paternal chromosomes. Yet by definition, sex chromosomes of the heterogametic sex lack a homologous partner. Recent studies in a number of systems have shed light on the unique meiotic behavior of heteromorphic sex chromosomes, and highlight both the commonalities and differences in divergent species. During meiotic prophase, the homology-dependent processes of pairing, synapsis, and recombination have ...

  12. Colored Kauffman homology and super-A-polynomials

    International Nuclear Information System (INIS)

    Nawata, Satoshi; Ramadevi, P.; Zodinmawia

    2014-01-01

    We study the structural properties of colored Kauffman homologies of knots. Quadruple-gradings play an essential role in revealing the differential structure of colored Kauffman homology. Using the differential structure, the Kauffman homologies carrying the symmetric tensor products of the vector representation for the trefoil and the figure-eight are determined. In addition, making use of relations from representation theory, we also obtain the HOMFLY homologies colored by rectangular Young tableaux with two rows for these knots. Furthermore, the notion of super-A-polynomials is extended in order to encompass two-parameter deformations of PSL(2,ℂ) character varieties

  13. The effects of specified chemical meals on food intake.

    Science.gov (United States)

    Koopmans, H S; Maggio, C A

    1978-10-01

    Rats received intragastric infusions of various specified chemical meals and were subsequently tested for a reduction in food intake. A second experiment, using a novel technique, tested for conditioned aversion to the meal infusions. The nonnutritive substances, kaolin clay and emulsified fluorocarbon, had no significant effect on food intake. Infusions of 1 M glucose and 1 M sorbitol reduced feeding behavior, but the 1 M sorbitol infusion also produced a conditioned aversion to flavored pellets paired with the sorbitol infusion, showing that the reduced feeding could have been caused by discomfort. Infusion of a high-fat meal consisting of emulsified triolein mixed with small amounts of sugar and protein or the rat's normal liquid diet, Nutrament, also reduced food intake, and both infusions failed to produce a conditioned aversion. The use of specified meals to understand the chemical basis of satiety requires a sensitive behavioral test to establish that the meal does not cause discomfort or other nonspecific effects.

  14. Model Checking Processes Specified In Join-Calculus Algebra

    Directory of Open Access Journals (Sweden)

    Sławomir Piotr Maludziński

    2014-01-01

    Full Text Available This article presents a model checking tool used to verify concurrent systems specified in join-calculus algebra. The temporal properties of systems under verification are expressed in CTL logic. Join-calculus algebra with its operational semantics defined by the chemical abstract machine serves as the basic method for the specification of concurrent systems and their synchronization mechanisms, and allows the examination of more complex systems.

  15. The prevalence of eating disorders not otherwise specified

    OpenAIRE

    Machado, Paulo P. P.; Machado, Bárbara César; Gonçalves, Sónia; Hoek, Hans W.

    2007-01-01

    Objective: Eating Disorders Not Otherwise Specified (EDNOS) represent the most common eating disorder diagnosed in specialized treatment settings. The purpose of the current study is to assess the prevalence of EDNOS in a nationwide community sample. Method: Participants were 2028 female students, aged 12 to 23, attending public schools in the 9th to 12th grades in Portugal. Participants completed the Eating Disorder Examination Questionnaire in Stage 1 of the study. In Stage 2, we selected a...

  16. The concept of homology as a basis for evaluating developmental mechanisms: exploring selective attention across the life-span.

    Science.gov (United States)

    Lickliter, Robert; Bahrick, Lorraine E

    2013-01-01

    Research with human infants as well as non-human animal embryos and infants has consistently demonstrated the benefits of intersensory redundancy for perceptual learning and memory for redundantly specified information during early development. Studies of infant affect discrimination, face discrimination, numerical discrimination, sequence detection, abstract rule learning, and word comprehension and segmentation have all shown that intersensory redundancy promotes earlier detection of these properties when compared to unimodal exposure to the same properties. Here we explore the idea that such intersensory facilitation is evident across the life-span and that this continuity is an example of a developmental behavioral homology. We present evidence that intersensory facilitation is most apparent during early phases of learning for a variety of tasks, regardless of developmental level, including domains that are novel or tasks that require discrimination of fine detail or speeded responses. Under these conditions, infants, children, and adults all show intersensory facilitation, suggesting a developmental homology. We discuss the challenge and propose strategies for establishing appropriate guidelines for identifying developmental behavioral homologies. We conclude that evaluating the extent to which continuities observed across development are homologous can contribute to a better understanding of the processes of development. Copyright © 2012 Wiley Periodicals, Inc.

  17. Complexity of hierarchically and 1-dimensional periodically specified problems

    Energy Technology Data Exchange (ETDEWEB)

    Marathe, M.V.; Hunt, H.B. III; Stearns, R.E.; Radhakrishnan, V.

    1995-08-23

    We study the complexity of various combinatorial and satisfiability problems when instances are specified using one of the following specifications: (1) the 1-dimensional finite periodic narrow specifications of Wanke and Ford et al. (2) the 1-dimensional finite periodic narrow specifications with explicit boundary conditions of Gale (3) the 2-way infinite1-dimensional narrow periodic specifications of Orlin et al. and (4) the hierarchical specifications of Lengauer et al. we obtain three general types of results. First, we prove that there is a polynomial time algorithm that given a 1-FPN- or 1-FPN(BC)specification of a graph (or a C N F formula) constructs a level-restricted L-specification of an isomorphic graph (or formula). This theorem along with the hardness results proved here provides alternative and unified proofs of many hardness results proved in the past either by Lengauer and Wagner or by Orlin. Second, we study the complexity of generalized CNF satisfiability problems of Schaefer. Assuming P {ne} PSPACE, we characterize completely the polynomial time solvability of these problems, when instances are specified as in (1), (2),(3) or (4). As applications of our first two types of results, we obtain a number of new PSPACE-hardness and polynomial time algorithms for problems specified as in (1), (2), (3) or(4). Many of our results also hold for O(log N) bandwidth bounded planar instances.

  18. The problem of the driverless vehicle specified path stability control

    Science.gov (United States)

    Buznikov, S. E.; Endachev, D. V.; Elkin, D. S.; Strukov, V. O.

    2018-02-01

    Currently the effort of many leading foreign companies is focused on creation of driverless transport for transportation of cargo and passengers. Among many practical problems arising while creating driverless vehicles, the problem of the specified path stability control occupies a central place. The purpose of this paper is formalization of the problem in question in terms of the quadratic functional of the control quality, the comparative analysis of the possible solutions and justification of the choice of the optimum technical solution. As square value of the integral of the deviation from the specified path is proposed as the quadratic functional of the control quality. For generation of the set of software and hardware solution variants the Zwicky “morphological box” method is used within the hardware and software environments. The heading control algorithms use the wheel steering angle data and the deviation from the lane centerline (specified path) calculated based on the navigation data and the data from the video system. Where the video system does not detect the road marking, the control is carried out based on the wheel navigation system data and where recognizable road marking exits - based on to the video system data. The analysis of the test results allows making the conclusion that the application of the combined navigation system algorithms that provide quasi-optimum solution of the problem while meeting the strict functional limits for the technical and economic indicators of the driverless vehicle control system under development is effective.

  19. Design of HIFU Transducers for Generating Specified Nonlinear Ultrasound Fields.

    Science.gov (United States)

    Rosnitskiy, Pavel B; Yuldashev, Petr V; Sapozhnikov, Oleg A; Maxwell, Adam D; Kreider, Wayne; Bailey, Michael R; Khokhlova, Vera A

    2017-02-01

    Various clinical applications of high-intensity focused ultrasound have different requirements for the pressure levels and degree of nonlinear waveform distortion at the focus. The goal of this paper is to determine transducer design parameters that produce either a specified shock amplitude in the focal waveform or specified peak pressures while still maintaining quasi-linear conditions at the focus. Multiparametric nonlinear modeling based on the Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation with an equivalent source boundary condition was employed. Peak pressures, shock amplitudes at the focus, and corresponding source outputs were determined for different transducer geometries and levels of nonlinear distortion. The results are presented in terms of the parameters of an equivalent single-element spherically shaped transducer. The accuracy of the method and its applicability to cases of strongly focused transducers were validated by comparing the KZK modeling data with measurements and nonlinear full diffraction simulations for a single-element source and arrays with 7 and 256 elements. The results provide look-up data for evaluating nonlinear distortions at the focus of existing therapeutic systems as well as for guiding the design of new transducers that generate specified nonlinear fields.

  20. Coordinating structural and functional synapse development: postsynaptic p21-activated kinase independently specifies glutamate receptor abundance and postsynaptic morphology.

    Science.gov (United States)

    Albin, Stephanie D; Davis, Graeme W

    2004-08-04

    Here, we show that postsynaptic p21-activated kinase (Pak) signaling diverges into two genetically separable pathways at the Drosophila neuromuscular junction. One pathway controls glutamate receptor abundance. Pak signaling within this pathway is specified by a required interaction with the adaptor protein Dreadlocks (Dock). We demonstrate that Dock is localized to the synapse via an Src homology 2-mediated protein interaction. Dock is not necessary for Pak localization but is necessary to restrict Pak signaling to control glutamate receptor abundance. A second genetically separable function of Pak kinase signaling controls muscle membrane specialization through the regulation of synaptic Discs-large. In this pathway, Dock is dispensable. We present a model in which divergent Pak signaling is able to coordinate two different features of postsynaptic maturation, receptor abundance, and muscle membrane specialization.

  1. Ozone oxidation of antidepressants in wastewater –Treatment evaluation and characterization of new by-products by LC-QToFMS

    Directory of Open Access Journals (Sweden)

    Lajeunesse André

    2013-01-01

    Full Text Available Abstract Background The fate of 14 antidepressants along with their respective N-desmethyl metabolites and the anticonvulsive drug carbamazepine was examined in a primary sewage treatment plant (STP and following advanced treatments with ozone (O3. The concentrations of each pharmaceutical compound were determined in raw sewage, effluent and sewage sludge samples by LC-MS/MS analysis. The occurrence of antidepressant by-products formed in treated effluent after ozonation was also investigated. Results Current primary treatments using physical and chemical processes removed little of the compounds (mean removal efficiency: 19%. Experimental sorption coefficients (Kd of each studied compounds were also calculated. Sorption of venlafaxine, desmethylvenlafaxine, and carbamazepine on sludge was assumed to be negligible (log Kd ≤ 2, but higher sorption behavior can be expected for sertraline (log Kd ≥ 4. Ozonation treatment with O3 (5 mg/L led to a satisfactory mean removal efficiency of 88% of the compounds. Screening of the final ozone-treated effluent samples by high resolution-mass spectrometry (LC-QqToFMS did confirm the presence of related N-oxide by-products. Conclusion Effluent ozonation led to higher mean removal efficiencies than current primary treatment, and therefore represented a promising strategy for the elimination of antidepressants in urban wastewaters. However, the use of O3 produced by-products with unknown toxicity.

  2. Smoking in preeclamptic women is associated with higher birthweight for gestational age and lower soluble fms-like tyrosine kinase-1 levels: a nested case control study

    Directory of Open Access Journals (Sweden)

    Kahn Susan R

    2011-11-01

    Full Text Available Abstract Background Smoking paradoxically increases the risk of small-for-gestational-age (SGA birth but protects against preeclampsia. Some studies have reported a "U-shaped" distribution of fetal growth in preeclamptic pregnancies, but reasons for this are unknown. We investigated whether cigarette smoking interacts with preeclampsia to affect fetal growth, and compared levels of soluble fms-like tyrosine kinase-1 (sFlt-1, a circulating anti-angiogenic protein, in preeclamptic smokers and non-smokers. Methods From a multicenter cohort of 5337 pregnant women, we prospectively identified 113 women who developed preeclampsia (cases and 443 controls. Smoking exposure was assessed by self-report and maternal hair nicotine levels. Fetal growth was assessed as z-score of birthweight for gestational age (BWGA. sFlt-1 was measured in plasma samples collected at the 24-26-week visit. Results In linear regression, smoking and preeclampsia were each associated with lower BWGA z-scores (β = -0.29; p = 0.008, and β = -0.67; p Conclusions Maternal smoking seems to protect against preeclampsia-associated fetal growth restriction and may account, at least partly, for the U-shaped pattern of fetal growth described in preeclamptic pregnancies. Smoking may exert this effect by reducing levels of the anti-angiogenic protein sFlt-1.

  3. Report of generation of the nuclear bank Presto-Warm (T=373 K) for the SVEA-96 fuel with the FMS codes

    International Nuclear Information System (INIS)

    Alonso V, G.

    1992-03-01

    In this work it is described in a general way the form in that was generated the Presto Warm database (TF=TM=373K) of the one SVEA-96 fuel for Laguna Verde. The formation of the bank it was carried out with the ECLIPSE 86-2D, RECORD 89-1A and POLGEN 88-1B of the FMS package installed in the VAX system of the offices of the National Commission of Nuclear Safety and Safeguards in Mexico D.F. The formed bank is denominated L1PG9109. All this was carried out following the 6F3/I/CN029/90/P1 procedure. The generated database contains information of the 10 nuclear parameters required in Presto without and with the effect of the control bar for the different arrangements of fuel bars present in the one assemble. All this included in what is known as Super option of the bank for Presto. (Author)

  4. Report of generation of the nuclear bank Presto-Warm (T=560 K) for the SVEA-96 fuel with the FMS codes

    International Nuclear Information System (INIS)

    Alonso V, G.

    1992-03-01

    In this work it is described in a general way the form in that was generated the Presto Warm database (TF=TM=560K) of the one SVEA-96 fuel for Laguna Verde. The formation of the bank it was carried out with the ECLIPSE 86-2D, RECORD 89-1A and POLGEN 88-1B of the FMS package installed in the VAX system of the offices of the National Commission of Nuclear Safety and Safeguards in Mexico D.F. The formed bank is denominated L1PG9109. All this was carried out following the 6F3/I/CN029/90/P1 procedure. The generated database contains information of the 10 nuclear parameters required in PRESTO without and with the effect of the control bar for the different arrangements of fuel bars present in the one assemble. All this included in what is known as SUPER option of the bank for PRESTO. (Author)

  5. Report of generation of the nuclear bank Presto-Cold (T=293 K) for the SVEA-96 fuel with the FMS codes

    International Nuclear Information System (INIS)

    Alonso V, G.

    1992-03-01

    In this work it is described in a general way the form in that was generated the Presto Cold database (TF=TM=293 K) of the one SVEA-96 fuel for Laguna Verde. The formation of the bank it was carried out with the ECLIPSE 86-2D, RECORD 89-1A and POLGEN 88-1B of the FMS package installed in the VAX system of the offices of the National Commission of Nuclear Safety and Safeguards in Mexico D.F. The formed bank is denominated L1PG9109. All this was carried out following the 6F3/I/CN029/90/P1 procedure. The generated database contains information of the 10 nuclear parameters required in PRESTO without and with the effect of the control bar for the different arrangements of fuel bars present in the one assemble. All this included in what is known as SUPER option of the bank for PRESTO. (Author)

  6. CBH1 homologs and varian CBH1 cellulase

    Energy Technology Data Exchange (ETDEWEB)

    Goedegebuur, Frits; Gualfetti, Peter; Mitchinson, Colin; Neefe, Paulien

    2014-07-01

    Disclosed are a number of homologs and variants of Hypocrea jecorina Cel7A (formerly Trichoderma reesei cellobiohydrolase I or CBH1), nucleic acids encoding the same and methods for producing the same. The homologs and variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted and/or deleted.

  7. The Causes of Quasi-homologous CMEs

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Lijuan; Wang, Yuming; Liu, Rui; Zhou, Zhenjun; Liu, Jiajia; Liu, Kai; Shen, Chenglong; Zhang, Quanhao [CAS Key Laboratory of Geospace Environment, Department of Geophysics and Planetary Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Temmer, M.; Thalmann, J. K.; Veronig, A. M., E-mail: ymwang@ustc.edu.cn, E-mail: ljliu@mail.ustc.edu.cn [Institute of Physics/IGAM, University of Graz, Universitätsplatz 5/II, A-8010 Graz (Austria)

    2017-08-01

    In this paper, we identified the magnetic source locations of 142 quasi-homologous (QH) coronal mass ejections (CMEs), of which 121 are from solar cycle (SC) 23 and 21 from SC 24. Among those CMEs, 63% originated from the same source location as their predecessor (defined as S-type), while 37% originated from a different location within the same active region as their predecessor (defined as D-type). Their distinctly different waiting time distributions, peaking around 7.5 and 1.5 hr for S- and D-type CMEs, suggest that they might involve different physical mechanisms with different characteristic timescales. Through detailed analysis based on nonlinear force-free coronal magnetic field modeling of two exemplary cases, we propose that the S-type QH CMES might involve a recurring energy release process from the same source location (by magnetic free energy replenishment), whereas the D-type QH CMEs can happen when a flux tube system is disturbed by a nearby CME.

  8. Torus actions, combinatorial topology, and homological algebra

    International Nuclear Information System (INIS)

    Bukhshtaber, V M; Panov, T E

    2000-01-01

    This paper is a survey of new results and open problems connected with fundamental combinatorial concepts, including polytopes, simplicial complexes, cubical complexes, and arrangements of subspaces. Attention is concentrated on simplicial and cubical subdivisions of manifolds, and especially on spheres. Important constructions are described that enable one to study these combinatorial objects by using commutative and homological algebra. The proposed approach to combinatorial problems is based on the theory of moment-angle complexes recently developed by the authors. The crucial construction assigns to each simplicial complex K with m vertices a T m -space Z K with special bigraded cellular decomposition. In the framework of this theory, well-known non-singular toric varieties arise as orbit spaces of maximally free actions of subtori on moment-angle complexes corresponding to simplicial spheres. It is shown that diverse invariants of simplicial complexes and related combinatorial-geometric objects can be expressed in terms of bigraded cohomology rings of the corresponding moment-angle complexes. Finally, it is shown that the new relationships between combinatorics, geometry, and topology lead to solutions of some well-known topological problems

  9. Statistical Inference for Porous Materials using Persistent Homology.

    Energy Technology Data Exchange (ETDEWEB)

    Moon, Chul [Univ. of Georgia, Athens, GA (United States); Heath, Jason E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mitchell, Scott A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-12-01

    We propose a porous materials analysis pipeline using persistent homology. We rst compute persistent homology of binarized 3D images of sampled material subvolumes. For each image we compute sets of homology intervals, which are represented as summary graphics called persistence diagrams. We convert persistence diagrams into image vectors in order to analyze the similarity of the homology of the material images using the mature tools for image analysis. Each image is treated as a vector and we compute its principal components to extract features. We t a statistical model using the loadings of principal components to estimate material porosity, permeability, anisotropy, and tortuosity. We also propose an adaptive version of the structural similarity index (SSIM), a similarity metric for images, as a measure to determine the statistical representative elementary volumes (sREV) for persistence homology. Thus we provide a capability for making a statistical inference of the uid ow and transport properties of porous materials based on their geometry and connectivity.

  10. Specifying the Behaviour of Python Programs: Language and Basic Examples

    Directory of Open Access Journals (Sweden)

    2010-04-01

    Full Text Available This manuscript describe BeSSY, a function-centric language for formal behavioural specification that requires no more than high-school mathematics on arithmetic, functions, Boolean algebra and sets theory. An object can be modelled as a union of data sets and functions whereas inherited object can be modelled as a union of supersets and a set of object-specific functions. Python list and dictionary operations will be specified in BeSSY for illustration.

  11. Homologous series of induced early mutants in indican rice. Pt.1. The production of homologous series of early mutants

    International Nuclear Information System (INIS)

    Chen Xiulan; Yang Hefeng; He Zhentian; Han Yuepeng; Liu Xueyu

    1999-01-01

    The percentage of homologous series of early mutants induced from the same Indican rice variety were almost the same (1.37%∼1.64%) in 1983∼1993, but the ones from the different eco-typical varieties were different. The early variety was 0.73%, the mid variety was 1.51%, and the late variety was 1.97%. The percentage of homologous series of early mutants from the varieties with the same pedigree and relationship were similar, but the one from the cog nation were lower than those from distant varieties. There are basic laws and characters in the homologous series of early mutants: 1. The inhibited phenotype is the basic of the homologous series of early mutants; 2. The production of the homologous series of early mutants is closely related with the growing period of the parent; 3. The parallel mutation of the stem and leaves are simultaneously happened with the variation of early or late maturing; 4. The occurrence of the homologous series of early mutants is in a state of imbalance. According to the law of parallel variability, the production of homologous series of early mutants can be predicted as long as the parents' classification of plant, pedigree and ecological type are identified. Therefore, the early breeding can be guided by the law of homologous series of early mutants

  12. Productive Homologous and Non-homologous Recombination of Hepatitis C Virus in Cell Culture

    Science.gov (United States)

    Li, Yi-Ping; Mikkelsen, Lotte S.; Gottwein, Judith M.; Bukh, Jens

    2013-01-01

    Genetic recombination is an important mechanism for increasing diversity of RNA viruses, and constitutes a viral escape mechanism to host immune responses and to treatment with antiviral compounds. Although rare, epidemiologically important hepatitis C virus (HCV) recombinants have been reported. In addition, recombination is an important regulatory mechanism of cytopathogenicity for the related pestiviruses. Here we describe recombination of HCV RNA in cell culture leading to production of infectious virus. Initially, hepatoma cells were co-transfected with a replicating JFH1ΔE1E2 genome (genotype 2a) lacking functional envelope genes and strain J6 (2a), which has functional envelope genes but does not replicate in culture. After an initial decrease in the number of HCV positive cells, infection spread after 13–36 days. Sequencing of recovered viruses revealed non-homologous recombinants with J6 sequence from the 5′ end to the NS2–NS3 region followed by JFH1 sequence from Core to the 3′ end. These recombinants carried duplicated sequence of up to 2400 nucleotides. HCV replication was not required for recombination, as recombinants were observed in most experiments even when two replication incompetent genomes were co-transfected. Reverse genetic studies verified the viability of representative recombinants. After serial passage, subsequent recombination events reducing or eliminating the duplicated region were observed for some but not all recombinants. Furthermore, we found that inter-genotypic recombination could occur, but at a lower frequency than intra-genotypic recombination. Productive recombination of attenuated HCV genomes depended on expression of all HCV proteins and tolerated duplicated sequence. In general, no strong site specificity was observed. Non-homologous recombination was observed in most cases, while few homologous events were identified. A better understanding of HCV recombination could help identification of natural recombinants

  13. Productive homologous and non-homologous recombination of hepatitis C virus in cell culture

    DEFF Research Database (Denmark)

    Scheel, Troels K H; Galli, Andrea; Li, Yi-Ping

    2013-01-01

    . In addition, recombination is an important regulatory mechanism of cytopathogenicity for the related pestiviruses. Here we describe recombination of HCV RNA in cell culture leading to production of infectious virus. Initially, hepatoma cells were co-transfected with a replicating JFH1ΔE1E2 genome (genotype 2a......) lacking functional envelope genes and strain J6 (2a), which has functional envelope genes but does not replicate in culture. After an initial decrease in the number of HCV positive cells, infection spread after 13-36 days. Sequencing of recovered viruses revealed non-homologous recombinants with J6...

  14. DockoMatic 2.0: high throughput inverse virtual screening and homology modeling.

    Science.gov (United States)

    Bullock, Casey; Cornia, Nic; Jacob, Reed; Remm, Andrew; Peavey, Thomas; Weekes, Ken; Mallory, Chris; Oxford, Julia T; McDougal, Owen M; Andersen, Timothy L

    2013-08-26

    DockoMatic is a free and open source application that unifies a suite of software programs within a user-friendly graphical user interface (GUI) to facilitate molecular docking experiments. Here we describe the release of DockoMatic 2.0; significant software advances include the ability to (1) conduct high throughput inverse virtual screening (IVS); (2) construct 3D homology models; and (3) customize the user interface. Users can now efficiently setup, start, and manage IVS experiments through the DockoMatic GUI by specifying receptor(s), ligand(s), grid parameter file(s), and docking engine (either AutoDock or AutoDock Vina). DockoMatic automatically generates the needed experiment input files and output directories and allows the user to manage and monitor job progress. Upon job completion, a summary of results is generated by Dockomatic to facilitate interpretation by the user. DockoMatic functionality has also been expanded to facilitate the construction of 3D protein homology models using the Timely Integrated Modeler (TIM) wizard. The wizard TIM provides an interface that accesses the basic local alignment search tool (BLAST) and MODELER programs and guides the user through the necessary steps to easily and efficiently create 3D homology models for biomacromolecular structures. The DockoMatic GUI can be customized by the user, and the software design makes it relatively easy to integrate additional docking engines, scoring functions, or third party programs. DockoMatic is a free comprehensive molecular docking software program for all levels of scientists in both research and education.

  15. Partially specified physics problems: university students' attitudes and performance

    International Nuclear Information System (INIS)

    Marusic, M; Erceg, N; Slisko, J

    2011-01-01

    In this research we asked the fourth year students (N = 50) of a technical faculty of the University of Split (Republic of Croatia) to solve a partially specified physics problem related to gravitational force. The task for the students was to decide whether the situation described in the problem is feasible or not. Nevertheless, the formulation of the problem is such that it does not give students any explicit advice regarding what to calculate or how to judge the feasibility of the given situation in the real world. The research was carried out using a structured written exam method. The worksheet was structured in order to assess explicitly a few elements of the students' problem-solving performance. Based on their results, the examinees were classified into four categories, depending on what they could or could not accomplish during problem solving. A majority of students were not able to solve the given physical problem completely. A selection of students' and professors' observations is also included. Our results show that traditionally formulated numerical exercises, which are mostly used in physics teaching, do not develop students' abilities in higher-order thinking (i.e. planning, decision making or result evaluation) to a desirable extent. We suggest that partially specified problems should be given to students, both in problem-solving sessions and exams, in order to prepare them for dealing with ill-structured tasks in real life.

  16. Detecting false positive sequence homology: a machine learning approach.

    Science.gov (United States)

    Fujimoto, M Stanley; Suvorov, Anton; Jensen, Nicholas O; Clement, Mark J; Bybee, Seth M

    2016-02-24

    Accurate detection of homologous relationships of biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that is essential to various evolutionary studies, ranging from building phylogenies to predicting functional gene annotations. There are many existing heuristic tools, most commonly based on bidirectional BLAST searches that are used to identify homologous genes and combine them into two fundamentally distinct classes: orthologs and paralogs. Due to only using heuristic filtering based on significance score cutoffs and having no cluster post-processing tools available, these methods can often produce multiple clusters constituting unrelated (non-homologous) sequences. Therefore sequencing data extracted from incomplete genome/transcriptome assemblies originated from low coverage sequencing or produced by de novo processes without a reference genome are susceptible to high false positive rates of homology detection. In this paper we develop biologically informative features that can be extracted from multiple sequence alignments of putative homologous genes (orthologs and paralogs) and further utilized in context of guided experimentation to verify false positive outcomes. We demonstrate that our machine learning method trained on both known homology clusters obtained from OrthoDB and randomly generated sequence alignments (non-homologs), successfully determines apparent false positives inferred by heuristic algorithms especially among proteomes recovered from low-coverage RNA-seq data. Almost ~42 % and ~25 % of predicted putative homologies by InParanoid and HaMStR respectively were classified as false positives on experimental data set. Our process increases the quality of output from other clustering algorithms by providing a novel post-processing method that is both fast and efficient at removing low quality clusters of putative homologous genes recovered by heuristic-based approaches.

  17. Edaravone inhibits hypoxia-induced trophoblast-soluble Fms-like tyrosine kinase 1 expression: a possible therapeutic approach to preeclampsia.

    Science.gov (United States)

    Zhao, Y; Zheng, Y F; Luo, Q Q; Yan, T; Liu, X X; Han, L; Zou, L

    2014-07-01

    To investigate the effects of edaravone, a potent free radical scavenger used clinically, on hypoxia-induced trophoblast-soluble Fms-like tyrosine kinase 1 (sFlt-1) expression. A trophoblast cell line (HRT-8/SVneo) impaired by cobalt chloride (CoCl2) was used as the cell model under hypoxic conditions. 3-[4, 5-dimethylthiazol-2-yl]-2, 5-diphenyl tetrazolium bromide (MTT) was used to measure the viability of cells exposed to CoCl2 and edaravone. The levels of intracellular reactive oxygen species (ROS) were analyzed by flow cytometry. mRNA expression of sFlt-1, vascular endothelial growth factor (VEGF), and placental growth factor (PlGF) in trophoblasts was measured by real-time polymerase chain reaction, and the secretion of sFlt-1, VEGF, and PlGF proteins was analyzed by enzyme-linked immunosorbent assays (ELISAs). A human umbilical vein endothelial cell (HUVEC) tube-formation assay was performed to identify the effects of CoCl2 and edaravone on vascular development. CoCl2 treatment caused the loss of trophoblast viability, the formation of ROS, and sFlt-1 mRNA and protein expression in a dose-dependent manner. Pretreatment with edaravone significantly inhibited hypoxia-induced oxidative stress formation and sFlt-1 expression in trophoblasts. Neither PlGF nor VEGF mRNA or protein expression was increased by CoCl2. In the in vitro tube formation assay, edaravone showed a protective role in vascular development under hypoxic conditions. This study demonstrated that hypoxia leading to increased sFlt-1 release in trophoblasts may contribute to the placental vascular formation abnormalities observed in preeclampsia and suggested that the free radical scavenger edaravone could be a candidate for the effective treatment of preeclampsia. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. A pesquisa como dispositivo para o exercício no PET-Saúde UFF/FMS Niterói

    Directory of Open Access Journals (Sweden)

    Ana Lúcia Abrahão

    Full Text Available O PET-Saúde (Programa de Educação pelo Trabalho para a Saúde proposto pela Universidade Federal Fluminense (UFF e pela Fundação Municipal de Saúde de Niterói (FMS iniciou suas atividades em abril de 2010 com a proposta de desenvolver o processo de ensino-aprendizagem de forma participativa, tendo como eixo central o trabalho no cotidiano dos serviços de saúde, utilizando as ferramentas da pesquisa e avaliação em saúde como elemento disparador do aprendizado. As atividades são desenvolvidas na perspectiva da construção de um diagnóstico de saúde da área de abrangência de cada unidade de saúde à qual o grupo PET está vinculado. A metodologia adotada pelos grupos consiste na investigação participativa, com o envolvimento de profissionais, alunos, usuários e docentes. Como ferramenta vem sendo utilizada a construção da história local, com levantamento de documentos e depoimentos da comunidade. Destaca-se a atividade de cadastramento e recadastramento de famílias e o levantamento do perfil epidemiológico dos territórios. Neste primeiro estágio, identificamos a interação em grupo multiprofissional como um desafio que vem proporcionando grandes avanços no entendimento do processo saúde-doença entre estudantes, docentes e profissionais.

  19. Sodium nitrite attenuates hypertension-in-pregnancy and blunts increases in soluble fms-like tyrosine kinase-1 and in vascular endothelial growth factor.

    Science.gov (United States)

    Gonçalves-Rizzi, Victor Hugo; Possomato-Vieira, Jose Sergio; Sales Graça, Tamiris Uracs; Nascimento, Regina Aparecida; Dias-Junior, Carlos A

    2016-07-01

    Preeclampsia is a pregnancy-associated disorder characterized by hypertension with uncertain pathogenesis. Increases in antiangiogenic soluble fms-like tyrosine kinase-1 (sFlt-1) and reductions in nitric oxide (NO) bioavailability have been observed in preeclamptic women. However, the specific mechanisms linking these detrimental changes to the hypertension-in-pregnancy are not clearly understood. In this regard, while recent findings have suggested that nitrite-derived NO formation exerts antihypertensive and antioxidant effects, no previous study has examined these responses to orally administered nitrite in hypertension-in-pregnancy. We then hypothesized restoring NO bioavailability with sodium nitrite in pregnant rats upon NO synthesis inhibition with N(omega)-nitro-l-arginine methyl ester (L-NAME) attenuates hypertension and high circulating levels of sFlt-1. Number and weight of pups and placentae were recorded to assess maternal-fetal interface. Plasma sFlt-1, vascular endothelial growth factor (VEGF) and biochemical determinants of NO formation and of antioxidant function were measured. We found that sodium nitrite blunts the hypertension-in-pregnancy and restores the NO bioavailability, and concomitantly prevents the L-NAME-induced high circulating sFlt-1 and VEGF levels. Also, our results suggest that nitrite-derived NO protected against reductions in litter size and placental weight caused by L-NAME, improving number of viable and resorbed fetuses and antioxidant function. Therefore, the present findings are consistent with the hypothesis that nitrite-derived NO may possibly be the driving force behind the maternal and fetal beneficial effects observed with sodium nitrite during hypertension-in-pregnancy. Certainly further investigations are required in preeclampsia, since counteracting the damages to the mother and fetal sides resulting from hypertension and elevated sFlt-1 levels may provide a great benefit in this gestational hypertensive disease

  20. Report of generation of the 'L1PG9321' nuclear bank of the CAORSO 3.26 collapsed assembly with the FMS codes

    International Nuclear Information System (INIS)

    Alonso V, G.

    1991-03-01

    In this work it is described in a general way the form in that the collapsed bank of the CAORSO 3.26 fuel as possible reload fuel for Laguna Verde it was generated. The formation of the bank was carried out with the ECLIPSE 86-2D, RECORD 89-1A and POLGEN 88-1B codes of the FMS package installed in the VAX system of the offices of the National Commission of Nuclear Safety and Safeguards in Mexico City. The formed bank is denominated L 1PG9321 . All this one was carried out following the '6F3/I/CN029/90/P1' procedure. To generate the bank, the five RECORD cells that compose the one assemble its were 'collapsed' in one alone, representing this to the complete assemble in what refers to the fuel bar distribution and enrichment. The one collapsed of the it assemble it is made averaging the content of UO 2 and Gd 2 O 3 in each fuel bar of the one assemble. Of this way is conserved the arrangement x-y of fuel bars but a representative fuel cell is obtained of everything the one it assembles being this the studied RECORD cell. In accordance with the requirements of nuclear information of FCS-II the nuclear information generated with RECORD should be of the one defined type as series 1 in the generation procedure of '6F3/I/CN029/90/P1' nuclear banks. This means that only the nuclear information as function of the burnt one of the fuel and of the hole in the fuel cell is required; however the bank also contains information of the defined type as series 2 with the control bar present for possible analysis of the reactor under these conditions. (Author)

  1. Report of the generation of the nuclear bank 'L1PG9121' of the SVEA-96 'collapsed' assemble for the FCS-II program with the FMS codes

    International Nuclear Information System (INIS)

    Alonso V, G.

    1992-01-01

    In this work it is described in a general way the form in that was generated the collapsed bank of the SVEA-96 fuel for Laguna Verde. The formation of the bank it was carried out with the ECLIPSE 86-2D, RECORD 89-1A and POLGEN 88-1B codes of the FMS package installed in the VAX system of the office of the National Commission of Nuclear Safety and Safeguards in Mexico D.F. The formed bank is denominated 'LlPG9121'. All this one carries out following the procedure '6F3/I/CN029/90/P1'. To generate the bank, both RECORD 'cells' that compose the assemble its were 'collapsed' in an alone one, representing this, the complete assemble in what refers to the distribution of fuel bar and enrichment. The collapsed of the assemble was made averaging the content of UO 2 and Gd 2 O 3 in each fuel bar of the one assemble. By this way the x-y array of fuel bars is conserved but a representative fuel cell of all the one assemble is obtained, being this the studied RECORD cell. In accordance with the requirements of nuclear information of FCS-II, the nuclear information generated with RECORD only was of the defined type as series 1 in the generation procedure of nuclear banks '6F3/I/CN029/90/P1'. This only means that only was generated nuclear information as function of the fuel burnt and of the vacuum in the fuel cell. Although the nuclear bank (L1PG9121) it was generated in these circumstances, it was also generates information of the defined type as series 2 with the present control bar for possible reactor analysis under these conditions. (Author)

  2. Transcription factor E93 specifies adult metamorphosis in hemimetabolous and holometabolous insects.

    Science.gov (United States)

    Ureña, Enric; Manjón, Cristina; Franch-Marro, Xavier; Martín, David

    2014-05-13

    All immature animals undergo remarkable morphological and physiological changes to become mature adults. In winged insects, metamorphic changes either are limited to a few tissues (hemimetaboly) or involve a complete reorganization of most tissues and organs (holometaboly). Despite the differences, the genetic switch between immature and adult forms in both types of insects relies on the disappearance of the antimetamorphic juvenile hormone (JH) and the transcription factors Krüppel-homolog 1 (Kr-h1) and Broad-Complex (BR-C) during the last juvenile instar. Here, we show that the transcription factor E93 is the key determinant that promotes adult metamorphosis in both hemimetabolous and holometabolous insects, thus acting as the universal adult specifier. In the hemimetabolous insect Blattella germanica, BgE93 is highly expressed in metamorphic tissues, and RNA interference (RNAi)-mediated knockdown of BgE93 in the nymphal stage prevented the nymphal-adult transition, inducing endless reiteration of nymphal development, even in the absence of JH. We also find that BgE93 down-regulated BgKr-h1 and BgBR-C expression during the last nymphal instar of B. germanica, a key step necessary for proper adult differentiation. This essential role of E93 is conserved in holometabolous insects as TcE93 RNAi in Tribolium castaneum prevented pupal-adult transition and produced a supernumerary second pupa. In this beetle, TcE93 also represses expression of TcKr-h1 and TcBR-C during the pupal stage. Similar results were obtained in the more derived holometabolous insect Drosophila melanogaster, suggesting that winged insects use the same regulatory mechanism to promote adult metamorphosis. This study provides an important insight into the understanding of the molecular basis of adult metamorphosis.

  3. The K-homology of nets of C∗-algebras

    Science.gov (United States)

    Ruzzi, Giuseppe; Vasselli, Ezio

    2014-12-01

    Let X be a space, intended as a possibly curved space-time, and A a precosheaf of C∗-algebras on X. Motivated by algebraic quantum field theory, we study the Kasparov and Θ-summable K-homology of A interpreting them in terms of the holonomy equivariant K-homology of the associated C∗-dynamical system. This yields a characteristic class for K-homology cycles of A with values in the odd cohomology of X, that we interpret as a generalized statistical dimension.

  4. Eating disorder not otherwise specified presentation in the US population.

    Science.gov (United States)

    Le Grange, Daniel; Swanson, Sonja A; Crow, Scott J; Merikangas, Kathleen R

    2012-07-01

    To examine prevalence and clinical correlates of eating disorder not otherwise specified (EDNOS) in the US population. Two cross-sectional surveys of adults and adolescents used the WHO CIDI to assess DSM-IV criteria for anorexia nervosa (AN), bulimia nervosa (BN), and EDNOS. Lifetime prevalence of EDNOS was 4.78% in adolescents and 4.64% in adults. The majority of adolescents and adults with an eating disorder presented with EDNOS. Three-quarters of participants with EDNOS met criteria for comorbid disorders, while one-quarter endorsed suicidality. Severity correlates were equally prevalent in EDNOS and AN, whereas comparisons between EDNOS and BN varied by specific correlate and sample. Adolescents with subthreshold AN (SAN) endorsed more anxiety than AN (p EDNOS. Eating disorder diagnostic nomenclature requires modification to capture the full spectrum. © 2012 by Wiley Periodicals, Inc. Int J Eat Disord 2012. Copyright © 2012 Wiley Periodicals, Inc.

  5. [Adolescent medicine: eating disorders not otherwise specified (EDNOS)].

    Science.gov (United States)

    Vust, S; Michaud, P A

    2008-01-09

    Young people (mostly females) suffering from eating disorders not otherwise specified (EDNOS) are more and more numerous and their difficulties pose serious problems to health care providers as well as the society. These situations correspond to eating disorders which do not totally meet the DSM-IV criteria for either anorexia or bulimia nervosa. The duration of the symptoms, the extent of suffering as well as the impact on daily life should be taken into account to set-up the treatment. The therapeutic approach to these disorders should ideally include both cognitive/dietary and psychodynamic approaches. The Multidisciplinary Unit for Adolescent Health in Lausanne has set-up a group treatment for these patients.

  6. A Language for Specifying Compiler Optimizations for Generic Software

    Energy Technology Data Exchange (ETDEWEB)

    Willcock, Jeremiah J. [Indiana Univ., Bloomington, IN (United States)

    2007-01-01

    Compiler optimization is important to software performance, and modern processor architectures make optimization even more critical. However, many modern software applications use libraries providing high levels of abstraction. Such libraries often hinder effective optimization — the libraries are difficult to analyze using current compiler technology. For example, high-level libraries often use dynamic memory allocation and indirectly expressed control structures, such as iteratorbased loops. Programs using these libraries often cannot achieve an optimal level of performance. On the other hand, software libraries have also been recognized as potentially aiding in program optimization. One proposed implementation of library-based optimization is to allow the library author, or a library user, to define custom analyses and optimizations. Only limited systems have been created to take advantage of this potential, however. One problem in creating a framework for defining new optimizations and analyses is how users are to specify them: implementing them by hand inside a compiler is difficult and prone to errors. Thus, a domain-specific language for librarybased compiler optimizations would be beneficial. Many optimization specification languages have appeared in the literature, but they tend to be either limited in power or unnecessarily difficult to use. Therefore, I have designed, implemented, and evaluated the Pavilion language for specifying program analyses and optimizations, designed for library authors and users. These analyses and optimizations can be based on the implementation of a particular library, its use in a specific program, or on the properties of a broad range of types, expressed through concepts. The new system is intended to provide a high level of expressiveness, even though the intended users are unlikely to be compiler experts.

  7. Homology of normal chains and cohomology of charges

    CERN Document Server

    Pauw, Th De; Pfeffer, W F

    2017-01-01

    The authors consider a category of pairs of compact metric spaces and Lipschitz maps where the pairs satisfy a linearly isoperimetric condition related to the solvability of the Plateau problem with partially free boundary. It includes properly all pairs of compact Lipschitz neighborhood retracts of a large class of Banach spaces. On this category the authors define homology and cohomology functors with real coefficients which satisfy the Eilenberg-Steenrod axioms, but reflect the metric properties of the underlying spaces. As an example they show that the zero-dimensional homology of a space in our category is trivial if and only if the space is path connected by arcs of finite length. The homology and cohomology of a pair are, respectively, locally convex and Banach spaces that are in duality. Ignoring the topological structures, the homology and cohomology extend to all pairs of compact metric spaces. For locally acyclic spaces, the authors establish a natural isomorphism between their cohomology and the �...

  8. Generalized local homology and cohomology for linearly compact modules

    International Nuclear Information System (INIS)

    Tran Tuan Nam

    2006-07-01

    We study generalized local homology for linearly compact modules. By duality, we get some properties of generalized local cohomology modules and extend well-known properties of local cohomology of A. Grothendieck. (author)

  9. On the homology and the cohomology of certain polycyclic groups

    International Nuclear Information System (INIS)

    Majumdar, S.

    1987-10-01

    The homology and the cohomology of infinite non-abelian split extensions of cyclic groups by cyclic groups have been computed through construction of nice free resolutions for these groups. (author). 16 refs

  10. Inhibitory Effect of Berberine on Zeste Homolog 2 (Ezh2 ...

    African Journals Online (AJOL)

    homolog 2 (Ezh2) expressions in KYSE450 human esophageal cancer cells. Methods: ... of the AXL receptor kinase. The results of ... effects of estrogen receptor antagonists on ..... protein EZH2 is involved in progression of prostate cancer.

  11. Matrix factorizations and homological mirror symmetry on the torus

    International Nuclear Information System (INIS)

    Knapp, Johanna; Omer, Harun

    2007-01-01

    We consider matrix factorizations and homological mirror symmetry on the torus T 2 using a Landau-Ginzburg description. We identify the basic matrix factorizations of the Landau-Ginzburg superpotential and compute the full spectrum taking into account the explicit dependence on bulk and boundary moduli. We verify homological mirror symmetry by comparing three-point functions in the A-model and the B-model

  12. Regulation of homologous recombination at telomeres in budding yeast

    DEFF Research Database (Denmark)

    Eckert-Boulet, Nadine; Lisby, Michael

    2010-01-01

    Homologous recombination is suppressed at normal length telomere sequences. In contrast, telomere recombination is allowed when telomeres erode in the absence of telomerase activity or as a consequence of nucleolytic degradation or incomplete replication. Here, we review the mechanisms that contr...... that contribute to regulating mitotic homologous recombination at telomeres and the role of these mechanisms in signalling short telomeres in the budding yeast Saccharomyces cerevisiae....

