Examining inter-family differences in intra-family (parent-adolescent) dynamics using grid-sequence analysis.

Science.gov (United States)

Brinberg, Miriam; Fosco, Gregory M; Ram, Nilam

2017-12-01

Family systems theorists have forwarded a set of theoretical principles meant to guide family scientists and practitioners in their conceptualization of patterns of family interaction-intra-family dynamics-that, over time, give rise to family and individual dysfunction and/or adaptation. In this article, we present an analytic approach that merges state space grid methods adapted from the dynamic systems literature with sequence analysis methods adapted from molecular biology into a "grid-sequence" method for studying inter-family differences in intra-family dynamics. Using dyadic data from 86 parent-adolescent dyads who provided up to 21 daily reports about connectedness, we illustrate how grid-sequence analysis can be used to identify a typology of intrafamily dynamics and to inform theory about how specific types of intrafamily dynamics contribute to adolescent behavior problems and family members' mental health. Methodologically, grid-sequence analysis extends the toolbox of techniques for analysis of family experience sampling and daily diary data. Substantively, we identify patterns of family level microdynamics that may serve as new markers of risk/protective factors and potential points for intervention in families. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing.

Science.gov (United States)

Wong, Lai-Ping; Lai, Jason Kuan-Han; Saw, Woei-Yuh; Ong, Rick Twee-Hee; Cheng, Anthony Youzhi; Pillai, Nisha Esakimuthu; Liu, Xuanyao; Xu, Wenting; Chen, Peng; Foo, Jia-Nee; Tan, Linda Wei-Lin; Koo, Seok-Hwee; Soong, Richie; Wenk, Markus Rene; Lim, Wei-Yen; Khor, Chiea-Chuen; Little, Peter; Chia, Kee-Seng; Teo, Yik-Ying

2014-05-01

South Asia possesses a significant amount of genetic diversity due to considerable intergroup differences in culture and language. There have been numerous reports on the genetic structure of Asian Indians, although these have mostly relied on genotyping microarrays or targeted sequencing of the mitochondria and Y chromosomes. Asian Indians in Singapore are primarily descendants of immigrants from Dravidian-language-speaking states in south India, and 38 individuals from the general population underwent deep whole-genome sequencing with a target coverage of 30X as part of the Singapore Sequencing Indian Project (SSIP). The genetic structure and diversity of these samples were compared against samples from the Singapore Sequencing Malay Project and populations in Phase 1 of the 1,000 Genomes Project (1 KGP). SSIP samples exhibited greater intra-population genetic diversity and possessed higher heterozygous-to-homozygous genotype ratio than other Asian populations. When compared against a panel of well-defined Asian Indians, the genetic makeup of the SSIP samples was closely related to South Indians. However, even though the SSIP samples clustered distinctly from the Europeans in the global population structure analysis with autosomal SNPs, eight samples were assigned to mitochondrial haplogroups that were predominantly present in Europeans and possessed higher European admixture than the remaining samples. An analysis of the relative relatedness between SSIP with two archaic hominins (Denisovan, Neanderthal) identified higher ancient admixture in East Asian populations than in SSIP. The data resource for these samples is publicly available and is expected to serve as a valuable complement to the South Asian samples in Phase 3 of 1 KGP.

[Study on Microbial Diversity of Peri-implantitis Subgingival by High-throughput Sequencing].

Science.gov (United States)

Li, Zhi-jie; Wang, Shao-guo; Li, Yue-hong; Tu, Dong-xiang; Liu, Shi-yun; Nie, Hong-bing; Li, Zhi-qiang; Zhang, Ju-mei

2015-07-01

To study microbial diversity of peri-implantitis subgingival with high-throughput sequencing, and investigate microbiological etiology of peri-implantitis. Subgingival plaques were sampled from the patients with peri-implantitis (D group) and non-peri-implantitis subjects (N group). The microbiological diversity of the subgingival plaques was detected by sequencing V4 region of 16S rRNA with Illumina Miseq platform. The diversity of the community structure was analyzed using Mothur software. A total of 156 507 gene sequences were detected in nine samples and 4 402 operational taxonomic units (OTUs) were found. Selenomonas, Pseudomonas, and Fusobacterium were dominant bacteria in D group, while Fusobacterium, Veillonella and Streptococcus were dominant bacteria in N group. Differences between peri-implantitis and non-peri-implantitis bacterial communities were observed at all phylogenetic levels by LEfSe, which was also found in PcoA test. The occurrence of peri-implantitis is not only related to periodontitis pathogenic microbe, but also related with the changes of oral microbial community structure. Treponema, Herbaspirillum, Butyricimonas and Phaeobacte may be closely related to the occurrence and development of peri-implantitis.

What is the optimal management of an intra-operative air leak in a colorectal anastomosis?

Science.gov (United States)

Mitchem, J B; Stafford, C; Francone, T D; Roberts, P L; Schoetz, D J; Marcello, P W; Ricciardi, R

2018-02-01

An airtight anastomosis on intra-operative leak testing has been previously demonstrated to be associated with a lower risk of clinically significant postoperative anastomotic leak following left-sided colorectal anastomosis. However, to date, there is no consistently agreed upon method for management of an intra-operative anastomotic leak. Therefore, we powered a noninferiority study to determine whether suture repair alone was an appropriate strategy for the management of an intra-operative air leak. This is a retrospective cohort analysis of prospectively collected data from a tertiary care referral centre. We included all consecutive patients with left-sided colorectal or ileorectal anastomoses and evidence of air leak during intra-operative leak testing. Patients were excluded if proximal diversion was planned preoperatively, a pre-existing proximal diversion was present at the time of surgery or an anastomosis was ultimately unable to be completed. The primary outcome measure was clinically significant anastomotic leak, as defined by the Surgical Infection Study Group at 30 days. From a sample of 2360 patients, 119 had an intra-operative air leak during leak testing. Sixty-eight patients underwent suture repair alone and 51 underwent proximal diversion or anastomotic reconstruction. The clinically significant leak rate was 9% (6/68; 95% CI: 2-15%) in the suture repair alone arm and 0% (0/51) in the diversion or reconstruction arm. Suture repair alone does not meet the criteria for noninferiority for the management of intra-operative air leak during left-sided colorectal anastomosis. Further repair of intra-operative air leak by suture repair alone should be reconsidered given these findings. Colorectal Disease © 2017 The Association of Coloproctology of Great Britain and Ireland.

A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

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Glass John I

2010-07-01

repeat may be disseminated by HGT and intra-genomic shuffling. Conclusions We describe novel features of PARCELs (Palindromic Amphipathic Repeat Coding ELements, a set of widely distributed repeat protein domains and coding sequences that were likely acquired through HGT by diverse unicellular microbes, further mobilized and diversified within genomes, and co-opted for expression in the membrane proteome of some taxa. Disseminated by multiple gene-centric vehicles, ORFs harboring these elements enhance accessory gene pools as part of the "mobilome" connecting genomes of various clades, in taxa sharing common niches.

High‑throughput sequencing analyses of oral microbial diversity in healthy people and patients with dental caries and periodontal disease.

Science.gov (United States)

Chen, Tingtao; Shi, Yan; Wang, Xiaolei; Wang, Xin; Meng, Fanjing; Yang, Shaoguo; Yang, Jian; Xin, Hongbo

2017-07-01

Recurrence of oral diseases caused by antibiotics has brought about an urgent requirement to explore the oral microbial diversity in the human oral cavity. In the present study, the high‑throughput sequencing method was adopted to compare the microbial diversity of healthy people and oral patients and sequence analysis was performed by UPARSE software package. The Venn results indicated that a mean of 315 operational taxonomic units (OTUs) was obtained, and 73, 64, 53, 19 and 18 common OTUs belonging to Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria, respectively, were identified in healthy people. Moreover, the reduction of Firmicutes and the increase of Proteobacteria in the children group, and the increase of Firmicutes and the reduction of Proteobacteria in the youth and adult groups, indicated that the age bracket and oral disease had largely influenced the tooth development and microbial development in the oral cavity. In addition, the traditional 'pathogenic bacteria' of Firmicutes, Proteobacteria and Bacteroidetes (accounted for >95% of the total sequencing number in each group) indicated that the 'harmful' bacteria may exert beneficial effects on oral health. Therefore, the data will provide certain clues for curing some oral diseases by the strategy of adjusting the disturbed microbial compositions in oral disease to healthy level.

Predictors of "occult" intra-abdominal injuries in blunt trauma patients.

Science.gov (United States)

Parreira, José Gustavo; Malpaga, Juliano Mangini Dias; Olliari, Camilla Bilac; Perlingeiro, Jacqueline A G; Soldá, Silvia C; Assef, José Cesar

2015-01-01

to assess predictors of intra-abdominal injuries in blunt trauma patients admitted without abdominal pain or abnormalities on the abdomen physical examination. We conducted a retrospective analysis of trauma registry data, including adult blunt trauma patients admitted from 2008 to 2010 who sustained no abdominal pain or abnormalities on physical examination of the abdomen at admission and were submitted to computed tomography of the abdomen and/or exploratory laparotomy. Patients were assigned into: Group 1 (with intra-abdominal injuries) or Group 2 (without intra-abdominal injuries). Variables were compared between groups to identify those significantly associated with the presence of intra-abdominal injuries, adopting ptrauma mechanism (ptrauma mechanism (p=0.008 - OR 2.85; 95%CI 1.13-6.22) and abnormal neurological physical exam at admission (p=0.015 - OR 0.44; 95%CI 0.22-0.85). Intra-abdominal injuries were predominantly associated with trauma mechanism and presence of chest injuries.

Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing.

Directory of Open Access Journals (Sweden)

Lai-Ping Wong

2014-05-01

Full Text Available South Asia possesses a significant amount of genetic diversity due to considerable intergroup differences in culture and language. There have been numerous reports on the genetic structure of Asian Indians, although these have mostly relied on genotyping microarrays or targeted sequencing of the mitochondria and Y chromosomes. Asian Indians in Singapore are primarily descendants of immigrants from Dravidian-language-speaking states in south India, and 38 individuals from the general population underwent deep whole-genome sequencing with a target coverage of 30X as part of the Singapore Sequencing Indian Project (SSIP. The genetic structure and diversity of these samples were compared against samples from the Singapore Sequencing Malay Project and populations in Phase 1 of the 1,000 Genomes Project (1 KGP. SSIP samples exhibited greater intra-population genetic diversity and possessed higher heterozygous-to-homozygous genotype ratio than other Asian populations. When compared against a panel of well-defined Asian Indians, the genetic makeup of the SSIP samples was closely related to South Indians. However, even though the SSIP samples clustered distinctly from the Europeans in the global population structure analysis with autosomal SNPs, eight samples were assigned to mitochondrial haplogroups that were predominantly present in Europeans and possessed higher European admixture than the remaining samples. An analysis of the relative relatedness between SSIP with two archaic hominins (Denisovan, Neanderthal identified higher ancient admixture in East Asian populations than in SSIP. The data resource for these samples is publicly available and is expected to serve as a valuable complement to the South Asian samples in Phase 3 of 1 KGP.

Characterization of Human Cytomegalovirus Genome Diversity in Immunocompromised Hosts by Whole-Genome Sequencing Directly From Clinical Specimens.

Science.gov (United States)

Hage, Elias; Wilkie, Gavin S; Linnenweber-Held, Silvia; Dhingra, Akshay; Suárez, Nicolás M; Schmidt, Julius J; Kay-Fedorov, Penelope C; Mischak-Weissinger, Eva; Heim, Albert; Schwarz, Anke; Schulz, Thomas F; Davison, Andrew J; Ganzenmueller, Tina

2017-06-01

Advances in next-generation sequencing (NGS) technologies allow comprehensive studies of genetic diversity over the entire genome of human cytomegalovirus (HCMV), a significant pathogen for immunocompromised individuals. Next-generation sequencing was performed on target enriched sequence libraries prepared directly from a variety of clinical specimens (blood, urine, breast milk, respiratory samples, biopsies, and vitreous humor) obtained longitudinally or from different anatomical compartments from 20 HCMV-infected patients (renal transplant recipients, stem cell transplant recipients, and congenitally infected children). De novo-assembled HCMV genome sequences were obtained for 57 of 68 sequenced samples. Analysis of longitudinal or compartmental HCMV diversity revealed various patterns: no major differences were detected among longitudinal, intraindividual blood samples from 9 of 15 patients and in most of the patients with compartmental samples, whereas a switch of the major HCMV population was observed in 6 individuals with sequential blood samples and upon compartmental analysis of 1 patient with HCMV retinitis. Variant analysis revealed additional aspects of minor virus population dynamics and antiviral-resistance mutations. In immunosuppressed patients, HCMV can remain relatively stable or undergo drastic genomic changes that are suggestive of the emergence of minor resident strains or de novo infection. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

[The use of 16S rDNA sequencing in species diversity analysis for sputum of patients with ventilator-associated pneumonia].

Science.gov (United States)

Yang, Xiaojun; Wang, Xiaohong; Liang, Zhijuan; Zhang, Xiaoya; Wang, Yanbo; Wang, Zhenhai

2014-05-01

To study the species and amount of bacteria in sputum of patients with ventilator-associated pneumonia (VAP) by using 16S rDNA sequencing analysis, and to explore the new method for etiologic diagnosis of VAP. Bronchoalveolar lavage sputum samples were collected from 31 patients with VAP. Bacterial DNA of the samples were extracted and identified by polymerase chain reaction (PCR). At the same time, sputum specimens were processed for routine bacterial culture. The high flux sequencing experiment was conducted on PCR positive samples with 16S rDNA macro genome sequencing technology, and sequencing results were analyzed using bioinformatics, then the results between the sequencing and bacteria culture were compared. (1) 550 bp of specific DNA sequences were amplified in sputum specimens from 27 cases of the 31 patients with VAP, and they were used for sequencing analysis. 103 856 sequences were obtained from those sputum specimens using 16S rDNA sequencing, yielding approximately 39 Mb of raw data. Tag sequencing was able to inform genus level in all 27 samples. (2) Alpha-diversity analysis showed that sputum samples of patients with VAP had significantly higher variability and richness in bacterial species (Shannon index values 1.20, Simpson index values 0.48). Rarefaction curve analysis showed that there were more species that were not detected by sequencing from some VAP sputum samples. (3) Analysis of 27 sputum samples with VAP by using 16S rDNA sequences yielded four phyla: namely Acitinobacteria, Bacteroidetes, Firmicutes, Proteobacteria. With genus as a classification, it was found that the dominant species included Streptococcus 88.9% (24/27), Limnohabitans 77.8% (21/27), Acinetobacter 70.4% (19/27), Sphingomonas 63.0% (17/27), Prevotella 63.0% (17/27), Klebsiella 55.6% (15/27), Pseudomonas 55.6% (15/27), Aquabacterium 55.6% (15/27), and Corynebacterium 55.6% (15/27). (4) Pyrophosphate sequencing discovered that Prevotella, Limnohabitans, Aquabacterium

The efficacy of superselective intra-arterial infusion in patients with T4 oral cancer. Comparison with conventional chemotherapy

International Nuclear Information System (INIS)

Arakaki, Keiichi; Arasaki, Akira; Kano, Takeshi

2009-01-01

Since 1985, we have applied systematic treatment to improve radicality and postoperative oral dysfunction, as well as maxillofacial deformity. However, most T4 cases of oral cancer have remained difficult to treat, and diverse methods and results for progressive cancer have been reported by many institutions. For high-grade malignancy cases, we changed the treatment from bleomycin or cisplatin in induction chemotherapy to targeted intra-arterial infusions of carboplatin with radiation-combined therapy. In this study, we compared the effects of conventional therapy with targeted intra-arterial infusions of carboplatin for T4 cases of oral cancer. In this retrospective review, we analyzed a subset of patients who were treated with induction chemotherapy using bleomycin (BLM) and targeted intra-arterial infusions of carboplatin (CBDCA) with radiation-combined therapy patients who received treatment between June 1985 and December 2006. Of the 105 patients who had T4 disease, the proportion with grade IIb to IV in the carboplatin with radiation-combined therapy (88.9%) was higher than that in induction chemotherapy (45.0%). Targeted chemoradiation therapy followed by surgical salvage is a highly effective approach for the regional control of patients with T4, although additional strategies are required to address the problem of distant metastases. (author)

Assessment of intra-species diversity among strains of Acinetobacter baumannii isolated from sites contaminated with petroleum hydrocarbons

International Nuclear Information System (INIS)

Manab Sarma, P.; Bhattacharya, D.; Krishnan, S.; Lal, B.

2004-01-01

Intra-species diversity among Acinetobacter baumannii strains isolated from crude oil-contaminated soils from different geographic regions in India was assessed, including their capability to degrade different fractions of total petroleum hydrocarbons. A total of 96 strains were isolated from five different sites. Of the 96 isolates, 25 strains were identified as Acinetobacter baumannii; all of these strains were biochemically profiled and grouped into eight phenovars on the basis of multivariate analysis of their substrate utilization profiles. All strains were able to degrade the total petroleum hydrocarbon fractions of crude oil. Intraspecies relatedness among the 25 strains was determined using tRNA intergenic spacer length polymorphism. Specific variants among the strains with different degradation capacities for different fractions of crude oil were detected. Environmental influences that cause intra-species diversity, such as functional resilience, within the selected strains of A. baumannii were also noted. It is suggested that such diversities may make it possible to select contaminant-specific strains for efficient biotechnological strategies in environmental remediation. 19 refs., 4 tabs., 3 figs

Assessment of intra-species diversity among strains of Acinetobacter baumannii isolated from sites contaminated with petroleum hydrocarbons

Energy Technology Data Exchange (ETDEWEB)

Manab Sarma, P.; Bhattacharya, D.; Krishnan, S. [TERI School of Advanced Studies, Center of Bioresources and Biotechnology, New Delhi (India); Lal, B. [TERI School of Advanced Studies, Microbial Biotechnology Division, New Delhi (India)

2004-06-01

Intra-species diversity among Acinetobacter baumannii strains isolated from crude oil-contaminated soils from different geographic regions in India was assessed, including their capability to degrade different fractions of total petroleum hydrocarbons. A total of 96 strains were isolated from five different sites. Of the 96 isolates, 25 strains were identified as Acinetobacter baumannii; all of these strains were biochemically profiled and grouped into eight phenovars on the basis of multivariate analysis of their substrate utilization profiles. All strains were able to degrade the total petroleum hydrocarbon fractions of crude oil. Intraspecies relatedness among the 25 strains was determined using tRNA intergenic spacer length polymorphism. Specific variants among the strains with different degradation capacities for different fractions of crude oil were detected. Environmental influences that cause intra-species diversity, such as functional resilience, within the selected strains of A. baumannii were also noted. It is suggested that such diversities may make it possible to select contaminant-specific strains for efficient biotechnological strategies in environmental remediation. 19 refs., 4 tabs., 3 figs.

Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions.

Science.gov (United States)

Silvas, Tania V; Hou, Shurong; Myint, Wazo; Nalivaika, Ellen; Somasundaran, Mohan; Kelch, Brian A; Matsuo, Hiroshi; Kurt Yilmaz, Nese; Schiffer, Celia A

2018-05-14

The APOBEC3 (A3) family of human cytidine deaminases is renowned for providing a first line of defense against many exogenous and endogenous retroviruses. However, the ability of these proteins to deaminate deoxycytidines in ssDNA makes A3s a double-edged sword. When overexpressed, A3s can mutate endogenous genomic DNA resulting in a variety of cancers. Although the sequence context for mutating DNA varies among A3s, the mechanism for substrate sequence specificity is not well understood. To characterize substrate specificity of A3A, a systematic approach was used to quantify the affinity for substrate as a function of sequence context, length, secondary structure, and solution pH. We identified the A3A ssDNA binding motif as (T/C)TC(A/G), which correlated with enzymatic activity. We also validated that A3A binds RNA in a sequence specific manner. A3A bound tighter to substrate binding motif within a hairpin loop compared to linear oligonucleotide, suggesting A3A affinity is modulated by substrate structure. Based on these findings and previously published A3A-ssDNA co-crystal structures, we propose a new model with intra-DNA interactions for the molecular mechanism underlying A3A sequence preference. Overall, the sequence and structural preferences identified for A3A leads to a new paradigm for identifying A3A's involvement in mutation of endogenous or exogenous DNA.

Global sequence diversity of the lactate dehydrogenase gene in Plasmodium falciparum.

Science.gov (United States)

Simpalipan, Phumin; Pattaradilokrat, Sittiporn; Harnyuttanakorn, Pongchai

2018-01-09

Antigen-detecting rapid diagnostic tests (RDTs) have been recommended by the World Health Organization for use in remote areas to improve malaria case management. Lactate dehydrogenase (LDH) of Plasmodium falciparum is one of the main parasite antigens employed by various commercial RDTs. It has been hypothesized that the poor detection of LDH-based RDTs is attributed in part to the sequence diversity of the gene. To test this, the present study aimed to investigate the genetic diversity of the P. falciparum ldh gene in Thailand and to construct the map of LDH sequence diversity in P. falciparum populations worldwide. The ldh gene was sequenced for 50 P. falciparum isolates in Thailand and compared with hundreds of sequences from P. falciparum populations worldwide. Several indices of molecular variation were calculated, including the proportion of polymorphic sites, the average nucleotide diversity index (π), and the haplotype diversity index (H). Tests of positive selection and neutrality tests were performed to determine signatures of natural selection on the gene. Mean genetic distance within and between species of Plasmodium ldh was analysed to infer evolutionary relationships. Nucleotide sequences of P. falciparum ldh could be classified into 9 alleles, encoding 5 isoforms of LDH. L1a was the most common allelic type and was distributed in P. falciparum populations worldwide. Plasmodium falciparum ldh sequences were highly conserved, with haplotype and nucleotide diversity values of 0.203 and 0.0004, respectively. The extremely low genetic diversity was maintained by purifying selection, likely due to functional constraints. Phylogenetic analysis inferred the close genetic relationship of P. falciparum to malaria parasites of great apes, rather than to other human malaria parasites. This study revealed the global genetic variation of the ldh gene in P. falciparum, providing knowledge for improving detection of LDH-based RDTs and supporting the candidacy of

Comparison of hyaluronic acid and PRP intra-articular injection with combined intra-articular and intraosseous PRP injections to treat patients with knee osteoarthritis.

Science.gov (United States)

Su, Ke; Bai, Yuming; Wang, Jun; Zhang, Haisen; Liu, Hao; Ma, Shiyun

2018-05-01

The aim of this study was to evaluate the benefit provided by intraosseous infiltration combined with intra-articular injection of platelet-rich plasma to treat mild and moderate stages of knee joint degeneration (Kellgren-Lawrence score II-III) compared with other treatments, specifically intra-articular injection of PRP and of HA. Eighty-six patients with grade II to grade III knee OA according to the Kellgren-Lawrence classification were randomly assigned to intra-articular combined with intraosseous injection of PRP (group A), intra-articular PRP (group B), or intra-articular HA (group C). Patients in group A received intra-articular combined with intraosseous injection of PRP (administered twice, 2 weeks apart). Patients in group B received intra-articular injection of PRP every 14 days. Patients in group C received a series of five intra-articular injections of HA every 7 days. All patients were evaluated using the Visual Analogue Scale (VAS) and Western Ontario and McMaster Universities (WOMAC) score before the treatment and at 1, 3, 6, 12, and 18 months after treatment. There were significant improvements at the end of the 1st month. Notably, group A patients had significantly superior VAS and WOMAC scores than were observed in groups B and C. The VAS scores were similar in groups B and group C after the 6th month. Regarding the WOMAC scores, groups B and C differed at the 1st, 3rd, 6th, and 12th months; however, no significant difference was observed at the 18th month. The combination of intraosseous with intra-articular injections of PRP resulted in a significantly superior clinical outcome, with sustained lower VAS and WOMAC scores and improvement in quality of life within 18 months.

De novo assembly of highly diverse viral populations

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Yang Xiao

2012-09-01

Full Text Available Abstract Background Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage. Results We present VICUNA, a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software. Conclusions We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.

Ethnic diversity and social capital in upward mobility systems: Problematizing the permeability of intra-organizational career boundaries

NARCIS (Netherlands)

Ossenkop, C.; Vinkenburg, C.J.; Jansen, P.G.W.; Ghorashi, H.

2015-01-01

Purpose – The purpose of this paper is to contribute to a better understanding of the complex relationship between ethnic diversity, social capital, and objective career success in upward mobility systems over time. The authors conceptualize the underlying process of why intra-organizational career

LOX: Inferring level of expression from diverse methods of census sequencing

KAUST Repository

Zhang, Zhang

2010-06-10

Summary: We present LOX (Level Of eXpression) that estimates the Level Of gene eXpression from high-throughput-expressed sequence datasets with multiple treatments or samples. Unlike most analyses, LOX incorporates a gene bias model that facilitates integration of diverse transcriptomic sequencing data that arises when transcriptomic data have been produced using diverse experimental methodologies. LOX integrates overall sequence count tallies normalized by total expressed sequence count to provide expression levels for each gene relative to all treatments as well as Bayesian credible intervals. © The Author 2010. Published by Oxford University Press. All rights reserved.

LOX: Inferring level of expression from diverse methods of census sequencing

KAUST Repository

Zhang, Zhang; Ló pez-Girá ldez, Francesc Francisco; Townsend, Jeffrey P.

2010-01-01

Summary: We present LOX (Level Of eXpression) that estimates the Level Of gene eXpression from high-throughput-expressed sequence datasets with multiple treatments or samples. Unlike most analyses, LOX incorporates a gene bias model that facilitates integration of diverse transcriptomic sequencing data that arises when transcriptomic data have been produced using diverse experimental methodologies. LOX integrates overall sequence count tallies normalized by total expressed sequence count to provide expression levels for each gene relative to all treatments as well as Bayesian credible intervals. © The Author 2010. Published by Oxford University Press. All rights reserved.

Predictors of cardiogenic shock in cardiac surgery patients receiving intra-aortic balloon pumps.

Science.gov (United States)

Iyengar, Amit; Kwon, Oh Jin; Bailey, Katherine L; Ashfaq, Adeel; Abdelkarim, Ayman; Shemin, Richard J; Benharash, Peyman

2018-02-01

Cardiogenic shock after cardiac surgery leads to severely increased mortality. Intra-aortic balloon pumps may be used during the preoperative period to increase coronary perfusion. The purpose of this study was to characterize predictors of postoperative cardiogenic shock in cardiac surgery patients with and without intra-aortic balloon pumps support. We performed a retrospective analysis of our institutional database of the Society of Thoracic Surgeons for patients operated between January 2008 to July 2015. Multivariable logistic regression was used to model postoperative cardiogenic shock in both the intra-aortic balloon pumps and matched control cohorts. Overall, 4,741 cardiac surgery patients were identified during the study period, of whom 192 (4%) received a preoperative intra-aortic balloon pump. Intra-aortic balloon pumps patients had a greater prevalence of diabetes, previous cardiac surgery, congestive heart failure, and an urgent/emergent status (P pumps patients also had greater 30-day mortality and more postoperative cardiogenic shock (9% vs 3%, P pumps cohort, only sex, previous percutaneous coronary intervention and preoperative arrhythmia remained significant on multivariable analysis (all P pumps and those who do not. Further analysis of the effects of prophylactic intra-aortic balloon pumps support is warranted. (Surgery 2017;160:XXX-XXX.). Copyright © 2017 Elsevier Inc. All rights reserved.

Intra-operative blood transfusion among adult surgical patients in a ...

African Journals Online (AJOL)

This retrospective study was designed to audit the pattern of intra-operative whole blood transfusion among adult surgical patients over a two-year period. Data were collected on the rate of intra-operative transfusion, estimated blood loss, units of donor blood transfused, pattern of use of autologous blood and circumstances ...

Fetal Intra-Peritoneal Transfusion for the Management of Very Early Spontaneous Twin Anemia-Polycythemia Sequence in an Obese Patient With a Whole Anterior Placenta.

Science.gov (United States)

Guenot, Cécile; Robyr, Romaine; Jastrow, Nicole; Vial, Yvan; Raio, Luigi; Baud, David

2016-04-01

Twin anemia-polycythemia sequence (TAPS) is a rare condition in monochorionic twin pregnancies. Small intertwin placental vascular communications allow transfusion, which results in a hemoglobin difference in the twins in the absence of oligohydramnios or polyhydramnios. We report here a case of TAPS diagnosed at 17 weeks' gestation in an obese patient (BMI 42) with a whole anterior placenta. The only possible treatment at this stage of pregnancy was intra-uterine transfusion (IUT), which was repeated weekly until photocoagulation of placental anastomoses was feasible. Fetoscopic laser surgery is the only curative treatment, but is challenging in TAPS because of the absence of polyhydramnios and the presence of minuscule anastomoses. An anterior placenta and high BMI can make the procedure even more challenging. This case report demonstrates that very early and rapidly progressing TAPS with technically complicated conditions (elevated BMI and anterior placenta) can be successfully managed with IUT until laser procedure is achievable.

Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections

Directory of Open Access Journals (Sweden)

Saliha Hammoumi

2016-09-01

Full Text Available Koi herpesvirus disease (KHVD is an emerging disease that causes mass mortality in koi and common carp, Cyprinus carpio L. Its causative agent is Cyprinid herpesvirus 3 (CyHV-3, also known as koi herpesvirus (KHV. Although data on the pathogenesis of this deadly virus is relatively abundant in the literature, still little is known about its genomic diversity and about the molecular mechanisms that lead to such a high virulence. In this context, we developed a new strategy for sequencing full-length CyHV-3 genomes directly from infected fish tissues. Total genomic DNA extracted from carp gill tissue was specifically enriched with CyHV-3 sequences through hybridization to a set of nearly 2 million overlapping probes designed to cover the entire genome length, using KHV-J sequence (GenBank accession number AP008984 as reference. Applied to 7 CyHV-3 specimens from Poland and Indonesia, this targeted genomic enrichment enabled recovery of the full genomes with >99.9% reference coverage. The enrichment rate was directly correlated to the estimated number of viral copies contained in the DNA extracts used for library preparation, which varied between ∼5000 and ∼2×107. The average sequencing depth was >200 for all samples, thus allowing the search for variants with high confidence. Sequence analyses highlighted a significant proportion of intra-specimen sequence heterogeneity, suggesting the presence of mixed infections in all investigated fish. They also showed that inter-specimen genetic diversity at the genome scale was very low (>99.95% of sequence identity. By enabling full genome comparisons directly from infected fish tissues, this new method will be valuable to trace outbreaks rapidly and at a reasonable cost, and in turn to understand the transmission routes of CyHV-3.

Dynamics of albumin synthetic response to intra-abdominal abscess in patients with gastrointestinal fistula.

Science.gov (United States)

Zhou, Bo; Ren, Jianan; Han, Gang; Chen, Yu; A, Jiye; Gu, Guosheng; Chen, Jun; Wang, Gefei; Li, Jieshou

2014-04-01

Low serum albumin concentration is a predictor of failure of source control for intra-abdominal infection. However, data on dynamics of albumin synthesis in these patients and to what extent these changes contribute to hypoalbuminemia are relatively scarce. We investigated in a group of patients with gastrointestinal fistula the dynamic response of liver albumin synthesis to intra-abdominal abscess and how these related to hypoalbuminemia and circulating endocrine hormone profiles. Eight gastrointestinal fistula patients scheduled to undergo percutaneous abscess sump drainage were enrolled prospectively to measure albumin synthesis rates at different stages of the inflammatory response (immediately after diagnosis and 7 d following sump drainage when clinical signs of intra-abdominal sepsis had been eradicated). Eight age-, sex-, and body mass index-matched intestinal fistula patients were studied as control patients. Consecutive arterial blood samples were drawn during a primed-constant infusion (priming dose: 4 micromol·kg(-1), infusion rate: 6 micromol·kg(-1)·min(-1)) to determine the incorporation rate of L-[ring-(2)H5]-phenylalanine directly into plasma albumin using gas chromatography/mass spectrometry analysis. Patients suffering from intra-abdominal infection had reduced plasma albumin and total plasma protein concentrations, compared with control patients. Albumin fractional synthesis rates in patients with intra-abdominal abscess were decreased, compared with those in the control group. When the source of infection was removed, albumin synthesis rates returned to control values, whereas albumin concentrations did not differ significantly from the corresponding concentrations in control subjects and patients with intra-abdominal abscess. Despite nutritional intervention, albumin synthesis rate is decreased in intestinal fistula patients with intra-abdominal abscess; albumin synthesis returns to control values during convalescence.

A comparison of 454 sequencing and clonal sequencing for the characterization of hepatitis C virus NS3 variants

NARCIS (Netherlands)

Ho, Cynthia K. Y.; Welkers, Matthijs R. A.; Thomas, Xiomara V.; Sullivan, James C.; Kieffer, Tara L.; Reesink, Henk W.; Rebers, Sjoerd P. H.; de Jong, Menno D.; Schinkel, Janke; Molenkamp, Richard

2015-01-01

We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were

Comparison of efficacy of intra-articular morphine and steroid in patients with knee osteoarthritis

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Serbülent Gökhan Beyaz

2012-01-01

Full Text Available Introduction: Primary therapeutic aim in treatment of osteoarthritis of the knee is to relieve the pain of osteoarthritis. The aim of this study was to compare the efficacy of intra-articular triamcinolone with intra-articular morphine in pain relief due to osteoarthritis of the knee in the elderly population. Materials and Methods: Patients between 50 and 80 years of age were randomized into three groups. Group M received morphine plus bupivacaine intra-articularly, Group T received triamcinolone plus bupivacaine intra-articularly, and Group C received saline plus bupivacaine intra-articularly. Patients were evaluated before injection and in 2nd, 4th, 6th, and 12th weeks after injection. First-line supplementary analgesic was oral paracetamol 1500 mg/day. If analgesia was insufficient with paracetamol, oral dexketoprofen trometamol 50 mg/day was recommended to patients. Results: After the intra-articular injection, there was statistically significant decrease in visual analog scale (VAS scores in Groups M and T, when compared to Group C. The decrease of VAS scores seen at the first 2 weeks continued steadily up to the end of 12th week. There was a significant decrease in Groups M and T in the WOMAC scores, when compared to Group C. There was no significant difference in the WOMAC scores between morphine and steroid groups. Significantly less supplementary analgesics was used in the morphine and steroid groups. Conclusion: Intra-articular morphine was as effective as intra-articular triamcinolone for analgesia in patients with osteoarthritis knee. Intra-articular morphine is possibly a better option than intra-articular steroid as it has lesser side effects.

Intra-articular gouty tophi of the knee: CT and MR imaging in 12 patients

International Nuclear Information System (INIS)

Chen, C.K.H.; Yeh Lee Ren; Pan Huay-Ben; Yang Chien-Fang; National Yang-Ming Univ., Taipei; Lu Yih-Chau; Wang Jyh-Seng; Resnick, D.; California Univ., Los Angeles, CA

1999-01-01

Objective. To define the imaging characteristics of intra-articular tophi of the knee. Design and patients. Twelve patients with intra-articular tophi in the knee were studied with routine MR imaging, gadolinium (Gd)-enhanced MR imaging, and CT over a 4-year period. There were 11 men and one woman, 25-82 years of age (mean age 48 years). Four patients did not have a documented history of gout at the time of the MR examination. The diagnosis of intra-articular tophi was provided by arthroscopy and histological examination (5 patients), by microscopic study of joint fluid (5 patients), or by characteristic clinical, laboratory and imaging findings (2 patients). Results. In 15 MR examinations the tophi were located purely intra-articularly in 10 knees. In the remaining five MR studies, periarticular soft tissues or bone, or both, were involved. All the intra-articular tophi manifested low to intermediate signal intensity on both T1- and T2-weighted images. All five Gd-enhanced MR examinations demonstrated a heterogeneous peripheral enhancement. All 10 CT scans showed varying degrees of stippled calcifications within the tophi. The nature of the calcifications was confirmed on histological examination in three patients. Conclusion. Presenting clinical manifestations of gout may relate to intra-articular tophaceous deposits. Such deposits present as masses on MR images with low to intermediate signal intensity on both T1- and T2-weighted images and a characteristic enhancement pattern following intravenous Gd administration. These features relate primarily to internal calcifications, which are most evident on CT images. MR evaluation (including Gd administration) supplemented, in some cases, with CT scanning allows accurate diagnosis of intra-articular tophaceous deposits. (orig.)

Next generation sequencing reveals the hidden diversity of zooplankton assemblages.

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Penelope K Lindeque

Full Text Available BACKGROUND: Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. METHODOLOGY/PRINCIPLE FINDINGS: Plankton net hauls (200 µm were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. CONCLUSIONS: Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may

Intracellular diversity of the V4 and V9 regions of the 18S rRNA in marine protists (radiolarians) assessed by high-throughput sequencing.

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Decelle, Johan; Romac, Sarah; Sasaki, Eriko; Not, Fabrice; Mahé, Frédéric

2014-01-01

Metabarcoding is a powerful tool for exploring microbial diversity in the environment, but its accurate interpretation is impeded by diverse technical (e.g. PCR and sequencing errors) and biological biases (e.g. intra-individual polymorphism) that remain poorly understood. To help interpret environmental metabarcoding datasets, we investigated the intracellular diversity of the V4 and V9 regions of the 18S rRNA gene from Acantharia and Nassellaria (radiolarians) using 454 pyrosequencing. Individual cells of radiolarians were isolated, and PCRs were performed with generalist primers to amplify the V4 and V9 regions. Different denoising procedures were employed to filter the pyrosequenced raw amplicons (Acacia, AmpliconNoise, Linkage method). For each of the six isolated cells, an average of 541 V4 and 562 V9 amplicons assigned to radiolarians were obtained, from which one numerically dominant sequence and several minor variants were found. At the 97% identity, a diversity metrics commonly used in environmental surveys, up to 5 distinct OTUs were detected in a single cell. However, most amplicons grouped within a single OTU whereas other OTUs contained very few amplicons. Different analytical methods provided evidence that most minor variants forming different OTUs correspond to PCR and sequencing artifacts. Duplicate PCR and sequencing from the same DNA extract of a single cell had only 9 to 16% of unique amplicons in common, and alignment visualization of V4 and V9 amplicons showed that most minor variants contained substitutions in highly-conserved regions. We conclude that intracellular variability of the 18S rRNA in radiolarians is very limited despite its multi-copy nature and the existence of multiple nuclei in these protists. Our study recommends some technical guidelines to conservatively discard artificial amplicons from metabarcoding datasets, and thus properly assess the diversity and richness of protists in the environment.

Genotypic Diversity within a Single Pseudomonas aeruginosa Strain Commonly Shared by Australian Patients with Cystic Fibrosis.

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Anna Sze Tai

Full Text Available In cystic fibrosis (CF, Pseudomonas aeruginosa undergoes intra-strain genotypic and phenotypic diversification while establishing and maintaining chronic lung infections. As the clinical significance of these changes is uncertain, we investigated intra-strain diversity in commonly shared strains from CF patients to determine if specific gene mutations were associated with increased antibiotic resistance and worse clinical outcomes. Two-hundred-and-one P. aeruginosa isolates (163 represented a dominant Australian shared strain, AUST-02 from two Queensland CF centres over two distinct time-periods (2001-2002 and 2007-2009 underwent mexZ and lasR sequencing. Broth microdilution antibiotic susceptibility testing in a subset of isolates was also performed. We identified a novel AUST-02 subtype (M3L7 in adults attending a single Queensland CF centre. This M3L7 subtype was multi-drug resistant and had significantly higher antibiotic minimum inhibitory concentrations than other AUST-02 subtypes. Prospective molecular surveillance using polymerase chain reaction assays determined the prevalence of the 'M3L7' subtype at this centre during 2007-2009 (170 patients and 2011 (173 patients. Three-year clinical outcomes of patients harbouring different strains and subtypes were compared. MexZ and LasR sequences from AUST-02 isolates were more likely in 2007-2009 than 2001-2002 to exhibit mutations (mexZ: odds ratio (OR = 3.8; 95% confidence interval (CI: 1.1-13.5 and LasR: OR = 2.5; 95%CI: 1.3-5.0. Surveillance at the adult centre in 2007-2009 identified M3L7 in 28/509 (5.5% P. aeruginosa isolates from 13/170 (7.6% patients. A repeat survey in 2011 identified M3L7 in 21/519 (4.0% P. aeruginosa isolates from 11/173 (6.4% patients. The M3L7 subtype was associated with greater intravenous antibiotic and hospitalisation requirements, and a higher 3-year risk of death/lung transplantation, than other AUST-02 subtypes (adjusted hazard ratio [HR] = 9.4; 95%CI: 2

Whole genome analysis of porcine astroviruses detected in Japanese pigs reveals genetic diversity and possible intra-genotypic recombination.

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Ito, Mika; Kuroda, Moegi; Masuda, Tsuneyuki; Akagami, Masataka; Haga, Kei; Tsuchiaka, Shinobu; Kishimoto, Mai; Naoi, Yuki; Sano, Kaori; Omatsu, Tsutomu; Katayama, Yukie; Oba, Mami; Aoki, Hiroshi; Ichimaru, Toru; Mukono, Itsuro; Ouchi, Yoshinao; Yamasato, Hiroshi; Shirai, Junsuke; Katayama, Kazuhiko; Mizutani, Tetsuya; Nagai, Makoto

2017-06-01

Porcine astroviruses (PoAstVs) are ubiquitous enteric virus of pigs that are distributed in several countries throughout the world. Since PoAstVs are detected in apparent healthy pigs, the clinical significance of infection is unknown. However, AstVs have recently been associated with a severe neurological disorder in animals, including humans, and zoonotic potential has been suggested. To date, little is known about the epidemiology of PoAstVs among the pig population in Japan. In this report, we present an analysis of nearly complete genomes of 36 PoAstVs detected by a metagenomics approach in the feces of Japanese pigs. Based on a phylogenetic analysis and pairwise sequence comparison, 10, 5, 15, and 6 sequences were classified as PoAstV2, PoAstV3, PoAstV4, and PoAstV5, respectively. Co-infection with two or three strains was found in individual fecal samples from eight pigs. The phylogenetic trees of ORF1a, ORF1b, and ORF2 of PoAstV2 and PoAstV4 showed differences in their topologies. The PoAstV3 and PoAstV5 strains shared high sequence identities within each genotype in all ORFs; however, one PoAstV3 strain and one PoAstV5 strain showed considerable sequence divergence from the other PoAstV3 and PoAstV5 strains, respectively, in ORF2. Recombination analysis using whole genomes revealed evidence of multiple possible intra-genotype recombination events in PoAstV2 and PoAstV4, suggesting that recombination might have contributed to the genetic diversity and played an important role in the evolution of Japanese PoAstVs. Copyright © 2017 Elsevier B.V. All rights reserved.

HIV-1 envelope sequence-based diversity measures for identifying recent infections.

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Alexis Kafando

Full Text Available Identifying recent HIV-1 infections is crucial for monitoring HIV-1 incidence and optimizing public health prevention efforts. To identify recent HIV-1 infections, we evaluated and compared the performance of 4 sequence-based diversity measures including percent diversity, percent complexity, Shannon entropy and number of haplotypes targeting 13 genetic segments within the env gene of HIV-1. A total of 597 diagnostic samples obtained in 2013 and 2015 from recently and chronically HIV-1 infected individuals were selected. From the selected samples, 249 (134 from recent versus 115 from chronic infections env coding regions, including V1-C5 of gp120 and the gp41 ectodomain of HIV-1, were successfully amplified and sequenced by next generation sequencing (NGS using the Illumina MiSeq platform. The ability of the four sequence-based diversity measures to correctly identify recent HIV infections was evaluated using the frequency distribution curves, median and interquartile range and area under the curve (AUC of the receiver operating characteristic (ROC. Comparing the median and interquartile range and evaluating the frequency distribution curves associated with the 4 sequence-based diversity measures, we observed that the percent diversity, number of haplotypes and Shannon entropy demonstrated significant potential to discriminate recent from chronic infections (p<0.0001. Using the AUC of ROC analysis, only the Shannon entropy measure within three HIV-1 env segments could accurately identify recent infections at a satisfactory level. The env segments were gp120 C2_1 (AUC = 0.806, gp120 C2_3 (AUC = 0.805 and gp120 V3 (AUC = 0.812. Our results clearly indicate that the Shannon entropy measure represents a useful tool for predicting HIV-1 infection recency.

Genetic diversity of the Andean tuber-bearing species, oca (Oxalis tuberosa Mol.), investigated by inter-simple sequence repeats.

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Pissard, A; Ghislain, M; Bertin, P

2006-01-01

The Andean tuber-bearing species, Oxalis tuberosa Mol., is a vegetatively propagated crop cultivated in the uplands of the Andes. Its genetic diversity was investigated in the present study using the inter-simple sequence repeat (ISSR) technique. Thirty-two accessions originating from South America (Argentina, Bolivia, Chile, and Peru) and maintained in vitro were chosen to represent the ecogeographic diversity of its cultivation area. Twenty-two primers were tested and 9 were selected according to fingerprinting quality and reproducibility. Genetic diversity analysis was performed with 90 markers. Jaccard's genetic distance between accessions ranged from 0 to 0.49 with an average of 0.28 +/- 0.08 (mean +/- SD). Dendrogram (UPGMA (unweighted pair-group method with arithmetic averaging)) and factorial correspondence analysis (FCA) showed that the genetic structure was influenced by the collection site. The two most distant clusters contained all of the Peruvian accessions, one from Bolivia, none from Argentina or Chile. Analysis by country revealed that Peru presented the greatest genetic distances from the other countries and possessed the highest intra-country genetic distance (0.30 +/- 0.08). This suggests that the Peruvian oca accessions form a distinct genetic group. The relatively low level of genetic diversity in the oca species may be related to its predominating reproduction strategy, i.e., vegetative propagation. The extent and structure of the genetic diversity of the species detailed here should help the establishment of conservation strategies.

Predictors of "occult" intra-abdominal injuries in blunt trauma patients

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José Gustavo Parreira

Full Text Available Objective: to assess predictors of intra-abdominal injuries in blunt trauma patients admitted without abdominal pain or abnormalities on the abdomen physical examination. Methods: We conducted a retrospective analysis of trauma registry data, including adult blunt trauma patients admitted from 2008 to 2010 who sustained no abdominal pain or abnormalities on physical examination of the abdomen at admission and were submitted to computed tomography of the abdomen and/or exploratory laparotomy. Patients were assigned into: Group 1 (with intra-abdominal injuries or Group 2 (without intra-abdominal injuries. Variables were compared between groups to identify those significantly associated with the presence of intra-abdominal injuries, adopting p<0.05 as significant. Subsequently, the variables with p<0.20 on bivariate analysis were selected to create a logistic regression model using the forward stepwise method. Results: A total of 268 cases met the inclusion criteria. Patients in Group I were characterized as having significantly (p<0.05 lower mean AIS score for the head segment (1.0±1.4 vs. 1.8±1.9, as well as higher mean AIS thorax score (1.6±1.7 vs. 0.9±1.5 and ISS (25.7±14.5 vs. 17,1±13,1. The rate of abdominal injuries was significantly higher in run-over pedestrians (37.3% and in motorcyclists (36.0% (p<0.001. The resultant logistic regression model provided 73.5% accuracy for identifying abdominal injuries. The variables included were: motorcyclist accident as trauma mechanism (p<0.001 - OR 5.51; 95%CI 2.40-12.64, presence of rib fractures (p<0.003 - OR 3.00; 95%CI 1.47-6.14, run-over pedestrian as trauma mechanism (p=0.008 - OR 2.85; 95%CI 1.13-6.22 and abnormal neurological physical exam at admission (p=0.015 - OR 0.44; 95%CI 0.22-0.85. Conclusion Intra-abdominal injuries were predominantly associated with trauma mechanism and presence of chest injuries.

Progress in strategies for sequence diversity library creation for ...

African Journals Online (AJOL)

As the simplest technique of protein engineering, directed evolution has been ... An experiment of directed evolution comprises mutant libraries creation and ... evolution, sequence diversity creation, novel strategy, computational design, ...

Sequence diversity and evolution of antimicrobial peptides in invertebrates.

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Tassanakajon, Anchalee; Somboonwiwat, Kunlaya; Amparyup, Piti

2015-02-01

Antimicrobial peptides (AMPs) are evolutionarily ancient molecules that act as the key components in the invertebrate innate immunity against invading pathogens. Several AMPs have been identified and characterized in invertebrates, and found to display considerable diversity in their amino acid sequence, structure and biological activity. AMP genes appear to have rapidly evolved, which might have arisen from the co-evolutionary arms race between host and pathogens, and enabled organisms to survive in different microbial environments. Here, the sequence diversity of invertebrate AMPs (defensins, cecropins, crustins and anti-lipopolysaccharide factors) are presented to provide a better understanding of the evolution pattern of these peptides that play a major role in host defense mechanisms. Copyright © 2014 Elsevier Ltd. All rights reserved.

Intra-arterial Ultra-low-Dose CT Angiography of Lower Extremity in Diabetic Patients

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Özgen, Ali, E-mail: draliozgen@hotmail.com [Yeditepe University Hospital, Department of Radiology (Turkey); Sanioğlu, Soner [Yeditepe University Hospital, Department of Cardiovascular Surgery (Turkey); Bingöl, Uğur Anıl [Yeditepe University Hospital, Department of Plastic Surgery (Turkey)

2016-08-15

PurposeTo image lower extremity arteries by CT angiography using a very low-dose intra-arterial contrast medium in patients with high risk of developing contrast-induced nephropathy (CIN).Materials and MethodsThree cases with long-standing diabetes mellitus and signs of lower extremity atherosclerotic disease were evaluated by CT angiography using 0.1 ml/kg of the body weight of contrast medium given via 10-cm-long 4F introducer by puncturing the CFA. Images were evaluated by an interventional radiologist and a cardiovascular surgeon. Density values of the lower extremity arteries were also calculated. Findings in two cases were compared with digital subtraction angiography images performed for percutaneous revascularization. Blood creatinine levels were followed for possible CIN.ResultsIntra-arterial CT angiography images were considered diagnostic in all patients and optimal in one patient. No patient developed CIN after intra-arterial CT angiography, while one patient developed CIN after percutaneous intervention.ConclusionIntra-arterial CT angiography of lower extremity might be performed in selected patients with high risk of developing CIN. Our limited experience suggests that as low as of 0.1 ml/kg of the body weight of contrast medium may result in adequate diagnostic imaging.

The Mobilome; A Major Contributor to Escherichia coli stx2-Positive O26:H11 Strains Intra-Serotype Diversity

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Sabine Delannoy

2017-09-01

Full Text Available Shiga toxin-producing Escherichia coli of serotype O26:H11/H- constitute a diverse group of strains and several clones with distinct genetic characteristics have been identified and characterized. Whole genome sequencing was performed using Illumina and PacBio technologies on eight stx2-positive O26:H11 strains circulating in France. Comparative analyses of the whole genome of the stx2-positive O26:H11 strains indicate that several clones of EHEC O26:H11 are co-circulating in France. Phylogenetic analysis of the French strains together with stx2-positive and stx-negative E. coli O26:H11 genomes obtained from Genbank indicates the existence of four clonal complexes (SNP-CCs separated in two distinct lineages, one of which comprises the “new French clone” (SNP-CC1 that appears genetically closely related to stx-negative attaching and effacing E. coli (AEEC strains. Interestingly, the whole genome SNP (wgSNP phylogeny is summarized in the cas gene phylogeny, and a simple qPCR assay targeting the CRISPR array specific to SNP-CC1 (SP_O26-E can distinguish between the two main lineages. The PacBio sequencing allowed a detailed analysis of the mobile genetic elements (MGEs of the strains. Numerous MGEs were identified in each strain, including a large number of prophages and up to four large plasmids, representing overall 8.7–19.8% of the total genome size. Analysis of the prophage pool of the strains shows a considerable diversity with a complex history of recombination. Each clonal complex (SNP-CC is characterized by a unique set of plasmids and phages, including stx-prophages, suggesting evolution through separate acquisition events. Overall, the MGEs appear to play a major role in O26:H11 intra-serotype clonal diversification.

The Mobilome; A Major Contributor to Escherichia coli stx2-Positive O26:H11 Strains Intra-Serotype Diversity.

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Delannoy, Sabine; Mariani-Kurkdjian, Patricia; Webb, Hattie E; Bonacorsi, Stephane; Fach, Patrick

2017-01-01

Shiga toxin-producing Escherichia coli of serotype O26:H11/H- constitute a diverse group of strains and several clones with distinct genetic characteristics have been identified and characterized. Whole genome sequencing was performed using Illumina and PacBio technologies on eight stx2 -positive O26:H11 strains circulating in France. Comparative analyses of the whole genome of the stx2 -positive O26:H11 strains indicate that several clones of EHEC O26:H11 are co-circulating in France. Phylogenetic analysis of the French strains together with stx2 -positive and stx -negative E. coli O26:H11 genomes obtained from Genbank indicates the existence of four clonal complexes (SNP-CCs) separated in two distinct lineages, one of which comprises the "new French clone" (SNP-CC1) that appears genetically closely related to stx -negative attaching and effacing E. coli (AEEC) strains. Interestingly, the whole genome SNP (wgSNP) phylogeny is summarized in the cas gene phylogeny, and a simple qPCR assay targeting the CRISPR array specific to SNP-CC1 (SP_O26-E) can distinguish between the two main lineages. The PacBio sequencing allowed a detailed analysis of the mobile genetic elements (MGEs) of the strains. Numerous MGEs were identified in each strain, including a large number of prophages and up to four large plasmids, representing overall 8.7-19.8% of the total genome size. Analysis of the prophage pool of the strains shows a considerable diversity with a complex history of recombination. Each clonal complex (SNP-CC) is characterized by a unique set of plasmids and phages, including stx -prophages, suggesting evolution through separate acquisition events. Overall, the MGEs appear to play a major role in O26:H11 intra-serotype clonal diversification.

Intra-tumor heterogeneity in head and neck cancer and its clinical implications

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Edmund A. Mroz

2016-06-01

Full Text Available The presence of heritable differences among cancer cells within a tumor, called intra-tumor genetic heterogeneity, has long been suspected of playing a role in poor responses to therapy. Research over the past decade has documented the existence of such heterogeneity within tumors of individual patients and documented its potential clinical significance. The research methods for identifying this heterogeneity were not, however, readily adaptable to widespread clinical application. After a brief review of this background, we describe the development of a measure of intra-tumor genetic heterogeneity, based on whole-exome sequencing of individual tumor samples, that could be applied to biopsy specimens in a clinical setting. This measure has now been used in head and neck squamous cell carcinoma (HNSCC to document, for the first time, a relation of high intra-tumor genetic heterogeneity to shorter overall survival in a large, multi-institutional study. The implications of heterogeneity for research and clinical care thus now need to be addressed. Keywords: Head and neck squamous cell carcinoma, Intra-tumor genetic heterogeneity, Next-generation sequencing, Targeted therapy

The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression

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Bodén Mikael

2010-04-01

Full Text Available Abstract Background Cajal bodies, nucleoli, PML nuclear bodies, and nuclear speckles are morpohologically distinct intra-nuclear structures that dynamically respond to cellular cues. Such nuclear bodies are hypothesized to play important regulatory roles, e.g. by sequestering and releasing transcription factors in a timely manner. While the nucleolus and nuclear speckles have received more attention experimentally, the PML nuclear body and the Cajal body are still incompletely characterized in terms of their roles and protein complement. Results By collating recent experimentally verified data, we find that almost 1000 proteins in the mouse nuclear proteome are known to associate with one or more of the nuclear bodies. Their gene ontology terms highlight their regulatory roles: splicing is confirmed to be a core activity of speckles and PML nuclear bodies house a range of proteins involved in DNA repair. We train support-vector machines to show that nuclear proteins contain discriminative sequence features that can be used to identify their intra-nuclear body associations. Prediction accuracy is highest for nucleoli and nuclear speckles. The trained models are also used to estimate the full protein complement of each nuclear body. Protein interactions are found primarily to link proteins in the nuclear speckles with proteins from other compartments. Cell cycle expression data provide support for increased activity in nucleoli, nuclear speckles and PML nuclear bodies especially during S and G2 phases. Conclusions The large-scale analysis of the mouse nuclear proteome sheds light on the functional organization of physically embodied intra-nuclear compartments. We observe partial support for the hypothesis that the physical organization of the nucleus mirrors functional modularity. However, we are unable to unambiguously identify proteins' intra-nuclear destination, suggesting that critical drivers behind of intra-nuclear translocation are yet to

Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform.

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Mitra, Abhishek; Skrzypczak, Magdalena; Ginalski, Krzysztof; Rowicka, Maga

2015-01-01

Sequencing microRNA, reduced representation sequencing, Hi-C technology and any method requiring the use of in-house barcodes result in sequencing libraries with low initial sequence diversity. Sequencing such data on the Illumina platform typically produces low quality data due to the limitations of the Illumina cluster calling algorithm. Moreover, even in the case of diverse samples, these limitations are causing substantial inaccuracies in multiplexed sample assignment (sample bleeding). Such inaccuracies are unacceptable in clinical applications, and in some other fields (e.g. detection of rare variants). Here, we discuss how both problems with quality of low-diversity samples and sample bleeding are caused by incorrect detection of clusters on the flowcell during initial sequencing cycles. We propose simple software modifications (Long Template Protocol) that overcome this problem. We present experimental results showing that our Long Template Protocol remarkably increases data quality for low diversity samples, as compared with the standard analysis protocol; it also substantially reduces sample bleeding for all samples. For comprehensiveness, we also discuss and compare experimental results from alternative approaches to sequencing low diversity samples. First, we discuss how the low diversity problem, if caused by barcodes, can be avoided altogether at the barcode design stage. Second and third, we present modified guidelines, which are more stringent than the manufacturer's, for mixing low diversity samples with diverse samples and lowering cluster density, which in our experience consistently produces high quality data from low diversity samples. Fourth and fifth, we present rescue strategies that can be applied when sequencing results in low quality data and when there is no more biological material available. In such cases, we propose that the flowcell be re-hybridized and sequenced again using our Long Template Protocol. Alternatively, we discuss how

Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform.

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Abhishek Mitra

Full Text Available Sequencing microRNA, reduced representation sequencing, Hi-C technology and any method requiring the use of in-house barcodes result in sequencing libraries with low initial sequence diversity. Sequencing such data on the Illumina platform typically produces low quality data due to the limitations of the Illumina cluster calling algorithm. Moreover, even in the case of diverse samples, these limitations are causing substantial inaccuracies in multiplexed sample assignment (sample bleeding. Such inaccuracies are unacceptable in clinical applications, and in some other fields (e.g. detection of rare variants. Here, we discuss how both problems with quality of low-diversity samples and sample bleeding are caused by incorrect detection of clusters on the flowcell during initial sequencing cycles. We propose simple software modifications (Long Template Protocol that overcome this problem. We present experimental results showing that our Long Template Protocol remarkably increases data quality for low diversity samples, as compared with the standard analysis protocol; it also substantially reduces sample bleeding for all samples. For comprehensiveness, we also discuss and compare experimental results from alternative approaches to sequencing low diversity samples. First, we discuss how the low diversity problem, if caused by barcodes, can be avoided altogether at the barcode design stage. Second and third, we present modified guidelines, which are more stringent than the manufacturer's, for mixing low diversity samples with diverse samples and lowering cluster density, which in our experience consistently produces high quality data from low diversity samples. Fourth and fifth, we present rescue strategies that can be applied when sequencing results in low quality data and when there is no more biological material available. In such cases, we propose that the flowcell be re-hybridized and sequenced again using our Long Template Protocol. Alternatively

Characterisation of the genetic diversity of Brucella by multilocus sequencing

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MacMillan Alastair P

2007-04-01

Full Text Available Abstract Background Brucella species include economically important zoonotic pathogens that can infect a wide range of animals. There are currently six classically recognised species of Brucella although, as yet unnamed, isolates from various marine mammal species have been reported. In order to investigate genetic relationships within the group and identify potential diagnostic markers we have sequenced multiple genetic loci from a large sample of Brucella isolates representing the known diversity of the genus. Results Nine discrete genomic loci corresponding to 4,396 bp of sequence were examined from 160 Brucella isolates. By assigning each distinct allele at a locus an arbitrary numerical designation the population was found to represent 27 distinct sequence types (STs. Diversity at each locus ranged from 1.03–2.45% while overall genetic diversity equated to 1.5%. Most loci examined represent housekeeping gene loci and, in all but one case, the ratio of non-synonymous to synonymous change was substantially Brucella species, B. abortus, B. melitensis, B. ovis and B. neotomae correspond to well-separated clusters. With the exception of biovar 5, B. suis isolates cluster together, although they form a more diverse group than other classical species with a number of distinct STs corresponding to the remaining four biovars. B. canis isolates are located on the same branch very closely related to, but distinguishable from, B. suis biovar 3 and 4 isolates. Marine mammal isolates represent a distinct, though rather weakly supported, cluster within which individual STs display one of three clear host preferences. Conclusion The sequence database provides a powerful dataset for addressing ongoing controversies in Brucella taxonomy and a tool for unambiguously placing atypical, phenotypically discordant or newly emerging Brucella isolates. Furthermore, by using the phylogenetic backbone described here, robust and rationally selected markers for use in

A taxonomy and cultural analysis of intra-hospital patient transfers.

