bluuebunny/crossref_metadata_2025_split huggingface dataset:
A study on the phylogeny and phylogeography of a marine cosmopolite diatom from the southern Black Sea
Authors: Baytut Özgür 
Published: January 2014

Abstract
A single-cell PCR method was applied to Pseudo-nitzschia pungens strains from the southern Black Sea. Based on the aligment set of the LSU D1-D3 region, a Bayesian molecular phylogeny analysis and a parsimony network analysis were used to investigate phylogenetic clades (Clades I-III) in P. pungens and to determine the ancestral clades. The parsimony network analysis also demonstrated that ancestral haplotypes belonged to Clade II, residing around the northeastern Pacific, while Clade I was distributed globally but antitropicaly. According to the findings of this study, the Black Sea strain (Clade III) shows a global phylogeographic pattern.
Warm currents affecting the spring and winter distributions of living coccolithophores in the Yellow Sea, China
Authors: Luan Qingshan , Sun Jianqiang , Niu Mingxiang , Wang Jun 
Published: January 2014

Abstract
Spring and winter distributions of living coccolithophores in the Yellow Sea were studied using a polarizing microscope based on two surveys in April 2010 and January 2011. Nine species were recorded, including Emiliania huxleyi and Gephyrocapsa oceanica as the predominant forms. The cell abundance of all coccolithophores in the spring was significantly higher than in the winter (p<0.01), with means of 15 387 and 2470 cells l-1, respectively. Notably, we observed a habitat selection of coccolithophores in the southeastern Yellow Sea (32–35°N, 123–125°E). This habitat was characterized by sharp temperature gradients during both seasons caused by water exchange between the shelf waters and the Yellow Sea Warm Current. Moreover, the cell abundance, standing crop and estimated fluxes of coccolithophores were abnormally high compared to other regions. The habitat preference of coccolithophores in the Yellow Sea was directly related to the hydrodynamic conditions. The unfavorable light conditions caused by the intense convective mixing were responsible for the low biomass of coccolithophores during the winter. However, the increasing temperature influenced by the warm current, in combination with water column stability, triggered the spring bloom of coccolithophores in the southern Yellow Sea.
Aquatic fungi and straminipilous organisms in lakes of the Augustowska Primeval Forest, Poland
Authors: Godlewska Anna , Kiziewicz Bożena , Muszyńska Elżbieta , Milewski Robert 
Published: January 2014

Abstract
We analyzed species composition of aquatic fungi and straminipilous organisms in six lakes located within the Augustowska Primeval Forest, Poland. Mycological observations conducted in the spring and autumn seasons together with hydrochemical analysis in the 2010–2012 revealed the presence of 44 species (10 aquatic fungi and 34 straminipilous organisms). Among the taxa detected, there were some potential pathogens of economically valuable fish species and spawn, including Achlya americana, Ac. polyandra, Saprolegnia ferax and S. parasitica. Some of the species were crustacean pathogens, such as Lagenidium giganteum, Myzocytium microsporum and M. zoophthorum. There were also some common human pathogens Aspergillus niger and Candida tropicalis. Some species, such as Achlya klebsiana, Ac. prolifera, Nowakowskiella elegans, N. macrospora, Pythium debaryanum, Py. inflatum, Rhizophlyctis rosea and Saprolegnia litoralis were common phytosaprobionts.
The largest number of species of fungi and straminipilous organisms was identified in Lake Sajenek (22), the fewest in Lake Białe (12).
The quantitative composition and qualitative differentiation of mycobiota were influenced by the content of biogenic compounds and the amount of organic substance. The elevated levels of these parameters (Lake Sajenek) stimulated the growth of fungi and straminipilous organisms, whereas very low concentrations of biogenic compounds and a small amount of organic matter (Lake Białe) had an inhibitory effect.
Statistical analysis of the results was conducted to determine the correlations between the number of fungal and straminipilous species and the hydrochemical parameters, i.e. water temperature, the level of nitrogen compounds (nitrate nitrogen, ammonium nitrogen), calcium carbohydrate, magnesium carbohydrate, water oxidizability and the content of dry residue, dissolved substances and suspension.
Spatial pattern of the planktonic ciliate community and its relationship with the environment in spring in the northern Beibu Gulf, South China Sea
Authors: Wang Yibo , Zhang Wenjing , Lin Yuanshao , Zheng Lianming , Cao Wenqing , Yang Jun 
Published: January 2014