  13. Zeroth Poisson Homology, Foliated Cohomology and Perfect Poisson Manifolds

    Science.gov (United States)

    Martínez-Torres, David; Miranda, Eva

    2018-01-01

    We prove that, for compact regular Poisson manifolds, the zeroth homology group is isomorphic to the top foliated cohomology group, and we give some applications. In particular, we show that, for regular unimodular Poisson manifolds, top Poisson and foliated cohomology groups are isomorphic. Inspired by the symplectic setting, we define what a perfect Poisson manifold is. We use these Poisson homology computations to provide families of perfect Poisson manifolds.

  14. ASPECT: An advanced specified-profile evaluation code for tokamaks

    International Nuclear Information System (INIS)

    Stotler, D.P.; Reiersen, W.T.; Bateman, G.

    1993-03-01

    A specified-profile, global analysis code has been developed to evaluate the performance of fusion reactor designs. Both steady-state and time-dependent calculations are carried out; the results of the former can be used in defining the parameters of the latter, if desired. In the steady-state analysis, the performance is computed at a density and temperature chosen to be consistent with input limits (e.g., density and beta) of several varieties. The calculation can be made at either the intersection of the two limits or at the point of optimum performance as the density and temperature are varied along the limiting boundaries. Two measures of performance are available for this purpose: the ignition margin or the confinement level required to achieve a prescribed ignition margin. The time-dependent calculation can be configured to yield either the evolution of plasma energy as a function of time or, via an iteration scheme, the amount of auxiliary power required to achieve a desired final plasma energy

  15. Measles virus-specified polypeptides in infected cells

    International Nuclear Information System (INIS)

    Vainionpaepae, R.

    1979-01-01

    The synthesis of wild-type measles virus-specified polypeptides in Vero cells in pulse-chase experiments, in cells with synchronized protein synthesis by high salt concentration, and in the presence of proteolytic enzyme inhibitors was analyzed by polyacrylamide slab-gel electrophoresis. Six major (L, G, 2, NP, 5 and M) structural polypeptides were identified in infected cells. The results of pulse-chase experiments suggested that most of the structural polypeptides were synthesized at their final length. Polypeptide M was found to be sensitive to trypsin. In TLCK-treated cells its molecular weight was about 1000-2000 daltons higher than in untreated cells. A minor virus-specific polypeptide with a molecular weight of about 23,000 was found as a very faint and diffuse band. In addition, three nonstructural polypeptides with molecular weights of 65,000, 38,000 and 18,000 were also detected. The experiments with proteolytic enzyme inhibitors and with synchronized protein synthesis suggested that the polypeptide with a molecular weight of 65,000 might be a precursor of the structural polypeptide 5. (author)

  16. Protein misfolding specifies recruitment to cytoplasmic inclusion bodies.

    Science.gov (United States)

    Bersuker, Kirill; Brandeis, Michael; Kopito, Ron R

    2016-04-25

    Inclusion bodies (IBs) containing aggregated disease-associated proteins and polyubiquitin (poly-Ub) conjugates are universal histopathological features of neurodegenerative diseases. Ub has been proposed to target proteins to IBs for degradation via autophagy, but the mechanisms that govern recruitment of ubiquitylated proteins to IBs are not well understood. In this paper, we use conditionally destabilized reporters that undergo misfolding and ubiquitylation upon removal of a stabilizing ligand to examine the role of Ub conjugation in targeting proteins to IBs that are composed of an N-terminal fragment of mutant huntingtin, the causative protein of Huntington's disease. We show that reporters are excluded from IBs in the presence of the stabilizing ligand but are recruited to IBs after ligand washout. However, we find that Ub conjugation is not necessary to target reporters to IBs. We also report that forced Ub conjugation by the Ub fusion degradation pathway is not sufficient for recruitment to IBs. Finally, we find that reporters and Ub conjugates are stable at IBs. These data indicate that compromised folding states, rather than conjugation to Ub, can specify recruitment to IBs. © 2016 Bersuker et al.

  17. Optimum heat power cycles for specified boundary conditions

    International Nuclear Information System (INIS)

    Ibrahim, O.M.; Klein, S.A.; Mitchell, J.W.

    1991-01-01

    In this paper optimization of the power output of Carnot and closed Brayton cycles is considered for both finite and infinite thermal capacitance rates of the external fluid streams. The method of Lagrange multipliers is used to solve for working fluid temperatures that yield maximum power. Analytical expressions for the maximum power and the cycle efficiency at maximum power are obtained. A comparison of the maximum power from the two cycles for the same boundary conditions, i.e., the same heat source/sink inlet temperatures, thermal capacitance rates, and heat exchanger conductances, shows that the Brayton cycle can produce more power than the Carnot cycle. This comparison illustrates that cycles exist that can produce more power than the Carnot cycle. The optimum heat power cycle, which will provide the upper limit of power obtained from any thermodynamic cycle for specified boundary conditions and heat exchanger conductances is considered. The optimum heat power cycle is identified by optimizing the sum of the power output from a sequence of Carnot cycles. The shape of the optimum heat power cycle, the power output, and corresponding efficiency are presented. The efficiency at maximum power of all cycles investigated in this study is found to be equal to (or well approximated by) η = 1 - sq. root T L.in /φT H.in where φ is a factor relating the entropy changes during heat rejection and heat addition

  18. Synthetic prions with novel strain-specified properties.

    Science.gov (United States)

    Moda, Fabio; Le, Thanh-Nhat T; Aulić, Suzana; Bistaffa, Edoardo; Campagnani, Ilaria; Virgilio, Tommaso; Indaco, Antonio; Palamara, Luisa; Andréoletti, Olivier; Tagliavini, Fabrizio; Legname, Giuseppe

    2015-12-01

    Prions are infectious proteins that possess multiple self-propagating structures. The information for strains and structural specific barriers appears to be contained exclusively in the folding of the pathological isoform, PrP(Sc). Many recent studies determined that de novo prion strains could be generated in vitro from the structural conversion of recombinant (rec) prion protein (PrP) into amyloidal structures. Our aim was to elucidate the conformational diversity of pathological recPrP amyloids and their biological activities, as well as to gain novel insights in characterizing molecular events involved in mammalian prion conversion and propagation. To this end we generated infectious materials that possess different conformational structures. Our methodology for the prion conversion of recPrP required only purified rec full-length mouse (Mo) PrP and common chemicals. Neither infected brain extracts nor amplified PrP(Sc) were used. Following two different in vitro protocols recMoPrP converted to amyloid fibrils without any seeding factor. Mouse hypothalamic GT1 and neuroblastoma N2a cell lines were infected with these amyloid preparations as fast screening methodology to characterize the infectious materials. Remarkably, a large number of amyloid preparations were able to induce the conformational change of endogenous PrPC to harbor several distinctive proteinase-resistant PrP forms. One such preparation was characterized in vivo habouring a synthetic prion with novel strain specified neuropathological and biochemical properties.

  19. 29 CFR 780.908 - Relation of employee's work to specified transportation.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Relation of employee's work to specified transportation... Relation of employee's work to specified transportation. In order for the exemption to apply to an employee... fruits or vegetables from the farm to the specified places within the same State. Engagement in other...

  20. 40 CFR 1065.514 - Cycle-validation criteria for operation over specified duty cycles.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Cycle-validation criteria for operation over specified duty cycles. 1065.514 Section 1065.514 Protection of Environment ENVIRONMENTAL... Over Specified Duty Cycles § 1065.514 Cycle-validation criteria for operation over specified duty...

  1. Multiscale analysis of nonlinear systems using computational homology

    Energy Technology Data Exchange (ETDEWEB)

    Konstantin Mischaikow; Michael Schatz; William Kalies; Thomas Wanner

    2010-05-24

    This is a collaborative project between the principal investigators. However, as is to be expected, different PIs have greater focus on different aspects of the project. This report lists these major directions of research which were pursued during the funding period: (1) Computational Homology in Fluids - For the computational homology effort in thermal convection, the focus of the work during the first two years of the funding period included: (1) A clear demonstration that homology can sensitively detect the presence or absence of an important flow symmetry, (2) An investigation of homology as a probe for flow dynamics, and (3) The construction of a new convection apparatus for probing the effects of large-aspect-ratio. (2) Computational Homology in Cardiac Dynamics - We have initiated an effort to test the use of homology in characterizing data from both laboratory experiments and numerical simulations of arrhythmia in the heart. Recently, the use of high speed, high sensitivity digital imaging in conjunction with voltage sensitive fluorescent dyes has enabled researchers to visualize electrical activity on the surface of cardiac tissue, both in vitro and in vivo. (3) Magnetohydrodynamics - A new research direction is to use computational homology to analyze results of large scale simulations of 2D turbulence in the presence of magnetic fields. Such simulations are relevant to the dynamics of black hole accretion disks. The complex flow patterns from simulations exhibit strong qualitative changes as a function of magnetic field strength. Efforts to characterize the pattern changes using Fourier methods and wavelet analysis have been unsuccessful. (4) Granular Flow - two experts in the area of granular media are studying 2D model experiments of earthquake dynamics where the stress fields can be measured; these stress fields from complex patterns of 'force chains' that may be amenable to analysis using computational homology. (5) Microstructure

  2. Multiscale analysis of nonlinear systems using computational homology

    Energy Technology Data Exchange (ETDEWEB)

    Konstantin Mischaikow, Rutgers University/Georgia Institute of Technology, Michael Schatz, Georgia Institute of Technology, William Kalies, Florida Atlantic University, Thomas Wanner,George Mason University

    2010-05-19

    This is a collaborative project between the principal investigators. However, as is to be expected, different PIs have greater focus on different aspects of the project. This report lists these major directions of research which were pursued during the funding period: (1) Computational Homology in Fluids - For the computational homology effort in thermal convection, the focus of the work during the first two years of the funding period included: (1) A clear demonstration that homology can sensitively detect the presence or absence of an important flow symmetry, (2) An investigation of homology as a probe for flow dynamics, and (3) The construction of a new convection apparatus for probing the effects of large-aspect-ratio. (2) Computational Homology in Cardiac Dynamics - We have initiated an effort to test the use of homology in characterizing data from both laboratory experiments and numerical simulations of arrhythmia in the heart. Recently, the use of high speed, high sensitivity digital imaging in conjunction with voltage sensitive fluorescent dyes has enabled researchers to visualize electrical activity on the surface of cardiac tissue, both in vitro and in vivo. (3) Magnetohydrodynamics - A new research direction is to use computational homology to analyze results of large scale simulations of 2D turbulence in the presence of magnetic fields. Such simulations are relevant to the dynamics of black hole accretion disks. The complex flow patterns from simulations exhibit strong qualitative changes as a function of magnetic field strength. Efforts to characterize the pattern changes using Fourier methods and wavelet analysis have been unsuccessful. (4) Granular Flow - two experts in the area of granular media are studying 2D model experiments of earthquake dynamics where the stress fields can be measured; these stress fields from complex patterns of 'force chains' that may be amenable to analysis using computational homology. (5) Microstructure

  3. RPA homologs and ssDNA processing during meiotic recombination.

    Science.gov (United States)

    Ribeiro, Jonathan; Abby, Emilie; Livera, Gabriel; Martini, Emmanuelle

    2016-06-01

    Meiotic homologous recombination is a specialized process that involves homologous chromosome pairing and strand exchange to guarantee proper chromosome segregation and genetic diversity. The formation and repair of DNA double-strand breaks (DSBs) during meiotic recombination differs from those during mitotic recombination in that the homologous chromosome rather than the sister chromatid is the preferred repair template. The processing of single-stranded DNA (ssDNA) formed on intermediate recombination structures is central to driving the specific outcomes of DSB repair during meiosis. Replication protein A (RPA) is the main ssDNA-binding protein complex involved in DNA metabolism. However, the existence of RPA orthologs in plants and the recent discovery of meiosis specific with OB domains (MEIOB), a widely conserved meiosis-specific RPA1 paralog, strongly suggest that multiple RPA complexes evolved and specialized to subdivide their roles during DNA metabolism. Here we review ssDNA formation and maturation during mitotic and meiotic recombination underlying the meiotic specific features. We describe and discuss the existence and properties of MEIOB and multiple RPA subunits in plants and highlight how they can provide meiosis-specific fates to ssDNA processing during homologous recombination. Understanding the functions of these RPA homologs and how they interact with the canonical RPA subunits is of major interest in the fields of meiosis and DNA repair.

  4. The OGCleaner: filtering false-positive homology clusters.

    Science.gov (United States)

    Fujimoto, M Stanley; Suvorov, Anton; Jensen, Nicholas O; Clement, Mark J; Snell, Quinn; Bybee, Seth M

    2017-01-01

    Detecting homologous sequences in organisms is an essential step in protein structure and function prediction, gene annotation and phylogenetic tree construction. Heuristic methods are often employed for quality control of putative homology clusters. These heuristics, however, usually only apply to pairwise sequence comparison and do not examine clusters as a whole. We present the Orthology Group Cleaner (the OGCleaner), a tool designed for filtering putative orthology groups as homology or non-homology clusters by considering all sequences in a cluster. The OGCleaner relies on high-quality orthologous groups identified in OrthoDB to train machine learning algorithms that are able to distinguish between true-positive and false-positive homology groups. This package aims to improve the quality of phylogenetic tree construction especially in instances of lower-quality transcriptome assemblies. https://github.com/byucsl/ogcleaner CONTACT: sfujimoto@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. Primary homologies of the circumorbital bones of snakes.

    Science.gov (United States)

    Palci, Alessandro; Caldwell, Michael W

    2013-09-01

    Some snakes have two circumorbital ossifications that in the current literature are usually referred to as the postorbital and supraorbital. We review the arguments that have been proposed to justify this interpretation and provide counter-arguments that reject those conjectures of primary homology based on the observation of 32 species of lizards and 81 species of snakes (both extant and fossil). We present similarity arguments, both topological and structural, for reinterpretation of the primary homologies of the dorsal and posterior orbital ossifications of snakes. Applying the test of similarity, we conclude that the posterior orbital ossification of snakes is topologically consistent as the homolog of the lacertilian jugal, and that the dorsal orbital ossification present in some snakes (e.g., pythons, Loxocemus, and Calabaria) is the homolog of the lacertilian postfrontal. We therefore propose that the terms postorbital and supraorbital should be abandoned as reference language for the circumorbital bones of snakes, and be replaced with the terms jugal and postfrontal, respectively. The primary homology claim for the snake "postorbital" fails the test of similarity, while the term "supraorbital" is an unnecessary and inaccurate application of the concept of a neomorphic ossification, for an element that passes the test of similarity as a postfrontal. This reinterpretation of the circumorbital bones of snakes is bound to have important repercussions for future phylogenetic analyses and consequently for our understanding of the origin and evolution of snakes. Copyright © 2013 Wiley Periodicals, Inc.

  6. An outpatient clinical study of dissociative disorder not otherwise specified.

    Science.gov (United States)

    Yanartaş, Ömer; Özmen, Hülya Akar; Citak, Serhat; Zincir, Selma Bozkurt; Sünbül, Esra Aydin

    2014-05-01

    The relatively high prevalence of the diagnosis of dissociative disorder not otherwise specified is frequently considered to be disproportionate. The disproportionate rate of this diagnosis is thought to be related to nosologic and/or diagnostic issues in dissociative identity disorder. We sought to investigate and compare the symptom patterns of these two clinical entities. We conducted a cross-sectional study involving 1314 participants who were screened with the Dissociative Experience Scale (DES) and the Somatoform Dissociation Questionnaire (SDQ). Of the participants, 272 who scored above the cut-off points for the screening questionnaires (DES score>30 and/or SDQ score>40 points) were invited to complete a structured interview using the Dissociative Disorders Interview Schedule (DDIS); of this subsample, only 190 participants agreed to participate in the second phase of the study. The mean score for the DES was 18.55±17.23, and the mean score for the SDQ was 30.19±13.32. Of the 190 participants, 167 patients were diagnosed as having a dissociative disorder (87.8%). We found that DD-NOS was the most prevalent category of dissociative disorder. There was a significantly larger percentage of patients in the DID group than in the DD-NOS group according to secondary features of DID and Schneiderian symptoms. The secondary features of DID and Schneiderian symptoms appeared to be more specific for DID, while no differences were detected between DID and DD-NOS based on most of the items on the SCL 90R. Further longitudinal studies are needed to determine the features that are similar and dissimilar between DD-NOS and DID. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. [Analysis of DNA-DNA homologies in obligate methylotrophic bacteria].

    Science.gov (United States)

    Doronina, N V; Govorukhina, N I; Lysenko, A M; Trotsenko, Iu A

    1988-01-01

    The genotypic affinity of 19 bacterial strains obligately dependent on methanol or methylamine as carbon and energy sources was studied by techniques of molecular DNA hybridization. The high homology level (35-88%) between motile strain Methylophilus methanolovorus V-1447D and nonmotile strain Methylobacillus sp. VSB-792 as well as other motile strains (Pseudomonas methanolica ATCC 21704, Methylomonas methanolica NRRL 5458, Pseudomonas sp. W6, strain A3) indicates that all of them belong to one genus. Rather high level of homology (62-63%) was found between Methylobacillus glycogenes ATCC 29475 and Pseudomonas insueta ATCC 21276 and strain G-10. The motile strain Methylophilus methylotrophus NCIB 10515 has a low homology (below 20%) to other of the studied obligate methylobacteria. Therefore, at least two genetically different genera of obligate methylobacteria can be distinguished, namely Methylophilus and Methylobacillus, the latter being represented by both motile and nonmotile forms.

  8. Induction of intrachromosomal homologous recombination in whole plants

    International Nuclear Information System (INIS)

    Puchta, H.; Swoboda, P.; Hohn, B.

    1995-01-01

    The influence of different factors on frequencies of intrachromosomal homologous recombination in whole Arabidopsis thaliana and tobacco plants was analyzed using a disrupted β-glucuronidase marker gene. Recombination frequencies were enhanced several fold by DNA damaging agents like UV-light or MMS (methyl methanesulfonate). Applying 3-methoxybenzamide (3-MB), an inhibitor of poly(ADP)ribose polymerase (PARP), an enzyme that is postulated to be involved in DNA repair, enhanced homologous recombination frequencies strongly. These findings indicate that homologous recombination is involved in DNA repair and can (at least partially) compensate for other DNA repair pathways. Indications that recombination in plants can be induced by environmental stress factors that are not likely to be involved in DNA metabolism were also found; Arabidopsis plants growing in a medium containing 0.1 M NaCl exhibited elevated recombination frequencies. The possible general effects of ‘environmental’ challenges on genome flexibility are discussed. (author)

  9. Khovanov homology for virtual knots with arbitrary coefficients

    International Nuclear Information System (INIS)

    Manturov, Vassily O

    2007-01-01

    The Khovanov homology theory over an arbitrary coefficient ring is extended to the case of virtual knots. We introduce a complex which is well-defined in the virtual case and is homotopy equivalent to the original Khovanov complex in the classical case. Unlike Khovanov's original construction, our definition of the complex does not use any additional prescription of signs to the edges of a cube. Moreover, our method enables us to construct a Khovanov homology theory for 'twisted virtual knots' in the sense of Bourgoin and Viro (including knots in three-dimensional projective space). We generalize a number of results of Khovanov homology theory (the Wehrli complex, minimality problems, Frobenius extensions) to virtual knots with non-orientable atoms

  10. Homology groups for particles on one-connected graphs

    Science.gov (United States)

    MaciÄ Żek, Tomasz; Sawicki, Adam

    2017-06-01

    We present a mathematical framework for describing the topology of configuration spaces for particles on one-connected graphs. In particular, we compute the homology groups over integers for different classes of one-connected graphs. Our approach is based on some fundamental combinatorial properties of the configuration spaces, Mayer-Vietoris sequences for different parts of configuration spaces, and some limited use of discrete Morse theory. As one of the results, we derive the closed-form formulae for ranks of the homology groups for indistinguishable particles on tree graphs. We also give a detailed discussion of the second homology group of the configuration space of both distinguishable and indistinguishable particles. Our motivation is the search for new kinds of quantum statistics.

  11. Khovanov-Rozansky Graph Homology and Composition Product

    DEFF Research Database (Denmark)

    Wagner, Emmanuel

    2008-01-01

    In analogy with a recursive formula for the HOMFLY-PT polynomial of links given by Jaeger, we give a recursive formula for the graph polynomial introduced by Kauffman and Vogel. We show how this formula extends to the Khovanov–Rozansky graph homology.......In analogy with a recursive formula for the HOMFLY-PT polynomial of links given by Jaeger, we give a recursive formula for the graph polynomial introduced by Kauffman and Vogel. We show how this formula extends to the Khovanov–Rozansky graph homology....

  12. Macdonald operators and homological invariants of the colored Hopf link

    International Nuclear Information System (INIS)

    Awata, Hidetoshi; Kanno, Hiroaki

    2011-01-01

    Using a power sum (boson) realization for the Macdonald operators, we investigate the Gukov, Iqbal, Kozcaz and Vafa (GIKV) proposal for the homological invariants of the colored Hopf link, which include Khovanov-Rozansky homology as a special case. We prove the polynomiality of the invariants obtained by GIKV's proposal for arbitrary representations. We derive a closed formula of the invariants of the colored Hopf link for antisymmetric representations. We argue that a little amendment of GIKV's proposal is required to make all the coefficients of the polynomial non-negative integers. (paper)

  13. Controlling meiotic recombinational repair - specifying the roles of ZMMs, Sgs1 and Mus81/Mms4 in crossover formation.

    Directory of Open Access Journals (Sweden)

    Ashwini Oke

    2014-10-01

    Full Text Available Crossovers (COs play a critical role in ensuring proper alignment and segregation of homologous chromosomes during meiosis. How the cell balances recombination between CO vs. noncrossover (NCO outcomes is not completely understood. Further lacking is what constrains the extent of DNA repair such that multiple events do not arise from a single double-strand break (DSB. Here, by interpreting signatures that result from recombination genome-wide, we find that synaptonemal complex proteins promote crossing over in distinct ways. Our results suggest that Zip3 (RNF212 promotes biased cutting of the double Holliday-junction (dHJ intermediate whereas surprisingly Msh4 does not. Moreover, detailed examination of conversion tracts in sgs1 and mms4-md mutants reveal distinct aberrant recombination events involving multiple chromatid invasions. In sgs1 mutants, these multiple invasions are generally multichromatid involving 3-4 chromatids; in mms4-md mutants the multiple invasions preferentially resolve into one or two chromatids. Our analysis suggests that Mus81/Mms4 (Eme1, rather than just being a minor resolvase for COs is crucial for both COs and NCOs in preventing chromosome entanglements by removing 3'- flaps to promote second-end capture. Together our results force a reevaluation of how key recombination enzymes collaborate to specify the outcome of meiotic DNA repair.

  14. Topological Hochschild homology and the Bass trace conjecture

    DEFF Research Database (Denmark)

    Berrick, A. J.; Hesselholt, Lars

    2015-01-01

    We use the methods of topological Hochschild homology to shed new light on groups satisfying the Bass trace conjecture. Factorization of the Hattori–Stallings rank map through the Bökstedt–Hsiang–Madsen cyclotomic trace map leads to Linnell's restriction on such groups. As a new consequence...

  15. The homological content of the Jones representations at $q = -1$

    DEFF Research Database (Denmark)

    Egsgaard, Jens Kristian; Fuglede Jørgensen, Søren

    We generalize a discovery of Kasahara and show that the Jones representations of braid groups, when evaluated at $q = -1$, are related to the action on homology of a branched double cover of the underlying punctured disk. As an application, we prove for a large family of pseudo-Anosov mapping...

  16. Topological quantum information, virtual Jones polynomials and Khovanov homology

    International Nuclear Information System (INIS)

    Kauffman, Louis H

    2011-01-01

    In this paper, we give a quantum statistical interpretation of the bracket polynomial state sum 〈K〉, the Jones polynomial V K (t) and virtual knot theory versions of the Jones polynomial, including the arrow polynomial. We use these quantum mechanical interpretations to give new quantum algorithms for these Jones polynomials. In those cases where the Khovanov homology is defined, the Hilbert space C(K) of our model is isomorphic with the chain complex for Khovanov homology with coefficients in the complex numbers. There is a natural unitary transformation U:C(K) → C(K) such that 〈K〉 = Trace(U), where 〈K〉 denotes the evaluation of the state sum model for the corresponding polynomial. We show that for the Khovanov boundary operator ∂:C(K) → C(K), we have the relationship ∂U + U∂ = 0. Consequently, the operator U acts on the Khovanov homology, and we obtain a direct relationship between the Khovanov homology and this quantum algorithm for the Jones polynomial. (paper)

  17. Homology of the open moduli space of curves

    DEFF Research Database (Denmark)

    Madsen, Ib Henning

    2012-01-01

    This is a survey on the proof of a generalized version of the Mumford conjecture obtained in joint work with M. Weiss stating that a certain map between some classifying spaces which a priori have different natures induces an isomorphism at the level of integral homology. We also discuss our proo...

  18. On the Cogosvili functor generated by a homology

    International Nuclear Information System (INIS)

    Abd El-Satter, A. Dabbour; Mahmoud, S.

    1991-09-01

    In the present work we discuss the Cogosvili functor generated by a homology, and study the construction of the corresponding groups and their induced homomorphisms. Moreover, we investigate the properties of this functor and prove that the set of such functors are isomorphic to the Bauer homotopy theory. (author). 19 refs

  19. Multiresolution persistent homology for excessively large biomolecular datasets

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Kelin; Zhao, Zhixiong [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Wei, Guo-Wei, E-mail: wei@math.msu.edu [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (United States)

    2015-10-07

    Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis. By appropriately tuning the resolution of the rigidity density, we are able to focus the topological lens on the scale of interest. The proposed multiresolution topological analysis is validated by a hexagonal fractal image which has three distinct scales. We further demonstrate the proposed method for extracting topological fingerprints from DNA molecules. In particular, the topological persistence of a virus capsid with 273 780 atoms is successfully analyzed which would otherwise be inaccessible to the normal point cloud method and unreliable by using coarse-grained multiscale persistent homology. The proposed method has also been successfully applied to the protein domain classification, which is the first time that persistent homology is used for practical protein domain analysis, to our knowledge. The proposed multiresolution topological method has potential applications in arbitrary data sets, such as social networks, biological networks, and graphs.

  20. Human Fanconi anemia monoubiquitination pathway promotes homologous DNA repair.

    Science.gov (United States)

    Nakanishi, Koji; Yang, Yun-Gui; Pierce, Andrew J; Taniguchi, Toshiyasu; Digweed, Martin; D'Andrea, Alan D; Wang, Zhao-Qi; Jasin, Maria

    2005-01-25

    Fanconi anemia (FA) is a recessive disorder characterized by congenital abnormalities, progressive bone-marrow failure, and cancer susceptibility. Cells from FA patients are hypersensitive to agents that produce DNA crosslinks and, after treatment with these agents, have pronounced chromosome breakage and other cytogenetic abnormalities. Eight FANC genes have been cloned, and the encoded proteins interact in a common cellular pathway. DNA-damaging agents activate the monoubiquitination of FANCD2, resulting in its targeting to nuclear foci that also contain BRCA1 and BRCA2/FANCD1, proteins involved in homology-directed DNA repair. Given the interaction of the FANC proteins with BRCA1 and BRCA2, we tested whether cells from FA patients (groups A, G, and D2) and mouse Fanca-/- cells with a targeted mutation are impaired for this repair pathway. We find that both the upstream (FANCA and FANCG) and downstream (FANCD2) FA pathway components promote homology-directed repair of chromosomal double-strand breaks (DSBs). The FANCD2 monoubiquitination site is critical for normal levels of repair, whereas the ATM phosphorylation site is not. The defect in these cells, however, is mild, differentiating them from BRCA1 and BRCA2 mutant cells. Surprisingly, we provide evidence that these proteins, like BRCA1 but unlike BRCA2, promote a second DSB repair pathway involving homology, i.e., single-strand annealing. These results suggest an early role for the FANC proteins in homologous DSB repair pathway choice.

  1. Intersection spaces, spatial homology truncation, and string theory

    CERN Document Server

    Banagl, Markus

    2010-01-01

    Intersection cohomology assigns groups which satisfy a generalized form of Poincaré duality over the rationals to a stratified singular space. The present monograph introduces a method that assigns to certain classes of stratified spaces cell complexes, called intersection spaces, whose ordinary rational homology satisfies generalized Poincaré duality. The cornerstone of the method is a process of spatial homology truncation, whose functoriality properties are analyzed in detail. The material on truncation is autonomous and may be of independent interest to homotopy theorists. The cohomology of intersection spaces is not isomorphic to intersection cohomology and possesses algebraic features such as perversity-internal cup-products and cohomology operations that are not generally available for intersection cohomology. A mirror-symmetric interpretation, as well as applications to string theory concerning massless D-branes arising in type IIB theory during a Calabi-Yau conifold transition, are discussed.

  2. A homology sound-based algorithm for speech signal interference

    Science.gov (United States)

    Jiang, Yi-jiao; Chen, Hou-jin; Li, Ju-peng; Zhang, Zhan-song

    2015-12-01

    Aiming at secure analog speech communication, a homology sound-based algorithm for speech signal interference is proposed in this paper. We first split speech signal into phonetic fragments by a short-term energy method and establish an interference noise cache library with the phonetic fragments. Then we implement the homology sound interference by mixing the randomly selected interferential fragments and the original speech in real time. The computer simulation results indicated that the interference produced by this algorithm has advantages of real time, randomness, and high correlation with the original signal, comparing with the traditional noise interference methods such as white noise interference. After further studies, the proposed algorithm may be readily used in secure speech communication.

  3. The endless tale of non-homologous end-joining.

    Science.gov (United States)

    Weterings, Eric; Chen, David J

    2008-01-01

    DNA double-strand breaks (DSBs) are introduced in cells by ionizing radiation and reactive oxygen species. In addition, they are commonly generated during V(D)J recombination, an essential aspect of the developing immune system. Failure to effectively repair these DSBs can result in chromosome breakage, cell death, onset of cancer, and defects in the immune system of higher vertebrates. Fortunately, all mammalian cells possess two enzymatic pathways that mediate the repair of DSBs: homologous recombination and non-homologous end-joining (NHEJ). The NHEJ process utilizes enzymes that capture both ends of the broken DNA molecule, bring them together in a synaptic DNA-protein complex, and finally repair the DNA break. In this review, all the known enzymes that play a role in the NHEJ process are discussed and a working model for the co-operation of these enzymes during DSB repair is presented.

  4. Homology and isomorphism: Bourdieu in conversation with New Institutionalism.

    Science.gov (United States)

    Wang, Yingyao

    2016-06-01

    Bourdieusian Field Theory (BFT) provided decisive inspiration for the early conceptual formulation of New Institutionalism (NI). This paper attempts to reinvigorate the stalled intellectual dialogue between NI and BFT by comparing NI's concept of isomorphism with BFT's notion of homology. I argue that Bourdieu's understanding of domination-oriented social action, transposable habitus, and a non-linear causality, embodied in his neglected concept of homology, provides an alternative theorization of field-level convergence to New Institutionalism's central idea of institutional isomorphism. To showcase how BFT can be useful for organizational research, I postulate a habitus-informed and field-conditioned theory of transference to enrich NI's spin-off thesis of 'diffusion'. I propose that while NI can benefit from BFT's potential of bringing social structure back into organizational research, BFT can enrich its social analysis by borrowing from NI's elaboration of the symbolic system of organizations. © London School of Economics and Political Science 2016.

  5. RTEL1 maintains genomic stability by suppressing homologous recombination.

    Science.gov (United States)

    Barber, Louise J; Youds, Jillian L; Ward, Jordan D; McIlwraith, Michael J; O'Neil, Nigel J; Petalcorin, Mark I R; Martin, Julie S; Collis, Spencer J; Cantor, Sharon B; Auclair, Melissa; Tissenbaum, Heidi; West, Stephen C; Rose, Ann M; Boulton, Simon J

    2008-10-17

    Homologous recombination (HR) is an important conserved process for DNA repair and ensures maintenance of genome integrity. Inappropriate HR causes gross chromosomal rearrangements and tumorigenesis in mammals. In yeast, the Srs2 helicase eliminates inappropriate recombination events, but the functional equivalent of Srs2 in higher eukaryotes has been elusive. Here, we identify C. elegans RTEL-1 as a functional analog of Srs2 and describe its vertebrate counterpart, RTEL1, which is required for genome stability and tumor avoidance. We find that rtel-1 mutant worms and RTEL1-depleted human cells share characteristic phenotypes with yeast srs2 mutants: lethality upon deletion of the sgs1/BLM homolog, hyperrecombination, and DNA damage sensitivity. In vitro, purified human RTEL1 antagonizes HR by promoting the disassembly of D loop recombination intermediates in a reaction dependent upon ATP hydrolysis. We propose that loss of HR control after deregulation of RTEL1 may be a critical event that drives genome instability and cancer.

  6. 36 CFR 223.84 - Small business bid form provisions on sales with specified road construction.

    Science.gov (United States)

    2010-07-01

    ... provisions on sales with specified road construction. 223.84 Section 223.84 Parks, Forests, and Public... specified road construction. For each sale described in § 223.82(b), the bid form must include provision for a small business concern: (a) To elect road construction by the Forest Service and where such...

  7. 75 FR 76940 - Specified Tax Return Preparers Required To File Individual Income Tax Returns Using Magnetic...

    Science.gov (United States)

    2010-12-10

    ... DEPARTMENT OF THE TREASURY Internal Revenue Service 26 CFR Parts 1 and 301 [REG-100194-10] RIN 1545-BJ52 Specified Tax Return Preparers Required To File Individual Income Tax Returns Using Magnetic... for ``specified tax return prepares,''. FOR FURTHER INFORMATION CONTACT: Keith L. Brau at (202) 622...

  8. 76 FR 22611 - Specified Tax Return Preparers Required To File Individual Income Tax Returns Using Magnetic...

    Science.gov (United States)

    2011-04-22

    ... Specified Tax Return Preparers Required To File Individual Income Tax Returns Using Magnetic Media... Register on Wednesday, March 30, 2011 (76 FR 17521) providing guidance to specified tax return preparers who prepare and file individual income tax returns using magnetic media pursuant to section 6011(e)(3...

  9. The Effects of Including a Callous-Unemotional Specifier for the Diagnosis of Conduct Disorder

    Science.gov (United States)

    Kahn, Rachel E.; Frick, Paul J.; Youngstrom, Eric; Findling, Robert L.; Youngstrom, Jennifer Kogos

    2012-01-01

    Background: "With Significant Callous-Unemotional Traits" has been proposed as a specifier for conduct disorder (CD) in the upcoming revision of the Diagnostic and Statistical Manual of Mental Disorders (DSM-V). The impact of this specifier on children diagnosed with CD should be considered. Methods: A multi-site cross-sectional design with…

  10. 31 CFR 560.803 - Customs procedures: Goods specified in § 560.201.

    Science.gov (United States)

    2010-07-01

    ... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Customs procedures: Goods specified... REGULATIONS Procedures § 560.803 Customs procedures: Goods specified in § 560.201. (a) With respect to goods... Customs officers shall not accept or allow any: (1) Entry for consumption or warehouse (including any...

  11. FastBLAST: homology relationships for millions of proteins.

    Directory of Open Access Journals (Sweden)

    Morgan N Price

    Full Text Available BACKGROUND: All-versus-all BLAST, which searches for homologous pairs of sequences in a database of proteins, is used to identify potential orthologs, to find new protein families, and to provide rapid access to these homology relationships. As DNA sequencing accelerates and data sets grow, all-versus-all BLAST has become computationally demanding. METHODOLOGY/PRINCIPAL FINDINGS: We present FastBLAST, a heuristic replacement for all-versus-all BLAST that relies on alignments of proteins to known families, obtained from tools such as PSI-BLAST and HMMer. FastBLAST avoids most of the work of all-versus-all BLAST by taking advantage of these alignments and by clustering similar sequences. FastBLAST runs in two stages: the first stage identifies additional families and aligns them, and the second stage quickly identifies the homologs of a query sequence, based on the alignments of the families, before generating pairwise alignments. On 6.53 million proteins from the non-redundant Genbank database ("NR", FastBLAST identifies new families 25 times faster than all-versus-all BLAST. Once the first stage is completed, FastBLAST identifies homologs for the average query in less than 5 seconds (8.6 times faster than BLAST and gives nearly identical results. For hits above 70 bits, FastBLAST identifies 98% of the top 3,250 hits per query. CONCLUSIONS/SIGNIFICANCE: FastBLAST enables research groups that do not have supercomputers to analyze large protein sequence data sets. FastBLAST is open source software and is available at http://microbesonline.org/fastblast.

  12. Homologous Recombination in Protozoan Parasites and Recombinase Inhibitors

    Directory of Open Access Journals (Sweden)

    Andrew A. Kelso

    2017-09-01

    Full Text Available Homologous recombination (HR is a DNA double-strand break (DSB repair pathway that utilizes a homologous template to fully repair the damaged DNA. HR is critical to maintain genome stability and to ensure genetic diversity during meiosis. A specialized class of enzymes known as recombinases facilitate the exchange of genetic information between sister chromatids or homologous chromosomes with the help of numerous protein accessory factors. The majority of the HR machinery is highly conserved among eukaryotes. In many protozoan parasites, HR is an essential DSB repair pathway that allows these organisms to adapt to environmental conditions and evade host immune systems through genetic recombination. Therefore, small molecule inhibitors, capable of disrupting HR in protozoan parasites, represent potential therapeutic options. A number of small molecule inhibitors were identified that disrupt the activities of the human recombinase RAD51. Recent studies have examined the effect of two of these molecules on the Entamoeba recombinases. Here, we discuss the current understandings of HR in the protozoan parasites Trypanosoma, Leishmania, Plasmodium, and Entamoeba, and we review the small molecule inhibitors known to disrupt human RAD51 activity.

  13. Phenylbutyrate inhibits homologous recombination induced by camptothecin and methyl methanesulfonate.

    Science.gov (United States)

    Kaiser, Gitte S; Germann, Susanne M; Westergaard, Tine; Lisby, Michael

    2011-08-01

    Homologous recombination is accompanied by extensive changes to chromatin organization at the site of DNA damage. Some of these changes are mediated through acetylation/deacetylation of histones. Here, we show that recombinational repair of DNA damage induced by the anti-cancer drug camptothecin (CPT) and the alkylating agent methyl methanesulfonate (MMS) is blocked by sodium phenylbutyrate (PBA) in the budding yeast Saccharomyces cerevisiae. In particular, PBA suppresses CPT- and MMS-induced genetic recombination as well as DNA double-strand break repair during mating-type interconversion. Treatment with PBA is accompanied by a dramatic reduction in histone H4 lysine 8 acetylation. Live cell imaging of homologous recombination proteins indicates that repair of CPT-induced DNA damage is redirected to a non-recombinogenic pathway in the presence of PBA without loss in cell viability. In contrast, the suppression of MMS-induced recombination by PBA is accompanied by a dramatic loss in cell viability. Taken together, our results demonstrate that PBA inhibits DNA damage-induced homologous recombination likely by mediating changes in chromatin acetylation. Moreover, the combination of PBA with genotoxic agents can lead to different cell fates depending on the type of DNA damage inflicted. 2011 Elsevier B.V. All rights reserved.

  14. Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily

    Directory of Open Access Journals (Sweden)

    Marc Lenoir

    2015-10-01

    Full Text Available The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the largest protein superfamilies, and have diverged to regulate many different signaling proteins and modules such as Dbl homology (DH and Tec homology (TH domains. The ligands of approximately 70 PH domains have been validated by binding assays and complexed structures, allowing meaningful extrapolation across the entire superfamily. Here the Membrane Optimal Docking Area (MODA program is used at a genome-wide level to identify all membrane docking PH structures and map their lipid-binding determinants. In addition to the linear sequence motifs which are employed for phosphoinositide recognition, the three dimensional structural features that allow peripheral membrane domains to approach and insert into the bilayer are pinpointed and can be predicted ab initio. The analysis shows that conserved structural surfaces distinguish which PH domains associate with membrane from those that do not. Moreover, the results indicate that lipid-binding PH domains can be classified into different functional subgroups based on the type of membrane insertion elements they project towards the bilayer.

  15. Prefiltering Model for Homology Detection Algorithms on GPU.

    Science.gov (United States)

    Retamosa, Germán; de Pedro, Luis; González, Ivan; Tamames, Javier

    2016-01-01

    Homology detection has evolved over the time from heavy algorithms based on dynamic programming approaches to lightweight alternatives based on different heuristic models. However, the main problem with these algorithms is that they use complex statistical models, which makes it difficult to achieve a relevant speedup and find exact matches with the original results. Thus, their acceleration is essential. The aim of this article was to prefilter a sequence database. To make this work, we have implemented a groundbreaking heuristic model based on NVIDIA's graphics processing units (GPUs) and multicore processors. Depending on the sensitivity settings, this makes it possible to quickly reduce the sequence database by factors between 50% and 95%, while rejecting no significant sequences. Furthermore, this prefiltering application can be used together with multiple homology detection algorithms as a part of a next-generation sequencing system. Extensive performance and accuracy tests have been carried out in the Spanish National Centre for Biotechnology (NCB). The results show that GPU hardware can accelerate the execution times of former homology detection applications, such as National Centre for Biotechnology Information (NCBI), Basic Local Alignment Search Tool for Proteins (BLASTP), up to a factor of 4.

  16. Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily.

    Science.gov (United States)

    Lenoir, Marc; Kufareva, Irina; Abagyan, Ruben; Overduin, Michael

    2015-10-23

    The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH) domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the largest protein superfamilies, and have diverged to regulate many different signaling proteins and modules such as Dbl homology (DH) and Tec homology (TH) domains. The ligands of approximately 70 PH domains have been validated by binding assays and complexed structures, allowing meaningful extrapolation across the entire superfamily. Here the Membrane Optimal Docking Area (MODA) program is used at a genome-wide level to identify all membrane docking PH structures and map their lipid-binding determinants. In addition to the linear sequence motifs which are employed for phosphoinositide recognition, the three dimensional structural features that allow peripheral membrane domains to approach and insert into the bilayer are pinpointed and can be predicted ab initio. The analysis shows that conserved structural surfaces distinguish which PH domains associate with membrane from those that do not. Moreover, the results indicate that lipid-binding PH domains can be classified into different functional subgroups based on the type of membrane insertion elements they project towards the bilayer.

  17. Genetic selection and DNA sequences of 4.5S RNA homologs

    DEFF Research Database (Denmark)

    Brown, S; Thon, G; Tolentino, E

    1989-01-01

    A general strategy for cloning the functional homologs of an Escherichia coli gene was used to clone homologs of 4.5S RNA from other bacteria. The genes encoding these homologs were selected by their ability to complement a deletion of the gene for 4.5S RNA. DNA sequences of the regions encoding...

  18. Study on homologous series of induced early mutants in Indica rice Ⅱ. the relationship between the homologous series of early mutants induced and the ecotype in Indica rice

    International Nuclear Information System (INIS)

    Chen Xiulan; Yang Hefeng; He Zhentian; Han Yuepeng; Liu Xueyu

    2001-01-01

    The induced mutation in light sensitivity of the Indica rice leads to induction of the homologous series of early mutants along with the variation of ecological character and the ecoclimate. The induction of mutants was closely related to the ecotype of Indica rice, the homologous series of early mutants in different level were derived from the different ecotype of the Indica rice, otherwise, the similar homologous series of early mutants were derived from the same ecotypic variety. The induction of the early ecotypic variety derived from the homologous series of early mutants provides the basis and possibility for accelerating the development of the new cultivars. (authors)

  19. p53 regulates the repair of DNA double-strand breaks by both homologous and non-homologous recombination

    International Nuclear Information System (INIS)

    Willers, H.; Powell, S.N.; Dahm-Daphi, J.

    2003-01-01

    Full text: p53 is known to suppress spontaneous homologous recombination (HR), while its role in non-homologous recombination (NHR) remains to be clarified. Here, we sought to determine the influence of p53 on the repair of chromosomal double-strand breaks (DSBs) by HR or NHR using specially designed recombination substrates that integrate into the genome. Isogenic mouse fibroblast pairs with or without expression of exogenous p53 protein were utilized. A reporter plasmid carrying a mutated XGPRT gene was chromosomally integrated and DSBs were generated within the plasmid by the I-SceI endonuclease. Subsequent homology-mediated repair from an episomal donor resulted in XGPRT reconstitution and cellular resistance to a selection antibiotic. Analogously, the repair of chromosomal I-SceI breaks by NHR using another novel reporter plasmid restored XGPRT translation. For p53-null cells, the mean frequency of I-SceI break repair via HR was 5.5 x 10 -4 . The p53-Val135 mutant, which previously has been shown to suppress spontaneous HR by 14-fold employing the same cell system and reporter gene, only caused a 2- to 3-fold suppression of break-induced HR. In contrast, a dramatic effect of p53 on repair via NHR was found. Preliminary sequence analysis indicated that there was at least a 1000-fold reduction of illegitimate repair events resulting in loss of sequence at the break sites. The observed effects were mediated by p53 mutants defective in regulation of the cell-cycle and apoptosis. The main findings were: (1) p53 virtually blocked illegitimate rejoining of chromosomal ends. (2) The suppression of homologous DSB repair was less pronounced than the inhibition of spontaneous HR. We hypothesize that p53 allows to a certain extent error-free homology-dependent repair to proceed, while blocking error-prone NHR. The data support and extent a previous model, in which p53 maintains genomic stability by regulating recombination independently of its transactivation function

  20. Aircraft model prototypes which have specified handling-quality time histories

    Science.gov (United States)

    Johnson, S. H.