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Rosenberg, Alana; Campbell Britton, Meredith; Feder, Shelli; Minges, Karl; Hodshon, Beth; Chaudhry, Sarwat I; Jenq, Grace Y; Emerson, Beth L

2018-05-02

Existing research on intra-hospital patient transitions focuses chiefly on handoffs, or exchanges of information, between clinicians. Less is known about patient transfers within hospitals, which include but extend beyond the exchange of information. Using participant observations and interviews at a 1,541-bed, academic, tertiary medical center, we explored the ways in which staff define and understand patient transfers between units. We conducted observations of staff (n = 16) working in four hospital departments and interviewed staff (n = 29) involved in transfers to general medicine floors from either the Emergency Department or the Medical Intensive Care Unit between February and September 2015. The collected data allowed us to understand transfers in the context of several hospital cultural microsystems. Decisions were made through the lens of the specific unit identity to which staff felt they belonged; staff actively strategized to manage workload; and empty beds were treated as a scarce commodity. Staff concepts informed the development of a taxonomy of intra-hospital transfers that includes five categories of activity: disposition, or determining the right floor and bed for the patient; notification to sending and receiving staff of patient assignment, departure and arrival; preparation to send and receive the patient; communication between sending and receiving units; and coordination to ensure that transfer components occur in a timely and seamless manner. This taxonomy widens the study of intra-hospital patient transfers from a communication activity to a complex cultural phenomenon with several categories of activity and views them as part of multidimensional hospital culture, as constructed and understood by staff. © 2018 Wiley Periodicals, Inc.

Effect of Intra Vitreal Injection of Bevacizumab on Intra-Occular Pressure

International Nuclear Information System (INIS)

Jaffar, S.; Tayyab, A.; Matin, Z. I.; Masrur, A.; Naqaish, R.

2016-01-01

Background: Bevacizumab has been in use as a therapeutic agent for macular oedema for several years. While its efficacy has been well documented, its use has been shown to cause a transient rise in the intra-ocular pressure. The aim of this study was to evaluate the long term effect of intra-vitreal injection of Bevacizumab on Intra-ocular pressure. Methods: One hundred eyes (n=100) of one hundred patients, requiring intra-vitreal injection of Bevacizumab for diabetic macular oedema were recruited from Shifa Foundation Community Health Centre (SFCHC) between January and December 2014. Patients of glaucoma, ocular hyper-tension, known allergy to Bevacizumab or had injections of Bevacizumab prior to the study were excluded. Intra-ocular pressure was measured using a Goldmann applanation tonometer, prior to, and at six and twelve months after the injection. The pre- and post- injection Intra-ocular pressure was entered into the database. Test of significance was applied to investigate whether there was a significant change in intra-ocular pressure after the injection. Results: The mean age of the patient was 56.97 years (±14.97). The mean intra-ocular pressure was 13.86 (±3.16) mmHg before injection, while post-injection mean Intra-Ocular pressure was 14.21 (±3.12) mmHg and 13.79 (±3.07) at six and twelve months respectively. Between baseline and six months there was a statistically significant difference in intra-ocular pressure (p=0.03), while no significant difference existed in the intra-ocular pressure between baseline and twelve months (p=0.92). Conclusion: Intra-vitreal injection of Bevacizumab is associated with a statically significant rise in intra-ocular pressure at six months, while no significant difference was seen at twelve months compared to baseline. (author)

Intra-Articular Analgesia and Steroid Reduce Pain Sensitivity in Knee OA Patients

DEFF Research Database (Denmark)

Jørgensen, Tanja Schjødt; Graven-Nielsen, Thomas; Ellegaard, Karen

2014-01-01

Objectives. To assess the effects of intra-articular therapy on pain sensitivity in the knee and surrounding tissues in knee OA patients. Methods. Twenty-five knee OA patients with symptomatic knee OA were included in this interventional cohort study. Pressure pain thresholds (PPT) were recorded...... muscles (control site). Results. Significantly increased PPTs were found following intra-articular injection, at both the knee (P effects were sustained for two weeks, and at some points the effect was even greater at two weeks (P 

Impact of intra-operative intraperitoneal chemotherapy on organ/space surgical site infection in patients with gastric cancer.

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Liu, X; Duan, X; Xu, J; Jin, Q; Chen, F; Wang, P; Yang, Y; Tang, X

2015-11-01

Various risk factors for surgical site infection (SSI) have been identified such as age, overweight, duration of surgery, blood loss, etc. Intraperitoneal chemotherapy during surgery is a common procedure in patients with gastric cancer, yet its impact on SSI has not been evaluated. To evaluate whether intra-operative intraperitoneal chemotherapy is a key risk factor for organ/space SSI in patients with gastric cancer. All patients with gastric cancer who underwent surgery at the Department of Gastrointestinal Surgery between January 2008 and December 2013 were studied. The organ/space SSI rates were compared between patients who received intra-operative intraperitoneal chemotherapy and patients who did not receive intra-operative intraperitoneal chemotherapy, and the risk factors for organ/space SSI were analysed by univariate and multi-variate regression analyses. The microbial causes of organ/space SSI were also identified. Of the eligible 845 patients, 356 received intra-operative intraperitoneal chemotherapy, and the organ/space SSI rate was higher in these patients compared with patients who did not receive intra-operative intraperitoneal chemotherapy (9.01% vs 3.88%; P = 0.002). Univariate analysis confirmed the significance of this finding (odds ratio 2.443; P = 0.003). As a result, hospital stay was increased in patients who received intra-operative intraperitoneal chemotherapy {mean 20.91 days [95% confidence interval (CI) 19.76-22.06] vs 29.72 days (95% CI 25.46-33.99); P = 0.000}. The results also suggested that intra-operative intraperitoneal chemotherapy may be associated with more Gram-negative bacterial infections. Intra-operative intraperitoneal chemotherapy is a significant risk factor for organ/space SSI in patients with gastric cancer. Copyright © 2015 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

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Manske, Magnus; Miotto, Olivo; Campino, Susana; Auburn, Sarah; Almagro-Garcia, Jacob; Maslen, Gareth; O’Brien, Jack; Djimde, Abdoulaye; Doumbo, Ogobara; Zongo, Issaka; Ouedraogo, Jean-Bosco; Michon, Pascal; Mueller, Ivo; Siba, Peter; Nzila, Alexis; Borrmann, Steffen; Kiara, Steven M.; Marsh, Kevin; Jiang, Hongying; Su, Xin-Zhuan; Amaratunga, Chanaki; Fairhurst, Rick; Socheat, Duong; Nosten, Francois; Imwong, Mallika; White, Nicholas J.; Sanders, Mandy; Anastasi, Elisa; Alcock, Dan; Drury, Eleanor; Oyola, Samuel; Quail, Michael A.; Turner, Daniel J.; Rubio, Valentin Ruano; Jyothi, Dushyanth; Amenga-Etego, Lucas; Hubbart, Christina; Jeffreys, Anna; Rowlands, Kate; Sutherland, Colin; Roper, Cally; Mangano, Valentina; Modiano, David; Tan, John C.; Ferdig, Michael T.; Amambua-Ngwa, Alfred; Conway, David J.; Takala-Harrison, Shannon; Plowe, Christopher V.; Rayner, Julian C.; Rockett, Kirk A.; Clark, Taane G.; Newbold, Chris I.; Berriman, Matthew; MacInnis, Bronwyn; Kwiatkowski, Dominic P.

2013-01-01

Malaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance. 1,2 Here we describe methods for large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short term culture. Analysis of 86,158 exonic SNPs that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genome-wide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome. PMID:22722859

Blood Glucose Levels Following Intra-Articular Steroid Injections in Patients with Diabetes: A Systematic Review.

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Choudhry, M N; Malik, R A; Charalambous, Charalambos Panayiotou

2016-03-22

Parenterally administered steroids have been shown to affect the metabolism of glucose and to cause abnormal blood glucose levels in diabetic patients. These abnormal blood glucose levels in diabetic patients raise concerns that intra-articular steroid injections also may affect blood glucose levels. We performed a systematic review of studies examining the effect of intra-articular steroid injections on blood glucose levels in patients with diabetes mellitus. A literature search of the PubMed, EMBASE, AMED, and CINAHL databases using all relevant keywords and phrases revealed 532 manuscripts. After the application of inclusion criteria, seven studies with a total of seventy-two patients were analyzed. All studies showed a rise in blood glucose levels following intra-articular steroid injection. Four of the seven studies showed a substantial increase in blood glucose. Peak values reached as high as 500 mg/dL. The peak increase in blood glucose did not occur immediately following intra-articular steroid injection, and in some cases it took several days to occur. In many patients, post-injection hyperglycemia occurred within twenty-four to seventy-two hours. Intra-articular steroid injections may cause hyperglycemia in patients with diabetes mellitus, and patients should be warned of this complication. Diabetic patients should be advised to regularly monitor their blood glucose levels for up to a week after injection and should seek medical advice if safe thresholds are breached. Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.

Relationship between ureB Sequence Diversity, Urease Activity and Genotypic Variations of Different Helicobacter pylori Strains in Patients with Gastric Disorders.

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Ghalehnoei, Hossein; Ahmadzadeh, Alireza; Farzi, Nastaran; Alebouyeh, Masoud; Aghdaei, Hamid Asadzadeh; Azimzadeh, Pendram; Molaei, Mahsa; Zali, Mohammad Reza

2016-01-01

Association of the severity of Helicobacter pylori induced diseases with virulence entity of the colonized strains was proven in some studies. Urease has been demonstrated as a potent virulence factor for H. pylori. The main aim of this study was investigation of the relationships of ureB sequence diversity, urease activity and virulence genotypes of different H. pylori strains with histopathological changes of gastric tissue in infected patients suffering from different gastric disorders. Analysis of the virulence genotypes in the isolated strains indicated significant associations between the presence of severe active gastritis and cagA+ (P = 0.039) or cagA/iceA1 genotypes (P = 0.026), and intestinal metaplasia and vacA m1 (P = 0.008) or vacA s1/m2 (P = 0.001) genotypes. Our results showed a 2.4-fold increased risk of peptic ulcer (95% CI: 0.483-11.93), compared with gastritis, in the infected patients who had dupA positive strains; however this association was not statistically significant. The results of urease activity showed a significant mean difference between the isolated strains from patients with PUD and NUD (P = 0.034). This activity was relatively higher among patients with intestinal metaplasia. Also a significant association was found between the lack of cagA and increased urease activity among the isolated strains (P = 0.036). While the greatest sequence variation of ureB was detected in a strain from a patient with intestinal metaplasia, the sole determined amino acid change in UreB sequence (Ala201Thr, 30%), showed no influence on urease activity. In conclusion, the supposed role of H. pylori urease to form peptic ulcer and advancing of intestinal metaplasia was postulated in this study. Higher urease activity in the colonizing H. pylori strains that present specific virulence factors was indicated as a risk factor for promotion of histopathological changes of gastric tissue that advance gastric malignancy.

Exploring fungal diversity in deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing

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Zhang, Xiao-Yong; Wang, Guang-Hua; Xu, Xin-Ya; Nong, Xu-Hua; Wang, Jie; Amin, Muhammad; Qi, Shu-Hua

2016-10-01

The present study investigated the fungal diversity in four different deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS1). A total of 40,297 fungal ITS1 sequences clustered into 420 operational taxonomic units (OTUs) with 97% sequence similarity and 170 taxa were recovered from these sediments. Most ITS1 sequences (78%) belonged to the phylum Ascomycota, followed by Basidiomycota (17.3%), Zygomycota (1.5%) and Chytridiomycota (0.8%), and a small proportion (2.4%) belonged to unassigned fungal phyla. Compared with previous studies on fungal diversity of sediments from deep-sea environments by culture-dependent approach and clone library analysis, the present result suggested that Illumina sequencing had been dramatically accelerating the discovery of fungal community of deep-sea sediments. Furthermore, our results revealed that Sordariomycetes was the most diverse and abundant fungal class in this study, challenging the traditional view that the diversity of Sordariomycetes phylotypes was low in the deep-sea environments. In addition, more than 12 taxa accounted for 21.5% sequences were found to be rarely reported as deep-sea fungi, suggesting the deep-sea sediments from Okinawa Trough harbored a plethora of different fungal communities compared with other deep-sea environments. To our knowledge, this study is the first exploration of the fungal diversity in deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing.

Characterization of sequence diversity in Plasmodium falciparum SERA5 from Indian isolates

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Rahul C.N

2015-06-01

Full Text Available Objective: To characterize the sequence diversity of blood-stage Plasmodium falciparum serine repeat antigen-5 (PfSERA5 which is lacking in a malaria-endemic country like India. Methods: In this study, parasitic DNA was obtained from field isolates collected from various geographic regions. Subsequently, PfSERA5 gene sequence was PCR amplified and DNA sequenced. Results: We reported the existence of unique repeat polymorphisms and novel haplotypes for both the octamer repeat (OR and serine repeat (SR regions of the N-terminal fragment of PfSERA5 from Indian isolates. Several isolates from India were identical to low-frequency African haplotypes. Unique finding of our study was an Indian isolate showing deletion in a perfectly conserved 14 mer sequence within octamer repeat. Indian haplotypes reported in this study were found to be distributed into the three earlier classified allelic clusters of FCR3, K1 and Honduras showcasing broad diversity as compared to worldwide haplotypes. Conclusions: This study is the first report on genetic diversity of PfSERA5 antigen from India. Further evaluation of these haplotypes by serotyping would provide useful information for investigating variant-specific immunity and aid in malaria vaccine research.

Sequence exploration reveals information bias among molecular markers used in phylogenetic reconstruction for Colletotrichum species.

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Rampersad, Sephra N; Hosein, Fazeeda N; Carrington, Christine Vf

2014-01-01

The Colletotrichum gloeosporioides species complex is among the most destructive fungal plant pathogens in the world, however, identification of isolates of quarantine importance to the intra-specific level is confounded by a number of factors that affect phylogenetic reconstruction. Information bias and quality parameters were investigated to determine whether nucleotide sequence alignments and phylogenetic trees accurately reflect the genetic diversity and phylogenetic relatedness of individuals. Sequence exploration of GAPDH, ACT, TUB2 and ITS markers indicated that the query sequences had different patterns of nucleotide substitution but were without evidence of base substitution saturation. Regions of high entropy were much more dispersed in the ACT and GAPDH marker alignments than for the ITS and TUB2 markers. A discernible bimodal gap in the genetic distance frequency histograms was produced for the ACT and GAPDH markers which indicated successful separation of intra- and inter-specific sequences in the data set. Overall, analyses indicated clear differences in the ability of these markers to phylogenetically separate individuals to the intra-specific level which coincided with information bias.

[Prediction of intra-abdominal hypertension risk in patients with acute colonic obstruction under epidural analgesia].

Science.gov (United States)

Stakanov, A V; Potseluev, E A; Musaeva, T S

2013-01-01

Purpose of the study was to identify prediction possibility of direct current potential level for intra-abdominal hypertension risk in patients with acute colonic obstruction under preoperative epidural analgesia. Prospective analysis of the preoperative period was carried out in 140 patients with acute colonic obstruction caused by colon cancer. Relations between preoperative level of permanent capacity and risk of intra-abdominal hypertension was identified Direct current potential level is an independent predictor of intra-abdominal hypertension. Diagnostic significance increases from first to fifth hour of preoperative period according to AUROC data from 0.821 to 0.905 and calibration 6.9 (p > 0.37) and 4.7 (p > 0.54) by Hosmer-Lemeshou criteria. The use of epidural analgesia in the complex intensive preoperative preparation is pathogenically justified. It reduces intra-abdominal hypertension in patients with acute colonic obstruction.

Estimating and comparing microbial diversity in the presence of sequencing errors

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Chiu, Chun-Huo

2016-01-01

Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here a nonparametric estimator of the true singleton count to replace the spurious singleton count in all methods/approaches. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons, provided these three frequency counts are reliable. To quantify microbial alpha diversity for an individual community, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an order q that determines the measures’ emphasis on rare or common species, include taxa richness (q = 0), Shannon diversity (q = 1, the exponential of Shannon entropy), and Simpson diversity (q = 2, the inverse of Simpson index). A diversity profile which depicts the Hill number as a function of order q conveys all information contained in a taxa abundance distribution. Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches (non-asymptotic and asymptotic) are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach refers to the comparison of estimated diversities of standardized samples with a common finite sample size or sample completeness. This

Low diversity in the mitogenome of sperm whales revealed by next-generation sequencing

Science.gov (United States)

Alana Alexander; Debbie Steel; Beth Slikas; Kendra Hoekzema; Colm Carraher; Matthew Parks; Richard Cronn; C. Scott Baker

2012-01-01

Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale (Physeter macrocephalus) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the sperm whale mitogenome are unknown. We sequenced 20...

A robust, simple genotyping-by-sequencing (GBS approach for high diversity species.

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Robert J Elshire

Full Text Available Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs. This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM and barley (Oregon Wolfe Barley recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

Intra-tumor heterogeneity in breast cancer has limited impact on transcriptomic-based molecular profiling.

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Karthik, Govindasamy-Muralidharan; Rantalainen, Mattias; Stålhammar, Gustav; Lövrot, John; Ullah, Ikram; Alkodsi, Amjad; Ma, Ran; Wedlund, Lena; Lindberg, Johan; Frisell, Jan; Bergh, Jonas; Hartman, Johan

2017-11-29

Transcriptomic profiling of breast tumors provides opportunity for subtyping and molecular-based patient stratification. In diagnostic applications the specimen profiled should be representative of the expression profile of the whole tumor and ideally capture properties of the most aggressive part of the tumor. However, breast cancers commonly exhibit intra-tumor heterogeneity at molecular, genomic and in phenotypic level, which can arise during tumor evolution. Currently it is not established to what extent a random sampling approach may influence molecular breast cancer diagnostics. In this study we applied RNA-sequencing to quantify gene expression in 43 pieces (2-5 pieces per tumor) from 12 breast tumors (Cohort 1). We determined molecular subtype and transcriptomic grade for all tumor pieces and analysed to what extent pieces originating from the same tumors are concordant or discordant with each other. Additionally, we validated our finding in an independent cohort consisting of 19 pieces (2-6 pieces per tumor) from 6 breast tumors (Cohort 2) profiled using microarray technique. Exome sequencing was also performed on this cohort, to investigate the extent of intra-tumor genomic heterogeneity versus the intra-tumor molecular subtype classifications. Molecular subtyping was consistent in 11 out of 12 tumors and transcriptomic grade assignments were consistent in 11 out of 12 tumors as well. Molecular subtype predictions revealed consistent subtypes in four out of six patients in this cohort 2. Interestingly, we observed extensive intra-tumor genomic heterogeneity in these tumor pieces but not in their molecular subtype classifications. Our results suggest that macroscopic intra-tumoral transcriptomic heterogeneity is limited and unlikely to have an impact on molecular diagnostics for most patients.

Endotracheal temperature and humidity measurements in laryngectomized patients: intra- and inter-patient variability

NARCIS (Netherlands)

Scheenstra, R.J.; Muller, S.H.; Vincent, A.; Sinaasappel, M.; Zuur, J.K.; Hilgers, F.J.M.

2009-01-01

This study assesses intra- and inter-patient variability in endotracheal climate (temperature and humidity) and effects of heat and moister exchangers (HME) in 16 laryngectomized individuals, measured repeatedly (N = 47). Inhalation Breath Length (IBL) was 1.35 s without HME and 1.05 s with HME (P <

Endotracheal temperature and humidity measurements in laryngectomized patients: intra- and inter-patient variability

NARCIS (Netherlands)

Scheenstra, R. J.; Muller, S. H.; Vincent, A.; Sinaasappel, M.; Zuur, J. K.; Hilgers, Frans J. M.

2009-01-01

This study assesses intra- and inter-patient variability in endotracheal climate (temperature and humidity) and effects of heat and moister exchangers (HME) in 16 laryngectomized individuals, measured repeatedly (N = 47). Inhalation Breath Length (IBL) was 1.35 s without HME and 1.05 s with HME (P

Propionibacterium acnes: disease-causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing

DEFF Research Database (Denmark)

Mollerup, Sarah; Friis-Nielsen, Jens; Vinner, Lasse

2016-01-01

Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions, but is also a proven contaminant of human samples and surgical wounds. Its...... significance as a pathogen is consequently a matter of debate.In the present study we investigated the presence of P. acnes DNA in 250 next generation sequencing datasets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were either subjected to microbial...... enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun-sequenced.We detected high proportions of P. acnes in enriched samples, particularly skin derived and other tissue samples, with levels being higher in enriched compared to shotgun-sequenced samples. P. acnes...

Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas

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Bodilis, Josselin; Nsigue-Meilo, Sandrine; Besaury, Ludovic; Quillet, Laurent

2012-01-01

Even though the 16S rRNA gene is the most commonly used taxonomic marker in microbial ecology, its poor resolution is still not fully understood at the intra-genus level. In this work, the number of rRNA gene operons, intra-genomic heterogeneities and lateral transfers were investigated at a fine-scale resolution, throughout the Pseudomonas genus. In addition to nineteen sequenced Pseudomonas strains, we determined the 16S rRNA copy number in four other Pseudomonas strains by Southern hybridization and Pulsed-Field Gel Electrophoresis, and studied the intra-genomic heterogeneities by Denaturing Gradient Gel Electrophoresis and sequencing. Although the variable copy number (from four to seven) seems to be correlated with the evolutionary distance, some close strains in the P. fluorescens lineage showed a different number of 16S rRNA genes, whereas all the strains in the P. aeruginosa lineage displayed the same number of genes (four copies). Further study of the intra-genomic heterogeneities revealed that most of the Pseudomonas strains (15 out of 19 strains) had at least two different 16S rRNA alleles. A great difference (5 or 19 nucleotides, essentially grouped near the V1 hypervariable region) was observed only in two sequenced strains. In one of our strains studied (MFY30 strain), we found a difference of 12 nucleotides (grouped in the V3 hypervariable region) between copies of the 16S rRNA gene. Finally, occurrence of partial lateral transfers of the 16S rRNA gene was further investigated in 1803 full-length sequences of Pseudomonas available in the databases. Remarkably, we found that the two most variable regions (the V1 and V3 hypervariable regions) had probably been laterally transferred from another evolutionary distant Pseudomonas strain for at least 48.3 and 41.6% of the 16S rRNA sequences, respectively. In conclusion, we strongly recommend removing these regions of the 16S rRNA gene during the intra-genus diversity studies. PMID:22545126

The Effect of Intra-articular Cocktail Versus Femoral Nerve Block for Patients Undergoing Hip Arthroscopy.

Science.gov (United States)

Childs, Sean; Pyne, Sonia; Nandra, Kiritpaul; Bakhsh, Wajeeh; Mustafa, S Atif; Giordano, Brian D

2017-12-01

To compare clinical efficacy and complication rate as measured by postoperative falls and development of peripheral neuritis between intra-articular blockade and femoral nerve block in patients undergoing arthroscopic hip surgery. An institutional review board approved retrospective review was conducted on a consecutive series of patients who underwent elective arthroscopic hip surgery by a single surgeon, between November 2013 and April 2015. Subjects were stratified into 2 groups: patients who received a preoperative femoral nerve block for perioperative pain control, and patients who received an intra-articular "cocktail" injection postoperatively. Demographic data, perioperative pain scores, narcotic consumption, incidence of falls, and iatrogenic peripheral neuritis were collected for analysis. Postoperative data were then collected at routine clinical visits. A total of 193 patients were included in this study (65 males, 125 females). Of them, 105 patients received preoperative femoral nerve blocks and 88 patients received an intraoperative intra-articular "cocktail." There were no significant differences in patient demographics, history of chronic pain (P = .35), worker's compensation (P = .24), preoperative pain scores (P = .69), or intraoperative doses of narcotics (P = .40). Patients who received preoperative femoral nerve blocks reported decreased pain during their time in PACU (P = .0001) and on hospital discharge (P = .28); however, there were no statistically significant differences in patient-reported pain scores at postoperative weeks 1 (P = .34), 3 (P = .64), and 6 (P = .70). Administration of an intra-articular block was associated with a significant reduction in the rate of postoperative falls (P = .009) and iatrogenic peripheral neuritis (P = .0001). Preoperative femoral nerve blocks are associated with decreased immediate postoperative pain, whereas intraoperative intra-articular anesthetic injections provide effective postoperative

Analysis of Urobilinogen and Urine Bilirubin for Intra-Abdominal Injury in Blunt Trauma Patients

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Gorchynski, Julie

2009-05-01

Full Text Available OBJECTIVE: To determine the point prevalence of urine bilirubin, urine hemoglobin and urobilinogen in blunt trauma patients, and to evaluate its utility as a screening tool for intra-abdominal injury.METHODS: Data analysis of 986 consecutive trauma patients of which 698 were adult blunt trauma patients. Five-hundred sixteen subjects had a urinalysis and a CT scan of the abdomen/pelvis or exploratory laparotomy. We reviewed initial urinalysis results from trauma patients in the emergency department (ED for the presence of urine hemoglobin, uroblinogen and urine bilirubin. Computed tomography (CT scan results and operative reports were reviewed from the trauma registry for evidence of liver laceration, spleen laceration, bowel or mesenteric injuries.RESULTS: There were 73 injuries and 57/516 patients (11% with intra-abdominal injury. Urinalysis was positive for urobilinogen in 28/516 (5.4% patients, urine bilirubin in 15/516 (2.9% patients and urine hemoglobin in 313/516 (61% patients. Nineteen/forty-seven (4% subjects had liver lacerations, 28/56 (5% splenic lacerations, and 15/5 (3% bowel or mesenteric injury. Comparing the proportion of patients that had urobilinogen detected in the group with and without intra-abdominal injury, 8/28 (29% subjects with urobilinogen, 5/15 (33% subjects with bilirubin and 47/313 (15% subjects with urine hemoglobin were found to have liver lacerations, spleen lacerations, or bowel/mesenteric injuries. Preexisting liver or biliary conditions were not statistically associated with elevation of urine bilirubin, urine hemoglobin or urobilinogen on initial urinalysis after blunt abdominal trauma. Point prevalence for urobilinogen, urine bilirubin and urine hemoglobin are 5.43% (28/516, 2.91% (15/516 and 60.7% (313/516 respectively.CONCLUSIONS: The utility of the initial routine urinalysis in the ED for adult blunt abdominal trauma patients should not be used as a screening tool for the evaluation of intra

Analysis of urobilinogen and urine bilirubin for intra-abdominal injury in blunt trauma patients.

Science.gov (United States)

Gorchynski, Julie; Dean, Kevin; Anderson, Craig L

2009-05-01

To determine the point prevalence of urine bilirubin, urine hemoglobin and urobilinogen in blunt trauma patients, and to evaluate its utility as a screening tool for intra-abdominal injury. Data analysis of 986 consecutive trauma patients of which 698 were adult blunt trauma patients. Five-hundred sixteen subjects had a urinalysis and a CT scan of the abdomen/pelvis or exploratory laparotomy. We reviewed initial urinalysis results from trauma patients in the emergency department (ED) for the presence of urine hemoglobin, uroblinogen and urine bilirubin. Computed tomography (CT) scan results and operative reports were reviewed from the trauma registry for evidence of liver laceration, spleen laceration, bowel or mesenteric injuries. There were 73 injuries and 57/516 patients (11%) with intra-abdominal injury. Urinalysis was positive for urobilinogen in 28/516 (5.4%) patients, urine bilirubin in 15/516 (2.9%) patients and urine hemoglobin in 313/516 (61%) patients. Nineteen/forty-seven (4%) subjects had liver lacerations, 28/56 (5%) splenic lacerations, and 15/5 (3%) bowel or mesenteric injury. Comparing the proportion of patients that had urobilinogen detected in the group with and without intra-abdominal injury, 8/28 (29%) subjects with urobilinogen, 5/15 (33%) subjects with bilirubin and 47/313 (15%) subjects with urine hemoglobin were found to have liver lacerations, spleen lacerations, or bowel/mesenteric injuries. Preexisting liver or biliary conditions were not statistically associated with elevation of urine bilirubin, urine hemoglobin or urobilinogen on initial urinalysis after blunt abdominal trauma. Point prevalence for urobilinogen, urine bilirubin and urine hemoglobin are 5.43% (28/516), 2.91% (15/516) and 60.7% (313/516) respectively. The utility of the initial routine urinalysis in the ED for adult blunt abdominal trauma patients should not be used as a screening tool for the evaluation of intra-abdominal injury.

Repeated Intra-Arterial Thrombectomy within 72 Hours in a Patient with a Clear Contraindication for Intravenous Thrombolysis

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Mona Laible

2015-01-01

Full Text Available Introduction. Treating patients with acute ischemic stroke, proximal arterial vessel occlusion, and absolute contraindication for administering intravenous recombinant tissue plasminogen activator (rtPA poses a therapeutic challenge. Intra-arterial thrombectomy constitutes an alternative treatment option. Materials and Methods. We report a case of a 57-year-old patient with concomitant gastric adenocarcinoma, who received three intra-arterial thrombectomies in 72 hours due to repeated occlusion of the left medial cerebral artery (MCA. Findings. Intra-arterial recanalization of the left medial cerebral artery was performed three times with initially good success. However, two days later, the right medial cerebral artery became occluded. Owing to the overall poor prognosis at that time and knowing the wishes of the patient, we decided not to perform another intra-arterial recanalization procedure. Conclusion. To our knowledge, this is the first case illustrating the use of repeated intra-arterial recanalization in early reocclusion of intracranial vessels.

Outbreak tracking of Aleutian mink disease virus (AMDV) using partial NS1 gene sequencing

DEFF Research Database (Denmark)

Ryt-Hansen, Pia; Hjulsager, Charlotte Kristiane; Hagberg, E. E.

2017-01-01

. However, in 2015, several outbreaks of AMDV occurred at mink farms throughout Denmark, and the sources of these outbreaks were not known. Partial NS1 gene sequencing, phylogenetic analyses data were utilized along with epidemiological to determine the origin of the outbreaks. The phylogenetic analyses...... not be excluded. This study confirmed that partial NS1 sequencing can be used in outbreak tracking to determine major viral clusters of AMDV. Using this method, two new distinct AMDV clusters with low intra-cluster sequence diversity were identified, and epidemiological data helped to reveal possible ways...

SU-E-T-250: New IMRT Sequencing Strategy: Towards Intra-Fraction Plan Adaptation for the MR-Linac

International Nuclear Information System (INIS)

Kontaxis, C; Bol, G; Lagendijk, J; Raaymakers, B

2014-01-01

Purpose: To develop a new sequencer for IMRT planning that during treatment makes the inclusion of external factors possible and by doing so accounts for intra-fraction anatomy changes. Given a real-time imaging modality that will provide the updated patient anatomy during delivery, this sequencer is able to take these changes into account during the calculation of subsequent segments. Methods: Pencil beams are generated for each beam angle of the treatment and a fluence optimization is performed. The pencil beams, together with the patient anatomy and the above optimal fluence form the input of our algorithm. During each iteration the following steps are performed: A fluence optimization is done and each beam's fluence is then split to discrete intensity levels. Deliverable segments are calculated for each one of these. Each segment's area multiplied by its intensity describes its efficiency. The most efficient segment among all beams is then chosen to deliver a part of the calculated fluence and the dose that will be delivered by this segment is calculated. This delivered dose is then subtracted from the remaining dose. This loop is repeated until 90% of the dose has been delivered and a final segment weight optimization is performed to reach full convergence. Results: This algorithm was tested in several prostate cases yielding results that meet all clinical constraints. Quality assurance was performed on Delta4 and film phantoms for one of these prostate cases and received clinical acceptance after passing both gamma analyses with the 3%/3mm criteria. Conclusion: A new sequencing algorithm was developed to facilitate the needs of intensity modulated treatment. The first results on static anatomy confirm that it can calculate clinical plans equivalent to those of the commercially available planning systems. We are now working towards 100% dose convergence which will allow us to handle anatomy deformations. This work is financially supported by Elekta

Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients.

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Matthias Merker

Full Text Available Multidrug-resistant (MDR Mycobacterium tuberculosis complex (MTBC strains represent a major threat for tuberculosis (TB control. Treatment of MDR-TB patients is long and less effective, resulting in a significant number of treatment failures. The development of further resistances leads to extensively drug-resistant (XDR variants. However, data on the individual reasons for treatment failure, e.g. an induced mutational burst, and on the evolution of bacteria in the patient are only sparsely available. To address this question, we investigated the intra-patient evolution of serial MTBC isolates obtained from three MDR-TB patients undergoing longitudinal treatment, finally leading to XDR-TB. Sequential isolates displayed identical IS6110 fingerprint patterns, suggesting the absence of exogenous re-infection. We utilized whole genome sequencing (WGS to screen for variations in three isolates from Patient A and four isolates from Patient B and C, respectively. Acquired polymorphisms were subsequently validated in up to 15 serial isolates by Sanger sequencing. We determined eight (Patient A and nine (Patient B polymorphisms, which occurred in a stepwise manner during the course of the therapy and were linked to resistance or a potential compensatory mechanism. For both patients, our analysis revealed the long-term co-existence of clonal subpopulations that displayed different drug resistance allele combinations. Out of these, the most resistant clone was fixed in the population. In contrast, baseline and follow-up isolates of Patient C were distinguished each by eleven unique polymorphisms, indicating an exogenous re-infection with an XDR strain not detected by IS6110 RFLP typing. Our study demonstrates that intra-patient microevolution of MDR-MTBC strains under longitudinal treatment is more complex than previously anticipated. However, a mutator phenotype was not detected. The presence of different subpopulations might confound phenotypic and

Clinical Analysis for the Correlation of Intra-abdominal Organ Injury in the Patients with Rib Fracture

OpenAIRE

Park, Seongsik

2012-01-01

Background Although it is rare for the fracture itself to become a life threatening injury in patients suffering from rib fracture, the lives of these patients are occasionally threatened by other associated injuries. Especially, early discovery of patients with rib fracture and intra-abdominal organ injury is extremely important to the prognosis. This study analyzed the link between rib fracture and intra-abdominal injury to achieve improved treatment. Materials and Methods Among trauma pati...

Microbial Culturomics Broadens Human Vaginal Flora Diversity: Genome Sequence and Description of Prevotella lascolaii sp. nov. Isolated from a Patient with Bacterial Vaginosis.

Science.gov (United States)

Diop, Khoudia; Diop, Awa; Levasseur, Anthony; Mediannikov, Oleg; Robert, Catherine; Armstrong, Nicholas; Couderc, Carine; Bretelle, Florence; Raoult, Didier; Fournier, Pierre-Edouard; Fenollar, Florence

2018-03-01

Microbial culturomics is a new subfield of postgenomic medicine and omics biotechnology application that has broadened our awareness on bacterial diversity of the human microbiome, including the human vaginal flora bacterial diversity. Using culturomics, a new obligate anaerobic Gram-stain-negative rod-shaped bacterium designated strain khD1 T was isolated in the vagina of a patient with bacterial vaginosis and characterized using taxonogenomics. The most abundant cellular fatty acids were C 15:0 anteiso (36%), C 16:0 (19%), and C 15:0 iso (10%). Based on an analysis of the full-length 16S rRNA gene sequences, phylogenetic analysis showed that the strain khD1 T exhibited 90% sequence similarity with Prevotella loescheii, the phylogenetically closest validated Prevotella species. With 3,763,057 bp length, the genome of strain khD1 T contained (mol%) 48.7 G + C and 3248 predicted genes, including 3194 protein-coding and 54 RNA genes. Given the phenotypical and biochemical characteristic results as well as genome sequencing, strain khD1 T is considered to represent a novel species within the genus Prevotella, for which the name Prevotella lascolaii sp. nov. is proposed. The type strain is khD1 T ( = CSUR P0109, = DSM 101754). These results show that microbial culturomics greatly improves the characterization of the human microbiome repertoire by isolating potential putative new species. Further studies will certainly clarify the microbial mechanisms of pathogenesis of these new microbes and their role in health and disease. Microbial culturomics is an important new addition to the diagnostic medicine toolbox and warrants attention in future medical, global health, and integrative biology postgraduate teaching curricula.

Molecular phylogeny of mangroves IV. nature and extent of intra-specific genetic variation and species diversity in mangroves

International Nuclear Information System (INIS)

Parida, A.; Parani, M.; Lakshmi, M.; Elango, S.; Ram, N.; Anuratha, C.S.

1998-01-01

Mangroves occupy estuarine ecosystems in the tropical regions of the world. Despite their highly productive nature and the protective roles they play in the coastal region, the ecosystem as a whole is under severe threat due to various climatic and anthropogenic factors. Therefore, the need for conservation of mangroves is widely emphasised. However, information on existing genetic diversity based on which a strategy for genetic conservation is to be drawn is not available for mangroves. This is primarily because conventional genetic analysis is difficult in these species for various reasons. Therefore, as an aid to our on-going conservation programme, efforts were made to assess the nature and extent of diversity in a number of mangrove species of the Indian coast using molecular markers. The nature and extent of intra-population diversity in sixteen mangrove species and detailed analysis of inter-population genetic polymorphism in four species, Acanthus ilicifolius, Excoecaria agallocha, Avicennia spp and Rhizophora (species and hybrid), is reported in the present communication. (author)

Intra-lesional spatial correlation of static and dynamic FET-PET parameters with MRI-based cerebral blood volume in patients with untreated glioma.

Science.gov (United States)

Göttler, Jens; Lukas, Mathias; Kluge, Anne; Kaczmarz, Stephan; Gempt, Jens; Ringel, Florian; Mustafa, Mona; Meyer, Bernhard; Zimmer, Claus; Schwaiger, Markus; Förster, Stefan; Preibisch, Christine; Pyka, Thomas

2017-03-01

18 F-fluorethyltyrosine-(FET)-PET and MRI-based relative cerebral blood volume (rCBV) have both been used to characterize gliomas. Recently, inter-individual correlations between peak static FET-uptake and rCBV have been reported. Herein, we assess the local intra-lesional relation between FET-PET parameters and rCBV. Thirty untreated glioma patients (27 high-grade) underwent simultaneous PET/MRI on a 3 T hybrid scanner obtaining structural and dynamic susceptibility contrast sequences. Static FET-uptake and dynamic FET-slope were correlated with rCBV within tumour hotspots across patients and intra-lesionally using a mixed-effects model to account for inter-individual variation. Furthermore, maximal congruency of tumour volumes defined by FET-uptake and rCBV was determined. While the inter-individual relationship between peak static FET-uptake and rCBV could be confirmed, our intra-lesional, voxel-wise analysis revealed significant positive correlations (median r = 0.374, p dynamic FET-PET variance and maximal overlap of respective tumour volumes was 37% on average. Our results show that the relation between peak values of MR-based rCBV and static FET-uptake can also be observed intra-individually on a voxel basis and also applies to a dynamic FET parameter, possibly determining hotspots of higher biological malignancy. However, just a small part of the FET-PET signal variance is explained by rCBV and tumour volumes determined by the two modalities showed only moderate overlap. These findings indicate that FET-PET and MR-based rCBV provide both congruent and complimentary information on glioma biology.

Clinical experience of intra-arterial therapy in patients with acute ischemic stroke from a single institute

International Nuclear Information System (INIS)

Park, So Young; Lee, Han Bin; Kim, Jong Guk; Oh, Seung Hun; Kim, Jin Kwon; Kim, Sang Heum; Kim, Ok Joon; Kim, Nam Keun

2016-01-01

To compare the efficacy and safety between intra-arterial therapy (IAT) and intra-venous and intra-arterial combined therapy (IVIACT) in patients with acute ischemic stroke in the anterior circulation territory. Forty-one patients treated with IAT using Solitaire were retrospectively reviewed. Nineteen patients were treated with IAT, twenty-two patients were treated with IVIACT, and ten patients of the forty-one patients were managed with multimodal treatment like stent, balloon angioplasty etc. We investigated the rate of recanalization and hemorrhage, NIH stroke scale and 3-month modified Rankin Scale. The overall recanalization rate was 93% and symptomatic ICH occurred in 10% of the patients. There was no difference in hemorrhage, recanalization rate, and early improvement between IAT and IVIACT. Good outcome was more frequently observed in 59% of the patients with IVIACT than 36% of the patients treated with IAT without any significant difference. The patients managed with multimodal treatment did not show any significant hemorrhage outcome. IAT using Solitaire is a useful treatment method without high risk in patients with acute ischemic stroke in the anterior circulation territory. Also, IVIACT and multimodal treatment might be considered as reasonable therapeutic options in these patients

Clinical experience of intra-arterial therapy in patients with acute ischemic stroke from a single institute

Energy Technology Data Exchange (ETDEWEB)

Park, So Young [Dept. Neurology, Seoul National University-Seoul Metropolitan Government Boramae Medical Center, Seoul (Korea, Republic of); Lee, Han Bin; Kim, Jong Guk; Oh, Seung Hun; Kim, Jin Kwon; Kim, Sang Heum; Kim, Ok Joon [CHA Bundang Medical Center, CHA University, Seongnam (Korea, Republic of); Kim, Nam Keun [Institute for Clinical Research, School of Medicine, CHA University, Seongnam (Korea, Republic of)

2016-11-15

To compare the efficacy and safety between intra-arterial therapy (IAT) and intra-venous and intra-arterial combined therapy (IVIACT) in patients with acute ischemic stroke in the anterior circulation territory. Forty-one patients treated with IAT using Solitaire were retrospectively reviewed. Nineteen patients were treated with IAT, twenty-two patients were treated with IVIACT, and ten patients of the forty-one patients were managed with multimodal treatment like stent, balloon angioplasty etc. We investigated the rate of recanalization and hemorrhage, NIH stroke scale and 3-month modified Rankin Scale. The overall recanalization rate was 93% and symptomatic ICH occurred in 10% of the patients. There was no difference in hemorrhage, recanalization rate, and early improvement between IAT and IVIACT. Good outcome was more frequently observed in 59% of the patients with IVIACT than 36% of the patients treated with IAT without any significant difference. The patients managed with multimodal treatment did not show any significant hemorrhage outcome. IAT using Solitaire is a useful treatment method without high risk in patients with acute ischemic stroke in the anterior circulation territory. Also, IVIACT and multimodal treatment might be considered as reasonable therapeutic options in these patients.

Origin, diversity and maturation of human antiviral antibodies analyzed by high-throughput sequencing

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Ponraj ePrabakaran

2012-08-01

Full Text Available Our understanding of how antibodies are generated and function could help develop effective vaccines and antibody-based therapeutics against viruses such as HIV-1, SARS Coronavirus (CoV, and Hendra and Nipah viruses (henipaviruses. Although broadly neutralizing antibodies (bnAbs against the HIV-1 were observed in patients, elicitation of such bnAbs remains a major challenge when compared to other viral targets. We previously hypothesized that HIV-1 could have evolved a strategy to evade the immune system due to absent or very weak binding of germline antibodies to the conserved epitopes that may not be sufficient to initiate and/or maintain an effective immune response. To further explore our hypothesis, we used the 454 sequence analysis of a large naïve library of human IgM antibodies which had been used for selecting antibodies against SARS Coronavirus (CoV receptor-binding domain (RBD, and soluble G proteins (sG of Hendra and Nipah viruses (henipaviruses. We found that the human IgM repertoires from the 454 sequencing have diverse germline usages, recombination patterns, junction diversity and a lower extent of somatic mutation. In this study, we identified germline intermediates of antibodies specific to HIV-1 and other viruses as observed in normal individuals, and compared their genetic diversity and somatic mutation level along with available structural and functional data. Further computational analysis will provide framework for understanding the underlying genetic and molecular determinants related to maturation pathways of antiviral bnAbs that could be useful for applying novel approaches to the design of effective vaccine immunogens and antibody-based therapeutics.

Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection.

Science.gov (United States)

Weiss, Eric R; Lamers, Susanna L; Henderson, Jennifer L; Melnikov, Alexandre; Somasundaran, Mohan; Garber, Manuel; Selin, Liisa; Nusbaum, Chad; Luzuriaga, Katherine

2018-01-15

Over 90% of the world's population is persistently infected with Epstein-Barr virus. While EBV does not cause disease in most individuals, it is the common cause of acute infectious mononucleosis (AIM) and has been associated with several cancers and autoimmune diseases, highlighting a need for a preventive vaccine. At present, very few primary, circulating EBV genomes have been sequenced directly from infected individuals. While low levels of diversity and low viral evolution rates have been predicted for double-stranded DNA (dsDNA) viruses, recent studies have demonstrated appreciable diversity in common dsDNA pathogens (e.g., cytomegalovirus). Here, we report 40 full-length EBV genome sequences obtained from matched oral wash and B cell fractions from a cohort of 10 AIM patients. Both intra- and interpatient diversity were observed across the length of the entire viral genome. Diversity was most pronounced in viral genes required for establishing latent infection and persistence, with appreciable levels of diversity also detected in structural genes, including envelope glycoproteins. Interestingly, intrapatient diversity declined significantly over time ( P < 0.01), and this was particularly evident on comparison of viral genomes sequenced from B cell fractions in early primary infection and convalescence ( P < 0.001). B cell-associated viral genomes were observed to converge, becoming nearly identical to the B95.8 reference genome over time (Spearman rank-order correlation test; r = -0.5589, P = 0.0264). The reduction in diversity was most marked in the EBV latency genes. In summary, our data suggest independent convergence of diverse viral genome sequences toward a reference-like strain within a relatively short period following primary EBV infection. IMPORTANCE Identification of viral proteins with low variability and high immunogenicity is important for the development of a protective vaccine. Knowledge of genome diversity within circulating viral

Intra-lesional spatial correlation of static and dynamic FET-PET parameters with MRI-based cerebral blood volume in patients with untreated glioma

Energy Technology Data Exchange (ETDEWEB)

Goettler, Jens; Preibisch, Christine [TU Muenchen, Department of Neuroradiology, Klinikum rechts der Isar, Munich (Germany); TU Muenchen, TUM Neuroimaging Center (TUM-NIC), Klinikum rechts der Isar, Munich (Germany); Lukas, Mathias; Mustafa, Mona; Schwaiger, Markus; Pyka, Thomas [TU Muenchen, Department of Nuclear Medicine, Klinikum rechts der Isar, Munich (Germany); Kluge, Anne; Kaczmarz, Stephan; Zimmer, Claus [TU Muenchen, Department of Neuroradiology, Klinikum rechts der Isar, Munich (Germany); Gempt, Jens; Ringel, Florian; Meyer, Bernhard [TU Muenchen, Department of Neurosurgery, Klinikum rechts der Isar, Munich (Germany); Foerster, Stefan [TU Muenchen, TUM Neuroimaging Center (TUM-NIC), Klinikum rechts der Isar, Munich (Germany); TU Muenchen, Department of Nuclear Medicine, Klinikum rechts der Isar, Munich (Germany); Klinikum Bayreuth, Department of Nuclear Medicine, Bayreuth (Germany)

2017-03-15

{sup 18}F-fluorethyltyrosine-(FET)-PET and MRI-based relative cerebral blood volume (rCBV) have both been used to characterize gliomas. Recently, inter-individual correlations between peak static FET-uptake and rCBV have been reported. Herein, we assess the local intra-lesional relation between FET-PET parameters and rCBV. Thirty untreated glioma patients (27 high-grade) underwent simultaneous PET/MRI on a 3 T hybrid scanner obtaining structural and dynamic susceptibility contrast sequences. Static FET-uptake and dynamic FET-slope were correlated with rCBV within tumour hotspots across patients and intra-lesionally using a mixed-effects model to account for inter-individual variation. Furthermore, maximal congruency of tumour volumes defined by FET-uptake and rCBV was determined. While the inter-individual relationship between peak static FET-uptake and rCBV could be confirmed, our intra-lesional, voxel-wise analysis revealed significant positive correlations (median r = 0.374, p < 0.0001). Similarly, significant inter- and intra-individual correlations were observed between FET-slope and rCBV. However, rCBV explained only 12% of the static and 5% of the dynamic FET-PET variance and maximal overlap of respective tumour volumes was 37% on average. Our results show that the relation between peak values of MR-based rCBV and static FET-uptake can also be observed intra-individually on a voxel basis and also applies to a dynamic FET parameter, possibly determining hotspots of higher biological malignancy. However, just a small part of the FET-PET signal variance is explained by rCBV and tumour volumes determined by the two modalities showed only moderate overlap. These findings indicate that FET-PET and MR-based rCBV provide both congruent and complimentary information on glioma biology. (orig.)

Clinical observation on treatment of Meibomian gland before IntraLase LASIK in patients with Meibomian gland dysfunction

Directory of Open Access Journals (Sweden)

He Huang

2016-04-01

Full Text Available AIM:To observe the changes of ocular surface inflammation and tear film state before and after the operation after preoperative targeted therapy for Meibomian gland in the patients scheduled for IntraLase-LASIK with Meibomian gland dysfunction(MGD. METHODS: Thirty-five patients(70 eyesscheduled for IntraLase-LASIK with different degrees of MGD from March to September 2014 were enrolled in this study. All patients were randomly divided into 2 groups, 17 patients(34 eyesin the observation group accepted preoperative targeted therapy for Meibomian gland; 18 patients(36 eyesin the control group did not give the treatment for Meibomian gland, the rest treatments were the same. The change of conjunctival congestion, photophobia, dry symptom score and tear break-up time(BUTwere observed at 1d and 1wk after IntraLase-LASIK. RESULTS: At 1d and 1wk postoperatively, the scores of conjunctival congestion, photophobia, dry symptom and BUT of the observation group were all lower than those of the control group, and the differences were significant(PCONCLUSION: For the patients scheduled for IntraLase-LASIK with MGD, preoperative targeted therapy for Meibomian gland can reduce the postoperative symptoms of ocular surface irritation, stabilize the tear film, improve the postoperative effect and improve the comfort of patients.

The Effect of Intra-articular Injection of Autologous Microfragmented Fat Tissue on Proteoglycan Synthesis in Patients with Knee Osteoarthritis

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Damir Hudetz

2017-10-01

Full Text Available Osteoarthritis (OA is one of the leading musculoskeletal disorders in the adult population. It is associated with cartilage damage triggered by the deterioration of the extracellular matrix tissue. The present study explores the effect of intra-articular injection of autologous microfragmented adipose tissue to host chondrocytes and cartilage proteoglycans in patients with knee OA. A prospective, non-randomized, interventional, single-center, open-label clinical trial was conducted from January 2016 to April 2017. A total of 17 patients were enrolled in the study, and 32 knees with osteoarthritis were assessed. Surgical intervention (lipoaspiration followed by tissue processing and intra-articular injection of the final microfragmented adipose tissue product into the affected knee(s was performed in all patients. Patients were assessed for visual analogue scale (VAS, delayed gadolinium-enhanced magnetic resonance imaging of cartilage (dGEMRIC and immunoglobulin G (IgG glycans at the baseline, three, six and 12 months after the treatment. Magnetic resonance sequence in dGEMRIC due to infiltration of the anionic, negatively charged contrast gadopentetate dimeglumine (Gd-DTPA2− into the cartilage indicated that the contents of cartilage glycosaminoglycans significantly increased in specific areas of the treated knee joint. In addition, dGEMRIC consequently reflected subsequent changes in the mechanical axis of the lower extremities. The results of our study indicate that the use of autologous and microfragmented adipose tissue in patients with knee OA (measured by dGEMRIC MRI increased glycosaminoglycan (GAG content in hyaline cartilage, which is in line with observed VAS and clinical results.

The role of interventional radiology in the management of intra-and extra-Peritoneal leakage in patients who have undergone continent urinary diversion

International Nuclear Information System (INIS)

Bodner, Leonard; Nosher, John L.; Siegel, Randall; Russer, Tadeus; Cummings, Kenneth; Kraus, Stephen

1997-01-01

Purpose. To assess how radiologic intervention altered the hospital course of patients undergoing continent urinary diversion. Methods. Thirty-seven consecutive patients with bladder cancer invading the muscular layer were treated with total cystectomy and construction of a continent urinary reservoir. Eleven of 37 patients suffered early and late anastomotic leakage; six had prolonged extraperitoneal leakage at the urethroenteric anastomosis, three had prolonged intraperitoneal pouch leaks, and two had delayed ureteroenteric leaks. Seven of these patients required radiologic intervention.Results. Intervention in the form of drainage catheter manipulation (n=4), percutaneous nephrostomy (n=4), or ureteral stent placement (n=2) resulted in cessation of leakage without surgical intervention in all seven patients. Intraperitoneal pouch leaks were more difficult to control than extraperitoneal leakage and required longer drainage intervals.Conclusion. Interventional radiologic procedures played a key role in the management of continent urinary diversion complications obviating the need for repeat surgical intervention in all instances

Evaluation of the microbial diversity in amyotrophic lateral sclerosis using high-throughput sequencing

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Xin Fang

2016-09-01

Full Text Available More and more evidences indicate that diseases of the central nervous system (CNS have been seriously affected by faecal microbes. However, little work is done to explore interaction between amyotrophic lateral sclerosis (ALS and faecal microbes. In the present study, high-throughput sequencing method was used to compare the intestinal microbial diversity of healthy people and ALS patients. The principal coordinate analysis (PCoA, Venn and unweighted pair-group method using arithmetic averages (UPGMA showed an obvious microbial changes between healthy people (group H and ALS patients (group A, and the average ratios of Bacteroides, Faecalibacterium, Anaerostipes, Prevotella, Escherichia and Lachnospira at genus level between ALS patients and healthy people were 0.78, 2.18, 3.41, 0.35, 0.79 and 13.07. Furthermore, the decreased Firmicutes/Bacteroidetes ratio at phylum level using LEfSE (LDA >4.0, together with the significant increased genus Dorea (harmful microorganisms and significant reduced genus Oscillibacter, Anaerostipes, Lachnospiraceae (beneficial microorganisms in ALS patients, indicated that the imbalance in intestinal microflora constitution had a strong association with the pathogenesis of ALS.

Evaluation of the Microbial Diversity in Amyotrophic Lateral Sclerosis Using High-Throughput Sequencing.

Science.gov (United States)

Fang, Xin; Wang, Xin; Yang, Shaoguo; Meng, Fanjing; Wang, Xiaolei; Wei, Hua; Chen, Tingtao

2016-01-01

More and more evidences indicate that diseases of the central nervous system have been seriously affected by fecal microbes. However, little work is done to explore interaction between amyotrophic lateral sclerosis (ALS) and fecal microbes. In the present study, high-throughput sequencing method was used to compare the intestinal microbial diversity of healthy people and ALS patients. The principal coordinate analysis, Venn and unweighted pair-group method using arithmetic averages (UPGMA) showed an obvious microbial changes between healthy people (group H) and ALS patients (group A), and the average ratios of Bacteroides , Faecalibacterium , Anaerostipes , Prevotella , Escherichia , and Lachnospira at genus level between ALS patients and healthy people were 0.78, 2.18, 3.41, 0.35, 0.79, and 13.07. Furthermore, the decreased Firmicutes/Bacteroidetes ratio at phylum level using LEfSE (LDA > 4.0), together with the significant increased genus Dorea (harmful microorganisms) and significant reduced genus Oscillibacter , Anaerostipes , Lachnospiraceae (beneficial microorganisms) in ALS patients, indicated that the imbalance in intestinal microflora constitution had a strong association with the pathogenesis of ALS.

Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify Dendrobium species.

Science.gov (United States)

Liu, Y T; Chen, R K; Lin, S J; Chen, Y C; Chin, S W; Chen, F C; Lee, C Y

2014-04-08

The Orchidaceae is one of the largest and most diverse families of flowering plants. The Dendrobium genus has high economic potential as ornamental plants and for medicinal purposes. In addition, the species of this genus are able to produce large crops. However, many Dendrobium varieties are very similar in outward appearance, making it difficult to distinguish one species from another. This study demonstrated that the 12 Dendrobium species used in this study may be divided into 2 groups by internal transcribed spacer (ITS) sequence analysis. Red and yellow flowers may also be used to separate these species into 2 main groups. In particular, the deciduous characteristic is associated with the ITS genetic diversity of the A group. Of 53 designed simple sequence repeat (SSR) primer pairs, 7 pairs were polymorphic for polymerase chain reaction products that were amplified from a specific band. The results of this study demonstrate that these 7 SSR primer pairs may potentially be used to identify Dendrobium species and their progeny in future studies.

Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping

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Gregory W. Peterson

2014-10-01

Full Text Available Genotyping-by-sequencing (GBS has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L. accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species.

Population diversity of Diaphorina citri (Hemiptera: Liviidae) in China based on whole mitochondrial genome sequences.

Science.gov (United States)

Wu, Fengnian; Jiang, Hongyan; Beattie, G Andrew C; Holford, Paul; Chen, Jianchi; Wallis, Christopher M; Zheng, Zheng; Deng, Xiaoling; Cen, Yijing

2018-04-24

Diaphorina citri (Asian citrus psyllid; ACP) transmits 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing (HLB). ACP has been reported in 11 provinces/regions in China, yet its population diversity remains unclear. In this study, we evaluated ACP population diversity in China using representative whole mitochondrial genome (mitogenome) sequences. Additional mitogenome sequences outside China were also acquired and evaluated. The sizes of the 27 ACP mitogenome sequences ranged from 14 986 to 15 030 bp. Along with three previously published mitogenome sequences, the 30 sequences formed three major mitochondrial groups (MGs): MG1, present in southwestern China and occurring at elevations above 1000 m; MG2, present in southeastern China and Southeast Asia (Cambodia, Indonesia, Malaysia, and Vietnam) and occurring at elevations below 180 m; and MG3, present in the USA and Pakistan. Single nucleotide polymorphisms in five genes (cox2, atp8, nad3, nad1 and rrnL) contributed mostly in the ACP diversity. Among these genes, rrnL had the most variation. Mitogenome sequences analyses revealed two major phylogenetic groups of ACP present in China as well as a possible unique group present currently in Pakistan and the USA. The information could have significant implications for current ACP control and HLB management. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

Echo-planar magnetic resonance imaging (EPI) with high-resolution matrix in intra-axial brain tumors

International Nuclear Information System (INIS)

Bruening, R.; Scheidler, J.; Porn, U.; Reiser, M.; Seelos, K.; Yousry, T.; Exner, H.; Rosen, B.R.

1999-01-01

The aim of this study was to assess the potential of high-speed interleaved echo-planar imaging (EPI) to achieve diagnostic image quality comparable to T2-weighted imaging in patients with brain tumors. Seventeen patients with intra-axial, supratentorial tumors (10 untreated gliomas, 7 radiated gliomas) were investigated on a 1.5-T scanner. The conventional scan (SE, TR/TE = 2200/80 ms, 18 slices) was acquired in 8 min, 4 s, and EPI (TR/TE = 3000/80 ms, 18 slices) was completed in 25 s. The films were compared in a blinded trail by three radiologists. On the general impression and anatomic display, both sequences were rated to be of similar quality. Artifacts were slightly more pronounced at the skull base and around surgical clips using EPI. Tumor delineation was nearly equivalent using EPI, compared with the T2-weighted sequence. Echo-planar imaging reached diagnostic quality in all patients. Interleaved high-resolution EPI yielded sufficient quality to depict intra-axial, supratentorial brain tumors. Since EPI can be obtained in a small fraction of the time needed for conventional spin echo, in addition to other indications it could be considered to study patients unable to cooperate. (orig.)