Abstract
Surface water samples were collected from 19 sites in the northern Beibu Gulf in April 2011. Species composition and abundance of planktonic ciliates were investigated. They were combined with environmental data to obtain the spatial pattern of the ciliate community and its relationship with the environment. A total of 36 species belonging to 13 genera and 3 orders (Oligotrichida, Haptorida and Tintinnida) were identified, including 10 dominant species. All 19 samples were divided into three groups using cluster analysis and multidimensional scaling (MDS) on the basis of the ciliate species composition and abundance. Group 1 was the least abundant. The species of the order Oligotrichida dominated in Group 2. In contrast, Mesodinium species were of increased importance in Group 3. Redundancy analysis (RDA) revealed that ciliate communities were more closely related to the level of nitrogen (total nitrogen, nitrate nitrogen, nitrite nitrogen) and phosphorus (total phosphorus, active phosphorus) rather than other variables. As the levels of nitrogen and phosphorus increased, communities dominated by species from the order Oligotrichida were replaced by those dominated by Mesodinium species.
New record of Geissleria declivis (Hust.) Lange-Bert. (Bacillariophyceae) in Europe, the first in Poland
Authors: Noga Teresa , Stanek-Tarkowska Jadwiga , Pajączek Anita , Peszek Łukasz 
Published: January 2014

Abstract
As a result of the research carried out in Lakes Duszatyńskie and the Olchowaty stream, a new European site with Geissleria declivis (Hust.) Lange-Bert. was found — a new species for Poland. The highest abundance of G. declivis has been observed on sandy substrate and small stones in the littoral zone of the Upper Lake during the spring season. The species occurred together with Achnanthidium minutissimum (Kütz.) Czarn. var. minutissimum, A. catenatum (Bily & Marvan), Fragilaria leptostauron (Ehrenb.) Hust. var. leptostauron and F. pinnata Ehrenb. var. pinnata. Our observations revealed that G. declivis develops in lentic water bodies with medium organic matter content and neutral pH. The species seems to prefer mesotrophic waters with low to medium electrolyte content and oligosaprobous. The species morphology and identity is documented in a series of light microscopic (LM) images and for the first time under a scanning electron microscope (SEM).
Ruby vs. Perl – the Languages of Bioinformatics
Authors: Goliński Maciej , Golińska Agnieszka Kitlas 
Published: January 2014

Abstract
Ruby and Perl are programming languages used in many fields. In this paper we would like to present their usefulness with regard to basic bioinformatic problems. We concentrate on a comparison of widely used Perl and relatively rarely used Ruby to show that Ruby can be a very efficient tool in bioinformatics. Both Perl and Ruby have a built-in regular expressions (or regexp) engine, which is essential in solving many problems in bioinformatics. We present some selected examples: printing the file content, removing comments from a FASTA file, using hashes, printing nucleotides included in a sequence, searching for a specific nucleotide in sequence and translating nucleotide sequences into protein sequences obtained in GenBank format. It is our belief that Ruby’s popularity will rise because of its simple syntax and the richness of its methods. Programs in Ruby are very easy to read and therefore easier to maintain and debug, which are the most important characteristics for a programming language.
MINING FLIES OF THE GENUS OPHIOMYIA (DIPTERA, AGROMYZIDAE) OF EASTERN UKRAINE AND ADJACENT TERRITORIES: REVIEW OF SPECIES WITH A FASCICULUS
Authors: Guglya Yu. A. 
Published: January 2014

Abstract
During 2009-2013, twenty-three species of agromyzid flies from the genus Ophiomyia Braschnikov, 1897 were collected in the territory of eastern and south-eastern Ukraine. Among them, six species are described as new for science: Ophiomyia australis sp. n., O. crispa sp. n., O. fasciculusalba sp. n., O. malalata sp. n., O. punctata sp. n. and O. versera sp. n. Male heads and genitalia are illustrated for all species. Pictures of the female genitalia are also provided for O. curvipalpis (Zetterstedt, 1848), O. disordens Pakalniškis, 1998, O. fennoniensis Spencer, 1976, O. maura (Meigen, 1832), O. melandricaulis Hering, 1943, O. ranunculicaulis Hering, 1949, O. slovaca Černý, 1994, O. skanensis Spencer, 1976 and O. submaura Hering, 1926. Information on distribution and host plants are also provided.
THE NATURE PROTECTION ASPECT OF THE BLACK SEA FISH MYXOSPOREAN STUDIES
Authors: Yurakhno V. M. 
Published: January 2014