    1978-01-01

    Several techniques for obtaining linear constant-coefficient airplane models from specified handling-quality time histories are discussed. The pseudodata method solves the basic problem, yields specified eigenvalues, and accommodates state-variable transfer-function zero suppression. The algebraic equations to be solved are bilinear, at worst. The disadvantages are reduced generality and no assurance that the resulting model will be airplane like in detail. The method is fully illustrated for a fourth-order stability-axis small motion model with three lateral handling quality time histories specified. The FORTRAN program which obtains and verifies the model is included and fully documented.

  1. EGL-13/SoxD specifies distinct O2 and CO2 sensory neuron fates in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Jakob Gramstrup Petersen

    2013-05-01

    Full Text Available Animals harbor specialized neuronal systems that are used for sensing and coordinating responses to changes in oxygen (O2 and carbon dioxide (CO2. In Caenorhabditis elegans, the O2/CO2 sensory system comprises functionally and morphologically distinct sensory neurons that mediate rapid behavioral responses to exquisite changes in O2 or CO2 levels via different sensory receptors. How the diversification of the O2- and CO2-sensing neurons is established is poorly understood. We show here that the molecular identity of both the BAG (O2/CO2-sensing and the URX (O2-sensing neurons is controlled by the phylogenetically conserved SoxD transcription factor homolog EGL-13. egl-13 mutant animals fail to fully express the distinct terminal gene batteries of the BAG and URX neurons and, as such, are unable to mount behavioral responses to changes in O2 and CO2. We found that the expression of egl-13 is regulated in the BAG and URX neurons by two conserved transcription factors-ETS-5(Ets factor in the BAG neurons and AHR-1(bHLH factor in the URX neurons. In addition, we found that EGL-13 acts in partially parallel pathways with both ETS-5 and AHR-1 to direct BAG and URX neuronal fate respectively. Finally, we found that EGL-13 is sufficient to induce O2- and CO2-sensing cell fates in some cellular contexts. Thus, the same core regulatory factor, egl-13, is required and sufficient to specify the distinct fates of O2- and CO2-sensing neurons in C. elegans. These findings extend our understanding of mechanisms of neuronal diversification and the regulation of molecular factors that may be conserved in higher organisms.

  2. The colocalization transition of homologous chromosomes at meiosis

    Science.gov (United States)

    Nicodemi, Mario; Panning, Barbara; Prisco, Antonella

    2008-06-01

    Meiosis is the specialized cell division required in sexual reproduction. During its early stages, in the mother cell nucleus, homologous chromosomes recognize each other and colocalize in a crucial step that remains one of the most mysterious of meiosis. Starting from recent discoveries on the system molecular components and interactions, we discuss a statistical mechanics model of chromosome early pairing. Binding molecules mediate long-distance interaction of special DNA recognition sequences and, if their concentration exceeds a critical threshold, they induce a spontaneous colocalization transition of chromosomes, otherwise independently diffusing.

  3. Homology and cohomology of a class of polycyclic groups

    International Nuclear Information System (INIS)

    Majumdar, S.

    1984-11-01

    The homology and the cohomology of the class of polycyclic groups G given by generators h 1 , h 2 ,..., hsub(n+1) and relations h 2 -1 h 1 h 2 =h 1 sup(m 1 ),h 3 -1 h 2 h 3 =h 2 sup(m 2 ),..., hsub(n+1) -1 hsub(n) hsub(n+1)=hsub(n)sup(msub(n)) are determined through the construction of a suitable free ZG resolution for the trivial ZG module Z. (author)

  4. 46 CFR 199.610 - Exemptions for vessels in specified services.

    Science.gov (United States)

    2010-10-01

    ... Specified Services Section or paragraph in this part Service Oceans Coastwise Great Lakes Lakes, Bays, and... helpless person can be observed from the navigating bridge; and A(iii) the vessel does not regularly engage...

  5. A Benchmark for Comparing Different Approaches for Specifying and Verifying Real-Time Systems

    Science.gov (United States)

    1993-01-01

    To be considered correct or useful, real - time systems must deliver results within specified time intervals, either without exception or with high...probability. Recently, a large number of formal methods have been invented for specifying and verifying real - time systems . It has been suggested that...these formal methods need to be tested out on actual real - time systems . Such testing will allow the scalability of the methods to be assessed and also

  6. Impact of homologous recombination on individual cellular radiosensitivity

    International Nuclear Information System (INIS)

    Koch, Kerstin; Wrona, Agnieszka; Dikomey, Ekkehard; Borgmann, Kerstin

    2009-01-01

    Purpose: Individual radiosensitivity as measured with in vitro irradiated lymphocytes using metaphase analysis can predict the risk of normal tissue effects after radiotherapy. This parameter is considered to be primarily determined by the cellular repair capacity of DNA double-strand breaks (DSBs). It is now tested to which extent this capacity also depends on homologous recombination (HR), which is a pathway available when cells are in S/G2 phase. Methods: Experiments were performed with CHO K1 cells, in which HR was suppressed via knock-down of RAD51 using RNA interference (RNAi). RAD51 was measured via western and foci formation, cell survival by colony forming, DSBs by γH2AX foci formation, and chromosomal damage using PCC, G0 or G2 assay. Results: In quiescent G1 cells DSB repair is completed 6 h after irradiation. But there is still a substantial fraction of non-repaired DSBs. Most of these DSBs are repaired when G1 cells are stimulated into cell cycle. Suppression of HR by down-regulation of RAD51 did not affect this repair. In contrast, repair was inhibited when cells were irradiated in late S/G2. In line with these data down-regulation of HR did affect survival of cells irradiated in late S/G2, but not in G1. Conclusions: Individual radiosensitivity as measured for G0/1 cells using metaphase analysis does not depend on homologous recombination

  7. On discrete symmetries and torsion homology in F-theory

    Energy Technology Data Exchange (ETDEWEB)

    Mayrhofer, Christoph [Arnold-Sommerfeld-Center, Ludwig-Maximilians-Universität München,München (Germany); Palti, Eran; Till, Oskar; Weigand, Timo [Institut für Theoretische Physik, Ruprecht-Karls-Universität Heidelberg,Heidelberg (Germany)

    2015-06-04

    We study the relation between discrete gauge symmetries in F-theory compactifications and torsion homology on the associated Calabi-Yau manifold. Focusing on the simplest example of a ℤ{sub 2} symmetry, we show that there are two physically distinct ways that such a discrete gauge symmetry can arise. First, compactifications of M-Theory on Calabi-Yau threefolds which support a genus-one fibration with a bi-section are known to be dual to six-dimensional F-theory vacua with a ℤ{sub 2} gauge symmetry. We show that the resulting five-dimensional theories do not have a ℤ{sub 2} symmetry but that the latter emerges only in the F-theory decompactification limit. Accordingly the genus-one fibred Calabi-Yau manifolds do not exhibit torsion in homology. Associated to the bi-section fibration is a Jacobian fibration which does support a section. Compactifying on these related but distinct varieties does lead to a ℤ{sub 2} symmetry in five dimensions and, accordingly, we find explicitly an associated torsion cycle. We identify the expected particle and membrane system of the discrete symmetry in terms of wrapped M2 and M5 branes and present a field-theory description of the physics for both cases in terms of circle reductions of six-dimensional theories. Our results and methods generalise straightforwardly to larger discrete symmetries and to four-dimensional compactifications.

  8. Structural analysis of zwitterionic liquids vs. homologous ionic liquids

    Science.gov (United States)

    Wu, Boning; Kuroda, Kosuke; Takahashi, Kenji; Castner, Edward W.

    2018-05-01

    Zwitterionic liquids (Zw-ILs) have been developed that are homologous to monovalent ionic liquids (ILs) and show great promise for controlled dissolution of cellulosic biomass. Using both high energy X-ray scattering and atomistic molecular simulations, this article compares the bulk liquid structural properties for novel Zw-ILs with their homologous ILs. It is shown that the significant localization of the charges on Zw-ILs leads to charge ordering similar to that observed for conventional ionic liquids with monovalent anions and cations. A low-intensity first sharp diffraction peak in the liquid structure factor S(q) is observed for both the Zw-IL and the IL. This is unexpected since both the Zw-IL and IL have a 2-(2-methoxyethoxy)ethyl (diether) functional group on the cationic imidazolium ring and ether functional groups are known to suppress this peak. Detailed analyses show that this intermediate range order in the liquid structure arises for slightly different reasons in the Zw-IL vs. the IL. For the Zw-IL, the ether tails in the liquid are shown to aggregate into nanoscale domains.

  9. Gimeracil sensitizes cells to radiation via inhibition of homologous recombination

    International Nuclear Information System (INIS)

    Takagi, Masaru; Sakata, Koh-ichi; Someya, Masanori; Tauchi, Hiroshi; Iijima, Kenta; Matsumoto, Yoshihisa; Torigoe, Toshihiko; Takahashi, Akari; Hareyama, Masato; Fukushima, Masakazu

    2010-01-01

    Background and purpose: 5-Chloro-2,4-dihydroxypyridine (Gimeracil) is a component of an oral fluoropyrimidine derivative S-1. Gimeracil is originally added to S-1 to yield prolonged 5-FU concentrations in tumor tissues by inhibiting dihydropyrimidine dehydrogenase, which degrades 5-FU. We found that Gimeracil by itself had the radiosensitizing effect. Methods and materials: We used various cell lines deficient in non-homologous end-joining (NHEJ) or homologous recombination (HR) as well as DLD-1 and HeLa in clonogenic assay. γ-H2AX focus formation and SCneo assay was performed to examine the effects of Gimeracil on DNA double strand break (DSB) repair mechanisms. Results: Results of γ-H2AX focus assay indicated that Gimeracil inhibited DNA DSB repair. It did not sensitize cells deficient in HR but sensitized those deficient in NHEJ. In SCneo assay, Gimeracil reduced the frequency of neo-positive clones. Additionally, it sensitized the cells in S-phase more than in G0/G1. Conclusions: Gimeracil inhibits HR. Because HR plays key roles in the repair of DSBH caused by radiotherapy, Gimeracil may enhance the efficacy of radiotherapy through the suppression of HR-mediated DNA repair pathways.

  10. Protein homology model refinement by large-scale energy optimization.

    Science.gov (United States)

    Park, Hahnbeom; Ovchinnikov, Sergey; Kim, David E; DiMaio, Frank; Baker, David

    2018-03-20

    Proteins fold to their lowest free-energy structures, and hence the most straightforward way to increase the accuracy of a partially incorrect protein structure model is to search for the lowest-energy nearby structure. This direct approach has met with little success for two reasons: first, energy function inaccuracies can lead to false energy minima, resulting in model degradation rather than improvement; and second, even with an accurate energy function, the search problem is formidable because the energy only drops considerably in the immediate vicinity of the global minimum, and there are a very large number of degrees of freedom. Here we describe a large-scale energy optimization-based refinement method that incorporates advances in both search and energy function accuracy that can substantially improve the accuracy of low-resolution homology models. The method refined low-resolution homology models into correct folds for 50 of 84 diverse protein families and generated improved models in recent blind structure prediction experiments. Analyses of the basis for these improvements reveal contributions from both the improvements in conformational sampling techniques and the energy function.

  11. HOMOLOGY MODELING AND MOLECULAR DYNAMICS STUDY OF MYCOBACTERIUM TUBERCULOSIS UREASE

    Directory of Open Access Journals (Sweden)

    Lisnyak Yu. V.

    2017-10-01

    Full Text Available Introduction. M. tuberculosis urease (MTU is an attractive target for chemotherapeutic intervention in tuberculosis by designing new safe and efficient enzyme inhibitors. A prerequisite for designing such inhibitors is an understanding of urease's three-dimensional (3D structure organization. 3D structure of M. tuberculosis urease is unknown. When experimental three-dimensional structure of a protein is not known, homology modeling, the most commonly used computational structure prediction method, is the technique of choice. This paper aimed to build a 3D-structure of M. tuberculosis urease by homology modeling and to study its stability by molecular dynamics simulations. Materials and methods. To build MTU model, five high-resolution X-ray structures of bacterial ureases with three-subunit composition (2KAU, 5G4H, 4UBP, 4СEU, and 4EPB have been selected as templates. For each template five stochastic alignments were created and for each alignment, a three-dimensional model was built. Then, each model was energy minimized and the models were ranked by quality Z-score. The MTU model with highest quality estimation amongst 25 potential models was selected. To further improve structure quality the model was refined by short molecular dynamics simulation that resulted in 20 snapshots which were rated according to their energy and the quality Z-score. The best scoring model having minimum energy was chosen as a final homology model of 3D structure for M. tuberculosis. The final model of MTU was also validated by using PDBsum and QMEAN servers. These checks confirmed good quality of MTU homology model. Results and discussion. Homology model of MTU is a nonamer (homotrimer of heterotrimers, (αβγ3 consisting of 2349 residues. In MTU heterotrimer, sub-units α, β, and γ tightly interact with each other at a surface of approximately 3000 Å2. Sub-unit α contains the enzyme active site with two Ni atoms coordinated by amino acid residues His347, His

  12. Homologous recombination and non-homologous end-joining repair pathways in bovine embryos with different developmental competence

    International Nuclear Information System (INIS)

    Henrique Barreta, Marcos; Garziera Gasperin, Bernardo; Braga Rissi, Vitor; Cesaro, Matheus Pedrotti de; Ferreira, Rogério; Oliveira, João Francisco de; Gonçalves, Paulo Bayard Dias; Bordignon, Vilceu

    2012-01-01

    This study investigated the expression of genes controlling homologous recombination (HR), and non-homologous end-joining (NHEJ) DNA-repair pathways in bovine embryos of different developmental potential. It also evaluated whether bovine embryos can respond to DNA double-strand breaks (DSBs) induced with ultraviolet irradiation by regulating expression of genes involved in HR and NHEJ repair pathways. Embryos with high, intermediate or low developmental competence were selected based on the cleavage time after in vitro insemination and were removed from in vitro culture before (36 h), during (72 h) and after (96 h) the expected period of embryonic genome activation. All studied genes were expressed before, during and after the genome activation period regardless the developmental competence of the embryos. Higher mRNA expression of 53BP1 and RAD52 was found before genome activation in embryos with low developmental competence. Expression of 53BP1, RAD51 and KU70 was downregulated at 72 h and upregulated at 168 h post-insemination in response to DSBs induced by ultraviolet irradiation. In conclusion, important genes controlling HR and NHEJ DNA-repair pathways are expressed in bovine embryos, however genes participating in these pathways are only regulated after the period of embryo genome activation in response to ultraviolet-induced DSBs.

  13. Homologous recombination and non-homologous end-joining repair pathways in bovine embryos with different developmental competence

    Energy Technology Data Exchange (ETDEWEB)

    Henrique Barreta, Marcos [Universidade Federal de Santa Catarina, Campus Universitario de Curitibanos, Curitibanos, SC (Brazil); Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS (Brazil); Garziera Gasperin, Bernardo; Braga Rissi, Vitor; Cesaro, Matheus Pedrotti de [Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS (Brazil); Ferreira, Rogerio [Centro de Educacao Superior do Oeste-Universidade do Estado de Santa Catarina, Chapeco, SC (Brazil); Oliveira, Joao Francisco de; Goncalves, Paulo Bayard Dias [Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS (Brazil); Bordignon, Vilceu, E-mail: vilceu.bordignon@mcgill.ca [Department of Animal Science, McGill University, Ste-Anne-De-Bellevue, QC (Canada)

    2012-10-01

    This study investigated the expression of genes controlling homologous recombination (HR), and non-homologous end-joining (NHEJ) DNA-repair pathways in bovine embryos of different developmental potential. It also evaluated whether bovine embryos can respond to DNA double-strand breaks (DSBs) induced with ultraviolet irradiation by regulating expression of genes involved in HR and NHEJ repair pathways. Embryos with high, intermediate or low developmental competence were selected based on the cleavage time after in vitro insemination and were removed from in vitro culture before (36 h), during (72 h) and after (96 h) the expected period of embryonic genome activation. All studied genes were expressed before, during and after the genome activation period regardless the developmental competence of the embryos. Higher mRNA expression of 53BP1 and RAD52 was found before genome activation in embryos with low developmental competence. Expression of 53BP1, RAD51 and KU70 was downregulated at 72 h and upregulated at 168 h post-insemination in response to DSBs induced by ultraviolet irradiation. In conclusion, important genes controlling HR and NHEJ DNA-repair pathways are expressed in bovine embryos, however genes participating in these pathways are only regulated after the period of embryo genome activation in response to ultraviolet-induced DSBs.

  14. Dynamics of Cellular Proliferation during 'Acute Homologous Disease' in Mice

    Energy Technology Data Exchange (ETDEWEB)

    Vitale, B.; Silobrcic, V.; Jurin, M.; Matosic, M.; Tomazic, Vesna [Laboratory for Transplantation and Tumour Immunology, Department of Biology, Institute Ruder Boskovic, Zagreb, Yugoslavia (Croatia)

    1968-08-15

    CBA mice, lethally irradiated and injected with 20 x 10{sup 6} bone-marrow cells derived from C57BL donors, develop a chronic form of 'homologous disease' and die between 20 and 40 days after treatment. If 10 x 10{sup 6} lymph node cells are added to the bone-marrow suspension, all recipients develop 'acute' homologous disease and die 6 to 10 days after irradiation. Different parameters of the disease were systematically observed. Among them, changes in spleen weight indicated early cell proliferation, which reached its maximum on day 4 and progressively decreased later on. Chromosomal analysis showed that all dividing cells in the spleen were of donor origin. Their number decreased concomitantly with the shrinkage and devastation of the organ, which started on day 6. The period of devastation of the spleen fully corresponds to the time in which all animals die. The use of cyclophosphamide in the treatment of 'acute' homologous disease transformed the disease into a chronic form with a mortality very similar to that obtained when only bone-marrow cells were injected. Among other effects, treatment with cyclophosphamide prevented early proliferation of donor cells in the spleen, and delayed spleen weight increase for about 10 days. After that period spleen weight increased, reaching its maximum on day 12. At first only donor type cells could be detected, but towards the end of the period in which spleen weight increase was registered host type cells appeared among the cells in mitosis. Their number gradually increased, and in some cases the majority or all of the dividing cells were of the host type. After a transitional decrease in spleen weight, another peak in cellular proliferation consisting of either host or donor or both types of cells was observed about day 30. In spite of the observed irregularities in the origin of dividing cells, all animals died by day 40 after application of cyclophosphamide. The relationship between proliferation of injected lymph node

  15. Caffeine suppresses homologous recombination through interference with RAD51-mediated joint molecule formation

    Science.gov (United States)

    Zelensky, Alex N.; Sanchez, Humberto; Ristic, Dejan; Vidic, Iztok; van Rossum-Fikkert, Sari E.; Essers, Jeroen; Wyman, Claire; Kanaar, Roland

    2013-01-01

    Caffeine is a widely used inhibitor of the protein kinases that play a central role in the DNA damage response. We used chemical inhibitors and genetically deficient mouse embryonic stem cell lines to study the role of DNA damage response in stable integration of the transfected DNA and found that caffeine rapidly, efficiently and reversibly inhibited homologous integration of the transfected DNA as measured by several homologous recombination-mediated gene-targeting assays. Biochemical and structural biology experiments revealed that caffeine interfered with a pivotal step in homologous recombination, homologous joint molecule formation, through increasing interactions of the RAD51 nucleoprotein filament with non-homologous DNA. Our results suggest that recombination pathways dependent on extensive homology search are caffeine-sensitive and stress the importance of considering direct checkpoint-independent mechanisms in the interpretation of the effects of caffeine on DNA repair. PMID:23666627

  16. Future trypanosomatid phylogenies: refined homologies, supertrees and networks

    Directory of Open Access Journals (Sweden)

    Stothard JR

    2000-01-01

    Full Text Available There has been good progress in inferring the evolutionary relationships within trypanosomes from DNA data as until relatively recently, many relationships have remained rather speculative. Ongoing molecular studies have provided data that have adequately shown Trypanosoma to be monophyletic and, rather surprisingly, that there are sharply contrasting levels of genetic variation within and between the major trypanosomatid groups. There are still, however, areas of research that could benefit from further development and resolution that broadly fall upon three questions. Are the current statements of evolutionary homology within ribosomal small sub-unit genes in need of refinement? Can the published phylograms be expanded upon to form `supertrees' depicting further relationships? Does a bifurcating tree structure impose an untenable dogma upon trypanosomatid phylogeny where hybridisation or reticulate evolutionary steps have played a part? This article briefly addresses these three questions and, in so doing, hopes to stimulate further interest in the molecular evolution of the group.

  17. Development and homology of the incisor teeth in the rabbit

    International Nuclear Information System (INIS)

    Muylle, S.; Simoens, P.; Lauwers, H.

    1996-01-01

    The morphology and development of the incisors were investigated stercomicroscopically, radiographically and by means of serial histologic sections in fetal, juvenile and adult New Zealand White rabbits. A vestigial and a major incisor develop on both sides of the upper and of the lower jaw, while a diphyodont minor incisor is located caudal to the major incisor on both sides of the upper jaw. The present study describes a unique case of incisor polyodontia in an adult wild rabbit, that exhibited all the characteristics of a typical atavistic dentition. From these observations it was deduced that the vestigial and the major incisors in the rabbit are monophyodont and correspond to the first and second incisors respectively, while the minor diphyodont incisor in the upper jaw is homologous with the third incisor

  18. Development and characterization of a homologous radioimmunoassay for equine prolactin

    International Nuclear Information System (INIS)

    Roser, J.F.; Chang, Y.S.; Papkoff, H.; Li, C.H.

    1984-01-01

    A specific and sensitive homologous radioimmunoassay has been developed for equine prolactin, suitable for measuring prolactin concentrations in serum of horses. The sensitivity of the assay ranged from 0.4 to 0.6 ng/ml and the intra- and inter-assay coefficients of variation averaged 6.9 and 15.4%, respectively, for five doses of hormone. Cross-reactivity with other mammalian and nonmammalian prolactins and growth hormones was less than 20 and 0.3%, respectively. Cross-reactivity with equine growth hormone was less than 0.07%. Equine serum and pituitary extracts showed parallel dilution-response curves with equine prolactin. The percentage recovery of exogenous equine prolactin in serum was 89%. Preliminary analysis of several physiological samples (stallions, pregnant, and nonpregnant mares) yielded values from 0.6 to 12.0 ng/ml

  19. Identification of rodent homologs of hepatitis C virus and pegiviruses

    DEFF Research Database (Denmark)

    Kapoor, Amit; Simmonds, Peter; Scheel, Troels K H

    2013-01-01

    UNLABELLED: Hepatitis C virus (HCV) and human pegivirus (HPgV or GB virus C) are globally distributed and infect 2 to 5% of the human population. The lack of tractable-animal models for these viruses, in particular for HCV, has hampered the study of infection, transmission, virulence, immunity...... into the origins of human infections and enhances our ability to study their pathogenesis and explore preventive and therapeutic interventions. Horses are the only reported host of nonprimate homologs of hepatitis C virus (HCV). Here, we report the discovery of HCV-like viruses in wild rodents. The majority of HCV...... of small-animal models for HCV, the most common infectious cause of liver failure and hepatocellular carcinoma after hepatitis B virus, and help to explore the health relevance of the highly prevalent human pegiviruses....

  20. The tedious task of finding homologous noncoding RNA genes

    DEFF Research Database (Denmark)

    Menzel, Karl Peter; Gorodkin, Jan; Stadler, Peter F

    2009-01-01

    User-driven in silico RNA homology search is still a nontrivial task. In part, this is the consequence of a limited precision of the computational tools in spite of recent exciting progress in this area, and to a certain extent, computational costs are still problematic in practice. An important......, and as we argue here, dominating issue is the dependence on good curated (secondary) structural alignments of the RNAs. These are often hard to obtain, not so much because of an inherent limitation in the available data, but because they require substantial manual curation, an effort that is rarely...... acknowledged. Here, we qualitatively describe a realistic scenario for what a "regular user" (i.e., a nonexpert in a particular RNA family) can do in practice, and what kind of results are likely to be achieved. Despite the indisputable advances in computational RNA biology, the conclusion is discouraging...

  1. On the homology of the shoulder girdle in turtles.

    Science.gov (United States)

    Nagashima, Hiroshi; Sugahara, Fumiaki; Takechi, Masaki; Sato, Noboru; Kuratani, Shigeru

    2015-05-01

    The shoulder girdle in turtles is encapsulated in the shell and has a triradiate morphology. Due to its unique configuration among amniotes, many theories have been proposed about the skeletal identities of the projections for the past two centuries. Although the dorsal ramus represents the scapular blade, the ventral two rami remain uncertain. In particular, the ventrorostral process has been compared to a clavicle, an acromion, and a procoracoid based on its morphology, its connectivity to the rest of the skeleton and to muscles, as well as with its ossification center, cell lineage, and gene expression. In making these comparisons, the shoulder girdle skeleton of anurans has often been used as a reference. This review traces the history of the debate on the homology of the shoulder girdle in turtles. And based on the integrative aspects of developmental biology, comparative morphology, and paleontology, we suggest acromion and procoracoid identities for the two ventral processes. © 2014 Wiley Periodicals, Inc.

  2. Homology of yeast photoreactivating gene fragment with human genomic digests

    International Nuclear Information System (INIS)

    Meechan, P.J.; Milam, K.M.; Cleaver, J.E.

    1984-01-01

    Enzymatic photoreactivation of UV-induced DNA lesions has been demonstrated for a variety of prokaryotic and eukaryotic organisms. Its presence in placental mammals, however, has not been clearly established. The authors attempted to resolve this question by assaying for the presence (or absence) of sequences in human DNA complimentary to a fragment of the photoreactivating gene from S. cerevisiae that has recently been cloned. In another study, DNA from human, chick E. coli and yeast cells was digested with either HindIII of BglII, electrophoresed on a 0.5% agarose gel, transferred (Southern blot) to a nylon membrane and probed for homology against a Sau3A restriction fragment from S. cerevisiae that compliments phr/sup -/ cells. Hybridization to human DNA digests was observed only under relatively non-stringent conditions indicating the gene is not conserved in placental mammals. These results are correlated with current literature data concerning photoreactivating enzymes

  3. Internal and External Reconnection Series Homologous Solar Flares

    Science.gov (United States)

    Sterling, Alphonse C.; Moore, Ronald L.

    2001-01-01

    Using data from the extreme ultraviolet imaging telescope (EIT) on SOHO and the soft X-ray telescope (SXT) on Yohkoh, we examine a series of morphologically homologous solar flares occurring in National Oceanic and Atmospheric Administration (NOAA) active region 8210 over May 1-2, 1998. An emerging flux region (EFR) impacted against a sunspot to the west and next to a coronal hole to the east is the source of the repeated flaring. An SXT sigmoid parallels the EFR's neutral line at the site of the initial flaring in soft X rays. In EIT each flaring episode begins with the formation of a crinkle pattern external to the EFR. These EIT crinkles move out from, and then in toward, the EFR with velocities approx. 20 km/ s. A shrinking and expansion of the width of the coronal hole coincides with the crinkle activity, and generation and evolution of a postflare loop system begins near the time of crinkle formation. Using a schematic based on magnetograms of the region, we suggest that these observations are consistent with the standard reconnection-based model for solar eruptions but are modified by the presence of the additional magnetic fields of the sunspot and coronal hole. In the schematic, internal reconnection begins inside of the EFR-associated fields, unleashing a flare, postflare loops, and a coronal mass ejection (CME). External reconnection, first occurring between the escaping CME and the coronal hole field and second occurring between fields formed as a result of the first external reconnection, results in the EIT crinkles and changes in the coronal hole boundary. By the end of the second external reconnection, the initial setup is reinstated; thus the sequence can repeat, resulting in morphologically homologous eruptions. Our inferred magnetic topology is similar to that suggested in the "breakout model" of eruptions although we cannot determine if our eruptions are released primarily by the breakout mechanism (external reconnection) or, alternatively

  4. Function of Rad51 paralogs in eukaryotic homologous recombinational repair

    International Nuclear Information System (INIS)

    Liu, N.; Skowronek, K.

    2003-01-01

    Full text: Homologous recombinational repair (HRR) is an important mechanism for maintaining genetic integrity and cancer prevention by accurately repair of DNA double strand breaks induced by environmental insults or occurred in DNA replication. A critical step in HRR is the polymerization of Rad51 on single stranded DNA to form nuclear protein filaments, the later conduct DNA strand paring and exchange between homologous strands. A number of proteins, including replication protein A (RPA), Rad52 and Rad51 paralogs, are suggested to modulate or facilitate the process of Rad51 filament formation. Five Rad51 paralogs, namely XRCC2, XRCC3, Rad51B, Rad51C and Rad51D have been identified in eucaryotic cells. These proteins show distant protein sequence identity to Rad51, to yeast Rad51 paralogs (Rad55 and Rad57) and to each other. Hamster or chicken mutants of Rad51 paralogs exhibit hypersensitivity to a variety of DNA damaging agents, especially cross-linking agents, and are defective in assembly of Rad51 onto HRR site after DNA damage. Recent data from our and other labs showed that Rad51 paralogs constitute two distinct complexes in cell extracts, one contains XRCC2, Rad51B, Rad51C and Rad51D, and the other contains Rad51C and XRCC3. Rad51C is involved in both complexes. Our results also showed that XRCC3-Rad51C complex interacts with Rad51 in vivo. Furthermore, overexpression of Rad52 can partially suppress the hypersensitivity of XRCC2 mutant irs1 to ionizing radiation and corrected the defects in Rad51 focus formation. These results suggest that XRCC2 and other Rad51 paralogs play a mediator function to Rad51 in the early stage of HRR

  5. DNA damage, homology-directed repair, and DNA methylation.

    Directory of Open Access Journals (Sweden)

    Concetta Cuozzo

    2007-07-01

    Full Text Available To explore the link between DNA damage and gene silencing, we induced a DNA double-strand break in the genome of Hela or mouse embryonic stem (ES cells using I-SceI restriction endonuclease. The I-SceI site lies within one copy of two inactivated tandem repeated green fluorescent protein (GFP genes (DR-GFP. A total of 2%-4% of the cells generated a functional GFP by homology-directed repair (HR and gene conversion. However, approximately 50% of these recombinants expressed GFP poorly. Silencing was rapid and associated with HR and DNA methylation of the recombinant gene, since it was prevented in Hela cells by 5-aza-2'-deoxycytidine. ES cells deficient in DNA methyl transferase 1 yielded as many recombinants as wild-type cells, but most of these recombinants expressed GFP robustly. Half of the HR DNA molecules were de novo methylated, principally downstream to the double-strand break, and half were undermethylated relative to the uncut DNA. Methylation of the repaired gene was independent of the methylation status of the converting template. The methylation pattern of recombinant molecules derived from pools of cells carrying DR-GFP at different loci, or from an individual clone carrying DR-GFP at a single locus, was comparable. ClustalW analysis of the sequenced GFP molecules in Hela and ES cells distinguished recombinant and nonrecombinant DNA solely on the basis of their methylation profile and indicated that HR superimposed novel methylation profiles on top of the old patterns. Chromatin immunoprecipitation and RNA analysis revealed that DNA methyl transferase 1 was bound specifically to HR GFP DNA and that methylation of the repaired segment contributed to the silencing of GFP expression. Taken together, our data support a mechanistic link between HR and DNA methylation and suggest that DNA methylation in eukaryotes marks homologous recombined segments.

  6. Meta-Analysis and Systematic Review to Assess the Role of Soluble FMS-Like Tyrosine Kinase-1 and Placenta Growth Factor Ratio in Prediction of Preeclampsia: The SaPPPhirE Study.

    Science.gov (United States)

    Agrawal, Swati; Cerdeira, Ana Sofia; Redman, Christopher; Vatish, Manu

    2018-02-01

    Preeclampsia is a major cause of morbidity and mortality worldwide. Numerous candidate biomarkers have been proposed for diagnosis and prediction of preeclampsia. Measurement of maternal circulating angiogenesis biomarker as the ratio of sFlt-1 (soluble FMS-like tyrosine kinase-1; an antiangiogenic factor)/PlGF (placental growth factor; an angiogenic factor) reflects the antiangiogenic balance that characterizes incipient or overt preeclampsia. The ratio increases before the onset of the disease and thus may help in predicting preeclampsia. We conducted a meta-analysis to explore the predictive accuracy of sFlt-1/PlGF ratio in preeclampsia. We included 15 studies with 534 cases with preeclampsia and 19 587 controls. The ratio has a pooled sensitivity of 80% (95% confidence interval, 0.68-0.88), specificity of 92% (95% confidence interval, 0.87-0.96), positive likelihood ratio of 10.5 (95% confidence interval, 6.2-18.0), and a negative likelihood ratio of 0.22 (95% confidence interval, 0.13-0.35) in predicting preeclampsia in both high- and low-risk patients. Most of the studies have not made a distinction between early- and late-onset disease, and therefore, the analysis for it could not be done. It can prove to be a valuable screening tool for preeclampsia and may also help in decision-making, treatment stratification, and better resource allocation. © 2017 American Heart Association, Inc.

  7. Oral Region Homologies in Paleozoic Crinoids and Other Plesiomorphic Pentaradial Echinoderms

    OpenAIRE

    Kammer, Thomas W.; Sumrall, Colin D.; Zamora, Samuel; Ausich, William I.; Deline, Bradley

    2013-01-01

    The phylogenetic relationships between major groups of plesiomorphic pentaradial echinoderms, the Paleozoic crinoids, blastozoans, and edrioasteroids, are poorly understood because of a lack of widely recognized homologies. Here, we present newly recognized oral region homologies, based on the Universal Elemental Homology model for skeletal plates, in a wide range of fossil taxa. The oral region of echinoderms is mainly composed of the axial, or ambulacral, skeleton, which apparently evolved ...

  8. Dnd Is a Critical Specifier of Primordial Germ Cells in the Medaka Fish

    Directory of Open Access Journals (Sweden)

    Ni Hong

    2016-03-01

    Full Text Available Primordial germ cell (PGC specification occurs early in development. PGC specifiers have been identified in Drosophila, mouse, and human but remained elusive in most animals. Here we identify the RNA-binding protein Dnd as a critical PGC specifier in the medaka fish (Oryzias latipes. Dnd depletion specifically abolished PGCs, and its overexpression boosted PGCs. We established a single-cell culture procedure enabling lineage tracing in vitro. We show that individual blastomeres from cleavage embryos at the 32- and 64-cell stages are capable of PGC production in culture. Importantly, Dnd overexpression increases PGCs via increasing PGC precursors. Strikingly, dnd RNA forms prominent particles that segregate asymmetrically. Dnd concentrates in germ plasm and stabilizes germ plasm RNA. Therefore, Dnd is a critical specifier of fish PGCs and utilizes particle partition as a previously unidentified mechanism for asymmetric segregation. These findings offer insights into PGC specification and manipulation in medaka as a lower vertebrate model.

  9. The Drosophila T-box transcription factor Midline functions within the Notch–Delta signaling pathway to specify sensory organ precursor cell fates and regulates cell survival within the eye imaginal disc

    Science.gov (United States)

    Das, Sudeshna; Chen, Q. Brent; Saucier, Joseph D.; Drescher, Brandon; Zong, Yan; Morgan, Sarah; Forstall, John; Meriwether, Andrew; Toranzo, Randy; Leal, Sandra M.

    2014-01-01

    We report that the T-box transcription factor Midline (Mid), an evolutionary conserved homolog of the vertebrate Tbx20 protein, functions within the Notch–Delta signaling pathway essential for specifying the fates of sensory organ precursor cells. This complements an established history of research showing that Mid regulates the cell-fate specification of diverse cell types within the developing heart, epidermis and central nervous system. Tbx20 has been detected in diverse neuronal and epithelial cells of embryonic eye tissues in both mice and humans. However, the mechanisms by which either Mid or Tbx20 function to regulate cell-fate specification or other critical aspects of eye development including cell survival have not yet been elucidated. We have also gathered preliminary evidence suggesting that Mid may play an indirect, but vital role in selecting SOP cells within the third-instar larval eye disc by regulating the expression of the proneural gene atonal. During subsequent pupal stages, Mid specifies SOP cell fates as a member of the Notch–Delta signaling hierarchy and is essential for maintaining cell viability within by inhibiting apoptotic pathways. We present several new hypotheses that seek to understand the role of Mid in regulating developmental processes downstream of the Notch receptor that are critical for specifying unique cell fates, patterning the adult eye and maintaining cellular homeostasis during eye disc morphogenesis. PMID:23962751

  10. The Drosophila T-box transcription factor Midline functions within the Notch-Delta signaling pathway to specify sensory organ precursor cell fates and regulates cell survival within the eye imaginal disc.

    Science.gov (United States)

    Das, Sudeshna; Chen, Q Brent; Saucier, Joseph D; Drescher, Brandon; Zong, Yan; Morgan, Sarah; Forstall, John; Meriwether, Andrew; Toranzo, Randy; Leal, Sandra M

    2013-01-01

    We report that the T-box transcription factor Midline (Mid), an evolutionary conserved homolog of the vertebrate Tbx20 protein, functions within the Notch-Delta signaling pathway essential for specifying the fates of sensory organ precursor (SOP) cells. These findings complement an established history of research showing that Mid regulates the cell-fate specification of diverse cell types within the developing heart, epidermis and central nervous system. Tbx20 has been detected in unique neuronal and epithelial cells of embryonic eye tissues in both mice and humans. However, the mechanisms by which either Mid or Tbx20 function to regulate cell-fate specification or other critical aspects of eye development including cell survival have not yet been elucidated. We have also gathered preliminary evidence suggesting that Mid may play an indirect, but vital role in selecting SOP cells within the third-instar larval eye disc by regulating the expression of the proneural gene atonal. During subsequent pupal stages, Mid specifies SOP cell fates as a member of the Notch-Delta signaling hierarchy and is essential for maintaining cell viability by inhibiting apoptotic pathways. We present several new hypotheses that seek to understand the role of Mid in regulating developmental processes downstream of the Notch receptor that are critical for specifying unique cell fates, patterning the adult eye and maintaining cellular homeostasis during eye disc morphogenesis. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  11. Homologous series of induced early mutants in Indica rice. Pt.3: The relationship between the induction of homologous series of early mutants and its different pedigree

    International Nuclear Information System (INIS)

    Chen Xiulan; Yang Hefeng; He Zhentian; Han Yuepeng; Liu Xueyu

    2002-01-01

    The percentage of homologous series of early mutants (PHSEM) induced by irradiation was closely related to its pedigree. This study showed that PHSEM for varieties with the same pedigree were similar, and there were three different level of dominance (high, low and normal) in the homologous series induced from different pedigree. The PHSEM for varieties derived form distant-relative-parents were higher than that derived from close-relative-parents. There was the dominance pedigree for the induction of homologous series of early mutants. IR8(Peta x DGWG), IR127 (Cpslo x Sigadis) and IR24 (IR8 x IR127) were dominant pedigree, and varieties derived from them could be easily induced the homologous series of early mutants

  12. Purging behavior in anorexia nervosa and eating disorder not otherwise specified

    DEFF Research Database (Denmark)

    Støving, René Klinkby; Andries, Alin; Brixen, Kim Torsten

    2012-01-01

    Purging behavior in eating disorders is associated with medical risks. We aimed to compare remission rates in purging and non-purging females with anorexia nervosa (AN) and eating disorder not otherwise specified (EDNOS) in a large retrospective single center cohort. A total of 339 patients...

  13. Understanding and Specifying Information Security Needs to Support the Delivery of High Quality Security Services

    NARCIS (Netherlands)

    Su, X.; Bolzoni, D.; van Eck, Pascal

    2006-01-01

    In this paper we present an approach for specifying and prioritizing information security requirements in organizations. It is important to prioritize security requirements since hundred per cent security is not achievable and the limited resources available should be directed to satisfy the most

  14. A Business Goal Driven Approach for Understanding and Specifying Information Security Requirements

    NARCIS (Netherlands)

    Su, X.; Bolzoni, D.; van Eck, Pascal

    In this paper we present an approach for specifying and prioritizing information security requirements in organizations. It is important to prioritize security requirements since hundred per cent security is not achievable and the limited resources available should be directed to satisfy the most

  15. Understanding and Specifying Information Security Needs to Support the Delivery of High Quality Security Services

    NARCIS (Netherlands)

    Su, X.; Bolzoni, D.; van Eck, Pascal

    2007-01-01

    In this paper we present an approach for specifying and prioritizing information security requirements in organizations. It is important to prioritize security requirements since hundred per cent security is not achievable and the limited resources available should be directed to satisfy the most

  16. 75 FR 43137 - Notice of Request for Revision of a Currently Approved Information Collection (Specified Risk...

    Science.gov (United States)

    2010-07-23

    ... via Listserv, a free e-mail subscription service consisting of industry, trade, and farm groups... addition, FSIS offers an e-mail subscription service which provides automatic and customized access to... approved information collection, Specified Risk Materials--Transport. DATES: Comments on this notice must...

  17. A bioinformatics approach to the development of immunoassays for specified risk material in canned meat products

    NARCIS (Netherlands)

    Reece, P.; Bremer, M.G.E.G.; Stones, R.; Danks, C.; Baumgartner, S.; Tomkies, V.; Hemetsberger, C.; Smits, N.G.E.; Lubbe, W.

    2009-01-01

    A bioinformatics approach to developing antibodies to specific proteins has been evaluated for the production of antibodies to heat-processed specified risk tissues from ruminants (brain and eye tissue). The approach involved the identification of proteins specific to ruminant tissues by

  18. An exploration of person perception abilities in children with a pervasive developmental disorder not otherwise specified

    NARCIS (Netherlands)

    Serra, M.; Minderaa, R.B; Van Geert, P. L. C.; Jackson, A.E.

    1995-01-01

    This explorative study investigates differences in person perception abilities between a group of children diagnosed as having a Pervasive Developmental Disorder Not Otherwise Specified (PDDNOS) and a group of normal children of the same age and sex. Person perception, a social-cognitive skill,

  19. 76 FR 18167 - Takes of Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the...

    Science.gov (United States)

    2011-04-01

    ..., many marine animals may need to remain in areas where they are exposed to chronic stimuli (Richardson... Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the Central Gulf of Alaska, June, 2011 AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric...

  20. 78 FR 34047 - Takes of Marine Mammals Incidental to Specified Activities; Navy Research, Development, Test and...

    Science.gov (United States)

    2013-06-06

    ... levels for these animals may be estimated using TTS data from marine mammals and relationships between... Marine Mammals Incidental to Specified Activities; Navy Research, Development, Test and Evaluation Activities at the Naval Surface Warfare Center Panama City Division AGENCY: National Marine Fisheries Service...

  1. 76 FR 77782 - Takes of Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the...

    Science.gov (United States)

    2011-12-14

    ..., 1963), but because of ecological or physiological requirements, many marine animals may need to remain... Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the Commonwealth of the Northern Mariana Islands, February to March 2012 AGENCY: National Marine Fisheries Service (NMFS), National...

  2. 77 FR 4765 - Takes of Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the...

    Science.gov (United States)

    2012-01-31

    ... physiological requirements, many marine animals may need to remain in areas where they are exposed to chronic... readily audible to the animals based on measured received levels and the hearing sensitivity of the marine... Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the Northwest Pacific...

  3. 78 FR 17359 - Takes of Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the...

    Science.gov (United States)

    2013-03-21

    ..., 1963), but because of ecological or physiological requirements, many marine animals may need to remain... Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the Northeast Atlantic Ocean, June to July, 2013 AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and...

  4. 76 FR 33246 - Takes of Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the...

    Science.gov (United States)

    2011-06-08

    ... ecological or physiological requirements, many marine animals may need to remain in areas where they are... Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the Central-Western Bering Sea, August 2011 AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and...

  5. 75 FR 8652 - Incidental Takes of Marine Mammals During Specified Activities; Marine Geophysical Survey in the...

    Science.gov (United States)

    2010-02-25

    ... for marine animals before and during airgun operations. NMFS believes that the realistic possibility... Takes of Marine Mammals During Specified Activities; Marine Geophysical Survey in the Commonwealth of the Northern Mariana Islands, April to June 2010 AGENCY: National Marine Fisheries Service (NMFS...