Reliability of intra-oral quantitative sensory testing (QST) in patients with atypical odontalgia and healthy controls - a multicentre study.

Science.gov (United States)

Baad-Hansen, L; Pigg, M; Yang, G; List, T; Svensson, P; Drangsholt, M

2015-02-01

The reliability of comprehensive intra-oral quantitative sensory testing (QST) protocol has not been examined systematically in patients with chronic oro-facial pain. The aim of the present multicentre study was to examine test-retest and interexaminer reliability of intra-oral QST measures in terms of absolute values and z-scores as well as within-session coefficients of variation (CV) values in patients with atypical odontalgia (AO) and healthy pain-free controls. Forty-five patients with AO and 68 healthy controls were subjected to bilateral intra-oral gingival QST and unilateral extratrigeminal QST (thenar) on three occasions (twice on 1 day by two different examiners and once approximately 1 week later by one of the examiners). Intra-class correlation coefficients and kappa values for interexaminer and test-retest reliability were computed. Most of the standardised intra-oral QST measures showed fair to excellent interexaminer (9-12 of 13 measures) and test-retest (7-11 of 13 measures) reliability. Furthermore, no robust differences in reliability measures or within-session variability (CV) were detected between patients with AO and the healthy reference group. These reliability results in chronic orofacial pain patients support earlier suggestions based on data from healthy subjects that intra-oral QST is sufficiently reliable for use as a part of a comprehensive evaluation of patients with somatosensory disturbances or neuropathic pain in the trigeminal region. © 2014 John Wiley & Sons Ltd.

Diagnosis of intra-abdominal infections and management of catastrophic outcomes

NARCIS (Netherlands)

Atema, J.J.

2015-01-01

Intra-abdominal infections are a diverse group of frequently encountered conditions of varying severity with various underlying pathologies. The first part of this thesis focused on the diagnostic work-up of suspected intra-abdominal infections. The diagnosticvalue of commonly used inflammatory

Intra-Tumour Signalling Entropy Determines Clinical Outcome in Breast and Lung Cancer

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Banerji, Christopher R. S.; Severini, Simone; Caldas, Carlos; Teschendorff, Andrew E.

2015-01-01

The cancer stem cell hypothesis, that a small population of tumour cells are responsible for tumorigenesis and cancer progression, is becoming widely accepted and recent evidence has suggested a prognostic and predictive role for such cells. Intra-tumour heterogeneity, the diversity of the cancer cell population within the tumour of an individual patient, is related to cancer stem cells and is also considered a potential prognostic indicator in oncology. The measurement of cancer stem cell abundance and intra-tumour heterogeneity in a clinically relevant manner however, currently presents a challenge. Here we propose signalling entropy, a measure of signalling pathway promiscuity derived from a sample’s genome-wide gene expression profile, as an estimate of the stemness of a tumour sample. By considering over 500 mixtures of diverse cellular expression profiles, we reveal that signalling entropy also associates with intra-tumour heterogeneity. By analysing 3668 breast cancer and 1692 lung adenocarcinoma samples, we further demonstrate that signalling entropy correlates negatively with survival, outperforming leading clinical gene expression based prognostic tools. Signalling entropy is found to be a general prognostic measure, valid in different breast cancer clinical subgroups, as well as within stage I lung adenocarcinoma. We find that its prognostic power is driven by genes involved in cancer stem cells and treatment resistance. In summary, by approximating both stemness and intra-tumour heterogeneity, signalling entropy provides a powerful prognostic measure across different epithelial cancers. PMID:25793737

Intra-tumour signalling entropy determines clinical outcome in breast and lung cancer.

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Christopher R S Banerji

2015-03-01

Full Text Available The cancer stem cell hypothesis, that a small population of tumour cells are responsible for tumorigenesis and cancer progression, is becoming widely accepted and recent evidence has suggested a prognostic and predictive role for such cells. Intra-tumour heterogeneity, the diversity of the cancer cell population within the tumour of an individual patient, is related to cancer stem cells and is also considered a potential prognostic indicator in oncology. The measurement of cancer stem cell abundance and intra-tumour heterogeneity in a clinically relevant manner however, currently presents a challenge. Here we propose signalling entropy, a measure of signalling pathway promiscuity derived from a sample's genome-wide gene expression profile, as an estimate of the stemness of a tumour sample. By considering over 500 mixtures of diverse cellular expression profiles, we reveal that signalling entropy also associates with intra-tumour heterogeneity. By analysing 3668 breast cancer and 1692 lung adenocarcinoma samples, we further demonstrate that signalling entropy correlates negatively with survival, outperforming leading clinical gene expression based prognostic tools. Signalling entropy is found to be a general prognostic measure, valid in different breast cancer clinical subgroups, as well as within stage I lung adenocarcinoma. We find that its prognostic power is driven by genes involved in cancer stem cells and treatment resistance. In summary, by approximating both stemness and intra-tumour heterogeneity, signalling entropy provides a powerful prognostic measure across different epithelial cancers.

Variation in Symbiodinium ITS2 sequence assemblages among coral colonies.

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Stat, Michael; Bird, Christopher E; Pochon, Xavier; Chasqui, Luis; Chauka, Leonard J; Concepcion, Gregory T; Logan, Dan; Takabayashi, Misaki; Toonen, Robert J; Gates, Ruth D

2011-01-05

Endosymbiotic dinoflagellates in the genus Symbiodinium are fundamentally important to the biology of scleractinian corals, as well as to a variety of other marine organisms. The genus Symbiodinium is genetically and functionally diverse and the taxonomic nature of the union between Symbiodinium and corals is implicated as a key trait determining the environmental tolerance of the symbiosis. Surprisingly, the question of how Symbiodinium diversity partitions within a species across spatial scales of meters to kilometers has received little attention, but is important to understanding the intrinsic biological scope of a given coral population and adaptations to the local environment. Here we address this gap by describing the Symbiodinium ITS2 sequence assemblages recovered from colonies of the reef building coral Montipora capitata sampled across Kāne'ohe Bay, Hawai'i. A total of 52 corals were sampled in a nested design of Coral Colony(Site(Region)) reflecting spatial scales of meters to kilometers. A diversity of Symbiodinium ITS2 sequences was recovered with the majority of variance partitioning at the level of the Coral Colony. To confirm this result, the Symbiodinium ITS2 sequence diversity in six M. capitata colonies were analyzed in much greater depth with 35 to 55 clones per colony. The ITS2 sequences and quantitative composition recovered from these colonies varied significantly, indicating that each coral hosted a different assemblage of Symbiodinium. The diversity of Symbiodinium ITS2 sequence assemblages retrieved from individual colonies of M. capitata here highlights the problems inherent in interpreting multi-copy and intra-genomically variable molecular markers, and serves as a context for discussing the utility and biological relevance of assigning species names based on Symbiodinium ITS2 genotyping.

Detection of Diverse Novel Bat Astrovirus Sequences in the Czech Republic.

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Dufkova, Lucie; Straková, Petra; Širmarová, Jana; Salát, Jiří; Moutelíková, Romana; Chrudimský, Tomáš; Bartonička, Tomáš; Nowotny, Norbert; Růžek, Daniel

2015-08-01

Astroviruses are a major cause of gastroenteritis in humans and animals. Recently, novel groups of astroviruses were identified in apparently healthy insectivorous bats. We report the detection of diverse novel astrovirus sequences in nine different European bat species: Eptesicus serotinus, Hypsugo savii, Myotis emarginatus, M. mystacinus, Nyctalus noctula, Pipistrellus nathusii or P. pygmaeus, P. pipistrellus, Vespertilio murinus, and Rhinolophus hipposideros. In six bat species, astrovirus sequences were detected for the first time. One astrovirus strain detected in R. hipposideros clustered phylogenetically with Chinese astrovirus strains originating from bats of the families Rhinolophidae and Hipposideridae. All other Czech astrovirus sequences from vesper bats formed, together with one Hungarian sequence, a separate monophyletic lineage within the bat astrovirus group. These findings provide new insights into the molecular epidemiology, ecology, and prevalence of astroviruses in European bat populations.

Multilocus sequence typing and rtxA toxin gene sequencing analysis of Kingella kingae isolates demonstrates genetic diversity and international clones.

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Romain Basmaci

Full Text Available BACKGROUND: Kingella kingae, a normal component of the upper respiratory flora, is being increasingly recognized as an important invasive pathogen in young children. Genetic diversity of this species has not been studied. METHODS: We analyzed 103 strains from different countries and clinical origins by a new multilocus sequence-typing (MLST schema. Putative virulence gene rtxA, encoding an RTX toxin, was also sequenced, and experimental virulence of representative strains was assessed in a juvenile-rat model. RESULTS: Thirty-six sequence-types (ST and nine ST-complexes (STc were detected. The main STc 6, 14 and 23 comprised 23, 17 and 20 strains respectively, and were internationally distributed. rtxA sequencing results were mostly congruent with MLST, and showed horizontal transfer events. Of interest, all members of the distantly related ST-6 (n = 22 and ST-5 (n = 4 harboured a 33 bp duplication or triplication in their rtxA sequence, suggesting that this genetic trait arose through selective advantage. The animal model revealed significant differences in virulence among strains of the species. CONCLUSION: MLST analysis reveals international spread of ST-complexes and will help to decipher acquisition and evolution of virulence traits and diversity of pathogenicity among K. kingae strains, for which an experimental animal model is now available.

Effect of intra-hepatic arterial infusion chemotherapy for patients with liver metastasis from breast cancer

International Nuclear Information System (INIS)

Liu Dezhong; Li Huai; Zeng Huiying; Yang Ling

2001-01-01

Objective: To evaluate the efficacy of intra-hepatic arterial infusion chemotherapy for patients with liver metastasis from breast cancer. Methods: 1993-1998 years, Thirty four patients with liver metastasis from breast cancer had received epi-adriamycin, cisplatin, mitomycin and 5-fluorouracil by intrahepatic arterial infusion chemotherapy. Twelve patients had received embolization. Results: Six patients (17.65%) had a complete response, 12 patients (35.29%) had a partial response. The overall response rate was 52.94%. Cumulative survival rates at 1, 2, 3 and 4 years were 56.90%, 25.00%, 5.00% and 5.00% respectively (Kaplan-Meier method). The median overall survival time was 11.5 months. Conclusion: Intra-hepatic arterial infusion chemotherapy is safe and effective for liver metastasis from breast cancer and should be the first choice of treatment for these patients

Intra-specific genetic diversity in wild olives (Olea europaea ssp cuspidata) in Hormozgan Province, Iran.

Science.gov (United States)

Noormohammadi, Z; Samadi-Molayousefi, H; Sheidai, M

2012-03-19

Wild olive (O. europaea ssp cuspidata) plants grow in various regions of Iran and are expected to have considerable genetic diversity due to adaptation to the various environmental conditions. We examined the genetic diversity of four populations of wild olive growing in Hormozgan Province located in southern Iran by using 30 RAPDs and 10 ISSR markers. The mean value of polymorphism for RAPD loci was 73.71%, while the value for ISSR loci was 81.74%. The Keshar population had the highest value of intra-population polymorphism for both RAPD and ISSR loci (66.86 and 62.71%, respectively), while the Tudar population had the lowest values (20.35 and 28.81%, respectively). Similarly, the highest and lowest number of effective alleles, Shannon index and Nei's genetic diversity were also found for these two populations. The highest value of H(pop)/H(sp) within population genetic diversity for RAPD and ISSR loci was found for the Keshar population (H(pop) = 0.85 and H(sp) = 0.90). OPA04-750, OPA13-650 and OPA02-350 RAPD bands were specific for Tudar, Bondon and Keshar populations, respectively, while no specific ISSR bands were observed. Analysis of molecular variance as well as the pairwise F(ST) test showed significant differences for RAPD and ISSR markers among the populations. The NJ and UPGMA trees also separated the wild olive populations from each other, indicating their genetic distinctness. UPGMA clustering of the four wild olive populations placed the Tudar population far from the other populations; Keshar and Bokhoon population samples revealed more similarity and were grouped together. We conclude that there is high genetic diversity among O. europaea ssp cuspidata populations located in southern Iran. We also found RAPD and ISSR markers to be useful molecular tools to discriminate and evaluate genetic variations in wild olive trees.

Intra-arterial Autologous Bone Marrow Cell Transplantation in a Patient with Upper-extremity Critical Limb Ischemia

International Nuclear Information System (INIS)

Madaric, Juraj; Klepanec, Andrej; Mistrik, Martin; Altaner, Cestmir; Vulev, Ivan

2013-01-01

Induction of therapeutic angiogenesis by autologous bone marrow mononuclear cell transplantation has been identified as a potential new option in patients with advanced lower-limb ischemia. There is little evidence of the benefit of intra-arterial cell application in upper-limb critical ischemia. We describe a patient with upper-extremity critical limb ischemia with digital gangrene resulting from hypothenar hammer syndrome successfully treated by intra-arterial autologous bone marrow mononuclear cell transplantation.

Molecular phylogeny of mangroves IV. nature and extent of intra-specific genetic variation and species diversity in mangroves

Energy Technology Data Exchange (ETDEWEB)

Parida, A; Parani, M; Lakshmi, M; Elango, S; Ram, N; Anuratha, C S [M.S. Swaminathan Research Foundation, Taramani, Madras (India)

1998-10-01

Mangroves occupy estuarine ecosystems in the tropical regions of the world. Despite their highly productive nature and the protective roles they play in the coastal region, the ecosystem as a whole is under severe threat due to various climatic and anthropogenic factors. Therefore, the need for conservation of mangroves is widely emphasised. However, information on existing genetic diversity based on which a strategy for genetic conservation is to be drawn is not available for mangroves. This is primarily because conventional genetic analysis is difficult in these species for various reasons. Therefore, as an aid to our on-going conservation programme, efforts were made to assess the nature and extent of diversity in a number of mangrove species of the Indian coast using molecular markers. The nature and extent of intra-population diversity in sixteen mangrove species and detailed analysis of inter-population genetic polymorphism in four species, Acanthus ilicifolius, Excoecaria agallocha, Avicennia spp and Rhizophora (species and hybrid), is reported in the present communication. (author) 25 refs, 2 figs, 2 tabs

A 25 million year macrofloral record (Carboniferous-Permian) in the Czech part of the Intra-Sudetic Basin, biostratigraphy, plant diversity and vegetation patterns

Czech Academy of Sciences Publication Activity Database

Opluštil, S.; Šimůnek, Z.; Pšenička, J.; Bek, Jiří; Libertín, M.

2017-01-01

Roč. 244, SEP 2017 (2017), s. 241-307 ISSN 0034-6667 R&D Projects: GA ČR GAP210/12/2053 Institutional support: RVO:67985831 Keywords : Early Permian * floral zonation * Intra-Sudetic Basin * Pennsylvanian * plant diversity * plant taphonomy * vegetation patterns Subject RIV: DB - Geology ; Mineralogy OBOR OECD: Paleontology Impact factor: 1.817, year: 2016

Genetic Diversity and Phylogenetic Analysis of the Iranian Leishmania Parasites Based on HSP70 Gene PCR-RFLP and Sequence Analysis.

Science.gov (United States)

Nemati, Sara; Fazaeli, Asghar; Hajjaran, Homa; Khamesipour, Ali; Anbaran, Mohsen Falahati; Bozorgomid, Arezoo; Zarei, Fatah

2017-08-01

Despite the broad distribution of leishmaniasis among Iranians and animals across the country, little is known about the genetic characteristics of the causative agents. Applying both HSP70 PCR-RFLP and sequence analyses, this study aimed to evaluate the genetic diversity and phylogenetic relationships among Leishmania spp. isolated from Iranian endemic foci and available reference strains. A total of 36 Leishmania isolates from almost all districts across the country were genetically analyzed for the HSP70 gene using both PCR-RFLP and sequence analysis. The original HSP70 gene sequences were aligned along with homologous Leishmania sequences retrieved from NCBI, and subjected to the phylogenetic analysis. Basic parameters of genetic diversity were also estimated. The HSP70 PCR-RFLP presented 3 different electrophoretic patterns, with no further intraspecific variation, corresponding to 3 Leishmania species available in the country, L. tropica, L. major, and L. infantum. Phylogenetic analyses presented 5 major clades, corresponding to 5 species complexes. Iranian lineages, including L. major, L. tropica, and L. infantum, were distributed among 3 complexes L. major, L. tropica, and L. donovani. However, within the L. major and L. donovani species complexes, the HSP70 phylogeny was not able to distinguish clearly between the L. major and L. turanica isolates, and between the L. infantum, L. donovani, and L. chagasi isolates, respectively. Our results indicated that both HSP70 PCR-RFLP and sequence analyses are medically applicable tools for identification of Leishmania species in Iranian patients. However, the reduced genetic diversity of the target gene makes it inevitable that its phylogeny only resolves the major groups, namely, the species complexes.

Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing

Science.gov (United States)

Yang, Yaping; Muzny, Donna M.; Xia, Fan; Niu, Zhiyv; Person, Richard; Ding, Yan; Ward, Patricia; Braxton, Alicia; Wang, Min; Buhay, Christian; Veeraraghavan, Narayanan; Hawes, Alicia; Chiang, Theodore; Leduc, Magalie; Beuten, Joke; Zhang, Jing; He, Weimin; Scull, Jennifer; Willis, Alecia; Landsverk, Megan; Craigen, William J.; Bekheirnia, Mir Reza; Stray-Pedersen, Asbjorg; Liu, Pengfei; Wen, Shu; Alcaraz, Wendy; Cui, Hong; Walkiewicz, Magdalena; Reid, Jeffrey; Bainbridge, Matthew; Patel, Ankita; Boerwinkle, Eric; Beaudet, Arthur L.; Lupski, James R.; Plon, Sharon E.; Gibbs, Richard A.; Eng, Christine M.

2015-01-01

IMPORTANCE Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders. OBJECTIVE To perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome. DESIGN, SETTING, AND PATIENTS Observational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014. Whole-exome sequencing tests were performed at a clinical genetics laboratory in the United States. Results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics. Tests were ordered by the patient’s physician. The patients were primarily pediatric (1756 [88%]; mean age, 6 years; 888 females [44%], 1101 males [55%], and 11 fetuses [1% gender unknown]), demonstrating diverse clinical manifestations most often including nervous system dysfunction such as developmental delay. MAIN OUTCOMES AND MEASURES Whole-exome sequencing diagnosis rate overall and by phenotypic category, mode of inheritance, spectrum of genetic events, and reporting of incidental findings. RESULTS A molecular diagnosis was reported for 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported. Molecular diagnosis rates for each phenotypic category were 143/526 (27.2%; 95% CI, 23.5%–31.2%) for the neurological group, 282/1147 (24.6%; 95% CI, 22.1%–27.2%) for the neurological plus other organ systems group, 30/83 (36.1%; 95% CI, 26.1%–47.5%) for the specific neurological group, and 49/244 (20.1%; 95% CI, 15.6%–25.8%) for the nonneurological group. The Mendelian disease patterns of the 527 molecular diagnoses included 280 (53.1%) autosomal dominant, 181 (34.3%) autosomal recessive (including 5 with uniparental disomy

Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data.

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Manal Helal

Full Text Available BACKGROUND: The intra- and inter-species genetic diversity of bacteria and the absence of 'reference', or the most representative, sequences of individual species present a significant challenge for sequence-based identification. The aims of this study were to determine the utility, and compare the performance of several clustering and classification algorithms to identify the species of 364 sequences of 16S rRNA gene with a defined species in GenBank, and 110 sequences of 16S rRNA gene with no defined species, all within the genus Nocardia. METHODS: A total of 364 16S rRNA gene sequences of Nocardia species were studied. In addition, 110 16S rRNA gene sequences assigned only to the Nocardia genus level at the time of submission to GenBank were used for machine learning classification experiments. Different clustering algorithms were compared with a novel algorithm or the linear mapping (LM of the distance matrix. Principal Components Analysis was used for the dimensionality reduction and visualization. RESULTS: The LM algorithm achieved the highest performance and classified the set of 364 16S rRNA sequences into 80 clusters, the majority of which (83.52% corresponded with the original species. The most representative 16S rRNA sequences for individual Nocardia species have been identified as 'centroids' in respective clusters from which the distances to all other sequences were minimized; 110 16S rRNA gene sequences with identifications recorded only at the genus level were classified using machine learning methods. Simple kNN machine learning demonstrated the highest performance and classified Nocardia species sequences with an accuracy of 92.7% and a mean frequency of 0.578. CONCLUSION: The identification of centroids of 16S rRNA gene sequence clusters using novel distance matrix clustering enables the identification of the most representative sequences for each individual species of Nocardia and allows the quantitation of inter- and intra

Human MLH1 suppresses the insertion of telomeric sequences at intra-chromosomal sites in telomerase-expressing cells

Science.gov (United States)

Jia, Pingping; Chastain, Megan; Zou, Ying; Her, Chengtao

2017-01-01

Abstract Aberrant formation of interstitial telomeric sequences (ITSs) promotes genome instabilities. However, it is unclear how aberrant ITS formation is suppressed in human cells. Here, we report that MLH1, a key protein involved in mismatch repair (MMR), suppresses telomeric sequence insertion (TSI) at intra-chromosomal regions. The frequency of TSI can be elevated by double-strand break (DSB) inducer and abolished by ATM/ATR inhibition. Suppression of TSI requires MLH1 recruitment to DSBs, indicating that MLH1's role in DSB response/repair is important for suppressing TSI. Moreover, TSI requires telomerase activity but is independent of the functional status of p53 and Rb. Lastly, we show that TSI is associated with chromosome instabilities including chromosome loss, micronuclei formation and chromosome breakage that are further elevated by replication stress. Our studies uncover a novel link between MLH1, telomerase, telomere and genome stability. PMID:28180301

Innovative design for a phase 1 trial with intra-patient dose escalation: The Crotoxin study

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Jacques Medioni

2017-09-01

Full Text Available Introduction: Crotoxin has a broad antitumor activity but has shown frequent neurotoxic toxicity. To induce tolerance and limit this toxicity, we propose a new design with intra-patient dose escalation. Methods: A new Dose Limiting Toxicity definition was used. The concept of Target Ceiling Dose was introduced. Results: Dose Limiting Toxicity was the inability to dose escalate twice. Target Ceiling Dose was the highest planned dose to be administered to a patient and could change for patients along time. Recommended Dose was defined similarly as in a (3 + 3 conventional design. Conclusion: This innovant design was used and the clinical trial is now closed for inclusions. Results will be presented later. Keywords: Clinical trial, Phase 1, Intra-patient dose escalation, Cancer

Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds.

Science.gov (United States)

Guo, H W; Li, C; Wang, X N; Li, Z J; Sun, G R; Li, G X; Liu, X J; Kang, X T; Han, R L

2017-10-01

1. To explore the genetic diversity of Chinese indigenous chicken breeds, a 585 bp fragment of the mitochondrial DNA (mtDNA) region was sequenced in 102 birds from the Xichuan black-bone chicken, Yunyang black-bone chicken and Lushi chicken. In addition, 30 mtDNA D-loop sequences of Silkie fowls were downloaded from NCBI. The mtDNA D-loop sequence polymorphism and maternal origin of 4 chicken breeds were analysed in this study. 2. The results showed that a total of 33 mutation sites and 28 haplotypes were detected in the 4 chicken breeds. The haplotype diversity and nucleotide diversity of these 4 native breeds were 0.916 ± 0.014 and 0.012 ± 0.002, respectively. Three clusters were formed in 4 Chinese native chickens and 12 reference breeds. Both the Xichuan black-bone chicken and Yunyang black-bone chicken were grouped into one cluster. Four haplogroups (A, B, C and E) emerged in the median-joining network in these breeds. 3. It was concluded that these 4 Chinese chicken breeds had high genetic diversity. The phylogenetic tree and median network profiles showed that Chinese native chickens and its neighbouring countries had at least two maternal origins, one from Yunnan, China and another from Southeast Asia or its surrounding area.

Intra-operative warming with a forced-air warmer in preventing hypothermia after tourniquet deflation in elderly patients.

Science.gov (United States)

Kim, Y-S; Jeon, Y-S; Lee, J-A; Park, W-K; Koh, H-S; Joo, J-D; In, J-H; Seo, K-W

2009-01-01

This randomized, single-blind study aimed to explore the effects of intra-operative warming with a forced-air warmer in the prevention of hypothermia after tourniquet deflation in elderly patients undergoing unilateral total knee replacement arthroplasty under general anaesthesia. Patients were randomized to receive either intra-operative warming using a forced-air warmer with an upper body blanket (warming group; n = 12) or no intra-operative warming (nonwarming group; n = 12). Oesophageal temperature was measured as core body temperature. At 30 min following tourniquet inflation, the core body temperature started to increase in the warming group whereas it continued to drop in the non-warming group. This difference was statistically significant. The final core body temperature after tourniquet deflation was significantly higher in the warming group (mean +/- SD 36.1 +/- 0.2 degrees C) than in the non-warming group (35.4 +/- 0.3 degrees C). Intra-operative forced-air warming increased the core body temperature before tourniquet deflation and prevented subsequent hypothermia in elderly patients under general anaesthesia.

Multilocus sequence analysis of Treponema denticola strains of diverse origin

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Mo Sisu

2013-02-01

Full Text Available Abstract Background The oral spirochete bacterium Treponema denticola is associated with both the incidence and severity of periodontal disease. Although the biological or phenotypic properties of a significant number of T. denticola isolates have been reported in the literature, their genetic diversity or phylogeny has never been systematically investigated. Here, we describe a multilocus sequence analysis (MLSA of 20 of the most highly studied reference strains and clinical isolates of T. denticola; which were originally isolated from subgingival plaque samples taken from subjects from China, Japan, the Netherlands, Canada and the USA. Results The sequences of the 16S ribosomal RNA gene, and 7 conserved protein-encoding genes (flaA, recA, pyrH, ppnK, dnaN, era and radC were successfully determined for each strain. Sequence data was analyzed using a variety of bioinformatic and phylogenetic software tools. We found no evidence of positive selection or DNA recombination within the protein-encoding genes, where levels of intraspecific sequence polymorphism varied from 18.8% (flaA to 8.9% (dnaN. Phylogenetic analysis of the concatenated protein-encoding gene sequence data (ca. 6,513 nucleotides for each strain using Bayesian and maximum likelihood approaches indicated that the T. denticola strains were monophyletic, and formed 6 well-defined clades. All analyzed T. denticola strains appeared to have a genetic origin distinct from that of ‘Treponema vincentii’ or Treponema pallidum. No specific geographical relationships could be established; but several strains isolated from different continents appear to be closely related at the genetic level. Conclusions Our analyses indicate that previous biological and biophysical investigations have predominantly focused on a subset of T. denticola strains with a relatively narrow range of genetic diversity. Our methodology and results establish a genetic framework for the discrimination and phylogenetic

Exploring the environmental diversity of kinetoplastid flagellates in the high-throughput DNA sequencing era

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Claudia Masini d’Avila-Levy

2015-01-01

Full Text Available The class Kinetoplastea encompasses both free-living and parasitic species from a wide range of hosts. Several representatives of this group are responsible for severe human diseases and for economic losses in agriculture and livestock. While this group encompasses over 30 genera, most of the available information has been derived from the vertebrate pathogenic genera Leishmaniaand Trypanosoma.Recent studies of the previously neglected groups of Kinetoplastea indicated that the actual diversity is much higher than previously thought. This article discusses the known segment of kinetoplastid diversity and how gene-directed Sanger sequencing and next-generation sequencing methods can help to deepen our knowledge of these interesting protists.

Differential sequence diversity at merozoite surface protein-1 locus of Plasmodium knowlesi from humans and macaques in Thailand.

Science.gov (United States)

Putaporntip, Chaturong; Thongaree, Siriporn; Jongwutiwes, Somchai

2013-08-01

To determine the genetic diversity and potential transmission routes of Plasmodium knowlesi, we analyzed the complete nucleotide sequence of the gene encoding the merozoite surface protein-1 of this simian malaria (Pkmsp-1), an asexual blood-stage vaccine candidate, from naturally infected humans and macaques in Thailand. Analysis of Pkmsp-1 sequences from humans (n=12) and monkeys (n=12) reveals five conserved and four variable domains. Most nucleotide substitutions in conserved domains were dimorphic whereas three of four variable domains contained complex repeats with extensive sequence and size variation. Besides purifying selection in conserved domains, evidence of intragenic recombination scattering across Pkmsp-1 was detected. The number of haplotypes, haplotype diversity, nucleotide diversity and recombination sites of human-derived sequences exceeded that of monkey-derived sequences. Phylogenetic networks based on concatenated conserved sequences of Pkmsp-1 displayed a character pattern that could have arisen from sampling process or the presence of two independent routes of P. knowlesi transmission, i.e. from macaques to human and from human to humans in Thailand. Copyright © 2013 Elsevier B.V. All rights reserved.

Oral treponeme major surface protein: Sequence diversity and distributions within periodontal niches.

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You, M; Chan, Y; Lacap-Bugler, D C; Huo, Y-B; Gao, W; Leung, W K; Watt, R M

2017-12-01

Treponema denticola and other species (phylotypes) of oral spirochetes are widely considered to play important etiological roles in periodontitis and other oral infections. The major surface protein (Msp) of T. denticola is directly implicated in several pathological mechanisms. Here, we have analyzed msp sequence diversity across 68 strains of oral phylogroup 1 and 2 treponemes; including reference strains of T. denticola, Treponema putidum, Treponema medium, 'Treponema vincentii', and 'Treponema sinensis'. All encoded Msp proteins contained highly conserved, taxon-specific signal peptides, and shared a predicted 'three-domain' structure. A clone-based strategy employing 'msp-specific' polymerase chain reaction primers was used to analyze msp gene sequence diversity present in subgingival plaque samples collected from a group of individuals with chronic periodontitis (n=10), vs periodontitis-free controls (n=10). We obtained 626 clinical msp gene sequences, which were assigned to 21 distinct 'clinical msp genotypes' (95% sequence identity cut-off). The most frequently detected clinical msp genotype corresponded to T. denticola ATCC 35405 T , but this was not correlated to disease status. UniFrac and libshuff analysis revealed that individuals with periodontitis and periodontitis-free controls harbored significantly different communities of treponeme clinical msp genotypes (Pdiversity than periodontitis-free controls (Mann-Whitney U-test, Pdiversity of Treponema clinical msp genotypes within their subgingival niches. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Intermediary metabolism in protists: a sequence-based view of facultative anaerobic metabolism in evolutionarily diverse eukaryotes.

Science.gov (United States)

Ginger, Michael L; Fritz-Laylin, Lillian K; Fulton, Chandler; Cande, W Zacheus; Dawson, Scott C

2010-12-01

Protists account for the bulk of eukaryotic diversity. Through studies of gene and especially genome sequences the molecular basis for this diversity can be determined. Evident from genome sequencing are examples of versatile metabolism that go far beyond the canonical pathways described for eukaryotes in textbooks. In the last 2-3 years, genome sequencing and transcript profiling has unveiled several examples of heterotrophic and phototrophic protists that are unexpectedly well-equipped for ATP production using a facultative anaerobic metabolism, including some protists that can (Chlamydomonas reinhardtii) or are predicted (Naegleria gruberi, Acanthamoeba castellanii, Amoebidium parasiticum) to produce H(2) in their metabolism. It is possible that some enzymes of anaerobic metabolism were acquired and distributed among eukaryotes by lateral transfer, but it is also likely that the common ancestor of eukaryotes already had far more metabolic versatility than was widely thought a few years ago. The discussion of core energy metabolism in unicellular eukaryotes is the subject of this review. Since genomic sequencing has so far only touched the surface of protist diversity, it is anticipated that sequences of additional protists may reveal an even wider range of metabolic capabilities, while simultaneously enriching our understanding of the early evolution of eukaryotes. Copyright © 2010 Elsevier GmbH. All rights reserved.

Low level of sequence diversity at merozoite surface protein-1 locus of Plasmodium ovale curtisi and P. ovale wallikeri from Thai isolates.

Science.gov (United States)

Putaporntip, Chaturong; Hughes, Austin L; Jongwutiwes, Somchai

2013-01-01

The merozoite surface protein-1 (MSP-1) is a candidate target for the development of blood stage vaccines against malaria. Polymorphism in MSP-1 can be useful as a genetic marker for strain differentiation in malarial parasites. Although sequence diversity in the MSP-1 locus has been extensively analyzed in field isolates of Plasmodium falciparum and P. vivax, the extent of variation in its homologues in P. ovale curtisi and P. ovale wallikeri, remains unknown. Analysis of the mitochondrial cytochrome b sequences of 10 P. ovale isolates from symptomatic malaria patients from diverse endemic areas of Thailand revealed co-existence of P. ovale curtisi (n = 5) and P. ovale wallikeri (n = 5). Direct sequencing of the PCR-amplified products encompassing the entire coding region of MSP-1 of P. ovale curtisi (PocMSP-1) and P. ovale wallikeri (PowMSP-1) has identified 3 imperfect repeated segments in the former and one in the latter. Most amino acid differences between these proteins were located in the interspecies variable domains of malarial MSP-1. Synonymous nucleotide diversity (πS) exceeded nonsynonymous nucleotide diversity (πN) for both PocMSP-1 and PowMSP-1, albeit at a non-significant level. However, when MSP-1 of both these species was considered together, πS was significantly greater than πN (pdiversity at this locus prior to speciation. Phylogenetic analysis based on conserved domains has placed PocMSP-1 and PowMSP-1 in a distinct bifurcating branch that probably diverged from each other around 4.5 million years ago. The MSP-1 sequences support that P. ovale curtisi and P. ovale wallikeri are distinct species. Both species are sympatric in Thailand. The low level of sequence diversity in PocMSP-1 and PowMSP-1 among Thai isolates could stem from persistent low prevalence of these species, limiting the chance of outcrossing at this locus.

Norrie disease gene sequence variants in an ethnically diverse population with retinopathy of prematurity.

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Hutcheson, Kelly A; Paluru, Prasuna C; Bernstein, Steven L; Koh, Jamie; Rappaport, Eric F; Leach, Richard A; Young, Terri L

2005-07-14

Retinopathy of prematurity (ROP) is a leading cause of visual loss in the pediatric population. Mutations in the Norrie disease gene (NDP) are associated with heritable retinal vascular disorders, and have been found in a small subset of patients with severe retinopathy of prematurity. Varying rates of progression to threshold disease in different races may have a genetic basis, as recent studies suggest that the incidence of NDP mutations may vary in different groups. African Americans, for example, are less likely to develop severe degrees of ROP. We screened a large cohort of ethnically diverse patients for mutations in the entire NDP. A total of 143 subjects of different ethnic backgrounds were enrolled in the study. Fifty-four patients had severe ROP (Stage 3 or worse). Of these, 38 were threshold in at least one eye (with a mean gestational age of 26.1 weeks and mean birth weight of 788.4 g). There were 36 patients with mild or no ROP, 31 parents with no history of retinal disease or prematurity, and 22 wild type (normal) controls. There were 70 African American subjects, 55 Caucasians, and 18 of other races. Severe ROP was noted in 29 African American subjects, 17 Caucasians, and 8 of other races. Seven polymerase chain reaction primer pairs spanning the NDP were optimized for denaturing high performance liquid chromatography and direct sequencing. Three primer pairs covered the coding region, and the remaining four spanned the 3' and 5' untranslated regions (UTR). Six of 54 (11%) infants with severe ROP had polymorphisms in the NDP. Five of the infants were African American, and one was Caucasian. Two parents were heterozygous for the same polymorphism as their child. One parent-child pair had a single base pair (bp) insertion in the 3' UTR region. Another parent-child pair had two mutations: a 14 bp deletion in the 5' UTR region of exon 1 and a single nucleotide polymorphism in the 5' UTR region of exon 2. No coding region sequence changes were found. No

Calf Compartment Syndrome associated with the Use of an Intra-osseous Line in an Adult Patient: A Case Report

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Malhotra R

2016-11-01

Full Text Available We present a case of a lower limb compartment syndrome associated with the use of an intra-osseous line inserted into the proximal tibia in an adult patient. An unconscious 59-year old male with multiple injuries presented to our Emergency Department after a road traffic accident. Bilateral proximal tibial intra osseous-lines were inserted due to poor venous access. After resuscitation his left leg was noted to be tense and swollen with absent pulses. Acute compartment syndrome was diagnosed both clinically and with compartment pressure measurement. Two incision fasciotomy on his left lower leg was performed. Intra osseous-lines in the proximal tibia are increasingly used in adult patients in the pre-hospital setting by paramedics and emergency physicians. Their use, along with the possible complications of these devices, such as the development of compartment syndrome or osteomyelitis leading to amputation, is well reported in the paediatric literature. To the best of our knowledge, there have not been any previous reports of complications in the adult patient. We present a case of lower leg compartment syndrome developing from the use of an intra-osseous line in the proximal tibia in an adult patient. With the increasing use of intra-osseous lines in adult patients, clinicians should be aware of the possibility of developing compartment syndrome which may lead to disability or amputation in severe cases.

Echo-planar magnetic resonance imaging (EPI) with high-resolution matrix in intra-axial brain tumors

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Bruening, R.; Scheidler, J.; Porn, U.; Reiser, M. [Institute of Diagnostic Radiology, Klinikum Grosshadern, University of Munich (Germany); Seelos, K.; Yousry, T. [Department of Neuroradiology, Institute of Diagnostic Radiology, Klinikum Grosshadern, University of Munich (Germany); Exner, H. [Institute for Medical Epidemiology, Klinikum Grosshadern, University of Munich, Munich (Germany); Rosen, B.R. [Department of Radiology, Massachusetts General Hospital, NMR Center, Charlestown, MA (United States)

1999-09-01

The aim of this study was to assess the potential of high-speed interleaved echo-planar imaging (EPI) to achieve diagnostic image quality comparable to T2-weighted imaging in patients with brain tumors. Seventeen patients with intra-axial, supratentorial tumors (10 untreated gliomas, 7 radiated gliomas) were investigated on a 1.5-T scanner. The conventional scan (SE, TR/TE = 2200/80 ms, 18 slices) was acquired in 8 min, 4 s, and EPI (TR/TE = 3000/80 ms, 18 slices) was completed in 25 s. The films were compared in a blinded trail by three radiologists. On the general impression and anatomic display, both sequences were rated to be of similar quality. Artifacts were slightly more pronounced at the skull base and around surgical clips using EPI. Tumor delineation was nearly equivalent using EPI, compared with the T2-weighted sequence. Echo-planar imaging reached diagnostic quality in all patients. Interleaved high-resolution EPI yielded sufficient quality to depict intra-axial, supratentorial brain tumors. Since EPI can be obtained in a small fraction of the time needed for conventional spin echo, in addition to other indications it could be considered to study patients unable to cooperate. (orig.) With 3 figs., 3 tabs., 27 refs.

Intra-cystic concentrations of albendazole-sulphoxide in human cystic echinococcosis: a systematic review and analysis of individual patient data.

Science.gov (United States)

Lötsch, Felix; Naderer, Judith; Skuhala, Tomislava; Groger, Mirjam; Auer, Herbert; Kaczirek, Klaus; Waneck, Fredrik; Ramharter, Michael

2016-08-01

Cystic echinococcosis (CE) is a widespread zoonosis caused by the species complex Echinococcus granulosus. Albendazole (ABZ)-the first-line anthelminthic drug for medical treatment of CE-is metabolized in vivo to the active derivative ABZ-sulphoxide (ABZ-SO). Target-site ABZ-SO concentrations in the hydatid cyst mediate the anthelminthic effect in CE. Primary outcome of this systematic review of individual patient data was the intra-cystic ABZ-SO concentration stratified by cyst size, location, calcification status and use of praziquantel. Studies reporting intra-cystic ABZ-SO concentrations in humans were identified by a systematic search. A pooled analysis of individual patient data was performed to assess intra-cystic concentrations. Pharmacokinetic data of 121 individual cysts were analysed. There was no correlation between plasma and intra-cystic ABZ-SO concentrations (rho = -0.03, p = 0.76). Intra-cystic drug concentrations were also not associated with sex and treatment duration. Use of praziquantel in combination with ABZ was associated with higher plasma (median 540 vs. 240 μg/L; p = 0.04) but not intra-cystic ABZ-SO concentrations (median 220 vs. 199 μg/L; p = 0.36). Relative drug concentrations in hepatic cysts were higher than in other cysts (0.8 vs. 0.4; p = 0.05). Intra-cystic concentrations were higher in calcified than non-calcified cysts (median 897 vs. 245 μg/L; p = 0.03). There was a trend towards higher intra-cystic concentrations in smaller sized cysts (β = -17.2 μg/L/cm; 95th CI, -35.9 to 1.6; p = 0.07). This study demonstrates that mean intra-cystic drug concentrations are similar to plasma concentrations on a population level. However, in individual patients plasma concentrations are not directly predictive for intra-cystic concentrations. The use of booster drugs was not associated with higher intra-cystic ABZ-SO concentrations in this analysis.

Intra-observer and interobserver reliability ofOne Leg Stand Test as a measure of posturalbalance in low back pain patients

DEFF Research Database (Denmark)

Maribo, Thomas; Iversen, Elena; Andersen, Niels Trolle

2009-01-01

Objective: To determine the absolute and relative reliability of intra-observer and interobserver To determine the absolute and relative reliability of intra-observer and interobserver measurements of postural balance using the One Leg Stand Test in patients with low back pain. Patients and methods...... to stand for the maximum time, and no further analysis was done. Eyes closed: intra-observer reliability was tested in 21 patients; absolute reliability showed a standard error of the measurement (SEM) of 2.48 s and a minimal detectable change (MDC) of 6.88. The relative reliability was acceptable...... with an intra class correlation coefficient (ICC) of 0.86. Interobserver reliability was tested in 27 patients; absolute reliability showed a SEM of 1.42 s and a MDC of 3.95. The relative reliability was acceptable with an ICC of 0.91. Conclusions: The One Leg Stand Test can be used to test postural balance...

Untargeted antifungal therapy in adult patients with complicated intra-abdominal infection

DEFF Research Database (Denmark)

Petersen, Marie Warrer; Perner, Anders; Sjövall, Fredrik

2017-01-01

who are critically ill have provided conflicting results, and clinical equipoise exists. Accordingly, we aim to assess patient-important benefits and harms of untargeted antifungal therapy versus placebo or no treatment in adult patients with complicated intra-abdominal infection. Methods and analysis......-cause mortality, and secondary outcomes include adverse events, duration of mechanical ventilation and inotropic support, need for renal replacement therapy, emergence of antibiotic resistance and intensive care unit and hospital length-of-stay. Conventional meta-analysis, including sensitivity and subgroup...

Complete sequence and diversity of a maize-associated Polerovirus in East Africa

Science.gov (United States)

Since 2011-2012, Maize lethal necrosis (MLN) has emerged in East Africa, causing massive yield loss and propelling research to identify viruses and virus populations present in maize. As expected, next generation sequencing (NGS) has revealed diverse and abundant viruses from the family Potyviridae,...

mtDNA sequence diversity of Hazara ethnic group from Pakistan.

Science.gov (United States)

Rakha, Allah; Fatima; Peng, Min-Sheng; Adan, Atif; Bi, Rui; Yasmin, Memona; Yao, Yong-Gang

2017-09-01

The present study was undertaken to investigate mitochondrial DNA (mtDNA) control region sequences of Hazaras from Pakistan, so as to generate mtDNA reference database for forensic casework in Pakistan and to analyze phylogenetic relationship of this particular ethnic group with geographically proximal populations. Complete mtDNA control region (nt 16024-576) sequences were generated through Sanger Sequencing for 319 Hazara individuals from Quetta, Baluchistan. The population sample set showed a total of 189 distinct haplotypes, belonging mainly to West Eurasian (51.72%), East & Southeast Asian (29.78%) and South Asian (18.50%) haplogroups. Compared with other populations from Pakistan, the Hazara population had a relatively high haplotype diversity (0.9945) and a lower random match probability (0.0085). The dataset has been incorporated into EMPOP database under accession number EMP00680. The data herein comprises the largest, and likely most thoroughly examined, control region mtDNA dataset from Hazaras of Pakistan. Copyright © 2017 Elsevier B.V. All rights reserved.

Genetic diversity analysis of Leuconostoc mesenteroides from Korean vegetables and food products by multilocus sequence typing.

Science.gov (United States)

Sharma, Anshul; Kaur, Jasmine; Lee, Sulhee; Park, Young-Seo

2018-06-01

In the present study, 35 Leuconostoc mesenteroides strains isolated from vegetables and food products from South Korea were studied by multilocus sequence typing (MLST) of seven housekeeping genes (atpA, groEL, gyrB, pheS, pyrG, rpoA, and uvrC). The fragment sizes of the seven amplified housekeeping genes ranged in length from 366 to 1414 bp. Sequence analysis indicated 27 different sequence types (STs) with 25 of them being represented by a single strain indicating high genetic diversity, whereas the remaining 2 were characterized by five strains each. In total, 220 polymorphic nucleotide sites were detected among seven housekeeping genes. The phylogenetic analysis based on the STs of the seven loci indicated that the 35 strains belonged to two major groups, A (28 strains) and B (7 strains). Split decomposition analysis showed that intraspecies recombination played a role in generating diversity among strains. The minimum spanning tree showed that the evolution of the STs was not correlated with food source. This study signifies that the multilocus sequence typing is a valuable tool to access the genetic diversity among L. mesenteroides strains from South Korea and can be used further to monitor the evolutionary changes.

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

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Walid Mottawea

2018-05-01

Full Text Available Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella. In this study, the prophage sequence diversity in different Salmonella serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of S. enterica representing 151 Salmonella serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in S. enterica genomes. Prophage sequences were highly variable among S. enterica serovars with a median ± interquartile range (IQR of 5 ± 3 prophage regions per genome. While some prophage sequences were highly conserved among the strains of specific serovars, few regions were lineage specific. Therefore, strains belonging to each serovar could be clustered separately based on their prophage content. Analysis of S. Enteritidis isolates from seven outbreaks generated distinct prophage profiles for each outbreak. Taken altogether, the diversity of the prophage sequences correlates with genome diversity. Prophage repertoires provide an additional marker for differentiating S. enterica subtypes during foodborne outbreaks.

Whole exome sequencing reveals concomitant mutations of multiple FA genes in individual Fanconi anemia patients.

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Chang, Lixian; Yuan, Weiping; Zeng, Huimin; Zhou, Quanquan; Wei, Wei; Zhou, Jianfeng; Li, Miaomiao; Wang, Xiaomin; Xu, Mingjiang; Yang, Fengchun; Yang, Yungui; Cheng, Tao; Zhu, Xiaofan

2014-05-15

Fanconi anemia (FA) is a rare inherited genetic syndrome with highly variable clinical manifestations. Fifteen genetic subtypes of FA have been identified. Traditional complementation tests for grouping studies have been used generally in FA patients and in stepwise methods to identify the FA type, which can result in incomplete genetic information from FA patients. We diagnosed five pediatric patients with FA based on clinical manifestations, and we performed exome sequencing of peripheral blood specimens from these patients and their family members. The related sequencing data were then analyzed by bioinformatics, and the FANC gene mutations identified by exome sequencing were confirmed by PCR re-sequencing. Homozygous and compound heterozygous mutations of FANC genes were identified in all of the patients. The FA subtypes of the patients included FANCA, FANCM and FANCD2. Interestingly, four FA patients harbored multiple mutations in at least two FA genes, and some of these mutations have not been previously reported. These patients' clinical manifestations were vastly different from each other, as were their treatment responses to androstanazol and prednisone. This finding suggests that heterozygous mutation(s) in FA genes could also have diverse biological and/or pathophysiological effects on FA patients or FA gene carriers. Interestingly, we were not able to identify de novo mutations in the genes implicated in DNA repair pathways when the sequencing data of patients were compared with those of their parents. Our results indicate that Chinese FA patients and carriers might have higher and more complex mutation rates in FANC genes than have been conventionally recognized. Testing of the fifteen FANC genes in FA patients and their family members should be a regular clinical practice to determine the optimal care for the individual patient, to counsel the family and to obtain a better understanding of FA pathophysiology.

Prognosis of patients with stage IIIb-IVa squamous cell carcinoma of the cervix following intra-arterial neoadjuvant chemotherapy

International Nuclear Information System (INIS)

Fujiwaki, R.; Maede, Y.; Ohnishi, Y.; Watanabe, Y.; Hata, K.; Miyazaki, K.

1999-01-01

The aim was to determine the long-term prognosis in patients with stage IIIb-IVa squamous cell carcinoma of the cervix who were treated with intra-arterial neoadjuvant chemotherapy (NAC), and to analyze factors related to prognostic value. The authors assessed the disease-free survival of 21 patients with FIGO stage IIIb-IVa squamous cell carcinoma of the cervix treated with intra-arterial NAC followed by irradiation therapy. Before chemotherapy, five factors (age, clinical stage, histologic type, parametrial involvement and serum level of SCC) were evaluated for their correlation with disease-free survival. Univariate Cox's proportional hazard model also demonstrated that age was a significant prognostic factor as a continuous variable. Intra-arterial NAC thus appeared to be effective in treating older patients with stage IIIb-IVa squamous cell carcinoma of the cervix

Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides.

Science.gov (United States)

Brown, Steven D; Utturkar, Sagar M; Klingeman, Dawn M; Johnson, Courtney M; Martin, Stanton L; Land, Miriam L; Lu, Tse-Yuan S; Schadt, Christopher W; Doktycz, Mitchel J; Pelletier, Dale A

2012-11-01

To aid in the investigation of the Populus deltoides microbiome, we generated draft genome sequences for 21 Pseudomonas strains and 19 other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium, and Variovorax were generated.

Intra-individual variability in tinnitus patients : current thoughts and perspectives.

Science.gov (United States)

Dauman, N; Erlandsson, S; Lundlin, L; Dauman, R

2015-04-01

Most tinnitus studies have attempted to compare groups of individuals, thus revealing inter-individuals differences, i.e., variations between compared subjects. For methodological reasons, inter-individual studies cannot take into account the variability of tinnitus experience, which has been known for decades to be relevant in daily practice with tinnitus patients. The concept of intra-individual variability has been promoted in the research literature, in order to shed light on this aspect of individual perception. In previous studies, unrelated to hearing, the concept of intra-individual variability implied inclusion of the environment (i.e., physical and social interactions) as a factor of individual performance. In tinnitus research, we believe that the concept of variability (within a person) could find a place beside the concept of variation (between groups of subjects). In this paper, four perspectives of tinnitus experiences from the clinical and research fields are described: (1) ENT consultation; (2) short-term group psychotherapy; (3) psychodynamic psychotherapy; and (4) clinical psychological research. Intra-individual variability stresses the importance of defining tinnitus in a dynamic way, contrary to the current definition of tinnitus as the perception of sound(s). In clinical practice, it is useful to embrace the perspective of the perceiver of tinnitus, and to include social and cultural circumstances as well as audiological/physical changes.

Genome sequence analysis of five Canadian isolates of strawberry mottle virus reveals extensive intra-species diversity and a longer RNA2 with increased coding capacity compared to a previously characterized European isolate.

Science.gov (United States)

Bhagwat, Basdeo; Dickison, Virginia; Ding, Xinlun; Walker, Melanie; Bernardy, Michael; Bouthillier, Michel; Creelman, Alexa; DeYoung, Robyn; Li, Yinzi; Nie, Xianzhou; Wang, Aiming; Xiang, Yu; Sanfaçon, Hélène

2016-06-01

In this study, we report the genome sequence of five isolates of strawberry mottle virus (family Secoviridae, order Picornavirales) from strawberry field samples with decline symptoms collected in Eastern Canada. The Canadian isolates differed from the previously characterized European isolate 1134 in that they had a longer RNA2, resulting in a 239-amino-acid extension of the C-terminal region of the polyprotein. Sequence analysis suggests that reassortment and recombination occurred among the isolates. Phylogenetic analysis revealed that the Canadian isolates are diverse, grouping in two separate branches along with isolates from Europe and the Americas.

Intra-specific diversity of Serratia marcescens in Anopheles mosquito midgut defines Plasmodium transmission capacity

Science.gov (United States)

Bando, Hironori; Okado, Kiyoshi; Guelbeogo, Wamdaogo M.; Badolo, Athanase; Aonuma, Hiroka; Nelson, Bryce; Fukumoto, Shinya; Xuan, Xuenan; Sagnon, N'Fale; Kanuka, Hirotaka

2013-01-01

A critical stage in malaria transmission occurs in the Anopheles mosquito midgut, when the malaria parasite, Plasmodium, ingested with blood, first makes contact with the gut epithelial surface. To understand the response mechanisms within the midgut environment, including those influenced by resident microbiota against Plasmodium, we focus on a midgut bacteria species' intra-specific variation that confers diversity to the mosquito's competency for malaria transmission. Serratia marcescens isolated from either laboratory-reared mosquitoes or wild populations in Burkina Faso shows great phenotypic variation in its cellular and structural features. Importantly, this variation is directly correlated with its ability to inhibit Plasmodium development within the mosquito midgut. Furthermore, this anti-Plasmodium function conferred by Serratia marcescens requires increased expression of the flagellum biosynthetic pathway that is modulated by the motility master regulatory operon, flhDC. These findings point to new strategies for controlling malaria through genetic manipulation of midgut bacteria within the mosquito. PMID:23571408

Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides

Energy Technology Data Exchange (ETDEWEB)

Brown, Steven D [ORNL; Utturkar, Sagar M [ORNL; Klingeman, Dawn Marie [ORNL; Johnson, Courtney M [ORNL; Martin, Stanton [ORNL; Land, Miriam L [ORNL; Lu, Tse-Yuan [ORNL; Schadt, Christopher Warren [ORNL; Doktycz, Mitchel John [ORNL; Pelletier, Dale A [ORNL

2012-01-01

To aid in the investigation of the Populus deltoides microbiome we generated draft genome sequences for twenty one Pseudomonas and twenty one other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Burkholderia, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium and Variovorax were generated.

Ultra-deep sequencing reveals the subclonal structure and genomic evolution of oral squamous cell carcinoma

DEFF Research Database (Denmark)

Tabatabaeifar, Siavosh; Thomassen, Mads; Larsen, Martin Jakob

Background: Oral squamous cell carcinoma (OSCC), a subgroup of head and neck squamous cell carcinoma (HNSCC), is primarily caused by alcohol consumption and tobacco use. Recent DNA sequencing studies suggests that HNSCC are very heterogeneous between patients; however the intra-patient subclonal...

HIV sequence diversity during the early phase of infection is associated with HIV DNA reductions during antiretroviral therapy.

Science.gov (United States)

Wang, Nidan; Li, Yijia; Han, Yang; Xie, Jing; Li, Taisheng

2017-06-01

The association between baseline human immunodeficiency virus (HIV) sequence diversity and HIV DNA decay after the initiation of antiretroviral therapy (ART) remains uncharacterized during the early stages of HIV infection. Samples were obtained from a cohort of 17 patients with early HIV infection (HIV-1 envelope (env) gene was amplified via single genome amplification (SGA) to determine the peripheral plasma HIV quasispecies. We categorized HIV quasispecies into two groups according to baseline viral sequence genetic distance, which was determined by the Poisson-Fitter tool. Total HIV DNA in peripheral blood mononuclear cells (PBMCs), viral load, and T cell subsets were measured prior to and after the initiation of ART. The median SGA sequence number was 17 (range 6-28). At baseline, we identified 7 patients with homogeneous viral populations (designated the Homogeneous group) and 10 patients with heterogeneous viral populations (designated the Heterogeneous group) based on SGA sequences. Both groups exhibited similar HIV DNA decay rates during the first 6 months of ART (P > 0.99), but the Homogenous group experienced more prominent decay than the Heterogeneous group after 6 months (P = 0.037). The Heterogeneous group had higher CD4 cell counts after ART initiation; however, both groups had comparable recovery in terms of CD4/CD8 ratios and CD8 T cell activation levels. Viral population homogeneity upon the initiation of ART is associated with a decrease in HIV DNA levels during ART. J. Med. Virol. 89:982-988, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

High levels of diversity characterize mandrill (Mandrillus sphinx) Mhc-DRB sequences.

Science.gov (United States)

Abbott, Kristin M; Wickings, E Jean; Knapp, Leslie A

2006-08-01

The major histocompatibility complex (MHC) is highly polymorphic in most primate species studied thus far. The rhesus macaque (Macaca mulatta) has been studied extensively and the Mhc-DRB region demonstrates variability similar to humans. The extent of MHC diversity is relatively unknown for other Old World monkeys (OWM), especially among genera other than Macaca. A molecular survey of the Mhc-DRB region in mandrills (Mandrillus sphinx) revealed extensive variability, suggesting that other OWMs may also possess high levels of Mhc-DRB polymorphism. In the present study, 33 Mhc-DRB loci were identified from only 13 animals. Eleven were wild-born and presumed to be unrelated and two were captive-born twins. Two to seven different sequences were identified for each individual, suggesting that some mandrills may have as many as four Mhc-DRB loci on a single haplotype. From these sequences, representatives of at least six Mhc-DRB loci or lineages were identified. As observed in other primates, some new lineages may have arisen through the process of gene conversion. These findings indicate that mandrills have Mhc-DRB diversity not unlike rhesus macaques and humans.

Cytogenetic Diversity of Simple Sequences Repeats in Morphotypes of Brassica rapa ssp. chinensis.

Science.gov (United States)

Zheng, Jin-Shuang; Sun, Cheng-Zhen; Zhang, Shu-Ning; Hou, Xi-Lin; Bonnema, Guusje

2016-01-01

A significant fraction of the nuclear DNA of all eukaryotes is comprised of simple sequence repeats (SSRs). Although these sequences are widely used for studying genetic variation, linkage mapping and evolution, little attention had been paid to the chromosomal distribution and cytogenetic diversity of these sequences. In this paper, we report the distribution characterization of mono-, di-, and tri-nucleotide SSRs in Brassica rapa ssp. chinensis. Fluorescence in situ hybridization was used to characterize the cytogenetic diversity of SSRs among morphotypes of B. rapa ssp. chinensis. The proportion of different SSR motifs varied among morphotypes of B. rapa ssp. chinensis, with tri-nucleotide SSRs being more prevalent in the genome of B. rapa ssp. chinensis. We determined the chromosomal locations of mono-, di-, and tri-nucleotide repeat loci. The results showed that the chromosomal distribution of SSRs in the different morphotypes is non-random and motif-dependent, and allowed us to characterize the relative variability in terms of SSR numbers and similar chromosomal distributions in centromeric/peri-centromeric heterochromatin. The differences between SSR repeats with respect to abundance and distribution indicate that SSRs are a driving force in the genomic evolution of B. rapa species. Our results provide a comprehensive view of the SSR sequence distribution and evolution for comparison among morphotypes B. rapa ssp. chinensis.

Efficacy and safety of combining intra-articular methylprednisolone and anti-TNF agent to achieve prolonged remission in patients with recurrent inflammatory monoarthritis.

LENUS (Irish Health Repository)

Haroon, Muhammad

2012-02-01

OBJECTIVE: To control local inflammation, the role of intra-articular corticosteroid is well established; similarly, with time there are more reports on the experience of intra-articular anti-TNF agent for localized joint inflammation. The aim of this study was to assess the safety, local tolerability and clinical response after combining intra-articular administration of corticosteroids and anti-TNF agents for recurrent inflammatory monoarthritis. METHODS: Patients with recurrent monoarthritis of the knee were recruited from our inflammatory arthritis clinics. These patients required intra-articular corticosteroids every 8-12 weeks, with good short-term results. Five such consecutive patients were invited to partake in this study. Patients were maintained on their baseline immunosuppressive therapy. After aspiration of knee joint, the involved joint was injected with 80mg of methylprednisolone mixed with 5ml of lignocaine 1%; this was followed by the injection of an anti-TNF agent. RESULTS: In majority of our patients (three out of five), combining anti-TNF agent and methylprednisolone led to prolonged anti-inflammatory response, and these patients remain in remission to date (mean follow-up of 12 months). These responders were noted to be naive to anti-TNF therapy. Conversely, the remaining two patients were found to be on baseline systemic anti-TNF therapy, and both of them failed to respond either partly or completely. CONCLUSION: Combining intra-articular corticosteroid and anti-TNF agent has proved to be safe in our cohort of patients. We conclude that in particular subset of patients who suffer from recurrent inflammatory monoarthritis or oligoarthritis, combination therapy of intra-articular corticosteroids and anti-TNF agents appears attractive and promising.