Abstract
The species composition and indices of the myxosporeans infecting fish from the different nature conservation Black Sea regions were considered on the base of the original investigations and literature data. Myxosporean inhabiting the Red Book fish hosts were investigated. The myxosporean species potentially pathogenic for the fish health were identified and epizootological situation was estimated.
Virological Escape in HCV Genotype-1-Infected Patients Receiving Daclatasvir plus Ribavirin and Peginterferon Alfa-2A or Alfa-2B
Authors: McPhee Fiona , Hernandez Dennis , Zhou Nannan , Yu Fei , Ueland Joseph , Monikowski Aaron , Chayama Kazuaki , Toyota Joji , Izumi Namiki , Yokosuka Osamu , Kawada Norifumi , Osaki Yukio , Hughes Eric A , Watanabe Hideaki , Ishikawa Hiroki , Kumada Hiromitsu 
Published: January 2014

Background Daclatasvir (DCV; BMS-790052) is a picomolar inhibitor of HCV non-structural protein 5A (NS5A) and has demonstrated efficacy in patients chronically infected with HCV. Methods In the double-blind, randomized studies AI444021 and AI444022, 71 Japanese patients chronically infected with HCV genotype 1 (predominantly genotype 1b) received DCV (10 mg or 60 mg) plus peginterferon alfa-2b or alfa-2a and ribavirin. Virological failure occurred in 14% (5/36) of treatment-naive patients and 54% (19/35) of prior alfa/ribavirin non-responders. Resistance testing was performed on baseline samples and samples with HCV RNA≥1,000 IU/ml at week 1 through post-treatment week 24. Results Baseline NS5A resistance-associated polymorphisms had less impact on virological response rates than IL28B genotype. All patients with virological failure had NS5A DCV-resistant variants at the time of failure. The predominant NS5A variants were L31V/M/I plus Y93H; this combination was detected in 100% (5/5) of treatment-naive patients and 74% (14/19) of non-responders with failure. Emergent resistance variants in prior non-responders (four viral breakthroughs, one relapse) were more varied with novel combinations such as L31F-DP32 and L28M-R30Q-A92K detected. Significant loss in DCV antiviral activity was generally only seen with ≥ two resistance-associated NS5A substitutions. All DCV-resistant variants were still detected at end of study. Conclusions Virological failure in HCV genotype 1b treatment-naive Japanese patients receiving DCV plus alfa-2a/ribavirin or alfa-2b/ribavirin was associated with enrichment of NS5A resistance variants L31V/M-Y93H. In prior non-responders, emergent variants associated with failure also included NS5A-A92K or NS5A-DP32. As with L31-Y93 variants, these variants persisted.
Daclatasvir Combined with Peginterferon Alfa-2A and Ribavirin in Japanese Patients Infected with Hepatitis C Genotype 1
Authors: Izumi Namiki , Yokosuka Osamu , Kawada Norifumi , Osaki Yukio , Yamamoto Kazuhide , Sata Michio , Ishikawa Hiroki , Ueki Tomoko , Hu Wenhua , McPhee Fiona , Hughes Eric A , Kumada Hiromitsu 
Published: January 2014

Background New direct-acting antiviral agents are currently being developed to treat chronic HCV. The efficacy and safety of daclatasvir combined with peginterferon alfa-2a (alfa-2a) and ribavirin were assessed in a randomized, double-blind Phase IIa study of Japanese patients with chronic HCV genotype-1 infection. Methods Japanese patients who were treatment-naive ( n=25) or prior null ( n=12) or partial ( n=5) responders received once-daily daclatasvir 10 mg or 60 mg or placebo in combination with alfa-2a and ribavirin. Daclatasvir recipients with a protocol-defined response (HCV RNA<15 IU/ml at week 4 and undetectable at week 12) were treated for 24 weeks; placebo recipients and patients without a protocol-defined response were treated for 48 weeks. Results Sustained virological response at 24 weeks post-treatment (SVR24) was achieved by 89% and 100% of treatment-naive patients receiving daclatasvir 10 mg and 60 mg, respectively, versus 75% in placebo recipients. Virological failure was more frequent in prior non-responder patients, with 50% and 78% achieving SVR24 in daclatasvir 10 mg and 60 mg groups, respectively. Adverse events occurred with similar frequency among treatment groups and were consistent with the adverse event profile of alfa-2a/ribavirin alone. The most commonly reported adverse events included pyrexia, alopecia, anaemia, lymphopenia, neutropenia, pruritus and diarrhoea. Three patients discontinued treatment due to anaemia. Conclusions Daclatasvir combined with alfa-2a/ribavirin in treatment-naive patients showed greater efficacy than alfa-2a/ribavirin alone and was generally well tolerated. The 60-mg dose of daclatasvir achieved the highest rates of SVR24 in both treatment-naive and non-responder populations and will be evaluated in a Phase III clinical trial.
Le président du groupe majoritaire
Authors: Benetti Julie 
Published: January 2014