  6. 77 FR 25966 - Takes of Marine Mammals Incidental to Specified Activities; Three Marine Geophysical Surveys in...

    Science.gov (United States)

    2012-05-02

    ..., 1963), but because of ecological or physiological requirements, many marine animals may need to remain... Marine Mammals Incidental to Specified Activities; Three Marine Geophysical Surveys in the Northeast Pacific Ocean, June Through July 2012 AGENCY: National Marine Fisheries Service, National Oceanic and...

  7. 78 FR 47282 - Takes of Marine Mammals Incidental to Specified Activities; Navy Research, Development, Test and...

    Science.gov (United States)

    2013-08-05

    ..., and location) and marine mammal and/or indicator presence, species, number of animals, their behavior... Marine Mammals Incidental to Specified Activities; Navy Research, Development, Test and Evaluation Activities at the Naval Surface Warfare Center Panama City Division AGENCY: National Marine Fisheries Service...

  8. 76 FR 6430 - Takes of Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the...

    Science.gov (United States)

    2011-02-04

    ..., many marine animals may need to remain in areas where they are exposed to chronic stimuli (Richardson... Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the Pacific Ocean off Costa Rica, April Through May, 2011 AGENCY: National Marine Fisheries Service (NMFS), National Oceanic...

  9. 76 FR 57959 - Takes of Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the...

    Science.gov (United States)

    2011-09-19

    ..., many marine animals may need to remain in areas where they are exposed to chronic stimuli (Richardson... Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the Central Pacific Ocean, November, 2011 Through January, 2012 AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and...

  10. 77 FR 58255 - Takes of Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey off the...

    Science.gov (United States)

    2012-09-19

    ... requirements, many marine animals may need to remain in areas where they are exposed to chronic stimuli... Vol. 77 Wednesday, No. 182 September 19, 2012 Part III Department of Commerce Takes of Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey off the Central Coast of California...

  11. 78 FR 33357 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to...

    Science.gov (United States)

    2013-06-04

    ... confidence in these values is unknown. Table 3--Marine Mammal Density Estimates Density Species (animals/km\\2... unintentional taking of marine animals occurring incidental to the shock testing which involved large explosives... Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental to Conducting...

  12. Public Key Encryption Supporting Plaintext Equality Test and User-Specified Authorization

    NARCIS (Netherlands)

    Tang, Qiang

    2011-01-01

    In this paper we investigate a category of public key encryption schemes which supports plaintext equality test and user-specified authorization. With this new primitive, two users, who possess their own public/private key pairs, can issue token(s) to a proxy to authorize it to perform plaintext

  13. Using the ACT-R architecture to specify 39 quantitative process models of decision making

    NARCIS (Netherlands)

    Marewski, Julian N.; Mehlhorn, Katja

    Hypotheses about decision processes are often formulated qualitatively and remain silent about the interplay of decision, memorial, and other cognitive processes. At the same time, existing decision models are specified at varying levels of detail, making it difficult to compare them. We provide a

  14. 76 FR 23306 - Takes of Marine Mammals Incidental to Specified Activities; Russian River Estuary Management...

    Science.gov (United States)

    2011-04-26

    ... Marine Mammals Incidental to Specified Activities; Russian River Estuary Management Activities AGENCY...) to incidentally harass, by Level B harassment only, three species of marine mammals during estuary... December 31, 2010; and Russian River Estuary Outlet Channel Adaptive Management Plan. NMFS' Environmental...

  15. 77 FR 24471 - Takes of Marine Mammals Incidental to Specified Activities; Russian River Estuary Management...

    Science.gov (United States)

    2012-04-24

    ... Marine Mammals Incidental to Specified Activities; Russian River Estuary Management Activities AGENCY...) to incidentally harass, by Level B harassment only, three species of marine mammals during estuary... Estuary Outlet Channel Adaptive Management Plan; and Feasibility of Alternatives to the Goat Rock State...

  16. Operational considerations in specifying legal weight vehicles for the highway transport of spent nuclear fuel

    International Nuclear Information System (INIS)

    Hill, C.V.; Rutenkroger, E.O.; Ratledge, J.E.

    1990-01-01

    This paper presents the results of a research project in which tractor manufacturers and carrier companies were interviewed to gather information on operational concerns in specifying a tractor to haul legal weight spent fuel casks. The interaction between driver fatigue,safety, and equipment is discussed, as are innovative operating strategies that could save weight

  17. Diagnosing, Conceptualizing, and Treating Eating Disorders Not Otherwise Specified: A Comprehensive Practice Model

    Science.gov (United States)

    Schwitzer, Alan M.

    2012-01-01

    This article presents research and evidence-based practices for identifying, understanding, diagnosing, conceptualizing, and providing a continuum of treatment for the most commonly experienced types of eating-related counseling concerns--namely, eating disorders not otherwise specified--among the population most likely to present these types of…

  18. Specifying Information Security Needs for the Delivery of High Quality Security Services

    NARCIS (Netherlands)

    Su, X.; Bolzoni, D.; van Eck, Pascal

    In this paper we present an approach for specifying and prioritizing information security requirements in organizations. We propose to explicitly link security requirements with the organizations' business vision, i.e. to provide business rationale for security requirements. The rationale is then

  19. 75 FR 42698 - Takes of Marine Mammals Incidental to Specified Activities; Installation of Meteorological Data...

    Science.gov (United States)

    2010-07-22

    ... or ingestion of proposed action-related trash and debris by marine mammals would not be expected... Marine Mammals Incidental to Specified Activities; Installation of Meteorological Data Collection Facilities in the Mid- Atlantic Outer Continental Shelf AGENCY: National Marine Fisheries Service (NMFS...

  20. Course of Subthreshold Bipolar Disorder in Youth: Diagnostic Progression from Bipolar Disorder Not Otherwise Specified

    Science.gov (United States)

    Axelson, David A.; Birmaher, Boris; Strober, Michael A.; Goldstein, Benjamin I.; Ha, Wonho; Gill, Mary Kay; Goldstein, Tina R.; Yen, Shirley; Hower, Heather; Hunt, Jeffrey I.; Liao, Fangzi; Iyengar, Satish; Dickstein, Daniel; Kim, Eunice; Ryan, Neal D.; Frankel, Erica; Keller, Martin B.

    2011-01-01

    Objective: To determine the rate of diagnostic conversion from an operationalized diagnosis of bipolar disorder not otherwise specified (BP-NOS) to bipolar I disorder (BP-I) or bipolar II disorder (BP-II) in youth over prospective follow-up and to identify factors associated with conversion. Method: Subjects were 140 children and adolescents…

  1. Differentiating Bipolar Disorder--Not Otherwise Specified and Severe Mood Dysregulation

    Science.gov (United States)

    Towbin, Kenneth; Axelson, David; Leibenluft, Ellen; Birmaher, Boris

    2013-01-01

    Objective: Bipolar disorder--not otherwise specified (BP-NOS) and severe mood dysregulation (SMD) are severe mood disorders that were defined to address questions about the diagnosis of bipolar disorder (BD) in youth. SMD and BP-NOS are distinct phenotypes that differ in clinical presentation and longitudinal course. The purpose of this review is…

  2. 76 FR 37285 - Fisheries in the Western Pacific; Mechanism for Specifying Annual Catch Limits and Accountability...

    Science.gov (United States)

    2011-06-27

    ... Limits and Accountability Measures AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and... procedures and timing for specifying annual catch limits (ACLs) and accountability measures (AMs) for western... accountability measures to ensure that the ACL is not exceeded. Restrictions may include, but are not limited to...

  3. 76 FR 14367 - Fisheries in the Western Pacific; Mechanism for Specifying Annual Catch Limits and Accountability...

    Science.gov (United States)

    2011-03-16

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration 50 CFR Part 665 RIN 0648-AY93 Fisheries in the Western Pacific; Mechanism for Specifying Annual Catch Limits and Accountability... limits (ACLs) and accountability measures (AMs), adopt the ecosystem component species classification...

  4. From the Pews to Policy: Specifying Evangelical Protestantism's Influence on States' Sexual Orientation Policies

    Science.gov (United States)

    Scheitle, Christopher P.; Hahn, Bryanna B.

    2011-01-01

    It is often assumed that the religious culture of a state can shape policies within the state, particularly concerning morality issues such as abortion or homosexuality. However, the precise manner in which religion shapes these policies has not been clearly specified. Drawing from social movements and policy literature, we argue that the…

  5. The syntax of appositive relativization : On specifying coordination, false free relatives, and promotion

    NARCIS (Netherlands)

    de Vries, Mark

    2006-01-01

    Appositive relative clauses differ in some essential respects from restrictive relative clauses. I argue that appositive relatives and appositions can be put together as a third class of coordination denoting specification. Thus, an appositive relative is a specifying conjunct to the visible

  6. Beyond a Definition: Toward a Framework for Designing and Specifying Mentoring Models

    Science.gov (United States)

    Dawson, Phillip

    2014-01-01

    More than three decades of mentoring research has yet to converge on a unifying definition of mentoring; this is unsurprising given the diversity of relationships classified as mentoring. This article advances beyond a definition toward a common framework for specifying mentoring models. Sixteen design elements were identified from the literature…

  7. 17 CFR 240.15d-20 - Plain English presentation of specified information.

    Science.gov (United States)

    2010-04-01

    ... 17 Commodity and Securities Exchanges 3 2010-04-01 2010-04-01 false Plain English presentation of specified information. 240.15d-20 Section 240.15d-20 Commodity and Securities Exchanges SECURITIES AND... Regulations Under the Securities Exchange Act of 1934 Other Reports § 240.15d-20 Plain English presentation of...

  8. 17 CFR 240.13a-20 - Plain English presentation of specified information.

    Science.gov (United States)

    2010-04-01

    ... 17 Commodity and Securities Exchanges 3 2010-04-01 2010-04-01 false Plain English presentation of specified information. 240.13a-20 Section 240.13a-20 Commodity and Securities Exchanges SECURITIES AND... Regulations Under the Securities Exchange Act of 1934 Other Reports § 240.13a-20 Plain English presentation of...

  9. Using eternity variables to specify and prove a serializable database interface

    NARCIS (Netherlands)

    Hesselink, Wim H.

    Eternity variables are introduced to specify and verify serializability of transactions of a distributed database. Eternity variables are a new kind of auxiliary variables. They do not occur in the implementation but are used in specification and verification. Elsewhere it has been proved that

  10. EMOTIONAL ROLE-TAKING ABILITIES OF CHILDREN WITH A PERVASIVE DEVELOPMENTAL DISORDER NOT OTHERWISE SPECIFIED

    NARCIS (Netherlands)

    Serra, M.; Minderaa, R.B; Van Geert, P. L. C.; Jackson, A.E.; Althaus, M.; Til, R.

    Seven to 12-year-old children with a Pervasive Developmental Disorder Not Otherwise Specified (PDDNOS) were compared with normal, healthy children of the same age and sex on three different emotional role-taking tasks. In these tasks, children had to use person-specific information to make an

  11. Effectiveness of psychotherapy in personality disorders not otherwise specified : A comparison of different treatment modalities

    NARCIS (Netherlands)

    Horn, E.K.; Bartak, A.; Meerman, A.M.M.A.; Rossum, B.V.; Ziegler, U.M.; Thunissen, M.A.G.; Soons, M.; Andrea, H.; Hamers, E.F.M.; Emmelkamp, P.M.G.; Stijnen, T.; Busschbach, J.J.V.; Verheul, R.

    2015-01-01

    Objective Although personality disorder not otherwise specified (PDNOS) is highly prevalent and associated with a high burden of disease, only a few treatment studies in this patient group exist. This study is the first to investigate the effectiveness of different modalities of psychotherapy in

  12. Counseling College Women Experiencing Eating Disorder Not Otherwise Specified: A Cognitive Behavior Therapy Model

    Science.gov (United States)

    Choate, Laura H.

    2010-01-01

    Eating disorder not otherwise specified (EDNOS; American Psychiatric Association, 2000) is, by far, the most common eating disorder that college counseling professionals encounter among their female clients. Empirical evidence and best practice guidelines support use of cognitive behavior therapy (CBT) with women experiencing EDNOS. This article…

  13. How doctors apply semantic components to specify search in work-related information retrieval

    DEFF Research Database (Denmark)

    Lykke, Marianne; Price, Susan L.; Delcambre, Lois L. M.

    2012-01-01

    Workplace searching is often context-specific and targets a “right answer” within some domain-specific aspect of the search topic. We have developed the semantic component (SC) model that allows searchers to specify a search within context-specific aspects of the main topic of documents. The goal...

  14. 31 CFR 515.803 - Customs procedures; merchandise specified in § 515.204.

    Science.gov (United States)

    2010-07-01

    ... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Customs procedures; merchandise... CONTROL REGULATIONS Procedures § 515.803 Customs procedures; merchandise specified in § 515.204. (a) With... thereto) whether or not such merchandise has been imported into the United States, collectors of customs...

  15. 76 FR 33721 - Takes of Marine Mammals Incidental to Specified Activities; Harbor Activities Related to the...

    Science.gov (United States)

    2011-06-09

    ..., incidental to conducting Delta Mariner harbor operations for one year. NMFS reviewed the ULA application and... vitulina), and Northern elephant seals (Mirounga angustirostris) hauled out on Small Haul-out Site 1 to... lions; and 43 Northern elephant seals by Level B harassment only. Description of the Specified...

  16. 75 FR 8677 - Takes of Marine Mammals Incidental to Specified Activities; Seabird and Pinniped Research...

    Science.gov (United States)

    2010-02-25

    ... not more than one year, by United States citizens who engage in a specified activity (other than.... Pinniped research activities involve monitoring breeding northern elephant seals (Mirounga angustirostris) to determine attendance patterns; resighting previously-tagged elephant seals; and conducting weekly...

  17. Mild, moderate, meaningful? Examining the psychological and functioning correlates of DSM-5 eating disorder severity specifiers.

    Science.gov (United States)

    Gianini, Loren; Roberto, Christina A; Attia, Evelyn; Walsh, B Timothy; Thomas, Jennifer J; Eddy, Kamryn T; Grilo, Carlos M; Weigel, Thomas; Sysko, Robyn

    2017-08-01

    This study evaluated the DSM-5 severity specifiers for treatment-seeking groups of participants with anorexia nervosa (AN), the purging form of bulimia nervosa (BN), and binge-eating disorder (BED). Hundred and sixty-two participants with AN, 93 participants with BN, and 343 participants with BED were diagnosed using semi-structured interviews, sub-categorized using DSM-5 severity specifiers and compared on demographic and cross-sectional clinical measures. In AN, the number of previous hospitalizations and the duration of illness increased with severity, but there was no difference across severity groups on measures of eating pathology, depression, or measures of self-reported physical or emotional functioning. In BN, the level of eating concerns increased across the severity groups, but the groups did not differ on measures of depression, self-esteem, and most eating pathology variables. In BN, support was also found for an alternative severity classification scheme based upon number of methods of purging. In BED, levels of several measures of eating pathology and self-reported physical and emotional functioning increased across the severity groups. For BED, however, support was also found for an alternative severity classification scheme based upon overvaluation of shape and weight. Preliminary evidence was also found for a transdiagnostic severity index based upon overvaluation of shape and weight. Overall, these data show limited support for the DSM-5 severity specifiers for BN and modest support for the DSM-5 severity specifiers for AN and BED. © 2017 Wiley Periodicals, Inc.

  18. Face recognition in children with a pervasive developmental disorder not otherwise specified

    NARCIS (Netherlands)

    Serra, M; Althaus, M; de Sonneville, LMJ; Stant, AD; Jackson, AE; Minderaa, RB

    This study investigates the accuracy and speed of face recognition in children with a Pervasive Developmental Disorder Not Otherwise Specified (PDDNOS; DSM-IV, American Psychiatric Association [APA], 1994). The study includes a clinical group of 26 nonretarded 7- to 10-year-old children with PDDNOS

  19. Insights into hydrocarbon formation by nitrogenase cofactor homologs.

    Science.gov (United States)

    Lee, Chi Chung; Hu, Yilin; Ribbe, Markus W

    2015-04-14

    The L-cluster is an all-iron homolog of nitrogenase cofactors. Driven by europium(II) diethylenetriaminepentaacetate [Eu(II)-DTPA], the isolated L-cluster is capable of ATP-independent reduction of CO and CN(-) to C1 to C4 and C1 to C6 hydrocarbons, respectively. Compared to its cofactor homologs, the L-cluster generates considerably more CH4 from the reduction of CO and CN(-), which could be explained by the presence of a "free" Fe atom that is "unmasked" by homocitrate as an additional site for methanation. Moreover, the elevated CH4 formation is accompanied by a decrease in the amount of longer hydrocarbons and/or the lengths of the hydrocarbon products, illustrating a competition between CH4 formation/release and C-C coupling/chain extension. These observations suggest the possibility of designing simpler synthetic clusters for hydrocarbon formation while establishing the L-cluster as a platform for mechanistic investigations of CO and CN(-) reduction without complications originating from the heterometal and homocitrate components. Nitrogenase is a metalloenzyme that is highly complex in structure and uniquely versatile in function. It catalyzes two reactions that parallel two important industrial processes: the reduction of nitrogen to ammonia, which parallels the Haber-Bosch process in ammonia production, and the reduction of carbon monoxide to hydrocarbons, which parallels the Fischer-Tropsch process in fuel production. Thus, the significance of nitrogenase can be appreciated from the perspective of the useful products it generates: (i) ammonia, the "fixed" nitrogen that is essential for the existence of the entire human population; and (ii) hydrocarbons, the "recycled" carbon fuel that could be used to directly address the worldwide energy shortage. This article provides initial insights into the catalytic characteristics of various nitrogenase cofactors in hydrocarbon formation. The reported assay system provides a useful tool for mechanistic

  20. Homologous Basal Ganglia Network Models in Physiological and Parkinsonian Conditions

    Directory of Open Access Journals (Sweden)

    Jyotika Bahuguna

    2017-08-01

    Full Text Available The classical model of basal ganglia has been refined in recent years with discoveries of subpopulations within a nucleus and previously unknown projections. One such discovery is the presence of subpopulations of arkypallidal and prototypical neurons in external globus pallidus, which was previously considered to be a primarily homogeneous nucleus. Developing a computational model of these multiple interconnected nuclei is challenging, because the strengths of the connections are largely unknown. We therefore use a genetic algorithm to search for the unknown connectivity parameters in a firing rate model. We apply a binary cost function derived from empirical firing rate and phase relationship data for the physiological and Parkinsonian conditions. Our approach generates ensembles of over 1,000 configurations, or homologies, for each condition, with broad distributions for many of the parameter values and overlap between the two conditions. However, the resulting effective weights of connections from or to prototypical and arkypallidal neurons are consistent with the experimental data. We investigate the significance of the weight variability by manipulating the parameters individually and cumulatively, and conclude that the correlation observed between the parameters is necessary for generating the dynamics of the two conditions. We then investigate the response of the networks to a transient cortical stimulus, and demonstrate that networks classified as physiological effectively suppress activity in the internal globus pallidus, and are not susceptible to oscillations, whereas parkinsonian networks show the opposite tendency. Thus, we conclude that the rates and phase relationships observed in the globus pallidus are predictive of experimentally observed higher level dynamical features of the physiological and parkinsonian basal ganglia, and that the multiplicity of solutions generated by our method may well be indicative of a natural

  1. Studies of Flerovium and Element 115 Homologs with Macrocyclic Extractants

    Energy Technology Data Exchange (ETDEWEB)

    Despotopulos, John D. [Univ. of Nevada, Las Vegas, NV (United States)

    2015-03-12

    Study of the chemistry of the heaviest elements, Z ≥ 104, poses a unique challenge due to their low production cross-sections and short half-lives. Chemistry also must be studied on the one-atom-at-a-time scale, requiring automated, fast, and very efficient chemical schemes. Recent studies of the chemical behavior of copernicium (Cn, element 112) and flerovium (Fl, element 114) together with the discovery of isotopes of these elements with half-lives suitable for chemical studies have spurred a renewed interest in the development of rapid systems designed to study the chemical properties of elements with Z ≥ 114. This dissertation explores both extraction chromatography and solvent extraction as methods for development of a rapid chemical separation scheme for the homologs of flerovium (Pb, Sn, Hg) and element 115 (Bi, Sb), with the goal of developing a chemical scheme that, in the future, can be applied to on-line chemistry of both Fl and element 115. Carrier-free radionuclides, used in these studies, of the homologs of Fl and element 115 were obtained by proton activation of high-purity metal foils at the Lawrence Livermore National Laboratory (LLNL) Center for Accelerator Mass Spectrometry (CAMS): natIn(p,n)113Sn, natSn(p,n)124Sb, and Au(p,n)197m,gHg. The carrier-free activity was separated from the foils by novel separation schemes based on ion exchange and extraction chromatography techniques. Carrier-free Pb and Bi isotopes were obtained from development of a novel generator based on cation exchange chromatography using the 232U parent to generate 212Pb and 212Bi. Macrocyclic extractants, specifically crown ethers and their derivatives, were chosen for these studies; crown ethers show high selectivity for metal ions. Finally. a potential chemical system for Fl was established based on the Eichrom Pb resin, and insight to an improved system based on thiacrown ethers is

  2. Topological data analysis as a morphometric method: using persistent homology to demarcate a leaf morphospace

    Science.gov (United States)

    Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in flowering plants and are sensitive to processing artifacts. Here we describe a persistent homology approach to measuring shape. Persistent homology is a topological method (concerned wit...

  3. Homology building as a means to define antigenic epitopes on dihydrofolate reductase (DHFR) from Plasmodium falciparum

    DEFF Research Database (Denmark)

    Alifrangis, Michael; Christensen, Inge T; Jørgensen, Flemming S

    2004-01-01

    in the gene coding for Pf-DHFR. Furthermore, we wanted to study the potential use of homology models in general and of Pf-DHFR in particular in predicting antigenic malarial surface epitopes. METHODS: A homology model of Pf-DHFR domain was employed to define an epitope for the development of site...

  4. Homologous Recombination as a Replication Fork Escort: Fork-Protection and Recovery

    Directory of Open Access Journals (Sweden)

    Audrey Costes

    2012-12-01

    Full Text Available Homologous recombination is a universal mechanism that allows DNA repair and ensures the efficiency of DNA replication. The substrate initiating the process of homologous recombination is a single-stranded DNA that promotes a strand exchange reaction resulting in a genetic exchange that promotes genetic diversity and DNA repair. The molecular mechanisms by which homologous recombination repairs a double-strand break have been extensively studied and are now well characterized. However, the mechanisms by which homologous recombination contribute to DNA replication in eukaryotes remains poorly understood. Studies in bacteria have identified multiple roles for the machinery of homologous recombination at replication forks. Here, we review our understanding of the molecular pathways involving the homologous recombination machinery to support the robustness of DNA replication. In addition to its role in fork-recovery and in rebuilding a functional replication fork apparatus, homologous recombination may also act as a fork-protection mechanism. We discuss that some of the fork-escort functions of homologous recombination might be achieved by loading of the recombination machinery at inactivated forks without a need for a strand exchange step; as well as the consequence of such a model for the stability of eukaryotic genomes.

  5. Density parameter estimation for finding clusters of homologous proteins-tracing actinobacterial pathogenicity lifestyles

    DEFF Research Database (Denmark)

    Röttger, Richard; Kalaghatgi, Prabhav; Sun, Peng

    2013-01-01

    Homology detection is a long-standing challenge in computational biology. To tackle this problem, typically all-versus-all BLAST results are coupled with data partitioning approaches resulting in clusters of putative homologous proteins. One of the main problems, however, has been widely neglecte...

  6. Failure of homologous synapsis and sex-specific reproduction problems

    Directory of Open Access Journals (Sweden)

    Hiroki eKurahashi

    2012-06-01

    Full Text Available The prophase of meiosis I ensures the correct segregation of chromosomes to each daughter cell. This includes the pairing, synapsis and recombination of homologous chromosomes. A subset of chromosomal abnormalities, including translocation and inversion, disturbs these processes, resulting in the failure to complete synapsis. This activates the meiotic pachytene checkpoint, and the gametes are fated to undergo cell cycle arrest and subsequent apoptosis. Spermatogenic cells appear to be more vulnerable to the pachytene checkpoint, and male carriers of chromosomal abnormalities are more susceptible to infertility. In contrast, oocytes tend to bypass the checkpoint and instead generate other problems, such as chromosome imbalance that often leads to recurrent pregnancy loss in female carriers. Recent advances in genetic manipulation technologies have increased our knowledge about the pachytene checkpoint and surveillance systems that detect chromosomal synapsis. This review focuses on the consequences of synapsis failure in humans and provides an overview of the mechanisms involved. We also discuss the sexual dimorphism of the involved pathways that leads to the differences in reproductive outcomes between males and females.

  7. Concerning the dynamic instability of actin homolog ParM

    International Nuclear Information System (INIS)

    Popp, David; Yamamoto, Akihiro; Iwasa, Mitsusada; Narita, Akihiro; Maeda, Kayo; Maeda, Yuichiro

    2007-01-01

    Using in vitro TIRF- and electron-microscopy, we reinvestigated the dynamics of native ParM, a prokaryotic DNA segregation protein and actin homolog. In contrast to a previous study, which used a cysteine ParM mutant, we find that the polymerization process of wild type ATP-ParM filaments consists of a polymerization phase and a subsequent steady state phase, which is dynamically unstable, like that of microtubules. We find that the apparent bidirectional polymerization of ParM, is not due to the intrinsic nature of this filament, but results from ParM forming randomly oriented bundles in the presence of crowding agents. Our results imply, that in the bacterium, ParM filaments spontaneously form bipolar bundles. Due to their intrinsic dynamic instability, ParM bundles can efficiently 'search' the cytoplasmic lumen for DNA, bind it equally well at the bipolar ends and segregate it approximately symmetrically, by the insertion of ParM subunits at either end

  8. Homologous radioimmunoassay for human epidermal growth factor (urogastrone)

    International Nuclear Information System (INIS)

    Dailey, G.E.; Kraus, J.W.; Orth, D.N.

    1978-01-01

    Epidermal growth factor (EGF), a polypeptide hormone originally discovered in the mouse submaxillary gland, stimulates growth in a variety of tissues in several species. This hormone has recently been identified in human urine. A homologous RIA for human EGF (RIA-hEGF) has been developed. In general, levels were similar to those recently reported using a heterologous RIA system. Twenty-four-hour urinary excretion of RIA-hEGF by normal adult males and females was 63.0 +- 3.0 and 52.0 +- 3.5 (mean +- SE) μg/total vol, or 29.7 +- 1.1 and 39.8 +- 1.7 μg/g creatinine, respectively. Excretion by females taking oral contraceptives was significantly greater (60.1 +- 2.7 μg/g creatinine; P 0.05). Several of those with very low values had histories of alcohol abuse. Excretion by patients with Cushing's syndrome was normal. Patients with psoriasis or recovering from major burns excreted both abnormally high and abnormally low levels of RIA-hEGF, with no obvious correlation to their clinical condition. There was no apparent diurnal or postprandial variation in urinary RIA-hEGF excretion by normal subjects. An excellent linear correlation was observed between RIA-hEGF and creatinine concentrations in each urine sample for each subject, suggesting that RIA-hEGF concentration in a random urine sample provides a valid index of 24-h RIA-hEGF excretion

  9. A persistent homology approach to collective behavior in insect swarms

    Science.gov (United States)

    Sinhuber, Michael; Ouellette, Nicholas T.

    Various animals from birds and fish to insects tend to form aggregates, displaying self-organized collective swarming behavior. Due to their frequent occurrence in nature and their implications for engineered, collective systems, these systems have been investigated and modeled thoroughly for decades. Common approaches range from modeling them with coupled differential equations on the individual level up to continuum approaches. We present an alternative, topology-based approach for describing swarming behavior at the macroscale rather than the microscale. We study laboratory swarms of Chironomus riparius, a flying, non-biting midge. To obtain the time-resolved three-dimensional trajectories of individual insects, we use a multi-camera stereoimaging and particle-tracking setup. To investigate the swarming behavior in a topological sense, we employ a persistent homology approach to identify persisting structures and features in the insect swarm that elude a direct, ensemble-averaging approach. We are able to identify features of sub-clusters in the swarm that show behavior distinct from that of the remaining swarm members. The coexistence of sub-swarms with different features resembles some non-biological systems such as active colloids or even thermodynamic systems.

  10. A somatic origin of homologous Robertsonian translocations and isochromosomes

    Energy Technology Data Exchange (ETDEWEB)

    Robinson, W.P.; Bernasconi, F.; Schinzel, A.A. (Univ. of Zurich (Switzerland)); Basaran, S.; Yueksel-Apak, M. (Univ. of Istanbul (Turkey)); Neri, G. (Universita Cattolica, Rome (Italy)); Serville, F. (Hopital d' Enfants Pellegrin, Bordeaux (France)); Balicek, P.; Haluza, R. (Univ. Hospital of Hradeck Kralove, Hradec Kralove (Czech Republic)); Farah, L.M.S. (Escuola Paulista de Medicina, Sao Paulo (Brazil)) (and others)

    1994-02-01

    One t(14q 14q), three t(15q 15q), two t(21q21q), and two t(22q22q) nonmosaic, apparently balanced, de novo Robertsonian translocation cases were investigated with polymorphic markers to establish the origin of the translocated chromosomes. Four cases had results indicative of an isochromosome: one t(14q14q) case with mild mental retardation and maternal uniparental disomy (UPD) for chromosome 14, one t(15q15q) case with the Prader-Willi syndrome and UPD(15), a phenotypically normal carrier of t(22q22q) with maternal UPD(22), and a phenotypically normal t(21q21q) case of paternal UPD(21). All UPD cases showed complete homozygosity throughout the involved chromosome, which is supportive of a postmeiotic origin. In the remaining four cases, maternal and paternal inheritance of the involved chromosome was found, which unambiguously implies a somatic origin. One t(15q15q) female had a child with a ring chromosome 15, which was also of probable postmeiotic origin as recombination between grandparental haplotypes had occurred prior to ring formation. UPD might be expected to result from de novo Robertsonian translocations of meiotic origin; however, all de novo homologous translocation cases, so far reported, with UPD of chromosomes 14, 15, 21, or 22 have been isochromosomes. These data provide the first direct evidence that nonmosaic Robertsonian translocations, as well as isochromosomes, are commonly the result of a mitotic exchange. 75 refs., 1 fig., 4 tabs.

  11. Dilogarithm identities in conformal field theory and group homology

    International Nuclear Information System (INIS)

    Dupont, J.L.

    1994-01-01

    Recently, Rogers' dilogarithm identities have attracted much attention in the setting of conformal field theory as well as lattice model calculations. One of the connecting threads is an identity of Richmond-Szekeres that appeared in the computation of central charges in conformal field theory. We show that the Richmond-Szekeres identity and its extension by Kirillov-Reshetikhin (equivalent to an identity found earlier by Lewin) can be interpreted as a lift of a generator of the third integral homology of a finite cyclic subgroup sitting inside the projective special linear group of all 2x2 real matrices viewed as a discrete group. This connection allows us to clarify a few of the assertions and conjectures stated in the work of Nahm-Recknagel-Terhoven concerning the role of algebraic K-theory and Thurston's program on hyperbolic 3-manifolds. Specifically, it is not related to hyperbolic 3-manifolds as suggested but is more appropriately related to the group manifold of the universal covering group of the projective special linear group of all 2x2 real matrices viewed as a topological group. This also resolves the weaker version of the conjecture as formulated by Kirillov. We end with a summary of a number of open conjectures on the mathematical side. (orig.)

  12. Predictive factors for homologous transfusion during paediatric scoliosis surgery.

    Science.gov (United States)

    Dupuis, Claire; Michelet, Daphné; Hilly, Julie; Diallo, Thierno; Vidal, Christophe; Delivet, Honorine; Nivoche, Yves; Mazda, Keyvan; Dahmani, Souhayl

    2015-12-01

    Blood saving strategies during paediatric spinal surgery often include recombinant erythropoietin (rEPO) and antifibrinolytic therapy (AFT). The goal of this study was to investigate additional preventive factors involved in the risk of blood transfusion. This prospective study was designed with the aim of identifying factors associated with the perioperative (defined as the intraoperative and the first postoperative day) probability of homologous red cell transfusion during scoliosis surgery in children operated during a one year period in our institution. The predictors analysed were: age, weight less than the 3rd percentile (W 255 minutes. ROC analysis for the latter model found an area under the curve of 0.9 (95% confidence interval: 0.8-0.97). The accuracy of the model was 92.3% (97.4% for non-transfusion and 69.2% for transfusion). Multivariate sensitivity analysis excluding patients with no preoperative administration of EPO found similar results. The current results indicate that optimising nutritional status might prevent allogenic blood transfusion and requires further investigation. Copyright © 2015 Société française d’anesthésie et de réanimation (Sfar). Published by Elsevier Masson SAS. All rights reserved.

  13. Homology among tet determinants in conjugative elements of streptococci

    Energy Technology Data Exchange (ETDEWEB)

    Smith, M.D.; Hazum, S.; Guild, W.R.

    1981-10-01

    A mutation to tetracycline sensitivity in a resistant strain of Streptococcus pneumoniae was shown by several criteria to be due to a point mutation in the conjugative o(cat-tet) element found in the chromosomes of strains derived from BM6001, a clinical strain resistant to tetracycline and chloramphenicol. Strains carrying the mutation were transformed back to tetracycline resistance with the high efficiency of a point marker by donor deoxyribonucleic acids from its ancestral strain and from nine other clinical isolates of pneumococcus and by deoxyribonucleic acids from Group D Streptococcus faecalis and Group B Streptococcus agalactiae strains that also carry conjugative tet elements in their chromosomes. It was not transformed to resistance by tet plasmid deoxyribonucleic acids from either gram-negative or gram-positive species, except for one that carried transposon TN916, the conjugative tet element present in the chromosomes of some S. faecalis strains. The results showed that the tet determinants in conjugative elements of several streptococcal species share a high degree of deoxyribonucleic acid sequence homology and suggested that they differ from other tet genes.

  14. Surface structure evolution in a homologous series of ionic liquids.

    Science.gov (United States)

    Haddad, Julia; Pontoni, Diego; Murphy, Bridget M; Festersen, Sven; Runge, Benjamin; Magnussen, Olaf M; Steinrück, Hans-Georg; Reichert, Harald; Ocko, Benjamin M; Deutsch, Moshe

    2018-02-06

    Interfaces of room temperature ionic liquids (RTILs) are important for both applications and basic science and are therefore intensely studied. However, the evolution of their interface structure with the cation's alkyl chain length [Formula: see text] from Coulomb to van der Waals interaction domination has not yet been studied for even a single broad homologous RTIL series. We present here such a study of the liquid-air interface for [Formula: see text], using angstrom-resolution X-ray methods. For [Formula: see text], a typical "simple liquid" monotonic surface-normal electron density profile [Formula: see text] is obtained, like those of water and organic solvents. For [Formula: see text], increasingly more pronounced nanoscale self-segregation of the molecules' charged moieties and apolar chains yields surface layering with alternating regions of headgroups and chains. The layering decays into the bulk over a few, to a few tens, of nanometers. The layering periods and decay lengths, their linear [Formula: see text] dependence, and slopes are discussed within two models, one with partial-chain interdigitation and the other with liquid-like chains. No surface-parallel long-range order is found within the surface layer. For [Formula: see text], a different surface phase is observed above melting. Our results also impact general liquid-phase issues like supramolecular self-aggregation and bulk-surface structure relations.

  15. Exploring the role of the DSM-5 performance-only specifier in adolescents with social anxiety disorder.

    Science.gov (United States)

    Fuentes-Rodriguez, Gema; Garcia-Lopez, Luis-Joaquin; Garcia-Trujillo, Veronica

    2018-03-23

    The DSM-5 social anxiety disorder section has recently added the performance-only specifier for individuals whose anxiety is limited to speaking or performing in public. The impact of the DSM-5 performance-only specifier remains a neglected area. The sample comprised 44 healthy controls and 50 adolescents with a clinical diagnosis of SAD (20% met criteria for the performance-only specifier). Findings revealed that adolescents with the specifier had a later age of onset; lower levels of depression, social anxiety symptomatology and clinical severity; and a lesser degree of comorbidity relative to adolescents with SAD but excluding the performance-only specifier. Specifiers only evidenced higher (cognitive) social anxiety symptomatology compared to healthy controls. Results of this study also suggested that the performance-only specifier may correspond to a mild form of social anxiety disorder. Data also revealed that SAD exists on a continuum of severity among healthy controls, specifier participants, and those with both interactional and performance fears, which is consistent with a dimensional structure for SAD. Finally, findings suggested a unique comorbid pattern for specifiers and those adolescents with SAD but excluding the performance-only specifier. The implications of these findings for the etiology, assessment, classification, and treatment of social anxiety in youth are discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Divergent Roles of RPA Homologs of the Model Archaeon Halobacterium salinarum in Survival of DNA Damage.

    Science.gov (United States)

    Evans, Jessica J; Gygli, Patrick E; McCaskill, Julienne; DeVeaux, Linda C

    2018-04-20

    The haloarchaea are unusual in possessing genes for multiple homologs to the ubiquitous single-stranded DNA binding protein (SSB or replication protein A, RPA) found in all three domains of life. Halobacterium salinarum contains five homologs: two are eukaryotic in organization, two are prokaryotic and are encoded on the minichromosomes, and one is uniquely euryarchaeal. Radiation-resistant mutants previously isolated show upregulation of one of the eukaryotic-type RPA genes. Here, we have created deletions in the five RPA operons. These deletion mutants were exposed to DNA-damaging conditions: ionizing radiation, UV radiation, and mitomycin C. Deletion of the euryarchaeal homolog, although not lethal as in Haloferax volcanii , causes severe sensitivity to all of these agents. Deletion of the other RPA/SSB homologs imparts a variable sensitivity to these DNA-damaging agents, suggesting that the different RPA homologs have specialized roles depending on the type of genomic insult encountered.

  17. PCR artifact in testing for homologous recombination in genomic editing in zebrafish.

    Directory of Open Access Journals (Sweden)

    Minho Won

    Full Text Available We report a PCR-induced artifact in testing for homologous recombination in zebrafish. We attempted to replace the lnx2a gene with a donor cassette, mediated by a TALEN induced double stranded cut. The donor construct was flanked with homology arms of about 1 kb at the 5' and 3' ends. Injected embryos (G0 were raised and outcrossed to wild type fish. A fraction of the progeny appeared to have undergone the desired homologous recombination, as tested by PCR using primer pairs extending from genomic DNA outside the homology region to a site within the donor cassette. However, Southern blots revealed that no recombination had taken place. We conclude that recombination happened during PCR in vitro between the donor integrated elsewhere in the genome and the lnx2a locus. We conclude that PCR alone may be insufficient to verify homologous recombination in genome editing experiments in zebrafish.

  18. Circulating free soluble fms-like tyrosine kinase-1 during late first trimester in relation with placental volume as a surrogate for trophoblastic production: a physiology study in low-risk cohort.

    Science.gov (United States)

    Manthati, Sudtawin; Pratumvinit, Busadee; Hanyongyuth, Ratchaneekorn; Udompunthurak, Suthipol; Phaophan, Amprapha; Wataganara, Tuangsit

    2017-08-01

    Data on first-trimester circulating soluble fms-like tyrosine kinase-1 (sFlt-1) and ischemic placental disease is limited and conflicting. This study aimed to study its physiology in relation to trophoblastic mass as the source of production. Low-risk (representing normal placentation) women from 11 0/7 to 13 6/7 weeks' gestation were prospectively enrolled. Selective measurement of serum free sFlt-1 using a new automated assay from 100 eligible subjects was analyzed with gestational age, maternal weight, fetal crown-rump length (CRL), and mean uterine artery Doppler pulsatility index (PI). Placental volume (surrogate for trophoblastic mass) was estimated using 3-dimensional ultrasound and was assessed for its association with serum free sFlt-1. There was no significant association between serum free sFlt-1 and placental volume in either arithmetic (r = 0.053, p = 0.600), logarithmic (r = 0.005, p = 0.963), or quartile (p = 0.703) scale. There was a significant negative correlation between free sFlt-1 level and maternal weight (r=-0.213, p = 0.033). No significant correlation was found between free sFlt-1 level and gestational age (r = 0.007, p = 0.947), CRL (r = 0.027, p = 0.788), and uterine artery Doppler mean PI (r = 0.020, p = 0.828). Lack of correlation between circulating free sFlt-1 level and placental volume suggests that trophoblasts are not its major source during first trimester with presumably physiologic placentation.

  19. Association between the high soluble fms-like tyrosine kinase-1 to placental growth factor ratio and adverse outcomes in asymptomatic women with early-onset fetal growth restriction.

    Science.gov (United States)

    Shinohara, Satoshi; Uchida, Yuzo; Kasai, Mayuko; Sunami, Rei

    2017-08-01

    To assess whether the high soluble fms-like tyrosine kinase-1 (sFlt-1) to placental growth factor (PlGF) ratio is associated with adverse outcomes (e.g., HELLP syndrome [hemolysis, elevated liver enzymes, and low platelets], severe hypertension uncontrolled by medication, non-reassuring fetal status, placental abruption, pulmonary edema, growth arrest, maternal death, or fetal death) and a shorter duration to delivery in early-onset fetal growth restriction (FGR). Thirty-four women with FGR diagnosed at Women who developed adverse outcomes within a week had a significantly higher sFlt-1/PlGF ratio than did those who did not develop complications. A cutoff value of 86.2 for the sFlt-1/PlGF ratio predicted adverse outcomes, with a sensitivity and specificity of 77.8% and 80.0%, respectively. Moreover, 58.4% of women with an sFlt-1/PlGF ratio ≥86.2 versus 9.1% of those with an sFlt-1/PlGF ratio <86.2 delivered within a week of presentation (p < 0.001). In multivariate analyses, an sFlt-1/PlGF ratio ≥86.2 (adjusted odds ratio 9.52; 95% confidence interval, 1.25-72.8) was associated with adverse maternal and neonatal outcomes. A high sFlt-1/PlGF ratio was associated with adverse outcomes and a shorter duration to delivery in early-onset FGR.

  20. A sensitive short read homology search tool for paired-end read sequencing data.

    Science.gov (United States)

    Techa-Angkoon, Prapaporn; Sun, Yanni; Lei, Jikai

    2017-10-16

    Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species. In particular, with the fast accumulation of transcriptomic data of non-model species and metagenomic data, profile homology search is widely adopted in integrated pipelines for functional analysis. While the state-of-the-art tool HMMER has achieved high sensitivity and accuracy in domain annotation, the sensitivity of HMMER on short reads declines rapidly. The low sensitivity on short read homology search can lead to inaccurate domain composition and abundance computation. Our experimental results showed that half of the reads were missed by HMMER for a RNA-Seq dataset. Thus, there is a need for better methods to improve the homology search performance for short reads. We introduce a profile homology search tool named Short-Pair that is designed for short paired-end reads. By using an approximate Bayesian approach employing distribution of fragment lengths and alignment scores, Short-Pair can retrieve the missing end and determine true domains. In particular, Short-Pair increases the accuracy in aligning short reads that are part of remote homologs. We applied Short-Pair to a RNA-Seq dataset and a metagenomic dataset and quantified its sensitivity and accuracy on homology search. The experimental results show that Short-Pair can achieve better overall performance than the state-of-the-art methodology of profile homology search. Short-Pair is best used for next-generation sequencing (NGS) data that lack reference genomes. It provides a complementary paired-end read homology search tool to HMMER. The source code is freely available at https://sourceforge.net/projects/short-pair/ .

  1. Hepatic receptors for homologous growth hormone in the eel

    International Nuclear Information System (INIS)

    Hirano, T.