High diversity of picornaviruses in rats from different continents revealed by deep sequencing.

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Hansen, Thomas Arn; Mollerup, Sarah; Nguyen, Nam-Phuong; White, Nicole E; Coghlan, Megan; Alquezar-Planas, David E; Joshi, Tejal; Jensen, Randi Holm; Fridholm, Helena; Kjartansdóttir, Kristín Rós; Mourier, Tobias; Warnow, Tandy; Belsham, Graham J; Bunce, Michael; Willerslev, Eske; Nielsen, Lars Peter; Vinner, Lasse; Hansen, Anders Johannes

2016-08-17

Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler's encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.

Wider-community Segregation and the Effect of Neighbourhood Ethnic Diversity on Social Capital: An Investigation into Intra-Neighbourhood Trust in Great Britain and London.

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Laurence, James

2017-10-01

Extensive research has demonstrated that neighbourhood ethnic diversity is negatively associated with intra-neighbourhood social capital. This study explores the role of segregation and integration in this relationship. To do so it applies three-level hierarchical linear models to two sets of data from across Great Britain and within London, and examines how segregation across the wider-community in which a neighbourhood is nested impacts trust amongst neighbours. This study replicates the increasingly ubiquitous finding that neighbourhood diversity is negatively associated with neighbour-trust. However, we demonstrate that this relationship is highly dependent on the level of segregation across the wider-community in which a neighbourhood is nested. Increasing neighbourhood diversity only negatively impacts neighbour-trust when nested in more segregated wider-communities. Individuals living in diverse neighbourhoods nested within integrated wider-communities experience no trust-penalty. These findings show that segregation plays a critical role in the neighbourhood diversity/trust relationship, and that its absence from the literature biases our understanding of how ethnic diversity affects social cohesion.

Sequence-Based Discovery Demonstrates That Fixed Light Chain Human Transgenic Rats Produce a Diverse Repertoire of Antigen-Specific Antibodies

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Katherine E. Harris

2018-04-01

Full Text Available We created a novel transgenic rat that expresses human antibodies comprising a diverse repertoire of heavy chains with a single common rearranged kappa light chain (IgKV3-15-JK1. This fixed light chain animal, called OmniFlic, presents a unique system for human therapeutic antibody discovery and a model to study heavy chain repertoire diversity in the context of a constant light chain. The purpose of this study was to analyze heavy chain variable gene usage, clonotype diversity, and to describe the sequence characteristics of antigen-specific monoclonal antibodies (mAbs isolated from immunized OmniFlic animals. Using next-generation sequencing antibody repertoire analysis, we measured heavy chain variable gene usage and the diversity of clonotypes present in the lymph node germinal centers of 75 OmniFlic rats immunized with 9 different protein antigens. Furthermore, we expressed 2,560 unique heavy chain sequences sampled from a diverse set of clonotypes as fixed light chain antibody proteins and measured their binding to antigen by ELISA. Finally, we measured patterns and overall levels of somatic hypermutation in the full B-cell repertoire and in the 2,560 mAbs tested for binding. The results demonstrate that OmniFlic animals produce an abundance of antigen-specific antibodies with heavy chain clonotype diversity that is similar to what has been described with unrestricted light chain use in mammals. In addition, we show that sequence-based discovery is a highly effective and efficient way to identify a large number of diverse monoclonal antibodies to a protein target of interest.

Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica.

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Shui-Lian He

Full Text Available Foxtail millet (Setaria italica (L. Beauv is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1 in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.

Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica).

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He, Shui-Lian; Yang, Yang; Morrell, Peter L; Yi, Ting-Shuang

2015-01-01

Foxtail millet (Setaria italica (L.) Beauv) is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP) and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1) in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.

An evaluation of the sociodemographic determinants of dental anxiety in patients scheduled for intra-alveolar extraction

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Peter E. Egbor

2014-09-01

Full Text Available Background: Studies on anxiety in patients having intra-alveolar extraction as well as the effect of patient's sociodemographic characteristics influencing level of associated anxiety are few in our environment. The aim of this study was to statistically analyze the sociodemographic determinants of dental anxiety in patients scheduled for intra-alveolar extraction. Methods: A cross-sectional study was conducted among 93 consecutive patients attending the outpatient clinic of the Department of Maxillofacial Surgery, University of Benin Teaching Hospital for intra-alveolar extraction in the months of November and December 2013. An interview-based questionnaire, Corah Dental Anxiety Scale Revised (DAS-R, was administered to evaluate levels of dental anxiety. Sociodemographic characteristics of the subjects were recorded. Descriptive statistics and regression models were done with the independent variables (sociodemographic factors and the dependent variable being the DAS-R. A P<0.05 was considered significant. Results: The internal consistency of the scale used as determined by Cronbach alpha was 0.76. Mean DAS score was 8.12±2.58. Dental anxiety and age of subjects showed significant inverse relationship. Females had a higher mean DAS score (8.76 than the males (7.37 (P=0.006. Residence (urban/rural was not statistically significant. Singles reported the highest DAS score (9.41 (P=0.006. The educational level attained was significantly related to dental anxiety (P=0.005. Those with secondary school education had the highest DAS score (9.26. Class V social status had the highest mean anxiety score (P=0.012. Stepwise linear regression showed that the best predictors for dental anxiety were sex (P=0.008 and marital status (P=0.026. Conclusion: This present study demonstrates that sex and marital status are the predictive factors for dental anxiety in the overall management of patients indicated for intra-alveolar extraction.

The Subclonal Structure and Genomic Evolution of Oral Squamous Cell Carcinoma Revealed by Ultra-deep Sequencing

DEFF Research Database (Denmark)

Tabatabaeifar, Siavosh; Thomassen, Mads; Larsen, Martin Jakob

Background: Oral squamous cell carcinoma (OSCC), a subgroup of head and neck squamous cell carcinoma (HNSCC), is primarily caused by alcohol consumption and tobacco use. Recent DNA sequencing studies suggests that HNSCC are very heterogeneous between patients; however the intra-patient subclonal...

Genome sequence diversity and clues to the evolution of variola (smallpox) virus.

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Esposito, Joseph J; Sammons, Scott A; Frace, A Michael; Osborne, John D; Olsen-Rasmussen, Melissa; Zhang, Ming; Govil, Dhwani; Damon, Inger K; Kline, Richard; Laker, Miriam; Li, Yu; Smith, Geoffrey L; Meyer, Hermann; Leduc, James W; Wohlhueter, Robert M

2006-08-11

Comparative genomics of 45 epidemiologically varied variola virus isolates from the past 30 years of the smallpox era indicate low sequence diversity, suggesting that there is probably little difference in the isolates' functional gene content. Phylogenetic clustering inferred three clades coincident with their geographical origin and case-fatality rate; the latter implicated putative proteins that mediate viral virulence differences. Analysis of the viral linear DNA genome suggests that its evolution involved direct descent and DNA end-region recombination events. Knowing the sequences will help understand the viral proteome and improve diagnostic test precision, therapeutics, and systems for their assessment.

Levels of Intra-specific AFLP Diversity in Tuber-Bearing Potato Species with Different Breeding Systems and Ploidy Levels

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Glenn J. Bryan

2017-09-01

Full Text Available DNA-based marker analysis of plant genebank material has become a useful tool in the evaluation of levels of genetic diversity and for the informed use and maintenance of germplasm. In this study, we quantify levels of amplified fragment length polymorphism (AFLP in representative accessions of wild and cultivated potato species of differing geographic origin, ploidy, and breeding system. We generated 449 polymorphic AFLP fragments in 619 plants, representing multiple plants (16–23 from 17 accessions of 14 potato taxa as well as single plants sampled from available accessions (from 3 to 56 of the same 14 taxa. Intra-accession diversities were compared to those of a synthetic ‘taxon-wide’ population comprising a single individual from a variable number of available accessions of each sampled taxon. Results confirm the expected considerably lower levels of polymorphism within accessions of self-compatible as compared to self-incompatible taxa. We observed broadly similar levels of ‘taxon-wide’ polymorphism among self-compatible and self-incompatible species, with self-compatible taxa showing only slightly lower rates of polymorphism. The most diverse accessions were the two cultivated potato accessions examined, the least diverse being the Mexican allohexaploids Solanum demissum and S. iopetalum. Generally allopolyploid self-compatible accessions exhibited lower levels of diversity. Some purported self-incompatible accessions showed relatively low levels of marker diversity, similar to the more diverse self-compatible material surveyed. Our data indicate that for self-compatible species a single plant is highly representative of a genebank accession. The situation for self-incompatible taxa is less clear, and sampling strategies used will depend on the type of investigation. These results have important implications for those seeking novel trait variation (e.g., disease resistance in gene banks as well as for the selection of individuals

Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture.

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Alicia R Martin

2014-08-01

Full Text Available Large-scale sequencing efforts have documented extensive genetic variation within the human genome. However, our understanding of the origins, global distribution, and functional consequences of this variation is far from complete. While regulatory variation influencing gene expression has been studied within a handful of populations, the breadth of transcriptome differences across diverse human populations has not been systematically analyzed. To better understand the spectrum of gene expression variation, alternative splicing, and the population genetics of regulatory variation in humans, we have sequenced the genomes, exomes, and transcriptomes of EBV transformed lymphoblastoid cell lines derived from 45 individuals in the Human Genome Diversity Panel (HGDP. The populations sampled span the geographic breadth of human migration history and include Namibian San, Mbuti Pygmies of the Democratic Republic of Congo, Algerian Mozabites, Pathan of Pakistan, Cambodians of East Asia, Yakut of Siberia, and Mayans of Mexico. We discover that approximately 25.0% of the variation in gene expression found amongst individuals can be attributed to population differences. However, we find few genes that are systematically differentially expressed among populations. Of this population-specific variation, 75.5% is due to expression rather than splicing variability, and we find few genes with strong evidence for differential splicing across populations. Allelic expression analyses indicate that previously mapped common regulatory variants identified in eight populations from the International Haplotype Map Phase 3 project have similar effects in our seven sampled HGDP populations, suggesting that the cellular effects of common variants are shared across diverse populations. Together, these results provide a resource for studies analyzing functional differences across populations by estimating the degree of shared gene expression, alternative splicing, and

Intra-procedural continuous dialysis to facilitate interventional catheterization in pediatric patients with severe renal failure.

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Opina, Angeline D; Qureshi, Athar M; Brewer, Eileen; Elenberg, Ewa; Swartz, Sarah; Michael, Mini; Justino, Henri

2017-11-01

Interventional catheterization procedures may be needed for patients with severe renal failure who are dependent on dialysis. To avoid the risk of fluid overload and electrolyte derangement during complex procedures in this oliguric/anuric patient population, we performed intra-procedural dialysis, either continuous renal replacement therapy (CRRT) or continous cycling peritoneal dialysis (CCPD). We performed a retrospective review of a cohort of pediatric patients, ages 0-18 years, with dialysis-dependent renal failure who received CRRT or CCPD during catheterization procedures from January 2013 to March 2016. Eight patients underwent a total of nine interventional catheterization procedures while receiving intra-procedural dialysis. Median age was 4.5 years (range 8 months to 17 years) and weight, 11.6 kg (11.2-62.6 kg). Six patients had end-stage renal disease (ESRD) and two patients had acute kidney injury (AKI), one due to hepatorenal syndrome and one due to multifactorial causes associated with congenital heart disease. The most common reason for catheterization was occlusive venous thrombosis requiring recanalization. CRRT was used during five cases and CCPD during four cases. Median procedure time was 337 min (95-651 min) and median contrast dose 4.2 mL kg -1 (1.2-8.2 mL kg -1 ). Euvolemia was maintained based on pre- and post-catheterizations weights, and no significant electrolyte abnormalities occurred based on lab monitoring during and post-procedure. Intra-procedural dialysis using CRRT or CCPD enables even small pediatric patients with severe renal failure to undergo long and complex interventional catheterizations by reducing the risk of fluid overload and electrolyte abnormalities. Collaboration between nephrology, cardiology, and dialysis teams is necessary for successful management of this challenging patient population. © 2017 Wiley Periodicals, Inc.

Experience with Extra Hepatic Intra Abdominal Hydatid Cyst

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Altaf Ahmed Talpur

2016-10-01

showed hydatid cyst spleen in 02 (18.1% patients, epigastrium in 04 (36.3% patients, beneath left crus of diaphragm in 02 (18.1% patients & right iliac fossa & pelvis in 1 (9.09% patient. In 02 (18.1% patients multiple Hydatid cysts were noted. Hydatid cysts liver found in 07 (63.6% patients. C.T scan Abdomen was performed in 09 (81.8% patients. Surgical procedures performed include Saucerization & omental packing in liver Hydatid cysts; Splenectomy for Splenic disease & complete excision of remaining intra-abdominal Hydatid cysts. Postoperative complications noted in 05 (45.4% patients. Conclusion: Extra hepatic intra abdominal is an infrequent disease presents signicant diagnostic & therapeutic challenge for surgeons.  Keywords: extra hepatic; hydatid disease; intra abdominal.

Intra-Hospital Outcomes in ST Elevation Myocardial Infarction: Comparison of Diabetic and Non-Diabetic Patients

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Toba Kazemi

2015-12-01

Full Text Available We read the interesting article entitled “the Effect of Diabetes Mellitus on Short Term Mortality and Morbidity after Isolated Coronary Artery Bypass Grafting Surgery” (1. We performed a study on intra-hospital complications in diabetic and non-diabetic patients with Acute Myocardial Infarction (AMI in Birjand, east of Iran in 2012. In our study, 479 patients with AMI (243 diabetics and 236 non-diabetics were assessed. The subjects’ mean age was 61.95 ± 13.18 years. Assessment of intra-hospital complications in the two groups revealed that recurrent angina and mortality were significantly higher in the diabetics compared to the non-diabetics (52.5% vs. 39.3%, P = 0.009; 11.2% vs. 2.6%, P = 0.012, respectively. Besides, the mean Ejection Fraction (EF was lower in the diabetics in comparison to the non-diabetics (45.26 ± 11.37% vs. 49.98 ± 10.39%, P = 0.014. Moreover, the incidence rates of intra-hospital mortality and heart failure were higher in the diabetics with AMI. This can be due to the higher prevalence of the associated risk factors, such as hypertension, dyslipidemia, and hyperglycemia, in diabetic patients and their effects on the heart. Hyperglycemia occurring after AMI is a strong and independent prognostic marker of post-MI complications. Stress, which occurs following AMI, increases insulin resistance and hyperglycemia and decreases glucose tolerance. Un-controlled diabetes in patients having AMI is accompanied by an unfavorable prognosis and may increase the risk of life-threatening complications (2. The increased risk of complications can be a possible explanation for the increase in intra-hospital mortality after AMI is diabetic patients. Various studies have indicated that initial hyperglycemia associated with failure of ST segment resolution after streptokinase infusion is followed by more extensive infarction revealed in Single-Photon Emission Computerized Tomography (SPECT, less blood flow in coronary arteries in

INTRA-ABDOMINAL HYPERTENSION AS A RISK FACTOR FOR ACUTE KIDNEY INJURY IN CRITICALLY ILL PATIENTS

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Sreelatha

2016-05-01

Full Text Available BACKGROUND AND AIMS Increased intra-abdominal pressure (IAP, also referred to as intra-abdominal hypertension (IAH, affects organ function in critically ill patients. The prevalence of IAH is between 32% - 65% in intensive care units. Normal IAP is ≈ 5–7 mmHg. According to WSACS definition, IAH = IAP ≥12 mmHg and is divided into 4 grades. They are Grade I (12-15 mmHg, Grade II (16-20 mmHg, Grade III (21-25 mmHg, Grade IV (>25 mmHg. Transvesical measurement of IAP currently is the most popular technique. Several systems with or without the need for electronic equipment are available that allow IAP measurement. The aim is to study the incidence of IAH in critically ill patients, to assess the risk factors for development of IAH, to study the role of IAH as a risk factor for Acute Kidney Injury (AKI, to assess the role of IAH as a risk factor for increased (Intensive Care Unit ICU mortality. SUBJECTS AND METHODS This is a prospective observational study. Study period was six months. The study included 52 patients admitted to Medical ICU in Government Medical College, Kozhikode, Kerala. RESULTS AND CONCLUSION There was a very high incidence of intra-abdominal hypertension in critically ill patients. IAH was significantly associated with risk factors like sepsis, mechanical ventilation, pancreatitis, capillary leak, ascites, cumulative fluid balance and cirrhosis. IAH is an independent risk factor for development of acute kidney injury. IAH is an independent predictor of mortality in critically ill patients.

K-shuff: A Novel Algorithm for Characterizing Structural and Compositional Diversity in Gene Libraries.

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Jangid, Kamlesh; Kao, Ming-Hung; Lahamge, Aishwarya; Williams, Mark A; Rathbun, Stephen L; Whitman, William B

2016-01-01

K-shuff is a new algorithm for comparing the similarity of gene sequence libraries, providing measures of the structural and compositional diversity as well as the significance of the differences between these measures. Inspired by Ripley's K-function for spatial point pattern analysis, the Intra K-function or IKF measures the structural diversity, including both the richness and overall similarity of the sequences, within a library. The Cross K-function or CKF measures the compositional diversity between gene libraries, reflecting both the number of OTUs shared as well as the overall similarity in OTUs. A Monte Carlo testing procedure then enables statistical evaluation of both the structural and compositional diversity between gene libraries. For 16S rRNA gene libraries from complex bacterial communities such as those found in seawater, salt marsh sediments, and soils, K-shuff yields reproducible estimates of structural and compositional diversity with libraries greater than 50 sequences. Similarly, for pyrosequencing libraries generated from a glacial retreat chronosequence and Illumina® libraries generated from US homes, K-shuff required >300 and 100 sequences per sample, respectively. Power analyses demonstrated that K-shuff is sensitive to small differences in Sanger or Illumina® libraries. This extra sensitivity of K-shuff enabled examination of compositional differences at much deeper taxonomic levels, such as within abundant OTUs. This is especially useful when comparing communities that are compositionally very similar but functionally different. K-shuff will therefore prove beneficial for conventional microbiome analysis as well as specific hypothesis testing.

Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus)

Science.gov (United States)

2011-01-01

Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58), we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP) were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of ompA as a fine

Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus

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Timms Peter

2011-04-01

Full Text Available Abstract Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58, we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of

[Influence of PCR cycle number on microbial diversity analysis through next generation sequencing].

Science.gov (United States)

An, Yunhe; Gao, Lijuan; Li, Junbo; Tian, Yanjie; Wang, Jinlong; Zheng, Xuejuan; Wu, Huijuan

2016-08-25

Using of high throughput sequencing technology to study the microbial diversity in complex samples has become one of the hottest issues in the field of microbial diversity research. In this study, the soil and sheep rumen chyme samples were used to extract DNA, respectively. Then the 25 ng total DNA was used to amplify the 16S rRNA V3 region with 20, 25, 30 PCR cycles, and the final sequencing library was constructed by mixing equal amounts of purified PCR products. Finally, the operational taxonomic unit (OUT) amount, rarefaction curve, microbial number and species were compared through data analysis. It was found that at the same amount of DNA template, the proportion of the community composition was not the best with more numbers of PCR cycle, although the species number was much more. In all, when the PCR cycle number is 25, the number of species and proportion of the community composition were the most optimal both in soil or chyme samples.

Refining intra-protein contact prediction by graph analysis

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Eyal Eran

2007-05-01

Full Text Available Abstract Background Accurate prediction of intra-protein residue contacts from sequence information will allow the prediction of protein structures. Basic predictions of such specific contacts can be further refined by jointly analyzing predicted contacts, and by adding information on the relative positions of contacts in the protein primary sequence. Results We introduce a method for graph analysis refinement of intra-protein contacts, termed GARP. Our previously presented intra-contact prediction method by means of pair-to-pair substitution matrix (P2PConPred was used to test the GARP method. In our approach, the top contact predictions obtained by a basic prediction method were used as edges to create a weighted graph. The edges were scored by a mutual clustering coefficient that identifies highly connected graph regions, and by the density of edges between the sequence regions of the edge nodes. A test set of 57 proteins with known structures was used to determine contacts. GARP improves the accuracy of the P2PConPred basic prediction method in whole proteins from 12% to 18%. Conclusion Using a simple approach we increased the contact prediction accuracy of a basic method by 1.5 times. Our graph approach is simple to implement, can be used with various basic prediction methods, and can provide input for further downstream analyses.

Medical complications of intra-hospital patient transports: implications for architectural design and research.

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Ulrich, Roger S; Zhu, Xuemei

2007-01-01

Literature on healthcare architecture and evidence-based design has rarely considered explicitly that patient outcomes may be worsened by intra-hospital transport (IHT), which is defined as transport of patients within the hospital. The article focuses on the effects of IHTs on patient complications and outcomes, and the implications of such impacts for designing safer, better hospitals. A review of 22 scientific studies indicates that IHTs are subject to a wide range of complications, many of which occur frequently and have distinctly detrimental effects on patient stability and outcomes. The research suggests that higher patient acuity and longer transport durations are associated with more frequent and serious IHT-related complications and outcome effects. It appears no rigorous research has compared different hospital designs and layouts with respect to having possibly differential effects on transport-related complications and worsened outcomes. Nonetheless, certain design implications can be extracted from the existing research literature, including the importance of minimizing transport delays due to restricted space and congestion, and creating layouts that shorten IHT times for high-acuity patients. Limited evidence raises the possibility that elevator-dependent vertical building layouts may increase susceptibility to transport delays that worsen complications. The strong evidence indicating that IHTs trigger complications and worsen outcomes suggests a powerful justification for adopting acuity-adaptable rooms and care models that substantially reduce transports. A program of studies is outlined to address gaps in knowledge.Key WordsPatient transports, transports within hospitals, patient safety, evidence-based design, hospital design, healthcare architecture, intra-hospital transport complications, acuity-adaptable care, elevators, outcomes.

Comparison of preoperative computerized tomography scan imaging of temporal bone with the intra-operative findings in patients undergoing mastiodectomy

International Nuclear Information System (INIS)

Gerami, H.; Naghavi, E.; Wahabi-Moghadam, M.; Forghanparast, K.; Akbar, Manzar H.

2009-01-01

Objective was to compare the consistency rates of pre- and intra-operative radiological findings in patients with chronic suppurative otitis media (CSOM). In a cross-sectional study, 80 patients with CSOM underwent pre-operative CT scanning and we compared the results with intra-operative clinical findings during mastiodectomy from 2000-2004 in the Otology Department, Amiralmomenin Hospital of Guilan Medical University, Rasht, Iran. Sensitivity, specificity, positive and negative predictive value of CT scan in tympanic and mastoid cholesteatoma, ossicular chain erosion, tegmentympani erosion, dehiscence of facial canal, lateral semicircular canal (LSCC) fistula were assessed. Then, correlation between radiological findings and intra-operative findings were calculated. The mean age of patients was 27.9+-16.3 years. Mostly were males (n=57 [71.3%]). Correlation of preoperative radiological images with intra-operative clinical findings were moderate to good on tympanic cholesteatoma, mastoid cholesteatoma and ossicular chain erosion, but weak and insignificant in cases of tegmen erosion, facial canal dehiscene and LSCC fistulae. Preoperative CT scan may be helpful in decision-making for surgery in cases of cholesteatoma and ossicular erosion. Despite of limitations radiological scanning is a useful adjunct to management of CSOM. (author)

AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.

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Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

2014-01-01

A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php.

Safety and Efficacy of Intra-articular Injection of Platelet-Rich Plasma in Patients With Ankle Osteoarthritis.

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Fukawa, Taisuke; Yamaguchi, Satoshi; Akatsu, Yorikazu; Yamamoto, Yohei; Akagi, Ryuichiro; Sasho, Takahisa

2017-06-01

An intra-articular injection of platelet-rich plasma (PRP) may be an effective treatment for osteoarthritis (OA). However, its efficacy in ankle OA has not been investigated yet. The purpose of this study was to assess the safety and efficacy of an intra-articular injection of PRP in patients with ankle OA during a 24-week period. Twenty ankles of 20 patients with varus-type ankle OA who received intra-articular injections of PRP were evaluated. PRP was extracted from whole blood by using the double-spin technique. Three injections of 2-mL PRP were administered to the ankle at an interval of 2 weeks under ultrasonographic guidance. Adverse events and efficacy were assessed at 4, 12, and 24 weeks after the last injection. Clinical outcomes were assessed by using the visual analog scale (VAS) for pain, the Japanese Society for Surgery of the Foot (JSSF) ankle/hindfoot scale, and the Self-Administered Foot Evaluation Questionnaire (SAFE-Q). No serious adverse effects were observed during the follow-up period. The VAS and JSSF scale scores significantly decreased from baseline to 4, 12, and 24 weeks after treatment ( P SAFE-Q significantly improved from baseline to 12 weeks after treatment ( P = .04). Overall, the amount of pain reduction was maximal at 12 weeks after the last injection, and the effect was reduced at 24 weeks. The patients with late-stage OA had worse scores in all outcomes than those with early-stage OA. Intra-articular injections of PRP resulted in no serious adverse effects and significantly reduced pain in the patients with ankle OA. PRP treatment can be safe and effective and may be an option in the treatment of ankle OA. Level IV, case series.

ITS2 sequence-structure phylogeny reveals diverse endophytic Pseudocercospora fungi on poplars.

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Yan, Dong-Hui; Gao, Qian; Sun, Xiaoming; Song, Xiaoyu; Li, Hongchang

2018-04-01

For matching the new fungal nomenclature to abolish pleomorphic names for a fungus, a genus Pseudocercospora s. str. was suggested to host holomorphic Pseudocercosproa fungi. But the Pseudocercosproa fungi need extra phylogenetic loci to clarify their taxonomy and diversity for their existing and coming species. Internal transcribed spacer 2 (ITS2) secondary structures have been promising in charactering species phylogeny in plants, animals and fungi. In present study, a conserved model of ITS2 secondary structures was confirmed on fungi in Pseudocercospora s. str. genus using RNAshape program. The model has a typical eukaryotic four-helix ITS2 secondary structure. But a single U base occurred in conserved motif of U-U mismatch in Helix 2, and a UG emerged in UGGU motif in Helix 3 to Pseudocercospora fungi. The phylogeny analyses based on the ITS2 sequence-secondary structures with compensatory base change characterizations are able to delimit more species for Pseudocercospora s. str. than phylogenic inferences of traditional multi-loci alignments do. The model was employed to explore the diversity of endophytic Pseudocercospora fungi in poplar trees. The analysis results also showed that endophytic Pseudocercospora fungi were diverse in species and evolved a specific lineage in poplar trees. This work suggested that ITS2 sequence-structures could become as additionally significant loci for species phylogenetic and taxonomic studies on Pseudocerospora fungi, and that Pseudocercospora endophytes could be important roles to Pseudocercospora fungi's evolution and function in ecology.

A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1.

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Binhua Liang

Full Text Available BACKGROUND: Pyrosequencing technology has the potential to rapidly sequence HIV-1 viral quasispecies without requiring the traditional approach of cloning. In this study, we investigated the utility of ultra-deep pyrosequencing to characterize genetic diversity of the HIV-1 gag quasispecies and assessed the possible contribution of pyrosequencing technology in studying HIV-1 biology and evolution. METHODOLOGY/PRINCIPAL FINDINGS: HIV-1 gag gene was amplified from 96 patients using nested PCR. The PCR products were cloned and sequenced using capillary based Sanger fluorescent dideoxy termination sequencing. The same PCR products were also directly sequenced using the 454 pyrosequencing technology. The two sequencing methods were evaluated for their ability to characterize quasispecies variation, and to reveal sites under host immune pressure for their putative functional significance. A total of 14,034 variations were identified by 454 pyrosequencing versus 3,632 variations by Sanger clone-based (SCB sequencing. 11,050 of these variations were detected only by pyrosequencing. These undetected variations were located in the HIV-1 Gag region which is known to contain putative cytotoxic T lymphocyte (CTL and neutralizing antibody epitopes, and sites related to virus assembly and packaging. Analysis of the positively selected sites derived by the two sequencing methods identified several differences. All of them were located within the CTL epitope regions. CONCLUSIONS/SIGNIFICANCE: Ultra-deep pyrosequencing has proven to be a powerful tool for characterization of HIV-1 genetic diversity with enhanced sensitivity, efficiency, and accuracy. It also improved reliability of downstream evolutionary and functional analysis of HIV-1 quasispecies.

Hunting down frame shifts: Ecological analysis of diverse functional gene sequences

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Michal eStrejcek

2015-11-01

Full Text Available Functional gene ecological analyses using amplicon sequencing can be challenging as translated sequences are often burdened with shifted reading frames. The aim of this work was to evaluate several bioinformatics tools designed to correct errors which arise during sequencing in an effort to reduce the number of frame-shifts (FS. Genes encoding for alpha subunits of biphenyl (bphA and benzoate (benA dioxygenases were used as model sequences. FrameBot, a FS correction tool, was able to reduce the number of detected FS to zero. However, up to 43.1% of sequences were discarded by FrameBot as non-specific targets. Therefore, we proposed a de novo mode of FrameBot for FS correction, which works on a similar basis as common chimera identifying platforms and is not dependent on reference sequences. By nature of FrameBot de novo design, it is crucial to provide it with data as error free as possible. We tested the ability of several publicly available correction tools to decrease the number of errors in the data sets. The combination of Maximum Expected Error (MEE filtering and single linkage pre-clustering (SLP proved the most efficient read procession. Applying FrameBot de novo on the processed data enabled analysis of BphA sequences with minimal losses of potentially functional sequences not homologous to those previously known. This experiment also demonstrated the extensive diversity of dioxygenases in soil. A script which performs FrameBot de novo is presented in the supplementary material to the study and the tool was implemented into FunGene Pipeline available at http://fungene.cme.msu.edu/FunGenePipeline/ and https://github.com/rdpstaff/Framebot.

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

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Holly J Atkinson

Full Text Available The dramatic increase in heterogeneous types of biological data--in particular, the abundance of new protein sequences--requires fast and user-friendly methods for organizing this information in a way that enables functional inference. The most widely used strategy to link sequence or structure to function, homology-based function prediction, relies on the fundamental assumption that sequence or structural similarity implies functional similarity. New tools that extend this approach are still urgently needed to associate sequence data with biological information in ways that accommodate the real complexity of the problem, while being accessible to experimental as well as computational biologists. To address this, we have examined the application of sequence similarity networks for visualizing functional trends across protein superfamilies from the context of sequence similarity. Using three large groups of homologous proteins of varying types of structural and functional diversity--GPCRs and kinases from humans, and the crotonase superfamily of enzymes--we show that overlaying networks with orthogonal information is a powerful approach for observing functional themes and revealing outliers. In comparison to other primary methods, networks provide both a good representation of group-wise sequence similarity relationships and a strong visual and quantitative correlation with phylogenetic trees, while enabling analysis and visualization of much larger sets of sequences than trees or multiple sequence alignments can easily accommodate. We also define important limitations and caveats in the application of these networks. As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships.

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

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Atkinson, Holly J; Morris, John H; Ferrin, Thomas E; Babbitt, Patricia C

2009-01-01

The dramatic increase in heterogeneous types of biological data--in particular, the abundance of new protein sequences--requires fast and user-friendly methods for organizing this information in a way that enables functional inference. The most widely used strategy to link sequence or structure to function, homology-based function prediction, relies on the fundamental assumption that sequence or structural similarity implies functional similarity. New tools that extend this approach are still urgently needed to associate sequence data with biological information in ways that accommodate the real complexity of the problem, while being accessible to experimental as well as computational biologists. To address this, we have examined the application of sequence similarity networks for visualizing functional trends across protein superfamilies from the context of sequence similarity. Using three large groups of homologous proteins of varying types of structural and functional diversity--GPCRs and kinases from humans, and the crotonase superfamily of enzymes--we show that overlaying networks with orthogonal information is a powerful approach for observing functional themes and revealing outliers. In comparison to other primary methods, networks provide both a good representation of group-wise sequence similarity relationships and a strong visual and quantitative correlation with phylogenetic trees, while enabling analysis and visualization of much larger sets of sequences than trees or multiple sequence alignments can easily accommodate. We also define important limitations and caveats in the application of these networks. As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships.

Intra-Ocular Pressure Measurement in a Patient with a Thin, Thick or Abnormal Cornea.

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Clement, Colin I; Parker, Douglas G A; Goldberg, Ivan

2016-01-01

Accurate measurement of intra-ocular pressure is a fundamental component of the ocular examination. The most common method of measuring IOP is by Goldmann applanation tonometry, the accuracy of which is influenced by the thickness and biomechanical properties of the cornea. Algorithms devised to correct for corneal thickness to estimate IOP oversimplify the effects of corneal biomechanics. The viscous and elastic properties of the cornea influence IOP measurements in unpredictable ways, a finding borne out in studies of patients with inherently abnormal and surgically altered corneal biomechanics. Dynamic contour tonometry, rebound tonometry and the ocular response analyzer provide useful alternatives to GAT in patients with abnormal corneas, such as those who have undergone laser vision correction or keratoplasty. This article reviews the various methods of intra-ocular pressure measurement available to the clinician and the ways in which their utility is influenced by variations in corneal thickness and biomechanics.

Atypical case of Wolfram syndrome revealed through targeted exome sequencing in a patient with suspected mitochondrial disease.

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Lieber, Daniel S; Vafai, Scott B; Horton, Laura C; Slate, Nancy G; Liu, Shangtao; Borowsky, Mark L; Calvo, Sarah E; Schmahmann, Jeremy D; Mootha, Vamsi K

2012-01-06

Mitochondrial diseases comprise a diverse set of clinical disorders that affect multiple organ systems with varying severity and age of onset. Due to their clinical and genetic heterogeneity, these diseases are difficult to diagnose. We have developed a targeted exome sequencing approach to improve our ability to properly diagnose mitochondrial diseases and apply it here to an individual patient. Our method targets mitochondrial DNA (mtDNA) and the exons of 1,600 nuclear genes involved in mitochondrial biology or Mendelian disorders with multi-system phenotypes, thereby allowing for simultaneous evaluation of multiple disease loci. Targeted exome sequencing was performed on a patient initially suspected to have a mitochondrial disorder. The patient presented with diabetes mellitus, diffuse brain atrophy, autonomic neuropathy, optic nerve atrophy, and a severe amnestic syndrome. Further work-up revealed multiple heteroplasmic mtDNA deletions as well as profound thiamine deficiency without a clear nutritional cause. Targeted exome sequencing revealed a homozygous c.1672C > T (p.R558C) missense mutation in exon 8 of WFS1 that has previously been reported in a patient with Wolfram syndrome. This case demonstrates how clinical application of next-generation sequencing technology can enhance the diagnosis of patients suspected to have rare genetic disorders. Furthermore, the finding of unexplained thiamine deficiency in a patient with Wolfram syndrome suggests a potential link between WFS1 biology and thiamine metabolism that has implications for the clinical management of Wolfram syndrome patients.

Atypical case of Wolfram syndrome revealed through targeted exome sequencing in a patient with suspected mitochondrial disease

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Lieber Daniel S

2012-01-01

Full Text Available Abstract Background Mitochondrial diseases comprise a diverse set of clinical disorders that affect multiple organ systems with varying severity and age of onset. Due to their clinical and genetic heterogeneity, these diseases are difficult to diagnose. We have developed a targeted exome sequencing approach to improve our ability to properly diagnose mitochondrial diseases and apply it here to an individual patient. Our method targets mitochondrial DNA (mtDNA and the exons of 1,600 nuclear genes involved in mitochondrial biology or Mendelian disorders with multi-system phenotypes, thereby allowing for simultaneous evaluation of multiple disease loci. Case Presentation Targeted exome sequencing was performed on a patient initially suspected to have a mitochondrial disorder. The patient presented with diabetes mellitus, diffuse brain atrophy, autonomic neuropathy, optic nerve atrophy, and a severe amnestic syndrome. Further work-up revealed multiple heteroplasmic mtDNA deletions as well as profound thiamine deficiency without a clear nutritional cause. Targeted exome sequencing revealed a homozygous c.1672C > T (p.R558C missense mutation in exon 8 of WFS1 that has previously been reported in a patient with Wolfram syndrome. Conclusion This case demonstrates how clinical application of next-generation sequencing technology can enhance the diagnosis of patients suspected to have rare genetic disorders. Furthermore, the finding of unexplained thiamine deficiency in a patient with Wolfram syndrome suggests a potential link between WFS1 biology and thiamine metabolism that has implications for the clinical management of Wolfram syndrome patients.

Learning of Sensory Sequences in Cerebellar Patients

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Frings, Markus; Boenisch, Raoul; Gerwig, Marcus; Diener, Hans-Christoph; Timmann, Dagmar

2004-01-01

A possible role of the cerebellum in detecting and recognizing event sequences has been proposed. The present study sought to determine whether patients with cerebellar lesions are impaired in the acquisition and discrimination of sequences of sensory stimuli of different modalities. A group of 26 cerebellar patients and 26 controls matched for…

Impairment in explicit visuomotor sequence learning is related to loss of microstructural integrity of the corpus callosum in multiple sclerosis patients with minimal disability.

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Bonzano, L; Tacchino, A; Roccatagliata, L; Sormani, M P; Mancardi, G L; Bove, M

2011-07-15

Sequence learning can be investigated by serial reaction-time (SRT) paradigms. Explicit learning occurs when subjects have to recognize a test sequence and has been shown to activate the frontoparietal network in both contralateral and ipsilateral hemispheres. Thus, the left and right superior longitudinal fasciculi (SLF), connecting the intra-hemispheric frontoparietal circuits, could have a role in explicit unimanual visuomotor learning. Also, as both hemispheres are involved, we could hypothesize that the corpus callosum (CC) has a role in this process. Pathological damage in both SLF and CC has been detected in patients with Multiple Sclerosis (PwMS), and microstructural alterations can be quantified by Diffusion Tensor Imaging (DTI). In light of these findings, we inquired whether PwMS with minimal disability showed impairments in explicit visuomotor sequence learning and whether this could be due to loss of white matter integrity in these intra- and inter-hemispheric white matter pathways. Thus, we combined DTI analysis with a modified version of SRT task based on finger opposition movements in a group of PwMS with minimal disability. We found that the performance in explicit sequence learning was significantly reduced in these patients with respect to healthy subjects; the amount of sequence-specific learning was found to be more strongly correlated with fractional anisotropy (FA) in the CC (r=0.93) than in the left (r=0.28) and right SLF (r=0.27) (p for interaction=0.005 and 0.04 respectively). This finding suggests that an inter-hemispheric information exchange between the homologous areas is required to successfully accomplish the task and indirectly supports the role of the right (ipsilateral) hemisphere in explicit visuomotor learning. On the other hand, we found no significant correlation of the FA in the CC and in the SLFs with nonspecific learning (assessed when stimuli are randomly presented), supporting the hypothesis that inter

Feasibility of MR urography in patients with urinary diversion

International Nuclear Information System (INIS)

Battal, Bilal; Kocaoglu, Murat; Ilica, Turan; Akgun, Veysel; Aydur, Emin; Dayanc, Murat

2011-01-01

The aims of this study were to determine the diagnostic value of MR urography and to compare the T2- and T1-weighted MR urography techniques in patients with urinary diversion. We retrospectively reviewed 19 MR urograms in 14 patients (13 male and one female, 8–77 years old, mean age: 54.2) with urinary diversion. Magnetic resonance urography examinations were performed with 1.5-T MR scanners. In addition to T2- and T1-weighted MR urography techniques, conventional T1- and T2-weighted axial and coronal sequences were also obtained. Collecting systems were evaluated in five segments (right proximal and distal collecting system, left proximal and distal collecting system and conduit or reservoir). Imaging features of the urinary collecting systems were evaluated with T2- and T1-weighted MR urography images. The clinical, laboratory data and follow-up imaging findings were regarded as standard. A cross table was formed to determine sensitivity, specificity and accuracy of MR urography techniques. T2-weighted MR urography, T1-weighted MR urography and combination of these two techniques could demonstrate 89.01, 87.65 and 93.83% of all collecting system segments, respectively. For the detection of the pathologic urinary segments, sensitivity, specificity and accuracy were 100, 95.29 and 95.6% in T2-weighted MR urography and 100, 93.42 and 93.82% in T1-weighted MR urography, respectively. Sensitivity, specificity and accuracy were 100% in combined T2- and T1-weighted MR urography technique. Magnetic resonance urography is an effective imaging method for the evaluation of the urinary system in patients with urinary diversion. T2-weighted MR urography alone has high sensitivity, specificity and accuracy, does not require intravenous contrast medium and can be obtained in 3–5 min. However, T1-weighted MR urography may provide additional information in some cases.

Fondaparinux for intra and perioperative anticoagulation in patients with heparin-induced thrombocytopenia candidates for peripheral vascular surgery: Report of 4 cases.

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Illuminati, Giulio; Calio', Francesco G; Pizzardi, Giulia; Amatucci, Chiara; Masci, Federica; Palumbo, Piergaspare

2016-01-01

Intra and perioperative anticoagulation in patients with heparin induced thrombocytopenia (HIT), candidates for peripheral vascular surgery remains a challenge, as the best alternative to heparin has not yet been established. We evaluated the off-label use of fondaparinux in four patients with HIT, undergoing peripheral vascular surgery procedures. Four patients of whom 3 men of a mean age of 66 years, with proven heparin induced thrombocytopenia (HIT) underwent two axillo-femoral bypasses, one femoro-popliteal bypass and one resection of a splenic artery aneurysm under fondaparinux. No intra or perioperative bleeding or thrombosis of new onset was observed. In the absence of a valid alternative to heparin for intra and perioperative anticoagulation in HIT, several other anticoagulants can be used in an off-label setting. However, no general consensus exist on which should be the one of choice. In this small series fondaparinux appeared to be both safe and effective. These preliminary results seem to justify the off-label use of fondaparinux for intra and perioperative anticoagulation in patients with HIT, candidates for peripheral vascular surgery interventions. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes

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Bruskiewich, Richard; Burris, Jason N.; Carrigan, Charlotte T.; Chase, Mark W.; Clarke, Neil D.; Covshoff, Sarah; dePamphilis, Claude W.; Edger, Patrick P.; Goh, Falicia; Graham, Sean; Greiner, Stephan; Hibberd, Julian M.; Jordon-Thaden, Ingrid; Kutchan, Toni M.; Leebens-Mack, James; Melkonian, Michael; Miles, Nicholas; Myburg, Henrietta; Patterson, Jordan; Pires, J. Chris; Ralph, Paula; Rolf, Megan; Sage, Rowan F.; Soltis, Douglas; Soltis, Pamela; Stevenson, Dennis; Stewart, C. Neal; Surek, Barbara; Thomsen, Christina J. M.; Villarreal, Juan Carlos; Wu, Xiaolei; Zhang, Yong; Deyholos, Michael K.; Wong, Gane Ka-Shu

2012-01-01

Next-generation sequencing plays a central role in the characterization and quantification of transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, there have been no large-scale empirical evaluations of the major determinants of sequencing success. We used a combination of existing and newly developed methods to isolate total RNA from 1115 samples from 695 plant species in 324 families, which represents >900 million years of phylogenetic diversity from green algae through flowering plants, including many plants of economic importance. We then sequenced 629 of these samples on Illumina GAIIx and HiSeq platforms and performed a large comparative analysis to identify predictors of RNA quality and the diversity of putative genes (scaffolds) expressed within samples. Tissue types (e.g., leaf vs. flower) varied in RNA quality, sequencing depth and the number of scaffolds. Tissue age also influenced RNA quality but not the number of scaffolds ≥1000 bp. Overall, 36% of the variation in the number of scaffolds was explained by metrics of RNA integrity (RIN score), RNA purity (OD 260/230), sequencing platform (GAIIx vs HiSeq) and the amount of total RNA used for sequencing. However, our results show that the most commonly used measures of RNA quality (e.g., RIN) are weak predictors of the number of scaffolds because Illumina sequencing is robust to variation in RNA quality. These results provide novel insight into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes. The methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers. PMID:23185583

Intra-cardiac echocardiography guided catheter ablation of a right posterior accessory pathway in a patient with Ebstein׳s anomaly

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Akira Shimane, MD

2014-12-01

Full Text Available We report a case of Ebstein׳s anomaly in which radiofrequency catheter ablation of an accessory pathway was successfully performed under intra-cardiac echocardiography. A 50-year-old woman was referred to our hospital for radiofrequency catheter ablation of a paroxysmal supraventricular tachycardia. A 12-lead surface electrocardiogram revealed ventricular pre-excitation associated with type B Wolff–Parkinson–White syndrome. In the baseline electrophysiological study, an orthodromic atrioventricular reciprocating tachycardia with a right posterior accessory pathway was induced. A phased-array intra-cardiac echo probe was positioned in the right atrium to visualize the atrioventricular junction. The key structures for catheter ablation, such as the atrialized right ventricle, atrioventricular junction, and tricuspid valve, were clearly visualized on intra-cardiac echocardiography. Radiofrequency current was successfully delivered at the atrioventricular junction, where a Kent potential was recorded. During a 6-month follow-up period, the patient was free from arrhythmias. The findings in this case suggest that phased-array intra-cardiac echocardiography is useful for ablation of right-sided accessory pathways in patients with Ebstein׳s anomaly.

Intra-fraction prostate displacement in radiotherapy estimated from pre- and post-treatment imaging of patients with implanted fiducial markers

International Nuclear Information System (INIS)

Kron, Tomas; Thomas, Jessica; Fox, Chris; Thompson, Ann; Owen, Rebecca; Herschtal, Alan; Haworth, Annette; Tai, Keen-Hun; Foroudi, Farshad

2010-01-01

Purpose: To determine intra-fraction displacement of the prostate gland from imaging pre- and post-radiotherapy delivery of prostate cancer patients with three implanted fiducial markers. Methods and materials: Data were collected from 184 patients who had two orthogonal X-rays pre- and post-delivery on at least 20 occasions using a Varian On Board kV Imaging system. A total of 5778 image pairs covering time intervals between 3 and 30 min between pre- and post-imaging were evaluated for intra-fraction prostate displacement. Results: The mean three dimensional vector shift between images was 1.7 mm ranging from 0 to 25 mm. No preferential direction of displacement was found; however, there was an increase of prostate displacement with time between images. There was a large variation in typical shifts between patients (range 1 ± 1 to 6 ± 2 mm) with no apparent trends throughout the treatment course. Images acquired in the first five fractions of treatment could be used to predict displacement patterns for individual patients. Conclusion: Intra-fraction motion of the prostate gland appears to be a limiting factor when considering margins for radiotherapy. Given the variation between patients, a uniform set of margins for all patients may not be satisfactory when high target doses are to be delivered.

Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences

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Alessandra Traini

2013-01-01

Full Text Available Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches.

Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences.

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Traini, Alessandra; Iorizzo, Massimo; Mann, Harpartap; Bradeen, James M; Carputo, Domenico; Frusciante, Luigi; Chiusano, Maria Luisa

2013-01-01

Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT) markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches.

Complete sequence and diversity of a maize-associated Polerovirus in East Africa.

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Massawe, Deogracious P; Stewart, Lucy R; Kamatenesi, Jovia; Asiimwe, Theodore; Redinbaugh, Margaret G

2018-06-01

Since 2011-2012, Maize lethal necrosis (MLN) has emerged in East Africa, causing massive yield loss and propelling research to identify viruses and virus populations present in maize. As expected, next generation sequencing (NGS) has revealed diverse and abundant viruses from the family Potyviridae, primarily sugarcane mosaic virus (SCMV), and maize chlorotic mottle virus (MCMV) (Tombusviridae), which are known to cause MLN by synergistic co-infection. In addition to these expected viruses, we identified a virus in the genus Polerovirus (family Luteoviridae) in 104/172 samples selected for MLN or other potential virus symptoms from Kenya, Uganda, Rwanda, and Tanzania. This polerovirus (MF974579) nucleotide sequence is 97% identical to maize-associated viruses recently reported in China, termed 'maize yellow mosaic virus' (MaYMV) and maize yellow dwarf virus (MaYMV; KU291101, KU291107, MYDV-RMV2; KT992824); and 99% identical to MaYMV (KY684356) infecting sugarcane and itch grass in Nigeria; 83% identical to a barley-associated polerovirus recently identified in Korea (BVG; KT962089); and 79% identical to the U.S. maize-infecting polerovirus maize yellow dwarf virus (MYDV-RMV; KT992824). Nucleotide sequences from ORF0 of 20 individual East African isolates collected from Kenya, Uganda, Rwanda, and Tanzania shared 98% or higher identity, and were detected in 104/172 (60.5%) of samples collected for virus-like symptoms, indicating extensive prevalence but limited diversity of this virus in East Africa. We refer to this virus as "MYDV-like polerovirus" until symptoms of the virus in maize are known.

Exploring Canadian Echinoderm Diversity through DNA Barcodes.

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Kara K S Layton

Full Text Available DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold between mean intra- (0.48% and inter- (12.0% specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs.

Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions

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Cheryl-Emiliane Tien Chow

2015-04-01

Full Text Available Viral diversity and virus-host interactions in oxygen-starved regions of the ocean, also known as oxygen minimum zones (OMZs, remain relatively unexplored. Microbial community metabolism in OMZs alters nutrient and energy flow through marine food webs, resulting in biological nitrogen loss and greenhouse gas production. Thus, viruses infecting OMZ microbes have the potential to modulate community metabolism with resulting feedback on ecosystem function. Here, we describe viral communities inhabiting oxic surface (10m and oxygen-starved basin (200m waters of Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia using viral metagenomics and complete viral fosmid sequencing on samples collected between April 2007 and April 2010. Of 6459 open reading frames (ORFs predicted across all 34 viral fosmids, 77.6% (n=5010 had no homology to reference viral genomes. These fosmids recruited a higher proportion of viral metagenomic sequences from Saanich Inlet than from nearby northeastern subarctic Pacific Ocean (Line P waters, indicating differences in the viral communities between coastal and open ocean locations. While functional annotations of fosmid ORFs were limited, recruitment to NCBI’s non-redundant ‘nr’ database and publicly available single-cell genomes identified putative viruses infecting marine thaumarchaeal and SUP05 proteobacteria to provide potential host linkages with relevance to coupled biogeochemical cycling processes in OMZ waters. Taken together, these results highlight the power of coupled analyses of multiple sequence data types, such as viral metagenomic and fosmid sequence data with prokaryotic single cell genomes, to chart viral diversity, elucidate genomic and ecological contexts for previously unclassifiable viral sequences, and identify novel host interactions in natural and engineered ecosystems.

Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing

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Li Xuehui

2012-10-01

Full Text Available Abstract Background Alfalfa, a perennial, outcrossing species, is a widely planted forage legume producing highly nutritious biomass. Currently, improvement of cultivated alfalfa mainly relies on recurrent phenotypic selection. Marker assisted breeding strategies can enhance alfalfa improvement efforts, particularly if many genome-wide markers are available. Transcriptome sequencing enables efficient high-throughput discovery of single nucleotide polymorphism (SNP markers for a complex polyploid species. Result The transcriptomes of 27 alfalfa genotypes, including elite breeding genotypes, parents of mapping populations, and unimproved wild genotypes, were sequenced using an Illumina Genome Analyzer IIx. De novo assembly of quality-filtered 72-bp reads generated 25,183 contigs with a total length of 26.8 Mbp and an average length of 1,065 bp, with an average read depth of 55.9-fold for each genotype. Overall, 21,954 (87.2% of the 25,183 contigs represented 14,878 unique protein accessions. Gene ontology (GO analysis suggested that a broad diversity of genes was represented in the resulting sequences. The realignment of individual reads to the contigs enabled the detection of 872,384 SNPs and 31,760 InDels. High resolution melting (HRM analysis was used to validate 91% of 192 putative SNPs identified by sequencing. Both allelic variants at about 95% of SNP sites identified among five wild, unimproved genotypes are still present in cultivated alfalfa, and all four US breeding programs also contain a high proportion of these SNPs. Thus, little evidence exists among this dataset for loss of significant DNA sequence diversity from either domestication or breeding of alfalfa. Structure analysis indicated that individuals from the subspecies falcata, the diploid subspecies caerulea, and the tetraploid subspecies sativa (cultivated tetraploid alfalfa were clearly separated. Conclusion We used transcriptome sequencing to discover large numbers of SNPs

Genetic Diversity and Phylogenetic Evolution of Tibetan Sheep Based on mtDNA D-Loop Sequences.

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Jianbin Liu

Full Text Available The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries is not well understood, and little is known about this species' genetic diversity. This knowledge gap is partly due to the difficulty of sample collection. This is the first work to address this question. Here, the genetic diversity and phylogenetic relationship of 636 individual Tibetan sheep from fifteen populations were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Samples were collected from the Qinghai-Tibetan Plateau area in China, and reference data were obtained from the six reference breed sequences available in GenBank. The length of the sequences varied considerably, between 1031 and 1259 bp. The haplotype diversity and nucleotide diversity were 0.992±0.010 and 0.019±0.001, respectively. The average number of nucleotide differences was 19.635. The mean nucleotide composition of the 350 haplotypes was 32.961% A, 29.708% T, 22.892% C, 14.439% G, 62.669% A+T, and 37.331% G+C. Phylogenetic analysis showed that all four previously defined haplogroups (A, B, C, and D were found in the 636 individuals of the fifteen Tibetan sheep populations but that only the D haplogroup was found in Linzhou sheep. Further, the clustering analysis divided the fifteen Tibetan sheep populations into at least two clusters. The estimation of the demographic parameters from the mismatch analyses showed that haplogroups A, B, and C had at least one demographic expansion in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau.

[Intra-anesthetic arterial hypotension in elderly patients during emergency surgery: what are the risk factors?

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Boubacar Ba, El Hadji; Leye, Papa Alassane; Traoré, Mamadou Mour; Ndiaye, Pape Ibrahima; Gaye, Ibrahima; Bah, Mamadou Diawo; Fall, Mamadou Lamine; Diouf, Elisabeth

2017-01-01

Emergency anesthesia in elderly patients aged 65 years and older is complex. The occurrence of intraoperative incidents and arterial hypotension is conditioned by patients' initial health status and by the quality of intraoperative management. This study aimed to determine the incidence of intra-anesthetic arterial hypotension in elderly patients during emergency surgery and to assess the involvement of certain factors in its occurrence: age, sex, patient's history, ASA class, anesthetic technique. We conducted a retrospective descriptive and analytical study in the Emergency Surgery Department at the Aristide Le Dantec University Hospital from 1 March 2014 to 28 February 2015. We collected data from 210 patients out of 224 elderly patients aged 65 years and older undergoing emergency anesthesias (10.93%). Data of 101 men and 109 women were included in the analysis, of whom 64.3% had at least one defect. Patients' preoperative status was assessed using American Society of Anesthesiology (ASA) classification: 71% of patients were ASA class 1 and 2 and 29% were ASA class 3 and 4. Locoregional anesthesia was the most practiced anesthetic technique (56.7%). 28 patients (13.33%) had intra-anesthetic arterial hypotension, of whom 16 under general anesthesia and 12 under locoregional anesthesia. It was more frequent in patients with high ASA class and a little less frequent in patients with PAH and underlying heart disease. Arterial hypotension in elderly patients during emergency surgery exposes the subject to the risk of not negligible intraoperative hypotension, especially in patients with high ASA class. Prevention is based on adequate preoperative assessment and anesthetic management.

Intra-articular injection of hyaluronic acid for treatment of osteoarthritis knee: comparative study to intra-articular corticosteroids

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Soad A Elsawy

2017-01-01

Conclusion Both HA and corticosteroid groups showed improvement in pain and knee function, but the intra-articular HA was superior to corticosteroid on long-term follow-up. This supports the potential rate of intra-articular HA as an effective long-term therapeutic option for patients with OA of the knee.

Simultaneous intra-arterial chemotherapy and radiotherapy for carcinoma of oropharynx without neck metastasis

International Nuclear Information System (INIS)

Tomita, Kichinobu; Higaki, Yuichiro

2000-01-01

We evaluated the usefulness of simultaneous intra-arterial chemotherapy and radiotherapy for oropharyngeal cancer without neck metastasis. Fifty eight cases without neck metastasis out of previously untreated 117 patients with oropharyngeal cancer treated at National Kyushu Cancer Center from 1972 to 1995 were examined. Seventeen patients were in T1, 27 in T2, 10 in T3, 4 in T4. Fourteen patients of 58 patients were treated by simultaneous intra-arterial chemotherapy and radiation therapy. The 5-year survival rate by Kaplan-Meier method for intra-arterial infusion group and non intra-arterial infusion group were 86% and 71%, respectively. Thirty one patients were treated with irradiation without surgery. In 31 cases without surgery, the 5-year survival rate for intra-arterial infusion group (13 cases) was 85%, while that for non intra-arterial infusion group (18 cases) was 60%, and the local control rate for intra-arterial infusion group is 92%, while that for non intra-arterial infusion group was 56%. Simultaneous intra-arterial chemotherapy and radiotherapy for oropharyngeal cancer without neck metastasis is useful to improve the prognosis with preserving the function. (author)

Genetic Diversity and Population Structure of F3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing.

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Eltaher, Shamseldeen; Sallam, Ahmed; Belamkar, Vikas; Emara, Hamdy A; Nower, Ahmed A; Salem, Khaled F M; Poland, Jesse; Baenziger, Peter S

2018-01-01

The availability of information on the genetic diversity and population structure in wheat ( Triticum aestivum L.) breeding lines will help wheat breeders to better use their genetic resources and manage genetic variation in their breeding program. The recent advances in sequencing technology provide the opportunity to identify tens or hundreds of thousands of single nucleotide polymorphism (SNPs) in large genome species (e.g., wheat). These SNPs can be utilized for understanding genetic diversity and performing genome wide association studies (GWAS) for complex traits. In this study, the genetic diversity and population structure were investigated in a set of 230 genotypes (F 3:6 ) derived from various crosses as a prerequisite for GWAS and genomic selection. Genotyping-by-sequencing provided 25,566 high-quality SNPs. The polymorphism information content (PIC) across chromosomes ranged from 0.09 to 0.37 with an average of 0.23. The distribution of SNPs markers on the 21 chromosomes ranged from 319 on chromosome 3D to 2,370 on chromosome 3B. The analysis of population structure revealed three subpopulations (G1, G2, and G3). Analysis of molecular variance identified 8% variance among and 92% within subpopulations. Of the three subpopulations, G2 had the highest level of genetic diversity based on three genetic diversity indices: Shannon's information index ( I ) = 0.494, diversity index ( h ) = 0.328 and unbiased diversity index (uh) = 0.331, while G3 had lowest level of genetic diversity ( I = 0.348, h = 0.226 and uh = 0.236). This high genetic diversity identified among the subpopulations can be used to develop new wheat cultivars.

Assessing inter- and intra-individual cognitive variability in patients at risk for cognitive impairment: the case of minimal hepatic encephalopathy.