Au Parlement, la majorité s’identifie au président du groupe majoritaire. Celui-ci personnifie son groupe ; il le représente en même temps qu’il le dirige. C’est pourquoi la révision constitutionnelle du 23 juillet 2008 aurait pu inaugurer une nouvelle conception de la présidence du groupe majoritaire, la rénovation de la majorité parlementaire s’incarnant dans son président. Mais la réforme entreprise n’a pas plus transformé la fonction de président du groupe majoritaire que le rôle de la majorité parlementaire elle-même. Garant de l’unité et de la discipline de son groupe, le président en reste avant tout la figure d’autorité et de commandement.
Interpretation of Public Feedback to Transportation Policy:
Authors: Krishen Anjala S. , Raschke Robyn L. , Kachroo Pushkin , Mejza Michael , Khan Alauddin 
Published: January 2014

AbstractDue to inadequate funding for road maintenance and expansion, many state governments are exploring the implementation of a vehicle-miles-traveled (VMT) policy. Such a policy requires adequate communication to the public that not only informs but also communicates the issues of concern to the constituents. As part of this communication, the Nevada Department of Transportation began by conducting workshops, while local newspapers allowed Internet-based response to the basic idea of this tax. Our article takes the qualitative data obtained from these multiple sources and analyzes it via a two-pronged qualitative methodology. First, we ascertain common profiles through iterative coding, and then we use concept maps to delve into the relationships between themes within these segments. Our findings indicate that by using qualitative segmentation followed by concept mapping of open-ended customer data, public policy officials can find genres or issues of interest to large segments and address those in communication endeavors.
Intra-Articular Injection of Human Meniscus Stem/Progenitor Cells Promotes Meniscus Regeneration and Ameliorates Osteoarthritis Through Stromal Cell-Derived Factor-1/CXCR4-Mediated Homing
Authors: Shen Weiliang , Chen Jialin , Zhu Ting , Chen Longkun , Zhang Wei , Fang Zhi , Heng Boon Chin , Yin Zi , Chen Xiao , Ji Junfeng , Chen Weishan , Ouyang Hong-Wei 
Published: January 2014

Abstract
Meniscus injury is frequently encountered in clinical practice. Current surgical therapy involving partial or complete meniscectomy relieves pain in the short-term but often leads to osteoarthritis (OA) in the long-term. In this study, we report a new strategy of articular cartilage protection by intra-articular injection of novel human meniscus stem/progenitor cells (hMeSPCs). We found that hMeSPCs displayed both mesenchymal stem cell characteristics and high expression levels of collagen II. In the rat meniscus injury model, hMeSPC transplantation not only led to more neo-tissue formation and better-defined shape but also resulted in more rounded cells and matured extracellular matrix. Stromal cell-derived factor-1 (SDF-1) enhanced the migration of hMeSPCs, whereas AMD3100 abolished the chemotactic effects of SDF-1 on hMeSPCs, both in vitro and in vivo. In an experimental OA model, transplantation of hMeSPCs effectively protected articular cartilage, as evidenced by reduced expression of OA markers such as collagen I, collagen X, and hypoxia-inducible factor 2α but increased expression of collagen II. Our study demonstrated for the first time that intra-articular injection of hMeSPCs enhanced meniscus regeneration through the SDF-1/CXCR4 axis. Our study highlights a new strategy of intra-articular injection of hMeSPCs for meniscus regeneration.
Sleep Problems, Posttraumatic Stress, and Mood Disorders Among Active-Duty Service Members
Authors: Lande R. Gregory 
Published: January 2014

Abstract

Context: Sleep problems among active-duty service members are pervasive and complicate the recovery from comorbid posttraumatic stress and mood disorders.

Objective: To better understand chronic sleep problems among active-duty service members.