    1991-01-01

    The specific binding of 125I-labeled eel growth hormone (eGH) to liver membranes of the eel was examined. The specific binding to the 10,000g pellet was greater than that to the 600g pellet. The specific binding was linear up to about 100 mg fresh tissue, and was saturable with increasing amounts of membrane. The specific binding was pH-, temperature-, and time-dependent, with the optimum pH at 7.4, and greater specific binding was obtained at 15 and 25 degrees than at 35 degrees. Scatchard analysis of liver binding gave an association constant of 1.1 x 10(9) M-1 and a capacity of 105 fmol/mg protein. The receptor preparation was highly specific for GHs. Natural and recombinant eel GHs as well as recombinant salmon GH competed equally with 125I-eGH for the receptor sites of the 10,000g liver membrane. Ovine GH was more potent in displacing the labeled eGH than the homologous eel hormone. Tilapia GH and ovine prolactin (PRL) were needed in greater amounts (40 times) than eGH to displace the labeled eGH. Salmon and tilapia PRLs were still less potent (500 times) than eGH. There was no displacement with eel PRL. No significant change in the specific binding was seen 1 week after hypophysectomy, whereas injection of eGH into the hypophysectomized eel caused a significant reduction after 24 hr. The binding to the membrane fractions from gills, kidney, muscle, intestine, and brain was low and exclusively nonspecific, indicating the presence of specific GH receptors predominantly in the liver

  2. Original Mycobacterial Sin, a consequence of highly homologous antigens?

    Science.gov (United States)

    Jenkins, A O; Michel, A; Rutten, V

    2017-05-01

    The role of antigens shared between Mycobacteria in in-vivo cross-reactive immune responses in host animals, have been reported to be responsible for reduced BCG vaccination efficacy as well reduced specificity of routine immunological diagnostic tests. This presents with significant disease control challenges in humans and animals. The present review highlights the results of previous studies on the effect of pre-sensitization to environmental mycobacteria on either pathogenic mycobacteria and/or M. bovis BCG, in experimental animals. It also takes an in-depth view into assessing the genetic similarities and relationships between atypical mycobacteria and Mycobacterium tuberculosis complex (MTBC) and how they might explain the immunological imprint of environmental mycobacteria in directing the hosts' immune response upon subsequent exposure to other classes of mycobacteria. The outcome of this review suggests that genetic closeness between particular atypical mycobacteria and MTBC usually indicate a higher level of homology for certain shared protective antigens. This ultimately results in a higher level of cross reactive immune responses as compared with other atypical mycobacteria that are further away genetically. This would explain the different effects of environmental mycobacteria on MTBC that have been reported in the different studies. In other words the direction of the host immune system in response to exposure to MTBC would depend on the type of environmental mycobacteria that was encountered in the initial exposure. We also explain these mycobacterial interactions in the context of the phenomenon of "Original Mycobacterial Sin". The effects of these inevitable mycobacterial interactions on field diagnosis and control by vaccination and how to circumvent them are discussed. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  3. Structural analysis of the Csk homologous kinase CHK

    International Nuclear Information System (INIS)

    Mulhern, T.; Chong, Y.-P.; Cheng, H.-C.

    2003-01-01

    Full text: CHK (Csk homologous kinase) is an intracellular protein tyrosine kinase, which is highly expressed in the haematopoietic system and the brain. The in vivo role of CHK is to specifically phosphorylate and deactivate the Src family of protein tyrosine kinases. The members of the Src family: Src, Blk, Fyn, Fgr, Hck, Lck, Lyn, Yes and Yrk are major players in numerous cell signalling pathways and exquisitely tuned control of Src family activity is fundamental to many processes in normal cells (reviewed in Lowell and Soriano, 1996). For example, the Src family kinase Fyn is highly expressed in the brain and its activity is vital for memory and learning. In the haematopoietic system, the Src family kinase Hck controls cytoskeletal reorganization, cell motility and immunologic activation. While the Csk family enzymes are closely related to the Src proteins (∼37% identity), the x-ray crystal structures of Src (Xu et al., 1997) and Csk (Ogawa et al., 2002) do display several important differences. Unlike Src, the Csk the SH2 and SH3 domains do not bind intramolecular ligands and they adopt a strikingly different disposition to that observed in Src. Another interesting feature is that the linkers between the SH3 and SH2 domains and between the SH2 and kinase domains, are in intimate contact with the N-lobe of kinase and both appear to play important roles in regulation of the kinase activity. However, the structural and functional basis of how this can be altered is still unclear. We describe the results of biochemical analyses of CHK mediated deactivation of Hck, which suggest that in addition to direct tail-phosphorylation, protein-protein interactions are important. We also describe heteronuclear NMR studies of the structure and ligand binding properties of the CHK SH2 and SH3 domains with a particular emphasis on the transmission of regulatory signals from the ligand binding sites to the interdomain linkers

  4. Image Watermarking Scheme for Specifying False Positive Probability and Bit-pattern Embedding

    Science.gov (United States)

    Sayama, Kohei; Nakamoto, Masayoshi; Muneyasu, Mitsuji; Ohno, Shuichi

    This paper treats a discrete wavelet transform(DWT)-based image watermarking with considering the false positive probability and bit-pattern embedding. We propose an iterative embedding algorithm of watermarking signals which are K sets pseudo-random numbers generated by a secret key. In the detection, K correlations between the watermarked DWT coefficients and watermark signals are computed by using the secret key. L correlations are made available for the judgment of the watermark presence with specified false positive probability, and the other K-L correlations are corresponding to the bit-pattern signal. In the experiment, we show the detection results with specified false positive probability and the bit-pattern recovery, and the comparison of the proposed method against JPEG compression, scaling down and cropping.

  5. An efficient approach for computing the geometrical optics field reflected from a numerically specified surface

    Science.gov (United States)

    Mittra, R.; Rushdi, A.

    1979-01-01

    An approach for computing the geometrical optic fields reflected from a numerically specified surface is presented. The approach includes the step of deriving a specular point and begins with computing the reflected rays off the surface at the points where their coordinates, as well as the partial derivatives (or equivalently, the direction of the normal), are numerically specified. Then, a cluster of three adjacent rays are chosen to define a 'mean ray' and the divergence factor associated with this mean ray. Finally, the ampilitude, phase, and vector direction of the reflected field at a given observation point are derived by associating this point with the nearest mean ray and determining its position relative to such a ray.

  6. Investigating the DSM-5 severity specifiers based on thinness for adults with anorexia nervosa.

    Science.gov (United States)

    Reas, Deborah Lynn; Rø, Øyvind

    2017-08-01

    The DSM-5 severity classification scheme for adults with anorexia nervosa (AN) is based upon current body mass index (BMI; kg/m 2 ). This study examined the utility of the DSM-5 severity specifiers for adults with AN in relation to core cognitive and behavioral features of eating pathology and associated psychosocial impairment. A clinical sample of 146 adult AN patients (140 women, 6 men) were categorized using DSM-5 current BMI severity specifiers and assessed with the Eating Disorder Examination-Questionnaire (EDE-Q) and Clinical Impairment Assessment (CIA). A total of 34 (23.3%) patients were categorized as mild (>=17.0 BMI), 35 (24.0%) as moderate (16-16.99 BMI), 32 (21.9%) as severe (15-15.99 BMI), and 45 (30.8%) as extreme (DSM-5 severity rating scheme to differentiate adults with AN in terms of core eating disorder pathology or associated psychosocial impairment. © 2017 Wiley Periodicals, Inc.

  7. Epidemiology of Adult DSM-5 Major Depressive Disorder and Its Specifiers in the United States.

    Science.gov (United States)

    Hasin, Deborah S; Sarvet, Aaron L; Meyers, Jacquelyn L; Saha, Tulshi D; Ruan, W June; Stohl, Malka; Grant, Bridget F

    2018-04-01

    No US national data are available on the prevalence and correlates of DSM-5-defined major depressive disorder (MDD) or on MDD specifiers as defined in DSM-5. To present current nationally representative findings on the prevalence, correlates, psychiatric comorbidity, functioning, and treatment of DSM-5 MDD and initial information on the prevalence, severity, and treatment of DSM-5 MDD severity, anxious/distressed specifier, and mixed-features specifier, as well as cases that would have been characterized as bereavement in DSM-IV. In-person interviews with a representative sample of US noninstitutionalized civilian adults (≥18 years) (n = 36 309) who participated in the 2012-2013 National Epidemiologic Survey on Alcohol and Related Conditions III (NESARC-III). Data were collected from April 2012 to June 2013 and were analyzed in 2016-2017. Prevalence of DSM-5 MDD and the DSM-5 specifiers. Odds ratios (ORs), adjusted ORs (aORs), and 95% CIs indicated associations with demographic characteristics and other psychiatric disorders. Of the 36 309 adult participants in NESARC-III, 12-month and lifetime prevalences of MDD were 10.4% and 20.6%, respectively. Odds of 12-month MDD were significantly lower in men (OR, 0.5; 95% CI, 0.46-0.55) and in African American (OR, 0.6; 95% CI, 0.54-0.68), Asian/Pacific Islander (OR, 0.6; 95% CI, 0.45-0.67), and Hispanic (OR, 0.7; 95% CI, 0.62-0.78) adults than in white adults and were higher in younger adults (age range, 18-29 years; OR, 3.0; 95% CI, 2.48-3.55) and those with low incomes ($19 999 or less; OR, 1.7; 95% CI, 1.49-2.04). Associations of MDD with psychiatric disorders ranged from an aOR of 2.1 (95% CI, 1.84-2.35) for specific phobia to an aOR of 5.7 (95% CI, 4.98-6.50) for generalized anxiety disorder. Associations of MDD with substance use disorders ranged from an aOR of 1.8 (95% CI, 1.63-2.01) for alcohol to an aOR of 3.0 (95% CI, 2.57-3.55) for any drug. Most lifetime MDD cases were moderate (39.7%) or severe

  8. VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern

    Directory of Open Access Journals (Sweden)

    Hu Qiang

    2012-01-01

    Full Text Available Abstract Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects. Conclusions VPA can be used as an automatic pipeline to prioritize variants for further functional exploration and hypothesis generation. The package is implemented in the R language and is freely available from http://vpa.r-forge.r-project.org.

  9. Studies of flerovium and element 115 homologs with macrocyclic extractants

    Science.gov (United States)

    Despotopulos, John Dustin

    Study of the chemistry of the heaviest elements, Z ? 104, poses a unique challenge due to their low production cross-sections and short half-lives. Chemistry also must be studied on the one-atom-at-a-time scale, requiring automated, fast, and very efficient chemical schemes. Recent studies of the chemical behavior of copernicium (Cn, element 112) and flerovium (Fl, element 114) together with the discovery of isotopes of these elements with half-lives suitable for chemical studies have spurred a renewed interest in the development of rapid systems designed to study the chemical properties of elements with Z ≥ 114. This dissertation explores both extraction chromatography and solvent extraction as methods for development of a rapid chemical separation scheme for the homologs of flerovium (Pb, Sn, Hg) and element 115 (Bi, Sb), with the goal of developing a chemical scheme that, in the future, can be applied to on-line chemistry of both Fl and element 115. Macrocyclic extractants, specifically crown ethers and their derivatives, were chosen for these studies. Carrier-free radionuclides, used in these studies, of the homologs of Fl and element 115 were obtained by proton activation of high purity metal foils at the Lawrence Livermore National Laboratory (LLNL) Center for Accelerator Mass Spectrometry (CAMS): natIn(p,n)113Sn, natSn(p,n)124Sb, and Au(p,n)197m,gHg. The carrier-free activity was separated from the foils by novel separation schemes based on ion exchange and extraction chromatography techniques. Carrier-free Pb and Bi isotopes were obtained from development of a novel generator based on cation exchange chromatography using the 232U parent to generate 212Pb and 212Bi. Crown ethers show high selectivity for metal ions based on their size compared to the negatively charged cavity of the ether. Extraction by crown ethers occur based on electrostatic ion-dipole interactions between the negatively charged ring atoms (oxygen, sulfur, etc.) and the positively

  10. A framework to specify agent-based models in geographic sciences

    OpenAIRE

    Grueau, Cédric; Araújo, João

    2015-01-01

    Agent-Based Modeling (ABM) and simulation have gained popularity in the Geographic Information Systems (GIS) domain. Despite the increasing number of models built by experts and users, it remains challenging for users to specify their models in a manner in which one can understand it. This constraint represents an inhibition to the development and acceptance of the ABM approach. In this paper, we raise the questions that need to be answered in order to cope with ABM specification issues. We r...

  11. Steroid Cell Ovarian Neoplasm, Not Otherwise Specified: A Case Report and Review of the Literature

    Directory of Open Access Journals (Sweden)

    Paul Singh

    2012-01-01

    Full Text Available Background. Steroid cell ovarian tumors, not otherwise specified, represent a unique cause of female virilization. Most commonly encountered in premenopausal women, these tumors can exist throughout a women’s lifetime, from before puberty until after menopause. Case. Steroid cell, not otherwise specified, was diagnosed in a 70-year-old female significant for hirsutism. The patient demonstrated elevated total testosterone levels with normal gonadotropins, DHEA, and DHEA-S levels. CT imaging revealed a right ovarian mass and subsequent laparoscopic right oophorectomy yielded clinical improvement promptly. Conclusion. Virilization in females can occur based on ovarian or adrenal pathology. In terms of ovarian-based female virilization, many tumors exist that may induce women to demonstrate masculine features, such as pure Sertoli, pure Leydig, Sertoli-Leydig combinations, and gynandroblastomas. Each of these tumor types possesses a unique histologic pattern that allows for pathologic identification after removal. A rare source of ovarian-based female virilization is steroid cell neoplasms, not otherwise specified, that do not demonstrate these specific histologic characteristics and thus represent a diagnosis of exclusion after other causes of ovarian-based female virilization have been ruled out.

  12. [Sequence analysis of LEAFY homologous gene from Dendrobium moniliforme and application for identification of medicinal Dendrobium].

    Science.gov (United States)

    Xing, Wen-Rui; Hou, Bei-Wei; Guan, Jing-Jiao; Luo, Jing; Ding, Xiao-Yu

    2013-04-01

    The LEAFY (LFY) homologous gene of Dendrobium moniliforme (L.) Sw. was cloned by new primers which were designed based on the conservative region of known sequences of orchid LEAFY gene. Partial LFY homologous gene was cloned by common PCR, then we got the complete LFY homologous gene Den LFY by Tail-PCR. The complete sequence of DenLFY gene was 3 575 bp which contained three exons and two introns. Using BLAST method, comparison analysis among the exon of LFY homologous gene indicted that the DenLFY gene had high identity with orchids LFY homologous, including the related fragment of PhalLFY (84%) in Phalaenopsis hybrid cultivar, LFY homologous gene in Oncidium (90%) and in other orchid (over 80%). Using MP analysis, Dendrobium is found to be the sister to Oncidium and Phalaenopsis. Homologous analysis demonstrated that the C-terminal amino acids were highly conserved. When the exons and introns were separately considered, exons and the sequence of amino acid were good markers for the function research of DenLFY gene. The second intron can be used in authentication research of Dendrobium based on the length polymorphism between Dendrobium moniliforme and Dendrobium officinale.

  13. Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress

    Science.gov (United States)

    Magdalou, Indiana; Machon, Christelle; Dardillac, Elodie; Técher, Hervé; Guitton, Jérôme; Debatisse, Michelle; Lopez, Bernard S.

    2016-01-01

    Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation

  14. Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress.

    Directory of Open Access Journals (Sweden)

    Therese Wilhelm

    2016-05-01

    Full Text Available Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es. Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3% rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing, and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and

  15. Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress.

    Science.gov (United States)

    Wilhelm, Therese; Ragu, Sandrine; Magdalou, Indiana; Machon, Christelle; Dardillac, Elodie; Técher, Hervé; Guitton, Jérôme; Debatisse, Michelle; Lopez, Bernard S

    2016-05-01

    Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation

  16. K-theory and periodic cyclic homology of some noncompact quantum algebras

    International Nuclear Information System (INIS)

    Do Ngoc Diep; Kuku, Aderemi O.

    2003-07-01

    We prove in this paper that the periodic cyclic homology of the quantized algebras of functions on coadjoint orbits of connected and simply connected Lie group, are isomorphic to the periodic cyclic homology of the quantized algebras of functions on coadjoint orbits of compact maximal subgroups, without localization. Some noncompact quantum groups and algebras were constructed and their irreducible representations were classified in recent works of Do Ngoc Diep and Nguyen Viet Hai [DH1]-[DH2] and Do Due Hanh [DD] by using deformation quantization. In this paper we compute their K-groups, periodic cyclic homology groups and their Chern characters. (author)

  17. 32 CFR 37.810 - What should my TIA's provisions specify for the method and frequency of recipients' payment...

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 1 2010-07-01 2010-07-01 false What should my TIA's provisions specify for the... TIA's provisions specify for the method and frequency of recipients' payment requests? The procedure... reimbursements or advance payments, your TIA must allow recipients to submit requests for payment at least...

  18. 77 FR 49277 - Takes of Marine Mammals During Specified Activities; Confined Blasting Operations by the U.S...

    Science.gov (United States)

    2012-08-15

    ... effects that confined blasting can have on marine animals near the blast (Keevin et al., 1999). The visual... Atmospheric Administration Takes of Marine Mammals During Specified Activities; Confined Blasting Operations... Marine Mammals During Specified Activities; Confined Blasting Operations by the U.S. Army Corps of...

  19. 7 CFR 70.13 - Ready-to-cook poultry and rabbits and specified poultry food products.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Ready-to-cook poultry and rabbits and specified... AGRICULTURE (CONTINUED) REGULATIONS AND STANDARDS UNDER THE AGRICULTURAL MARKETING ACT OF 1946 AND THE EGG... Poultry Products and Rabbit Products General § 70.13 Ready-to-cook poultry and rabbits and specified...

  20. Prevalence and Red Flags Regarding Specified Causes of Back Pain in Older Adults Presenting in General Practice

    NARCIS (Netherlands)

    Enthoven, Wendy T. M.; Geuze, Judith; Scheele, Jantine; Bierma-Zeinstra, Sita M. A.; Bueving, Herman J.; Bohnen, Arthur M.; Peul, Wilco C.; van Tulder, Maurits W.; Berger, Marjolein Y.; Koes, Bart W.; Luijsterburg, Pim A. J.

    BACKGROUND: In a small proportion of patients experiencing unspecified back pain a specified underlying pathology is present. OBJECTIVE: To identify the prevalence of physician-specified causes of back pain and to assess associations between red flags and vertebral fractures, as diagnosed by the

  1. An Approach for Zika Virus Inhibition Using Homology Structure of the Envelope Protein

    Czech Academy of Sciences Publication Activity Database

    Fernando, S.; Fernando, T.; Štefánik, M.; Eyer, Luděk; Růžek, Daniel

    2016-01-01

    Roč. 58, č. 12 (2016), s. 801-806 ISSN 1073-6085 Institutional support: RVO:60077344 Keywords : Zika virus * homology model * druggability * drug discovery Subject RIV: EE - Microbiology, Virology Impact factor: 1.634, year: 2016

  2. Regulation of homologous recombination repair protein Rad51 by Ku70

    International Nuclear Information System (INIS)

    Du Liqing; Liu Qiang; Wang Yan; Xu Chang; Cao Jia; Fu Yue; Chen Fenghua; Fan Feiyue

    2013-01-01

    Objective: To explore the regulative effect of non-homologous end joining (NHEJ)protein Ku70 on homologous recombination repair protein Rad51, and to investigate the synergistic mechanism of homologous recombination repair in combination with NHEJ. Methods: Observed Rad51 protein expression after transfect Ku70 small interfering RNA or Ku70 plasmid DNA into tumor cells using Western blot. Results: Expression of Rad51 was obviously reduced after pretreated with Ku70 small interfering RNA. And with the increasing expression of Ku70 protein after transfection of Ku70 plasmid DNA PGCsi3.0-hKu70 into tumor cell lines, the Rad51 protein expression was increased. Conclusion: Ku70 protein has regulating effect on gene expression of Rad51, and it might participate in the collaboration between homologous recombination repair and NHEJ. (authors)

  3. Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs

    NARCIS (Netherlands)

    Sanders, Ashley D; Falconer, Ester; Hills, Mark; Spierings, Diana C J; Lansdorp, Peter M.

    The ability to distinguish between genome sequences of homologous chromosomes in single cells is important for studies of copy-neutral genomic rearrangements (such as inversions and translocations), building chromosome-length haplotypes, refining genome assemblies, mapping sister chromatid exchange

  4. Integration of vectors by homologous recombination in the plant pathogen Glomerella cingulata.

    Science.gov (United States)

    Rikkerink, E H; Solon, S L; Crowhurst, R N; Templeton, M D

    1994-03-01

    An homologous transformation system has been developed for the plant pathogenic fungus Glomerella cingulata (Colletotrichum gloeosporioides). A transformation vector containing the G. cingulata gpdA promoter fused to the hygromycin phosphotransferase gene was constructed. Southern analyses indicated that this vector integrated at single sites in most transformants. A novel method of PCR amplification across the recombination junction point indicated that the integration event occurred by homologous recombination in more than 95% of the transformants. Deletion studies demonstrated that 505 bp (the minimum length of homologous promoter DNA analysed which was still capable of promoter function) was sufficient to target integration events. Homologous integration of the vector resulted in duplication of the gdpA promoter region. When transformants were grown without selective pressure, a high incidence of vector excision by recombination between the duplicated regions was evident. The significance of these recombination characteristics is discussed with reference to the feasibility of performing gene disruption experiments.

  5. CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2010-01-01

    CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.......0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models.......3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is...

  6. Competition between replicative and translesion polymerases during homologous recombination repair in Drosophila.

    Directory of Open Access Journals (Sweden)

    Daniel P Kane

    Full Text Available In metazoans, the mechanism by which DNA is synthesized during homologous recombination repair of double-strand breaks is poorly understood. Specifically, the identities of the polymerase(s that carry out repair synthesis and how they are recruited to repair sites are unclear. Here, we have investigated the roles of several different polymerases during homologous recombination repair in Drosophila melanogaster. Using a gap repair assay, we found that homologous recombination is impaired in Drosophila lacking DNA polymerase zeta and, to a lesser extent, polymerase eta. In addition, the Pol32 protein, part of the polymerase delta complex, is needed for repair requiring extensive synthesis. Loss of Rev1, which interacts with multiple translesion polymerases, results in increased synthesis during gap repair. Together, our findings support a model in which translesion polymerases and the polymerase delta complex compete during homologous recombination repair. In addition, they establish Rev1 as a crucial factor that regulates the extent of repair synthesis.

  7. On some homological functors of a Bieberbach group with symmetric point group

    Science.gov (United States)

    Ting, Tan Yee; Idrus, Nor'ashiqin Mohd; Masri, Rohaidah; Ladi, Nor Fadzilah Abdul

    2017-05-01

    Bieberbach groups with symmetric point group are polycyclic. The properties of the groups can be explored by computing their homological functors. In this paper, some homological functors of a Bieberbach group with symmetric point group, such as the Schur multiplier and the G-trivial subgroup of the nonabelian tensor square, are generalized up to finite dimension and are represented in the form of direct product of cyclic groups.

  8. Double Strand Break Repair, one mechanism can hide another: Alternative non-homologous end joining

    International Nuclear Information System (INIS)

    Rass, E.; Grabarz, A.; Bertrand, P.; Lopez, B.S.

    2012-01-01

    DNA double strand breaks are major cytotoxic lesions encountered by the cells. They can be induced by ionizing radiation or endogenous stress and can lead to genetic instability. Two mechanisms compete for the repair of DNA double strand breaks: homologous recombination and non-homologous end joining (NHEJ). Homologous recombination requires DNA sequences homology and is initiated by single strand resection. Recently, advances have been made concerning the major steps and proteins involved in resection. NHEJ, in contrast, does not require sequence homology. The existence of a DNA double strand break repair mechanism, independent of KU and ligase IV, the key proteins of the canonical non homologous end joining pathway, has been revealed lately and named alternative non homologous end joining. The hallmarks of this highly mutagenic pathway are deletions at repair junctions and frequent use of distal micro-homologies. This mechanism is also initiated by a single strand resection of the break. The aim of this review is firstly to present recent data on single strand resection, and secondly the alternative NHEJ pathway, including a discussion on the fidelity of NHEJ. Based on current knowledge, canonical NHEJ does not appear as an intrinsically mutagenic mechanism, but in contrast, as a conservative one. The structure of broken DNA ends actually dictates the quality repair of the alternative NHEJ and seems the actual responsible for the mutagenesis attributed beforehand to the canonical NHEJ. The existence of this novel DNA double strand breaks repair mechanism needs to be taken into account in the development of radiosensitizing strategies in order to optimise the efficiency of radiotherapy. (authors)

  9. Somatic association of telocentric chromosomes carrying homologous centromeres in common wheat.

    Science.gov (United States)

    Mello-Sampayo, T

    1973-01-01

    Measurements of distances between telocentric chromosomes, either homologous or representing the opposite arms of a metacentric chromosome (complementary telocentrics), were made at metaphase in root tip cells of common wheat carrying two homologous pairs of complementary telocentrics of chromosome 1 B or 6 B (double ditelosomic 1 B or 6 B). The aim was to elucidate the relative locations of the telocentric chromosomes within the cell. The data obtained strongly suggest that all four telocentrics of chromosome 1 B or 6 B are spacially and simultaneously co-associated. In plants carrying two complementary (6 B (S) and 6 B (L)) and a non-related (5 B (L)) telocentric, only the complementary chromosomes were found to be somatically associated. It is thought, therefore, that the somatic association of chromosomes may involve more than two chromosomes in the same association and, since complementary telocentrics are as much associated as homologous, that the homology between centromeres (probably the only homologous region that exists between complementary telocentrics) is a very important condition for somatic association of chromosomes. The spacial arrangement of chromosomes was studied at anaphase and prophase and the polar orientation of chromosomes at prophase was found to resemble anaphase orientation. This was taken as good evidence for the maintenance of the chromosome arrangement - the Rabl orientation - and of the peripheral location of the centromere and its association with the nuclear membrane. Within this general arrangement homologous telocentric chromosomes were frequently seen to have their centromeres associated or directed towards each other. The role of the centromere in somatic association as a spindle fibre attachment and chromosome binder is discussed. It is suggested that for non-homologous chromosomes to become associated in root tips, the only requirement needed should be the homology of centromeres such as exists between complementary

  10. Recovery of arrested replication forks by homologous recombination is error-prone.

    Directory of Open Access Journals (Sweden)

    Ismail Iraqui

    Full Text Available Homologous recombination is a universal mechanism that allows repair of DNA and provides support for DNA replication. Homologous recombination is therefore a major pathway that suppresses non-homology-mediated genome instability. Here, we report that recovery of impeded replication forks by homologous recombination is error-prone. Using a fork-arrest-based assay in fission yeast, we demonstrate that a single collapsed fork can cause mutations and large-scale genomic changes, including deletions and translocations. Fork-arrest-induced gross chromosomal rearrangements are mediated by inappropriate ectopic recombination events at the site of collapsed forks. Inverted repeats near the site of fork collapse stimulate large-scale genomic changes up to 1,500 times over spontaneous events. We also show that the high accuracy of DNA replication during S-phase is impaired by impediments to fork progression, since fork-arrest-induced mutation is due to erroneous DNA synthesis during recovery of replication forks. The mutations caused are small insertions/duplications between short tandem repeats (micro-homology indicative of replication slippage. Our data establish that collapsed forks, but not stalled forks, recovered by homologous recombination are prone to replication slippage. The inaccuracy of DNA synthesis does not rely on PCNA ubiquitination or trans-lesion-synthesis DNA polymerases, and it is not counteracted by mismatch repair. We propose that deletions/insertions, mediated by micro-homology, leading to copy number variations during replication stress may arise by progression of error-prone replication forks restarted by homologous recombination.

  11. Csk Homologous Kinase, a Potential Regulator of CXCR4-mediated Breast Cancer Cell Metastasis

    Science.gov (United States)

    2010-08-31

    SH2 ) and SH3 domains and lacks the consensus tyrosine phosphorylation and myristylation sites found in Src family kinases . CHK has been shown to...0350 TITLE: Csk Homologous Kinase , a Potential Regulator of CXCR4-mediated Breast Cancer Cell Metastasis PRINCIPAL INVESTIGATOR: Byeong-Chel...1 AUG 2009 - 31 JUL 2010 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER W81XWH-09-1-0350 Csk Homologous Kinase , a Potential Regulator

  12. A scanning tunneling microscope capable of imaging specified micron-scale small samples.

    Science.gov (United States)

    Tao, Wei; Cao, Yufei; Wang, Huafeng; Wang, Kaiyou; Lu, Qingyou

    2012-12-01

    We present a home-built scanning tunneling microscope (STM) which allows us to precisely position the tip on any specified small sample or sample feature of micron scale. The core structure is a stand-alone soft junction mechanical loop (SJML), in which a small piezoelectric tube scanner is mounted on a sliding piece and a "U"-like soft spring strip has its one end fixed to the sliding piece and its opposite end holding the tip pointing to the sample on the scanner. Here, the tip can be precisely aligned to a specified small sample of micron scale by adjusting the position of the spring-clamped sample on the scanner in the field of view of an optical microscope. The aligned SJML can be transferred to a piezoelectric inertial motor for coarse approach, during which the U-spring is pushed towards the sample, causing the tip to approach the pre-aligned small sample. We have successfully approached a hand cut tip that was made from 0.1 mm thin Pt∕Ir wire to an isolated individual 32.5 × 32.5 μm(2) graphite flake. Good atomic resolution images and high quality tunneling current spectra for that specified tiny flake are obtained in ambient conditions with high repeatability within one month showing high and long term stability of the new STM structure. In addition, frequency spectra of the tunneling current signals do not show outstanding tip mount related resonant frequency (low frequency), which further confirms the stability of the STM structure.

  13. A scanning tunneling microscope capable of imaging specified micron-scale small samples

    Science.gov (United States)

    Tao, Wei; Cao, Yufei; Wang, Huafeng; Wang, Kaiyou; Lu, Qingyou

    2012-12-01

    We present a home-built scanning tunneling microscope (STM) which allows us to precisely position the tip on any specified small sample or sample feature of micron scale. The core structure is a stand-alone soft junction mechanical loop (SJML), in which a small piezoelectric tube scanner is mounted on a sliding piece and a "U"-like soft spring strip has its one end fixed to the sliding piece and its opposite end holding the tip pointing to the sample on the scanner. Here, the tip can be precisely aligned to a specified small sample of micron scale by adjusting the position of the spring-clamped sample on the scanner in the field of view of an optical microscope. The aligned SJML can be transferred to a piezoelectric inertial motor for coarse approach, during which the U-spring is pushed towards the sample, causing the tip to approach the pre-aligned small sample. We have successfully approached a hand cut tip that was made from 0.1 mm thin Pt/Ir wire to an isolated individual 32.5 × 32.5 μm2 graphite flake. Good atomic resolution images and high quality tunneling current spectra for that specified tiny flake are obtained in ambient conditions with high repeatability within one month showing high and long term stability of the new STM structure. In addition, frequency spectra of the tunneling current signals do not show outstanding tip mount related resonant frequency (low frequency), which further confirms the stability of the STM structure.

  14. A scheme of quantum state discrimination over specified states via weak-value measurement

    Science.gov (United States)

    Chen, Xi; Dai, Hong-Yi; Liu, Bo-Yang; Zhang, Ming

    2018-04-01

    The commonly adopted projective measurements are invalid in the specified task of quantum state discrimination when the discriminated states are superposition of planar-position basis states whose complex-number probability amplitudes have the same magnitude but different phases. Therefore we propose a corresponding scheme via weak-value measurement and examine the feasibility of this scheme. Furthermore, the role of the weak-value measurement in quantum state discrimination is analyzed and compared with one in quantum state tomography in this Letter.

  15. Chronic Eosinophilic Leukemia—Not Otherwise Specified (NOS in the Background of a Large Cell Lymphoma

    Directory of Open Access Journals (Sweden)

    Wilson I. Gonsalves

    2013-01-01

    Full Text Available Clonal eosinophilic disorders are rare among hematological malignancies. Most eosinophilia tends to be due to secondary causes such as infections, hypersensitivity conditions, drug reactions, and connective tissue disorders. The presence of a primary clonal eosinophilic disorder such as chronic eosinophilic leukemia—not otherwise specified (NOS in the presence of a synchronous large cell lymphoma—is rare making the diagnosis challenging. We present a case of a 51-year-old female with the aforementioned presentation and demonstrate the extensive workup performed to identify the diagnosis.

  16. GLASSgo – Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence

    Directory of Open Access Journals (Sweden)

    Steffen C. Lott

    2018-04-01

    Full Text Available Bacterial small RNAs (sRNAs are important post-transcriptional regulators of gene expression. The functional and evolutionary characterization of sRNAs requires the identification of homologs, which is frequently challenging due to their heterogeneity, short length and partly, little sequence conservation. We developed the GLobal Automatic Small RNA Search go (GLASSgo algorithm to identify sRNA homologs in complex genomic databases starting from a single sequence. GLASSgo combines an iterative BLAST strategy with pairwise identity filtering and a graph-based clustering method that utilizes RNA secondary structure information. We tested the specificity, sensitivity and runtime of GLASSgo, BLAST and the combination RNAlien/cmsearch in a typical use case scenario on 40 bacterial sRNA families. The sensitivity of the tested methods was similar, while the specificity of GLASSgo and RNAlien/cmsearch was significantly higher than that of BLAST. GLASSgo was on average ∼87 times faster than RNAlien/cmsearch, and only ∼7.5 times slower than BLAST, which shows that GLASSgo optimizes the trade-off between speed and accuracy in the task of finding sRNA homologs. GLASSgo is fully automated, whereas BLAST often recovers only parts of homologs and RNAlien/cmsearch requires extensive additional bioinformatic work to get a comprehensive set of homologs. GLASSgo is available as an easy-to-use web server to find homologous sRNAs in large databases.

  17. Partially specified physics problems: university students' attitudes and performance

    Energy Technology Data Exchange (ETDEWEB)

    Marusic, M [Prva Gimnazija, Teslina 10, 21000 Split (Croatia); Erceg, N [Department of Physics, University of Rijeka, Omladinska 14, 51000 Rijeka (Croatia); Slisko, J, E-mail: mirko@marusic.inf, E-mail: nerceg@phy.uniri.hr, E-mail: jslisko@fcfm.buap.mx [Benemerita Universidad Autonoma de Puebla, Apartado Postal 1152, Puebla, Puebla CP 72000 (Mexico)

    2011-05-15

    In this research we asked the fourth year students (N = 50) of a technical faculty of the University of Split (Republic of Croatia) to solve a partially specified physics problem related to gravitational force. The task for the students was to decide whether the situation described in the problem is feasible or not. Nevertheless, the formulation of the problem is such that it does not give students any explicit advice regarding what to calculate or how to judge the feasibility of the given situation in the real world. The research was carried out using a structured written exam method. The worksheet was structured in order to assess explicitly a few elements of the students' problem-solving performance. Based on their results, the examinees were classified into four categories, depending on what they could or could not accomplish during problem solving. A majority of students were not able to solve the given physical problem completely. A selection of students' and professors' observations is also included. Our results show that traditionally formulated numerical exercises, which are mostly used in physics teaching, do not develop students' abilities in higher-order thinking (i.e. planning, decision making or result evaluation) to a desirable extent. We suggest that partially specified problems should be given to students, both in problem-solving sessions and exams, in order to prepare them for dealing with ill-structured tasks in real life.

  18. Artificial ground motion compatible with specified peak ground displacement and target multi-damping response spectra

    International Nuclear Information System (INIS)

    Zhang Yushan; Zhao Fengxin

    2010-01-01

    With respect to the design ground motion of nuclear power plant (NPP), the Regular Guide 1.60 of the US not only defined the standard multi-damping response spectra, i.e. the RG1.60 spectra, but also definitely prescribed the peak ground displacement (PGD) value corresponding to the standard spectra. However, in the engineering practice of generating multi-damping-spectra-compatible artificial ground motion for the seismic design of NPP, the PGD value had been neglected. Addressing this issue, this paper proposed a synthesizing method which generates the artificial ground motion compatible with not only the target multi-damping response spectra but also the specified PGD value. Firstly, by the transfer formula between the power spectrum and the response spectrum, an initial uniformly modulated acceleration time history is synthesized by multiplying the stationary Gaussian process with the prescribed intensity envelope to simulate the amplitude-non-stationarity of earthquake ground motion. And then by superimposing a series of narrow-band time histories in the time domain, the initial time history is modified in the iterative manner to match the target PGD as well as the target multi-damping spectra with the pre-specified matching precisions. Numerical examples are provided to demonstrate the matching precisions of the proposed method to the target values.

  19. Using the ACT-R architecture to specify 39 quantitative process models of decision making

    Directory of Open Access Journals (Sweden)

    Julian N. Marewski

    2011-08-01

    Full Text Available Hypotheses about decision processes are often formulated qualitatively and remain silent about the interplay of decision, memorial, and other cognitive processes. At the same time, existing decision models are specified at varying levels of detail, making it difficult to compare them. We provide a methodological primer on how detailed cognitive architectures such as ACT-R allow remedying these problems. To make our point, we address a controversy, namely, whether noncompensatory or compensatory processes better describe how people make decisions from the accessibility of memories. We specify 39 models of accessibility-based decision processes in ACT-R, including the noncompensatory recognition heuristic and various other popular noncompensatory and compensatory decision models. Additionally, to illustrate how such models can be tested, we conduct a model comparison, fitting the models to one experiment and letting them generalize to another. Behavioral data are best accounted for by race models. These race models embody the noncompensatory recognition heuristic and compensatory models as a race between competing processes, dissolving the dichotomy between existing decision models.

  20. Measures of the DSM-5 mixed-features specifier of major depressive disorder.

    Science.gov (United States)

    Zimmerman, Mark

    2017-04-01

    During the past two decades, a number of studies have found that depressed patients frequently have manic symptoms intermixed with depressive symptoms. While the frequency of mixed syndromes are more common in bipolar than in unipolar depressives, mixed states are also common in patients with major depressive disorder. The admixture of symptoms may be evident when depressed patients present for treatment, or they may emerge during ongoing treatment. In some patients, treatment with antidepressant medication might precipitate the emergence of mixed states. It would therefore be useful to systematically inquire into the presence of manic/hypomanic symptoms in depressed patients. We can anticipate that increased attention will likely be given to mixed depression because of changes in the DSM-5. In the present article, I review instruments that have been utilized to assess the presence and severity of manic symptoms and therefore could be potentially used to identify the DSM-5 mixed-features specifier in depressed patients and to evaluate the course and outcome of treatment. In choosing which measure to use, clinicians and researchers should consider whether the measure assesses both depression and mania/hypomania, assesses all or only some of the DSM-5 criteria for the mixed-features specifier, or assesses manic/hypomanic symptoms that are not part of the DSM-5 definition. Feasibility, more so than reliability and validity, will likely determine whether these measures are incorporated into routine clinical practice.

  1. High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

    Directory of Open Access Journals (Sweden)

    Mikihiko eKawai

    2014-03-01

    Full Text Available Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5 and 107.0 mbsf at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB, key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.

  2. Partial amino acid sequence of apolipoprotein(a) shows that it is homologous to plasminogen

    International Nuclear Information System (INIS)

    Eaton, D.L.; Fless, G.M.; Kohr, W.J.; McLean, J.W.; Xu, Q.T.; Miller, C.G.; Lawn, R.M.; Scanu, A.M.

    1987-01-01

    Apolipoprotein(a) [apo(a)] is a glycoprotein with M/sub r/ ∼ 280,000 that is disulfide linked to apolipoprotein B in lipoprotein(a) particles. Elevated plasma levels of lipoprotein(a) are correlated with atherosclerosis. Partial amino acid sequence of apo(a) shows that it has striking homology to plasminogen. Plasminogen is a plasma serine protease zymogen that consists of five homologous and tandemly repeated domains called kringles and a trypsin-like protease domain. The amino-terminal sequence obtained for apo(a) is homologous to the beginning of kringle 4 but not the amino terminus of plasminogen. Apo(a) was subjected to limited proteolysis by trypsin or V8 protease, and fragments generated were isolated and sequenced. Sequences obtained from several of these fragments are highly (77-100%) homologous to plasminogen residues 391-421, which reside within kringle 4. Analysis of these internal apo(a) sequences revealed that apo(a) may contain at least two kringle 4-like domains. A sequence obtained from another tryptic fragment also shows homology to the end of kringle 4 and the beginning of kringle 5. Sequence data obtained from the two tryptic fragments shows homology with the protease domain of plasminogen. One of these sequences is homologous to the sequences surrounding the activation site of plasminogen. Plasminogen is activated by the cleavage of a specific arginine residue by urokinase and tissue plasminogen activator; however, the corresponding site in apo(a) is a serine that would not be cleaved by tissue plasminogen activator or urokinase. Using a plasmin-specific assay, no proteolytic activity could be demonstrated for lipoprotein(a) particles. These results suggest that apo(a) contains kringle-like domains and an inactive protease domain

  3. Identification and localization of a gene that specifies production of Escherichia coli DNA topoisomerase I

    International Nuclear Information System (INIS)

    Trucksis, M.; Depew, R.E.

    1981-01-01

    A gene that specifies production of Escherichia coli DNA topoisomerase I (ω protein) was identified with the aid of a radioimmunoassay for this protein. E. coli DNA topoisomerase I was produced by Salmonella typhimurium merodiploids that harbored E. coli plasmid F' 123, but not by strains that lost this plasmid. Analysis of strains with spontaneous deletions of F' 123 showed that the gene, topA, required for production of the E. coli ω protein was between the trp operon and the cysB gene. Deletions that eliminated topA also eliminated the supX gene. We suggest that topA is the structural gene of E. coli DNA topoisomerase I and that topA is identical to supX

  4. Storing files in a parallel computing system based on user-specified parser function

    Science.gov (United States)

    Faibish, Sorin; Bent, John M; Tzelnic, Percy; Grider, Gary; Manzanares, Adam; Torres, Aaron

    2014-10-21

    Techniques are provided for storing files in a parallel computing system based on a user-specified parser function. A plurality of files generated by a distributed application in a parallel computing system are stored by obtaining a parser from the distributed application for processing the plurality of files prior to storage; and storing one or more of the plurality of files in one or more storage nodes of the parallel computing system based on the processing by the parser. The plurality of files comprise one or more of a plurality of complete files and a plurality of sub-files. The parser can optionally store only those files that satisfy one or more semantic requirements of the parser. The parser can also extract metadata from one or more of the files and the extracted metadata can be stored with one or more of the plurality of files and used for searching for files.

  5. SGV: a code to evaluate plasma reaction rates to a specified accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Devoto, R.S.; Hanson, J.D.

    1978-09-22

    A FORTRAN code to evaluate binary reaction rates (sigmav) for a plasma to a specified accuracy is described. Distribution functions permitted are (1) two Maxwellian species at different temperatures, (2) beam-Maxwellian, (3) cold gas with Maxwellian, and (4) beam-plasma with mirror distribution of the form f(v) varies as f(v) M (cos theta). Several functional forms are permitted for f(v) and M(cos theta). Cross-section subroutines for a number of interactions involving hydrogen, helium, and electrons are included, as is a routine allowing input of numerical data. The code is written as a subroutine to allow ready incorporation into larger plasma codes.

  6. A Computer Program for Simplifying Incompletely Specified Sequential Machines Using the Paull and Unger Technique

    Science.gov (United States)

    Ebersole, M. M.; Lecoq, P. E.

    1968-01-01

    This report presents a description of a computer program mechanized to perform the Paull and Unger process of simplifying incompletely specified sequential machines. An understanding of the process, as given in Ref. 3, is a prerequisite to the use of the techniques presented in this report. This process has specific application in the design of asynchronous digital machines and was used in the design of operational support equipment for the Mariner 1966 central computer and sequencer. A typical sequential machine design problem is presented to show where the Paull and Unger process has application. A description of the Paull and Unger process together with a description of the computer algorithms used to develop the program mechanization are presented. Several examples are used to clarify the Paull and Unger process and the computer algorithms. Program flow diagrams, program listings, and a program user operating procedures are included as appendixes.

  7. Eating disorder not otherwise specified: the view from a tertiary care treatment center.

    Science.gov (United States)

    Rockert, Wendi; Kaplan, Allan S; Olmsted, Marion P

    2007-11-01

    This study sought to characterize a large number of adult outpatients diagnosed with eating disorder not otherwise specified (EDNOS). The sample consisted of 1,449 patients who were classified as anorexia nervosa (AN), bulimia nervosa (BN), or assigned to one of six EDNOS categories. Eating disorder groups were compared on demographic features, symptom frequencies, and psychological functioning. Forty percent of the sample was categorized as EDNOS. A subgroup of purging only patients closely resembled the BN purging subtype. Although EDNOS subthreshold BN patients reported less psychopathology than full syndrome BN they, nevertheless, displayed clinical levels of disturbance. Patients who binge-eat once a week demonstrate a profile of psychological functioning similar to those who binge eat twice a week. Consistent with previous research, in this sample there were subgroups embedded in the EDNOS category that both share similarities with and differ from full syndrome BN. (c) 2007 by Wiley Periodicals, Inc.

  8. Planning GPS Measurements of a Linear Object for a Specified Time Interval

    Directory of Open Access Journals (Sweden)

    Specht Cezary

    2017-12-01

    Full Text Available The previous measurement campaigns planning used in geodesy is conducted exclusively for individual points. For the natural process aimed at the adoption of the introduction of the planning (prediction of constellation state in navigation, which is characterized by the movement, one should adopt measurement campaigns planning for linear objects. In contrast to the existing planning solutions, focused on point presentation of the state of the constellation of navigation system, the author of this article rearranges the proposal of determination of geometrical factors, and their summation. In the presented simulation, one has specified the route of passing at certain times and it was assumed that the receiver will move with variable motion. One has defined the geometric ratios (PDOP, which allow to distinguish the results corresponding to the adopted criteria for the measurement of linear object to be conducted with the best possible accuracy.