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Bisiacchi, Patrizia; Cona, Giorgia; Tarantino, Vincenza; Schiff, Sami; Montagnese, Sara; Amodio, Piero; Capizzi, Giovanna

2014-12-01

Recent evidence reveals that inter- and intra-individual variability significantly affects cognitive performance in a number of neuropsychological pathologies. We applied a flexible family of statistical models to elucidate the contribution of inter- and intra-individual variables on cognitive functioning in healthy volunteers and patients at risk for hepatic encephalopathy (HE). Sixty-five volunteers (32 patients with cirrhosis and 33 healthy volunteers) were assessed by means of the Inhibitory Control Task (ICT). A Generalized Additive Model for Location, Scale and Shape (GAMLSS) was fitted for jointly modeling the mean and the intra-variability of Reaction Times (RTs) as a function of socio-demographic and task related covariates. Furthermore, a Generalized Linear Mixed Model (GLMM) was fitted for modeling accuracy. When controlling for the covariates, patients without minimal hepatic encephalopathy (MHE) did not differ from patients with MHE in the low-demanding condition, both in terms of RTs and accuracy. Moreover, they showed a significant decline in accuracy compared to the control group. Compared to patients with MHE, patients without MHE showed faster RTs and higher accuracy only in the high-demanding condition. The results revealed that the application of GAMLSS and GLMM models are able to capture subtle cognitive alterations, previously not detected, in patients' subclinical pathologies.

INTRA graphical package - INTRA-Graph 1.0

International Nuclear Information System (INIS)

Hofman, D.; Edlund, O.

2001-04-01

INTRA-Graph 1.0 has been developed at Studsvik Eco and Safety AB in the frame of the European Fusion Technology Programme for application in the safety analysis using the INTRA code. INTRA-Graph 1.0 is a graphical package producing 2-dimensional plots of results generated by the INTRA code. INTRA-Graph 1.0 has been developed by extending the Grace package source code, distributed under the terms of GNU General Public License. The changes in the Grace source files are limited to provide easy updates of the INTRA-Graph when a new version of Grace will be released. The INTRA-related functionality has been implemented in new source files. The present report describes and gives complete listing of these files. The changes in the Grace source files are also described and the listing of the changed parts of the files is presented. The report gives detailed explanations and examples of files required for installation and configuration of INTRA-Graph on the different types of Unix workstations

Population Pharmacokinetics of Artesunate and Dihydroartemisinin following Intra-Rectal Dosing of Artesunate in Malaria Patients

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Simpson, Julie A; Agbenyega, Tsiri; Barnes, Karen I; Perri, Gianni Di; Folb, Peter; Gomes, Melba; Krishna, Sanjeev; Krudsood, Srivicha; Looareesuwan, Sornchai; Mansor, Sharif; McIlleron, Helen; Miller, Raymond; Molyneux, Malcolm; Mwenechanya, James; Navaratnam, Visweswaran; Nosten, Francois; Olliaro, Piero; Pang, Lorrin; Ribeiro, Isabela; Tembo, Madalitso; van Vugt, Michele; Ward, Steve; Weerasuriya, Kris; Win, Kyaw; White, Nicholas J

2006-01-01

Background Intra-rectal artesunate has been developed as a potentially life-saving treatment of severe malaria in rural village settings where administration of parenteral antimalarial drugs is not possible. We studied the population pharmacokinetics of intra-rectal artesunate and the relationship with parasitological responses in patients with moderately severe falciparum malaria. Methods and Findings Adults and children in Africa and Southeast Asia with moderately severe malaria were recruited in two Phase II studies (12 adults from Southeast Asia and 11 children from Africa) with intensive sampling protocols, and three Phase III studies (44 children from Southeast Asia, and 86 children and 26 adults from Africa) with sparse sampling. All patients received 10 mg/kg artesunate as a single intra-rectal dose of suppositories. Venous blood samples were taken during a period of 24 h following dosing. Plasma artesunate and dihydroartemisinin (DHA, the main biologically active metabolite) concentrations were measured by high-performance liquid chromatography with electrochemical detection. The pharmacokinetic properties of DHA were determined using nonlinear mixed-effects modelling. Artesunate is rapidly hydrolysed in vivo to DHA, and this contributes the majority of antimalarial activity. For DHA, a one-compartment model assuming complete conversion from artesunate and first-order appearance and elimination kinetics gave the best fit to the data. The mean population estimate of apparent clearance (CL/F) was 2.64 (l/kg/h) with 66% inter-individual variability. The apparent volume of distribution (V/F) was 2.75 (l/kg) with 96% inter-individual variability. The estimated DHA population mean elimination half-life was 43 min. Gender was associated with increased mean CL/F by 1.14 (95% CI: 0.36–1.92) (l/kg/h) for a male compared with a female, and weight was positively associated with V/F. Larger V/Fs were observed for the patients requiring early rescue treatment compared

Population pharmacokinetics of artesunate and dihydroartemisinin following intra-rectal dosing of artesunate in malaria patients.

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Julie A Simpson

2006-11-01

Full Text Available Intra-rectal artesunate has been developed as a potentially life-saving treatment of severe malaria in rural village settings where administration of parenteral antimalarial drugs is not possible. We studied the population pharmacokinetics of intra-rectal artesunate and the relationship with parasitological responses in patients with moderately severe falciparum malaria.Adults and children in Africa and Southeast Asia with moderately severe malaria were recruited in two Phase II studies (12 adults from Southeast Asia and 11 children from Africa with intensive sampling protocols, and three Phase III studies (44 children from Southeast Asia, and 86 children and 26 adults from Africa with sparse sampling. All patients received 10 mg/kg artesunate as a single intra-rectal dose of suppositories. Venous blood samples were taken during a period of 24 h following dosing. Plasma artesunate and dihydroartemisinin (DHA, the main biologically active metabolite concentrations were measured by high-performance liquid chromatography with electrochemical detection. The pharmacokinetic properties of DHA were determined using nonlinear mixed-effects modelling. Artesunate is rapidly hydrolysed in vivo to DHA, and this contributes the majority of antimalarial activity. For DHA, a one-compartment model assuming complete conversion from artesunate and first-order appearance and elimination kinetics gave the best fit to the data. The mean population estimate of apparent clearance (CL/F was 2.64 (l/kg/h with 66% inter-individual variability. The apparent volume of distribution (V/F was 2.75 (l/kg with 96% inter-individual variability. The estimated DHA population mean elimination half-life was 43 min. Gender was associated with increased mean CL/F by 1.14 (95% CI: 0.36-1.92 (l/kg/h for a male compared with a female, and weight was positively associated with V/F. Larger V/Fs were observed for the patients requiring early rescue treatment compared with the remainder

Population pharmacokinetics of artesunate and dihydroartemisinin following intra-rectal dosing of artesunate in malaria patients.

Science.gov (United States)

Simpson, Julie A; Agbenyega, Tsiri; Barnes, Karen I; Di Perri, Gianni; Folb, Peter; Gomes, Melba; Krishna, Sanjeev; Krudsood, Srivicha; Looareesuwan, Sornchai; Mansor, Sharif; McIlleron, Helen; Miller, Raymond; Molyneux, Malcolm; Mwenechanya, James; Navaratnam, Visweswaran; Nosten, Francois; Olliaro, Piero; Pang, Lorrin; Ribeiro, Isabela; Tembo, Madalitso; van Vugt, Michele; Ward, Steve; Weerasuriya, Kris; Win, Kyaw; White, Nicholas J

2006-11-01

Intra-rectal artesunate has been developed as a potentially life-saving treatment of severe malaria in rural village settings where administration of parenteral antimalarial drugs is not possible. We studied the population pharmacokinetics of intra-rectal artesunate and the relationship with parasitological responses in patients with moderately severe falciparum malaria. Adults and children in Africa and Southeast Asia with moderately severe malaria were recruited in two Phase II studies (12 adults from Southeast Asia and 11 children from Africa) with intensive sampling protocols, and three Phase III studies (44 children from Southeast Asia, and 86 children and 26 adults from Africa) with sparse sampling. All patients received 10 mg/kg artesunate as a single intra-rectal dose of suppositories. Venous blood samples were taken during a period of 24 h following dosing. Plasma artesunate and dihydroartemisinin (DHA, the main biologically active metabolite) concentrations were measured by high-performance liquid chromatography with electrochemical detection. The pharmacokinetic properties of DHA were determined using nonlinear mixed-effects modelling. Artesunate is rapidly hydrolysed in vivo to DHA, and this contributes the majority of antimalarial activity. For DHA, a one-compartment model assuming complete conversion from artesunate and first-order appearance and elimination kinetics gave the best fit to the data. The mean population estimate of apparent clearance (CL/F) was 2.64 (l/kg/h) with 66% inter-individual variability. The apparent volume of distribution (V/F) was 2.75 (l/kg) with 96% inter-individual variability. The estimated DHA population mean elimination half-life was 43 min. Gender was associated with increased mean CL/F by 1.14 (95% CI: 0.36-1.92) (l/kg/h) for a male compared with a female, and weight was positively associated with V/F. Larger V/Fs were observed for the patients requiring early rescue treatment compared with the remainder, independent

The ITS1-5.8S-ITS2 sequence region in the Musaceae: structure, diversity and use in molecular phylogeny.

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Eva Hřibová

2011-03-01

Full Text Available Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this work we report on the structure and diversity of the ITS region in 87 representatives of the family Musaceae. We provide the first detailed information on ITS sequence diversity in the genus Musa and describe the presence of more than one type of ITS sequence within individual species. Both Sanger sequencing of amplified ITS regions and whole genome 454 sequencing lead to similar phylogenetic inferences. We show that it is necessary to identify putative pseudogenic ITS sequences, which may have negative effect on phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstruction based on ITS sequence showed that the genus Musa is divided into two distinct clades--Callimusa and Australimusa and Eumusa and Rhodochlamys. Most of the intraspecific banana hybrids analyzed contain conserved parental ITS sequences, indicating incomplete concerted evolution of rDNA loci. Independent evolution of parental rDNA in hybrids enables determination of genomic constitution of hybrids using ITS. The observation of only one type of ITS sequence in some of the presumed interspecific hybrid clones warrants further study to confirm their hybrid origin and to unravel processes leading to evolution of their genomes.

Evaluation of the genetic diversity of Plum pox virus in a single plum tree.

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Predajňa, Lukáš; Šubr, Zdeno; Candresse, Thierry; Glasa, Miroslav

2012-07-01

Genetic diversity of Plum pox virus (PPV) and its distribution within a single perennial woody host (plum, Prunus domestica) has been evaluated. A plum tree was triply infected by chip-budding with PPV-M, PPV-D and PPV-Rec isolates in 2003 and left to develop untreated under open field conditions. In September 2010 leaf and fruit samples were collected from different parts of the tree canopy. A 745-bp NIb-CP fragment of PPV genome, containing the hypervariable region encoding the CP N-terminal end was amplified by RT-PCR from each sample and directly sequenced to determine the dominant sequence. In parallel, the PCR products were cloned and a total of 105 individual clones were sequenced. Sequence analysis revealed that after 7 years of infection, only PPV-M was still detectable in the tree and that the two other isolates (PPV-Rec and PPV-D) had been displaced. Despite the fact that the analysis targeted a relatively short portion of the genome, a substantial amount of intra-isolate variability was observed for PPV-M. A total of 51 different haplotypes could be identified from the 105 individual sequences, two of which were largely dominant. However, no clear-cut structuration of the viral population by the tree architecture could be highlighted although the results obtained suggest the possibility of intra-leaf/fruit differentiation of the viral population. Comparison of the consensus sequence with the original source isolate showed no difference, suggesting within-plant stability of this original isolate under open field conditions. Copyright © 2012 Elsevier B.V. All rights reserved.

Continuous intra-arterial nimodipine infusion in patients with severe refractory cerebral vasospasm after aneurysmal subarachnoid hemorrhage: a feasibility study and outcome results.

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Bele, Sylvia; Proescholdt, Martin A; Hochreiter, Andreas; Schuierer, Gerhard; Scheitzach, Judith; Wendl, Christina; Kieninger, Martin; Schneiker, Andre; Bründl, Elisabeth; Schödel, Petra; Schebesch, Karl-Michael; Brawanski, Alexander

2015-12-01

Severe cerebral vasospasm is a major cause of death and disability in patients with aneurysmal subarachnoid hemorrhage. No causative treatment is yet available and hypertensive hypervolemic therapy (HHT) is often insufficient to avoid delayed cerebral ischemia and neurological deficits. We compared patients receiving continuous intra-arterial infusion of the calcium-antagonist nimodipine with a historical group treated with HHT and oral nimodipine alone. Between 0.5 and 1.2 mg/h of nimodipine were continuously administered by intra-arterial infusion via microcatheters either into the internal carotid or vertebral artery or both, depending on the areas of vasospasm. The effect was controlled via multimodal neuromonitoring and transcranial Doppler sonography. Outcome was determined by means of the Glasgow Outcome Scale at discharge and 6 months after the hemorrhage and compared to a historical control group. Twenty-one patients received 28 intra-arterial nimodipine infusions. Six months after discharge, the occurrence of cerebral infarctions was significantly lower (42.6 %) in the nimodipine group than in the control group (75.0 %). This result was reflected by a significantly higher proportion (76.0 %) of patients with good outcome in the nimodipine-treated group, when compared to 10.0 % good outcome in the control group. Median GOS was 4 in the nimodipine group and 2 in the control group (p = 0.001). Continuous intra-arterial nimodipine infusion is an effective treatment for patients with severe cerebral vasospasm who fail to respond to HHT and oral nimodipine alone. Key to the effective administration of continuous intra-arterial nimodipine is multimodal neuromonitoring and the individual adaptation of dosage and time of infusion for each patient.

Detection of intra-cardiac and intra-arterial thrombi using labelled platelets

International Nuclear Information System (INIS)

Bernard, P.J.; Laforte, C. de

1990-01-01

Scintigraphy with 111 Indium labelled platelets is a powerful tool to detect platelet deposits in vessels. This quantitative and functional imaging method needs a labeling procedure which completely preserves the properties of the platelets and allows the concept of hematologically active clot. Three main groups of patients were examined. 1-91 hematologically active intra-cardiac thrombi were detected. The follow-up of 19 of them shows 5 deaths and 7 cerebral embolisms. 2-372 patients with lower limb ischemia, mainly in the case of blue toe syndrome were examined. 158 times a comparison with the surgical patterns was possible, there were 3 false positive and 9 false negative results. 3-In a group of 310 patients with transient cerebro-vascular accidents, 38 times the records were poorly significant. In 27 patients we were able to compare the morphological examinations (including platelet scintigraphy) to the anatomical findings. Sensitivity was only 64% and specificity 71%. As in the cases of intra-cardiac thrombi, the method allows the follow-up of pharmacological therapy. Platelets labelled with 111 Indium provide the means for sensitive and specific detection of hematologically active clots in cardiac and arterial pathology [fr

Genetic plasticity of the Shigella virulence plasmid is mediated by intra- and inter-molecular events between insertion sequences.

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Pilla, Giulia; McVicker, Gareth; Tang, Christoph M

2017-09-01

Acquisition of a single copy, large virulence plasmid, pINV, led to the emergence of Shigella spp. from Escherichia coli. The plasmid encodes a Type III secretion system (T3SS) on a 30 kb pathogenicity island (PAI), and is maintained in a bacterial population through a series of toxin:antitoxin (TA) systems which mediate post-segregational killing (PSK). The T3SS imposes a significant cost on the bacterium, and strains which have lost the plasmid and/or genes encoding the T3SS grow faster than wild-type strains in the laboratory, and fail to bind the indicator dye Congo Red (CR). Our aim was to define the molecular events in Shigella flexneri that cause loss of Type III secretion (T3S), and to examine whether TA systems exert positional effects on pINV. During growth at 37°C, we found that deletions of regions of the plasmid including the PAI lead to the emergence of CR-negative colonies; deletions occur through intra-molecular recombination events between insertion sequences (ISs) flanking the PAI. Furthermore, by repositioning MvpAT (which belongs to the VapBC family of TA systems) near the PAI, we demonstrate that the location of this TA system alters the rearrangements that lead to loss of T3S, indicating that MvpAT acts both globally (by reducing loss of pINV through PSK) as well as locally (by preventing loss of adjacent sequences). During growth at environmental temperatures, we show for the first time that pINV spontaneously integrates into different sites in the chromosome, and this is mediated by inter-molecular events involving IS1294. Integration leads to reduced PAI gene expression and impaired secretion through the T3SS, while excision of pINV from the chromosome restores T3SS function. Therefore, pINV integration provides a reversible mechanism for Shigella to circumvent the metabolic burden imposed by pINV. Intra- and inter-molecular events between ISs, which are abundant in Shigella spp., mediate plasticity of S. flexneri pINV.

High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High-Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers

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Weiguo Hou

2018-05-01

Full Text Available Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length encoding the cyanophage gp23 major capsid protein (MCP. Diverse viral communities were detected in all samples. The fragments of 142-, 145-, and 148-bp in length were most abundant in the amplicons, and most sequences (>92% belonged to cyanophages. Additionally, different sequencing depths resulted in different diversity estimates of the viral community. Operational taxonomic units obtained from deep sequencing of the MCP gene covered the majority of those obtained from shallow sequencing, suggesting that deep sequencing exhibited a more complete picture of cyanophage community than shallow sequencing. Our results also revealed a wide geographic distribution of marine myocyanophages, i.e., higher dissimilarities of the myocyanophage communities corresponded with the larger distances between the sampling sites. Collectively, this study suggests that the newly designed primer pair can be effectively used to study the community and diversity of myocyanophage from different environments, and the high-throughput sequencing represents a good method to understand viral diversity.

Using high-throughput sequencing to leverage surveillance of genetic diversity and oseltamivir resistance: a pilot study during the 2009 influenza A(H1N1 pandemic.

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Juan Téllez-Sosa

Full Text Available BACKGROUND: Influenza viruses display a high mutation rate and complex evolutionary patterns. Next-generation sequencing (NGS has been widely used for qualitative and semi-quantitative assessment of genetic diversity in complex biological samples. The "deep sequencing" approach, enabled by the enormous throughput of current NGS platforms, allows the identification of rare genetic viral variants in targeted genetic regions, but is usually limited to a small number of samples. METHODOLOGY AND PRINCIPAL FINDINGS: We designed a proof-of-principle study to test whether redistributing sequencing throughput from a high depth-small sample number towards a low depth-large sample number approach is feasible and contributes to influenza epidemiological surveillance. Using 454-Roche sequencing, we sequenced at a rather low depth, a 307 bp amplicon of the neuraminidase gene of the Influenza A(H1N1 pandemic (A(H1N1pdm virus from cDNA amplicons pooled in 48 barcoded libraries obtained from nasal swab samples of infected patients (n  =  299 taken from May to November, 2009 pandemic period in Mexico. This approach revealed that during the transition from the first (May-July to second wave (September-November of the pandemic, the initial genetic variants were replaced by the N248D mutation in the NA gene, and enabled the establishment of temporal and geographic associations with genetic diversity and the identification of mutations associated with oseltamivir resistance. CONCLUSIONS: NGS sequencing of a short amplicon from the NA gene at low sequencing depth allowed genetic screening of a large number of samples, providing insights to viral genetic diversity dynamics and the identification of genetic variants associated with oseltamivir resistance. Further research is needed to explain the observed replacement of the genetic variants seen during the second wave. As sequencing throughput rises and library multiplexing and automation improves, we foresee that

Ibrutinib Therapy Increases T Cell Repertoire Diversity in Patients with Chronic Lymphocytic Leukemia.

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Yin, Qingsong; Sivina, Mariela; Robins, Harlan; Yusko, Erik; Vignali, Marissa; O'Brien, Susan; Keating, Michael J; Ferrajoli, Alessandra; Estrov, Zeev; Jain, Nitin; Wierda, William G; Burger, Jan A

2017-02-15

The Bruton's tyrosine kinase inhibitor ibrutinib is a highly effective, new targeted therapy for chronic lymphocytic leukemia (CLL) that thwarts leukemia cell survival, growth, and tissue homing. The effects of ibrutinib treatment on the T cell compartment, which is clonally expanded and thought to support the growth of malignant B cells in CLL, are not fully characterized. Using next-generation sequencing technology, we characterized the diversity of TCRβ-chains in peripheral blood T cells from 15 CLL patients before and after 1 y of ibrutinib therapy. We noted elevated CD4 + and CD8 + T cell numbers and a restricted TCRβ repertoire in all pretreatment samples. After 1 y of ibrutinib therapy, elevated peripheral blood T cell numbers and T cell-related cytokine levels had normalized, and T cell repertoire diversity increased significantly. Dominant TCRβ clones in pretreatment samples declined or became undetectable, and the number of productive unique clones increased significantly during ibrutinib therapy, with the emergence of large numbers of low-frequency TCRβ clones. Importantly, broader TCR repertoire diversity was associated with clinical efficacy and lower rates of infections during ibrutinib therapy. These data demonstrate that ibrutinib therapy increases diversification of the T cell compartment in CLL patients, which contributes to cellular immune reconstitution. Copyright © 2017 by The American Association of Immunologists, Inc.

Metagenomic analysis of viral diversity in respiratory samples from patients with respiratory tract infections in Kuwait.

Science.gov (United States)

Madi, Nada; Al-Nakib, Widad; Mustafa, Abu Salim; Habibi, Nazima

2018-03-01

A metagenomic approach based on target independent next-generation sequencing has become a known method for the detection of both known and novel viruses in clinical samples. This study aimed to use the metagenomic sequencing approach to characterize the viral diversity in respiratory samples from patients with respiratory tract infections. We have investigated 86 respiratory samples received from various hospitals in Kuwait between 2015 and 2016 for the diagnosis of respiratory tract infections. A metagenomic approach using the next-generation sequencer to characterize viruses was used. According to the metagenomic analysis, an average of 145, 019 reads were identified, and 2% of these reads were of viral origin. Also, metagenomic analysis of the viral sequences revealed many known respiratory viruses, which were detected in 30.2% of the clinical samples. Also, sequences of non-respiratory viruses were detected in 14% of the clinical samples, while sequences of non-human viruses were detected in 55.8% of the clinical samples. The average genome coverage of the viruses was 12% with the highest genome coverage of 99.2% for respiratory syncytial virus, and the lowest was 1% for torque teno midi virus 2. Our results showed 47.7% agreement between multiplex Real-Time PCR and metagenomics sequencing in the detection of respiratory viruses in the clinical samples. Though there are some difficulties in using this method to clinical samples such as specimen quality, these observations are indicative of the promising utility of the metagenomic sequencing approach for the identification of respiratory viruses in patients with respiratory tract infections. © 2017 Wiley Periodicals, Inc.

Intra-arterial and intra-venous chemotherapy combined with radiation in the treatment of brain tumours

International Nuclear Information System (INIS)

Watne, K.

1992-01-01

The present investigations were undertaken to study the effect of combining different modalities of chemotherapy with radiation in post-operative treatment of brain tumours. The conclusions and clinical implication of the investigations are as follows: The combination of combined intra-arterial chemotherapy followed by radiation leads to an increased median survival with more long term survivors in patients with anaplastic astrocytomas and in patients older than 40 years with astrocytomas. In patients with glioblastoma multiforme, this modality of treatment do not improve median survival, but an increased number of long-term survivors may be seen. Patients younger than 40 years with astrocytomas do not benefit from this modality of treatment. A parallelism exists between sensitivity to chemotherapy and response to radiotherapy. Patients who will benefit from the treatment may be selected early, normally two months after treatment start. Combining intra-arterial chemotherapy and radiation does not lead to an increased incidence of adverse CNS reactions. Specific transient abnormalities in the brain may occur during the first year after treatment and may be misinterpreted as tumour recurrence. EEG may be valuable in predicting adverse CNS reactions following treatment. Nuclear brain scan may be of valuable in selecting the patients who are in danger of developing adverse CNS reactions. Intra-arterial chemotherapy does have an effect in patients with brain tumours who have recurrent tumour after radiation. The most important prognostic factors are age, corticosteroid dependency at treatment start, performance status, histology and frontal lobe location. 103 refs., 2 tabs

Interaction between intra-abdominal pressure and positive-end expiratory pressure

Directory of Open Access Journals (Sweden)

Jamili Anbar Torquato

2009-02-01

Full Text Available OBJECTIVE: The aim of this study was to quantify the interaction between increased intra-abdominal pressure and Positive-End Expiratory Pressure. METHODS: In 30 mechanically ventilated ICU patients with a fixed tidal volume, respiratory system plateau and abdominal pressure were measured at a Positive-End Expiratory Pressure level of zero and 10 cm H2O. The measurements were repeated after placing a 5 kg weight on the patients' belly. RESULTS: After the addition of 5 kg to the patients' belly at zero Positive-End Expiratory Pressure, both intra-abdominal pressure (p<0.001 and plateau pressures (p=0.005 increased significantly. Increasing the Positive-End Expiratory Pressure levels from zero to 10 cm H2O without weight on the belly did not result in any increase in intra-abdominal pressure (p=0.165. However, plateau pressures increased significantly (p< 0.001. Increasing Positive-End Expiratory Pressure from zero to 10 cm H2O and adding 5 kg to the belly increased intra-abdominal pressure from 8.7 to 16.8 (p<0.001 and plateau pressure from 18.26 to 27.2 (p<0.001. Maintaining Positive-End Expiratory Pressure at 10 cm H2O and placing 5 kg on the belly increased intra-abdominal pressure from 12.3 +/- 1.7 to 16.8 +/- 1.7 (p<0.001 but did not increase plateau pressure (26.6+/-1.2 to 27.2 +/-1.1 -p=0.83. CONCLUSIONS: The addition of a 5kg weight onto the abdomen significantly increased both IAP and the airway plateau pressure, confirming that intra-abdominal hypertension elevates the plateau pressure. However, plateau pressure alone cannot be considered a good indicator for the detection of elevated intra-abdominal pressure in patients under mechanical ventilation using PEEP. In these patients, the intra-abdominal pressure must also be measured.

Endophytic bacterial diversity in grapevine (Vitis vinifera L.) leaves described by 16S rRNA gene sequence analysis and length heterogeneity-PCR.

Science.gov (United States)

Bulgari, Daniela; Casati, Paola; Brusetti, Lorenzo; Quaglino, Fabio; Brasca, Milena; Daffonchio, Daniele; Bianco, Piero Attilio

2009-08-01

Diversity of bacterial endophytes associated with grapevine leaf tissues was analyzed by cultivation and cultivation-independent methods. In order to identify bacterial endophytes directly from metagenome, a protocol for bacteria enrichment and DNA extraction was optimized. Sequence analysis of 16S rRNA gene libraries underscored five diverse Operational Taxonomic Units (OTUs), showing best sequence matches with gamma-Proteobacteria, family Enterobacteriaceae, with a dominance of the genus Pantoea. Bacteria isolation through cultivation revealed the presence of six OTUs, showing best sequence matches with Actinobacteria, genus Curtobacterium, and with Firmicutes genera Bacillus and Enterococcus. Length Heterogeneity-PCR (LH-PCR) electrophoretic peaks from single bacterial clones were used to setup a database representing the bacterial endophytes identified in association with grapevine tissues. Analysis of healthy and phytoplasma-infected grapevine plants showed that LH-PCR could be a useful complementary tool for examining the diversity of bacterial endophytes especially for diversity survey on a large number of samples.

Intra-abdominal pressure and abdominal compartment syndrome in acute general surgery.

LENUS (Irish Health Repository)

Sugrue, Michael

2012-01-31

BACKGROUND: Intra-abdominal pressure (IAP) is a harbinger of intra-abdominal mischief, and its measurement is cheap, simple to perform, and reproducible. Intra-abdominal hypertension (IAH), especially grades 3 and 4 (IAP > 18 mmHg), occurs in over a third of patients and is associated with an increase in intra-abdominal sepsis, bleeding, renal failure, and death. PATIENTS AND METHODS: Increased IAP reading may provide an objective bedside stimulus for surgeons to expedite diagnostic and therapeutic work-up of critically ill patients. One of the greatest challenges surgeons and intensivists face worldwide is lack of recognition of the known association between IAH, ACS, and intra-abdominal sepsis. This lack of awareness of IAH and its progression to ACS may delay timely intervention and contribute to excessive patient resuscitation. CONCLUSIONS: All patients entering the intensive care unit (ICU) after emergency general surgery or massive fluid resuscitation should have an IAP measurement performed every 6 h. Each ICU should have guidelines relating to techniques of IAP measurement and an algorithm for management of IAH.

Diversity analysis of gut microbiota in osteoporosis and osteopenia patients

Directory of Open Access Journals (Sweden)

Jihan Wang

2017-06-01

Full Text Available Some evidence suggests that bone health can be regulated by gut microbiota. To better understand this, we performed 16S ribosomal RNA sequencing to analyze the intestinal microbial diversity in primary osteoporosis (OP patients, osteopenia (ON patients and normal controls (NC. We observed an inverse correlation between the number of bacterial taxa and the value of bone mineral density. The diversity estimators in the OP and ON groups were increased compared with those in the NC group. Beta diversity analyses based on hierarchical clustering and principal coordinate analysis (PCoA could discriminate the NC samples from OP and ON samples. Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria constituted the four dominant phyla in all samples. Proportion of Firmicutes was significantly higher and Bacteroidetes was significantly lower in OP samples than that in NC samples (p < 0.05, Gemmatimonadetes and Chloroflexi were significantly different between OP and NC group as well as between ON and NC group (p < 0.01. A total of 21 genera with proportions above 1% were detected and Bacteroides accounted for the largest proportion in all samples. The Blautia, Parabacteroides and Ruminococcaceae genera differed significantly between the OP and NC group (p < 0.05. Linear discriminant analysis (LDA results showed one phylum community and seven phylum communities were enriched in ON and OP, respectively. Thirty-five genus communities, five genus communities and two genus communities were enriched in OP, ON and NC, respectively. The results of this study indicate that gut microbiota may be a critical factor in osteoporosis development, which can further help us search for novel biomarkers of gut microbiota in OP and understand the interaction between gut microbiota and bone health.

Diversity analysis of gut microbiota in osteoporosis and osteopenia patients.

Science.gov (United States)

Wang, Jihan; Wang, Yangyang; Gao, Wenjie; Wang, Biao; Zhao, Heping; Zeng, Yuhong; Ji, Yanhong; Hao, Dingjun

2017-01-01

Some evidence suggests that bone health can be regulated by gut microbiota. To better understand this, we performed 16S ribosomal RNA sequencing to analyze the intestinal microbial diversity in primary osteoporosis (OP) patients, osteopenia (ON) patients and normal controls (NC). We observed an inverse correlation between the number of bacterial taxa and the value of bone mineral density. The diversity estimators in the OP and ON groups were increased compared with those in the NC group. Beta diversity analyses based on hierarchical clustering and principal coordinate analysis (PCoA) could discriminate the NC samples from OP and ON samples. Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria constituted the four dominant phyla in all samples. Proportion of Firmicutes was significantly higher and Bacteroidetes was significantly lower in OP samples than that in NC samples ( p  < 0.05), Gemmatimonadetes and Chloroflexi were significantly different between OP and NC group as well as between ON and NC group ( p  < 0.01). A total of 21 genera with proportions above 1% were detected and Bacteroides accounted for the largest proportion in all samples. The Blautia, Parabacteroides and Ruminococcaceae genera differed significantly between the OP and NC group ( p  < 0.05). Linear discriminant analysis (LDA) results showed one phylum community and seven phylum communities were enriched in ON and OP, respectively. Thirty-five genus communities, five genus communities and two genus communities were enriched in OP, ON and NC, respectively. The results of this study indicate that gut microbiota may be a critical factor in osteoporosis development, which can further help us search for novel biomarkers of gut microbiota in OP and understand the interaction between gut microbiota and bone health.

Sequence diversity and copy number variation of Mutator-like transposases in wheat

Directory of Open Access Journals (Sweden)

Nobuaki Asakura

2008-01-01

Full Text Available Partial transposase-coding sequences of Mutator-like elements (MULEs were isolated from a wild einkorn wheat, Triticum urartu, by degenerate PCR. The isolated sequences were classified into a MuDR or Class I clade and divided into two distinct subclasses (subclass I and subclass II. The average pair-wise identity between members of both subclasses was 58.8% at the nucleotide sequence level. Sequence diversity of subclass I was larger than that of subclass II. DNA gel blot analysis showed that subclass I was present as low copy number elements in the genomes of all Triticum and Aegilops accessions surveyed, while subclass II was present as high copy number elements. These two subclasses seemed uncapable of recognizing each other for transposition. The number of copies of subclass II elements was much higher in Aegilops with the S, Sl and D genomes and polyploid Triticum species than in diploid Triticum with the A genome, indicating that active transposition occurred in S, Sl and D genomes before polyploidization. DNA gel blot analysis of six species selected from three subfamilies of Poaceae demonstrated that only the tribe Triticeae possessed both subclasses. These results suggest that the differentiation of these two subclasses occurred before or immediately after the establishment of the tribe Triticeae.

Molecular sequence data of hepatitis B virus and genetic diversity after vaccination.

Science.gov (United States)

van Ballegooijen, W Marijn; van Houdt, Robin; Bruisten, Sylvia M; Boot, Hein J; Coutinho, Roel A; Wallinga, Jacco

2009-12-15

The effect of vaccination programs on transmission of infectious disease is usually assessed by monitoring programs that rely on notifications of symptomatic illness. For monitoring of infectious diseases with a high proportion of asymptomatic cases or a low reporting rate, molecular sequence data combined with modern coalescent-based techniques offer a complementary tool to assess transmission. Here, the authors investigate the added value of using viral sequence data to monitor a vaccination program that was started in 1998 and was targeted against hepatitis B virus in men who have sex with men in Amsterdam, the Netherlands. The incidence in this target group, as estimated from the notifications of acute infections with hepatitis B virus, was low; therefore, there was insufficient power to show a significant change in incidence. In contrast, the genetic diversity, as estimated from the viral sequence collected from the target group, revealed a marked decrease after vaccination was introduced. Taken together, the findings suggest that introduction of vaccination coincided with a change in the target group toward behavior with a higher risk of infection. The authors argue that molecular sequence data provide a powerful additional monitoring instrument, next to conventional case registration, for assessing the impact of vaccination.

Intra-arterial port implantation for intra-arterial chemotherapy : comparison between PIPS(Percutaneously Implantable Port System) and port system

International Nuclear Information System (INIS)

Yoon, Sang Jin; Shim, Hyung Jin; Jung, Hun Young; Choi, Yong Ho; Kim, Yang Soo; Song, In Sup; Kwak, Byung Kook

1999-01-01

To compare the techniques and complications of intra-arterial port implantation for intra-arterial chemotherapy between PIPS and the port system. For intra-arterial port implantation, 27 cases in 27 patients were retrospectively evaluated using PIPS(PIPS-200, William Cook Europe, Denmark) while for 21 cases in 19 patients a pediatric venous port system(Port-A-Cath, 5.8F, SIMS Deltec, U. S. A.) was used. All intra-arterial port implantation was performed percuteneously in an angiographic ward. Hepatocellular carcinoma was diagnosed in 18 patients and hepatic metastasis in 16. Peripheral cholangiocarcinoma, and pancreatic gastric, ovarian, renal cell and colon carcinoma were included. We compared the techniques and complications between PIPS and the port system. The follow up period ranged from 23 to 494(mean, 163) days in PIPS and from 12 to 431(mean, 150) days in the port system. In all cases, intra-arterial port implantations were technically successful. Port catheter tips were located in the common hepatic artery(n=8), proper hepatic artery(n=7), right hepatic artery(n=5), gastroduodenal artery(n=2), left hepatic artery(n=1), pancreaticoduodenal artery(n=1), inferior mesenteric artery(n=1), lumbar artery(n=1), and renal artery(n=1) in PIPS, and in the proper hepatic artery(n=6), gastroduodenal artery(n=6), common hepatic artery(n=3), right hepatic artery(n=4), inferior mesenteric artery(n=1), and internal iliac artery(n=1) in the port system. Port chambers were buried in infrainguinal subcutaneous tissue. Using PIPS, complications developed in seven cases(25.9%) and of these, four (57.1%) were catheter or chamber related. In the port system, catheter or chamber related complications developed in four cases(19.0%). Because PIPS and the port system have relative merits and demetrits, successful intra-arterial port implantation is possible if equipment is properly selected

Patient doses during intra-oral radiography in dental offices

International Nuclear Information System (INIS)

Sakaino, Rie; Harata, Yasuo; Okano, Tomohiro; Sato, Kenji; Yosue, Takashi; Nishikawa, Keiichi; Sano, Tsukasa; Kobayashi, Ikuo

2011-01-01

Measurement of patient entrance dose (PED) and dose area product (DAP) at various dental offices in the Tokyo bay area and comparison of PEDs with the existing diagnostic reference levels recommended in the United Kingdom (UK). The survey included 28 dental clinics categorized by the type of intra-oral radiography used. PED was measured by placing an optically stimulated luminescence dosimeter (OSLD) at the tip of the cone. Exposure parameters were those used for the adult mandibular molar region in the respective clinics. The OSLD readings were calibrated using an ionizing chamber manufactured according to standards of the Japan Quality Assurance Organization. The area (A), of the X-ray beam, was calculated by exposing an X-ray film placed at the tip of the cone and measuring the exposed area. Then the DAP was calculated as the product of PED times A. The PED estimated at various dental clinics differed by a factor of 120. The mean, minimum, maximum, median and third quartile values of PEDs were 4.99, 0.18, 21.7, 3.60 and 5.76 mGy, respectively. At 60-70 kV, PEDs observed in clinics using digital imaging systems were below 2.1 mGy which was lower than that of clinics using films that were E-speed or faster. It was also observed that PEDs were directly proportional to the tube current and exposure time. The mean, minimum, maximum, median and third quartile of DAPs were 13.0, 0.45, 61.4, 9.34 and 13.4 cGy cm 2 , respectively. The DAP values showed a linear correlation coefficient of 0.99 with PED values. Measurement of PED and DAP using OSLD and X-ray film can play a useful role in optimization of radiation protection for patients during intra-oral radiography. This method can be conveniently applied to set up diagnostic reference levels by carrying out mass surveys in Japan. (author)

Phylogenetic diversity in the core group of Peziza inferred from ITS sequences and morphology

DEFF Research Database (Denmark)

Hansen, K.; Læssøe, Thomas; Pfister, D.H.

2002-01-01

Species delimitation within the core group of Peziza is highly controversial. The group, typified by P. vesiculosa, is morphologically coherent and in previous analyses of LSU rDNA sequences it formed a highly supported clade. Phylogenetic diversity and species limits were investigated within......), shallowly cup- to disc-shaped apothecia (A) and large (up to 15 cm), deeply cup-shaped to expanded apothecia (B). The overall exciple structure (a stratified or non-stratified medullary layer) and to some degree spore surface relief, likewise support the groupings. Clade A contains taxa with smooth...... that populations on a diverse array of substrates may be closely related, or indeed, conspecific....

[Bacterial diversity in sequencing batch biofilm reactor (SBBR) for landfill leachate treatment using PCR-DGGE].

Science.gov (United States)

Xiao, Yong; Yang, Zhao-hui; Zeng, Guang-ming; Ma, Yan-he; Liu, You-sheng; Wang, Rong-juan; Xu, Zheng-yong

2007-05-01

For studying the bacterial diversity and the mechanism of denitrification in sequencing bath biofilm reactor (SBBR) treating landfill leachate to provide microbial evidence for technique improvements, total microbial DNA was extracted from samples which were collected from natural landfill leachate and biofilm of a SBBR that could efficiently remove NH4+ -N and COD of high concentration. 16S rDNA fragments were amplified from the total DNA successfully using a pair of universal bacterial 16S rDNA primer, GC341F and 907R, and then were used for denaturing gradient gel electrophoresis (DGGE) analysis. The bands in the gel were analyzed by statistical methods and excided from the gel for sequencing, and the sequences were used for homology analysis and then two phylogenetic trees were constructed using DNAStar software. Results indicated that the bacterial diversity of the biofilm in SBBR and the landfill leachate was abundant, and no obvious change of community structure happened during running in the biofilm, in which most bacteria came from the landfill leachate. There may be three different modes of denitrification in the reactor because several different nitrifying bacteria, denitrifying bacteria and anaerobic ammonia oxidation bacteria coexisted in it. The results provided some valuable references for studying microbiological mechanism of denitrification in SBBR.

Cultural diversity and patient teaching.

Science.gov (United States)

Price, J L; Cordell, B

1994-01-01

Cultural diversity challenges health care providers to facilitate bridging cross-cultural gaps with clients. It is through providing culturally relevant care that health care practitioners truly serve the needs of all clients in our diverse society. A theory of Cultural Care Diversity and Universality offers a framework for building linkages of clinical knowledge to cultural care. A four-step approach to providing culturally sensitive patient teaching is described: (1) health care providers should assess their own cultural beliefs and be aware of general ethnic, regional, and religious beliefs and practices in their area; (2) develop a teaching plan; (3) implement the plan; (4) evaluate the success of the teaching-learning process and make alterations based on evaluation. When providers assess clients' beliefs and practices and incorporate them into the teaching plan design, teaching becomes more relevant and clients become more successful at learning.

Diversity analysis in Cannabis sativa based on large-scale development of expressed sequence tag-derived simple sequence repeat markers.

Science.gov (United States)

Gao, Chunsheng; Xin, Pengfei; Cheng, Chaohua; Tang, Qing; Chen, Ping; Wang, Changbiao; Zang, Gonggu; Zhao, Lining

2014-01-01

Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SSRs were identified from 3,624 ESTs. From there, a total of 3,442 complementary primer pairs were designed as SSR markers. Among these markers, trinucleotide repeat motifs (50.99%) were the most abundant, followed by hexanucleotide (25.13%), dinucleotide (16.34%), tetranucloetide (3.8%), and pentanucleotide (3.74%) repeat motifs, respectively. The AAG/CTT trinucleotide repeat (17.96%) was the most abundant motif detected in the SSRs. One hundred and seventeen EST-SSR markers were randomly selected to evaluate primer quality in 24 cannabis varieties. Among these 117 markers, 108 (92.31%) were successfully amplified and 87 (74.36%) were polymorphic. Forty-five polymorphic primer pairs were selected to evaluate genetic diversity and relatedness among the 115 cannabis genotypes. The results showed that 115 varieties could be divided into 4 groups primarily based on geography: Northern China, Europe, Central China, and Southern China. Moreover, the coefficient of similarity when comparing cannabis from Northern China with the European group cannabis was higher than that when comparing with cannabis from the other two groups, owing to a similar climate. This study outlines the first large-scale development of SSR markers for cannabis. These data may serve as a foundation for the development of genetic linkage, quantitative trait loci mapping, and marker-assisted breeding of cannabis.

Angiographic evaluation of the effect of intra-arterial milrinone therapy in patients with vasospasm from aneurysmal subarachnoid hemorrhage.

Science.gov (United States)

Shankar, Jai Jai Shiva; dos Santos, Marlise P; Deus-Silva, Leonardo; Lum, Cheemun

2011-02-01

Several methods have been used to treat cerebral vasospasm, which is a major cause of morbidity and mortality in patients with aneurysmal subarachnoid hemorrhage (SAH). Here, we examined the effectiveness and safety of intra-arterial injection of milrinone for the treatment of vasospasm. Consecutive patients with angiographically confirmed vasospasm received intra-arterial milrinone between January 2006 and December 2007. The improvement in diameter of vessel (in millimeters) following treatment was assessed by paired t test for statistical significance. The angiographic improvement of supraclinoid internal carotid artery, M1 segment of middle cerebral artery, and A1 and A2 segment of anterior cerebral artery was compared with the modified Rankin score of the patients at discharge. A total of 15 milrinone treatments were performed in 14 patients (11 females and 3 males) with mean age of 52.7 years (31-68 years). There was significant angiographic improvement after milrinone therapy (p milrinone was a safe and effective treatment of cerebral vasospasm following aneurysmal SAH.

Comparison of the Diversity of Basidiomycetes from Dead Wood of the Manchurian fir (Abies holophylla) as Evaluated by Fruiting Body Collection, Mycelial Isolation, and 454 Sequencing.

Science.gov (United States)

Jang, Yeongseon; Jang, Seokyoon; Min, Mihee; Hong, Joo-Hyun; Lee, Hanbyul; Lee, Hwanhwi; Lim, Young Woon; Kim, Jae-Jin

2015-10-01

In this study, three different methods (fruiting body collection, mycelial isolation, and 454 sequencing) were implemented to determine the diversity of wood-inhabiting basidiomycetes from dead Manchurian fir (Abies holophylla). The three methods recovered similar species richness (26 species from fruiting bodies, 32 species from mycelia, and 32 species from 454 sequencing), but Fisher's alpha, Shannon-Wiener, Simpson's diversity indices of fungal communities indicated fruiting body collection and mycelial isolation displayed higher diversity compared with 454 sequencing. In total, 75 wood-inhabiting basidiomycetes were detected. The most frequently observed species were Heterobasidion orientale (fruiting body collection), Bjerkandera adusta (mycelial isolation), and Trichaptum fusco-violaceum (454 sequencing). Only two species, Hymenochaete yasudae and Hypochnicium karstenii, were detected by all three methods. This result indicated that Manchurian fir harbors a diverse basidiomycetous fungal community and for complete estimation of fungal diversity, multiple methods should be used. Further studies are required to understand their ecology in the context of forest ecosystems.

Donepezil treatment in ethnically diverse patients with Alzheimer disease.

Science.gov (United States)

Tinklenberg, Jared R; Kraemer, Helena C; Yaffe, Kristine; O'Hara, Ruth; Ringman, John M; Ashford, John W; Yesavage, Jerome A; Taylor, Joy L

2015-04-01

To compare the outcome of donepezil treatment in ethnically diverse Alzheimer disease (AD) patients with ethnically diverse AD patients who did not receive donepezil. Patients meeting NINCDS-ADRA criteria for probable or possible AD from a consortium of California sites were systematically followed for at least 1 year in this prospective, observational study. Their treatment regimens, including prescription of donepezil, were determined by their individual physician according to his or her usual criteria. Patients self-identified their ethnicity. The 64 ethnically diverse AD patients who completed the study and received donepezil treatment had an average 1-year decline of 2.30 points (standard deviation: 3.9) on the 30-point Mini-Mental State Exam compared with a 1.70-point (standard deviation: 4.2) decline in the 74 ethnically diverse completers who received no donepezil or other anti-AD drugs during the study period. This difference was not statistically significant. The overall Cohen effect size of this treatment-associated difference was estimated at -0.15. After using propensity analyses and other techniques to assess factors that could bias prescribing decisions, the lack of benefits associated with donepezil treatment remained. The lack of donepezil benefits also remained when more traditional analyses were applied to these data. Ethnically diverse AD patients in this study apparently did not benefit from 1 year of donepezil treatment. These unpromising results are in contrast to modest benefits of donepezil treatment measured in a directly comparable California study involving white non-Latino AD patients. Published by Elsevier Inc.

Molecular detection and sequence characterization of diverse rhabdoviruses in bats, China.

Science.gov (United States)

Xu, Lin; Wu, Jianmin; Jiang, Tinglei; Qin, Shaomin; Xia, Lele; Li, Xingyu; He, Biao; Tu, Changchun

2018-01-15

The Rhabdoviridae is among the most diverse families of RNA viruses and currently classified into 18 genera with some rhabdoviruses lethal to humans and other animals. Herein, we describe genetic characterization of three novel rhabdoviruses from bats in China. Of these, two viruses (Jinghong bat virus and Benxi bat virus) found in Rhinolophus bats showed a phylogenetic relationship with vesiculoviruses, and sequence analyses indicate that they represent two new species within the genus Vesiculovirus. The remaining Yangjiang bat virus found in Hipposideros larvatus bats were only distantly related to currently known rhabdoviruses. Copyright © 2017 Elsevier B.V. All rights reserved.

GROUPING WEB ACCESS SEQUENCES uSING SEQUENCE ALIGNMENT METHOD

OpenAIRE

BHUPENDRA S CHORDIA; KRISHNAKANT P ADHIYA

2011-01-01

In web usage mining grouping of web access sequences can be used to determine the behavior or intent of a set of users. Grouping websessions is how to measure the similarity between web sessions. There are many shortcomings in traditional measurement methods. The taskof grouping web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-groupsimilarity is done using sequence alignment method. This paper introduces a new method to group we...

Does intra-abdominal fluid increase the resting energy expenditure?

Science.gov (United States)

Zarling, E J; Grande, A; Hano, J

1997-10-01

In patients with intra-abdominal fluid collection, caloric needs are based on an estimated dry weight. This is done because intra-abdominal fluid has been assumed to be metabolically inactive. One recent study of patients with slowly resolving ascites suggested otherwise. In our study, the effect of intra-abdominal fluid on the resting energy expenditure (REE) and apparent lean body mass was determined in 10 stable patients requiring peritoneal dialysis. For each subject, in both the empty and full state, we measured REE by indirect calorimetry, and body composition by the bioelectric impedance method. In the full state, the VCO2 was significantly increased (210 +/- 11 versus 197 +/- 9 mL/min, P empty state. This caused an increase in the calculated resting energy expenditure (1531 +/- 88 kcal/d empty versus 1593 +/- 94 kcal/d full, P calories derived from glucose absorbed out of the dialysate. Estimates of body fat, lean body mass, and total water also were not affected by the intra-abdominal fluid. We conclude that intra-abdominal fluid will not affect the measured REE and hence may be considered to be metabolically inactive.

Intra-Hospital Transport of Patients on Non-Invasive Ventilation: Review, Analysis, and Key Practical Recommendations by the International NIV Committee

Directory of Open Access Journals (Sweden)

Annia Schreiber

2017-12-01

Full Text Available Intra-hospital transport is often needed for diagnostic and therapeutic procedures that cannot be performed at the bedside. However, moving patients from the safe environment of an Intensive Care Unit (ICU can lead to a variety of complications and adverse events, the risk is even higher in ventilated patients. This review is intended as a guide on how to prevent and avoid these adverse events during intra-hospital transport of patients on non-invasive ventilation (NIV. Greater attention should be paid to NIV indications and the selection of the patients to be transported. Detailed planning, preparation, and communication between the ward of origin and destination site, appropriate equipment, skilled staff, and continuous monitoring are the key major determinants of success in transporting critically ill patients on NIV. These points are discussed and analyzed in detail.

Reliability of Ultrasound Diameter Measurements in Patients with a Small Asymptomatic Popliteal Artery Aneurysm: An Intra- and Inter-observer Agreement Study.

Science.gov (United States)

Zwiers, I; Hoogland, C M T; Mackaay, A J C

2016-03-01

In this study the intra- and inter-observer variability of ultrasound measurements of the diameter of the popliteal artery were tested in a group of patients under surveillance for a small (diameter 10-20 mm), asymptomatic popliteal artery aneurysm (PAA). From a group of patients under ultrasound surveillance for bilateral, asymptomatic PAAs, 13 consecutive patients agreed to participate in the study and provided informed consent. The maximum diameter of the popliteal arteries was assessed by a vascular technologist. The same assessment was repeated by a second vascular technologist, unaware of the results of the first measurement. After a week, this protocol was repeated. The intra- and inter-observer reliability of this measurement was calculated using intra-class correlation coefficients (ICCs) and Bland and Altman plots. Of the 10 patients with bilateral and three patients with unilateral PAA, 12 completed the 2 week protocol. A total of 86 measurements were analyzed. The mean diameter of the popliteal arteries was 13.5 ± 3.4 mm. The ICC for the intra-observer reliability of observer 1 was 0.96 (95% CI 0.92-0.99), p .47. The absolute magnitude of the systematic error of both observers was less than 0.135 mm (median 0.00). Ultrasound measurement of the maximum diameter of the popliteal artery is reproducible; hence, it is suitable for making a clinical treatment decision. Its use for surveillance of small, asymptomatic PAAs is justified. Copyright © 2015 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

Dengue 1 diversity and microevolution, French Polynesia 2001-2006: connection with epidemiology and clinics.

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Elodie Descloux

Full Text Available BACKGROUND: Dengue fever (DF is an emerging infectious disease in the tropics and subtropics. Determinants of DF epidemiology and factors involved in severe cases-dengue haemorrhagic fever (DHF and dengue shock syndrome (DSS-remain imperfectly characterized. Since 2000, serotype 1 (DENV-1 has predominated in the South Pacific. The aim of this study was (i to determine the origin and (ii to study the evolutionary relationships of DENV-1 viruses that have circulated in French Polynesia (FP from the severe 2001 outbreak to the recent 2006 epidemic, and (iii to analyse the viral intra-host genetic diversity according to clinical presentation. METHODOLOGY/PRINCIPAL FINDINGS: Sequences of 181 envelope gene and 12 complete polyproteins of DENV-1 viruses obtained from human sera in FP during the 2001-2006 period were generated. Phylogenetic analysis showed that all DENV-1 FP strains belonged to genotype IV-"South Pacific" and derived from a single introduction event from South-East Asia followed by a 6-year in situ evolution. Although the ratio of nonsynonymous/synonymous substitutions per site indicated strong negative selection, a mutation in the envelope glycoprotein (S222T appeared in 2002 and was subsequently fixed. It was noted that genetic diversification was very significant during the 2002-2005 period of endemic DENV-1 circulation. For nine DF sera and eight DHF/DSS sera, approximately 40 clones/serum of partial envelope gene were sequenced. Importantly, analysis revealed that the intra-host genetic diversity was significantly lower in severe cases than in classical DF. CONCLUSIONS/SIGNIFICANCE: First, this study showed that DENV-1 epidemiology in FP was different from that described in other South-Pacific islands, characterized by a long sustained viral circulation and the absence of new viral introduction over a 6-year period. Second, a significant part of DENV-1 evolution was observed during the endemic period characterized by the rapid

DS-CDMA satellite diversity reception for personal satellite communication: Downlink performance analysis

Science.gov (United States)

DeGaudenzi, Riccardo; Giannetti, Filippo

1995-01-01

The downlink of a satellite-mobile personal communication system employing power-controlled Direct Sequence Code Division Multiple Access (DS-CDMA) and exploiting satellite-diversity is analyzed and its performance compared with a more traditional communication system utilizing single satellite reception. The analytical model developed has been thoroughly validated by means of extensive Monte Carlo computer simulations. It is shown how the capacity gain provided by diversity reception shrinks considerably in the presence of increasing traffic or in the case of light shadowing conditions. Moreover, the quantitative results tend to indicate that to combat system capacity reduction due to intra-system interference, no more than two satellites shall be active over the same region. To achieve higher system capacity, differently from terrestrial cellular systems, Multi-User Detection (MUD) techniques are likely to be required in the mobile user terminal, thus considerably increasing its complexity.

Genetic diversity and molecular evolution of Naga King Chili inferred from internal transcribed spacer sequence of nuclear ribosomal DNA.

Science.gov (United States)

Kehie, Mechuselie; Kumaria, Suman; Devi, Khumuckcham Sangeeta; Tandon, Pramod

2016-02-01

Sequences of the Internal Transcribed Spacer (ITS1-5.8S-ITS2) of nuclear ribosomal DNAs were explored to study the genetic diversity and molecular evolution of Naga King Chili. Our study indicated the occurrence of nucleotide polymorphism and haplotypic diversity in the ITS regions. The present study demonstrated that the variability of ITS1 with respect to nucleotide diversity and sequence polymorphism exceeded that of ITS2. Sequence analysis of 5.8S gene revealed a much conserved region in all the accessions of Naga King Chili. However, strong phylogenetic information of this species is the distinct 13 bp deletion in the 5.8S gene which discriminated Naga King Chili from the rest of the Capsicum sp. Neutrality test results implied a neutral variation, and population seems to be evolving at drift-mutation equilibrium and free from directed selection pressure. Furthermore, mismatch analysis showed multimodal curve indicating a demographic equilibrium. Phylogenetic relationships revealed by Median Joining Network (MJN) analysis denoted a clear discrimination of Naga King Chili from its closest sister species (Capsicum chinense and Capsicum frutescens). The absence of star-like network of haplotypes suggested an ancient population expansion of this chili.

Intentional intra-arterial injection of midazolam in a patient with status epilepticus in the intensive care unit

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Muhammad Asghar Ali

2017-01-01

Full Text Available Fundamental medical care includes intravenous (IV access which provides prompt resuscitation and reliable delivery of analgesics, antibiotics, and vasoactive medication. Difficult access populations, especially in critical area, continue to challenge providers to consider and utilize alternative means to provide IV access. Potential options under such circumstances include intramuscular, intraosseous, and intratracheal drug administration, but in extreme cases where no other options are available, intra-arterial route might be considered. We present a case where midazolam was intentionally injected intra-arterially to abort seizure activity in a patient with status epilepticus in the Intensive Care Unit.

Mechanical ventilation and intra-abdominal hypertension: 'Beyond Good and Evil'

OpenAIRE

Pelosi, Paolo; Vargas, Maria

2012-01-01

Intra-abdominal hypertension is frequent in surgical and medical critically ill patients. Intra-abdominal hypertension has a serious impact on the function of respiratory as well as peripheral organs. In the presence of alveolar capillary damage, which occurs in acute respiratory distress syndrome (ARDS), intra-abdominal hypertension promotes lung injury as well as edema, impedes the pulmonary lymphatic drainage, and increases intra-thoracic pressures, leading to atelectasis, airway closure, ...

A case study in intra-abdominal sepsis.

Science.gov (United States)

Paul, Jasmeet S; Ridolfi, Timothy J

2012-12-01

Intra-abdominal infections are a common problem for the general surgeon and major sources of morbidity and mortality in the intensive care unit. Some of these patients present with peritonitis that can rapidly progress to septic shock. The basic principles of care include prompt resuscitation, antibiotics, and source control. This article will use a detailed case study to outline the management of a patient with severe intra-abdominal infection from diverticulitis from initial resuscitation to reconstruction. Components of the Surviving Sepsis Campaign as they pertain to surgical patients are discussed and updated, and the concept of damage control general surgery is applied. Copyright © 2012. Published by Elsevier Inc.

Intra- and inter-rater reliability of the Knee Society Knee Score when used by two physiotherapists in patients post total knee arthroplasty

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S. Gopal

2010-01-01

Full Text Available Background and Purpose: It has yet to be shown whether routine physiotherapy plays a role in the rehabilitation of patients post totalknee arthroplasty (Rajan et al 2004. Physiotherapists should be using validoutcome measures to provide evidence of the benefit of their intervention. The aim of this study was to establish the intra and inter-rater reliability of the Knee Society Knee Score, a scoring system developed by Insall et al(1989. The Knee Society Knee Score can be used to assess the integrity of theknee joint of patients undergoing total knee arthroplasty. Since the scoreinvolves clinical testing, the intra-rater reliability of the clinician should be established prior to using the scores as datain clinical research. W here multiple clinicians are involved, inter-rater reliability should also be established.Design: This was a correlation study.Subjects: A  sample of thirty patients post total knee arthroplasty attending the arthroplasty clinic at Johannesburg Hospital between six weeks and twelve months postoperatively.M ethod: Recruited patients were evaluated twice with a time interval of one hour between each assessment. Statistical A nalysis: The intra- and inter-rater reliability were estimated using Intraclass Correlation Coefficient (ICC. R esults: The intra-rater reliability showed excellent reliability (h= 0.95 for Examiner A  and good reliability (h= 0.71for Examiner B. The inter-rater reliability showed moderate reliability (h= 0.67 during test one and h= 0.66 during test two.Conclusion: The KSKS has good intra-rater reliability when tested within a period of one hour. The KSKS demonstrated moderate agreement for inter rater reliability.

New Technique of Direct Intra-abdominal Pressure Measurement

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Elena Risin

2006-10-01

Conclusion: Direct measurement of intra-abdominal pressure using 14-Fr PVC round drain is a newly described technique that is simple, fast and credible. Future investigation will be needed to confirm the reliability of this method during postoperative follow-up of intra-abdominal pressures in selected patients.

Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region

KAUST Repository

Arif, Chatchanit; Daniels, Camille; Bayer, Till; Banguera Hinestroza, Eulalia; Barbrook, Adrian; Howe, Christopher J.; LaJeunesse, Todd C.; Voolstra, Christian R.

2014-01-01

The persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.

Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region

KAUST Repository

Arif, Chatchanit

2014-09-01

The persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.