Methods: Medical records for active-duty service members who completed enhanced sleep assessments during an 18-month period beginning in October 2010 at the Walter Reed National Military Medical Centers' Psychiatry Continuity Service were retrospectively reviewed. Sleep assessment measures included the Pittsburgh Insomnia Rating Scale, the Alcohol Use Disorders Identification Test, the Zung Self-Rating Depression Scale, the Zung Self-Rating Anxiety Scale, the Posttraumatic Stress Disorder Checklist – Military Version, the Epworth Sleepiness Scale, the Pre-Sleep Arousal Scale, and a home sleep study.

Results: A total of 76 records met the study criteria. Twenty-two participants (29%) had an apnea/hypopnea index that suggested mild to moderate sleep apnea. Service members with higher self-reported posttraumatic stress scores also reported a higher degree of both somatic and cognitive factors interfering with sleep initiation. Compared with those who had low self-reported posttraumatic stress scores, service members with high posttraumatic stress scores also had less total sleep time (mean difference, 38 minutes) and higher scores on the apnea/hypopnea index, the respiratory disturbance index, and the oxygen saturation index.

Conclusion: Enhanced sleep assessments that include traditional self-report tests and a home sleep study can help identify previously undiscovered behavioral and respiratory problems among service members, particularly those with higher posttraumatic stress scores.
Preventing Early Cardiovascular Death in Patients With Familial Hypercholesterolemia
Authors: Repas Thomas B. , Tanner J. Ross 
Published: January 2014

Abstract
Familial hypercholesterolemia (FH) is an autosomal dominant disorder resulting in severe elevation of total and low-density lipoprotein cholesterol levels. There are more than 600,000 individuals in the United States with FH. Individuals with FH tend to experience premature cardiovascular disease and often die from sudden cardiac death at a young age. Statins alone or in combination with other lipid-lowering medications are effective in managing FH and preventing cardiovascular events. For patients who do not respond to or are intolerant of pharmacotherapy, low-density lipoprotein apheresis is available as a nonpharmacologic treatment option. Despite the prevalence of FH, it is undiagnosed and untreated in the majority of patients. Screening, combined with appropriate drug therapy, can save lives. The authors review the screening, diagnosis, and management of FH.
Mini–Medical School Programs Are an Effective Tool to Introduce Students to Osteopathic Medicine
Authors: Kaye Kathryn E. , Berns Alyssa L. , Cress Lyndsi R. , Nazar Andrea M. 
Published: January 2014

Abstract

Context: Mini–medical school programs are designed to give participants, usually high school students, a more realistic perception of medicine and to leave students with a stronger desire to pursue a career in medicine.

Objective: To determine if the annual High School Mini–Medical School program hosted by the West Virginia School of Osteopathic Medicine increased interest in osteopathic medicine among high school students.

Design: A survey was conducted before and after the program to test the program's effectiveness.

Setting: West Virginia School of Osteopathic Medicine's Clinical Education Center.

Participants: High school students from Charleston, Fairmont, and the Greenbrier Valley in West Virginia.

Interventions: The participants attended an outreach program designed to interest them in a career in medicine and specifically osteopathic medicine.

Results: Sixty-nine participants came away with an improved understanding of a physician's life and medical school after the program. There was a mean increase in positive responses for the survey items “I understand what medical school life is truly like” (P=.0066) and “I understand what life as a doctor is really like” (P=.0004). Participants left the program with a stronger desire to pursue a career in medicine (P<.0001).

Conclusion: Mini–medical school programs are an effective tool to inspire high school students to pursue careers in medicine, including osteopathic medicine.
Osteopathic Manipulative Treatment in the Management of Biliary Dyskinesia
Authors: Heineman Katherine 
Published: January 2014

Abstract
Biliary dyskinesia is a functional gastrointestinal disorder of the gallbladder and sphincter of Oddi. Diagnosis is made on the basis of symptoms of biliary colic in the absence of cholelithiasis and gallbladder inflammation. Palpatory findings of tissue texture changes at midthoracic levels (T6-T9) may correspond to visceral dysfunction related to the biliary system. Osteopathic manipulative treatment (OMT) of the T6-T9 segments can remove the feedback related to the somatic component, thereby affecting nociceptive facilitation at the spinal level and allowing the body to restore autonomic balance. Few reports in the current literature provide examples of treatment for patients with biliary dyskinesia using OMT. The author describes the case of a 51-year-old woman who presented with symptoms consistent with biliary dyskinesia. Her biliary colic completely resolved after OMT. Osteopathic evaluation and OMT should be considered a safe and effective option for conservative management of biliary dyskinesia.