  9. Operational considerations in specifying legal weight vehicles for the highway transport of spent nuclear fuel

    International Nuclear Information System (INIS)

    Hill, C.V.; Rutenkroger, E.O.; Ratledge, J.E.

    1990-01-01

    This paper presents the results of a research project in which tractor manufacturers and carrier companies were interviewed to gather information on operational concerns in specifying a tractor to haul legal weight spent fuel casks. The system was assumed to operate very close to the 80,000 pound legal weight limit. Safety, performance, reliability, and maintainability of equipment were factors given particular attention. The interaction between driver fatigue, safety, and equipment was also discussed. Innovative operating strategies that could save weight were discussed. The paper concluded that operational considerations require that planners working with standard off-the-shelf tractor equipment should allow at least 17,350 pounds for the weight of the tractor as a starting point from which further weight reduction analysis can proceed. 4 refs., 3 figs

  10. Violation of Bloch's Law That Specifies Reciprocity of Intensity and Duration with Brief Light Flashes

    Directory of Open Access Journals (Sweden)

    Ernest Greene

    2013-12-01

    Full Text Available For more than a century researchers have been reporting that the visual impact of a very brief flash is determined by the quantity of photons that the flash delivers. This has been variously described as the Bunsen-Roscoe Law or Bloch's Law, often specified as reciprocity of intensity × duration. Prior research found no evidence for such reciprocity when microsecond-duration flashes from a light-emitting diode array were used to display the major contours of nameable shapes. The present work tested with flash durations ranging up to 100 ms and also found no reciprocity. This departure from classic principles might be due to the specific range of wavelengths of the light-emitting diodes and to a mesopic level of ambient light, which together would preclude activation of rods. The reciprocity of intensity and duration may only be valid with full dark adaptation and very dim flashes that activate rods.

  11. Use of a concise prescription for specifying absolute dose distribution in external beam radiation therapy

    International Nuclear Information System (INIS)

    Viggers, D.A.; Shalev, S.

    1989-01-01

    Radiation therapy dose distributions are usually calculated relative to some normalization point to which a prescribed dose in grays is to be delivered. Often the radiation therapist requests that the prescribed dose be delivered to some other point(s), such as the 90% isodose. Therefore the prescribed dose is not well defined. Furthermore, this procedure leaves the shape of the dose distribution unspecified. The authors have used a dose prescription specifying the volumes of target and nontarget tissue that must lie within dose limits stated in grays. These dose-volume limits determine the magnitude and shape of the dose distribution. The prescription is well defined while allowing the absolute dose at a chosen point to be adjusted so that the dose distribution satisfies the prescription

  12. [Non-autistic pervasive developmental disorders: Rett syndrome, disintegrative disorder and pervasive developmental disorder not otherwise specified

    NARCIS (Netherlands)

    Mercadante, M.T.; Gaag, R.J. van der; Schwartzman, J.S.

    2006-01-01

    The category "Pervasive Developmental Disorders" includes autistic disorder, Asperger's syndrome, Rett's syndrome, childhood disintegrative disorder, and a residual category, named pervasive developmental disorder not otherwise specified. In this review, Rett's syndrome and childhood disintegrative

  13. Assembly and dynamics of the bacteriophage T4 homologous recombination machinery

    Directory of Open Access Journals (Sweden)

    Morrical Scott W

    2010-12-01

    Full Text Available Abstract Homologous recombination (HR, a process involving the physical exchange of strands between homologous or nearly homologous DNA molecules, is critical for maintaining the genetic diversity and genome stability of species. Bacteriophage T4 is one of the classic systems for studies of homologous recombination. T4 uses HR for high-frequency genetic exchanges, for homology-directed DNA repair (HDR processes including DNA double-strand break repair, and for the initiation of DNA replication (RDR. T4 recombination proteins are expressed at high levels during T4 infection in E. coli, and share strong sequence, structural, and/or functional conservation with their counterparts in cellular organisms. Biochemical studies of T4 recombination have provided key insights on DNA strand exchange mechanisms, on the structure and function of recombination proteins, and on the coordination of recombination and DNA synthesis activities during RDR and HDR. Recent years have seen the development of detailed biochemical models for the assembly and dynamics of presynaptic filaments in the T4 recombination system, for the atomic structure of T4 UvsX recombinase, and for the roles of DNA helicases in T4 recombination. The goal of this chapter is to review these recent advances and their implications for HR and HDR mechanisms in all organisms.

  14. Regulation of Rad51-Mediated Homologous Recombination by BRCA2, DSS1 and RAD52

    DEFF Research Database (Denmark)

    Rants, Louise Olthaver Juhl

    Homologous recombination (HR) provides a mechanism to restore integrity and maintain stability of the genetic material. HR is a major pathway for repair of DNA double-strand breaks (DSB), recovery of broken replication forks and generation of meiotic crossovers. The defining step in HR is homolog......Homologous recombination (HR) provides a mechanism to restore integrity and maintain stability of the genetic material. HR is a major pathway for repair of DNA double-strand breaks (DSB), recovery of broken replication forks and generation of meiotic crossovers. The defining step in HR...... is homologous strand exchange directed by the RecA-related recombinase Rad51. BRCA2 participates in HR by mediating Rad51 homology-directed repair. Both BRCA2 and Rad51 are essential for HR, DNA repair, and the maintenance of genome stability. In the present study, we seek to understand the mechanism of BRCA2...... with RAD52-mediated repair at sites of CPT-induced DNA damage. The synthetic lethality approach using RAD52 small molecule inhibitors in brca-deficient cancers is a promising therapeutic strategy for cancer treatment....

  15. Evaluation of the DSM-5 Severity Specifier for Bulimia Nervosa in Treatment-Seeking Youth.

    Science.gov (United States)

    Dakanalis, Antonios; Colmegna, Fabrizia; Zanetti, Maria Assunta; Di Giacomo, Ester; Riva, Giuseppe; Clerici, Massimo

    2018-02-01

    A new severity specifier for bulimia nervosa (BN), based on the frequency of inappropriate weight compensatory behaviours (e.g., laxative misuse, self-induced vomiting, fasting, diuretic misuse, and excessive exercise), has been added to the most recent (fifth) edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) as a means of addressing variability and heterogeneity in the severity of the disorder. While existing research provides support for the DSM-5 severity specifier for BN in adult patients, evidence for its validity and clinical utility in youth is currently lacking. To address this gap, data from 272 treatment-seeking adolescents with DSM-5 BN (94.2% female, M age  = 15.3 years, SD 1.7) were analysed to examine whether these patients, sub-grouped based on the DSM-5 severity definitions, would show meaningful differences in a broad range of clinical variables and demographic and physical characteristics. Analyses revealed that participants categorized with mild, moderate, severe, and extreme severity of BN significantly differed from each other in 15 variables regarding eating disorder pathological features and putative maintenance factors (i.e., core low self-esteem, perfectionism, social appearance anxiety, body surveillance, and mood intolerance), health-related quality of life and comorbid psychiatric (i.e., affective and anxiety) disorders (large effect sizes). Between-group differences in demographics, body mass index, or age-of-BN onset were not observed. Collectively, our findings provide support for the utility of the frequency of inappropriate weight compensatory behaviours as a severity indicator for BN and suggest that age-at-onset of BN is probably more disorder- than severity-dependent. Implications for future research are outlined.

  16. Schedules of requirements for the transport of specified types of radioactive material consignments

    International Nuclear Information System (INIS)

    1986-01-01

    These Schedules have been prepared as a companion document to the 1985 Edition of the Transport Regulations (Safety Series No. 6). As presented here, the Schedules also reflect the corrections and changes implemented by the 1986 Supplement to the Regulations for the Safe Transport of Radioactive Material. Direct cross-referencing to the paragraphs, tables and figures in the Regulations is made, and the use of both the International System of Units (SI) and the formerly accepted, traditional units is continued. In many cases, due to rounding off the numbers, the two values for a given parameter for the two units may differ somewhat. To move toward international use of SI units and to avoid inconsistencies, the values for the SI units are controlling in all cases. These Schedules are provided only as an aid to users of the Regulations and the provisions of the Regulations take precedence over the Schedules. These Schedules also serve as a generic model of the Schedules which are part of modal international regulatory documents, such as the International Maritime Dangerous Goods (IMDG) Code of the International Maritime Organization (IMO), the European Agreement Concerning the International Carriage of Dangerous Goods by Road (ADR) and the International Convention Concerning the Carriage of Dangerous Goods by Rail (CIM/RID). For regulatory purposes, reference shall be made to the detailed provisions of the Regulations specified in Safety Series No. 6. The Schedules do not reproduce the provisions of the Regulations in detail nor do they contain any additional requirements. They merely provide a summary of the main provisions for each specified type of radioactive material, references being provided to the relevant detailed provisions of the Regulations to enable these to be consulted where necessary. A table summarizing package, shipment approval, and notification requirements of the Regulations is provided

  17. A Test of the Empirical Profile and Coherence of the DSM-5 Psychopathy Specifier.

    Science.gov (United States)

    Miller, Joshua D; Lamkin, Joanna; Maples-Keller, Jessica L; Sleep, Chelsea E; Lynam, Donald R

    2017-11-13

    The Diagnostic and Statistical Manual of Mental Disorders-5th edition (DSM-5; American Psychiatric Association, 2013) introduced a psychopathy specifier (DSM-5 PS) as part of the Section III diagnostic model of antisocial personality disorder. Designed to capture the construct of fearless dominance/boldness, the DSM-5 PS is assessed on the basis of the presence of low scores on traits of withdrawal and anxiousness, and high scores on attention seeking. These constructs have garnered attention in the past decade but are the subject of substantial debate as to their role in the conceptualization and assessment of psychopathy, given their limited relations to the maladaptive outcomes typically associated with this personality disorder. In the current study (N = 340 undergraduates; 170 informants), we examined the DSM-5 PS, both in composite form and its trait subscales, to investigate the degree to which the DSM-5 PS manifested empirical profiles associated with psychopathy and its maladaptive correlates. Consistent with prior fearless dominance/boldness research, the DSM-5 PS manifested limited relations with other components of psychopathy, symptoms of DSM-5 Section II and III antisocial personality disorder, and self- and informant-related impairment scores. When examined at the individual subscale level, the 3 DSM-5 PS subscales manifested only partially overlapping profiles and only 1 of the 3-Attention Seeking-demonstrated an association with maladaptivity (e.g., externalizing behaviors). These findings raise important concerns about the coherence and utility of the DSM-5 PS as a diagnostic specifier included in a psychiatric nosology. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  18. Zebrafish Mnx proteins specify one motoneuron subtype and suppress acquisition of interneuron characteristics

    Directory of Open Access Journals (Sweden)

    Seredick Steve D

    2012-11-01

    Full Text Available Abstract Background Precise matching between motoneuron subtypes and the muscles they innervate is a prerequisite for normal behavior. Motoneuron subtype identity is specified by the combination of transcription factors expressed by the cell during its differentiation. Here we investigate the roles of Mnx family transcription factors in specifying the subtypes of individually identified zebrafish primary motoneurons. Results Zebrafish has three Mnx family members. We show that each of them has a distinct and temporally dynamic expression pattern in each primary motoneuron subtype. We also show that two Mnx family members are expressed in identified VeLD interneurons derived from the same progenitor domain that generates primary motoneurons. Surprisingly, we found that Mnx proteins appear unnecessary for differentiation of VeLD interneurons or the CaP motoneuron subtype. Mnx proteins are, however, required for differentiation of the MiP motoneuron subtype. We previously showed that MiPs require two temporally-distinct phases of Islet1 expression for normal development. Here we show that in the absence of Mnx proteins, the later phase of Islet1 expression is initiated but not sustained, and MiPs become hybrids that co-express morphological and molecular features of motoneurons and V2a interneurons. Unexpectedly, these hybrid MiPs often extend CaP-like axons, and some MiPs appear to be entirely transformed to a CaP morphology. Conclusions Our results suggest that Mnx proteins promote MiP subtype identity by suppressing both interneuron development and CaP axon pathfinding. This is, to our knowledge, the first report of transcription factors that act to distinguish CaP and MiP subtype identities. Our results also suggest that MiP motoneurons are more similar to V2 interneurons than are CaP motoneurons.

  19. Validity and utility of the DSM-5 severity specifier for binge-eating disorder.

    Science.gov (United States)

    Dakanalis, Antonios; Colmegna, Fabrizia; Riva, Giuseppe; Clerici, Massimo

    2017-08-01

    To test both the concurrent and predictive significance of the new DSM-5 severity specifier for binge-eating disorder (BED) in adult outpatients. Existing data from 195 adults with DSM-5 BED who received evidence-based treatment (manual-based cognitive-behavioral therapy) in an outpatient setting were re-analysed to examine whether these patients sub-grouped according to the DSM-5 severity levels, defined by the frequency of binge-eating (BE) episodes, would show meaningful differences in a range of variables of clinical interest assessed at pre-treatment and end-of treatment abstinence from BE. Participants categorized with mild (33.3% of the sample), moderate (35.4%), severe (15.9%), and extreme (15.4%) severity of BED, based on their pre-treatment clinician-rated frequency of BE episodes, differed significantly from each other in physical characteristics (body mass index) and another sixteen variables of clinical interest assessed at pre-treatment regarding eating disorder psychopathology and putative maintenance factors, lifetime and current psychiatric disorder comorbidity, general psychiatric distress, and psychosocial impairment. The four DSM-5 severity groups were statistically indistinguishable in demographics or age-of-BED onset. However, significant between-group differences were observed in the treatment outcome, i.e., abstinence from BE, achieved by 98.5%, 66.7%, 38.7% and 6.7% of participants categorized with mild, moderate, severe, and extreme severity respectively. The outcome analyses repeated in the completer sample (n = 187) yielded the same pattern of the aforementioned intent-to-treat (N = 195) results. The findings provide support for the severity specifier for BED introduced in the DSM-5 as a means of addressing within-group variability in severity. © 2017 Wiley Periodicals, Inc.

  20. Budgetary and Economic Outcomes Under Paths for Federal Revenues and Noninterest Spending Specified by Chairman Price, March 2016

    Science.gov (United States)

    2016-03-01

    Budgetary and Economic Outcomes Under Paths for Federal Revenues and Noninterest Spending Specified by Chairman Price , March 2016 March 2016CONGRESS... Price and His Staff 1 The Extended Baseline and Three Illustrative Paths 1 How CBO Analyzed the Effects of the Budgetary Paths 3 What Would Outcomes...Be Under Current Law? 4 What Paths for Federal Revenues and Noninterest Spending Did Chairman Price Specify? 6 What Would Budgetary and Economic

  1. Carboxy-terminal truncation activates glp-1 protein to specify vulval fates in Caenorhabditis elegans.

    Science.gov (United States)

    Mango, S E; Maine, E M; Kimble, J

    1991-08-29

    The glp-1 and lin-12 genes encode homologous transmembrane proteins that may act as receptors for cell interactions during development. The glp-1 product is required for induction of germ-line proliferation and for embryogenesis. By contrast, lin-12 mediates somatic cell interactions, including those between the precursor cells that form the vulval hypodermis (VPCs). Here we analyse an unusual allele of glp-1, glp-1(q35), which displays a semidominant multivulva phenotype (Muv), as well as the typical recessive, loss-of-function Glp phenotypes (sterility and embryonic lethality). We find that the effects of glp-1(q35) on VPC development mimic those of dominant lin-12 mutations, even in the absence of lin-12 activity. The glp-1(q35) gene bears a nonsense mutation predicted to eliminate the 122 C-terminal amino acids, including a ProGluSerThr (PEST) sequence thought to destabilize proteins. We suggest that the carboxy terminus bears a negative regulatory domain which normally inactivates glp-1 in the VPCs. We propose that inappropriate glp-1(q35) activity can substitute for lin-12 to determine vulval fate, perhaps by driving the VPCs to proliferate.

  2. Transcription patterns of genes encoding four metallothionein homologs in Daphnia pulex exposed to copper and cadmium are time- and homolog-dependent

    International Nuclear Information System (INIS)

    Asselman, Jana; Shaw, Joseph R.; Glaholt, Stephen P.; Colbourne, John K.; De Schamphelaere, Karel A.C.

    2013-01-01

    Highlights: •Transcription patterns of 4 metallothionein isoforms in Daphnia pulex. •Under cadmium and copper stress these patterns are time-dependent. •Under cadmium and copper stress these patterns are homolog-dependent. •The results stress the complex regulation of metallothioneins. -- Abstract: Metallothioneins are proteins that play an essential role in metal homeostasis and detoxification in nearly all organisms studied to date. Yet discrepancies between outcomes of chronic and acute exposure experiments hamper the understanding of the regulatory mechanisms of their isoforms following metal exposure. Here, we investigated transcriptional differences among four identified homologs (mt1–mt4) in Daphnia pulex exposed across time to copper and cadmium relative to a control. Transcriptional upregulation of mt1 and mt3 was detected on day four following exposure to cadmium, whereas that of mt2 and mt4 was detected on day two and day eight following exposure to copper. These results confirm temporal and metal-specific differences in the transcriptional induction of genes encoding metallothionein homologs upon metal exposure which should be considered in ecotoxicological monitoring programs of metal-contaminated water bodies. Indeed, the mRNA expression patterns observed here illustrate the complex regulatory system associated with metallothioneins, as these patterns are not only dependent on the metal, but also on exposure time and the homolog studied. Further phylogenetic analysis and analysis of regulatory elements in upstream promoter regions revealed a high degree of similarity between metallothionein genes of Daphnia pulex and Daphnia magna, a species belonging to the same genus. These findings, combined with a limited amount of available expression data for D. magna metallothionein genes, tentatively suggest a potential generalization of the metallothionein response system between these Daphnia species

  3. Transcription patterns of genes encoding four metallothionein homologs in Daphnia pulex exposed to copper and cadmium are time- and homolog-dependent

    Energy Technology Data Exchange (ETDEWEB)

    Asselman, Jana, E-mail: jana.asselman@ugent.be [Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, Ghent (Belgium); Shaw, Joseph R.; Glaholt, Stephen P. [The School of Public and Environmental Affairs, Indiana University, Bloomington, IN (United States); Colbourne, John K. [School of Biosciences, The University of Birmingham, Birmingham (United Kingdom); De Schamphelaere, Karel A.C. [Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, Ghent (Belgium)

    2013-10-15

    Highlights: •Transcription patterns of 4 metallothionein isoforms in Daphnia pulex. •Under cadmium and copper stress these patterns are time-dependent. •Under cadmium and copper stress these patterns are homolog-dependent. •The results stress the complex regulation of metallothioneins. -- Abstract: Metallothioneins are proteins that play an essential role in metal homeostasis and detoxification in nearly all organisms studied to date. Yet discrepancies between outcomes of chronic and acute exposure experiments hamper the understanding of the regulatory mechanisms of their isoforms following metal exposure. Here, we investigated transcriptional differences among four identified homologs (mt1–mt4) in Daphnia pulex exposed across time to copper and cadmium relative to a control. Transcriptional upregulation of mt1 and mt3 was detected on day four following exposure to cadmium, whereas that of mt2 and mt4 was detected on day two and day eight following exposure to copper. These results confirm temporal and metal-specific differences in the transcriptional induction of genes encoding metallothionein homologs upon metal exposure which should be considered in ecotoxicological monitoring programs of metal-contaminated water bodies. Indeed, the mRNA expression patterns observed here illustrate the complex regulatory system associated with metallothioneins, as these patterns are not only dependent on the metal, but also on exposure time and the homolog studied. Further phylogenetic analysis and analysis of regulatory elements in upstream promoter regions revealed a high degree of similarity between metallothionein genes of Daphnia pulex and Daphnia magna, a species belonging to the same genus. These findings, combined with a limited amount of available expression data for D. magna metallothionein genes, tentatively suggest a potential generalization of the metallothionein response system between these Daphnia species.

  4. Comparative anatomy, evolution, and homologies of tetrapod hindlimb muscles, comparison with forelimb muscles, and deconstruction of the forelimb-hindlimb serial homology hypothesis.

    Science.gov (United States)

    Diogo, Rui; Molnar, Julia

    2014-06-01

    For more than two centuries, the idea that the forelimb and hindlimb are serially homologous structures has been accepted without serious question. This study presents the first detailed analysis of the evolution and homologies of all hindlimb muscles in representatives of each major tetrapod group and proposes a unifying nomenclature for these muscles. These data are compared with information obtained previously about the forelimb muscles of tetrapods and the muscles of other gnathostomes in order to address one of the most central and enigmatic questions in evolutionary and comparative anatomy: why are the pelvic and pectoral appendages of gnathostomes generally so similar to each other? An integrative analysis of the new myological data, combined with a review of recent paleontological, developmental, and genetic works and of older studies, does not support serial homology between the structures of these appendages. For instance, many of the strikingly similar forelimb and hindlimb muscles found in each major extant tetrapod taxon were acquired at different geological times and/or have different embryonic origins. These similar muscles are not serial homologues, but the result of evolutionary parallelism/convergence due to a complex interplay of ontogenetic, functional, topological, and phylogenetic constraints/factors. Copyright © 2014 Wiley Periodicals, Inc.

  5. Biochemical and Structural Analysis of Hormone-sensitive Lipase Homolog EstE7: Insight into the Stabilized Dimerization of HSL-Homolog Proteins

    International Nuclear Information System (INIS)

    Nam, Ki Hyun; Park, Sung Ha; Lee, Won Ho; Hwang, Kwang Yeon

    2010-01-01

    Hormone sensitive lipase (HSL) plays a major role in energy homeostasis and lipid metabolism. Several crystal structures of HSL-homolog proteins have been identified, which has led to a better understanding of its molecular function. HSLhomolog proteins exit as both monomer and dimer, but the biochemical and structural basis for such oligomeric states has not been successfully elucidated. Therefore, we determined the crystal structure of HSL-homolog protein EstE7 from a metagenome library at 2.2 A resolution and characterized the oligomeric states of EstE7 both structurally and biochemically. EstE7 protein prefers the dimeric state in solution, which is supported by its higher enzymatic activity in the dimeric state. In the crystal form, EstE7 protein shows two-types of dimeric interface. Specifically, dimerization via the external β8-strand occurred through tight association between two pseudosymmetric folds via salt bridges, hydrogen bonds and van der Waals interactions. This dimer formation was similar to that of other HSL-homolog protein structures such as AFEST, BEFA, and EstE1. We anticipate that our results will provide insight into the oligomeric state of HSLhomolog proteins

  6. Analysis of ultraviolet and X-ray observations of three homologous solar flares from SMM

    Science.gov (United States)

    Cheng, Chung-Chieh; Pallavicini, Roberto

    1987-01-01

    Three homologous flares observed in the UV lines of Fe XXI and O V and in X-rays from the SMM were studied. It was found that: (1) the homology of the flares was most noticeable in Fe XXI and soft X-ray emissions; (2) the three flares shared many of the same loop footprints which were located in O V bright kernals associated with hard X-ray bursts; and (3) in spite of the strong spatial homology, the temporal evolution in UV and X-ray emissions varied from flare to flare. A comparison between the UV observations and photospheric magnetograms revealed that the basic flare configuration was a complex loop system consisting of many loops or bundles of loops.

  7. Homological Order in Three and Four dimensions: Wilson Algebra, Entanglement Entropy and Twist Defects

    Science.gov (United States)

    Roy, Abhishek; Chen, Xiao; Teo, Jeffrey

    2013-03-01

    We investigate homological orders in two, three and four dimensions by studying Zk toric code models on simplicial, cellular or in general differential complexes. The ground state degeneracy is obtained from Wilson loop and surface operators, and the homological intersection form. We compute these for a series of closed 3 and 4 dimensional manifolds and study the projective representations of mapping class groups (modular transformations). Braiding statistics between point and string excitations in (3+1)-dimensions or between dual string excitations in (4+1)-dimensions are topologically determined by the higher dimensional linking number, and can be understood by an effective topological field theory. An algorithm for calculating entanglemnent entropy of any bipartition of closed manifolds is presented, and its topological signature is completely characterized homologically. Extrinsic twist defects (or disclinations) are studied in 2,3 and 4 dimensions and are shown to carry exotic fusion and braiding properties. Simons Fellowship

  8. Coal and biomass-based chemicals via carbonylation, hydroformylation and homologation reactions

    Energy Technology Data Exchange (ETDEWEB)

    Sunavala, P.D.; Raghunath, B.

    The paper emphasizes the importance of carbonylation, hydroformylation and homologation reactions in the manufacture of organic chemicals (such as acetic acid, acetic anhydride, cellulose acetate, vinyl acetate monomer, aliphatic amines, isocyanates, methanol, ethanol, n-butanol, ethylene glycol, acrylic acid, etc.) from coal and biomass feedstocks. Topics covered are: synthesis of acetic acid; manufacture of acetic anhydride; synthesis of vinyl acetate monomer by carbonylation; synthesis of aliphatic amines by hydroformylation; synthesis of organic diisocyanates; ethanol synthesis by homologation of methanol; synthesis of ethylene glycol via hydroformylation of formaldehyde; synthesis of n- butanol and n-butyraldehyde by propylene formylation; synthesis of acrylic acid; homologation reaction of carboxylic acid esters with ruthenium catalysts; and synthesis of phenyl isocyanate from nitrobenzene by reductive carbonylation. 26 refs.

  9. Current status of grafts and implants in rhinoplasty: Part II. Homologous grafts and allogenic implants.

    Science.gov (United States)

    Sajjadian, Ali; Naghshineh, Nima; Rubinstein, Roee

    2010-03-01

    After reading this article, the participant should be able to: 1. Understand the challenges in restoring volume and structural integrity in rhinoplasty. 2. Identify the appropriate uses of various homologous grafts and allogenic implants in reconstruction, including: (a) freeze-dried acellular allogenic cadaveric dermis grafts, (b) irradiated cartilage grafts, (c) hydroxyapatite mineral matrix, (d) silicone implants, (e) high-density polyethylene implants, (f) polytetrafluoroethylene implants, and (g) injectable filler materials. 3. Identify the advantages and disadvantages of each of these biomaterials. 4. Understand the specific techniques that may aid in the use these grafts or implants. This review specifically addresses the use of homologous grafts and allogenic implants in rhinoplasty. It is important to stress that autologous materials remain the preferred graft material for use in rhinoplasty, owing to their high biocompatibility and low risk of infection and extrusion. However, concerns of donor-site morbidity, graft availability, and graft resorption have motivated the development and use of homologous and allogenic implants.

  10. FBH1 helicase disrupts RAD51 filaments in vitro and modulates homologous recombination in mammalian cells

    DEFF Research Database (Denmark)

    Simandlova, Jitka; Zagelbaum, Jennifer; Payne, Miranda J

    2013-01-01

    Efficient repair of DNA double strand breaks and interstrand cross-links requires the homologous recombination (HR) pathway, a potentially error-free process that utilizes a homologous sequence as a repair template. A key player in HR is RAD51, the eukaryotic ortholog of bacterial RecA protein. RAD......51 can polymerize on DNA to form a nucleoprotein filament that facilitates both the search for the homologous DNA sequences and the subsequent DNA strand invasion required to initiate HR. Because of its pivotal role in HR, RAD51 is subject to numerous positive and negative regulatory influences...... filaments on DNA through its ssDNA translocase function. Consistent with this, a mutant mouse embryonic stem cell line with a deletion in the FBH1 helicase domain fails to limit RAD51 chromatin association and shows hyper-recombination. Our data are consistent with FBH1 restraining RAD51 DNA binding under...

  11. Uptake and Persistence of Homologous and Heterologous Zooxanthellae in the Temperate Sea Anemone Cereus pedunculatus (Pennant).

    Science.gov (United States)

    Davy, S K; Lucas, I A N; Turner, J R

    1997-04-01

    The uptake and persistence of symbiotic dinoflagellates (zooxanthellae) were measured in the temperate sea anemone Cereus pedunculatus (Pennant). Aposymbiotic specimens of C. pedunculatus were inoculated with zooxanthellae freshly isolated from a range of temperate and subtropical Anthozoa. Each inoculate consisted of zooxanthellae from a single host species and was either homologous (zooxanthellae from a host of the same species as the one being inoculated) or heterologous (from a host of a different species than the one being inoculated). The densities of zooxanthellae in host tissues were determined at regular intervals. C. pedunculatus took up homologous and heterologous zooxanthellae to similar degrees, except for zooxanthellae from the temperate Anthopleura ballii, which were taken up to a lesser extent. The densities of all zooxanthellae declined between 4 hours and 4 days after uptake, indicating that zooxanthellae were expelled, digested, or both during this period. The densities of all zooxanthellae increased between 2 and 8 weeks after inoculation, indicating zooxanthella growth. Over the entire 8-week period after uptake, densities of homologous zooxanthellae were always greater than those of heterologous zooxanthellae. Between 8 and 36 weeks after infection, densities of homologous zooxanthellae declined markedly and densities of some heterologous zooxanthellae increased further, resulting in homologous and heterologous zooxanthella densities being the same at 36 weeks. These densities were the same as those in naturally infected C. pedunculatus of similar size. The results suggest that zooxanthellae from a range of host species and environments can establish symbioses with C. pedunculatus and that, over long periods under laboratory conditions, heterologous zooxanthellae may populate C. pedunculatus to the same extent as homologous zooxanthellae.

  12. Long-term use and follow-up of autologous and homologous cartilage graft in rhinoplasty

    Directory of Open Access Journals (Sweden)

    Ghasemali Khorasani

    2016-05-01

    Full Text Available Background: Cartilage grafting is used in rhinoplasty and reconstructive surgeries. Autologous rib and nasal septum cartilage (auto graft is the preferred source of graft material in rhinoplasty, however, homologous cartilage (allograft has been extensively used to correct the nasal framework in nasal deformities. Autologous cartilage graft usage is restricted with complication of operation and limiting availability of tissue for extensive deformities. Alternatively, preserved costal cartilage allograft represents a readily available and easily contoured material. The current study was a formal systematic review of complications associated with autologous versus homologous cartilage grafting in rhinoplasty patients. Methods: In this cohort retrospective study, a total of 124 patients undergone primary or revision rhinoplasty using homologous or autologus grafts with postoperative follow-up ranging from 6 to 60 months were studied. The types of grafts and complications related to the grafts were evaluated. This included evaluation for warping, infection, resorption, mobility and fracture. Results: The total complications related to the cartilage grafts were 7 cases, which included 1 warped in auto graft group, three cases of graft displacement (two in allograft group and one in auto graft group and three fractures in allograft group. No infection and resorption was recorded. Complication rate (confidence interval 0.95 in autologous and homologous group were 1.25(0.4-3.88 and 2.08(0.78-5.55 in 1000 months follow up. There was no statistically significant difference between autologous and homologous group complications. Onset of complication in autologous and homologous group were 51.23(49.27-53.19 and 58.7(54.51-62.91 month respectively (P=0.81. Conclusion: The allograft cartilage has the advantage of avoiding donor-site scar. Moreover, it provides the same benefits as autologous costal cartilage with comparable complication rate. Therefore, it

  13. Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.

    Science.gov (United States)

    Omelchenko, Marina V; Galperin, Michael Y; Wolf, Yuri I; Koonin, Eugene V

    2010-04-30

    Evolutionarily unrelated proteins that catalyze the same biochemical reactions are often referred to as analogous - as opposed to homologous - enzymes. The existence of numerous alternative, non-homologous enzyme isoforms presents an interesting evolutionary problem; it also complicates genome-based reconstruction of the metabolic pathways in a variety of organisms. In 1998, a systematic search for analogous enzymes resulted in the identification of 105 Enzyme Commission (EC) numbers that included two or more proteins without detectable sequence similarity to each other, including 34 EC nodes where proteins were known (or predicted) to have distinct structural folds, indicating independent evolutionary origins. In the past 12 years, many putative non-homologous isofunctional enzymes were identified in newly sequenced genomes. In addition, efforts in structural genomics resulted in a vastly improved structural coverage of proteomes, providing for definitive assessment of (non)homologous relationships between proteins. We report the results of a comprehensive search for non-homologous isofunctional enzymes (NISE) that yielded 185 EC nodes with two or more experimentally characterized - or predicted - structurally unrelated proteins. Of these NISE sets, only 74 were from the original 1998 list. Structural assignments of the NISE show over-representation of proteins with the TIM barrel fold and the nucleotide-binding Rossmann fold. From the functional perspective, the set of NISE is enriched in hydrolases, particularly carbohydrate hydrolases, and in enzymes involved in defense against oxidative stress. These results indicate that at least some of the non-homologous isofunctional enzymes were recruited relatively recently from enzyme families that are active against related substrates and are sufficiently flexible to accommodate changes in substrate specificity.

  14. Simulation methods supporting homologation of Electronic Stability Control in vehicle variants

    Science.gov (United States)

    Lutz, Albert; Schick, Bernhard; Holzmann, Henning; Kochem, Michael; Meyer-Tuve, Harald; Lange, Olav; Mao, Yiqin; Tosolin, Guido

    2017-10-01

    Vehicle simulation has a long tradition in the automotive industry as a powerful supplement to physical vehicle testing. In the field of Electronic Stability Control (ESC) system, the simulation process has been well established to support the ESC development and application by suppliers and Original Equipment Manufacturers (OEMs). The latest regulation of the United Nations Economic Commission for Europe UN/ECE-R 13 allows also for simulation-based homologation. This extends the usage of simulation from ESC development to homologation. This paper gives an overview of simulation methods, as well as processes and tools used for the homologation of ESC in vehicle variants. The paper first describes the generic homologation process according to the European Regulation (UN/ECE-R 13H, UN/ECE-R 13/11) and U.S. Federal Motor Vehicle Safety Standard (FMVSS 126). Subsequently the ESC system is explained as well as the generic application and release process at the supplier and OEM side. Coming up with the simulation methods, the ESC development and application process needs to be adapted for the virtual vehicles. The simulation environment, consisting of vehicle model, ESC model and simulation platform, is explained in detail with some exemplary use-cases. In the final section, examples of simulation-based ESC homologation in vehicle variants are shown for passenger cars, light trucks, heavy trucks and trailers. This paper is targeted to give a state-of-the-art account of the simulation methods supporting the homologation of ESC systems in vehicle variants. However, the described approach and the lessons learned can be used as reference in future for an extended usage of simulation-supported releases of the ESC system up to the development and release of driver assistance systems.

  15. Evolutionary origin and divergence of GnIH and its homologous peptides.

    Science.gov (United States)

    Tsutsui, Kazuyoshi; Osugi, Tomohiro

    2009-03-01

    Probing undiscovered hypothalamic neuropeptides that play important roles in the regulation of pituitary function in vertebrates is essential for the progress of neuroendocrinology. In 2000, we discovered a novel hypothalamic dodecapeptide inhibiting gonadotropin release in quail and termed it gonadotropin-inhibitory hormone (GnIH). GnIH acts on the pituitary and gonadotropin-releasing hormone (GnRH) neurons in the hypothalamus via a novel G protein-coupled receptor for GnIH to inhibit gonadal development and maintenance by decreasing gonadotropin release and synthesis. Similar findings were observed in other avian species. Thus, GnIH is a key factor controlling avian reproduction. To give our findings a broader perspective, we also found GnIH homologous peptides in the hypothalamus of other vertebrates, such as mammals, reptiles, amphibians and teleosts. GnIH and its homologs share a common C-terminal LPXRFamide (X=L or Q) motif. A mammalian GnIH homolog also inhibited gonadotropin release in mammals like the GnIH action in birds. In contrast to higher vertebrates, hypophysiotropic activities of GnIH homologs were different in lower vertebrates. To clarify the evolutionary origin of GnIH and its homologs, we further sought to identify novel LPXRFamide peptides from the brain of sea lamprey and hagfish, two extant groups of the oldest lineage of vertebrates, Agnatha. In these agnathans, LPXRFamide peptide and its cDNA were identified only from the brain of hagfish. Based on these findings over the past decade, this paper summarizes the evolutionary origin and divergence of GnIH and its homologous peptides.

  16. Homological functor of a torsion free crystallographic group of dimension five with a nonabelian point group

    Science.gov (United States)

    Ting, Tan Yee; Idrus, Nor'ashiqin Mohd.; Masri, Rohaidah; Sarmin, Nor Haniza; Hassim, Hazzirah Izzati Mat

    2014-06-01

    Torsion free crystallographic groups, called Bieberbach groups, appear as fundamental groups of compact, connected, flat Riemannian manifolds and have many interesting properties. New properties of the group can be obtained by, not limited to, exploring the groups and by computing their homological functors such as nonabelian tensor squares, the central subgroup of nonabelian tensor squares, the kernel of the mapping of nonabelian tensor squares of a group to the group and many more. In this paper, the homological functor, J(G) of a centerless torsion free crystallographic group of dimension five with a nonabelian point group which is a dihedral point group is computed using commutator calculus.

  17. Two zebrafish G2A homologs activate multiple intracellular signaling pathways in acidic environment

    Energy Technology Data Exchange (ETDEWEB)

    Ichijo, Yuta; Mochimaru, Yuta [Laboratory of Cell Signaling Regulation, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571 (Japan); Azuma, Morio [Laboratory of Regulatory Biology, Graduate School of Science and Engineering, University of Toyama, 3190-Gofuku, Toyama 930-8555 (Japan); Satou, Kazuhiro; Negishi, Jun [Laboratory of Cell Signaling Regulation, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571 (Japan); Nakakura, Takashi [Department of Anatomy, Graduate School of Medicine, Teikyo University, 2-11-1 Itabashi-Ku, Tokyo 173-8605 (Japan); Oshima, Natsuki [Laboratory of Cell Signaling Regulation, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571 (Japan); Mogi, Chihiro; Sato, Koichi [Laboratory of Signal Transduction, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512 (Japan); Matsuda, Kouhei [Laboratory of Regulatory Biology, Graduate School of Science and Engineering, University of Toyama, 3190-Gofuku, Toyama 930-8555 (Japan); Okajima, Fumikazu [Laboratory of Signal Transduction, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512 (Japan); Tomura, Hideaki, E-mail: tomurah@meiji.ac.jp [Laboratory of Cell Signaling Regulation, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571 (Japan)

    2016-01-01

    Human G2A is activated by various stimuli such as lysophosphatidylcholine (LPC), 9-hydroxyoctadecadienoic acid (9-HODE), and protons. The receptor is coupled to multiple intracellular signaling pathways, including the G{sub s}-protein/cAMP/CRE, G{sub 12/13}-protein/Rho/SRE, and G{sub q}-protein/phospholipase C/NFAT pathways. In the present study, we examined whether zebrafish G2A homologs (zG2A-a and zG2A-b) could respond to these stimuli and activate multiple intracellular signaling pathways. We also examined whether histidine residue and basic amino acid residue in the N-terminus of the homologs also play roles similar to those played by human G2A residues if the homologs sense protons. We found that the zG2A-a showed the high CRE, SRE, and NFAT activities, however, zG2A-b showed only the high SRE activity under a pH of 8.0. Extracellular acidification from pH 7.4 to 6.3 ameliorated these activities in zG2A-a-expressing cells. On the other hand, acidification ameliorated the SRE activity but not the CRE and NFAT activities in zG2A-b-expressing cells. LPC or 9-HODE did not modify any activity of either homolog. The substitution of histidine residue at the 174{sup th} position from the N-terminus of zG2A-a to asparagine residue attenuated proton-induced CRE and NFAT activities but not SRE activity. The substitution of arginine residue at the 32nd position from the N-terminus of zG2A-a to the alanine residue also attenuated its high and the proton-induced CRE and NFAT activities. On the contrary, the substitution did not attenuate SRE activity. The substitution of the arginine residue at the 10th position from the N-terminus of zG2A-b to the alanine residue also did not attenuate its high or the proton-induced SRE activity. These results indicate that zebrafish G2A homologs were activated by protons but not by LPC and 9-HODE, and the activation mechanisms of the homologs were similar to those of human G2A. - Highlights: • Zebrafish two G2A homologs are proton

  18. An HMM posterior decoder for sequence feature prediction that includes homology information

    DEFF Research Database (Denmark)

    Käll, Lukas; Krogh, Anders Stærmose; Sonnhammer, Erik L. L.

    2005-01-01

    Motivation: When predicting sequence features like transmembrane topology, signal peptides, coil-coil structures, protein secondary structure or genes, extra support can be gained from homologs. Results: We present here a general hidden Markov model (HMM) decoding algorithm that combines probabil......Motivation: When predicting sequence features like transmembrane topology, signal peptides, coil-coil structures, protein secondary structure or genes, extra support can be gained from homologs. Results: We present here a general hidden Markov model (HMM) decoding algorithm that combines......://phobius.cgb.ki.se/poly.html . An implementation of the algorithm is available on request from the authors....

  19. Activation barriers for series of exothermic homologous reactions. VI. Reactions of lanthanide and transition metal atoms.

    Science.gov (United States)

    Blue, Alan S.; Fontijn, Arthur

    2001-09-01

    Semiempirical configuration interaction (SECI) theory to predict activation barriers, E, as given by k(T)=ATn exp(-E(RT), has been applied to homologous series of lanthanide (LN) and transition metal (TM) atom oxidation reactions. This was achieved by considering as homologous series reactions of elements differing only by the number of electrons in one subshell. Comparison between SECI and experimental results leads to an average deviation for the LN+N2O reactions of 0.66 kJ mol-1, and up to 5.5 kJ mol-1 for other series. Thirty-one activation barriers are reported.

  20. The mechanism of non-homologous end-joining: a synopsis of synapsis.

    Science.gov (United States)

    Weterings, Eric; van Gent, Dik C

    2004-11-02

    Repair of DNA double-strand breaks (DSBs) by non-homologous end-joining (NHEJ) is required for resistance to genotoxic agents, such as ionizing radiation, but also for proper development of the vertebrate immune system. Much progress has been made in identifying the factors that are involved in this repair pathway. We are now entering the phase in which we begin to understand basic concepts of the reaction mechanism and regulation of non-homologous end-joining. This review concentrates on novel insights into damage recognition and subsequent tethering, processing and joining of DNA ends.

  1. OCCURRENCE OF SMALL HOMOLOGOUS AND COMPLEMENTARY FRAGMENTS IN HUMAN VIRUS GENOMES AND THEIR POSSIBLE ROLE

    Directory of Open Access Journals (Sweden)

    E. P. Kharchenko

    2017-01-01

    Full Text Available With computer analysis occurrence of small homologous and complementary fragments (21 nucleotides in length has been studied in genomes of 14 human viruses causing most dangerous infections. The sample includes viruses with (+ and (– single stranded RNA and DNA-containing hepatitis A virus. Analysis of occurrence of homologous sequences has shown the existence two extreme situations. On the one hand, the same virus contains homologous sequences to almost all other viruses (for example, Ebola virus, severe acute respiratory syndrome-related coronavirus, and mumps virus, and numerous homologous sequences to the same other virus (especially in severe acute respiratory syndrome-related coronavirus to Dengue virus and in Ebola virus to poliovirus. On the other hand, there are rare occurrence and not numerous homologous sequences in genomes of other viruses (rubella virus, hepatitis A virus, and hepatitis B virus. Similar situation exists for occurrence of complementary sequences. Rubella virus, the genome of which has the high content of guanine and cytosine, has no complementary sequences to almost all other viruses. Most viruses have moderate level of occurrence for homologous and complementary sequences. Autocomplementary sequences are numerous in most viruses and one may suggest that the genome of single stranded RNA viruses has branched secondary structure. In addition to possible role in recombination among strains autocomplementary sequences could be regulators of translation rate of virus proteins and determine its optimal proportion in virion assembly with genome and mRNA folding. Occurrence of small homologous and complementary sequences in RNA- and DNA-containing viruses may be the result of multiple recombinations in the past and the present and determine their adaptation and variability. Recombination may take place in coinfection of human and/or common hosts. Inclusion of homologous and complementary sequences into genome could not

  2. Specifying the Concept of Future Generations for Addressing Issues Related to High-Level Radioactive Waste.

    Science.gov (United States)

    Kermisch, Celine

    2016-12-01

    The nuclear community frequently refers to the concept of "future generations" when discussing the management of high-level radioactive waste. However, this notion is generally not defined. In this context, we have to assume a wide definition of the concept of future generations, conceived as people who will live after the contemporary people are dead. This definition embraces thus each generation following ours, without any restriction in time. The aim of this paper is to show that, in the debate about nuclear waste, this broad notion should be further specified and to clarify the related implications for nuclear waste management policies. Therefore, we provide an ethical analysis of different management strategies for high-level waste in the light of two principles, protection of future generations-based on safety and security-and respect for their choice. This analysis shows that high-level waste management options have different ethical impacts across future generations, depending on whether the memory of the waste and its location is lost, or not. We suggest taking this distinction into account by introducing the notions of "close future generations" and "remote future generations", which has important implications on nuclear waste management policies insofar as it stresses that a retrievable disposal has fewer benefits than usually assumed.