Translational and rotational intra- and inter-fractional errors in patient and target position during a short course of frameless stereotactic body radiotherapy

International Nuclear Information System (INIS)

Josipovic, Mirjana; Fredberg Persson, Gitte; Logadottir, Aashildur; Smulders, Bob; Westmann, Gunnar; Bangsgaard, Jens Peter

2012-01-01

Background. Implementation of cone beam computed tomography (CBCT) in frameless stereotactic body radiotherapy (SBRT) of lung tumours enables setup correction based on tumour position. The aim of this study was to compare setup accuracy with daily soft tissue matching to bony anatomy matching and evaluate intra- and inter-fractional translational and rotational errors in patient and target positions. Material and methods. Fifteen consecutive SBRT patients were included in the study. Vacuum cushions were used for immobilisation. SBRT plans were based on midventilation phase of four-dimensional (4D)-CT or three-dimensional (3D)-CT from PET/CT. Margins of 5 mm in the transversal plane and 10 mm in the cranio-caudal (CC) direction were applied. SBRT was delivered in three fractions within a week. At each fraction, CBCT was performed before and after the treatment. Setup accuracy comparison between soft tissue matching and bony anatomy matching was evaluated on pretreatment CBCTs. From differences in pre- and post-treatment CBCTs, we evaluated the extent of translational and rotational intra-fractional changes in patient position, tumour position and tumour baseline shift. All image registration was rigid with six degrees of freedom. Results. The median 3D difference between patient position based on bony anatomy matching and soft tissue matching was 3.0 mm (0-8.3 mm). The median 3D intra-fractional change in patient position was 1.4 mm (0-12.2 mm) and 2.2 mm (0-13.2 mm) in tumour position. The median 3D intra-fractional baseline shift was 2.2 mm (0-4.7 mm). With correction of translational errors, the remaining systematic and random errors were approximately 1deg. Conclusion. Soft tissue tumour matching improved precision of treatment delivery in frameless SBRT of lung tumours compared to image guidance using bone matching. The intra-fractional displacement of the target position was affected by both translational and rotational changes in tumour baseline position

Usefulness of intra-aortic balloon pump counterpulsation in patients with cardiogenic shock from acute myocardial infarction

NARCIS (Netherlands)

Cheng, Jin M.; Valk, Suzanne D. A.; den Uil, Corstiaan A.; van der Ent, Martin; Lagrand, Wim K.; van de Sande, Meike; van Domburg, Ron T.; Simoons, Maarten L.

2009-01-01

Although intra-aortic balloon pump (IABP) counterpulsation is increasingly being used for the treatment of patients with cardiogenic shock from acute myocardial infarction, data on the long-term outcomes are lacking. The aim of the present study was to evaluate the 30-day and long-term mortality and

Genome-Wide Diversity and Phylogeography of Mycobacterium avium subsp. paratuberculosis in Canadian Dairy Cattle.

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Christina Ahlstrom

Full Text Available Mycobacterium avium subsp. paratuberculosis (MAP is the causative bacterium of Johne's disease (JD in ruminants. The control of JD in the dairy industry is challenging, but can be improved with a better understanding of the diversity and distribution of MAP subtypes. Previously established molecular typing techniques used to differentiate MAP have not been sufficiently discriminatory and/or reliable to accurately assess the population structure. In this study, the genetic diversity of 182 MAP isolates representing all Canadian provinces was compared to the known global diversity, using single nucleotide polymorphisms identified through whole genome sequencing. MAP isolates from Canada represented a subset of the known global diversity, as there were global isolates intermingled with Canadian isolates, as well as multiple global subtypes that were not found in Canada. One Type III and six "Bison type" isolates were found in Canada as well as one Type II subtype that represented 86% of all Canadian isolates. Rarefaction estimated larger subtype richness in Québec than in other Canadian provinces using a strict definition of MAP subtypes and lower subtype richness in the Atlantic region using a relaxed definition. Significant phylogeographic clustering was observed at the inter-provincial but not at the intra-provincial level, although most major clades were found in all provinces. The large number of shared subtypes among provinces suggests that cattle movement is a major driver of MAP transmission at the herd level, which is further supported by the lack of spatial clustering on an intra-provincial scale.

Time from ACL injury to reconstruction and the prevalence of additional intra-articular pathology: is patient age an important factor?

Science.gov (United States)

Magnussen, Robert A; Pedroza, Angela D; Donaldson, Christopher T; Flanigan, David C; Kaeding, Christopher C

2013-09-01

Meniscus and cartilage lesions have been reported to be prevalent during delayed reconstruction of anterior cruciate ligament (ACL) injuries. Relatively, little work has been done exploring the influence of patient age on this relationship. The purpose of this study is to determine whether the effect of time from ACL injury to reconstruction on the prevalence of associated meniscal and chondral injury is influenced by patient age. It was hypothesized that patients in whom the time from ACL injury to reconstruction exceeds 12 weeks will exhibit an increased prevalence of medial compartment pathology relative to those reconstructed within 12 weeks of injury in patients of all ages. Data detailing time from ACL injury to reconstruction and the prevalence of intra-articular findings were obtained in 311 of 489 consecutive patients undergoing primary isolated ACL reconstruction. Patients were divided into two groups based on whether the time from ACL injury to reconstruction was time from ACL injury to reconstruction exceeded 12 weeks. The prevalence of lateral meniscal injury did not increase with increasing time ACL injury to surgery. Among patients aged 22 years and under, there was no increase in the prevalence of intra-articular pathology in any compartment in the late reconstruction group. In contrast, among patients over the age of 22, there was a significant increase in the prevalence of medial chondral injury (p = 0.042) in the late reconstruction group. The prevalence of injuries to the meniscus and articular cartilage in the medial compartment of the knee is increased with increasing time from ACL injury to reconstruction. This relationship may vary depending on patient age. Patients over the age of 22 exhibit a higher prevalence of intra-articular injury with delayed reconstruction, while no such differences are noted among younger patients. Retrospective comparative study, level III.

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing.

Science.gov (United States)

Zhang, Yanying; Yang, Qingsong; Ling, Juan; Van Nostrand, Joy D; Shi, Zhou; Zhou, Jizhong; Dong, Junde

2017-01-01

Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata , Avicennia marina , and Ceriops tagal , was undertaken using high - throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing

Directory of Open Access Journals (Sweden)

Yanying Zhang

2017-10-01

Full Text Available Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata, Avicennia marina, and Ceriops tagal, was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.

Endoscopic Ultrasound-Guided Drainage of Intra-Abdominal Abscess after Gastric Perforation in a Patient Receiving Ramucirumab and Paclitaxel for Advanced Gastric Cancer

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Koichiro Mandai

2017-01-01

Full Text Available Gastrointestinal perforation is a serious adverse event that occurs in approximately 1% of patients receiving ramucirumab and paclitaxel. A 67-year-old man with unresectable advanced gastric cancer was admitted to our hospital and treated with ramucirumab and paclitaxel. Gastric perforation occurred during the second cycle of chemotherapy. Although the patient’s condition improved without surgery, an abscess developed in the intra-abdominal fluid collection resulting from the perforation. We performed endoscopic ultrasound-guided abscess drainage. The patient improved and was discharged in satisfactory condition. Endoscopic ultrasound-guided drainage is a treatment option for patients with intra-abdominal abscess following gastric perforation due to ramucirumab.

Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity

Science.gov (United States)

Fujimoto, Masanori; Moyerbrailean, Gregory A.; Noman, Sifat; Gizicki, Jason P.; Ram, Michal L.; Green, Phyllis A.; Ram, Jeffrey L.

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (pbased principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies. PMID:25222021

Intra-articular distribution pattern after ultrasound-guided injections in wrist joints of patients with rheumatoid arthritis

DEFF Research Database (Denmark)

Boesen, Mikael; Jensen, Karl Erik; Torp-Pedersen, Søren

2007-01-01

OBJECTIVE: To investigate the distribution of an ultrasound-guided intra-articular (IA) injection in the wrist joint of patients with rheumatoid arthritis (RA). METHODS: An ultrasound-guided IA drug injection into the wrist joint was performed in 17 patients with 1 ml methylprednisolone (40 mg...... with the MRI OMERACT synovitis score (r=0.60, p=0.014), but not with the erosions, bonemarrow oedema scores or any clinical parameters. CONCLUSION: The distribution of contrast on MRI showed patient specific and random patterns after IA injections in active RA wrist joints. The degree of distribution increased...

Intra-abdominal fibrosis in a recent cohort of patients with neuroendocrine ('carcinoid') tumours of the small bowel.

Science.gov (United States)

Druce, M R; Bharwani, N; Akker, S A; Drake, W M; Rockall, A; Grossman, A B

2010-03-01

Fibrosis is a hallmark of neuroendocrine tumours (NETs) arising in the jejunum and ileum and may manifest in the mesentery and elsewhere. It is clinically important and once-established, there are few effective therapies. To examine the frequency, radiological manifestations and clinical significance of intra-abdominal fibrosis in a patient cohort using modern cross-sectional imaging. Current prevalence is compared to historical series and correlation with cardiac fibrosis evaluated. Cross-sectional, retrospective survey of a cohort of patients with mid-gut NETs from a single centre. Review of clinical features, biochemistry and imaging of patients with sporadic mid-gut NET and available imaging between 2002 and 2008. Thirty-one patients were included: 26 (83.9%) had liver metastases and 11 (35.4%) had small-bowel wall thickening; 17 patients (55%) had mesenteric involvement, with a mass, which contained coarse calcification in seven patients and fine calcification in a further two. There was soft-tissue stranding in 13 patients (plus in a further patient with no mass) and 'indrawing' of tissues in 11 patients. Two patients had a 'misty' mesentery and two had early retroperitoneal fibrosis. Mesenteric involvement was unrelated to gender and urinary 5HIAA excretion. Intra-abdominal fibrosis can be detected radiologically in around half of patients with mid-gut NET using contemporary cross-sectional imaging. Although not statistically significant, small-bowel obstruction was seen more frequently in the group with fibrosis. There was no relationship with cardiac fibrosis. Prospective studies are needed to evaluate predictors of fibrosis onset and clinical course and determine optimal methods of prevention and treatment.

Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.

Science.gov (United States)

Noyes, Noelle R; Weinroth, Maggie E; Parker, Jennifer K; Dean, Chris J; Lakin, Steven M; Raymond, Robert A; Rovira, Pablo; Doster, Enrique; Abdo, Zaid; Martin, Jennifer N; Jones, Kenneth L; Ruiz, Jaime; Boucher, Christina A; Belk, Keith E; Morley, Paul S

2017-10-17

Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias. The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins. These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.

Phylogeny and genetic diversity of Bridgeoporus nobilissimus inferred using mitochondrial and nuclear rDNA sequences

Science.gov (United States)

Redberg, G.L.; Hibbett, D.S.; Ammirati, J.F.; Rodriguez, R.J.

2003-01-01

The genetic diversity and phylogeny of Bridgeoporus nobilissimus have been analyzed. DNA was extracted from spores collected from individual fruiting bodies representing six geographically distinct populations in Oregon and Washington. Spore samples collected contained low levels of bacteria, yeast and a filamentous fungal species. Using taxon-specific PCR primers, it was possible to discriminate among rDNA from bacteria, yeast, a filamentous associate and B. nobilissimus. Nuclear rDNA internal transcribed spacer (ITS) region sequences of B. nobilissimus were compared among individuals representing six populations and were found to have less than 2% variation. These sequences also were used to design dual and nested PCR primers for B. nobilissimus-specific amplification. Mitochondrial small-subunit rDNA sequences were used in a phylogenetic analysis that placed B. nobilissimus in the hymenochaetoid clade, where it was associated with Oxyporus and Schizopora.

Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster.

Science.gov (United States)

Miller, Danny E; Cook, Kevin R; Yeganeh Kazemi, Nazanin; Smith, Clarissa B; Cockrell, Alexandria J; Hawley, R Scott; Bergman, Casey M

2016-03-08

Multiply inverted balancer chromosomes that suppress exchange with their homologs are an essential part of the Drosophila melanogaster genetic toolkit. Despite their widespread use, the organization of balancer chromosomes has not been characterized at the molecular level, and the degree of sequence variation among copies of balancer chromosomes is unknown. To map inversion breakpoints and study potential diversity in descendants of a structurally identical balancer chromosome, we sequenced a panel of laboratory stocks containing the most widely used X chromosome balancer, First Multiple 7 (FM7). We mapped the locations of FM7 breakpoints to precise euchromatic coordinates and identified the flanking sequence of breakpoints in heterochromatic regions. Analysis of SNP variation revealed megabase-scale blocks of sequence divergence among currently used FM7 stocks. We present evidence that this divergence arose through rare double-crossover events that replaced a female-sterile allele of the singed gene (sn(X2)) on FM7c with a sequence from balanced chromosomes. We propose that although double-crossover events are rare in individual crosses, many FM7c chromosomes in the Bloomington Drosophila Stock Center have lost sn(X2) by this mechanism on a historical timescale. Finally, we characterize the original allele of the Bar gene (B(1)) that is carried on FM7, and validate the hypothesis that the origin and subsequent reversion of the B(1) duplication are mediated by unequal exchange. Our results reject a simple nonrecombining, clonal mode for the laboratory evolution of balancer chromosomes and have implications for how balancer chromosomes should be used in the design and interpretation of genetic experiments in Drosophila.

Breaking down the silos to decrease internal diversions and patient flow delays.

Science.gov (United States)

Driscoll, Molly; Tobis, Kristen; Gurka, David; Serafin, Frederick; Carlson, Elizabeth

2015-01-01

Hospitals strive to admit patients to the units where caregiver competencies align with the patient's condition. When the hospital's census peaks, internal diversions and the associated risks increase, which are intensified when silos exist, as segregated care negatively impacts collaboration and patient safety. In this study, a 600+-bed academic, tertiary care specialty hospital experienced an increase in internal diversions. Within the neuroscience service line, emergent neuroscience transfers from outside hospitals had been declined or internally diverted because of capacity limitations. Formalized processes for improving collaboration between health care providers related to capacity issues were required to decrease internal diversions and improve patient flow and patient safety. A pilot project was conducted on neuroscience units during a process improvement initiative. A hospital-wide internal diversion plan was developed, identifying primary and secondary placement options for all patients requiring hospitalization to support patient flow and patient safety. Forecasting tools were developed to provide units' leadership with current information on expected admissions. Daily capacity huddles were instituted to increase collaboration between patient care units. The interventions trialed during the pilot decreased internal diversions and improved patient flow. The improved collaboration resulted in an 80% decrease in declinations of emergent intensive care unit transfers from outside hospitals due to capacity limitations and a 50% decrease in the number of these patients being internally diverted to alternate intensive care units. The interventions implemented minimized internal diversions and improved patient flow. The transparency of the patient placement process led to an increased collaboration between all participants.

Coil Embolization of an Arteriobiliary Fistula Caused by Hepatic Intra-Arterial Chemotherapy

International Nuclear Information System (INIS)

Takao, Hidemasa; Doi, Ippei; Makita, Kohzoh; Watanabe, Toshiaki

2005-01-01

Arteriobiliary fistula is a rare complication of hepatic intra-arterial chemotherapy. We report successful coil embolization of an arteriobiliary fistula. An 80-year-old woman underwent percutaneous placement of an indwelling catheter into the replaced right hepatic artery for intra-arterial chemotherapy of liver metastases. Coil embolization of the left hepatic artery was not performed. The patient complained of abdominal pain during intra-arterial chemotherapy. Angiography revealed a fistula between the replaced right hepatic artery and the common bile duct. The fistula was successfully treated by coil embolization via the indwelling catheter, and the indwelling catheter was removed. Although such complications usually herald the termination of intra-arterial chemotherapy, the patient underwent percutaneous implantation of a new catheter-port system, and intra-arterial chemotherapy was restarted

Correlation between trans and intra-thoracic impedance and conductance in patients with chronic heart failure.

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Malfatto, Gabriella; Villani, Alessandra; Rosa, Francesco Della; Rella, Valeria; Oldani, Matteo; Giglio, Alessia; Facchini, Mario; Parati, Gianfranco

2016-04-01

In chronic heart failure, changes of intra-thoracic impedance (Z0IT) may suggest impending pulmonary congestion; a similar result has been found by measuring trans-thoracic conductance (TFCTT = 1/Z0 = 1/kΩ). We assumed that a relationship could exist between Z0IT and TFCTT. We collected 140 measurements from 70 patients carrying an implantable cardioverter-defibrillator/cardiac resynchronization device with the CareLink function (71 ± 9 years, New York Heart Association (NYHA) 2.4 ± 0.9, ejection fraction 31 ± 8%, optimal treatment); they were studied during system alarms and after appropriate treatment (diuretics and/or vasodilators, n = 42) or during clinical stability and at the time of a system alarm (n = 28); correspondent BNP values were obtained. We related Z0IT obtained by the device, with TFCTT obtained with a commercial system. A strong relationship was found between Z0IT and TFCTT. Changes in the variables after treatment or during worsening conditions were of the same direction and order of magnitude, and were related to BNP levels obtained simultaneously. Trans-thoracic conductance, similarly to intra-thoracic impedance, may noninvasively point to pulmonary congestion and be useful in patients not carrying an implanted device. The possibility of remotely obtaining this variable should be evaluated for the telemonitoring of heart failure patients.

Bacterial diversity in Adélie penguin, Pygoscelis adeliae, guano: molecular and morpho-physiological approaches.

Science.gov (United States)

Zdanowski, Marek K; Weglenski, Piotr; Golik, Pawel; Sasin, Joanna M; Borsuk, Piotr; Zmuda, Magdalena J; Stankovic, Anna

2004-11-01

The total number of bacteria and culturable bacteria in Adélie penguin (Pygoscelis adeliae) guano was determined during 42 days of decomposition in a location adjacent to the rookery in Admiralty Bay, King George Island, Antarctica. Of the culturable bacteria, 72 randomly selected colonies were described using 49 morpho-physiological tests, 27 of which were subsequently considered significant in characterizing and differentiating the isolates. On the basis of the nucleotide sequence of a fragment of the 16S rRNA gene in each of 72 pure isolates, three major phylogenetic groups were identified, namely the Moraxellaceae/Pseudomonadaceae (29 isolates), the Flavobacteriaceae (14), and the Micrococcaceae (29). Grouping of the isolates on the basis of morpho-physiological tests (whether 49 or 27 parameters) showed similar results to those based on 16S rRNA gene sequences. Clusters were characterized by considerable intra-cluster variation in both 16S rRNA gene sequences and morpho-physiological responses. High diversity in abundance and morphometry of total bacterial communities during penguin guano decomposition was supported by image analysis of epifluorescence micrographs. The results indicate that the bacterial community in penguin guano is not only one of the richest in Antarctica, but is extremely diverse, both phylogenetically and morpho-physiologically.

Safety and efficacy of bi-annual intra-articular LBSA0103 injections in patients with knee osteoarthritis.

Science.gov (United States)

Lee, Jin Kyu; Choi, Chong-Hyuk; Oh, Kwang-Jun; Kyung, Hee-Soo; Yoo, Ju-Hyung; Ha, Chul-Won; Bin, Seong-Il; Kang, Seung-Baik; Kim, Myung Ku; Lee, Ju-Hong; Lee, Myung Chul

2017-11-01

The objective of this study is to assess the safety and efficacy of repeated intra-articular injection of high molecular weight hyaluronic acid (LBSA0103) at a 26-week interval, in patients with osteoarthritis of the knee. The study was an open-label, single arm, multicentre prospective trial conducted in patients with symptomatic knee osteoarthritis. The intervention consisted of two intra-articular injections of LBSA0103, with the second injection performed 26 weeks after the first injection. The primary outcome was the incidence of adverse drug reactions related to each injection. Assessment of efficacy of repeated injections in terms of maintenance of pain relief was a secondary objective of this study. Of the 185 patients screened, 174 patients received the first injection and 153 patients received both injections of LBSA0103. Nine adverse drug reactions occurred in seven patients (4.02%) after the first injection, while only one adverse drug reaction occurred (0.65%) after the second injection. As a secondary outcome measure, the improvements in the efficacy parameters including total WOMAC score and weight-bearing pain were all significant at both week 13 and 39 compared to the baseline value (P injection were consistent with those after the initial injection of LBSA0103 (between week 26 and week 39, P injection of LBSA0103 at a 26-week interval is safe without increased risk of adverse drug reactions. Additionally, LBSA0103 is effective in reduction of osteoarthritis knee pain and in maintenance of pain reduction for a 39-week period when a second injection is administered.

Chemoradiotherapy using retrograde superselective intra-arterial infusion for advanced oral cancer

International Nuclear Information System (INIS)

Mitsudo, Kenji; Iwai, Toshinori; Mitsunaga, Sachiyo

2011-01-01

Concurrent chemoradiotherapy using retrograde superselective intra-arterial infusion demonstrates good local control and overall survival rates due to the advantage of simultaneous infusion of anticancer agent with the synergistic effects of chemotherapy and radiotherapy. This study evaluated the therapeutic results, overall survival and local control rates in patients with advanced oral cancer treated with definitive concurrent chemoradiotherapy using retrograde superselective intra-arterial infusion. A total of 688 patients with carcinoma of the head and neck were referred to our institution between January 2001 and December 2006. Among them, 175 patients with carcinoma of the oral cavity underwent definitive concurrent chemoradiotherapy using retrograde superselective intra-arterial infusion. Treatment consisted of superselective intra-arterial infusions (docetaxel, total 60 mg/m 2 , cisplatin, total 125-150 mg/m 2 ) and daily concurrent radiotherapy (total 50-60 Gy) for 5-6 weeks. Four weeks after the completion of all treatments, patients underwent biopsy of the primary lesion and radiological examinations. Complete response (CR) of the primary site was achieved in 160 (91.4%) of the 175 patients. Residual disease at the primary site was seen in 15 patients (8.6%), and 14 patients (8.0%) showed local recurrence during follow-up. Five-year survival and local control rates were 71.6% and 82.2%, respectively. (author)

High incidence of nephropathy in neurosurgical patients after intra-arterial administration of low-osmolar and iso-osmolar contrast media.

Science.gov (United States)

Serafin, Zbigniew; Karolkiewicz, Maciej; Gruszka, Marzena; Strózecki, Pawel; Lasek, Wladyslaw; Odrowaz-Sypniewska, Grazyna; Manitius, Jacek; Beuth, Wojciech

2011-05-01

Percutaneous endovascular examinations and interventions require significant amounts of iodinated contrast media (CM) and have been reported to be complicated by an increased incidence of post-contrast nephropathy. To evaluate renal function, the incidence of post-contrast nephropathy, and risk factors after interventional procedures in neurosurgical patients after intra-arterial administration of a low-osmolar contrast medium (LOCM) versus an iso-osmolar contrast medium (IOCM). This single-center, prospective, randomized, double-blinded study included 92 patients in its final analysis (mean age 49.6 ± 12.6 years, 29.3% men, mean eGFR 97.8 ± 26.3 mL/min/1.73 m(2)). LOCM was used in 48 patients (52.2%) and IOCM in 44 patients (47.8%). The patients were given an average of 151.2 ± 52.1 mL of contrast medium intra-arterially. Serum creatinine (SCr), urinary N-acetyl-β-glucosaminidase (NAG) excretion, and creatinine clearance (CCr) were measured at baseline, and on days 1 and 3 after the procedure. Baseline risk factors, renal functional parameters, and average CM doses were not statistically different between the two groups. SCr, NAG, and CCr values did not differ significantly between the LOCM and IOCM groups on days 1 and 3 after CM administration. Nephropathy developed in 21 cases (22.8%): 13 (27.1%) after LOCM use and 8 (18.2%) after IOCM; (P = NS). The only significant risk factors of CIN were the diabetes (P = 0.0466) and atherosclerosis (P = 0.0498). We found a high incidence of nephropathy in neurosurgical patients after intra-arterial CM administration. The renal function values and incidence of nephropathy following LOCM administration were not statistically different from those following IOCM administration.

Patients' views on incidental findings from clinical exome sequencing

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Kristin E. Clift

2015-03-01

Full Text Available This article characterizes the opinions of patients and family members of patients undergoing clinical genomic-based testing regarding the return of incidental findings from these tests. Over sixteen months, we conducted 55 in-depth interviews with individuals to explore their preferences regarding which types of results they would like returned to them. Responses indicate a diversity of attitudes toward the return of incidental findings and a diversity of justifications for those attitudes. The majority of participants also described an imperative to include the patient in deciding which results to return rather than having universal, predetermined rules governing results disclosure. The results demonstrate the importance of a patient centered-approach to returning incidental findings.

Impact of Human Immunodeficiency Virus Type-1 Sequence Diversity on Antiretroviral Therapy Outcomes

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Allison Langs-Barlow

2014-10-01

Full Text Available Worldwide circulating HIV-1 genomes show extensive variation represented by different subtypes, polymorphisms and drug-resistant strains. Reports on the impact of sequence variation on antiretroviral therapy (ART outcomes are mixed. In this review, we summarize relevant published data from both resource-rich and resource-limited countries in the last 10 years on the impact of HIV-1 sequence diversity on treatment outcomes. The prevalence of transmission of drug resistant mutations (DRMs varies considerably, ranging from 0% to 27% worldwide. Factors such as geographic location, access and availability to ART, duration since inception of treatment programs, quality of care, risk-taking behaviors, mode of transmission, and viral subtype all dictate the prevalence in a particular geographical region. Although HIV-1 subtype may not be a good predictor of treatment outcome, review of emerging evidence supports the fact that HIV-1 genome sequence-resulting from natural polymorphisms or drug-associated mutations-matters when it comes to treatment outcomes. Therefore, continued surveillance of drug resistant variants in both treatment-naïve and treatment-experienced populations is needed to reduce the transmission of DRMs and to optimize the efficacy of the current ART armamentarium.

Higher dose intra-arterial milrinone and intra-arterial combined milrinone-nimodipine infusion as a rescue therapy for refractory cerebral vasospasm.

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Duman, Enes; Karakoç, Fatma; Pinar, H Ulas; Dogan, Rafi; Fırat, Ali; Yıldırım, Erkan

2017-12-01

Background Cerebral vasospasm (CV) is a major cause of delayed morbidity and mortality in patients with subarachnoid hemorrhage (SAH). Various cerebral protectants have been tested in patients with aneurysmal SAH. We aimed to research the success rate of treatment of CV via intra-arterial milrinone injection and aggressive pharmacological therapy for refractory CV. Methods A total of 25 consecutive patients who received intra-arterial milrinone and nimodipine treatment for CV following SAH between 2014 and 2017 were included in the study. Patients who underwent surgical clipping were excluded. Refractory vasospasm was defined as patients with CV refractory to therapies requiring ≥3 endovascular interventions. Overall, six patients had refractory CV. Long-term neurological outcome was assessed 6-18 months after SAH using a modified Rankin score and Barthel index. Results The median modified Rankin scores were 1 (min: 0, max: 3) and Barthel index scores were 85 (min: 70, max: 100) From each vasospastic territory maximal 10-16 mg milrinone was given to patients; a maximum of 24 mg milrinone was given to each patient in a session and a maximum of 42 mg milrinone was given to a patient in a day. Both milrinone and nimodipine were given to three patients. There was a large vessel diameter increase after milrinone and nimodipine injections. No patient died due to CV; only one patient had motor dysfunction on the right lower extremity. Conclusion Higher doses of milrinone can be used effectively to control refractory CV. For exceptional patients with refractory CV, high dose intra-arterial nimodipine and milrinone infusion can be used as a rescue therapy.

Shallow magma diversions during explosive diatreme-forming eruptions.

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Le Corvec, Nicolas; Muirhead, James D; White, James D L

2018-04-13

The diversion of magma is an important mechanism that may lead to the relocation of a volcanic vent. Magma diversion is known to occur during explosive volcanic eruptions generating subterranean excavation and remobilization of country and volcanic rocks. However, feedbacks between explosive crater formation and intrusion processes have not been considered previously, despite their importance for understanding evolving hazards during volcanic eruptions. Here, we apply numerical modeling to test the impacts of excavation and subsequent infilling of diatreme structures on stress states and intrusion geometries during the formation of maar-diatreme complexes. Explosive excavation and infilling of diatremes affects local stress states which inhibits magma ascent and drives lateral diversion at various depths, which are expected to promote intra-diatreme explosions, host rock mixing, and vent migration. Our models demonstrate novel mechanisms explaining the generation of saucer-shaped sills, linked with magma diversion and enhanced intra-diatreme explosive fragmentation during maar-diatreme volcanism. Similar mechanisms will occur at other volcanic vents producing crater-forming eruptions.

When and how should we measure intra- abdominal pressure?

African Journals Online (AJOL)

2008-11-11

Nov 11, 2008 ... developing intra-abdominal hypertension (IAH) and. ACS. This may be ... the development of systemic inflammatory response syndrome (SIRS) ... of this technique are that it places the patient at increased risk for .... 9. Malbrain ML. Different techniques to measure intra-abdominal pressure (IAP): time for a.

The Pfirrmann classification of lumbar intervertebral disc degeneration: an independent inter- and intra-observer agreement assessment.

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Urrutia, Julio; Besa, Pablo; Campos, Mauricio; Cikutovic, Pablo; Cabezon, Mario; Molina, Marcelo; Cruz, Juan Pablo

2016-09-01

Grading inter-vertebral disc degeneration (IDD) is important in the evaluation of many degenerative conditions, including patients with low back pain. Magnetic resonance imaging (MRI) is considered the best imaging instrument to evaluate IDD. The Pfirrmann classification is commonly used to grade IDD; the authors describing this classification showed an adequate agreement using it; however, there has been a paucity of independent agreement studies using this grading system. The aim of this study was to perform an independent inter- and intra-observer agreement study using the Pfirrmann classification. T2-weighted sagittal images of 79 patients consecutively studied with lumbar spine MRI were classified using the Pfirrmann grading system by six evaluators (three spine surgeons and three radiologists). After a 6-week interval, the 79 cases were presented to the same evaluators in a random sequence for repeat evaluation. The intra-class correlation coefficient (ICC) and the weighted kappa (wκ) were used to determine the inter- and intra-observer agreement. The inter-observer agreement was excellent, with an ICC = 0.94 (0.93-0.95) and wκ = 0.83 (0.74-0.91). There were no differences between spine surgeons and radiologists. Likewise, there were no differences in agreement evaluating the different lumbar discs. Most differences among observers were only of one grade. Intra-observer agreement was also excellent with ICC = 0.86 (0.83-0.89) and wκ = 0.89 (0.85-0.93). In this independent study, the Pfirrmann classification demonstrated an adequate agreement among different observers and by the same observer on separate occasions. Furthermore, it allows communication between radiologists and spine surgeons.

Characterization of Intestinal Microbiomes of Hirschsprung's Disease Patients with or without Enterocolitis Using Illumina-MiSeq High-Throughput Sequencing.

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Yuqing Li

Full Text Available Hirschsprung-associated enterocolitis (HAEC is a life-threatening complication of Hirschsprung's disease (HD. Although the pathological mechanisms are still unclear, studies have shown that HAEC has a close relationship with the disturbance of intestinal microbiota. This study aimed to investigate the characteristics of the intestinal microbiome of HD patients with or without enterocolitis. During routine or emergency surgery, we collected 35 intestinal content samples from five patients with HAEC and eight HD patients, including three HD patients with a history of enterocolitis who were in a HAEC remission (HAEC-R phase. Using Illumina-MiSeq high-throughput sequencing, we sequenced the V4 region of bacterial 16S rRNA, and operational taxonomic units (OTUs were defined by 97% sequence similarity. Principal coordinate analysis (PCoA of weighted UniFrac distances was performed to evaluate the diversity of each intestinal microbiome sample. The microbiota differed significantly between the HD patients (characterized by the prevalence of Bacteroidetes and HAEC patients (characterized by the prevalence of Proteobacteria, while the microbiota of the HAEC-R patients was more similar to that of the HAEC patients. We also observed that the specimens from different intestinal sites of each HD patient differed significantly, while the specimens from different intestinal sites of each HAEC and HAEC-R patient were more similar. In conclusion, the microbiome pattern of the HAEC-R patients was more similar to that of the HAEC patients than to that of the HD patients. The HD patients had a relatively distinct, more stable community than the HAEC and HAEC-R patients, suggesting that enterocolitis may either be caused by or result in a disruption of the patient's uniquely adapted intestinal flora. The intestinal microbiota associated with enterocolitis may persist following symptom resolution and can be implicated in the symptom recurrence.

Sequence diversity and natural selection at domain I of the apical membrane antigen 1 among Indian Plasmodium falciparum populations

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Kumar Ashwani

2007-11-01

Full Text Available Abstract Background The Plasmodium falciparum apical membrane antigen 1 (AMA1 is a leading malaria vaccine candidate antigen. The complete AMA1 protein is comprised of three domains where domain I exhibits high sequence polymorphism and is thus named as the hyper-variable region (HVR. The present study describes the extent of genetic polymorphism and natural selection at domain I of the ama1 gene among Indian P. falciparum isolates. Methods The part of the ama1 gene covering domain I was PCR amplified and sequenced from 157 P. falciparum isolates collected from five different geographical regions of India. Statistical and phylogenetic analyses of the sequences were done using DnaSP ver. 4. 10. 9 and MEGA version 3.0 packages. Results A total of 57 AMA1 haplotypes were observed among 157 isolates sequenced. Forty-six of these 57 haplotypes are being reported here for the first time. The parasites collected from the high malaria transmission areas (Assam, Orissa, and Andaman and Nicobar Islands showed more haplotypes (H and nucleotide diversity π as compared to low malaria transmission areas (Uttar Pradesh and Goa. The comparison of all five Indian P. falciparum subpopulations indicated moderate level of genetic differentiation and limited gene flow (Fixation index ranging from 0.048 to 0.13 between populations. The difference between rates of non-synonymous and synonymous mutations, Tajima's D and McDonald-Kreitman test statistics suggested that the diversity at domain I of the AMA1 antigen is due to positive natural selection. The minimum recombination events were also high indicating the possible role of recombination in generating AMA1 allelic diversity. Conclusion The level of genetic diversity and diversifying selection were higher in Assam, Orissa, and Andaman and Nicobar Islands populations as compared to Uttar Pradesh and Goa. The amounts of gene flow among these populations were moderate. The data reported here will be valuable for the

Genome-wide-analyses of Listeria monocytogenes from food-processing plants reveal clonal diversity and date the emergence of persisting sequence types.

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Knudsen, Gitte M; Nielsen, Jesper Boye; Marvig, Rasmus L; Ng, Yin; Worning, Peder; Westh, Henrik; Gram, Lone

2017-08-01

Whole genome sequencing is increasing used in epidemiology, e.g. for tracing outbreaks of food-borne diseases. This requires in-depth understanding of pathogen emergence, persistence and genomic diversity along the food production chain including in food processing plants. We sequenced the genomes of 80 isolates of Listeria monocytogenes sampled from Danish food processing plants over a time-period of 20 years, and analysed the sequences together with 10 public available reference genomes to advance our understanding of interplant and intraplant genomic diversity of L. monocytogenes. Except for three persisting sequence types (ST) based on Multi Locus Sequence Typing being ST7, ST8 and ST121, long-term persistence of clonal groups was limited, and new clones were introduced continuously, potentially from raw materials. No particular gene could be linked to the persistence phenotype. Using time-based phylogenetic analyses of the persistent STs, we estimate the L. monocytogenes evolutionary rate to be 0.18-0.35 single nucleotide polymorphisms/year, suggesting that the persistent STs emerged approximately 100 years ago, which correlates with the onset of industrialization and globalization of the food market. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats.

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de Lange, Orlando; Wolf, Christina; Thiel, Philipp; Krüger, Jens; Kleusch, Christian; Kohlbacher, Oliver; Lahaye, Thomas

2015-11-16

Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genetic diversity of Taenia asiatica from Thailand and other geographical locations as revealed by cytochrome c oxidase subunit 1 sequences.

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Anantaphruti, Malinee Thairungroj; Thaenkham, Urusa; Watthanakulpanich, Dorn; Phuphisut, Orawan; Maipanich, Wanna; Yoonuan, Tippayarat; Nuamtanong, Supaporn; Pubampen, Somjit; Sanguankiat, Surapol

2013-02-01

Twelve 924 bp cytochrome c oxidase subunit 1 (cox1) mitochondrial DNA sequences from Taenia asiatica isolates from Thailand were aligned and compared with multiple sequence isolates from Thailand and 6 other countries from the GenBank database. The genetic divergence of T. asiatica was also compared with Taenia saginata database sequences from 6 different countries in Asia, including Thailand, and 3 countries from other continents. The results showed that there were minor genetic variations within T. asiatica species, while high intraspecies variation was found in T. saginata. There were only 2 haplotypes and 1 polymorphic site found in T. asiatica, but 8 haplotypes and 9 polymorphic sites in T. saginata. Haplotype diversity was very low, 0.067, in T. asiatica and high, 0.700, in T. saginata. The very low genetic diversity suggested that T. asiatica may be at a risk due to the loss of potential adaptive alleles, resulting in reduced viability and decreased responses to environmental changes, which may endanger the species.

Neoadjuvant intra-arterial chemotherapy combined with radiotherapy and surgery in patients with advanced maxillary sinus cancer

Energy Technology Data Exchange (ETDEWEB)

Kim, Won Tae; Kim, Yong Kan; Lee, Ju Hye; Kim, Dong Hyun; Park, Dahl; Cho, Kyu Sup; Kim, Dong Won [Pusan National University Hospital, Pusan National University School of Medicine, Busan (Korea, Republic of); Nam, Ji Ho; Roh, Hwan Jung [Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Yangsan (Korea, Republic of)

2013-09-15

The optimal treatment of advanced maxillary sinus cancer has been challenging for several decades. Intra-arterial chemotherapy (IAC) for head and neck cancer has been controversial. We have analyzed the long-term outcome of neoadjuvant IAC followed by radiation therapy (RT) and surgery. Twenty-seven patients with advanced maxillary sinus cancer were treated between 1989 and 2002. Five-fluorouracil (5-FU, 500 mg/m2) was infused intra-arterially, and followed by RT (total 50.4 Gy/28 fractions). A planned surgery was performed 3 to 4 weeks after completion of IAC and RT. At a median follow-up of 77 months (range, 12 to 169 months), the 5-year rates of overall survival in all patients were 63%. The 5-year rates of overall survival of stage T3/T4 patients were 70.0% and 58.8%, respectively. Seven of fourteen patients with disease recurrence had a local recurrence alone. The 5-year actuarial local control rates in patients with stage T3/T4, and in all patients were 20.0%, 32.3%, and 27.4%, respectively. Overall response rate after the completion of IAC and RT was 70.3%. During the follow-up, seven patients (25.9%) showed mild to moderate late complications. The tumor extent (i.e., the involvement of either orbit and/or base of skull) appeared to be related with local recurrence. Neoadjuvant IAC with 5-FU followed by RT and surgery may be effective to improve local tumor control in the patients with advanced maxillary sinus cancer. However, local failure was still the major cause of death. Further investigations are required to determine the optimal treatment schedule, radiotherapy techniques and chemotherapy regimens.

Genetic diversity studies in pea (Pisum sativum L.) using simple sequence repeat markers.

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Kumari, P; Basal, N; Singh, A K; Rai, V P; Srivastava, C P; Singh, P K

2013-03-13

The genetic diversity among 28 pea (Pisum sativum L.) genotypes was analyzed using 32 simple sequence repeat markers. A total of 44 polymorphic bands, with an average of 2.1 bands per primer, were obtained. The polymorphism information content ranged from 0.657 to 0.309 with an average of 0.493. The variation in genetic diversity among these cultivars ranged from 0.11 to 0.73. Cluster analysis based on Jaccard's similarity coefficient using the unweighted pair-group method with arithmetic mean (UPGMA) revealed 2 distinct clusters, I and II, comprising 6 and 22 genotypes, respectively. Cluster II was further differentiated into 2 subclusters, IIA and IIB, with 12 and 10 genotypes, respectively. Principal component (PC) analysis revealed results similar to those of UPGMA. The first, second, and third PCs contributed 21.6, 16.1, and 14.0% of the variation, respectively; cumulative variation of the first 3 PCs was 51.7%.

Genotyping-by-Sequencing Analysis for Determining Population Structure of Finger Millet Germplasm of Diverse Origins

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Anil Kumar

2016-07-01

Full Text Available Finger millet [ (L. Gaertn.] is grown mainly by subsistence farmers in arid and semiarid regions of the world. To broaden its genetic base and to boost its production, it is of paramount importance to characterize and genotype the diverse gene pool of this important food and nutritional security crop. However, as a result of nonavailability of the genome sequence of finger millet, the progress could not be made in realizing the molecular basis of unique qualities of the crop. In the present investigation, attempts have been made to characterize the genetically diverse collection of 113 finger millet accessions through whole-genome genotyping-by-sequencing (GBS, which resulted in a genome-wide set of 23,000 single-nucleotide polymorphisms (SNPs segregating across the entire collection and several thousand SNPs segregating within every accession. A model-based population structure analysis reveals the presence of three subpopulations among the finger millet accessions, which are in parallel with the results of phylogenetic analysis. The observed population structure is consistent with the hypothesis that finger millet was domesticated first in Africa, and from there it was introduced to India some 3000 yr ago. A total of 1128 gene ontology (GO terms were assigned to SNP-carrying genes for three main categories: biological process, cellular component, and molecular function. Facilitated access to high-throughput genotyping and sequencing technologies are likely to improve the breeding process in developing countries, and as such, this data will be very useful to breeders who are working for the genetic improvement of finger millet.

Genotyping-by-Sequencing Analysis for Determining Population Structure of Finger Millet Germplasm of Diverse Origins.

Science.gov (United States)

Kumar, Anil; Sharma, Divya; Tiwari, Apoorv; Jaiswal, J P; Singh, N K; Sood, Salej

2016-07-01

Finger millet [ (L.) Gaertn.] is grown mainly by subsistence farmers in arid and semiarid regions of the world. To broaden its genetic base and to boost its production, it is of paramount importance to characterize and genotype the diverse gene pool of this important food and nutritional security crop. However, as a result of nonavailability of the genome sequence of finger millet, the progress could not be made in realizing the molecular basis of unique qualities of the crop. In the present investigation, attempts have been made to characterize the genetically diverse collection of 113 finger millet accessions through whole-genome genotyping-by-sequencing (GBS), which resulted in a genome-wide set of 23,000 single-nucleotide polymorphisms (SNPs) segregating across the entire collection and several thousand SNPs segregating within every accession. A model-based population structure analysis reveals the presence of three subpopulations among the finger millet accessions, which are in parallel with the results of phylogenetic analysis. The observed population structure is consistent with the hypothesis that finger millet was domesticated first in Africa, and from there it was introduced to India some 3000 yr ago. A total of 1128 gene ontology (GO) terms were assigned to SNP-carrying genes for three main categories: biological process, cellular component, and molecular function. Facilitated access to high-throughput genotyping and sequencing technologies are likely to improve the breeding process in developing countries, and as such, this data will be very useful to breeders who are working for the genetic improvement of finger millet. Copyright © 2016 Crop Science Society of America.

Whole Exome Sequencing in Pediatric Neurology Patients: Clinical Implications and Estimated Cost Analysis.

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Nolan, Danielle; Carlson, Martha

2016-06-01

Genetic heterogeneity in neurologic disorders has been an obstacle to phenotype-based diagnostic testing. The authors hypothesized that information compiled via whole exome sequencing will improve clinical diagnosis and management of pediatric neurology patients. The authors performed a retrospective chart review of patients evaluated in the University of Michigan Pediatric Neurology clinic between 6/2011 and 6/2015. The authors recorded previous diagnostic testing, indications for whole exome sequencing, and whole exome sequencing results. Whole exome sequencing was recommended for 135 patients and obtained in 53 patients. Insurance barriers often precluded whole exome sequencing. The most common indication for whole exome sequencing was neurodevelopmental disorders. Whole exome sequencing improved the presumptive diagnostic rate in the patient cohort from 25% to 48%. Clinical implications included family planning, medication selection, and systemic investigation. Compared to current second tier testing, whole exome sequencing can result in lower long-term charges and more timely diagnosis. Overcoming barriers related to whole exome sequencing insurance authorization could allow for more efficient and fruitful diagnostic neurological evaluations. © The Author(s) 2016.

Intra-arterial chemotherapy combined with irradiation for invasive bladder cancer

International Nuclear Information System (INIS)

Fujimoto, Naohiro; Sato, Hideki; Harada, Shuji; Matsumoto, Tetsuro; Ikuyama, Toshihiro

2004-01-01

Total cystectomy and urinary diversion are the standard treatments for invasive bladder cancer. However, total cystectomy is not possible in some patients due to advanced age, a poor general condition, or refusal to undergo cystectomy. In such cases, intra-arterial chemotherapy (IAC) and/or radiotherapy are the alternative treatments. We performed IAC with cisplatin and adriamycin in 9 patients with invasive bladder cancer and obtained complete response (CR) in 5 out of the 9 patients (55.6%). However, 3 of these 5 CR patients developed local recurrence within 1 year. In an effort to improve the efficacy, we performed combination therapy comprising IAC plus radiotherapy in 12 patients with invasive bladder cancer. CR was obtained in 58.3% and the bladder was preserved in 91.7% with this combination therapy. However, distant metastases developed in 33.3% after the combined treatment of IAC plus radiation therapy. These findings suggest that the combination of radiotherapy and IAC is useful for local control of invasive bladder cancer. Data from more cases and results from a longer follow-up are needed to fully confirm the efficacy of this type of treatment. In addition, therapeutic modalities to prevent distant metastasis need to be considered. (author)

On the Use of Diversity Measures in Longitudinal Sequencing Studies of Microbial Communities.

Science.gov (United States)

Wagner, Brandie D; Grunwald, Gary K; Zerbe, Gary O; Mikulich-Gilbertson, Susan K; Robertson, Charles E; Zemanick, Edith T; Harris, J Kirk

2018-01-01

Identification of the majority of organisms present in human-associated microbial communities is feasible with the advent of high throughput sequencing technology. As substantial variability in microbiota communities is seen across subjects, the use of longitudinal study designs is important to better understand variation of the microbiome within individual subjects. Complex study designs with longitudinal sample collection require analytic approaches to account for this additional source of variability. A common approach to assessing community changes is to evaluate the change in alpha diversity (the variety and abundance of organisms in a community) over time. However, there are several commonly used alpha diversity measures and the use of different measures can result in different estimates of magnitude of change and different inferences. It has recently been proposed that diversity profile curves are useful for clarifying these differences, and may provide a more complete picture of the community structure. However, it is unclear how to utilize these curves when interest is in evaluating changes in community structure over time. We propose the use of a bi-exponential function in a longitudinal model that accounts for repeated measures on each subject to compare diversity profiles over time. Furthermore, it is possible that no change in alpha diversity (single community/sample) may be observed despite the presence of a highly divergent community composition. Thus, it is also important to use a beta diversity measure (similarity between multiple communities/samples) that captures changes in community composition. Ecological methods developed to evaluate temporal turnover have currently only been applied to investigate changes of a single community over time. We illustrate the extension of this approach to multiple communities of interest (i.e., subjects) by modeling the beta diversity measure over time. With this approach, a rate of change in community

Genetic diversity based on 28S rDNA sequences among populations of Culex quinquefasciatus collected at different locations in Tamil Nadu, India.

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Sakthivelkumar, S; Ramaraj, P; Veeramani, V; Janarthanan, S

2015-09-01

The basis of the present study was to distinguish the existence of any genetic variability among populations of Culex quinquefasciatus which would be a valuable tool in the management of mosquito control programmes. In the present study, population of Cx. quinquefasciatus collected at different locations in Tamil Nadu were analyzed for their genetic variation based on 28S rDNA D2 region nucleotide sequences. A high degree of genetic polymorphism was detected in the sequences of D2 region of 28S rDNA on the predicted secondary structures in spite of high nucleotide sequence similarity. The findings based on secondary structure using rDNA sequences suggested the existence of a complex genotypic diversity of Cx. quinquefasciatus population collected at different locations of Tamil Nadu, India. This complexity in genetic diversity in a single mosquito population collected at different locations is considered an important issue towards their influence and nature of vector potential of these mosquitoes.

Randomized Comparison of Intra-Arterial Chemotherapy Versus Intra-Arterial Chemotherapy and Gelfoam Embolization for Treatment of Advanced Cervical Carcinoma

International Nuclear Information System (INIS)

Ikeda, O.; Mizukami, N.; Murata, Y.; Arakawa, A.; Katabuchi, H.; Okamoto, H.; Yasunaga, T.; Tsunawaki, A.; Yamashita, Y.

2005-01-01

Purpose:We evaluated the effects of intra-arterial infusion therapy by comparing the results obtained with a combination of intra-arterial anticancer drugs with and without transcatheter arterial embolization (TAE) in patients with cervical cancer.Methods:Between April 1999 and March 2003, intra-arterial therapy was administered to 45 patients (mean age 49 years) with cervical cancer. Of these, 18 had stage IIb , 4 had stage IIIa, 19 had stage IIIb, and 4 had stage IVb cancer; the histopathologic types were squamous cell carcinoma (n = 35), adenocarcinoma (n = 8), and adenosquamous carcinoma (n = 2). A total of 45 patients gave their informed consent and were randomized on a continuous basis into one of three groups according to the therapeutic protocols: group A consisted of 15 patients who received cisplatin, group B consisted of 17 patients who received cisplatin, mitomycin, doxorubicin hydrochloride, and 5-fluorouracil, and group C consisted of 13 patients who received cisplatin and TAE. Each protocol was administered twice with a 3 week interval between treatments. The efficacy of treatment was evaluated on the basis of the tumor reduction ratio (%) using MR imaging and the side effects were analyzed.Results:In groups A, B, and C, the tumor reduction ratio was 54%, 84%, and 86%, respectively; it was significantly greater in groups B and C than in group A (p < 0.01). The difference between groups B and C was not statistically significant. Although all group C patients developed severe pain after TAE, the pain was controlled with analgesics. Thrombocytopenia occurred in 6 of 17 (35%) group B patients.Conclusion:Group B and C patients had better tumor reduction than those in group A. Fewer hematologic complications occurred in group C patients compared with group B

The Increase of Intra-Abdominal Pressure Can Affect Intraocular Pressure

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Ilhan Ece

2015-01-01

Full Text Available Objective. This study aims to explore the usage of intraocular pressure measurements as the early indicator of the increase in intra-abdominal pressure. Methods. In this prospective study, 40 patients undergoing elective surgery were included. Patients were divided into four groups of 10 patients. The control group (Group C was not subjected to laparoscopic intervention. Laparoscopic surgery was, respectively, performed with an intra-abdominal pressure of 9, 12, and 15 mmHg in Groups L (low, M (medium, and H (high pressure. Intraocular pressure was measured binocularly in each patient at three different times (before, during, and end of surgery using a contact tonometer. Results. Patients’ gender, age, body mass index (BMI, American Society of Anesthesiology (ASA class, and operative times were not different among the groups. No complications occurred with either the surgery or measurement of intraocular pressure. Intubation was associated with a severe rise in IOP (P<0.05. An increase in intraocular pressure was seen in groups M and H (P<0.05. Conclusion. Intraocular pressure was increased in the groups with an intra-abdominal pressure of 12 mmHg or more. Measuring the intraocular pressure might be a useful method to estimate the intra-abdominal pressure. This trial is registered with NCT02319213.

Intra-articular ganglion cysts of the knee: clinical and MR imaging features

International Nuclear Information System (INIS)

Kim, M.G.; Cho, W.H.; Kim, B.H.; Choi, J.A.; Lee, N.J.; Chung, K.B.; Choi, Y.S.; Cho, S.B.; Lim, H.C.

2001-01-01

The purpose of this study was to present clinical and MR imaging features of intra-articular ganglion cysts of the knee. Retrospective review of 1685 consecutive medical records and MR examinations of the knee performed at three imaging centers allowed identification of 20 patients (13 men and 7 women; mean age 35 years), in whom evidence of intra-articular ganglion cyst was seen. Of the 20 ganglion cysts, 5 were found in the infrapatellar fat pad, 10 arose from the posterior cruciate ligament, and 5 from the anterior cruciate ligament. Three of five patients with ganglion cyst in the infrapatellar fat pad had a palpable mass. In 7 of 15 patients with ganglion cyst in the intercondylar notch, exacerbation of pain occurred in a squatting position. On four MR arthrographies, ganglion cysts were an intra-articular round, lobulated, low signal intensity lesion. Five cases of fat-suppressed contrast-enhanced T1-weighted SE images demonstrated peripheral thin rim enhancement. The clinical presentation of intra-articular ganglion cyst is varied according to its intra-articular location. The MR appearance of intra-articular ganglion cyst is characteristic and usually associated with the cruciate ligament or the infrapatellar fat pad. Magnetic resonance arthrography has no definite advantage over conventional MR in the evaluation of the lesion. For intra-articular ganglion cyst in the infrapatellar fat pad, fat-suppressed contrast-enhanced MR imaging could be useful, because a thin, rim-enhancing feature of intra-articular ganglion cyst allows it to be distinguished from synovial hemangioma and synovial sarcoma. (orig.)

Comparing Ecological and Genetic Diversity Within the Marine Diatom Genus Pseudo-nitzschia: A Multiregional Synthesis

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Hubbard, K.; Bruzek, S.

2016-02-01

The globally distributed marine diatom genus Pseudo-nitzschia consists of approximately 40 species, more than half of which occur in US coastal waters. Here, sensitive genetic tools targeting a variable portion of the internal transcribed spacer 1 (ITS1) region of the rRNA gene were used to assess Pseudo-nitzschia spp. diversity in more than 600 environmental DNA samples collected from US Atlantic, Pacific, and Gulf of Mexico waters. Community-based approaches employed genus-specific primers for environmental DNA fingerprinting and targeted sequencing. For the Gulf of Mexico samples especially, a nested PCR approach (with or without degenerate primers) improved resolution of species diversity. To date, more than 40 unique ITS1 amplicon sizes have been repeatedly observed in ITS1 fingerprints. Targeted sequencing of environmental DNA as well as single chains isolated from live samples indicate that many of these represent novel and known inter- and intra-specific Pseudo-nitzschia diversity. A few species (e.g., P. pungens, P. cuspidata) occur across all three regions, whereas other species and intraspecific variants occurred at local to regional spatial scales only. Generally, species frequently co-occur in complex assemblages, and transitions in Pseudo-nitzschia community composition occur seasonally, prior to bloom initiation, and across (cross-shelf, latitudinal, and vertical) environmental gradients. These observations highlight the dynamic nature of diatom community composition in the marine environment and the importance of classifying diversity at relevant ecological and/or taxonomic scales.

Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

Science.gov (United States)

Fujimoto, Masanori; Moyerbrailean, Gregory A; Noman, Sifat; Gizicki, Jason P; Ram, Michal L; Green, Phyllis A; Ram, Jeffrey L

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (pPCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies.

Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity

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Andrea Hahn

2018-05-01

Full Text Available Cystic fibrosis (CF is an autosomal recessive disease associated with recurrent lung infections that can lead to morbidity and mortality. The impact of antibiotics for treatment of acute pulmonary exacerbations on the CF airway microbiome remains unclear with prior studies giving conflicting results and being limited by their use of 16S ribosomal RNA sequencing. Our primary objective was to validate the use of true single molecular sequencing (tSMS and PathoScope in the analysis of the CF airway microbiome. Three control samples were created with differing amounts of Burkholderia cepacia, Pseudomonas aeruginosa, and Prevotella melaninogenica, three common bacteria found in cystic fibrosis lungs. Paired sputa were also obtained from three study participants with CF before and >6 days after initiation of antibiotics. Antibiotic resistant B. cepacia and P. aeruginosa were identified in concurrently obtained respiratory cultures. Direct sequencing was performed using tSMS, and filtered reads were aligned to reference genomes from NCBI using PathoScope and Kraken and unique clade-specific marker genes using MetaPhlAn. A total of 180–518 K of 6–12 million filtered reads were aligned for each sample. Detection of known pathogens in control samples was most successful using PathoScope. In the CF sputa, alpha diversity measures varied based on the alignment method used, but similar trends were found between pre- and post-antibiotic samples. PathoScope outperformed Kraken and MetaPhlAn in our validation study of artificial bacterial community controls and also has advantages over Kraken and MetaPhlAn of being able to determine bacterial strains and the presence of fungal organisms. PathoScope can be confidently used when evaluating metagenomic data to determine CF airway microbiome diversity.

A not-so-big crisis: re-reading Silurian conodont diversity in a sequence-stratigraphic framework

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Jarochowska, Emilia; Munnecke, Axel

2016-04-01

Conodonts are extensively used in Ordovician through Triassic biostratigraphy and fossil-based geochemistry. However, their distribution in rock successions is commonly taken at face value, without taking into account their diverse and poorly understood ecology. Multielement taxonomy, ontogenetic and environmental variability, difficulties in extraction, and relative rarity all contribute to the general lack of quantitative studies on conodont stratigraphic distribution and temporal turnover. With respect to Silurian conodonts, the concept of recurrent conodont extinction events - the so called Ireviken, Mulde and Lau events - has become a standard in the stratigraphic literature. The concept has been proposed based on qualitative observations of local extirpations of open-marine pelagic or nekto-benthic taxa and temporary dominance of shallow-water species in the Silurian succession of the Swedish island of Gotland. These changes coincided with positive carbon isotope excursions, abrupt facies shifts, "blooms" of benthic fauna, and changes in reef communities, which have all been combined into a general view of Silurian bio-geochemical events. This view posits a deterministic, reproducible pattern in Silurian conodont diversity, attributed to recurrent ecological or geochemical conditions. The growing body of sequence-stratigraphic interpretations across these events in Gotland and other sections worldwide indicate that in all cases the Silurian "events" are associated with rapid global regressions. This suggests that faunal changes such as the dominance of shallow-water, low-diversity conodont fauna and the increase of benthic invertebrate diversity and abundance represent predictable consequences of the variation in the completeness of the rock record and preservation potential of different environments. Our studies in Poland and Ukraine indicate that the magnitude of change in the taxonomic composition of conodont assemblages across the middle Silurian global

Sequence variation in mitochondrial cox1 and nad1 genes of ascaridoid nematodes in cats and dogs from Iran.

Science.gov (United States)

Mikaeili, F; Mirhendi, H; Mohebali, M; Hosseini, M; Sharbatkhori, M; Zarei, Z; Kia, E B

2015-07-01

The study was conducted to determine the sequence variation in two mitochondrial genes, namely cytochrome c oxidase 1 (pcox1) and NADH dehydrogenase 1 (pnad1) within and among isolates of Toxocara cati, Toxocara canis and Toxascaris leonina. Genomic DNA was extracted from 32 isolates of T. cati, 9 isolates of T. canis and 19 isolates of T. leonina collected from cats and dogs in different geographical areas of Iran. Mitochondrial genes were amplified by polymerase chain reaction (PCR) and sequenced. Sequence data were aligned using the BioEdit software and compared with published sequences in GenBank. Phylogenetic analysis was performed using Bayesian inference and maximum likelihood methods. Based on pairwise comparison, intra-species genetic diversity within Iranian isolates of T. cati, T. canis and T. leonina amounted to 0-2.3%, 0-1.3% and 0-1.0% for pcox1 and 0-2.0%, 0-1.7% and 0-2.6% for pnad1, respectively. Inter-species sequence variation among the three ascaridoid nematodes was significantly higher, being 9.5-16.6% for pcox1 and 11.9-26.7% for pnad1. Sequence and phylogenetic analysis of the pcox1 and pnad1 genes indicated that there is significant genetic diversity within and among isolates of T. cati, T. canis and T. leonina from different areas of Iran, and these genes can be used for studying genetic variation of ascaridoid nematodes.

Frozen section is superior to imprint cytology for the intra-operative assessment of sentinel lymph node metastasis in Stage I Breast cancer patients

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Makita Masujiro

2006-05-01

Full Text Available Abstract Background A standard intra-operative procedure for assessing sentinel lymph node metastasis in breast cancer patients has not yet been established. Patients and methods One hundred and thirty-eight patients with stage I breast cancer who underwent sentinel node biopsy using both imprint cytology and frozen section were analyzed. Results Seventeen of the 138 patients had sentinel node involvement. Results of imprint cytology included nine false negative cases (sensitivity, 47.1%. In contrast, only two cases of false negatives were found on frozen section (sensitivity, 88.2%. There were two false positive cases identified by imprint cytology (specificity, 98.3%. On the other hand, frozen section had 100% specificity. Conclusion These findings suggest that frozen section is superior to imprint cytology for the intra-operative determination of sentinel lymph node metastasis in stage I breast cancer patients.