  3. Biohydrogen production from specified risk materials co-digested with cattle manure

    Energy Technology Data Exchange (ETDEWEB)

    Gilroyed, Brandon H. [Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta T1J 4B1 (Canada); Department of Civil Engineering, Schulich School of Engineering, University of Calgary, Calgary, Alberta T2N 1N4 (Canada); Li, Chunli; Hao, Xiying; McAllister, Tim A. [Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta T1J 4B1 (Canada); Chu, Angus [Department of Civil Engineering, Schulich School of Engineering, University of Calgary, Calgary, Alberta T2N 1N4 (Canada)

    2010-02-15

    Biohydrogen production from the anaerobic digestion of specified risk materials (SRM) co-digested with cattle manure was assessed in a 3 x 5 factorial design. Total organic loading rates (OLR) of 10, 20, and 40 g L{sup -1} volatile solids (VS) were tested using manure:SRM (wt/wt) mixtures of 100:0 (control), 90:10, 80:20, 60:40, and 50:50 using five 2 L continuously stirred biodigesters operating at 55 C. Gas samples were taken daily to determine hydrogen production, and slurry samples were analyzed daily for volatile fatty acid (VFA) concentration, total ammonia nitrogen (TAN), and VS degradation. Hydrogen production (mL g{sup -1} VS fed) varied quadratically according to OLR (P < 0.01), with maximum production at OLR20, while production decreased linearly (P < 0.0001) as SRM concentration increased. Reduced hydrogen production associated with SRM inclusion at >10% VS may be attributed to a rapid increase in TAN (r = -0.55) or other inhibitors such as long chain fatty acids. Reduced hydrogen production (P < 0.01) at OLR40 versus OLR20 may be related to increased rate of VFA accumulation and final VFA concentration (P < 0.001), as well as inhibition due to hydrogen accumulation (P < 0.001). Biohydrogen production from SRM co-digested with cattle manure may not be feasible on an industrial scale due to reduced hydrogen production with increasing levels of SRM. (author)

  4. Combining Multiple Forms Of Visual Information To Specify Contact Relations In Spatial Layout

    Science.gov (United States)

    Sedgwick, Hal A.

    1990-03-01

    An expert system, called Layout2, has been described, which models a subset of available visual information for spatial layout. The system is used to examine detailed interactions between multiple, partially redundant forms of information in an environment-centered geometrical model of an environment obeying certain rather general constraints. This paper discusses the extension of Layout2 to include generalized contact relations between surfaces. In an environment-centered model, the representation of viewer-centered distance is replaced by the representation of environmental location. This location information is propagated through the representation of the environment by a network of contact relations between contiguous surfaces. Perspective information interacts with other forms of information to specify these contact relations. The experimental study of human perception of contact relations in extended spatial layouts is also discussed. Differences between human results and Layout2 results reveal limitations in the human ability to register available information; they also point to the existence of certain forms of information not yet formalized in Layout2.

  5. On the design of high-rise buildings with a specified level of reliability

    Science.gov (United States)

    Dolganov, Andrey; Kagan, Pavel

    2018-03-01

    High-rise buildings have a specificity, which significantly distinguishes them from traditional buildings of high-rise and multi-storey buildings. Steel structures in high-rise buildings are advisable to be used in earthquake-proof regions, since steel, due to its plasticity, provides damping of the kinetic energy of seismic impacts. These aspects should be taken into account when choosing a structural scheme of a high-rise building and designing load-bearing structures. Currently, modern regulatory documents do not quantify the reliability of structures. Although the problem of assigning an optimal level of reliability has existed for a long time. The article shows the possibility of designing metal structures of high-rise buildings with specified reliability. Currently, modern regulatory documents do not quantify the reliability of high-rise buildings. Although the problem of assigning an optimal level of reliability has existed for a long time. It is proposed to establish the value of reliability 0.99865 (3σ) for constructions of buildings and structures of a normal level of responsibility in calculations for the first group of limiting states. For increased (construction of high-rise buildings) and reduced levels of responsibility for the provision of load-bearing capacity, it is proposed to assign respectively 0.99997 (4σ) and 0.97725 (2σ). The coefficients of the use of the cross section of a metal beam for different levels of security are given.

  6. Multiple zebrafish atoh1 genes specify a diversity of neuronal types in the zebrafish cerebellum.

    Science.gov (United States)

    Kidwell, Chelsea U; Su, Chen-Ying; Hibi, Masahiko; Moens, Cecilia B

    2018-06-01

    A single Atoh1 basic-helix-loop-helix transcription factor specifies multiple neuron types in the mammalian cerebellum and anterior hindbrain. The zebrafish genome encodes three paralagous atoh1 genes whose functions in cerebellum and anterior hindbrain development we explore here. With use of a transgenic reporter, we report that zebrafish atoh1c-expressing cells are organized in two distinct domains that are separated both by space and developmental time. An early isthmic expression domain gives rise to an extracerebellar population in rhombomere 1 and an upper rhombic lip domain gives rise to granule cell progenitors that migrate to populate all four granule cell territories of the fish cerebellum. Using genetic mutants we find that of the three zebrafish atoh1 paralogs, atoh1c and atoh1a are required for the full complement of granule neurons. Surprisingly, the two genes are expressed in non-overlapping granule cell progenitor populations, indicating that fish use duplicate atoh1 genes to generate granule cell diversity that is not detected in mammals. Finally, live imaging of granule cell migration in wildtype and atoh1c mutant embryos reveals that while atoh1c is not required for granule cell specification per se, it is required for granule cells to delaminate and migrate away from the rhombic lip. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. Introducing the Guard-Stage-Milestone Approach for Specifying Business Entity Lifecycles

    Science.gov (United States)

    Hull, Richard; Damaggio, Elio; Fournier, Fabiana; Gupta, Manmohan; Heath, Fenno (Terry); Hobson, Stacy; Linehan, Mark; Maradugu, Sridhar; Nigam, Anil; Sukaviriya, Piyawadee; Vaculin, Roman

    A promising approach to managing business operations is based on business entities with lifecycles (BEL's) (a.k.a. business artifacts), i.e., key conceptual entities that are central to guiding the operations of a business, and whose content changes as they move through those operations. A BEL type includes both an information model that captures, in either materialized or virtual form, all of the business-relevant data about entities of that type, and a lifecycle model, that specifies the possible ways an entity of that type might progress through the business by responding to events and invoking services, including human activities. Most previous work on BEL's has focused on the use of lifecycle models based on variants of finite state machines. This paper introduces the Guard-Stage-Milestone (GSM) meta-model for lifecycles, which is an evolution of the previous work on BEL's. GSM lifecycles are substantially more declarative than the finite state machine variants, and support hierarchy and parallelism within a single entity instance. The GSM operational semantics are based on a form of Event-Condition-Action (ECA) rules, and provide a basis for formal verification and reasoning. This paper provides an informal, preliminary introduction to the GSM approach, and briefly overviews selected research directions.

  8. OPM Scheme Editor 2: A graphical editor for specifying object-protocol structures

    Energy Technology Data Exchange (ETDEWEB)

    Chen, I-Min A.; Markowitz, V.M.; Pang, F.; Ben-Shachar, O.

    1993-07-01

    This document describes an X-window based Schema Editor for the Object-Protocol Model (OPM). OPM is a data model that supports the specification of complex object and protocol classes. objects and protocols are qualified in OPM by attributes that are defined over (associated with) value classes. Connections of object and protocol classes are expressed in OPM via attributes. OPM supports the specification (expansion) of protocols in terms of alternative and sequences of component (sub) protocols. The OPM Schema Editor allows specifying, displaying, modifying, and browsing through OPM schemas. The OPM Schema Editor generates an output file that can be used as input to an OPM schema translation tool that maps OPM schemas into definitions for relational database management systems. The OPM Schema Editor was implemented using C++ and the X11 based Motif toolkit, on Sun SPARCstation under Sun Unix OS 4.1. This document consists of the following parts: (1) A tutorial consisting of seven introductory lessons for the OPM Schema Editor. (2) A reference manual describing all the windows and functions of the OPM Schema Editor. (3) An appendix with an overview of OPM.

  9. Performance characteristics of specified power reactors in multidimensional neutron diffusion problems

    International Nuclear Information System (INIS)

    Kim, M.G.

    1980-01-01

    The multigroup neutron diffusion equations with the constraint of specified power distributions are investigated by the application of the straight-line method which can be considered as the limiting case of zero mesh space in the finite difference method. The standard partial differential form of the diffusion equation is reduced to sets of ordinary differential equations and then converted into sets of integral equations by using Green's functions defined on the pseudo straight lines. Coupling of each straight line to the adjacent lines arises from the application of a three-point central difference formula. The interfaces encountered between two regions are taken into account by imposing the continuity conditions for the grown fluxes and net currents with Taylor expansions of internal fluxes at the interface positions. A few sample problems are selected to test the validity of the method. It is found that the proposed method of solution is similar to the finite Fourier sine transform. Numerical results for the solutions obtained by the method of straight lines are compared with the results of the exact analytical solutions for simple geometries. These comparisons indicate that the proposed method is compatible with the analytical method, and in some problems considered the straight-line solutions are much more efficient than the exact solutions. The method is also extended to the reactor kinetics problem by expressing the kinetics parameters in terms of the basis functions which are used to obtain the solutions of the steady-state neutron diffusion equations

  10. Enhancing the Adhesive Strength of a Plywood Adhesive Developed from Hydrolyzed Specified Risk Materials

    Directory of Open Access Journals (Sweden)

    Birendra B. Adhikari

    2016-08-01

    Full Text Available The current production of wood composites relies mostly on formaldehyde-based adhesives such as urea formaldehyde (UF and phenol formaldehyde (PF resins. As these resins are produced from non-renewable resources, and there are some ongoing issues with possible health hazard due to formaldehyde emission from such products, the purpose of this research was to develop a formaldehyde-free plywood adhesive utilizing waste protein as a renewable feedstock. The feedstock for this work was specified risk material (SRM, which is currently being disposed of either by incineration or by landfilling. In this report, we describe a technology for utilization of SRM for the development of an environmentally friendly plywood adhesive. SRM was thermally hydrolyzed using a Canadian government-approved protocol, and the peptides were recovered from the hydrolyzate. The recovered peptides were chemically crosslinked with polyamidoamine-epichlorohydrin (PAE resin to develop an adhesive system for bonding of plywood specimens. The effects of crosslinking time, peptides/crosslinking agent ratio, and temperature of hot pressing of plywood specimens on the strength of formulated adhesives were investigated. Formulations containing as much as 78% (wt/wt peptides met the ASTM (American Society for Testing and Materials specifications of minimum dry and soaked shear strength requirement for UF resin type adhesives. Under the optimum conditions tested, the peptides–PAE resin-based formulations resulted in plywood specimens having comparable dry as well as soaked shear strength to that of commercial PF resin.

  11. Methods for Specifying Scientific Data Standards and Modeling Relationships with Applications to Neuroscience

    Science.gov (United States)

    Rübel, Oliver; Dougherty, Max; Prabhat; Denes, Peter; Conant, David; Chang, Edward F.; Bouchard, Kristofer

    2016-01-01

    Neuroscience continues to experience a tremendous growth in data; in terms of the volume and variety of data, the velocity at which data is acquired, and in turn the veracity of data. These challenges are a serious impediment to sharing of data, analyses, and tools within and across labs. Here, we introduce BRAINformat, a novel data standardization framework for the design and management of scientific data formats. The BRAINformat library defines application-independent design concepts and modules that together create a general framework for standardization of scientific data. We describe the formal specification of scientific data standards, which facilitates sharing and verification of data and formats. We introduce the concept of Managed Objects, enabling semantic components of data formats to be specified as self-contained units, supporting modular and reusable design of data format components and file storage. We also introduce the novel concept of Relationship Attributes for modeling and use of semantic relationships between data objects. Based on these concepts we demonstrate the application of our framework to design and implement a standard format for electrophysiology data and show how data standardization and relationship-modeling facilitate data analysis and sharing. The format uses HDF5, enabling portable, scalable, and self-describing data storage and integration with modern high-performance computing for data-driven discovery. The BRAINformat library is open source, easy-to-use, and provides detailed user and developer documentation and is freely available at: https://bitbucket.org/oruebel/brainformat. PMID:27867355

  12. Whole-Body Motion Planning for Humanoid Robots by Specifying Via-Points

    Directory of Open Access Journals (Sweden)

    ChangHyun Sung

    2013-07-01

    Full Text Available We design a framework about the planning of whole body motion for humanoid robots. Motion planning with various constraints is essential to success the task. In this research, we propose a motion planning method corresponding to various conditions for achieving the task. We specify some via-points to deal with the conditions for target achievement depending on various constraints. Together with certain constraints including task accomplishment, the via-point representation plays a crucial role in the optimization process of our method. Furthermore, the via-points as the optimization parameters are related to some physical conditions. We applied this method to generate the kicking motion of a humanoid robot HOAP-3. We have confirmed that the robot was able to complete the task of kicking a ball over an obstacle into a goal in addition to changing conditions of the location of a ball. These results show that the proposed motion planning method using via-point representation can increase articulation of the motion.

  13. An attempt to specify thermal history in CZ silicon wafers and possibilities for its modification

    International Nuclear Information System (INIS)

    Kissinger, G.; Sattler, A.; Mueller, T.; Ammon, W. von

    2007-01-01

    The term thermal history of silicon wafers represents the whole variety of process parameters of crystal growth. The aim of this contribution is an attempt to specify thermal history by one parameter that is directly correlated to the bulk microdefect density. The parameter that reflects thermal history and correlates it with nucleation of oxide precipitates is the concentration of VO 2 complexes. The VO 2 concentration in silicon wafers is too low to be measured by FTIR but it can be obtained from the loss of interstitial oxygen during a standardized thermal treatment. Based on this, the vacancy concentration frozen during crystal cooling in the ingot can be calculated. RTA treatments above 1150 deg. C create a well defined level of the VO 2 concentration in silicon wafers. This means that a well controlled modification of the thermal history is possible. We also investigated the kinetics of reduction of the as-grown excess VO 2 concentration during RTA treatments at 950 deg. C and 1050 deg. C and the effectiveness of this attempt to totally delete the thermal history

  14. Specifying residential retrofit packages for 30 % reductions in energy consumption in hot-humid climate zones

    Energy Technology Data Exchange (ETDEWEB)

    Burgett, J.M.; Chini, A.R.; Oppenheim, P. [University of Florida, 573 Rinker Hall, Newell Drive, Gainesville, FL 32611 (United States)

    2013-08-15

    The purpose of this research was to demonstrate the application of energy simulation as an effective tool for specifying cost-effective residential retrofit packages that will reduce energy consumption by 30 %. Single-family homes in the hot-humid climate type of the Southeastern USA were used to demonstrate the application. US census data from both state and federal studies were used to create 12 computer simulation homes representing the most common characteristics of single-family houses specific to this area. Well-recognized energy efficiency measures (EEMs) were simulated to determine their cumulative energy reduction potential. Detailed cost estimates were created for cost-to-benefit analysis. For each of the 12 simulated homes, 4 packages of EEMs were created. The four packages provided home owners options for reducing their energy by 30 % along with the estimated up-front cost and simple payback periods. The simple payback period was used to determine how cost-effective a measure was. The packages are specific to a geographic area to provide a higher degree of confidence in the projected cost and energy savings. The study provides a generic methodology to create a similar 30 % energy reduction packages for other locations and a detailed description of a case study to serve as an example. The study also highlights the value that computer simulation models can have to develop energy efficiency packages cost-effectively and specific to home owner's location and housing type.

  15. Development of wide range charge integration application specified integrated circuit for photo-sensor

    Energy Technology Data Exchange (ETDEWEB)

    Katayose, Yusaku, E-mail: katayose@ynu.ac.jp [Department of Physics, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501 (Japan); Ikeda, Hirokazu [Institute of Space and Astronautical Science (ISAS)/Japan Aerospace Exploration Agency (JAXA), 3-1-1 Yoshinodai, Chuo-ku, Sagamihara, Kanagawa 252-5210 (Japan); Tanaka, Manobu [National Laboratory for High Energy Physics, KEK, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Shibata, Makio [Department of Physics, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501 (Japan)

    2013-01-21

    A front-end application specified integrated circuit (ASIC) is developed with a wide dynamic range amplifier (WDAMP) to read-out signals from a photo-sensor like a photodiode. The WDAMP ASIC consists of a charge sensitive preamplifier, four wave-shaping circuits with different amplification factors and Wilkinson-type analog-to-digital converter (ADC). To realize a wider range, the integrating capacitor in the preamplifier can be changed from 4 pF to 16 pF by a two-bit switch. The output of a preamplifier is shared by the four wave-shaping circuits with four gains of 1, 4, 16 and 64 to adapt the input range of ADC. A 0.25-μm CMOS process (of UMC electronics CO., LTD) is used to fabricate the ASIC with four-channels. The dynamic range of four orders of magnitude is achieved with the maximum range over 20 pC and the noise performance of 0.46 fC + 6.4×10{sup −4} fC/pF. -- Highlights: ► A front-end ASIC is developed with a wide dynamic range amplifier. ► The ASIC consists of a CSA, four wave-shaping circuits and pulse-height-to-time converters. ► The dynamic range of four orders of magnitude is achieved with the maximum range over 20 pC.

  16. Separate transcriptionally regulated pathways specify distinct classes of sister dendrites in a nociceptive neuron.

    Science.gov (United States)

    O'Brien, Barbara M J; Palumbos, Sierra D; Novakovic, Michaela; Shang, Xueying; Sundararajan, Lakshmi; Miller, David M

    2017-12-15

    The dendritic processes of nociceptive neurons transduce external signals into neurochemical cues that alert the organism to potentially damaging stimuli. The receptive field for each sensory neuron is defined by its dendritic arbor, but the mechanisms that shape dendritic architecture are incompletely understood. Using the model nociceptor, the PVD neuron in C. elegans, we determined that two types of PVD lateral branches project along the dorsal/ventral axis to generate the PVD dendritic arbor: (1) Pioneer dendrites that adhere to the epidermis, and (2) Commissural dendrites that fasciculate with circumferential motor neuron processes. Previous reports have shown that the LIM homeodomain transcription factor MEC-3 is required for all higher order PVD branching and that one of its targets, the claudin-like membrane protein HPO-30, preferentially promotes outgrowth of pioneer branches. Here, we show that another MEC-3 target, the conserved TFIIA-like zinc finger transcription factor EGL-46, adopts the alternative role of specifying commissural dendrites. The known EGL-46 binding partner, the TEAD transcription factor EGL-44, is also required for PVD commissural branch outgrowth. Double mutants of hpo-30 and egl-44 show strong enhancement of the lateral branching defect with decreased numbers of both pioneer and commissural dendrites. Thus, HPO-30/Claudin and EGL-46/EGL-44 function downstream of MEC-3 and in parallel acting pathways to direct outgrowth of two distinct classes of PVD dendritic branches. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Microbial communities and greenhouse gas emissions associated with the biodegradation of specified risk material in compost

    International Nuclear Information System (INIS)

    Xu, Shanwei; Reuter, Tim; Gilroyed, Brandon H.; Tymensen, Lisa; Hao, Yongxin; Hao, Xiying; Belosevic, Miodrag; Leonard, Jerry J.; McAllister, Tim A.

    2013-01-01

    Highlights: ► Addition of feathers altered bacterial and fungal communities in compost. ► Microbial communities degrading SRM and compost matrix were distinct. ► Addition of feathers may enrich for microbial communities that degrade SRM. ► Inclusion of feather in compost increased both CH 4 and N 2 O emissions from compost. ► Density of methanogens and methanotrophs were weakly associated with CH 4 emissions. - Abstract: Provided that infectious prions (PrP Sc ) are inactivated, composting of specified risk material (SRM) may be a viable alternative to rendering and landfilling. In this study, bacterial and fungal communities as well as greenhouse gas emissions associated with the degradation of SRM were examined in laboratory composters over two 14 day composting cycles. Chicken feathers were mixed into compost to enrich for microbial communities involved in the degradation of keratin and other recalcitrant proteins such as prions. Feathers altered the composition of bacterial and fungal communities primarily during the first cycle. The bacterial genera Saccharomonospora, Thermobifida, Thermoactinomycetaceae, Thiohalospira, Pseudomonas, Actinomadura, and Enterobacter, and the fungal genera Dothideomycetes, Cladosporium, Chaetomium, and Trichaptum were identified as candidates involved in SRM degradation. Feathers increased (P 4 primarily during the early stages of the first cycle and N 2 O during the second. Although inclusion of feathers in compost increases greenhouse gas emissions, it may promote the establishment of microbial communities that are more adept at degrading SRM and recalcitrant proteins such as keratin and PrP Sc

  18. Distributed Consensus Tracking for Second-Order Nonlinear Multiagent Systems with a Specified Reference State

    Directory of Open Access Journals (Sweden)

    Guoguang Wen

    2014-01-01

    Full Text Available This paper mainly addresses the distributed consensus tracking problem for second-order nonlinear multiagent systems with a specified reference trajectory. The dynamics of each follower consists of two terms: nonlinear inherent dynamics and a simple communication protocol relying only on the position and velocity information of its neighbors. The consensus reference is taken as a virtual leader, whose output is only its position and velocity information that is available to only a subset of a group of followers. To achieve consensus tracking, a class of nonsmooth control protocols is proposed which reply on the relative information among the neighboring agents. Then some corresponding sufficient conditions are derived. It is shown that if the communication graph associated with the virtual leader and followers is connected at each time instant, the consensus can be achieved at least globally exponentially with the proposed protocol. Rigorous proofs are given by using graph theory, matrix theory, and Lyapunov theory. Finally, numerical examples are presented to illustrate the theoretical analysis.

  19. Generation of Stationary Non-Gaussian Time Histories with a Specified Cross-spectral Density

    Directory of Open Access Journals (Sweden)

    David O. Smallwood

    1997-01-01

    Full Text Available The paper reviews several methods for the generation of stationary realizations of sampled time histories with non-Gaussian distributions and introduces a new method which can be used to control the cross-spectral density matrix and the probability density functions (pdfs of the multiple input problem. Discussed first are two methods for the specialized case of matching the auto (power spectrum, the skewness, and kurtosis using generalized shot noise and using polynomial functions. It is then shown that the skewness and kurtosis can also be controlled by the phase of a complex frequency domain description of the random process. The general case of matching a target probability density function using a zero memory nonlinear (ZMNL function is then covered. Next methods for generating vectors of random variables with a specified covariance matrix for a class of spherically invariant random vectors (SIRV are discussed. Finally the general case of matching the cross-spectral density matrix of a vector of inputs with non-Gaussian marginal distributions is presented.

  20. Determining the optimum length of a bridge opening with a specified reliability level of water runoff

    Directory of Open Access Journals (Sweden)

    Evdokimov Sergey

    2017-01-01

    Full Text Available Current trends in construction are aimed at providing reliability and safety of engineering facilities. According to the latest government regulations for construction, the scientific approach to engineering research, design, construction and operation of construction projects is a key priority. The reliability of a road depends on a great number of factors and characteristics of their statistical compounds (sequential and parallel. A part of a road with such man-made structures as a bridge or a pipe is considered as a system with a sequential element connection. The overall reliability is the multiplication of the reliability of these elements. The parameters of engineering structures defined by analytical dependences are highly volatile because of the inaccuracy of the defining factors. However each physical parameter is statistically unstable that is evaluated by variable coefficient of their values. It causes the fluctuation in the parameters of engineering structures. Their study may result in the changes in general and particular design rules in order to increase the reliability. The paper gives the grounds for these changes by the example of a bridge. It allows calculating its optimum length with a specified reliability level of water runoff under the bridge.

  1. Exclusion of overlapping symptoms in DSM-5 mixed features specifier: heuristic diagnostic and treatment implications.

    Science.gov (United States)

    Malhi, Gin S; Byrow, Yulisha; Outhred, Tim; Fritz, Kristina

    2017-04-01

    This article focuses on the controversial decision to exclude the overlapping symptoms of distractibility, irritability, and psychomotor agitation (DIP) with the introduction of the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) mixed features specifier. In order to understand the placement of mixed states within the current classification system, we first review the evolution of mixed states. Then, using Kraepelin's original classification of mixed states, we compare and contrast his conceptualization with modern day definitions. The DSM-5 workgroup excluded DIP symptoms, arguing that they lack the ability to differentiate between manic and depressive states; however, accumulating evidence suggests that DIP symptoms may be core features of mixed states. We suggest a return to a Kraepelinian approach to classification-with mood, ideation, and activity as key axes-and reintegration of DIP symptoms as features that are expressed across presentations. An inclusive definition of mixed states is urgently needed to resolve confusion in clinical practice and to redirect future research efforts.

  2. Avian metapneumovirus excretion in vaccinated and non-vaccinated specified pathogen free laying chickens.

    Science.gov (United States)

    Hess, M; Huggins, M B; Mudzamiri, R; Heincz, U

    2004-02-01

    Vaccinated and non-vaccinated specified pathogen-free White Leghorn laying chickens were challenged at peak of lay by the intravenous or oculonasal route with a virulent avian metapneumovirus (aMPV) subtype B chicken strain. Severe clinical signs and a drop in egg production were induced in the non-vaccinated intravenously challenged birds whereas the vaccinates were not affected. Live virus excretion was demonstrated in the faeces and respiratory tract of non-vaccinated hens for up to 7 days post intravenous challenge. After oculonasal challenge, virus excretion could only be demonstrated in the respiratory tract for up to 5 days. No live virus excretion was found in either the faeces or the respiratory tract of vaccinated birds. Concurrent with live virus isolation, the presence of viral RNA was demonstrated by single reverse transcription-polymerase chain reaction (RT-PCR). Nested RT-PCR was more sensitive and viral RNA could be detected in non-vaccinated birds up to 28 days post either intravenous or oculonasal challenge, at which time the experiment was terminated. Viral RNA was detected for up to 12 days in vaccinated birds. This is the first study investigating excretion of aMPV and viral RNA in vaccinated and non-vaccinated laying hens challenged under experimental conditions. The results are of importance with regard to the persistence of aMPV and the appropriate diagnostic detection method in laying birds.

  3. Symptomatic ovarian steroid cell tumor not otherwise specified in a post-menopausal woman

    Directory of Open Access Journals (Sweden)

    Neha Sood

    2016-06-01

    Full Text Available Steroid cell tumor not otherwise specified (NOS is a rare subtype of sex cord stromal tumor of the ovary and contributes less than 0.1% of all ovarian neoplasms. The majority of tumors occur in pre-menopausal women (mean age: 43 years, in which 56-77% of patients present with virilization due to excess testosterone. An 80-year-old woman with worsening alopecia and excessive growth of coarse hair on abdomen and genital area was found to have elevated serum testosterone level (462 ng/mL. Radiologic studies were consistent with bilateral adrenal adenomas. Bilateral adrenal venous sampling ruled out the adrenal gland as origin of hormone secretion. A diagnostic and therapeutic bilateral salpingooophorectomy confirmed steroid cell tumor NOS of the left ovary. Post-operatively, the patient had complete resolution of her symptoms and normalization of testosterone level. Our case emphasizes the importance of a clinical suspicion for an occult testosterone secreting ovarian tumor in a symptomatic patient without obvious ovarian mass on imaging.

  4. Isolation and identification of the human homolog of a new p53-binding protein, Mdmx

    NARCIS (Netherlands)

    Shvarts, A.; Bazuine, M.; Dekker, P.; Ramos, Y. F.; Steegenga, W. T.; Merckx, G.; van Ham, R. C.; van der Houven van Oordt, W.; van der Eb, A. J.; Jochemsen, A. G.

    1997-01-01

    We recently reported the identification of a mouse cDNA encoding a new p53-associating protein that we called Mdmx because of its structural similarity to Mdm2, a well-known p53-binding protein. Here we report the isolation of a cDNA encoding the human homolog of Mdmx. The ORF of the cDNA encodes a

  5. Vitamin E homologs and ¿-oryzanol levels in rice (Oryza sativa L.) during seed development

    Science.gov (United States)

    Vitamin E homologs (tocopherols and tocotrienols) and gamma-oryzanol have gained significant attention due to their proposed health benefits and ability to increase vegetable oil stability. Changes in the levels of these phytochemicals were examined during seed development. Rapid accumulation of toc...

  6. Identification of the porcine homologous of human disease causing trinucleotide repeat sequences

    DEFF Research Database (Denmark)

    Madsen, Lone Bruhn; Thomsen, Bo; Sølvsten, Christina Ane Elisabeth

    2007-01-01

    in this paper the identification of porcine noncoding and polyglutamine-encoding TNR regions and the comparison to the homologous TNRs from human, chimpanzee, dog, opossum, rat, and mouse. Several of the porcine TNR regions are highly polymorphic both within and between different breeds. The TNR regions...

  7. Evolution and homology of the astragalus in early amniotes: new fossils, new perspectives.

    Science.gov (United States)

    O'Keefe, F Robin; Sidor, Christian A; Larsson, Hans C E; Maga, Abdoudaye; Ide, Oumarou

    2006-04-01

    The reorganization of the ankle in basal amniotes has long been considered a key innovation allowing the evolution of more terrestrial and cursorial behavior. Understanding how this key innovation arose is a complex problem that largely concerns the homologizing of the amniote astragalus with the various ossifications in the anamniote tarsus. Over the last century, several hypotheses have been advanced homologizing the amniote astragalus with the many ossifications in the ankle of amphibian-grade tetrapods. There is an emerging consensus that the amniote astragalus is a complex structure emerging via the co-ossification of several originally separate elements, but the identities of these elements remain unclear. Here we present new fossil evidence bearing on this contentious question. A poorly ossified, juvenile astragalus of the large captorhinid Moradisaurus grandis shows clear evidence of four ossification centers, rather than of three centers or one center as posited in previous models of astragalus homology. Comparative material of the captorhinid Captorhinikos chozaensis is also interpretable as demonstrating four ossification centers. A new, four-center model for the homology of the amniote astragalus is advanced, and is discussed in the context of the phylogeny of the Captorhinidae in an attempt to identify the developmental transitions responsible for the observed pattern of ossification within this clade. Lastly, the broader implications for amniote phylogeny are discussed, concluding that the neomorphic pattern of astragalus ossification seen in all extant reptiles (including turtles) arose within the clade Diapsida.

  8. Resistance of hypoxic cells to ionizing radiation is influenced by homologous recombination status

    International Nuclear Information System (INIS)

    Sprong, Debbie; Janssen, Hilde L.; Vens, Conchita; Begg, Adrian C.

    2006-01-01

    Purpose: To determine the role of DNA repair in hypoxic radioresistance. Methods and Materials: Chinese hamster cell lines with mutations in homologous recombination (XRCC2, XRCC3, BRAC2, RAD51C) or nonhomologous end-joining (DNA-PKcs) genes were irradiated under normoxic (20% oxygen) and hypoxic (<0.1% oxygen) conditions, and the oxygen enhancement ratio (OER) was calculated. In addition, Fanconi anemia fibroblasts (complementation groups C and G) were compared with fibroblasts from nonsyndrome patients. RAD51 foci were studied using immunofluorescence. Results: All hamster cell lines deficient in homologous recombination showed a decrease in OER (1.5-2.0 vs. 2.6-3.0 for wild-types). In contrast, the OER for the DNA-PKcs-deficient line was comparable to wild-type controls. The two Fanconi anemia cell strains also showed a significant reduction in OER. The OER for RAD51 foci formation at late times after irradiation was considerably lower than that for survival in wild-type cells. Conclusion: Homologous recombination plays an important role in determining hypoxic cell radiosensitivity. Lower OERs have also been reported in cells deficient in XPF and ERCC1, which, similar to homologous recombination genes, are known to play a role in cross-link repair. Because Fanconi anemia cells are also sensitive to cross-linking agents, this strengthens the notion that the capacity to repair cross-links determines hypoxic radiosensitivity

  9. Refinement of homology-based protein structures by molecular dynamics simulation techniques

    NARCIS (Netherlands)

    Fan, H; Mark, AE

    The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to

  10. Direct Single-Molecule Observation of Mode and Geometry of RecA-Mediated Homology Search.

    Science.gov (United States)

    Lee, Andrew J; Endo, Masayuki; Hobbs, Jamie K; Wälti, Christoph

    2018-01-23

    Genomic integrity, when compromised by accrued DNA lesions, is maintained through efficient repair via homologous recombination. For this process the ubiquitous recombinase A (RecA), and its homologues such as the human Rad51, are of central importance, able to align and exchange homologous sequences within single-stranded and double-stranded DNA in order to swap out defective regions. Here, we directly observe the widely debated mechanism of RecA homology searching at a single-molecule level using high-speed atomic force microscopy (HS-AFM) in combination with tailored DNA origami frames to present the reaction targets in a way suitable for AFM-imaging. We show that RecA nucleoprotein filaments move along DNA substrates via short-distance facilitated diffusions, or slides, interspersed with longer-distance random moves, or hops. Importantly, from the specific interaction geometry, we find that the double-stranded substrate DNA resides in the secondary DNA binding-site within the RecA nucleoprotein filament helical groove during the homology search. This work demonstrates that tailored DNA origami, in conjunction with HS-AFM, can be employed to reveal directly conformational and geometrical information on dynamic protein-DNA interactions which was previously inaccessible at an individual single-molecule level.

  11. Interference of Homologous Sequences on the SNP Study of CYP2A13 Gene

    Directory of Open Access Journals (Sweden)

    Qinghua ZHOU

    2010-02-01

    Full Text Available Background and objective It has been proven that cytochrome P450 enzyme 2A13 (CYP2A13 played an important role in the association between single nucleotide polymorphisms (SNP and human diseases. Cytochrome P450 enzymes are a group of isoenzymes, whose sequence homology may interfere with the study for SNP. The aim of this study is to explore the interference on the SNP study of CYP2A13 caused by homologous sequences. Methods Taqman probe was applied to detect distribution of rs8192789 sites in 573 subjects, and BLAST method was used to analyze the amplified sequences. Partial sequences of CYP2A13 were emplified by PCR from 60 cases. The emplified sequences were TA cloned and sequenced. Results For rs8192789 loci in 573 cases, only 3 cases were TT, while the rest were CT heterozygotes, which was caused by homologous sequences. There are a large number of overlapping peaks in identical sequences of 60 cases, and the SNP of 101 amino acid site reported in the SNP database is not found. The cloned sequences are 247 bp, 235 bp fragments. Conclusion The homologous sequences may interfere the study for SNP of CYP2A13, and some SNP may not exist.

  12. Metabolism of homologous and heterologous serum proteins in garter snakes (Thamnophis ordinoides)

    International Nuclear Information System (INIS)

    Leong, D.; Coe, J.E.

    1978-01-01

    The half-life (Tsub(1/2) of serum immunoglobulin (Ig) and albumin from snakes and mammals were determined in both garter snakes (Thamnophis ordinoides) and mice (Mus musculus). Metabolism of serum proteins in snakes was similar to mammalian protein metabolism in that homologous serum albumin had shorter Tsub(1/2) (16 days) than IgG (38 days). Also, reptilian and mammalian serum proteins had a relatively longer Tsub(1/2) when injected into closely related species. Thus mammalian serum Ig (rabbit gamma globulin (RGG)) had a shorter Tsub(1/2) (6.3 days) in snake than did homologous snake IgG (38 days), whereas in mice, RGG had a longer Tsub(1/2) (3.8 days) than snake Ig (0.9 days). Differences between metabolism of homologous and heterologous albumins were apparent only in snakes in which the Tsub(1/2) of homologous albumin was approximately 8-fold greater than mammalian albumin. These results indicate that metabolism of both Ig and albumin in snakes is regulated by specific receptors whereas albumin receptors have been difficult to demonstrate in mammals. The results of this study suggest that one of the factors determining the metabolism of a protein is its foreignness to the host perhaps because of receptor cross reactions. (author)

  13. In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration

    KAUST Repository

    Suzuki, Keiichiro; Tsunekawa, Yuji; Herná ndez-Bení tez, Reyna; Wu, Jun; Zhu, Jie; Kim, Euiseok J.; Hatanaka, Fumiyuki; Yamamoto, Mako; Araoka, Toshikazu; Li, Zhe; Kurita, Masakazu; Hishida, Tomoaki; Li, Mo; Aizawa, Emi; Guo, Shicheng; Chen, Song; Goebl, April; Soligalla, Rupa Devi; Qu, Jing; Jiang, Tingshuai; Fu, Xin; Jafari, Maryam; Esteban, Concepcion Rodriguez; Berggren, W. Travis; Lajara, Jeronimo; Nuñ ez-Delicado, Estrella; Guillen, Pedro; Campistol, Josep M.; Matsuzaki, Fumio; Liu, Guang-Hui; Magistretti, Pierre J.; Zhang, Kun; Callaway, Edward M.; Zhang, Kang; Belmonte, Juan Carlos Izpisua

    2016-01-01

    regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9)3, 4 technology, here we devise a homology-independent targeted integration (HITI) strategy, which allows for robust DNA knock-in in both dividing and non-dividing cells in vitro and, more

  14. Homology modeling of the serotonin transporter: Insights into the primary escitalopram-binding Site

    DEFF Research Database (Denmark)

    Jørgensen, Anne Marie; Tagmose, L.; Jørgensen, A.M.M.

    2007-01-01

    -ray structure of the closely related amino acid transporter, Aquifex aeolicus leucine transporter (LeuT), provides an opportunity to develop a three-dimensional model of the structure of SERT. We present herein a homology model of SERT using LeuT as the template and containing escitalopram as a bound ligand...

  15. Mammalian Sir2 homolog SIRT3 regulates global mitochondrial lysine acetylation

    DEFF Research Database (Denmark)

    Lombard, David B; Alt, Frederick W; Cheng, Hwei-Ling

    2007-01-01

    Homologs of the Saccharomyces cerevisiae Sir2 protein, sirtuins, promote longevity in many organisms. Studies of the sirtuin SIRT3 have so far been limited to cell culture systems. Here, we investigate the localization and function of SIRT3 in vivo. We show that endogenous mouse SIRT3 is a solubl...

  16. Uncoupling protein homologs may provide a link between mitochondria, metabolism and lifespan.

    Science.gov (United States)

    Wolkow, Catherine A; Iser, Wendy B

    2006-05-01

    Uncoupling proteins (UCPs), which dissipate the mitochondrial proton gradient, have the ability to decouple mitochodrial respiration from ATP production. Since mitochondrial electron transport is a major source of free radical production, it is possible that UCP activity might impact free radical production. Free radicals can react with and damage cellular proteins, DNA and lipids. Accumulated damage from oxidative stress is believed to be a major contributor to cellular decline during aging. If UCP function were to impact mitochondrial free radical production, then one would expect to find a link between UCP activity and aging. This theory has recently been tested in a handful of organisms whose genomes contain UCP1 homologs. Interestingly, these experiments indicate that UCP homologs can affect lifespan, although they do not support a simple relationship between UCP activity and aging. Instead, UCP-like proteins appear to have a variety of effects on lifespan, and on pathways implicated in lifespan regulation. One possible explanation for this complex picture is that UCP homologs may have tissue-specific effects that complicate their effects on aging. Furthermore, the functional analysis of UCP1 homologs is incomplete. Thus, these proteins may perform functions in addition to, or instead of, mitochondrial uncoupling. Although these studies have not revealed a clear picture of UCP effects on aging, they have contributed to the growing knowledge base for these interesting proteins. Future biochemical and genetic investigation of UCP-like proteins will do much to clarify their functions and to identify the regulatory networks in which they are involved.

  17. Searching remote homology with spectral clustering with symmetry in neighborhood cluster kernels.

    Directory of Open Access Journals (Sweden)

    Ujjwal Maulik

    Full Text Available Remote homology detection among proteins utilizing only the unlabelled sequences is a central problem in comparative genomics. The existing cluster kernel methods based on neighborhoods and profiles and the Markov clustering algorithms are currently the most popular methods for protein family recognition. The deviation from random walks with inflation or dependency on hard threshold in similarity measure in those methods requires an enhancement for homology detection among multi-domain proteins. We propose to combine spectral clustering with neighborhood kernels in Markov similarity for enhancing sensitivity in detecting homology independent of "recent" paralogs. The spectral clustering approach with new combined local alignment kernels more effectively exploits the unsupervised protein sequences globally reducing inter-cluster walks. When combined with the corrections based on modified symmetry based proximity norm deemphasizing outliers, the technique proposed in this article outperforms other state-of-the-art cluster kernels among all twelve implemented kernels. The comparison with the state-of-the-art string and mismatch kernels also show the superior performance scores provided by the proposed kernels. Similar performance improvement also is found over an existing large dataset. Therefore the proposed spectral clustering framework over combined local alignment kernels with modified symmetry based correction achieves superior performance for unsupervised remote homolog detection even in multi-domain and promiscuous domain proteins from Genolevures database families with better biological relevance. Source code available upon request.sarkar@labri.fr.

  18. Cloning and homologic analysis of Tpn I gene in silkworm Bombyx ...

    African Journals Online (AJOL)

    GREGO

    2007-03-19

    Mar 19, 2007 ... 1Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, P. R. China. ... Key words: Tpn I, Bombyx mori, troponin, homology. ... cycles (94ºC for 30 s, 58ºC for 30 s, 72ºC for 3 min) in a Gene Amp.

  19. A recurrent translocation is mediated by homologous recombination between HERV-H elements

    Directory of Open Access Journals (Sweden)

    Hermetz Karen E

    2012-01-01

    Full Text Available Abstract Background Chromosome rearrangements are caused by many mutational mechanisms; of these, recurrent rearrangements can be particularly informative for teasing apart DNA sequence-specific factors. Some recurrent translocations are mediated by homologous recombination between large blocks of segmental duplications on different chromosomes. Here we describe a recurrent unbalanced translocation casued by recombination between shorter homologous regions on chromosomes 4 and 18 in two unrelated children with intellectual disability. Results Array CGH resolved the breakpoints of the 6.97-Megabase (Mb loss of 18q and the 7.30-Mb gain of 4q. Sequencing across the translocation breakpoints revealed that both translocations occurred between 92%-identical human endogenous retrovirus (HERV elements in the same orientation on chromosomes 4 and 18. In addition, we find sequence variation in the chromosome 4 HERV that makes one allele more like the chromosome 18 HERV. Conclusions Homologous recombination between HERVs on the same chromosome is known to cause chromosome deletions, but this is the first report of interchromosomal HERV-HERV recombination leading to a translocation. It is possible that normal sequence variation in substrates of non-allelic homologous recombination (NAHR affects the alignment of recombining segments and influences the propensity to chromosome rearrangement.

  20. FBH1 influences DNA replication fork stability and homologous recombination through ubiquitylation of RAD51

    DEFF Research Database (Denmark)

    Chu, Wai Kit; Payne, Miranda J; Beli, Petra

    2015-01-01

    Unscheduled homologous recombination (HR) can lead to genomic instability, which greatly increases the threat of neoplastic transformation in humans. The F-box DNA helicase 1 (FBH1) is a 3'-5' DNA helicase with a putative function as a negative regulator of HR. It is the only known DNA helicase t...

  1. Cloning and homologic analysis of Tpn I gene in silkworm Bombyx ...

    African Journals Online (AJOL)

    Cloning and homologic analysis of Tpn I gene in silkworm Bombyx mori. Y Zhao, Yao Q, X Tang, Q Wang, H Yin, Z Hu, J Lu, K Chen. Abstract. The troponin complex is composed of three subunits, Troponin C (the calcium sensor component) and Troponin T and I (structural proteins). Tpn C is encoded by multiple genes in ...

  2. Role of nitric oxide and flavohemoglobin homolog genes in Aspergillus nidulans sexual development and mycotoxin production

    Science.gov (United States)

    Flavohemoglobins are widely distributed proteins in both prokaryotic and eukaryotic organisms, conferring resistance against nitrosative stress. In the present study we investigated the role of two flavohemoglobin homologous genes, fhbA and fhbB, in morphogenesis and in the production of the mycotox...

  3. [Preparation of monoclonal antibody against 4-amylphenol and homology modeling of its Fv fragment].

    Science.gov (United States)

    Cheng, Lei; Wu, Haizhen; Fei, Jing; Zhang, Lujia; Ye, Jiang; Zhang, Huizhan

    2017-03-01

    Objective To prepare and characterize a monoclonal antibody (mAb) against 4-amylphenol (4-AP), clone its cDNA sequence and make homology modeling for its Fv fragment. Methods A high-affinity anti-4-AP mAb was generated from a hybridoma cell line F10 using electrofusion between splenocytes from APA-BSA-immunized mouse and Sp2/0 myeloma cells. Then we extracted the mRNA of F10 cells and cloned the cDNA of mAb. The homology modeling and molecular docking of its Fv fragment was conducted with biological software. Results Under the optimum conditions, the ic-ELISA equation was y=A 2 +(A 1 -A 2 )/(1+(x/x 0 ) p ) (A 1 =1.28; A 2 =-0.066; x 0 =12560.75; p=0.74) with a correlation coefficient (R 2 ) of 0.997. The lowest detectable limit was 0.65 μg/mL. The heavy and light chains of mAb respectively belonged to IgG1 and Kappa. The homology modeling and molecular docking studies revealed that the binding of 4-Ap and mAb was attributed to the hydrogen bond and hydrophobic interactions. Conclusion The study successfully established a stable 4-AP mAb-secreting hybridoma cell line. The study on spatial structure of Fv fragment using homology modeling provided a reference for the development and design of single chain variable fragments.

  4. Liver receptor homolog-1 is a critical determinant of methyl-pool metabolism

    Science.gov (United States)

    Balance of labile methyl groups (choline, methionine, betaine, and folate) is important for normal liver function. Quantitatively, a significant use of labile methyl groups is in the production of phosphatidylcholines (PCs), which are ligands for the nuclear liver receptor homolog-1 (LRH-1). We stud...

  5. Genes homologous to glycopeptide resistance vanA are widespread in soil microbial communities

    DEFF Research Database (Denmark)

    Guardabassi, L.; Agersø, Yvonne

    2006-01-01

    -Ala : D-Ala ligase genes unrelated to vanA. In order to enhance detection of vanA-homologous genes, a third PCR step was added using primers targeting vanA in soil Paenibacillus. Sequencing of 25 clones obtained by this method allowed recovery of 23 novel sequences having 86-100% identity with van...

  6. Homologous histamine H1 receptor desensitization results in reduction of H1 receptor agonist efficacy

    NARCIS (Netherlands)

    Leurs, R; Smit, M J; Bast, A; Timmerman, H

    1991-01-01

    Prolonged exposure of the guinea-pig intestinal longitudinal smooth muscle to histamine caused homologous desensitization of the H1 receptor, which led to reduced H1 receptor-mediated production of [3H]inositol phosphates as well as to reduced H1 agonist-induced contractions. [3H]Mepyramine binding

  7. The murine retinoblastoma homolog maps to chromosome 14 near Es-10

    NARCIS (Netherlands)

    Stone, J.C.; Crosby, J.J.; Kozak, C.A.; Schievella, A.R.; Bernards, R.A.; Nadeau, J.H.

    1989-01-01

    Restriction fragment length variants have been exploited to map genetically Rb-1, the murine homolog of the human retinoblastoma gene. Rb-1 localized to mouse chromosome 14 on the basis of results from analysis of somatic cell hybrids. In an interspecific backcross involving Mus spretus, Rb-1 and

  8. Disruption of mouse RAD54 reduces ionizing radiation resistance and homologous recombination.

    NARCIS (Netherlands)

    J. Essers (Jeroen); R.W. Hendriks (Rudi); S.M.A. Swagemakers (Sigrid); C. Troelstra (Christine); J. de Wit (Jan); D. Bootsma (Dirk); J.H.J. Hoeijmakers (Jan); R. Kanaar (Roland)

    1997-01-01

    textabstractDouble-strand DNA break (DSB) repair by homologous recombination occurs through the RAD52 pathway in Saccharomyces cerevisiae. Its biological importance is underscored by the conservation of many RAD52 pathway genes, including RAD54, from fungi to humans. We have analyzed the phenotype

  9. CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles.

    Science.gov (United States)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole; Petersen, Thomas Nordahl

    2010-07-01

    CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models for 94% of the targets (117 out of 128), 74% were predicted as high reliability models (87 out of 117). These achieved an average RMSD of 4.6 A when superimposed to the 3D structure. The remaining 26% low reliably models (30 out of 117) could superimpose to the true 3D structure with an average RMSD of 9.3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is web server is available at http://www.cbs.dtu.dk/services/CPHmodels/.

  10. New Proposal of Setal Homology in Schizomida and Revision of Surazomus (Hubbardiidae) from Ecuador.

    Science.gov (United States)

    Manzanilla, Osvaldo Villarreal; de Miranda, Gustavo Silva; Giupponi, Alessandro Ponce de Leão

    2016-01-01

    The homology of three somatic systems in Schizomida is studied yielding the following results: (1) proposal of homology and chaetotaxy of abdominal setae in Surazomus; (2) revision of the cheliceral chaetotaxy in Schizomida, with suggestion of new homology scheme between Hubbardiidae and Protoschizomidae, description of a new group of setae in Hubbardiinae (G7), and division of setae group 5 in two subgroups, G5A and G5B; (3) proposal of segmental homology between trimerous and tetramerous female flagellum in Hubbardiinae with association of segment III of tri-segmented species to segments III + IV of tetra-segmented species. Considerations about the dorsal microsetae on the male flagellum are made. The genus Surazomus in Ecuador is revised. The sympatric species Surazomus palenque sp. nov. and S. kitu sp. nov. (Ecuador, Pichincha) are described and illustrated. The female of S. cuenca (Rowland and Reddell, 1979) is described, with two new distributional records for the species. Surazomus cumbalensis (Kraus, 1957) is recorded for the first time from Ecuador (Pichincha).

  11. Metazoan Scc4 homologs link sister chromatid cohesion to cell and axon migration guidance

    NARCIS (Netherlands)

    V.C. Seitan (Vlad); P.A. Banks (Peter); S. Laval (Steve); N.A. Majid (Nazia); D. Dorsett (Dale); A. Rana (Amer); J. Smith (Jeremy); A. Bateman (Alex); S. Krpic (Sanja); A. Hostert (Arnd); S.M. Rollins; H. Erdjument-Bromage (Hediye); P. Tempst (Paul); C.Y. Benard (Claire); S. Hekimi (Siegfried); S.F. Newbury (Sarah); T. Strachan (Tom)

    2006-01-01

    textabstractSaccharomyces cerevisiae Scc2 binds Scc4 to form an essential complex that loads cohesin onto chromosomes. The prevalence of Scc2 orthologs in eukaryotes emphasizes a conserved role in regulating sister chromatid cohesion, but homologs of Scc4 have not hitherto been identified outside

  12. Pleckstrin Homology Domain Diffusion in Dictyostelium Cytoplasm Studied Using Fluorescence Correlation Spectroscopy

    NARCIS (Netherlands)

    Engel, Ruchira; Hink, Mark A.; Bosgraaf, Leonard; Haastert, Peter J.M. van; Visser, Antonie J.W.G.

    2004-01-01

    The translocation of pleckstrin homology (PH) domain-containing proteins from the cytoplasm to the plasma membrane plays an important role in the chemotaxis mechanism of Dictyostelium cells. The diffusion of three PH domain-green fluorescent protein (GFP) fusions (PH2-GFP, PH10-GFP, and PH-CRAC

  13. Pleckstrin homology domain diffusion in Dictyostelium cytoplasm studied using fluorescence correlation spectroscopy

    NARCIS (Netherlands)

    Ruchira, A.; Hink, M.A.; Bosgraaf, L.; Haastert, van P.J.M.; Visser, A.J.W.G.

    2004-01-01

    The translocation of pleckstrin homology (PH) domain-containing proteins from the cytoplasm to the plasma membrane plays an important role in the chemotaxis mechanism of Dictyostelium cells. The diffusion of three PH domain-green fluorescent protein (GFP) fusions (PH2-GFP, PH10-GFP, and PH-CRAC

  14. 29 CFR 4.2 - Payment of minimum wage specified in section 6(a)(1) of the Fair Labor Standards Act of 1938...

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 1 2010-07-01 2010-07-01 true Payment of minimum wage specified in section 6(a)(1) of the... and Procedures § 4.2 Payment of minimum wage specified in section 6(a)(1) of the Fair Labor Standards... employees shall pay any employees engaged in such work less than the minimum wage specified in section 6(a...

  15. Sequence homology at the breakpoint and clinical phenotype of mitochondrial DNA deletion syndromes.

    Science.gov (United States)

    Sadikovic, Bekim; Wang, Jing; El-Hattab, Ayman W; Landsverk, Megan; Douglas, Ganka; Brundage, Ellen K; Craigen, William J; Schmitt, Eric S; Wong, Lee-Jun C

    2010-12-20

    Mitochondrial DNA (mtDNA) deletions are a common cause of mitochondrial disorders. Large mtDNA deletions can lead to a broad spectrum of clinical features with different age of onset, ranging from mild mitochondrial myopathies (MM), progressive external ophthalmoplegia (PEO), and Kearns-Sayre syndrome (KSS), to severe Pearson syndrome. The aim of this study is to investigate the molecular signatures surrounding the deletion breakpoints and their association with the clinical phenotype and age at onset. MtDNA deletions in 67 patients were characterized using array comparative genomic hybridization (aCGH) followed by PCR-sequencing of the deletion junctions. Sequence homology including both perfect and imperfect short repeats flanking the deletion regions were analyzed and correlated with clinical features and patients' age group. In all age groups, there was a significant increase in sequence homology flanking the deletion compared to mtDNA background. The youngest patient group (deletion distribution in size and locations, with a significantly lower sequence homology flanking the deletion, and the highest percentage of deletion mutant heteroplasmy. The older age groups showed rather discrete pattern of deletions with 44% of all patients over 6 years old carrying the most common 5 kb mtDNA deletion, which was found mostly in muscle specimens (22/41). Only 15% (3/20) of the young patients (deletion, which is usually present in blood rather than muscle. This group of patients predominantly (16 out of 17) exhibit multisystem disorder and/or Pearson syndrome, while older patients had predominantly neuromuscular manifestations including KSS, PEO, and MM. In conclusion, sequence homology at the deletion flanking regions is a consistent feature of mtDNA deletions. Decreased levels of sequence homology and increased levels of deletion mutant heteroplasmy appear to correlate with earlier onset and more severe disease with multisystem involvement.

  16. Illustrating and homology modeling the proteins of the Zika virus [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Sean Ekins

    2016-09-01

    Full Text Available The Zika virus (ZIKV is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening.

  17. Homology and homoplasy of swimming behaviors and neural circuits in the Nudipleura (Mollusca, Gastropoda, Opisthobranchia)

    Science.gov (United States)

    Newcomb, James M.; Sakurai, Akira; Lillvis, Joshua L.; Gunaratne, Charuni A.; Katz, Paul S.

    2012-01-01

    How neural circuit evolution relates to behavioral evolution is not well understood. Here the relationship between neural circuits and behavior is explored with respect to the swimming behaviors of the Nudipleura (Mollusca, Gastropoda, Opithobranchia). Nudipleura is a diverse monophyletic clade of sea slugs among which only a small percentage of species can swim. Swimming falls into a limited number of categories, the most prevalent of which are rhythmic left–right body flexions (LR) and rhythmic dorsal–ventral body flexions (DV). The phylogenetic distribution of these behaviors suggests a high degree of homoplasy. The central pattern generator (CPG) underlying DV swimming has been well characterized in Tritonia diomedea and in Pleurobranchaea californica. The CPG for LR swimming has been elucidated in Melibe leonina and Dendronotus iris, which are more closely related. The CPGs for the categorically distinct DV and LR swimming behaviors consist of nonoverlapping sets of homologous identified neurons, whereas the categorically similar behaviors share some homologous identified neurons, although the exact composition of neurons and synapses in the neural circuits differ. The roles played by homologous identified neurons in categorically distinct behaviors differ. However, homologous identified neurons also play different roles even in the swim CPGs of the two LR swimming species. Individual neurons can be multifunctional within a species. Some of those functions are shared across species, whereas others are not. The pattern of use and reuse of homologous neurons in various forms of swimming and other behaviors further demonstrates that the composition of neural circuits influences the evolution of behaviors. PMID:22723353

  18. Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts

    KAUST Repository

    Huang, Chao-Li

    2015-03-15

    Background: Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in Xanthomonas pathogenic to various plants. Results: Using whole-genome sequences, we examined the genetic divergence in Xanthomonas campestris that infected Brassicaceae, and X. citri, pathogenic to a wider host range. Genetic differentiation between two incipient races of X. citri pv. mangiferaeindicae was attributable to a DNA fragment introduced by phages. In contrast to most portions of the genome that had nearly equivalent levels of genetic divergence between subspecies as a result of the accumulation of point mutations, 10% of the core genome involving with homologous recombination contributed to the diversification in Xanthomonas, as revealed by the correlation between homologous recombination and genomic divergence. Interestingly, 179 genes were under positive selection; 98 (54.7%) of these genes were involved in homologous recombination, indicating that foreign genetic fragments may have caused the adaptive diversification, especially in lineages with nutritional transitions. Homologous recombination may have provided genetic materials for the natural selection, and host shifts likely triggered ecological adaptation in Xanthomonas. To a certain extent, we observed positive selection nevertheless contributed to ecological divergence beyond host shifting. Conclusion: Altogether, mediated with lasting gene flow, species formation in Xanthomonas was likely governed by natural selection that played a key role in helping the deviating populations to explore novel niches (hosts) or respond to environmental cues, subsequently triggering species diversification. © Huang et al.

  19. A family of cell-adhering peptides homologous to fibrinogen C-termini

    International Nuclear Information System (INIS)

    Levy-Beladev, Liron; Levdansky, Lilia; Gaberman, Elena; Friedler, Assaf; Gorodetsky, Raphael

    2010-01-01

    Research highlights: → Cell-adhesive sequences homologous to fibrinogen C-termini exist in other proteins. → The extended homologous cell-adhesive C-termini peptides family is termed Haptides. → In membrane-like environment random coiled Haptides adopt a helical conformation. → Replacing positively charged residues with alanine reduces Haptides activity. -- Abstract: A family of cell-adhesive peptides homologous to sequences on different chains of fibrinogen was investigated. These homologous peptides, termed Haptides, include the peptides Cβ, preCγ, and CαE, corresponding to sequences on the C-termini of fibrinogen chains β, γ, and αE, respectively. Haptides do not affect cell survival and rate of proliferation of the normal cell types tested. The use of new sensitive assays of cell adhesion clearly demonstrated the ability of Haptides, bound to inert matrices, to mediate attachment of different matrix-dependent cell types including normal fibroblasts, endothelial, and smooth muscle cells. Here we present new active Haptides bearing homologous sequences derived from the C-termini of other proteins, such as angiopoietin 1 and 2, tenascins C and X, and microfibril-associated glycoprotein-4. The cell adhesion properties of all the Haptides were found to be associated mainly with their 11 N-terminal residues. Mutated preCγ peptides revealed that positively charged residues account for their attachment effect. These results suggest a mechanism of direct electrostatic interaction of Haptides with the cell membrane. The extended Haptides family may be applied in modulating adhesion of cells to scaffolds for tissue regeneration and for enhancement of nanoparticulate transfection into cells.

  20. Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts

    KAUST Repository

    Huang, Chao-Li; Pu, Pei-Hua; Huang, Hao-Jen; Sung, Huang-Mo; Liaw, Hung-Jiun; Chen, Yi-Min; Chen, Chien-Ming; Huang, Ming-Ban; Osada, Naoki; Gojobori, Takashi; Pai, Tun-Wen; Chen, Yu-Tin; Hwang, Chi-Chuan; Chiang, Tzen-Yuh

    2015-01-01

    Background: Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in Xanthomonas pathogenic to various plants. Results: Using whole-genome sequences, we examined the genetic divergence in Xanthomonas campestris that infected Brassicaceae, and X. citri, pathogenic to a wider host range. Genetic differentiation between two incipient races of X. citri pv. mangiferaeindicae was attributable to a DNA fragment introduced by phages. In contrast to most portions of the genome that had nearly equivalent levels of genetic divergence between subspecies as a result of the accumulation of point mutations, 10% of the core genome involving with homologous recombination contributed to the diversification in Xanthomonas, as revealed by the correlation between homologous recombination and genomic divergence. Interestingly, 179 genes were under positive selection; 98 (54.7%) of these genes were involved in homologous recombination, indicating that foreign genetic fragments may have caused the adaptive diversification, especially in lineages with nutritional transitions. Homologous recombination may have provided genetic materials for the natural selection, and host shifts likely triggered ecological adaptation in Xanthomonas. To a certain extent, we observed positive selection nevertheless contributed to ecological divergence beyond host shifting. Conclusion: Altogether, mediated with lasting gene flow, species formation in Xanthomonas was likely governed by natural selection that played a key role in helping the deviating populations to explore novel niches (hosts) or respond to environmental cues, subsequently triggering species diversification. © Huang et al.

  1. The clinical usefulness of the new LPE specifier for subtyping adolescents with conduct disorder in the DSM 5.

    Science.gov (United States)

    Jambroes, Tijs; Jansen, Lucres M C; Vermeiren, Robert R J M; Doreleijers, Theo A H; Colins, Olivier F; Popma, Arne

    2016-08-01

    In DSM 5, conduct disorder (CD) has been expanded with a new specifier 'with Limited Prosocial Emotions' (LPE) in addition to the age-of-onset (AoO) subtyping, and is thought to identify a severe antisocial subgroup of CD. However, research in clinical practice has been scarce. Therefore, the current study will examine differences in clinical symptoms between subtypes of CD, based on both subtyping schemes. Subsequently, it will investigate whether the LPE specifier explains unique variance in aggression, added to the AoO subtyping. A sample of 145 adolescents with CD (51 % male, mean age 15.0) from a closed treatment institution participated in this study. CD diagnoses and AoO subtype were assessed using a structured diagnostic interview. The LPE specifier was assessed using the callous-unemotional dimension of the Youth Psychopathy Traits Inventory (YPI). Self-reported proactive and reactive aggression, rule-breaking behavior and internalizing problems within the subtypes were compared. Youth with childhood-onset CD and LPE showed significantly more aggression than adolescent-onset CD without LPE (proactive aggression: F = 3.1, p < 0.05, reactive aggression: F = 3.7, p < 0.05). Hierarchical regression revealed that the LPE specifier uniquely explained 7 % of the variance in reactive aggression, additionally to the AoO subtyping. For proactive aggression, the interaction between AoO and the LPE added 4.5 % to the explained variance. Although the LPE specifier may help to identify a more aggressive subtype of CD in adolescents, the incremental utility seems to be limited. Therefore, clinical relevance of the LPE specifier in high-risk adolescent samples still needs to be investigated thoroughly.

  2. Class Position and Musical Tastes: A Sing-Off between the Cultural Omnivorism and Bourdieusian Homology Frameworks.

    Science.gov (United States)

    Veenstra, Gerry

    2015-05-01

    The longstanding debate between the homology and omnivorism approaches to the class bases of cultural tastes and practices rages on in cultural sociology. The homology thesis claims that class positions throughout the class hierarchy are accompanied by specified cultural tastes and specialized modes of appreciating them while the cultural omnivorism thesis contends that elites are (increasingly) characterized by a breadth of cultural tastes of any and all kinds. This study tests the applicability of these theses to musical tastes in Canada through the application of multiple correspondence analysis, latent class analysis, and logistic regression modeling to original telephone survey data (n = 1,595) from Toronto and Vancouver. I find that musical omnivorism, an appreciation for diverse musical styles, is not dispersed along class lines. Instead I find a homology between class position and musical tastes that designates blues, choral, classical, jazz, musical theater, opera, pop, reggae, rock, and world/international as relatively highbrow and country, disco, easy listening, golden oldies, heavy metal, and rap as relatively lowbrow. Of the highbrow tastes, all but jazz are disliked by lower class people, and of the lowbrow tastes, country, easy listening, and golden oldies are concurrently disliked by higher class people. Consistent with the homology thesis, it appears that class position is aligned with specific musical likes and dislikes. Le vieux débat entre les approches de l'homologie et de l'omnivorisme aux bases des classes des goûts et des pratiques culturels fait rage dans la sociologie culturelle. La thèse de l'homologie prétend que les positions des classes à travers la hiérarchie des classes sont accompagnées par des goûts culturels spécifiés et des modes spécialisés permettant leur appréciation. La thèse de l'omnivorisme culturel, en revanche, soutient que les élites sont (de plus en plus) caractérisées par un éventail de go

  3. Microbial communities and greenhouse gas emissions associated with the biodegradation of specified risk material in compost

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Shanwei [Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5 (Canada); Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1 (Canada); Reuter, Tim [Alberta Agriculture and Rural Development, Lethbridge, Alberta, Canada T1J 4V6 (Canada); Gilroyed, Brandon H. [Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1 (Canada); Tymensen, Lisa [Alberta Agriculture and Rural Development, Lethbridge, Alberta, Canada T1J 4V6 (Canada); Hao, Yongxin; Hao, Xiying [Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1 (Canada); Belosevic, Miodrag [Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada T6G 2E9 (Canada); Leonard, Jerry J. [Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5 (Canada); McAllister, Tim A., E-mail: tim.mcallister@agr.gc.ca [Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1 (Canada)

    2013-06-15

    Highlights: ► Addition of feathers altered bacterial and fungal communities in compost. ► Microbial communities degrading SRM and compost matrix were distinct. ► Addition of feathers may enrich for microbial communities that degrade SRM. ► Inclusion of feather in compost increased both CH{sub 4} and N{sub 2}O emissions from compost. ► Density of methanogens and methanotrophs were weakly associated with CH{sub 4} emissions. - Abstract: Provided that infectious prions (PrP{sup Sc}) are inactivated, composting of specified risk material (SRM) may be a viable alternative to rendering and landfilling. In this study, bacterial and fungal communities as well as greenhouse gas emissions associated with the degradation of SRM were examined in laboratory composters over two 14 day composting cycles. Chicken feathers were mixed into compost to enrich for microbial communities involved in the degradation of keratin and other recalcitrant proteins such as prions. Feathers altered the composition of bacterial and fungal communities primarily during the first cycle. The bacterial genera Saccharomonospora, Thermobifida, Thermoactinomycetaceae, Thiohalospira, Pseudomonas, Actinomadura, and Enterobacter, and the fungal genera Dothideomycetes, Cladosporium, Chaetomium, and Trichaptum were identified as candidates involved in SRM degradation. Feathers increased (P < 0.05) headspace concentrations of CH{sub 4} primarily during the early stages of the first cycle and N{sub 2}O during the second. Although inclusion of feathers in compost increases greenhouse gas emissions, it may promote the establishment of microbial communities that are more adept at degrading SRM and recalcitrant proteins such as keratin and PrP{sup Sc}.

  4. Epitope-Specific Tolerance Modes Differentially Specify Susceptibility to Proteolipid Protein-Induced Experimental Autoimmune Encephalomyelitis

    Directory of Open Access Journals (Sweden)

    Lei Wang

    2017-11-01

    Full Text Available Immunization with myelin components can elicit experimental autoimmune encephalomyelitis (EAE. EAE susceptibility varies between mouse strains, depending on the antigen employed. BL/6 mice are largely resistant to EAE induction with proteolipid protein (PLP, probably a reflection of antigen-specific tolerance. However, the extent and mechanism(s of tolerance to PLP remain unclear. Here, we identified three PLP epitopes in PLP-deficient BL/6 mice. PLP-sufficient mice did not respond against two of these, whereas tolerance was “leaky” for an epitope with weak predicted MHCII binding, and only this epitope was encephalitogenic. In TCR transgenic mice, the “EAE-susceptibility-associated” epitope was “ignored” by specific CD4 T cells, whereas the “resistance-associated” epitope induced clonal deletion and Treg induction in the thymus. Central tolerance was autoimmune regulator dependent and required expression and presentation of PLP by thymic epithelial cells (TECs. TEC-specific ablation of PLP revealed that peripheral tolerance, mediated by dendritic cells through recessive tolerance mechanisms (deletion and anergy, could largely compensate for a lack of central tolerance. However, adoptive EAE was exacerbated in mice lacking PLP in TECs, pointing toward a non-redundant role of the thymus in dominant tolerance to PLP. Our findings reveal multiple layers of tolerance to a central nervous system autoantigen that vary among epitopes and thereby specify disease susceptibility. Understanding how different modalities of tolerance apply to distinct T cell epitopes of a target in autoimmunity has implications for antigen-specific strategies to therapeutically interfere with unwanted immune reactions against self.

  5. Anterior Visceral Endoderm SMAD4 Signaling Specifies Anterior Embryonic Patterning and Head Induction in Mice

    Science.gov (United States)

    Li, Cuiling; Li, Yi-Ping; Fu, Xin-Yuan; Deng, Chu-Xia

    2010-01-01

    SMAD4 serves as a common mediator for signaling of TGF-β superfamily. Previous studies illustrated that SMAD4-null mice die at embryonic day 6.5 (E6.5) due to failure of mesoderm induction and extraembryonic defects; however, functions of SMAD4 in each germ layer remain elusive. To investigate this, we disrupted SMAD4 in the visceral endoderm and epiblast, respectively, using a Cre-loxP mediated approach. We showed that mutant embryos lack of SMAD4 in the visceral endoderm (Smad4Co/Co;TTR-Cre) died at E7.5-E9.5 without head-fold and anterior embryonic structures. We demonstrated that TGF-β regulates expression of several genes, such as Hex1, Cer1, and Lim1, in the anterior visceral endoderm (AVE), and the failure of anterior embryonic development in Smad4Co/Co;TTR-Cre embryos is accompanied by diminished expression of these genes. Consistent with this finding, SMAD4-deficient embryoid bodies showed impaired responsiveness to TGF-β-induced gene expression and morphological changes. On the other hand, embryos carrying Cre-loxP mediated disruption of SMAD4 in the epiblasts exhibited relatively normal mesoderm and head-fold induction although they all displayed profound patterning defects in the later stages of gastrulation. Cumulatively, our data indicate that SMAD4 signaling in the epiblasts is dispensable for mesoderm induction although it remains critical for head patterning, which is significantly different from SMAD4 signaling in the AVE, where it specifies anterior embryonic patterning and head induction. PMID:20941375

  6. The role of auxin and cytokinin signalling in specifying the root architecture of Arabidopsis thaliana

    KAUST Repository

    Muraro, Daniele

    2013-01-01

    Auxin and cytokinin are key hormonal signals that control the cellular architecture of the primary root and the initiation of new lateral root organs in the plant Arabidopsis thaliana. Both developmental processes are regulated by cross-talk between these hormones and their signalling pathways. In this paper, sub-cellular and multi-cellular mathematical models are developed to investigate how interactions between auxin and cytokinin influence the size and location of regions of division and differentiation within the primary root, and describe how their cross-regulation may cause periodic branching of lateral roots. We show how their joint activity may influence tissue-specific oscillations in gene expression, as shown in Moreno-Risueno et al. (2010) and commented upon in Traas and Vernoux (2010), and we propose mechanisms that may generate synchronisation of such periodic behaviours inside a cell and with its neighbours. Using a multi-cellular model, we also analyse the roles of cytokinin and auxin in specifying the three main regions of the primary root (elongation, transition and division zones), our simulation results being in good agreement with independent experimental observations. We then use our model to generate testable predictions concerning the effect of varying the concentrations of the auxin efflux transporters on the sizes of the different root regions. In particular, we predict that over-expression of the transporters will generate a longer root with a longer elongation zone and a smaller division zone than that of a wild type root. This root will contain fewer cells than its wild type counterpart. We conclude that our model can provide a useful tool for investigating the response of cell division and elongation to perturbations in hormonal signalling. © 2012 Elsevier Ltd.

  7. "Subthreshold" depression: is the distinction between depressive disorder not otherwise specified and adjustment disorder valid?

    Science.gov (United States)

    Zimmerman, Mark; Martinez, Jennifer H; Dalrymple, Kristy; Chelminski, Iwona; Young, Diane

    2013-05-01

    Patients with clinically significant symptoms of depression who do not meet the criteria for major depressive disorder or dysthymic disorder are considered to have subthreshold depression. According to DSM-IV, such patients should be diagnosed with depressive disorder not otherwise specified (NOS) if the development of the symptoms is not attributable to a stressful event or with adjustment disorder if the symptoms follow a stressor. Research on the treatment of subthreshold depression rarely addresses the distinction between depressive disorder NOS and adjustment disorder. In the present report from the Rhode Island Methods to Improve Diagnostic Assessment and Services (MIDAS) project, we examined the validity of this distinction. From December 1995 to June 2011, 3,400 psychiatric patients presenting to the Rhode Island Hospital outpatient practice were evaluated with semistructured diagnostic interviews for DSM-IV Axis I and Axis II disorders and measures of psychosocial morbidity. Slightly less than 10% (n = 300) of the 3,400 patients were diagnosed with depressive disorder NOS or adjustment disorder with depressed mood. The patients with depressive disorder NOS were significantly more often diagnosed with social phobia (P depressive disorder NOS reported more anhedonia, increased appetite, increased sleep, and indecisiveness, whereas the patients with adjustment disorder reported more weight loss, reduced appetite, and insomnia. There was no significant difference between the groups in overall level of severity of depression or impaired functioning. The patients with depressive disorder NOS had a nonsignificantly elevated morbid risk of depression in their first-degree relatives. Clinically significant subthreshold depression was common in psychiatric outpatients, and the present results support the validity of distinguishing between depressive disorder NOS and adjustment disorder with depressed mood. Future studies of the treatment of subthreshold depression

  8. Ectopic expression of RNF168 and 53BP1 increases mutagenic but not physiological non-homologous end joining

    DEFF Research Database (Denmark)

    Zong, Dali; Callén, Elsa; Pegoraro, Gianluca

    2015-01-01

    DNA double strand breaks (DSBs) formed during S phase are preferentially repaired by homologous recombination (HR), whereas G1 DSBs, such as those occurring during immunoglobulin class switch recombination (CSR), are repaired by non-homologous end joining (NHEJ). The DNA damage response proteins ...

  9. On some homological functors of Bieberbach group of dimension four with dihedral point group of order eight

    Science.gov (United States)

    Mohammad, Siti Afiqah; Ali, Nor Muhainiah Mohd; Sarmin, Nor Haniza; Idrus, Nor'ashiqin Mohd; Masri, Rohaidah

    2014-06-01

    A Bieberbach group is a torsion free crystallographic group, which is an extension of a free abelian group of finite rank by a finite point group, while homological functors of a group include nonabelian tensor square, exterior square and Schur Multiplier. In this paper, some homological functors of a Bieberbach group of dimension four with dihedral point group of order eight are computed.

  10. Modeling Human Serum Albumin Tertiary Structure to Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics

    Science.gov (United States)

    Petrovic, Dus?an; Zlatovic´, Mario

    2015-01-01

    A homology modeling laboratory experiment has been developed for an introductory molecular modeling course for upper-division undergraduate chemistry students. With this experiment, students gain practical experience in homology model preparation and assessment as well as in protein visualization using the educational version of PyMOL…

  11. An analytical procedure for computing smooth transitions between two specified cross sections with applications to blended wing body configuration

    Science.gov (United States)

    Barger, R. L.

    1982-01-01

    An analytical procedure is described for designing smooth transition surfaces for blended wing-body configurations. Starting from two specified cross section shapes, the procedure generates a gradual transition from one cross section shape to the other as an analytic blend of the two shapes. The method utilizes a conformal mapping, with subsequent translation and scaling, to transform the specified and shapes to curves that can be combined more smoothly. A sample calculation is applied to a blended wing-body missile type configuration with a top mounted inlet.

  12. Either non-homologous ends joining or homologous recombination is required to repair double-strand breaks in the genome of macrophage-internalized Mycobacterium tuberculosis.

    Science.gov (United States)

    Brzostek, Anna; Szulc, Izabela; Klink, Magdalena; Brzezinska, Marta; Sulowska, Zofia; Dziadek, Jaroslaw

    2014-01-01

    The intracellular pathogen Mycobacterium tuberculosis (Mtb) is constantly exposed to a multitude of hostile conditions and is confronted by a variety of potentially DNA-damaging assaults in vivo, primarily from host-generated antimicrobial toxic radicals. Exposure to reactive nitrogen species and/or reactive oxygen species causes different types of DNA damage, including oxidation, depurination, methylation and deamination, that can result in single- or double-strand breaks (DSBs). These breaks affect the integrity of the whole genome and, when left unrepaired, can lead to cell death. Here, we investigated the role of the DSB repair pathways, homologous recombination (HR) and non-homologous ends joining (NHEJ), in the survival of Mtb inside macrophages. To this end, we constructed Mtb strains defective for HR (ΔrecA), NHEJ [Δ(ku,ligD)], or both DSB repair systems [Δ(ku,ligD,recA)]. Experiments using these strains revealed that either HR or NHEJ is sufficient for the survival and propagation of tubercle bacilli inside macrophages. Inhibition of nitric oxide or superoxide anion production with L-NIL or apocynin, respectively, enabled the Δ(ku,ligD,recA) mutant strain lacking both systems to survive intracellularly. Complementation of the Δ(ku,ligD,recA) mutant with an intact recA or ku-ligD rescued the ability of Mtb to propagate inside macrophages.

  13. Either non-homologous ends joining or homologous recombination is required to repair double-strand breaks in the genome of macrophage-internalized Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Anna Brzostek

    Full Text Available The intracellular pathogen Mycobacterium tuberculosis (Mtb is constantly exposed to a multitude of hostile conditions and is confronted by a variety of potentially DNA-damaging assaults in vivo, primarily from host-generated antimicrobial toxic radicals. Exposure to reactive nitrogen species and/or reactive oxygen species causes different types of DNA damage, including oxidation, depurination, methylation and deamination, that can result in single- or double-strand breaks (DSBs. These breaks affect the integrity of the whole genome and, when left unrepaired, can lead to cell death. Here, we investigated the role of the DSB repair pathways, homologous recombination (HR and non-homologous ends joining (NHEJ, in the survival of Mtb inside macrophages. To this end, we constructed Mtb strains defective for HR (ΔrecA, NHEJ [Δ(ku,ligD], or both DSB repair systems [Δ(ku,ligD,recA]. Experiments using these strains revealed that either HR or NHEJ is sufficient for the survival and propagation of tubercle bacilli inside macrophages. Inhibition of nitric oxide or superoxide anion production with L-NIL or apocynin, respectively, enabled the Δ(ku,ligD,recA mutant strain lacking both systems to survive intracellularly. Complementation of the Δ(ku,ligD,recA mutant with an intact recA or ku-ligD rescued the ability of Mtb to propagate inside macrophages.

  14. HomPPI: a class of sequence homology based protein-protein interface prediction methods

    Directory of Open Access Journals (Sweden)

    Dobbs Drena

    2011-06-01

    Full Text Available Abstract Background Although homology-based methods are among the most widely used methods for predicting the structure and function of proteins, the question as to whether interface sequence conservation can be effectively exploited in predicting protein-protein interfaces has been a subject of debate. Results We studied more than 300,000 pair-wise alignments of protein sequences from structurally characterized protein complexes, including both obligate and transient complexes. We identified sequence similarity criteria required for accurate homology-based inference of interface residues in a query protein sequence. Based on these analyses, we developed HomPPI, a class of sequence homology-based methods for predicting protein-protein interface residues. We present two variants of HomPPI: (i NPS-HomPPI (Non partner-specific HomPPI, which can be used to predict interface residues of a query protein in the absence of knowledge of the interaction partner; and (ii PS-HomPPI (Partner-specific HomPPI, which can be used to predict the interface residues of a query protein with a specific target protein. Our experiments on a benchmark dataset of obligate homodimeric complexes show that NPS-HomPPI can reliably predict protein-protein interface residues in a given protein, with an average correlation coefficient (CC of 0.76, sensitivity of 0.83, and specificity of 0.78, when sequence homologs of the query protein can be reliably identified. NPS-HomPPI also reliably predicts the interface residues of intrinsically disordered proteins. Our experiments suggest that NPS-HomPPI is competitive with several state-of-the-art interface prediction servers including those that exploit the structure of the query proteins. The partner-specific classifier, PS-HomPPI can, on a large dataset of transient complexes, predict the interface residues of a query protein with a specific target, with a CC of 0.65, sensitivity of 0.69, and specificity of 0.70, when homologs of

  15. Geometry-specified troposphere decorrelation for subcentimeter real-time kinematic solutions over long baselines

    Science.gov (United States)

    Li, Bofeng; Feng, Yanming; Shen, Yunzhong; Wang, Charles

    2010-11-01

    Real-time kinematic (RTK) GPS techniques have been extensively developed for applications including surveying, structural monitoring, and machine automation. Limitations of the existing RTK techniques that hinder their applications for geodynamics purposes are twofold: (1) the achievable RTK accuracy is on the level of a few centimeters and the uncertainty of vertical component is 1.5-2 times worse than those of horizontal components and (2) the RTK position uncertainty grows in proportional to the base-to-rover distances. The key limiting factor behind the problems is the significant effect of residual tropospheric errors on the positioning solutions, especially on the highly correlated height component. This paper develops the geometry-specified troposphere decorrelation strategy to achieve the subcentimeter kinematic positioning accuracy in all three components. The key is to set up a relative zenith tropospheric delay (RZTD) parameter to absorb the residual tropospheric effects and to solve the established model as an ill-posed problem using the regularization method. In order to compute a reasonable regularization parameter to obtain an optimal regularized solution, the covariance matrix of positional parameters estimated without the RZTD parameter, which is characterized by observation geometry, is used to replace the quadratic matrix of their "true" values. As a result, the regularization parameter is adaptively computed with variation of observation geometry. The experiment results show that new method can efficiently alleviate the model's ill condition and stabilize the solution from a single data epoch. Compared to the results from the conventional least squares method, the new method can improve the long-range RTK solution precision from several centimeters to the subcentimeter in all components. More significantly, the precision of the height component is even higher. Several geosciences applications that require subcentimeter real-time solutions can

  16. Stat5 signaling specifies basal versus stress erythropoietic responses through distinct binary and graded dynamic modalities.

    Directory of Open Access Journals (Sweden)

    Ermelinda Porpiglia

    2012-08-01

    Full Text Available Erythropoietin (Epo-induced Stat5 phosphorylation (p-Stat5 is essential for both basal erythropoiesis and for its acceleration during hypoxic stress. A key challenge lies in understanding how Stat5 signaling elicits distinct functions during basal and stress erythropoiesis. Here we asked whether these distinct functions might be specified by the dynamic behavior of the Stat5 signal. We used flow cytometry to analyze Stat5 phosphorylation dynamics in primary erythropoietic tissue in vivo and in vitro, identifying two signaling modalities. In later (basophilic erythroblasts, Epo stimulation triggers a low intensity but decisive, binary (digital p-Stat5 signal. In early erythroblasts the binary signal is superseded by a high-intensity graded (analog p-Stat5 response. We elucidated the biological functions of binary and graded Stat5 signaling using the EpoR-HM mice, which express a "knocked-in" EpoR mutant lacking cytoplasmic phosphotyrosines. Strikingly, EpoR-HM mice are restricted to the binary signaling mode, which rescues these mice from fatal perinatal anemia by promoting binary survival decisions in erythroblasts. However, the absence of the graded p-Stat5 response in the EpoR-HM mice prevents them from accelerating red cell production in response to stress, including a failure to upregulate the transferrin receptor, which we show is a novel stress target. We found that Stat5 protein levels decline with erythroblast differentiation, governing the transition from high-intensity graded signaling in early erythroblasts to low-intensity binary signaling in later erythroblasts. Thus, using exogenous Stat5, we converted later erythroblasts into high-intensity graded signal transducers capable of eliciting a downstream stress response. Unlike the Stat5 protein, EpoR expression in erythroblasts does not limit the Stat5 signaling response, a non-Michaelian paradigm with therapeutic implications in myeloproliferative disease. Our findings show how the

  17. Effectiveness of Psychotherapy in Personality Disorders Not Otherwise Specified: A Comparison of Different Treatment Modalities.

    Science.gov (United States)

    Horn, Eva K; Bartak, Anna; Meerman, Anke M M A; Rossum, Bert V; Ziegler, Uli M; Thunnissen, Moniek; Soons, Mirjam; Andrea, Helene; Hamers, Elisabeth F M; Emmelkamp, Paul M G; Stijnen, Theo; Busschbach, Jan J V; Verheul, Roel

    2015-01-01

    Although personality disorder not otherwise specified (PDNOS) is highly prevalent and associated with a high burden of disease, only a few treatment studies in this patient group exist. This study is the first to investigate the effectiveness of different modalities of psychotherapy in patients with PDNOS, i.e., short-term (up to 6 months) and long-term (more than 6 months) outpatient, day hospital, and inpatient psychotherapy. A total of 205 patients with PDNOS were assigned to one of six treatment modalities. Effectiveness was assessed over 60 months after baseline. The primary outcome measure was symptom severity, and the secondary outcome measures included psychosocial functioning and quality of life. The study design was quasi-experimental, and the multiple propensity score was used to control for initial differences between treatment groups. All treatment modalities showed positive outcomes, especially in terms of improvements of symptom severity and social role functioning. At 12-month follow-up, after adjustment for initial differences between the treatment groups, short-term outpatient psychotherapy and short-term inpatient psychotherapy showed most improvement and generally outperformed the other modalities concerning symptom severity. At 60 months after baseline, effectiveness remained but observed differences between modalities mostly diminished. Patients with PDNOS benefit from psychotherapy both at short-term and long-term follow-up. Short-term outpatient psychotherapy and short-term inpatient psychotherapy seem to be superior to the other treatment modalities at 12-month follow-up. At 60-month follow-up, treatments showed mostly comparable effectiveness. The effectiveness of different modalities of psychotherapy in patients with PDNOS (i.e., short-term vs long-term; outpatient versus day hospital versus inpatient psychotherapy) has not yet been compared. Different modalities of psychotherapy are effective for patients with PDNOS, and positive

  18. Dectin-1 Polymorphism: A Genetic Disease Specifier in Autism Spectrum Disorders?

    Directory of Open Access Journals (Sweden)

    Meriem Bennabi

    Full Text Available In autism spectrum disorders (ASD, complex gene-environment interactions contribute to disease onset and progress. Given that gastro-intestinal dysfunctions are common in ASD, we postulated involvement of microbial dysbiosis in ASD and investigated, under a case-control design, the influence of DNA polymorphisms in the CLEC7A gene that encodes a pivotal fungal sensor, Dectin-1.DNAs from 478 ASD patients and 351 healthy controls (HC were analyzed for the CLEC7A rs16910631G/A and rs2078178 A/G single nucleotide polymorphisms (SNPs. Differences in the distribution of allele, genotype and haplotype by Chi-square testing and nonparametric analysis by Kruskal-Wallis/Mann-Whitney tests, where appropriate, were performed. The free statistical package R.2.13 software was used for the statistical analysis.We found that the CLEC7A rs2078178 G allele and GG genotype were more prevalent in HC as compared to ASD but failed to reach statistical significance for the latter (pc = 0.01, 0.06 respectively. However, after phenotype-based stratification, the CLEC7A rs2078178 G allele and GG genotype were found to be significantly more frequent in the Asperger group as compared to other ASD subsets (pc = 0.02, 0.01, a finding reinforced by haplotype analysis (rs2078178/rs16910631 G-G/G-G (pc = 0.002. Further, intellectual quotient (IQ-based stratification of ASD patients revealed that IQ values increase linearly along the CLEC7A rs2078178 AA, AG and GG genotypes (p = 0.05 and in a recessive manner (GG vs. AA+AG p = 0.02, further confirmed by haplotype distribution (CLEC7A rs2078178-16910631; A-G/A-G, A-G/G-G and G-G/G-G, p = 0.02, G-G/G-G vs. others, p = 0.01.Our data suggest that the genetic diversity of CLEC7A gene influences the ASD phenotype by behaving as a disease specifier and imply that the genetic control of innate immune response could determine the ASD phenotype.

  19. 75 FR 54095 - Takes of Marine Mammals Incidental to Specified Activities; Low-Energy Marine Seismic Survey in...

    Science.gov (United States)

    2010-09-03

    ... Marine Mammals Incidental to Specified Activities; Low- Energy Marine Seismic Survey in the Eastern... low-energy marine seismic survey. Pursuant to the Marine Mammal Protection Act (MMPA), NMFS is... funding provided by the National Science Foundation, a low-energy marine seismic survey. NMFS reviewed SIO...

  20. 76 FR 68720 - Takes of Marine Mammals Incidental to Specified Activities; Low-Energy Marine Geophysical Survey...

    Science.gov (United States)

    2011-11-07

    ... Marine Mammals Incidental to Specified Activities; Low- Energy Marine Geophysical Survey in the Western... conducting a low-energy marine geophysical (i.e., seismic) survey in the western tropical Pacific Ocean... Science Foundation (NSF), and ``Environmental Assessment of a Low-Energy Marine Geophysical Survey by the...