Multilocus sequence analysis (MLSA) of Bradyrhizobium strains: revealing high diversity of tropical diazotrophic symbiotic bacteria.

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Delamuta, Jakeline Renata Marçon; Ribeiro, Renan Augusto; Menna, Pâmela; Bangel, Eliane Villamil; Hungria, Mariangela

2012-04-01

Symbiotic association of several genera of bacteria collectively called as rhizobia and plants belonging to the family Leguminosae (=Fabaceae) results in the process of biological nitrogen fixation, playing a key role in global N cycling, and also bringing relevant contributions to the agriculture. Bradyrhizobium is considered as the ancestral of all nitrogen-fixing rhizobial species, probably originated in the tropics. The genus encompasses a variety of diverse bacteria, but the diversity captured in the analysis of the 16S rRNA is often low. In this study, we analyzed twelve Bradyrhizobium strains selected from previous studies performed by our group for showing high genetic diversity in relation to the described species. In addition to the 16S rRNA, five housekeeping genes (recA, atpD, glnII, gyrB and rpoB) were analyzed in the MLSA (multilocus sequence analysis) approach. Analysis of each gene and of the concatenated housekeeping genes captured a considerably higher level of genetic diversity, with indication of putative new species. The results highlight the high genetic variability associated with Bradyrhizobium microsymbionts of a variety of legumes. In addition, the MLSA approach has proved to represent a rapid and reliable method to be employed in phylogenetic and taxonomic studies, speeding the identification of the still poorly known diversity of nitrogen-fixing rhizobia in the tropics.

Sequence-Dependent Self-Assembly and Structural Diversity of Islet Amyloid Polypeptide-Derived β-Sheet Fibrils

International Nuclear Information System (INIS)

Wang, Shih-Ting; Lin, Yiyang; Spencer, Ryan K.; Thomas, Michael R.; Nguyen, Andy I.

2017-01-01

Determining the structural origins of amyloid fibrillation is essential for understanding both the pathology of amyloidosis and the rational design of inhibitors to prevent or reverse amyloid formation. In this work, the decisive roles of peptide structures on amyloid self-assembly and morphological diversity were investigated by the design of eight amyloidogenic peptides derived from islet amyloid polypeptide. Among the segments, two distinct morphologies were highlighted in the form of twisted and planar (untwisted) ribbons with varied diameters, thicknesses, and lengths. In particular, transformation of amyloid fibrils from twisted ribbons into untwisted structures was triggered by substitution of the C-terminal serine with threonine, where the side chain methyl group was responsible for the distinct morphological change. This effect was confirmed following serine substitution with alanine and valine and was ascribed to the restriction of intersheet torsional strain through the increased hydrophobic interactions and hydrogen bonding. We also studied the variation of fibril morphology (i.e., association and helicity) and peptide aggregation propensity by increasing the hydrophobicity of the peptide side group, capping the N-terminus, and extending sequence length. Lastly, we anticipate that our insights into sequence-dependent fibrillation and morphological diversity will shed light on the structural interpretation of amyloidogenesis and development of structure-specific imaging agents and aggregation inhibitors.

Fondaparinux for intra and perioperative anticoagulation in patients with heparin-induced thrombocytopenia candidates for peripheral vascular surgery: Report of 4 cases

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Giulio Illuminati, MD

2016-01-01

Conclusions: These preliminary results seem to justify the off-label use of fondaparinux for intra and perioperative anticoagulation in patients with HIT, candidates for peripheral vascular surgery interventions.

Case volumes of intra-arterial and intravenous treatment of ischemic stroke in the USA.

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Hirsch, J A; Yoo, A J; Nogueira, R G; Verduzco, L A; Schwamm, L H; Pryor, J C; Rabinov, J D; González, R G

2009-07-01

Ischemic stroke is a major cause of disability and death in the USA. Intravenous tissue plasminogen activator (t-PA) remains underutilized. With the development of newer intra-arterial reperfusion therapies, there is increased opportunity to address the more devastating large-vessel occlusions. We seek to identify the numbers of patients with stroke treated with intravenous and intra-arterial therapies, as well as to estimate the potential number of intra-arterial cases in the foreseeable future. We performed a literature search to determine case volumes of intravenous t-PA use. We extrapolated the current case volume of intra-arterial stroke therapies from the numbers of cases in which the Merci retrieval device was used. In order to estimate the potential numbers of intra-arterial stroke cases, we characterized the percentage of patients with stroke who received intra-arterial therapy at two leading stroke centers. We applied these percentages to the numbers of patients with stroke seen at the top 100, 200 and 500 stroke centers by volume. The rate of intravenous t-PA use is 2.4-3.6%, resulting in 15 000-22 000 cases/year in the USA. The estimated case volume of intra-arterial therapies is 3500-7200 in 2006. Based on data from St. Luke's Brain and Stroke Institute and Massachusetts General Hospital, approximately 5-20% of patients with ischemic stroke can be treated with intra-arterial therapies. Extrapolating this to the top 500 stroke centers by volume, the potential number of intra-arterial cases in the USA is 10 400-41 500/year. Based on the current numbers of intra-arterial cases, our theoretical model identifies a potential for significant growth of this stroke therapy.

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh

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2011-01-01

Background Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. Results In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. Conclusion We developed 550 validated genic

Computational optimisation of targeted DNA sequencing for cancer detection

DEFF Research Database (Denmark)

Martinez, Pierre; McGranahan, Nicholas; Birkbak, Nicolai Juul

2013-01-01

Despite recent progress thanks to next-generation sequencing technologies, personalised cancer medicine is still hampered by intra-tumour heterogeneity and drug resistance. As most patients with advanced metastatic disease face poor survival, there is need to improve early diagnosis. Analysing...... detection. Dividing 4,467 samples into one discovery and two independent validation cohorts, we show that up to 76% of 10 cancer types harbour at least one mutation in a panel of only 25 genes, with high sensitivity across most tumour types. Our analyses demonstrate that targeting "hotspot" regions would...

Use of next-generation sequencing in oral cavity cancer

DEFF Research Database (Denmark)

Tabatabaeifar, Siavosh; Kruse, Torben A; Thomassen, Mads

Background: Oral cavity cancer is a subgroup of head and neck cancer which is the world’s 6th most common cancer form. Oral squamous cell carcinomas (OSCC) constitute almost all oral cavity cancers, and OSCC are primarily attributed by excessive alcohol consumption and tobacco exposure...... of tumour cells exists. Conclusions: Use of next generation sequencing in oral cavity cancer can give valuable insight into the biology of the disease. By investigating intra tumour heterogeneity we see that the different tumour specimens in each patient are quite homogenous, but evidence of heterogeneous...

Sequence analysis of measles virus strains collected during the pre- and early-vaccination era in Denmark reveals a considerable diversity of ancient strains

DEFF Research Database (Denmark)

Christensen, Laurids Siig; Schöller, S.; Schierup, M. H.

2002-01-01

A total of 199 serum samples from patients with measles collected in Denmark, Greenland and the Faroe Islands from 1964 to 1983 were analysed by PCR. Measles virus (MV) RNA could be detected in 38 (19%) of the samples and a total of 18 strains were subjected to partial sequence analysis of the he......A total of 199 serum samples from patients with measles collected in Denmark, Greenland and the Faroe Islands from 1964 to 1983 were analysed by PCR. Measles virus (MV) RNA could be detected in 38 (19%) of the samples and a total of 18 strains were subjected to partial sequence analysis...... of the hemagglutinin gene. The strains exhibited a considerable genomic diversity, which is at odds with the assumption that one genome type prevailed among globally circulating MV strains prior to the advent of live-attenuated vaccines. Our data indicate that the similarity of the various vaccine strains...... is attributed to their having originated from the same primary isolate. Consequently, it is implied that a small number of clinical manifestations of MV worldwide from which strains similar to the vaccine strain were identified were vaccine related rather than being caused by members of a persistently...

Combined intra-articular glucocorticoid, bupivacaine and morphine reduces pain and convalescence after diagnostic knee arthroscopy

DEFF Research Database (Denmark)

Rasmussen, Sten; Lorentzen, Jan S; Larsen, Allan S

2002-01-01

We studied the effect of intra-articullar saline vs. bupivacaine + morphine or bupivacaine morphine + methylprednisolone after diagnostic knee arthroscopy. In a double-blind randomized study, 60 patients undergoing diagnostic knee arthroscopy without a therapeutic procedure were allocated to groups...... receiving intra-articular saline, intra-articular bupivacaine 150 mg + morphine 4 mg or the same dose of bupivacaine + morphine + intra-articular methylprednisolone 40 mg at the end of arthroscopy during general anesthesia. All patients were instructed to resume normal activities immediately after...

Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing

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M. Michelle Malmberg

2018-04-01

Full Text Available Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD. Complexity reduction genotyping-by-sequencing (GBS methods, including GBS-transcriptomics (GBS-t, enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs, and identify structural variants (SVs. Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.

Intra-individual comparison of CAIPIRINHA VIBE technique with conventional VIBE sequences in contrast-enhanced MRI of focal liver lesions

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Albrecht, M.H., E-mail: MoritzAlbrecht@gmx.net [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Medical University of South Carolina, Department of Radiology and Radiological Science, Charleston, SC (United States); Bodelle, B., E-mail: boris.bodelle@kgu.de [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Varga-Szemes, A., E-mail: vargaasz@musc.edu [Medical University of South Carolina, Department of Radiology and Radiological Science, Charleston, SC (United States); Dewes, P., E-mail: patricia.dewes@kgu.de [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Bucher, A.M., E-mail: andreas.bucher@kgu.de [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Ball, B.D., E-mail: BallBr@musc.edu [Medical University of South Carolina, Department of Radiology and Radiological Science, Charleston, SC (United States); De Cecco, C.N., E-mail: dececco@musc.edu [Medical University of South Carolina, Department of Radiology and Radiological Science, Charleston, SC (United States); Schoepf, U.J., E-mail: schoepf@musc.edu [Medical University of South Carolina, Department of Radiology and Radiological Science, Charleston, SC (United States); Zhu, X., E-mail: zhuxun@shzu.edu.cn [Shihezi University, Department of Psychology, Beisi Road, Xinjiang (China); Zangos, S., E-mail: Zangos@em.uni-frankfurt.de [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Gruber-Rouh, T., E-mail: tatjanagruber2004@yahoo.de [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Wichmann, J.L., E-mail: dochwichmann@gmail.com [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); and others

2017-01-15

Purpose: To evaluate the impact of controlled aliasing in parallel imaging results in higher acceleration (CAIPIRINHA) volume interpolated breath-hold examination (VIBE) magnetic resonance imaging (MRI) technique on image quality, reader confidence, and inter-observer agreement for the assessment of focal liver lesions in comparison with the standard VIBE approach. Material and methods: In this IRB-approved intra-individual comparison study, abdominal arterial and portal-venous contrast-enhanced MRI studies were retrospectively analyzed in 38 patients with malignant liver lesions. Each patient underwent both CAIPIRINHA and conventional VIBE 3 T MRI within 3 months, showing stable disease. Images were evaluated using 5-point rating scales by two blinded radiologists with more than 20 and 5 years of experience in MRI, respectively. Readers scored dignity of liver lesions and assessed which liver segments were affected by malignancy (ranging from 1 = definitely benign/not affected to 5 = definitely malignant/affected by malignancy). Readers also rated overall image quality, sharpness of intrahepatic veins, and diagnostic confidence (ranging from 1 = poor to 5 = excellent). Results: Reviewers achieved a higher inter-observer reliability using CAIPIRINHA when they reported which liver segments were affected by malignancy compared to traditional VIBE series (κ = 0.62 and 0.54, respectively, p < 0.05). Similarly, CAIPIRINHA showed a slightly higher inter-rater agreement for the dignity of focal liver lesions versus the standard VIBE images (κ = 0.50 and 0.49, respectively, p < 0.05). CAIPIRINHA series also scored higher in comparison to standard VIBE sequences (mean scores: image quality, 4.2 and 3.5; sharpness of intrahepatic vessels, 3.8 and 3.2, respectively, p < 0.05) for both reviewers and allowed for higher subjective diagnostic confidence (ratings, 3.8 and 3.2, respectively, p < 0.05). Conclusion: Compared to the standard VIBE approach, CAIPIRINHA VIBE technique

Digital histology quantification of intra-hepatic fat in patients undergoing liver resection.

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Parkin, E; O'Reilly, D A; Plumb, A A; Manoharan, P; Rao, M; Coe, P; Frystyk, J; Ammori, B; de Liguori Carino, N; Deshpande, R; Sherlock, D J; Renehan, A G

2015-08-01

High intra-hepatic fat (IHF) content is associated with insulin resistance, visceral adiposity, and increased morbidity and mortality following liver resection. However, in clinical practice, IHF is assessed indirectly by pre-operative imaging [for example, chemical-shift magnetic resonance (CS-MR)]. We used the opportunity in patients undergoing liver resection to quantify IHF by digital histology (D-IHF) and relate this to CT-derived anthropometrics, insulin-related serum biomarkers, and IHF estimated by CS-MR. A reproducible method for quantification of D-IHF using 7 histology slides (inter- and intra-rater concordance: 0.97 and 0.98) was developed. In 35 patients undergoing resection for colorectal cancer metastases, we measured: CT-derived subcutaneous and visceral adipose tissue volumes, Homeostasis Model Assessment of Insulin Resistance (HOMA-IR), fasting serum adiponectin, leptin and fetuin-A. We estimated relative IHF using CS-MR and developed prediction models for IHF using a factor-clustered approach. The multivariate linear regression models showed that D-IHF was best predicted by HOMA-IR (Beta coefficient(per doubling): 2.410, 95% CI: 1.093, 5.313) and adiponectin (β(per doubling): 0.197, 95% CI: 0.058, 0.667), but not by anthropometrics. MR-derived IHF correlated with D-IHF (rho: 0.626; p = 0.0001), but levels of agreement deviated in upper range values (CS-MR over-estimated IHF: regression versus zero, p = 0.009); this could be adjusted for by a correction factor (CF: 0.7816). Our findings show IHF is associated with measures of insulin resistance, but not measures of visceral adiposity. CS-MR over-estimated IHF in the upper range. Larger studies are indicated to test whether a correction of imaging-derived IHF estimates is valid. Copyright © 2015 Elsevier Ltd. All rights reserved.

Rehabilitation of a Patient with an Intra Oral Prosthesis and an Extra Oral Orbital Prosthesis Retained with Magnets

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Pattanaik, Seema; Wadkar, Aarti P.

2011-01-01

This clinical case report deals with a rehabilitation of a patient with an extensive maxillary and orbital defect using an intra oral prosthesis obturating the maxillary defect and extra oral orbital prosthesis retained with rare-earth magnets for secondary retention; primary retention was derived by snug fit of the prosthesis to underlying and adjacent tissues. The rehabilitation resulted in improved function, esthetics and comfort to the patient thus enabling him to lead a normal life.

Orchiopexy for intra-abdominal testes: factors predicting success.

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Stec, Andrew A; Tanaka, Stacy T; Adams, Mark C; Pope, John C; Thomas, John C; Brock, John W

2009-10-01

Intra-abdominal testes can be treated with several surgical procedures. We evaluated factors influencing the outcome of orchiopexy for intra-abdominal testis. We retrospectively reviewed 156 consecutive orchiopexies performed for intra-abdominal testis, defined as a nonpalpable testis on examination and located in the abdomen at surgery. All surgical approaches were included in the study. Primary outcome was the overall success rate and secondary outcomes were success based on surgical approach, age and a patent processus vaginalis. Success was considered a testis with normal texture and size compared to the contralateral testis at followup. Multivariate analysis was performed to determine factors predictive of success. The overall success rate of all orchiopexies was 79.5%. Median patient age at orchiopexy was 12 months and mean followup was 16 months. Of the patients 117 had a patent processus vaginalis at surgery. One-stage abdominal orchiopexy was performed in 92 testes with 89.1% success. Of these cases 32 were performed laparoscopically with 96.9% success. One-stage Fowler-Stephens orchiopexy was performed in 27 testes and 2-stage Fowler-Stephens orchiopexy was performed in 37 with success in 63.0% and 67.6%, respectively. Multivariate analysis revealed that 1-stage orchiopexy without vessel division had more successful outcomes than 1 and 2-stage Fowler-Stephens orchiopexy (OR 0.24, p = 0.007 and 0.29, p = 0.19, respectively). Neither age at surgery nor an open internal ring was significant (p = 0.49 and 0.12, respectively). The overall success of orchiopexy for intra-abdominal testis is 79.5%. While patient selection remains a critical factor, 1-stage orchiopexy without vessel division was significantly more successful and a laparoscopic approach was associated with the fewest failures for intra-abdominal testes.

Intra-uterine hematoma in pregnancy

DEFF Research Database (Denmark)

Glavind, K; Nøhr, S; Nielsen, P H

1991-01-01

In 60 patients with a live fetus and an intra-uterine hematoma (IUH) proven by ultrasonic scanning the outcome of pregnancy was spontaneous abortion in 12% and premature delivery in 10%. No correlation between the outcome of the pregnancy and the maximum size of the hematoma or the week...

Genetic diversity of Trichomonas vaginalis clinical isolates from Henan province in central China.

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Mao, Meng; Liu, Hui Li

2015-07-01

Trichomonas vaginalis is a flagellated protozoan parasite that infects the human urogenital tract, causing the most common non-viral, sexually transmitted disease worldwide. In this study, genetic variants of T. vaginalis were identified in Henan Province, China. Fragments of the small subunit of nuclear ribosomal RNA (18S rRNA) were amplified from 32 T. vaginalis isolates obtained from seven regions of Henan Province. Overall, 18 haplotypes were determined from the 18S rRNA sequences. Each sampled population and the total population displayed high haplotype diversity (Hd), accompanied by very low nucleotide diversity (Pi). In these molecular genetic variants, 91.58% genetic variation was derived from intra-regions. Phylogenetic analysis revealed no correlation between phylogeny and geographic distribution. Demographic analysis supported population expansion of T. vaginalis isolates from central China. Our findings showing moderate-to-high genetic variations in the 32 isolates of T. vaginalis provide useful knowledge for monitoring changes in parasite populations for the development of future control strategies.

Intra-articular hyaluronan is without clinical effect in knee osteoarthritis: a multicentre, randomised, placebo-controlled, double-blind study of 337 patients followed for 1 year

DEFF Research Database (Denmark)

Jørgensen, Anette; Stengaard-Pedersen, Kristian; Simonsen, Ole

2010-01-01

OBJECTIVE: To examine the long-term efficacy and safety of five intra-articular injections with hyaluronan in knee osteoarthritis. METHODS: A multicentre, randomised, placebo-controlled double-blind study of 337 patients fulfilling the American College of Rheumatology (ACR) criteria for knee...... osteoarthritis (clinical and laboratory) and with a Lequesne algofunctional index score (LFI) of 10 or greater. Patients received a hyaluronan product (sodium hyaluronate; Hyalgan) (n=167) or saline (n=170) intra-articularly weekly for 5 weeks and were followed up to 1 year. Time to recurrence was the primary...... the ACR criteria for osteoarthritis of the knee with moderate to severe disease activity (LFI > or = 10), five intra-articular injections of hyaluronan did not improve pain, function, paracetamol consumption or other efficacy parameters 3, 6, 9 and 12 months after the treatment....

Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a

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Xue Ying

2006-07-01

Full Text Available Abstract Background Shigella bacteria cause dysentery, which remains a significant threat to public health. Shigella flexneri is the most common species in both developing and developed countries. Five Shigella genomes have been sequenced, revealing dynamic and diverse features. To investigate the intra-species diversity of S. flexneri genomes further, we have sequenced the complete genome of S. flexneri 5b strain 8401 (abbreviated Sf8401 and compared it with S. flexneri 2a (Sf301. Results The Sf8401 chromosome is 4.5-Mb in size, a little smaller than that of Sf301, mainly because the former lacks the SHI-1 pathogenicity island (PAI. Compared with Sf301, there are 6 inversions and one translocation in Sf8401, which are probably mediated by insertion sequences (IS. There are clear differences in the known PAIs between these two genomes. The bacteriophage SfV segment remaining in SHI-O of Sf8401 is clearly larger than the remnants of bacteriophage SfII in Sf301. SHI-1 is absent from Sf8401 but a specific related protein is found next to the pheV locus. SHI-2 is involved in one intra-replichore inversion near the origin of replication, which may change the expression of iut/iuc genes. Moreover, genes related to the glycine-betaine biosynthesis pathway are present only in Sf8401 among the known Shigella genomes. Conclusion Our data show that the two S. flexneri genomes are very similar, which suggests a high level of structural and functional conservation between the two serotypes. The differences reflect different selection pressures during evolution. The ancestor of S. flexneri probably acquired SHI-1 and SHI-2 before SHI-O was integrated and the serotypes diverged. SHI-1 was subsequently deleted from the S. flexneri 5b genome by recombination, but stabilized in the S. flexneri 2a genome. These events may have contributed to the differences in pathogenicity and epidemicity between the two serotypes of S. flexneri.

SCREENING OF PROTEASE INHIBITORS RESISTANCE MUTATIONS IN HEPATITIS C VIRUS ISOLATES INFECTING ROMANIAN PATIENTS UNEXPOSED TO TRIPLE THERAPY.

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Dinu, Sorin; Calistru, Petre-Iacob; Ceauşu, Emanoil; Târdeil, Graţiela; Oprişan, Gabriela

2015-01-01

Although the European recommendations include the use of new antiviral drugs for the treatment of hepatitis C, in Romania the current treatment remains interferon plus ribavirin. First generation viral protease inhibitors (i.e. boceprevir, telaprevir), which have raised the chances of obtaining viral clearance in up to 70% of infection cases produced by genotype 1 isolates, have not been introduced yet as standard treatment in our country. The success of these new antivirals is limited by the occurrence and selection of resistance mutations during therapy. We set-up a molecular study aiming to detect any resistance mutations to boceprevir and telaprevir harbored by hepatitis C isolates infecting Romanian patients naïve to viral protease inhibitors. Since these new antivirals are efficient and approved for genotype 1 infection, viral samples were genotyped following a protocol previously developed by our research group. We analyzed by both population sequencing and molecular cloning and sequencing the NS3 protease region of hepatitis C virus isolates infecting patients which were not previously exposed to boceprevir and telaprevir. All the analyzed samples were subtype 1b and resembled the samples collected in recent years from Romanian patients. Molecular cloning followed by sequencing showed great intra-host diversity, which is known to represent the source of isolates with different resistance phenotypes. Both population sequencing and molecular cloning followed by clone sequencing revealed two boceprevir resistance mutations (T54S and V55A), respectively, a telaprevir resistance mutation (T54S) in the sequences obtained from a patient with chronic hepatitis C. To our knowledge, this is the first study indicating the existence of pre-treatment resistance mutations to boceprevir and telaprevir in hepatitis C virus isolates infecting Romanian patients.

Fungal Diversity in Field Mold-Damaged Soybean Fruits and Pathogenicity Identification Based on High-Throughput rDNA Sequencing

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Jiang Liu

2017-05-01

Full Text Available Continuous rain and an abnormally wet climate during harvest can easily lead to soybean plants being damaged by field mold (FM, which can reduce seed yield and quality. However, to date, the underlying pathogen and its resistance mechanism have remained unclear. The objective of the present study was to investigate the fungal diversity of various soybean varieties and to identify and confirm the FM pathogenic fungi. A total of 62,382 fungal ITS1 sequences clustered into 164 operational taxonomic units (OTUs with 97% sequence similarity; 69 taxa were recovered from the samples by internal transcribed spacer (ITS region sequencing. The fungal community compositions differed among the tested soybeans, with 42 OTUs being amplified from all varieties. The quadratic relationships between fungal diversity and organ-specific mildew indexes were analyzed, confirming that mildew on soybean pods can mitigate FM damage to the seeds. In addition, four potentially pathogenic fungi were isolated from FM-damaged soybean fruits; morphological and molecular identification confirmed these fungi as Aspergillus flavus, A. niger, Fusarium moniliforme, and Penicillium chrysogenum. Further re-inoculation experiments demonstrated that F. moniliforme is dominant among these FM pathogenic fungi. These results lay the foundation for future studies on mitigating or preventing FM damage to soybean.

Analysis on the use of Multi-Sequence MRI Series for Segmentation of Abdominal Organs

International Nuclear Information System (INIS)

Selver, M A; Selvi, E; Kavur, E; Dicle, O

2015-01-01

Segmentation of abdominal organs from MRI data sets is a challenging task due to various limitations and artefacts. During the routine clinical practice, radiologists use multiple MR sequences in order to analyze different anatomical properties. These sequences have different characteristics in terms of acquisition parameters (such as contrast mechanisms and pulse sequence designs) and image properties (such as pixel spacing, slice thicknesses and dynamic range). For a complete understanding of the data, computational techniques should combine the information coming from these various MRI sequences. These sequences are not acquired in parallel but in a sequential manner (one after another). Therefore, patient movements and respiratory motions change the position and shape of the abdominal organs. In this study, the amount of these effects is measured using three different symmetric surface distance metrics performed to three dimensional data acquired from various MRI sequences. The results are compared to intra and inter observer differences and discussions on using multiple MRI sequences for segmentation and the necessities for registration are presented

Study of Inter- and Intra-fraction Motion in Brain Tumor Patients Undergoing VMAT Treatment

International Nuclear Information System (INIS)

Ascencion Ybarra, Y.; Alfonso Laguardia, R.; Yartsev, S.

2015-01-01

Conforming dose to the tumor and sparing normal tissue can be challenging for brain tumors with complex shapes in close proximity to critical structures. The goal of this study was to evaluate the inter- and intra-fraction motion in brain tumor patients undergoing volumetric modulated arc therapy (VMAT). The image matching software was found to be very sensitive to the choice of the region of matching. It is recommended to use the same region of interest for comparing the image sets and perform the automatic matching based on bony landmarks in brain tumor cases. (Author)

Role of static fluid MR urography in detecting post urinary diversion complications

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Amr Farouk Ibrahim Moustafa

2018-06-01

Full Text Available Aim of work: The aim of the study was to assess the diagnostic performance of static MR urography in detection of post cystectomy complications & the ability of static fluid MR urography in visualization of urinary tract segments. Material & methods: We prospectively reviewed 21 MR urograms with urinary diversion. The most common surgical procedures included Ileal conduit & Ileocecal neobladder diversion.Magnetic resonance urography examinations were performed with 1.5-T MR scanners. T2 weighted (static fluid MR urography techniques were done, in addition to conventional T1- and T2-weighted axial and coronal sequences. Urinary tract was divided in different parts: pelvicalyceal systems, upper, mid and lower ureteric segments & the reservoir or conduit Imaging features of the urinary collecting systems were evaluated for their visualization and complications detection. Results: T2-weighted MR urography could demonstrate 95% of urinary tract segments & together with conventional MR sequences all urinary tract segments can be visualized. Urinary diversion related complications were encountered included in 15 patients (71.4% & no urological complications were seen in 6 patients (28.6%. Conclusion: Comprehensive T2-weighted MR urography is an effective imaging method for the visualization of the urinary system and detection of early and late postoperative complications in patients with urinary diversion. Keywords: MR urography, Urinary diversion, Cancer bladder

Joint lavage followed by intra-articular injection of hyaluronic acid and/or corticosteroids in patients with severe hemophilic arthropathy of the knee: Is this intervention really effective?

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Rodriguez-Merchan, E Carlos; Valentino, Leonard A

2018-05-10

The aim of this review is to explore the scientific rationale and evidence for a potential benefit of joint lavage followed by intra-articular injection of hyaluronic acid and/or corticosteroids in patients with severe hemophilic arthropathy of the knee (SHAK). Areas covered: This article is a narrative review of the evidence for potential benefits of joint lavage followed by intra-articular injection of hyaluronic acid and corticosteroids in SHAK compared with osteoarthritis of the knee in non-hemophilia patients. Expert commentary: Although some reports on hemophilic arthropathy with a low-grade of evidence seem to indicate a benefit of joint lavage followed by intra-articular injection of hyaluronic acid and/or corticosteroids in patients with SHAK, the short-lived improvements afforded by hyaluronic acid, and the doubtful benefits of corticosteroids and joint lavage in hemophilia, do not warrant their use in hemophilic patients. The scientific rationale of these procedures is poor and they are not recommended.

Intra-operative removal of chest tube in video-assisted thoracoscopic procedures

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Moustafa M. El-Badry

2017-12-01

Conclusions: Intra-operative removal of chest tube during VATS procedures was a safe technique in well selected patients with an intra-operative successful air-leak test with radiological and clinical follow-up. This technique provided lesser post-operative pain with shorter hospital stay.

Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences.

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Jeanbille, M; Buée, M; Bach, C; Cébron, A; Frey-Klett, P; Turpault, M P; Uroz, S

2016-02-01

Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.

Partial sequence homogenization in the 5S multigene families may generate sequence chimeras and spurious results in phylogenetic reconstructions.

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Galián, José A; Rosato, Marcela; Rosselló, Josep A

2014-03-01

Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclear 5S rDNA gene family rarely used contiguous 5S coding sequences due to the routine use of head-to-tail polymerase chain reaction primers that are anchored to the coding region. Moreover, the 5S coding sequences have been concatenated with independent, adjacent gene units in many studies, creating simulated chimeric genes as the raw data for evolutionary analysis. This practice is based on the tacitly assumed, but rarely tested, hypothesis that strict intra-locus concerted evolution processes are operating in 5S rDNA genes, without any empirical evidence as to whether it holds for the recovered data. The potential pitfalls of analysing the patterns of molecular evolution and reconstructing phylogenies based on these chimeric genes have not been assessed to date. Here, we compared the sequence integrity and phylogenetic behavior of entire versus concatenated 5S coding regions from a real data set obtained from closely related plant species (Medicago, Fabaceae). Our results suggest that within arrays sequence homogenization is partially operating in the 5S coding region, which is traditionally assumed to be highly conserved. Consequently, concatenating 5S genes increases haplotype diversity, generating novel chimeric genotypes that most likely do not exist within the genome. In addition, the patterns of gene evolution are distorted, leading to incorrect haplotype relationships in some evolutionary reconstructions.

Evaluation of genetic diversity amongst Descurainia sophia L. genotypes by inter-simple sequence repeat (ISSR) marker.

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Saki, Sahar; Bagheri, Hedayat; Deljou, Ali; Zeinalabedini, Mehrshad

2016-01-01

Descurainia sophia is a valuable medicinal plant in family of Brassicaceae. To determine the range of diversity amongst D. sophia in Iran, 32 naturally distributed plants belonging to six natural populations of the Iranian plateau were investigated by inter-simple sequence repeat (ISSR) markers. The average percentage of polymorphism produced by 12 ISSR primers was 86 %. The PIC values for primers ranged from 0.22 to 0.40 and Rp values ranged between 6.5 and 19.9. The relative genetic diversity of the populations was not high (Gst =0.32). However, the value of gene flow revealed by the ISSR marker was high (Nm = 1.03). UPGMA clustering method based on Jaccard similarity coefficient grouped the genotypes into two major clusters. Graph results from Neighbor-Net Network generated after a 1000 bootstrap test using Jaccard coefficient, and STRUCTURE analysis confirmed the UPGMA clustering. The first three PCAs represented 57.31 % of the total variation. The high levels of genetic diversity were observed within populations, which is useful in breeding and conservation programs. ISSR is found to be an eligible marker to study genetic diversity of D. sophia.

Usability of Commercially Available Mobile Applications for Diverse Patients.

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Sarkar, Urmimala; Gourley, Gato I; Lyles, Courtney R; Tieu, Lina; Clarity, Cassidy; Newmark, Lisa; Singh, Karandeep; Bates, David W

2016-12-01

Mobile applications or 'apps' intended to help people manage their health and chronic conditions are widespread and gaining in popularity. However, little is known about their acceptability and usability for low-income, racially/ethnically diverse populations who experience a disproportionate burden of chronic disease and its complications. The objective of this study was to investigate the usability of existing mobile health applications ("apps") for diabetes, depression, and caregiving, in order to facilitate development and tailoring of patient-facing apps for diverse populations. Usability testing, a mixed-methods approach that includes interviewing and direct observation of participant technology use, was conducted with participants (n = 9 caregivers; n = 10 patients with depression; and n = 10 patients with diabetes) on a total of 11 of the most popular health apps (four diabetes apps, four depression apps, and three caregiver apps) on both iPad and Android tablets. The participants were diverse: 15 (58 %) African Americans, seven (27 %) Whites, two (8 %) Asians, two (8 %) Latinos with either diabetes, depression, or who were caregivers. Participants were given condition-specific tasks, such as entering a blood glucose value into a diabetes app. Participant interviews were video recorded and were coded using standard methods to evaluate attempts and completions of tasks. We performed inductive coding of participant comments to identify emergent themes. Participants completed 79 of 185 (43 %) tasks across 11 apps without assistance. Three themes emerged from participant comments: lack of confidence with technology, frustration with design features and navigation, and interest in having technology to support their self-management. App developers should employ participatory design strategies in order to have an impact on chronic conditions such as diabetes and depression that disproportionately affect vulnerable populations. While patients

Intra-artery thrombolytic therapy for acute ischemic cerebral infarction

International Nuclear Information System (INIS)

Du Wei; Shao Chengmin; Wang Jianlin; Lei Jin; Jia Fan; Cao Lanfang; Chai Ruchang; Su Wei; Gu Jinchuan

2004-01-01

Objective: To evaluate the clinical effects of intra-arterial thrombolytic therapy for acute ischemic cerebral infarction and analyze the factors influencing the clinical prognosis. Methods: 32 patients were treated with intra-arterial thrombolysis using urokinase (median dose, 65 x 10 4 U) within 2-20 hours, after the onset. The patient's condition was assessed by neurologists using National Institutes of Health Stroke Scale (NIHSS) score right at the admission. Clinical outcome was assessed after 3 months and graded as good for Modified Rankin Scale (MRS) scores of 0 to 3 and poor for MRS scores of 4 or 5 and death. Results: Follow up cerebral angiography of 14 cases treated within 6 hours after onset showed complete/partial recanalization in 13 cases. Other 18 patients whose treatment started beyond 6 hours after onset out-came with complete/partial in 7. 20 (62.5%) of the 32 patients had good out-come, 12(37.5%) had poor outcome and two patients(9.4%) died. Cerebral hemorrhage occurred in 2 of the 32 patients. Good outcome was associated with an initial NIHSS score of <20 (P<0.01) and vascular recanalization (P<0.025). Recanalization was more likely to be obtained if thrombolysis began within 6 hours (P<0.05). Conclusion: Intra-arterial thrombolysis is a safe and effective therapy for acute ischemic cerebral infarction. (authors)

Intra-fraction motion of the prostate during treatment with helical tomotherapy

International Nuclear Information System (INIS)

Thomas, Simon J.; Ashburner, Mark; Tudor, George Samuel J.; Treeby, Jo; Dean, June; Routsis, Donna; Rimmer, Yvonne L.; Russell, Simon G.; Burnet, Neil G.

2013-01-01

Background and purpose: To measure the geometric uncertainty resulting from intra-fraction motion and intra-observer image matching, for patients having image-guided prostate radiotherapy on TomoTherapy. Material and methods: All patients had already been selected for prostate radiotherapy on TomoTherapy, with daily MV-CT imaging. The study involved performing an additional MV-CT image at the end of treatment, on 5 occasions during the course of 37 treatments. 54 patients were recruited to the study. A new formula was derived to calculate the PTV margin for intra-fraction motion. Results: The mean values of the intra-fraction differences were 0.0 mm, 0.5 mm, 0.5 mm and 0.0° for LR, SI, AP and roll, respectively. The corresponding standard deviations were 1.1 mm, 0.8 mm, 0.8 mm and 0.6° for systematic uncertainties (Σ), 1.3 mm, 2.0 mm, 2.2 mm and 0.3° for random uncertainties (σ). This intra-fraction motion requires margins of 2.2 mm in LR, 2.1 mm in SI and 2.1 mm in AP directions. Inclusion of estimates of the effect of rotations and matching errors increases these margins to approximately 4 mm in LR and 5 mm in SI and AP directions. Conclusions: A new margin recipe has been developed to calculate margins for intra-fraction motion. This recipe is applicable to any measurement technique that is based on the difference between images taken before and after treatment

NS5A Sequence Heterogeneity and Mechanisms of Daclatasvir Resistance in Hepatitis C Virus Genotype 4 Infection.

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Zhou, Nannan; Hernandez, Dennis; Ueland, Joseph; Yang, Xiaoyan; Yu, Fei; Sims, Karen; Yin, Philip D; McPhee, Fiona

2016-01-15

Daclatasvir is an NS5A inhibitor approved for treatment of infection due to hepatitis C virus (HCV) genotypes (GTs) 1-4. To support daclatasvir use in HCV genotype 4 infection, we examined a diverse genotype 4-infected population for HCV genotype 4 subtype prevalence, NS5A polymorphisms at residues associated with daclatasvir resistance (positions 28, 30, 31, or 93), and their effects on daclatasvir activity in vitro and clinically. We performed phylogenetic analysis of genotype 4 NS5A sequences from 186 clinical trial patients and 43 sequences from the European HCV database, and susceptibility analyses of NS5A polymorphisms and patient-derived NS5A sequences by using genotype 4 NS5A hybrid genotype 2a replicons. The clinical trial patients represented 14 genotype 4 subtypes; most prevalent were genotype 4a (55%) and genotype 4d (27%). Daclatasvir 50% effective concentrations for 10 patient-derived NS5A sequences representing diverse phylogenetic clusters were ≤0.080 nM. Most baseline sequences had ≥1 NS5A polymorphism at residues associated with daclatasvir resistance; however, only 3 patients (1.6%) had polymorphisms conferring ≥1000-fold daclatasvir resistance in vitro. Among 46 patients enrolled in daclatasvir trials, all 20 with baseline resistance polymorphisms achieved a sustained virologic response. Circulating genotype 4 subtypes are genetically diverse. Polymorphisms conferring high-level daclatasvir resistance in vitro are uncommon before therapy, and clinical data suggest that genotype 4 subtype and baseline polymorphisms have minimal impact on responses to daclatasvir-containing regimens. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America.

Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation.

Science.gov (United States)

Kim, Sang Hu; Clark, Shawn T; Surendra, Anuradha; Copeland, Julia K; Wang, Pauline W; Ammar, Ron; Collins, Cathy; Tullis, D Elizabeth; Nislow, Corey; Hwang, David M; Guttman, David S; Cowen, Leah E

2015-11-01

The microbiome shapes diverse facets of human biology and disease, with the importance of fungi only beginning to be appreciated. Microbial communities infiltrate diverse anatomical sites as with the respiratory tract of healthy humans and those with diseases such as cystic fibrosis, where chronic colonization and infection lead to clinical decline. Although fungi are frequently recovered from cystic fibrosis patient sputum samples and have been associated with deterioration of lung function, understanding of species and population dynamics remains in its infancy. Here, we coupled high-throughput sequencing of the ribosomal RNA internal transcribed spacer 1 (ITS1) with phenotypic and genotypic analyses of fungi from 89 sputum samples from 28 cystic fibrosis patients. Fungal communities defined by sequencing were concordant with those defined by culture-based analyses of 1,603 isolates from the same samples. Different patients harbored distinct fungal communities. There were detectable trends, however, including colonization with Candida and Aspergillus species, which was not perturbed by clinical exacerbation or treatment. We identified considerable inter- and intra-species phenotypic variation in traits important for host adaptation, including antifungal drug resistance and morphogenesis. While variation in drug resistance was largely between species, striking variation in morphogenesis emerged within Candida species. Filamentation was uncoupled from inducing cues in 28 Candida isolates recovered from six patients. The filamentous isolates were resistant to the filamentation-repressive effects of Pseudomonas aeruginosa, implicating inter-kingdom interactions as the selective force. Genome sequencing revealed that all but one of the filamentous isolates harbored mutations in the transcriptional repressor NRG1; such mutations were necessary and sufficient for the filamentous phenotype. Six independent nrg1 mutations arose in Candida isolates from different patients

Genetic diversity in two Japanese flounder populations from China seas inferred using microsatellite markers and COI sequences

Science.gov (United States)

Xu, Dongdong; Li, Sanlei; Lou, Bao; Zhang, Yurong; Zhan, Wei; Shi, Huilai

2012-07-01

Japanese flounder is one of the most important commercial species in China; however, information on the genetic background of natural populations in China seas is scarce. The lack of genetic data has hampered fishery management and aquaculture development programs for this species. In the present study, we have analyzed the genetic diversity in natural populations of Japanese flounder sampled from the Yellow Sea (Qingdao population, QD) and East China Sea (Zhoushan population, ZS) using 10 polymorphic microsatellite loci and cytochrome c oxidase subunit I (COI) sequencing data. A total of 68 different alleles were observed over 10 microsatellite loci. The total number of alleles per locus ranged from 2 to 9, and the number of genotypes per locus ranged from 3 to 45. The observed heterozygosity and expected heterozygosity in QD were 0.733 and 0.779, respectively, and in ZS the heterozygosity values were 0.708 and 0.783, respectively. Significant departures from Hardy-Weinberg equilibrium were observed in 7 of the 10 microsatellite loci in each of the two populations. The COI sequencing analysis revealed 25 polymorphic sites and 15 haplotypes in the two populations. The haplotype diversity and nucleotide diversity in the QD population were 0.746±0.072 8 and 0.003 34±0.001 03 respectively, and in ZS population the genetic diversity values were 0.712±0.047 0 and 0.003 18±0.000 49, respectively. The microsatellite data ( F st =0.048 7, P <0.001) and mitochondrial DNA data ( F st =0.128, P <0.001) both revealed significant genetic differentiation between the two populations. The information on the genetic variation and differentiation in Japanese flounder obtained in this study could be used to set up suitable guidelines for the management and conservation of this species, as well as for managing artificial selection programs. In future studies, more geographically diverse stocks should be used to obtain a deeper understanding of the population structure of Japanese

Imatinib mesylate induces responses in patients with liver metastases from gastrointestinal stromal tumor failing intra-arterial hepatic chemotherapy

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Fiorentini Giammaria

2006-01-01

Full Text Available Background: Imatinib mesylate represents a real major paradigm shift in cancer therapy, targeting the specific molecular abnormalities, crucial in the etiology of tumor. Intra-arterial hepatic chemotherapy (IAHC followed by embolization, has been considered an interesting palliative option for patients with liver metastases from gastrointestinal stromal tumor (GIST, due to the typically hypervascular pattern of the tumor. Aims: We report our experience with IAHC followed by Imatinib mesylate, in order to show the superiority of the specific molecular approach in liver metastases from GIST. Materials and Methods: Three patients (pts with pretreated massive liver metastases from GIST, received IAHC with Epirubicin 50 mg/mq, every 3 weeks for 6 cycles. At the evidence of progression, they received Imatinib mesylate. Results: We observed progressive diseases in all cases. In 1998, one patient underwent Thalidomide at 150 mg orally, every day for 4 months, with evidence of stable disease and clinical improvement. In 2001, two patients received Imatinib mesylate at 400 mg orally, every day, with evidence of partial response lasting 18+ months and 16 months. One of them had grade 3 neutropenia, with suspension of therapy for 3 weeks. Conclusion: No patient treated with IAHC, reported objective responses, but two of them obtained partial response after the assumption of Imatinib mesylate and one showed temporary stabilization with thalidomide. Imatinib mesylate represents a new opportunity in GIST therapy, targeting the specific molecular alteration. It seems to be superior to conventional intra arterial hepatic chemotherapy.

Intra-tumor genetic heterogeneity and mortality in head and neck cancer: analysis of data from the Cancer Genome Atlas.

Science.gov (United States)

Mroz, Edmund A; Tward, Aaron D; Tward, Aaron M; Hammon, Rebecca J; Ren, Yin; Rocco, James W

2015-02-01

Although the involvement of intra-tumor genetic heterogeneity in tumor progression, treatment resistance, and metastasis is established, genetic heterogeneity is seldom examined in clinical trials or practice. Many studies of heterogeneity have had prespecified markers for tumor subpopulations, limiting their generalizability, or have involved massive efforts such as separate analysis of hundreds of individual cells, limiting their clinical use. We recently developed a general measure of intra-tumor genetic heterogeneity based on whole-exome sequencing (WES) of bulk tumor DNA, called mutant-allele tumor heterogeneity (MATH). Here, we examine data collected as part of a large, multi-institutional study to validate this measure and determine whether intra-tumor heterogeneity is itself related to mortality. Clinical and WES data were obtained from The Cancer Genome Atlas in October 2013 for 305 patients with head and neck squamous cell carcinoma (HNSCC), from 14 institutions. Initial pathologic diagnoses were between 1992 and 2011 (median, 2008). Median time to death for 131 deceased patients was 14 mo; median follow-up of living patients was 22 mo. Tumor MATH values were calculated from WES results. Despite the multiple head and neck tumor subsites and the variety of treatments, we found in this retrospective analysis a substantial relation of high MATH values to decreased overall survival (Cox proportional hazards analysis: hazard ratio for high/low heterogeneity, 2.2; 95% CI 1.4 to 3.3). This relation of intra-tumor heterogeneity to survival was not due to intra-tumor heterogeneity's associations with other clinical or molecular characteristics, including age, human papillomavirus status, tumor grade and TP53 mutation, and N classification. MATH improved prognostication over that provided by traditional clinical and molecular characteristics, maintained a significant relation to survival in multivariate analyses, and distinguished outcomes among patients having

3D-Flair sequence at 3T in cochlear otosclerosis

International Nuclear Information System (INIS)

Lombardo, Francesco; De Cori, Sara; Aghakhanyan, Gayane; Montanaro, Domenico; De Marchi, Daniele; Frijia, Francesca; Canapicchi, Raffaello; Fortunato, Susanna; Forli, Francesca; Berrettini, Stefano; Chiappino, Dante

2016-01-01

To assess the capability of three-dimensional fluid-attenuated inversion recovery (3D-FLAIR) sequences in detecting signal alterations of the endolabyrinthine fluid in patients with otosclerosis. 3D-FLAIR before and after (-/+) gadolinium (Gd) administration was added to the standard MR protocol and acquired in 13 patients with a clinical/audiological diagnosis of severe/profound hearing loss in otosclerosis who were candidates for cochlear implantation and in 11 control subjects using 3-T magnetic resonance imaging (MRI) equipment. The MRI signal of the fluid-filled cochlea was assessed both visually and calculating the signal intensity ratio (SIR = signal intensity cochlea/brainstem). We revealed no endocochlear signal abnormalities on T1-weighted -/+ Gd images for either group, while on 3D-FLAIR we found bilateral hyperintensity with enhancement after Gd administration in eight patients and bilateral hyperintensity without enhancement in one patient. No endocochlear signal abnormalities were detected in other patients or the control group. Using 3-T MRI equipment, the 3D-FLAIR -/+ Gd sequence is able to detect the blood-labyrinth barrier (BLB) breakdown responsible for alterations of the endolabyrinthine fluid in patients with cochlear otosclerosis. We believe that 3D-FLAIR +/- Gd is an excellent imaging modality to assess the intra-cochlear damage in otosclerosis patients. (orig.)

3D-Flair sequence at 3T in cochlear otosclerosis

Energy Technology Data Exchange (ETDEWEB)

Lombardo, Francesco; De Cori, Sara; Aghakhanyan, Gayane; Montanaro, Domenico; De Marchi, Daniele; Frijia, Francesca; Canapicchi, Raffaello [Fondazione CNR Regione Toscana ' ' G. Monasterio' ' , Neuroradiology Unit, Pisa (Italy); Fortunato, Susanna; Forli, Francesca; Berrettini, Stefano [University of Pisa, ENT Audiology Phoniatry Unit, Department of Neuroscience, Pisa (Italy); Chiappino, Dante [Fondazione CNR Regione Toscana ' ' G. Monasterio' ' , Department of Radiology, Massa (Italy)

2016-10-15

To assess the capability of three-dimensional fluid-attenuated inversion recovery (3D-FLAIR) sequences in detecting signal alterations of the endolabyrinthine fluid in patients with otosclerosis. 3D-FLAIR before and after (-/+) gadolinium (Gd) administration was added to the standard MR protocol and acquired in 13 patients with a clinical/audiological diagnosis of severe/profound hearing loss in otosclerosis who were candidates for cochlear implantation and in 11 control subjects using 3-T magnetic resonance imaging (MRI) equipment. The MRI signal of the fluid-filled cochlea was assessed both visually and calculating the signal intensity ratio (SIR = signal intensity cochlea/brainstem). We revealed no endocochlear signal abnormalities on T1-weighted -/+ Gd images for either group, while on 3D-FLAIR we found bilateral hyperintensity with enhancement after Gd administration in eight patients and bilateral hyperintensity without enhancement in one patient. No endocochlear signal abnormalities were detected in other patients or the control group. Using 3-T MRI equipment, the 3D-FLAIR -/+ Gd sequence is able to detect the blood-labyrinth barrier (BLB) breakdown responsible for alterations of the endolabyrinthine fluid in patients with cochlear otosclerosis. We believe that 3D-FLAIR +/- Gd is an excellent imaging modality to assess the intra-cochlear damage in otosclerosis patients. (orig.)

Usefulness of fluoroscopy-guided intra-articular injection of the knee

Energy Technology Data Exchange (ETDEWEB)

Myung, Jae Sung; Lee, Joon Woo [Seoul National University Bundang Hospital, Seongnam (Korea, Republic of); Lee, Ji Yeon [Kangwon National University College of Medicine, Chuncheon (Korea, Republic of)] (and others)

2007-06-15

To determine the accuracy of the intra-articular location of hyaluronic acid injection using a blind approach and to establish the usefulness of fluoroscopy-guided intra-articular injection. A fluoroscopy unit was used for 368 intra-articular injections of hyaluronic acid to 93 knees in 65 patients. Initially, blind needle positioning was conducted on the fluoroscopy table. The failure rate of the blind approach among the 368 injections was evaluated, and a relationship between the Kellgren-Lawrence grade (K-L grade) and the incidence of repeated failures using the blind approach was determined for injections to 52 knees in 37 patients who received a complete cycle of injections (five consecutive injections with a one-week interval between injections). Using a blind approach, 298 of 368 trials (81.2%) resulted in a needle tip being placed in an intra-articular location, while 70 of 368 trials resulted in an extra-articular placement of the needle tip. Among 52 knees to which a complete cycle of injection (five consecutive injections with a one-week interval between injections) was administered, repeated failure of intra-articular placement using the blind approach was seen for 18 knees (34.6%); a more severe K-L grade assigned was associated with a higher rate of repeated failure. However, the trend was not statistically significant based on the Chi-squared test ({rho} value = 0.14). Fluoroscopy-guided needle placement may be helpful to ensure therapeutic intra-articular injection of the knee.

Usefulness of fluoroscopy-guided intra-articular injection of the knee

International Nuclear Information System (INIS)

Myung, Jae Sung; Lee, Joon Woo; Lee, Ji Yeon

2007-01-01

To determine the accuracy of the intra-articular location of hyaluronic acid injection using a blind approach and to establish the usefulness of fluoroscopy-guided intra-articular injection. A fluoroscopy unit was used for 368 intra-articular injections of hyaluronic acid to 93 knees in 65 patients. Initially, blind needle positioning was conducted on the fluoroscopy table. The failure rate of the blind approach among the 368 injections was evaluated, and a relationship between the Kellgren-Lawrence grade (K-L grade) and the incidence of repeated failures using the blind approach was determined for injections to 52 knees in 37 patients who received a complete cycle of injections (five consecutive injections with a one-week interval between injections). Using a blind approach, 298 of 368 trials (81.2%) resulted in a needle tip being placed in an intra-articular location, while 70 of 368 trials resulted in an extra-articular placement of the needle tip. Among 52 knees to which a complete cycle of injection (five consecutive injections with a one-week interval between injections) was administered, repeated failure of intra-articular placement using the blind approach was seen for 18 knees (34.6%); a more severe K-L grade assigned was associated with a higher rate of repeated failure. However, the trend was not statistically significant based on the Chi-squared test (ρ value = 0.14). Fluoroscopy-guided needle placement may be helpful to ensure therapeutic intra-articular injection of the knee

Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

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Masanori Fujimoto

Full Text Available The impact of NaOH as a ballast water treatment (BWT on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12 treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001. UniFrac distance based principal coordinate analysis (PCoA plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new

Genetic Diversity and Sequence Variations at Growth Hormone Loci among Composite and Hereford Populations of Beef Cattle

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ALAN J. LYMBERY

2000-07-01

Full Text Available A total of 194 Hereford and 235 composite breed cattle from Wokalup Research Station were used in this study. The aims of the study were to: Investigate polymorphisms in the growth hormone gene in the composite and purebred Hereford herds from the Wokalup selection experiment, compare genetic diversity in the growth hormone gene of the breeds, sequencing and compare the sequences of growth hormone loci between composite and purebred Hereford herds with published sequence from Genebank. The genomic DNA was extracted using Wizard genomic DNA purification system from Promega. Two fragments of growth hormone gene were amplified using PCR and continued with RFLP. Each genotype in both loci was sequenced. PCR products of each genotypes were cloned into PCR II, transformed, colonies selection, plasmid DNA extraction continued with cycle sequencing. Polymorphisms were found in both breeds of cattle in both loci of GH-L1 and GH-L2 of the growth hormone gene by PCR-RFLP analysis. Sequencing analysis confirmed the RFLPs data, polymorphism detected using AluI at GH-L1 is due to substitution between leusin/ valine at position 127, while polymorphism at the MspI restriction site was caused by transition of C to T at +837 position.

DNA barcode sequencing from old type specimens as a tool in taxonomy: a case study in the diverse genus Eois (Lepidoptera: Geometridae.

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Patrick Strutzenberger

Full Text Available In this study we report on the sequencing of the COI barcode region from 96 historical specimens (92 type specimens +4 non-types of Eois. Eois is a diverse clade of tropical geometrid moths and is the target of a number of ongoing studies on life-histories, phylogeny, co-evolution with host plants or parasitoids, and diversity patterns across temporal and spatial dimensions. The unequivocal application of valid names is crucial for all aspects of biodiversity research as well as monitoring and conservation efforts. The availability of barcodes from historical type specimens has the potential to facilitate the much-needed acceleration of species description. We performed non-destructive DNA extraction on the abdomens of Eois specimens between 79 and 157 years of age. We used six primer combinations (recovering between 109 and 130 bp each to target the full-length barcode sequence of each specimen. We were able to obtain sequences for 91 of 96 specimens (success rate 94.8%. Sequence length ranged from 121 bp to full barcode sequences (658 bp, the average sequence length was ~500 bp. We detected a moderately strong and statistically significant negative correlation between specimen age and total sequence length, which is in agreement with expectations. The abdomen proved to be an exceedingly valuable source of DNA in old specimens of Lepidoptera. Barcode sequences obtained in this study are currently being used in an effort towards a step-wise taxonomic revision of Eois. We encourage that DNA barcodes obtained from types specimens should be included in all species descriptions and revisions whenever feasible.

Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea

KAUST Repository

Pearman, John K.

2015-11-01

The present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based on extracellular DNA. High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. High levels of alpha-diversity were detected with 16,089 operational taxonomic units (OTUs) being identified. The majority of the OTUs were assigned to Metazoa (29.2%), Alveolata (22.4%) and Stramenopiles (17.8%). Stramenopiles (Diatomea) and Alveolata (Ciliophora) were frequent in a lagoon and in shallower coastal stations, whereas metazoans (Arthropoda: Maxillopoda) were dominant in deeper offshore stations. Only 24.6% of total OTUs were shared among all areas. Beta-diversity was generally lower between the lagoon and Jeddah (nearshore) than between either of those and the offshore area, suggesting a nearshore–offshore biodiversity gradient. The current approach allowed for a broad-range of benthic eukaryotic biodiversity to be analysed with significantly less labour than would be required by other traditional taxonomic approaches. Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales.

Photobiont diversity in lichens from metal-rich substrata based on ITS rDNA sequences.

Science.gov (United States)

Backor, Martin; Peksa, Ondrej; Skaloud, Pavel; Backorová, Miriam

2010-05-01

The photobiont is considered as the more sensitive partner of lichen symbiosis in metal pollution. For this reason the presence of a metal tolerant photobiont in lichens may be a key factor of ecological success of lichens growing on metal polluted substrata. The photobiont inventory was examined for terricolous lichen community growing in Cu mine-spoil heaps derived by historical mining. Sequences of internal transcribed spacer (ITS) were phylogenetically analyzed using maximum likelihood analyses. A total of 50 ITS algal sequences were obtained from 22 selected lichen taxa collected at three Cu mine-spoil heaps and two control localities. Algae associated with Cladonia and Stereocaulon were identified as members of several Asterochloris lineages, photobionts of cetrarioid lichens clustered with Trebouxia hypogymniae ined. We did not find close relationship between heavy metal content (in localities as well as lichen thalli) and photobiont diversity. Presence of multiple algal genotypes in single lichen thallus has been confirmed. Copyright 2009 Elsevier Inc. All rights reserved.

The impact of cross-cultural interactions on medical students' preparedness to care for diverse patients.

Science.gov (United States)

Niu, Nina N; Syed, Zeba A; Krupat, Edward; Crutcher, Betty N; Pelletier, Stephen R; Shields, Helen M

2012-11-01

Medical students who graduate from schools with diverse student populations are more likely to rate themselves as prepared to care for diverse patients compared with students who graduate from more homogenous schools. This study aimed to identify the types of cross-cultural interactions associated with students' self-rated preparedness. In 2010, the authors developed and administered a Web-based survey that queried Harvard Medical School students about their voluntary interethnic interactions (studying, socializing), participation in diversity-related extracurricular activities, and self-rated preparedness to care for diverse patients. The authors separated students' responses regarding interethnic interactions and participation in diversity-related extracurricular activities into high and low participation, then determined the association between these responses and those to questions about students' self-rated preparedness to care for diverse patients. They used ANOVA and Z tests of proportion to analyze their data. Of 724 eligible students, 460 completed the survey (64%). Seventy-five percent (324/433) believed they were prepared to care for patients from backgrounds different from their own. Students who spent >75% of their study time with students from different backgrounds or who participated in a greater number of diversity-related extracurricular activities were more likely to rate themselves as prepared to care for diverse patients overall and to perform seven other skills. Voluntary cross-cultural interactions, both studying and socializing, are associated with higher self-rated preparedness to care for patients from diverse backgrounds. Medical schools should continue to support multicultural pursuits to prepare students to become physicians sensitive to the needs of diverse patients.

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.

Science.gov (United States)

Sharpton, Thomas J; Jospin, Guillaume; Wu, Dongying; Langille, Morgan G I; Pollard, Katherine S; Eisen, Jonathan A

2012-10-13

New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences. We implemented fully automated and high-throughput procedures to de novo cluster proteins into families based upon global alignment similarity. Our approach employs an iterative clustering strategy in which homologs of known families are sifted out of the search for new families. The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. We refer to protein families identified through this approach as "Sifting Families," or SFams. Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. We validated the quality of SFam clustering through statistical as well as network topology-based analyses. We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (http://edhar.genomecenter.ucdavis.edu/sifting_families/).

Ultra-deep sequencing reveals high prevalence and broad structural diversity of hepatitis B surface antigen mutations in a global population.

Science.gov (United States)

Gencay, Mikael; Hübner, Kirsten; Gohl, Peter; Seffner, Anja; Weizenegger, Michael; Neofytos, Dionysios; Batrla, Richard; Woeste, Andreas; Kim, Hyon-Suk; Westergaard, Gaston; Reinsch, Christine; Brill, Eva; Thu Thuy, Pham Thi; Hoang, Bui Huu; Sonderup, Mark; Spearman, C Wendy; Pabinger, Stephan; Gautier, Jérémie; Brancaccio, Giuseppina; Fasano, Massimo; Santantonio, Teresa; Gaeta, Giovanni B; Nauck, Markus; Kaminski, Wolfgang E

2017-01-01

The diversity of the hepatitis B surface antigen (HBsAg) has a significant impact on the performance of diagnostic screening tests and the clinical outcome of hepatitis B infection. Neutralizing or diagnostic antibodies against the HBsAg are directed towards its highly conserved major hydrophilic region (MHR), in particular towards its "a" determinant subdomain. Here, we explored, on a global scale, the genetic diversity of the HBsAg MHR in a large, multi-ethnic cohort of randomly selected subjects with HBV infection from four continents. A total of 1553 HBsAg positive blood samples of subjects originating from 20 different countries across Africa, America, Asia and central Europe were characterized for amino acid variation in the MHR. Using highly sensitive ultra-deep sequencing, we found 72.8% of the successfully sequenced subjects (n = 1391) demonstrated amino acid sequence variation in the HBsAg MHR. This indicates that the global variation frequency in the HBsAg MHR is threefold higher than previously reported. The majority of the amino acid mutations were found in the HBV genotypes B (28.9%) and C (25.4%). Collectively, we identified 345 distinct amino acid mutations in the MHR. Among these, we report 62 previously unknown mutations, which extends the worldwide pool of currently known HBsAg MHR mutations by 22%. Importantly, topological analysis identified the "a" determinant upstream flanking region as the structurally most diverse subdomain of the HBsAg MHR. The highest prevalence of "a" determinant region mutations was observed in subjects from Asia, followed by the African, American and European cohorts, respectively. Finally, we found that more than half (59.3%) of all HBV subjects investigated carried multiple MHR mutations. Together, this worldwide ultra-deep sequencing based genotyping study reveals that the global prevalence and structural complexity of variation in the hepatitis B surface antigen have, to date, been significantly underappreciated.

Intra-parotid dermoid cyst: excision through a face lift incision.

Science.gov (United States)

Shakeel, M; Keh, S M; Chapman, A; Hussain, A

2014-11-01

Intra-parotid dermoid cysts are extremely rare. Clinically, they present like any other parotid lump and pre-operative diagnosis is rarely possible. A 62 years old Caucasian man presented with a painless lump in his right parotid region. The Magnetic Resonance Imaging (MRI) scan revealed a 3 x 3 cm mass in the parotid tail. Cytological examination was unhelpful. The patient underwent successful excision of the cyst through a small face lift incision. No drain was inserted and the patient was discharged home the same day. The patient made an uneventful recovery and was highly satisfied with the aesthetic outcome. The definite histopathological diagnosis was an intra-parotid dermoid cyst.

Sequence diversity and differential expression of major phenylpropanoid-flavonoid biosynthetic genes among three mango varieties.

Science.gov (United States)

Hoang, Van L T; Innes, David J; Shaw, P Nicholas; Monteith, Gregory R; Gidley, Michael J; Dietzgen, Ralf G

2015-07-30

Mango fruits contain a broad spectrum of phenolic compounds which impart potential health benefits; their biosynthesis is catalysed by enzymes in the phenylpropanoid-flavonoid (PF) pathway. The aim of this study was to reveal the variability in genes involved in the PF pathway in three different mango varieties Mangifera indica L., a member of the family Anacardiaceae: Kensington Pride (KP), Irwin (IW) and Nam Doc Mai (NDM) and to determine associations with gene expression and mango flavonoid profiles. A close evolutionary relationship between mango genes and those from the woody species poplar of the Salicaceae family (Populus trichocarpa) and grape of the Vitaceae family (Vitis vinifera), was revealed through phylogenetic analysis of PF pathway genes. We discovered 145 SNPs in total within coding sequences with an average frequency of one SNP every 316 bp. Variety IW had the highest SNP frequency (one SNP every 258 bp) while KP and NDM had similar frequencies (one SNP every 369 bp and 360 bp, respectively). The position in the PF pathway appeared to influence the extent of genetic diversity of the encoded enzymes. The entry point enzymes phenylalanine lyase (PAL), cinnamate 4-mono-oxygenase (C4H) and chalcone synthase (CHS) had low levels of SNP diversity in their coding sequences, whereas anthocyanidin reductase (ANR) showed the highest SNP frequency followed by flavonoid 3'-hydroxylase (F3'H). Quantitative PCR revealed characteristic patterns of gene expression that differed between mango peel and flesh, and between varieties. The combination of mango expressed sequence tags and availability of well-established reference PF biosynthetic genes from other plant species allowed the identification of coding sequences of genes that may lead to the formation of important flavonoid compounds in mango fruits and facilitated characterisation of single nucleotide polymorphisms between varieties. We discovered an association between the extent of sequence variation and

Randomised Phase I/II trial assessing the safety and efficacy of radiolabelled anti-carcinoembryonic antigen I131 KAb201 antibodies given intra-arterially or intravenously in patients with unresectable pancreatic adenocarcinoma

International Nuclear Information System (INIS)

Sultana, Asma; Garvey, Conall; Sutton, Robert; Neoptolemos, John P; Ghaneh, Paula; Shore, Susannah; Raraty, Michael GT; Vinjamuri, Sobhan; Evans, Jonathan E; Smith, Catrin Tudur; Lane, Steven; Chauhan, Seema; Bosonnet, Lorraine

2009-01-01

Advanced pancreatic cancer has a poor prognosis, and the current standard of care (gemcitabine based chemotherapy) provides a small survival advantage. However the drawback is the accompanying systemic toxicity, which targeted treatments may overcome. This study aimed to evaluate the safety and tolerability of KAb201, an anti-carcinoembryonic antigen monoclonal antibody, labelled with I 131 in pancreatic cancer (ISRCTN 16857581). Patients with histological/cytological proven inoperable adenocarcinoma of the head of pancreas were randomised to receive KAb 201 via either the intra-arterial or intravenous delivery route. The dose limiting toxicities within each group were determined. Patients were assessed for safety and efficacy and followed up until death. Between February 2003 and July 2005, 25 patients were enrolled. Nineteen patients were randomised, 9 to the intravenous and 10 to the intra-arterial arms. In the intra-arterial arm, dose limiting toxicity was seen in 2/6 (33%) patients at 50 mCi whereas in the intravenous arm, dose limiting toxicity was noted in 1/6 patients at 50 mCi, but did not occur at 75 mCi (0/3). The overall response rate was 6% (1/18). Median overall survival was 5.2 months (95% confidence interval = 3.3 to 9 months), with no significant difference between the intravenous and intra-arterial arms (log rank test p = 0.79). One patient was still alive at the time of this analysis. Dose limiting toxicity for KAb201 with I 131 by the intra-arterial route was 50 mCi, while dose limiting toxicity was not reached in the intravenous arm

Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time

KAUST Repository

Bagchi, Samik; Garcia Tellez, Berenice; Rao, Hari Ananda; Lamendella, Regina; Saikaly, Pascal

2014-01-01

In this study, 16S rRNA gene pyrosequencing was applied in order to provide a better insight on the diversity and dynamics of total, dominant, and rare bacterial taxa in replicate lab-scale sequencing batch reactors (SBRs) operated at different

The comparative study of CT guided and ultrasound guided percutaneous ethanol injection in the treatment of intra-abdominal cyst

International Nuclear Information System (INIS)

Li Heping; Yang Jianyong; Chen Wei; Zhuang Wenquan; Huang Yulian; Chen Jianye

2005-01-01

Objective: An comparative study of the interventional approach of CT guided and ultiasound guided percutaneous ethanol injection(PEI) in the treatment of intra-abdominal cyst. Methods: CT guided PEI was performed in the treatment of intra-abdominal cyst in 38 patients while ultrasound guided PEI was performed in 45 cases. Results: The puncture procedure of CT guided PEI was totally performed 83 times in treating 56 intra-abdominal cysts in 38 patients and CT guided PEI was unsuccessful in 6 patients. The puncture procedure of ultrasound guided PEI were performed 87 times in treating 71 intra-abdominal cysts in 55 patients and ultrasound guided PEI only failed only in 1 patient. Conclusion: Ultrasound guided PEI is superior to CT guided PEI in the treatment of intra-abdominal cyst. (authors)

Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing

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Muhammad Naveed

2014-09-01

Full Text Available In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ. Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization.

Chemical meningitis related to intra-CSF liposomal cytarabine.

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Durand, Bénédicte; Zairi, Fahed; Boulanger, Thomas; Bonneterre, Jacques; Mortier, Laurent; Le Rhun, Emilie

2017-10-01

Therapeutic options of leptomeningeal metastases include intra-cerebrospinal fluid (CSF) chemotherapy. Among intra-CSF agents, liposomal cytarabine has advantages but can induce specific toxicities. A BRAF-V600E-mutated melanoma leptomeningeal metastases patient, treated by dabrafenib and liposomal cytarabine, presented after the first injection of liposomal cytarabine with hyperthermia and headaches. Despite sterile CSF/blood analyses, extended intravenous antibiotics were given and the second injection was delayed. The diagnosis of chemical meningitis was finally made. Dose reduction and appropriate symptomatic treatment permitted the administration of 15 injections of liposomal cytarabine combined with dabrafenib. A confirmation of the diagnosis of chemical meningitis is essential in order (1) not to delay intra-CSF or systemic chemotherapy or (2) to limit the administration of unnecessary but potentially toxic antibiotics.

Correlation between intra-abdominal pressure and pulmonary volumes after superior and inferior abdominal surgery

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Roberto de Cleva

2014-07-01

Full Text Available OBJECTIVE:Patients undergoing abdominal surgery are at risk for pulmonary complications. The principal cause of postoperative pulmonary complications is a significant reduction in pulmonary volumes (FEV1 and FVC to approximately 65-70% of the predicted value. Another frequent occurrence after abdominal surgery is increased intra-abdominal pressure. The aim of this study was to correlate changes in pulmonary volumes with the values of intra-abdominal pressure after abdominal surgery, according to the surgical incision in the abdomen (superior or inferior.METHODS:We prospectively evaluated 60 patients who underwent elective open abdominal surgery with a surgical time greater than 240 minutes. Patients were evaluated before surgery and on the 3rd postoperative day. Spirometry was assessed by maximal respiratory maneuvers and flow-volume curves. Intra-abdominal pressure was measured in the postoperative period using the bladder technique.RESULTS:The mean age of the patients was 56±13 years, and 41.6% 25 were female; 50 patients (83.3% had malignant disease. The patients were divided into two groups according to the surgical incision (superior or inferior. The lung volumes in the preoperative period showed no abnormalities. After surgery, there was a significant reduction in both FEV1 (1.6±0.6 L and FVC (2.0±0.7 L with maintenance of FEV1/FVC of 0.8±0.2 in both groups. The maximum intra-abdominal pressure values were similar (p= 0.59 for the two groups. There was no association between pulmonary volumes and intra-abdominal pressure measured in any of the groups analyzed.CONCLUSIONS:Our results show that superior and inferior abdominal surgery determines hypoventilation, unrelated to increased intra-abdominal pressure. Patients at high risk of pulmonary complications should receive respiratory care even if undergoing inferior abdominal surgery.

Correlation between intra-abdominal pressure and pulmonary volumes after superior and inferior abdominal surgery.

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Cleva, Roberto de; Assumpção, Marianna Siqueira de; Sasaya, Flavia; Chaves, Natalia Zuniaga; Santo, Marco Aurelio; Fló, Claudia; Lunardi, Adriana C; Jacob Filho, Wilson

2014-07-01

Patients undergoing abdominal surgery are at risk for pulmonary complications. The principal cause of postoperative pulmonary complications is a significant reduction in pulmonary volumes (FEV1 and FVC) to approximately 65-70% of the predicted value. Another frequent occurrence after abdominal surgery is increased intra-abdominal pressure. The aim of this study was to correlate changes in pulmonary volumes with the values of intra-abdominal pressure after abdominal surgery, according to the surgical incision in the abdomen (superior or inferior). We prospectively evaluated 60 patients who underwent elective open abdominal surgery with a surgical time greater than 240 minutes. Patients were evaluated before surgery and on the 3rd postoperative day. Spirometry was assessed by maximal respiratory maneuvers and flow-volume curves. Intra-abdominal pressure was measured in the postoperative period using the bladder technique. The mean age of the patients was 56 ± 13 years, and 41.6% 25 were female; 50 patients (83.3%) had malignant disease. The patients were divided into two groups according to the surgical incision (superior or inferior). The lung volumes in the preoperative period showed no abnormalities. After surgery, there was a significant reduction in both FEV1 (1.6 ± 0.6 L) and FVC (2.0 ± 0.7 L) with maintenance of FEV1/FVC of 0.8 ± 0.2 in both groups. The maximum intra-abdominal pressure values were similar (p=0.59) for the two groups. There was no association between pulmonary volumes and intra-abdominal pressure measured in any of the groups analyzed. Our results show that superior and inferior abdominal surgery determines hypoventilation, unrelated to increased intra-abdominal pressure. Patients at high risk of pulmonary complications should receive respiratory care even if undergoing inferior abdominal surgery.

Predicting Where a Radiation Will Occur: Acoustic and Molecular Surveys Reveal Overlooked Diversity in Indian Ocean Island Crickets (Mogoplistinae: Ornebius.

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Ben H Warren

Full Text Available Recent theory suggests that the geographic location of island radiations (local accumulation of species diversity due to cladogenesis can be predicted based on island area and isolation. Crickets are a suitable group for testing these predictions, as they show both the ability to reach some of the most isolated islands in the world, and to speciate at small spatial scales. Despite substantial song variation between closely related species in many island cricket lineages worldwide, to date this characteristic has not received attention in the western Indian Ocean islands; existing species descriptions are based on morphology alone. Here we use a combination of acoustics and DNA sequencing to survey these islands for Ornebius crickets. We uncover a small but previously unknown radiation in the Mascarenes, constituting a three-fold increase in the Ornebius species diversity of this archipelago (from two to six species. A further new species is detected in the Comoros. Although double archipelago colonisation is the best explanation for species diversity in the Seychelles, in situ cladogenesis is the best explanation for the six species in the Mascarenes and two species of the Comoros. Whether the radiation of Mascarene Ornebius results from intra- or purely inter- island speciation cannot be determined on the basis of the phylogenetic data alone. However, the existence of genetic, song and ecological divergence at the intra-island scale is suggestive of an intra-island speciation scenario in which ecological and mating traits diverge hand-in-hand. Our results suggest that the geographic location of Ornebius radiations is partially but not fully explained by island area and isolation. A notable anomaly is Madagascar, where our surveys are consistent with existing accounts in finding no Ornebius species present. Possible explanations are discussed, invoking ecological differences between species and differences in environmental history between

Intra-articular morphine versus bupivacaine for knee motion among patients with osteoarthritis: randomized double-blind clinical trial

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Miriam Bellini Gazi

Full Text Available CONTEXT AND OBJECTIVE: Osteoarthritis causes pain and disability in a high percentage of elderly people. The aim of the present study was to assess the efficacy of intra-articular morphine and bupivacaine on the joint flexion and extension angles of patients with knee osteoarthritis. DESIGN AND SETTING: A randomized double-blind study was performed at a pain clinic of Universidade Federal de São Paulo. METHODS: Thirty-nine patients with pain for more than three months, of intensity greater than three on a numerical scale (zero to 10, were included. G1 patients received 1 mg (1 ml of morphine diluted in 9 ml of saline, intra-articularly, and G2 patients received 25 mg (10 ml of 0.25% bupivacaine without epinephrine. Pain was assessed on a numerical scale and knee flexion and extension angles were measured after administration of the drugs at rest and during movement. The total amount of analgesic supplementation using 500 mg doses of paracetamol was also determined. RESULTS: No significant difference in pain intensity was observed between G1 and G2. Significant decreases in pain at rest and during movement and significant increases in mean flexion and extension angles were observed in both groups, with no significant difference between the two groups. The mean total amount of paracetamol used over a seven-day period was 3578 mg in G1 and 5333 mg in G2 (P = 0.2355; Mann-Whitney test. CONCLUSION: The analgesic effects of 1 mg of morphine and 25 mg of 0.25% bupivacaine were similar among patients with osteoarthritis of the knee.

Comparative performance of double-digest RAD sequencing across divergent arachnid lineages.

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Burns, Mercedes; Starrett, James; Derkarabetian, Shahan; Richart, Casey H; Cabrero, Allan; Hedin, Marshal

2017-05-01

Next-generation sequencing technologies now allow researchers of non-model systems to perform genome-based studies without the requirement of a (often unavailable) closely related genomic reference. We evaluated the role of restriction endonuclease (RE) selection in double-digest restriction-site-associated DNA sequencing (ddRADseq) by generating reduced representation genome-wide data using four different RE combinations. Our expectation was that RE selections targeting longer, more complex restriction sites would recover fewer loci than RE with shorter, less complex sites. We sequenced a diverse sample of non-model arachnids, including five congeneric pairs of harvestmen (Opiliones) and four pairs of spiders (Araneae). Sample pairs consisted of either conspecifics or closely related congeneric taxa, and in total 26 sample pair analyses were tested. Sequence demultiplexing, read clustering and variant calling were performed in the pyRAD program. The 6-base pair cutter EcoRI combined with methylated site-specific 4-base pair cutter MspI produced, on average, the greatest numbers of intra-individual loci and shared loci per sample pair. As expected, the number of shared loci recovered for a sample pair covaried with the degree of genetic divergence, estimated with cytochrome oxidase I sequences, although this relationship was non-linear. Our comparative results will prove useful in guiding protocol selection for ddRADseq experiments on many arachnid taxa where reference genomes, even from closely related species, are unavailable. © 2016 John Wiley & Sons Ltd.

Occult HCV Infection (OCI) Diagnosis in Cirrhotic and Non-cirrhotic Naïve Patients by Intra-PBMC Nested Viral RNA PCR.

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Abd Alla, Mohamed Darwish Ahmed; Elibiary, Saleh Ahmed; Wu, George Y; El-Awady, Mostafa Kamel

2017-12-28

Background and Aims: Occult HCV infections (OCIs) include IgG antibody seronegative cryptogenic (COCIs), as well as seropositive secondary naïve (SNOCIs) and experienced (SEOCIs) cases. We used peripheral-blood-mononuclear-cell (PBMC)-PCR to evaluate COCIs and SNOCIs prevalence, serum HCV spontaneous disappearance (SCSD) in naïve cirrhotics and non-cirrhotics, intra-PBMC HCV-RNA strands in relation to cirrhosis density in naïve non-viremia cases, and HCV-RNA seroconversion after 1 year of solitary naïve intra-PBMC infection. Methods: The anti-HCV IgG antibody-positive naïve-patients ( n = 785) were classified into viremic ( n = 673) and non-viremic [ n = 112, including non-cirrhotics ( n = 55) and cirrhotics ( n = 57)], and 62 controls without evidence of HCV-infection. Controls and post-HCV non-viremia cases ( n = 62+112 = 174) were submitted to hepatic Fibroscan-Elastography evaluation. All subjects ( n = 847) were screened for intra-PBMC HCV-RNA sense and antisense strands by nested-PCR. Results: Naïve-OCI cases (4.84%) that were diagnosed by PBMC-PCR significantly raised the total numbers of HCV-infection to 714 ( p = 0.01). The percent positivity of SNOCIs (34.82%) was significantly higher than for asymptomatic-COCIs (3.125%, p = 0.0001). Comparing PBMC-PCR with single-step-reverse-transcription (SRT)-PCR for identification of SCSD in naïve IgG antibody-positive non-viremia patients ( n = 112) revealed a decline in SCSD prevalence by PBMC-PCR (from 14.27% to 9.3%), regardless of presence of hepatic cirrhosis ( p = 0.03). SCSD was found to be higher by PBMC-PCR in non-cirrhotics compared to cirrhotics ( p = 0.0001), with an insignificant difference when using SRT-PCR ( p = 0.45). Intra-PBMC HCV-RNA infection was significantly more frequent in cirrhotics compared to both non-cirrhotics and controls ( p < 0.0005). An increased hepatic fibrosis density was recognized in intra-PBMC HCV-RNA infection with sense ( p = 0.0001) or antisense strand ( p = 0

Diversity spurs diversification in ecological communities

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Calcagno, Vincent; Jarne, Philippe; Loreau, Michel; Mouquet, Nicolas; David, Patrice

2017-06-01

Diversity is a fundamental, yet threatened, property of ecological systems. The idea that diversity can itself favour diversification, in an autocatalytic process, is very appealing but remains controversial. Here, we study a generalized model of ecological communities and investigate how the level of initial diversity influences the possibility of evolutionary diversification. We show that even simple models of intra- and inter-specific ecological interactions can predict a positive effect of diversity on diversification: adaptive radiations may require a threshold number of species before kicking-off. We call this phenomenon DDAR (diversity-dependent adaptive radiations) and identify mathematically two distinct pathways connecting diversity to diversification, involving character displacement and the positive diversity-productivity relationship. Our results may explain observed delays in adaptive radiations at the macroscale and diversification patterns reported in experimental microbial communities, and shed new light on the dynamics of ecological diversity, the diversity-dependence of diversification rates, and the consequences of biodiversity loss.

Diversity spurs diversification in ecological communities.

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Calcagno, Vincent; Jarne, Philippe; Loreau, Michel; Mouquet, Nicolas; David, Patrice

2017-06-09

Diversity is a fundamental, yet threatened, property of ecological systems. The idea that diversity can itself favour diversification, in an autocatalytic process, is very appealing but remains controversial. Here, we study a generalized model of ecological communities and investigate how the level of initial diversity influences the possibility of evolutionary diversification. We show that even simple models of intra- and inter-specific ecological interactions can predict a positive effect of diversity on diversification: adaptive radiations may require a threshold number of species before kicking-off. We call this phenomenon DDAR (diversity-dependent adaptive radiations) and identify mathematically two distinct pathways connecting diversity to diversification, involving character displacement and the positive diversity-productivity relationship. Our results may explain observed delays in adaptive radiations at the macroscale and diversification patterns reported in experimental microbial communities, and shed new light on the dynamics of ecological diversity, the diversity-dependence of diversification rates, and the consequences of biodiversity loss.

Diagnostic value of hepatobiliary sequence scintigraphy in patients with postcholecystectomy syndrome

International Nuclear Information System (INIS)

Frey, H.; Jorke, D.; Gottschild, D.; Langbein, T.; Zinner, G.; Kob, D.

1992-01-01

The autors report about the possibility of registration from functionally disturbances of gall fluid with the help of hepatobiliary sequence-scintigraphy in patients with postcholecystectomy-syndrome. The diagnostic importance of this methode and the meaning of other usually procedures is discussed. A selection of patients succeed in objective manner with hepatobiliary sequence-scintigraphy together with clinically dates of laboratory. In patients with postcholecystectomy-syndrome the procedure can show functionally disturbances in the area of extrahepatic gall ways. (orig.) [de

Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing

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Pruckler James M

2008-11-01

Full Text Available Abstract Background Bacillus cereus is most commonly associated with foodborne illness (diarrheal and emetic but is also an opportunistic pathogen that can cause severe and fatal infections. Several multilocus sequence typing (MLST schemes have recently been developed to genotype B. cereus and analysis has suggested a clonal or weakly clonal population structure for B. cereus and its close relatives B. anthracis and B. thuringiensis. In this study we used MLST to determine if B. cereus isolates associated with illnesses of varying severity (e.g., severe, systemic vs. gastrointestinal (GI illness were clonal or formed clonal complexes. Results A retrospective analysis of 55 clinical B. cereus isolates submitted to the Centers for Disease Control and Prevention between 1954 and 2004 was conducted. Clinical isolates from severe infections (n = 27, gastrointestinal (GI illness (n = 18, and associated isolates from food (n = 10 were selected for analysis using MLST. The 55 isolates were diverse and comprised 38 sequence types (ST in two distinct clades. Of the 27 isolates associated with serious illness, 13 clustered in clade 1 while 14 were in clade 2. Isolates associated with GI illness were also found throughout clades 1 and 2, while no isolates in this study belonged to clade 3. All the isolates from this study belonging to the clade 1/cereus III lineage were associated with severe disease while isolates belonging to clade1/cereus II contained isolates primarily associated with severe disease and emetic illness. Only three STs were observed more than once for epidemiologically distinct isolates. Conclusion STs of clinical B. cereus isolates were phylogenetically diverse and distributed among two of three previously described clades. Greater numbers of strains will need to be analyzed to confirm if specific lineages or clonal complexes are more likely to contain clinical isolates or be associated with specific illness, similar to B. anthracis and

Structural Conservation Despite Huge Sequence Diversity Allows EPCR Binding by the PfEMP1 Family Implicated in Severe Childhood Malaria

DEFF Research Database (Denmark)

Lau, Clinton K.Y.; Turner, Louise; Jespersen, Jakob S.

2015-01-01

with severe childhood malaria. We combine crystal structures of CIDRa1:EPCR complexes with analysis of 885 CIDRa1 sequences, showing that the EPCR-binding surfaces of CIDRa1 domains are conserved in shape and bonding potential, despite dramatic sequence diversity. Additionally, these domains mimic features...... of the natural EPCR ligand and can block this ligand interaction. Using peptides corresponding to the EPCR-binding region, antibodies can be purified from individuals in malaria-endemic regions that block EPCR binding of diverse CIDRa1 variants. This highlights the extent to which such a surface protein family......The PfEMP1 family of surface proteins is central for Plasmodium falciparum virulence and must retain the ability to bind to host receptors while also diversifying to aid immune evasion. The interaction between CIDRa1 domains of PfEMP1 and endothelial protein C receptor (EPCR) is associated...

Do intra-articular hyaluronic acid injections delay total knee replacement in patients with osteoarthritis - A Cox model analysis.

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Delbarre, Angélique; Amor, Bernard; Bardoulat, Isabelle; Tetafort, Aymeric; Pelletier-Fleury, Nathalie

2017-01-01

This study aimed to describe patients treated for knee osteoarthritis between 2006 and 2013 in France and to compare the delay from diagnosis to total knee replacement between patients who received intra-articular hyaluronic acid injections and those who did not receive the injections. A second objective was to compare direct medical costs for ambulatory care between treatment groups. Patients were selected from a representative sample of the real world administrative claims database using an algorithm developed by experts from the scientific committee of the study. Data were matched with the medico-administrative database for hospital care. A Cox proportional hazards model was stratified for the treatment group and adjusted for available socio-demographic and medical covariates to compare restricted mean survival times at different time points (1, 3, 5 and 7.5 years) between groups. Costs were expressed in 2013 euros. A total of 14,782 patients were treated for knee osteoarthritis (67% women; mean age = 68 years). Among this population, 1,662 patients had total knee replacement (11.2%). At each time point, restricted mean survival time without total knee replacement was significantly higher (p-valueshyaluronic acid group, from +51 to +217 days at 1 and 7.5 years, respectively. For the year preceding total knee replacement, the means for total direct medical costs were similar between groups, €744 vs €805 for treatment and control groups, respectively, (p-value = 0.104). Intra-articular injections accounted for less than 10% of the total costs. This is the first retrospective longitudinal study involving knee osteoarthritis patients using medico-administrative databases in France. The results support the effectiveness of hyaluronic acid injections in delaying total knee replacement and show that patients treated with hyaluronic acid have similar direct medical costs for ambulatory care compared to patients treated with corticosteroids only.

Radiation therapy with concurrent retrograde superselective intra-arterial chemotherapy for gingival carcinoma

International Nuclear Information System (INIS)

Mukai, Y.; Hata, M.; Koike, I.; Inoue, T.; Mitsudo, K.; Koizumi, T.; Oguri, S.; Kioi, M.; Tohnai, I.; Omura, M.

2014-01-01

The aim of this study was to review the efficacy and toxicity of radiation therapy with concurrent retrograde superselective intra-arterial chemotherapy in the treatment of gingival carcinoma. In all, 34 patients (21 men and 13 women) with squamous cell carcinoma of the gingiva underwent radiation therapy with concurrent retrograde superselective intra-arterial chemotherapy. Treatment consisted of daily external irradiation and concurrent retrograde superselective intra-arterial infusion with cisplatin and docetaxel. A median total dose of 60 Gy in 30 fractions was delivered to tumors. Of the 34 patients, 29 (85 %) achieved a complete response (CR) and 5 had residual tumors. Of the 29 patients with a CR, 2 had local recurrences and 1 had distant metastasis 1-15 months after treatment. Twenty-six of the 36 patients had survived at a median follow-up time of 36 months (range 12-79 months); 4 died of cancer and 4 died of non-cancer-related causes. At both 3 and 5 years after treatment, the overall survival rates were 79 % and the cause-specific survival rates were 85 %. Osteoradionecrosis of the mandibular bone only developed in 1 patient after treatment. Radiation therapy with concurrent retrograde superselective intra-arterial chemotherapy was effective and safe in the treatment of gingival carcinoma. This treatment may be a promising curative and organ-preserving treatment option for gingival carcinoma. (orig.) [de

The pioneering use of ISSR (Inter Simple Sequence Repeat in Neotropical anurans: preliminary assessment of genetic diversity in populations of Physalaemus cuvieri (Amphibia, Leiuperidae

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Rafaela M Moresco

2013-01-01

Full Text Available The greatest diversity of anurans in the world is in Brazil and one of the major challenges is to reconcile the accelerated economic development with strategies that aim to maintain this diversity in forest fragments, often representing ESUs of some biomes. This study aimed to obtain data that will support conservation projects through the pioneering use of ISSR analysis in Neotropical anurans, estimating the intra- and interpopulation genetic diversity of four populations of P. cuvieri (Paraná and São Paulo regions. Of the 65 loci scored 58 were polymorphic, with 0.797 intrapopulation variation and 0.203 interpopulation variation. The index of interpopulation genetic differentiation (Fst proved to be high among the population of Marmeleiro-PR and the three populations of SP (Fst > 0.288; genetic dissimilarity was related to the geographical distance. The ISSR proved to be efficient and useful molecular markers in comparison with other markers most widely used for preliminary diagnosis of genetic diversity in populations of amphibians, and could be applied as a tool for future conservation projects, since they could identify potential ESUs and influence decisions on the preservation of fragments.

Rapid non-contrast magnetic resonance imaging for post appendectomy intra-abdominal abscess in children

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Lee, Megan H. [Washington University School of Medicine in St. Louis, Mallinckrodt Institute of Radiology, St. Louis, MO (United States); Eutsler, Eric P.; Khanna, Geetika [Washington University School of Medicine in St. Louis, Pediatric Radiology, Mallinckrodt Institute of Radiology, St. Louis, MO (United States); Sheybani, Elizabeth F. [Mercy Hospital St. Louis, Department of Radiology, St. Louis, MO (United States)

2017-07-15

Acute appendicitis, especially if perforated at presentation, is often complicated by postoperative abscess formation. The detection of a postoperative abscess relies primarily on imaging. This has traditionally been done with contrast-enhanced computed tomography. Non-contrast magnetic resonance imaging (MRI) has the potential to accurately detect intra-abdominal abscesses, especially with the use of diffusion-weighted imaging (DWI). To evaluate our single-center experience with a rapid non-contrast MRI protocol evaluating post-appendectomy abscesses in children with persistent postsurgical symptoms. In this retrospective, institutional review board-approved study, all patients underwent a clinically indicated non-contrast 1.5- or 3-Tesla abdomen/pelvis MRI consisting of single-shot fast spin echo, inversion recovery and DWI sequences. All MRI studies were reviewed by two blinded pediatric radiologists to identify the presence of a drainable fluid collection. Each fluid collection was further characterized as accessible or not accessible for percutaneous or transrectal drainage. Imaging findings were compared to clinical outcome. Seven of the 15 patients had a clinically significant fluid collection, and 5 of these patients were treated with percutaneous drain placement or exploratory laparotomy. The other patients had a phlegmon or a clinically insignificant fluid collection and were discharged home within 48 h. Rapid non-contrast MRI utilizing fluid-sensitive and DWI sequences can be used to identify drainable fluid collections in post-appendectomy patients. This protocol can be used to triage patients between conservative management vs. abscess drainage without oral/intravenous contrast or exposure to ionizing radiation. (orig.)

Rapid non-contrast magnetic resonance imaging for post appendectomy intra-abdominal abscess in children

International Nuclear Information System (INIS)

Lee, Megan H.; Eutsler, Eric P.; Khanna, Geetika; Sheybani, Elizabeth F.

2017-01-01

Acute appendicitis, especially if perforated at presentation, is often complicated by postoperative abscess formation. The detection of a postoperative abscess relies primarily on imaging. This has traditionally been done with contrast-enhanced computed tomography. Non-contrast magnetic resonance imaging (MRI) has the potential to accurately detect intra-abdominal abscesses, especially with the use of diffusion-weighted imaging (DWI). To evaluate our single-center experience with a rapid non-contrast MRI protocol evaluating post-appendectomy abscesses in children with persistent postsurgical symptoms. In this retrospective, institutional review board-approved study, all patients underwent a clinically indicated non-contrast 1.5- or 3-Tesla abdomen/pelvis MRI consisting of single-shot fast spin echo, inversion recovery and DWI sequences. All MRI studies were reviewed by two blinded pediatric radiologists to identify the presence of a drainable fluid collection. Each fluid collection was further characterized as accessible or not accessible for percutaneous or transrectal drainage. Imaging findings were compared to clinical outcome. Seven of the 15 patients had a clinically significant fluid collection, and 5 of these patients were treated with percutaneous drain placement or exploratory laparotomy. The other patients had a phlegmon or a clinically insignificant fluid collection and were discharged home within 48 h. Rapid non-contrast MRI utilizing fluid-sensitive and DWI sequences can be used to identify drainable fluid collections in post-appendectomy patients. This protocol can be used to triage patients between conservative management vs. abscess drainage without oral/intravenous contrast or exposure to ionizing radiation. (orig.)

Persistent renal enhancement after intra-arterial versus intravenous iodixanol administration

International Nuclear Information System (INIS)

Chou, Shinn-Huey; Wang, Zhen J.; Kuo, Jonathan; Cabarrus, Miguel; Fu Yanjun; Aslam, Rizwan; Yee, Judy; Zimmet, Jeffrey M.; Shunk, Kendrick; Elicker, Brett; Yeh, Benjamin M.

2011-01-01

Purpose: To examine the clinical significance of persistent renal enhancement after iodixanol administration. Methods: We retrospectively studied 166 consecutive patients who underwent non-enhanced abdominopelvic CT within 7 days after receiving intra-arterial (n = 99) or intravenous (n = 67) iodixanol. Renal attenuation was measured for each non-enhanced CT scan. Persistent renal enhancement was defined as CT attenuation >55 Hounsfield units (HU). Contrast-induced nephropathy (CIN) was defined as a rise in serum creatinine >0.5 mg/dL within 5 days after contrast administration. Results: While the intensity and frequency of persistent renal enhancement was higher after intra-arterial (mean CT attenuation of 73.7 HU, seen in 54 of 99 patients, or 55%) than intravenous contrast material administration (51.8 HU, seen in 21 of 67, or 31%, p < 0.005), a multivariate regression model showed that the independent predictors of persistent renal enhancement were a shorter time interval until the subsequent non-enhanced CT (p < 0.001); higher contrast dose (p < 0.001); higher baseline serum creatinine (p < 0.01); and older age (p < 0.05). The route of contrast administration was not a predictor of persistent renal enhancement in this model. Contrast-induced nephropathy was noted in 9 patients who received intra-arterial (9%) versus 3 who received intravenous iodixanol (4%), and was more common in patients with persistent renal enhancement (p < 0.01). Conclusion: Persistent renal enhancement at follow-up non-contrast CT suggests a greater risk for contrast-induced nephropathy, but the increased frequency of striking renal enhancement in patients who received intra-arterial rather than intravenous contrast material also reflects the larger doses of contrast and shorter time to subsequent follow-up CT scanning for such patients.

The prevalence and characteristics of intra-atrial right coronary artery anomaly in 9,284 patients referred for coronary computed tomography angiography

International Nuclear Information System (INIS)

Opolski, Maksymilian P.; Pregowski, Jerzy; Kruk, Mariusz; Staruch, Adam D.; Witkowski, Adam; Demkow, Marcin; Hryniewiecki, Tomasz; Michalek, Piotr; Ruzyllo, Witold; Kepka, Cezary

2014-01-01

Objective: To determine the prevalence, radiologic patterns and clinical characteristics of intra-atrial right coronary artery (IARCA) among adult coronary computed tomography angiography (CCTA) population. Methods: We included 9,284 consecutive subjects who underwent CCTA at a single high-volume center. The presence of IARCA including the number, length and diameter of IARCA segments with accompanying atherosclerosis and coronary anomalies were evaluated. Additionally, clinical characteristics and midterm follow-up of IARCA patients were recorded. Results: The IARCA prevalence was 0.15% (14/9,284) with 15 intra-atrial segments. The intra-atrial segment length ranged from 14 to 53 mm, and the mean diameter proximal to the entry site was 3.3 ± 0.7 mm. IARCA was more often associated with intramuscular course of the left anterior descending coronary artery (29% vs. 4%, p = 0.001) and anomalous origin of the left circumflex artery from the right aortic sinus (14% vs. 0.3%, p = 0.001) compared with non-IARCA cases. The majority of IARCA patients were women (86%) presenting with supraventricular arrhythmia (71%). Compared with computed tomographic population without IARCA, IARCA subjects were younger (60 ± 12 vs. 54 ± 14 years, p = 0.037) and more often women (51% vs. 86%, p = 0.013). At a mean of 20 months follow-up of IARCA patients there were no adverse cardiac events except for supraventricular tachycardia episodes occurring in 36% of subjects. Conclusions: IARCA occurs rarely and is often associated with additional coronary anomalies. The clinical profile of IARCA patients is most often represented by middle-aged women with supraventricular arrhythmia showing favorable midterm prognosis

Decreased HIV diversity after allogeneic stem cell transplantation of an HIV-1 infected patient: a case report

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Thielen Alexander

2010-03-01

Full Text Available Abstract The human immunodeficiency virus type 1 (HIV-1 coreceptor use and viral evolution were analyzed in blood samples from an HIV-1 infected patient undergoing allogeneic stem cell transplantation (SCT. Coreceptor use was predicted in silico from sequence data obtained from the third variable loop region of the viral envelope gene with two software tools. Viral diversity and evolution was evaluated on the same samples by Bayesian inference and maximum likelihood methods. In addition, phenotypic analysis was done by comparison of viral growth in peripheral blood mononuclear cells and in a CCR5 (R5-deficient T-cell line which was controlled by a reporter assay confirming viral tropism. In silico coreceptor predictions did not match experimental determinations that showed a consistent R5 tropism. Anti-HIV directed antibodies could be detected before and after the SCT. These preexisting antibodies did not prevent viral rebound after the interruption of antiretroviral therapy during the SCT. Eventually, transplantation and readministration of anti-retroviral drugs lead to sustained increase in CD4 counts and decreased viral load to undetectable levels. Unexpectedly, viral diversity decreased after successful SCT. Our data evidence that only R5-tropic virus was found in the patient before and after transplantation. Therefore, blocking CCR5 receptor during stem cell transplantation might have had beneficial effects and this might apply to more patients undergoing allogeneic stem cell transplantation. Furthermore, we revealed a scenario of HIV-1 dynamic different from the commonly described ones. Analysis of viral evolution shows the decrease of viral diversity even during episodes with bursts in viral load.

Intra-Arterial Treatment in Patients with Acute Massive Gastrointestinal Bleeding after Endoscopic Failure: Comparisons between Positive versus Negative Contrast Extravasation Groups

International Nuclear Information System (INIS)

Chang, Wei Chou; Liu, Chang Hsien; Hsu, Hsian He; Huang, Guo Shu; Hsieh, Tasi Yuan; Tsai, Shin Hung; Hsieh, Chung Bao; Yu, Chin Yung; Tung, Ho Jui

2011-01-01

To determine whether treatment outcome is associated with visualization of contrast extravasation in patients with acute massive gastrointestinal bleeding after endoscopic failure. From January 2007 to December 2009, patients that experienced a first attack of acute gastrointestinal bleeding after failure of initial endoscopy were referred to our interventional department for intra-arterial treatment. We enrolled 79 patients and divided them into two groups: positive and negative extravasation. For positive extravasation, patients were treated by coil embolization; and in negative extravasation, patients were treated with intra-arterial vasopressin infusion. The two groups were compared for clinical parameters, hemodynamics, laboratory findings, endoscopic characteristics, and mortality rates. Forty-eight patients had detectable contrast extravasation (positive extravasation), while 31 patients did not (negative extravasation). Fifty-six patients survived from this bleeding episode (overall clinical success rate, 71%). An elevation of hemoglobin level was observed in the both two groups; significantly greater in the positive extravasation group compared to the negative extravasation group. Although these patients were all at high risk of dying, the 90-day mortality rate was significantly lower in the positive extravasation than in the negative extravasation (20% versus 42%, p < 0.05). A multivariate analysis suggested that successful hemo stasis (odds ratio [OR] = 28.66) is the most important predictor affecting the mortality in the two groups of patients. Visualization of contrast extravasation on angiography usually can target the bleeding artery directly, resulting in a higher success rate to control of hemorrhage.

Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates

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Black, PA

2015-10-24

Background Whole genome sequencing has revolutionised the interrogation of mycobacterial genomes. Recent studies have reported conflicting findings on the genomic stability of Mycobacterium tuberculosis during the evolution of drug resistance. In an age where whole genome sequencing is increasingly relied upon for defining the structure of bacterial genomes, it is important to investigate the reliability of next generation sequencing to identify clonal variants present in a minor percentage of the population. This study aimed to define a reliable cut-off for identification of low frequency sequence variants and to subsequently investigate genetic heterogeneity and the evolution of drug resistance in M. tuberculosis. Methods Genomic DNA was isolated from single colonies from 14 rifampicin mono-resistant M. tuberculosis isolates, as well as the primary cultures and follow up MDR cultures from two of these patients. The whole genomes of the M. tuberculosis isolates were sequenced using either the Illumina MiSeq or Illumina HiSeq platforms. Sequences were analysed with an in-house pipeline. Results Using next-generation sequencing in combination with Sanger sequencing and statistical analysis we defined a read frequency cut-off of 30 % to identify low frequency M. tuberculosis variants with high confidence. Using this cut-off we demonstrated a high rate of genetic diversity between single colonies isolated from one population, showing that by using the current sequencing technology, single colonies are not a true reflection of the genetic diversity within a whole population and vice versa. We further showed that numerous heterogeneous variants emerge and then disappear during the evolution of isoniazid resistance within individual patients. Our findings allowed us to formulate a model for the selective bottleneck which occurs during the course of infection, acting as a genomic purification event. Conclusions Our study demonstrated true levels of genetic diversity

HIV populations are large and accumulate high genetic diversity in a nonlinear fashion.

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Maldarelli, Frank; Kearney, Mary; Palmer, Sarah; Stephens, Robert; Mican, JoAnn; Polis, Michael A; Davey, Richard T; Kovacs, Joseph; Shao, Wei; Rock-Kress, Diane; Metcalf, Julia A; Rehm, Catherine; Greer, Sarah E; Lucey, Daniel L; Danley, Kristen; Alter, Harvey; Mellors, John W; Coffin, John M

2013-09-01

HIV infection is characterized by rapid and error-prone viral replication resulting in genetically diverse virus populations. The rate of accumulation of diversity and the mechanisms involved are under intense study to provide useful information to understand immune evasion and the development of drug resistance. To characterize the development of viral diversity after infection, we carried out an in-depth analysis of single genome sequences of HIV pro-pol to assess diversity and divergence and to estimate replicating population sizes in a group of treatment-naive HIV-infected individuals sampled at single (n = 22) or multiple, longitudinal (n = 11) time points. Analysis of single genome sequences revealed nonlinear accumulation of sequence diversity during the course of infection. Diversity accumulated in recently infected individuals at rates 30-fold higher than in patients with chronic infection. Accumulation of synonymous changes accounted for most of the diversity during chronic infection. Accumulation of diversity resulted in population shifts, but the rates of change were low relative to estimated replication cycle times, consistent with relatively large population sizes. Analysis of changes in allele frequencies revealed effective population sizes that are substantially higher than previous estimates of approximately 1,000 infectious particles/infected individual. Taken together, these observations indicate that HIV populations are large, diverse, and slow to change in chronic infection and that the emergence of new mutations, including drug resistance mutations, is governed by both selection forces and drift.

Evolutionary insight from whole-genome sequencing of Pseudomonas aeruginosa from cystic fibrosis patients

DEFF Research Database (Denmark)

Marvig, Rasmus Lykke; Madsen Sommer, Lea Mette; Jelsbak, Lars

2015-01-01

is suggested to be due to the large genetic repertoire of P. aeruginosa and its ability to genetically adapt to the host environment. Here, we review the recent work that has applied whole-genome sequencing to understand P. aeruginosa population genomics, within-host microevolution and diversity, mutational...

Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes

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Vaishali P. Waman

2016-08-01

Full Text Available Background Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae. There are four serotypes of Dengue Virus (DENV-1 to DENV-4, each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages. Methods Complete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches. Results DENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach. Discussion Complete genome-based analysis

Intra- and inter-rater reliabilities of measurement of ultrasound imaging for muscle thickness and pennation angle of tibialis anterior muscle in stroke patients.

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Cho, Ki Hun; Lee, Hwang Jae; Lee, Wan Hee

2017-07-01

Dysfunction of skeletal muscle has been commonly reported in stroke patients. The purpose of this study was to investigate the intra- and inter-rater reliabilities of measurement of ultrasound imaging (USI) for pennation angle (PA) and muscle thickness (MT) of tibialis anterior muscle in stroke patients. Thirty-four stroke patients (19 men) participated in this study. USI was used for measurement of PA and MT of the tibialis anterior muscles at rest and during maximum voluntary contraction (MVC). Two examiners acquired images from all participants during two separate testing sessions, seven days apart. Intra-class correlation coefficients (ICCs), confidence interval (CI), standard error of measurement, minimal detectable change, and Bland-Altman plots were used for estimation of reliability. In the intra-rater reliability between measures, for all variables (PA and MT of the paretic and non-paretic sides of tibialis anterior muscles at rest and during MVC), the ICCs ranged between 0.639 and 0.998 and the CI was within an acceptable range of 0.388-0.999. In inter-rater reliability between examiners for the two tests, for all variables, the ICCs ranged between 0.690 and 0.995 and the CI was within an acceptable range of 0.463-0.997. In addition, significant difference was observed between the paretic and non-paretic sides of the tibialis anterior muscle architecture (p stroke patients. In addition, objective and quantitative measurements of tibialis anterior muscle using USI may provide appropriate management for the walking recovery of stroke patients.

Diagnosis of intra abdominal inflammatory processes with 111In-labelled leucocytes

International Nuclear Information System (INIS)

Roevekamp, M.H.; Brummelkamp, W.H.; Schoot, J.B. van der; Reinders Folmer, S.Chr.C.; Royen, E.A. van

1982-01-01

Over a two and a half year period, 225 scintigrams with indium-111 oxinate labelled leukocytes were performed in 184 patients suspected of an intra-abdominal, retroperitoneal or pelvic inflammatory process. In patients suspected of an upper abdominal process, an indium-111 leukocyte-99Tc-Sn colloid subtraction was performed, in order to eliminate the normal liver and spleen uptake. 123 Scintigrams were considered true positive and 73 true negative. A diagnostic accuracy of 87% was calculated. With 18 false-positive scans an 80%-specificity and with 11 false-negative a 92%-sensitivity were obtained. False-positive results in the majority of the scintigrams were based on leukocyte accumulations, due to aspecific cellular inflammatory reactions. False-negative results were mainly related to intra-hepatic, intra-splenic or older lesions. In 150 patients, ultrasonography and/or computed tomography was also performed. A higher diagnostic accuracy was observed with leukocyte scintigraphy compared to ultrasonography. (Auth.)

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource

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Sharpton Thomas J

2012-10-01

Full Text Available Abstract Background New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences. Results We implemented fully automated and high-throughput procedures to de novo cluster proteins into families based upon global alignment similarity. Our approach employs an iterative clustering strategy in which homologs of known families are sifted out of the search for new families. The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. We refer to protein families identified through this approach as “Sifting Families,” or SFams. Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. We validated the quality of SFam clustering through statistical as well as network topology–based analyses. Conclusions We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (http://edhar.genomecenter.ucdavis.edu/sifting_families/.

Molecular epidemiological analysis of env and pol sequences in newly diagnosed HIV type 1-infected, untreated patients in Hungary.

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Mezei, Mária; Ay, Eva; Koroknai, Anita; Tóth, Renáta; Balázs, Andrea; Bakos, Agnes; Gyori, Zoltán; Bánáti, Ferenc; Marschalkó, Márta; Kárpáti, Sarolta; Minárovits, János

2011-11-01

The aim of our study was to monitor the diversity of HIV-1 strains circulating in Hungary and investigate the prevalence of resistance-associated mutations to reverse transcriptase (RT) and protease (PR) inhibitors in newly diagnosed, drug-naive patients. A total of 30 HIV-1-infected patients without prior antiretroviral treatment diagnosed during the period 2008-2010 were included into this study. Viral subtypes and the presence of RT, PR resistance-associated mutations were established by sequencing. Classification of HIV-1 strains showed that 29 (96.6%) patients were infected with subtype B viruses and one patient (3.3%) with subtype A virus. The prevalence of HIV-1 strains with transmitted drug resistance mutations in newly diagnosed individuals was 16.6% (5/30). This study showed that HIV-1 subtype B is still highly predominant in Hungary and documented a relatively high transmission rate of drug resistance in our country.

Diversity of Indo-West Pacific Siphonaria (Mollusca: Gastropoda: Euthyneura).

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Dayrat, Benoît; Goulding, Tricia C; White, Tracy R

2014-03-14

Species of the limpet genus Siphonaria (Gastropoda: Euthyneura) are commonly found in the rocky intertidal, worldwide, except in the Arctic. In total, 205 species-group names are available and not permanently invalid. However, estimating the actual species diversity of Siphonaria has remained challenging, mainly because past authors have interpreted differently the variation of shell characters, resulting in different taxonomic accounts. Species diversity of Siphonaria is evaluated for the first time here based on DNA sequence data (three mitochondrial gene fragments: COI, 12S, and 16S) and a large sampling focusing on the tropical and subtropical Indo-West Pacific (from eastern Africa to Hawaii): new sequences are provided for 153 individuals, 123 of which were collected from 93 locations throughout the Indo-West Pacific. In total, 41 species (molecular units) are recognized worldwide (31 from the Indo-West Pacific), all of which are strongly supported. Potential names are discussed for those 41 species, based on traditional taxonomy. The shells of 66 of the individuals from which DNA was extracted are illustrated: intra- and inter-specific variation is documented in detail and discussed in the light of new molecular results. It is shown that many species could hardly be identified based on the shell only, because the variation of shell characters is too high and overlaps between species. Geographically, no species is found across the entire Indo-West Pacific, where quite a few species seem to be endemic to restricted areas. The biogeography of Siphonaria in the Indo-West Pacific is compared to other groups.

Core genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis.

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Cavanagh, Jorunn Pauline; Klingenberg, Claus; Hanssen, Anne-Merethe; Fredheim, Elizabeth Aarag; Francois, Patrice; Schrenzel, Jacques; Flægstad, Trond; Sollid, Johanna Ericson

2012-06-01

The notoriously multi-resistant Staphylococcus haemolyticus is an emerging pathogen causing serious infections in immunocompromised patients. Defining the population structure is important to detect outbreaks and spread of antimicrobial resistant clones. Currently, the standard typing technique is pulsed-field gel electrophoresis (PFGE). In this study we describe novel molecular typing schemes for S. haemolyticus using multi locus sequence typing (MLST) and multi locus variable number of tandem repeats (VNTR) analysis. Seven housekeeping genes (MLST) and five VNTR loci (MLVF) were selected for the novel typing schemes. A panel of 45 human and veterinary S. haemolyticus isolates was investigated. The collection had diverse PFGE patterns (38 PFGE types) and was sampled over a 20 year-period from eight countries. MLST resolved 17 sequence types (Simpsons index of diversity [SID]=0.877) and MLVF resolved 14 repeat types (SID=0.831). We found a low sequence diversity. Phylogenetic analysis clustered the isolates in three (MLST) and one (MLVF) clonal complexes, respectively. Taken together, neither the MLST nor the MLVF scheme was suitable to resolve the population structure of this S. haemolyticus collection. Future MLVF and MLST schemes will benefit from addition of more variable core genome sequences identified by comparing different fully sequenced S. haemolyticus genomes. Copyright © 2012 Elsevier B.V. All rights reserved.

Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts.

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Webster, Nicole S; Taylor, Michael W; Behnam, Faris; Lücker, Sebastian; Rattei, Thomas; Whalan, Stephen; Horn, Matthias; Wagner, Michael

2010-08-01

Marine sponges contain complex bacterial communities of considerable ecological and biotechnological importance, with many of these organisms postulated to be specific to sponge hosts. Testing this hypothesis in light of the recent discovery of the rare microbial biosphere, we investigated three Australian sponges by massively parallel 16S rRNA gene tag pyrosequencing. Here we show bacterial diversity that is unparalleled in an invertebrate host, with more than 250,000 sponge-derived sequence tags being assigned to 23 bacterial phyla and revealing up to 2996 operational taxonomic units (95% sequence similarity) per sponge species. Of the 33 previously described 'sponge-specific' clusters that were detected in this study, 48% were found exclusively in adults and larvae - implying vertical transmission of these groups. The remaining taxa, including 'Poribacteria', were also found at very low abundance among the 135,000 tags retrieved from surrounding seawater. Thus, members of the rare seawater biosphere may serve as seed organisms for widely occurring symbiont populations in sponges and their host association might have evolved much more recently than previously thought. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus.

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Elizabeth M Driebe

Full Text Available Staphylococcus aureus is an important clinical pathogen worldwide and understanding this organism's phylogeny and, in particular, the role of recombination, is important both to understand the overall spread of virulent lineages and to characterize outbreaks. To further elucidate the phylogeny of S. aureus, 35 diverse strains were sequenced using whole genome sequencing. In addition, 29 publicly available whole genome sequences were included to create a single nucleotide polymorphism (SNP-based phylogenetic tree encompassing 11 distinct lineages. All strains of a particular sequence type fell into the same clade with clear groupings of the major clonal complexes of CC8, CC5, CC30, CC45 and CC1. Using a novel analysis method, we plotted the homoplasy density and SNP density across the whole genome and found evidence of recombination throughout the entire chromosome, but when we examined individual clonal lineages we found very little recombination. However, when we analyzed three branches of multiple lineages, we saw intermediate and differing levels of recombination between them. These data demonstrate that in S. aureus, recombination occurs across major lineages that subsequently expand in a clonal manner. Estimated mutation rates for the CC8 and CC5 lineages were different from each other. While the CC8 lineage rate was similar to previous studies, the CC5 lineage was 100-fold greater. Fifty known virulence genes were screened in all genomes in silico to determine their distribution across major clades. Thirty-three genes were present variably across clades, most of which were not constrained by ancestry, indicating horizontal gene transfer or gene loss.

A comparative study to validate the use of ultrasonography and computed tomography in patients with post-operative intra-abdominal sepsis

International Nuclear Information System (INIS)

Go, H.L.S.; Baarslag, H.J.; Vermeulen, H.; Lameris, J.S.; Legemate, D.A.

2005-01-01

Purpose: To validate abdominal ultrasonography and helical computed tomography in detecting causes for sepsis in patients after abdominal surgery and to determine improved criteria for its use. Materials and methods: Eighty-five consecutive surgical patients primarily operated for non-infectious disease were included in this prospective study. Forty-one patients were admitted to the intensive care unit. All patients were suspected of an intra-abdominal sepsis after abdominal surgery. Both ultrasonography (US) and helical abdominal computed tomography (CT) were performed to investigate the origin of an intra-abdominal sepsis. The images of both US and CT were interpreted on a four-point scale by different radiologists or residents in radiology, the investigators were blinded of each other's test. Interpretations of US and CT were compared with a reference standard which was defined by the result of diagnostic aspiration of suspected fluid collections (re)laparotomy, clinical course or the opinion of an independent panel. Likelihood ratios and post-test probabilities were calculated and interobserver agreement was determined using κ statistics. Results: The overall prevalence of an abdominal infection was 0.49. The likelihood ratio (LR) of a positive test-result for US was 1.33 (95% CI: 0.8-2.5) and for CT scan 2.53 (95% CI: 1.4-5.0); corresponding post-test probabilities for US 0.57 (95% CI: 0.42-0.70) and for CT 0.71 (95% CI: 0.57-0.83). The LR of a negative test-result was, respectively, 0.60 (95% CI: 0.3-1.3) and 0.18 (95% CI: 0.06-0.5); corresponding post-test probabilities for US 0.37 (95% CI: 0.20-0.57) and for CT 0.15 (95% CI: 0.06-0.32) were calculated. Conclusion: Computed tomography can be used as the imaging modality of choice in patients suspected of intra-abdominal sepsis after abdominal surgery. Because of the low discriminatory power ultrasonography should not be performed as initial diagnostic test

Low diversity Cryptococcus neoformans variety grubii multilocus sequence types from Thailand are consistent with an ancestral African origin.

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Sitali P Simwami

2011-04-01

Full Text Available The global burden of HIV-associated cryptococcal meningitis is estimated at nearly one million cases per year, causing up to a third of all AIDS-related deaths. Molecular epidemiology constitutes the main methodology for understanding the factors underpinning the emergence of this understudied, yet increasingly important, group of pathogenic fungi. Cryptococcus species are notable in the degree that virulence differs amongst lineages, and highly-virulent emerging lineages are changing patterns of human disease both temporally and spatially. Cryptococcus neoformans variety grubii (Cng, serotype A constitutes the most ubiquitous cause of cryptococcal meningitis worldwide, however patterns of molecular diversity are understudied across some regions experiencing significant burdens of disease. We compared 183 clinical and environmental isolates of Cng from one such region, Thailand, Southeast Asia, against a global MLST database of 77 Cng isolates. Population genetic analyses showed that Thailand isolates from 11 provinces were highly homogenous, consisting of the same genetic background (globally known as VNI and exhibiting only ten nearly identical sequence types (STs, with three (STs 44, 45 and 46 dominating our sample. This population contains significantly less diversity when compared against the global population of Cng, specifically Africa. Genetic diversity in Cng was significantly subdivided at the continental level with nearly half (47% of the global STs unique to a genetically diverse and recombining population in Botswana. These patterns of diversity, when combined with evidence from haplotypic networks and coalescent analyses of global populations, are highly suggestive of an expansion of the Cng VNI clade out of Africa, leading to a limited number of genotypes founding the Asian populations. Divergence time testing estimates the time to the most common ancestor between the African and Asian populations to be 6,920 years ago (95% HPD

Comparison of intra-articular injections of Hyaluronic Acid and Corticosteroid in the treatment of Osteoarthritis of the hip in comparison with intra-articular injections of Bupivacaine. Design of a prospective, randomized, controlled study with blinding of the patients and outcome assessors

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Bellemans Johan

2010-11-01

Full Text Available Abstract Background Although intra-articular hyaluronic acid is well established as a treatment for osteoarthritis of the knee, its use in hip osteoarthritis is not based on large randomized controlled trials. There is a need for more rigorously designed studies on hip osteoarthritis treatment as this subject is still very much under debate. Methods/Design Randomized, controlled trial with a three-armed, parallel-group design. Approximately 315 patients complying with the inclusion and exclusion criteria will be randomized into one of the following treatment groups: infiltration of the hip joint with hyaluronic acid, with a corticosteroid or with 0.125% bupivacaine. The following outcome measure instruments will be assessed at baseline, i.e. before the intra-articular injection of one of the study products, and then again at six weeks, 3 and 6 months after the initial injection: Pain (100 mm VAS, Harris Hip Score and HOOS, patient assessment of their clinical status (worse, stable or better then at the time of enrollment and intake of pain rescue medication (number per week. In addition patients will be asked if they have complications/adverse events. The six-month follow-up period for all patients will begin on the date the first injection is administered. Discussion This randomized, controlled, three-arm study will hopefully provide robust information on two of the intra-articular treatments used in hip osteoarthritis, in comparison to bupivacaine. Trial registration NCT01079455