bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathogenic mechanisms linking benign prostatic hyperplasia, lower urinary tract symptoms and erectile dysfunction
Authors: Glina Sidney , Glina Felipe Placco Araujo 
Published: May 2013

Introduction: Erectile dysfunction (ED) and lower urinary tract symptoms (LUTS) caused by benign prostatic hyperplasia (BPH) are clinical entities very prevalent in men aged over 50 years. There is evidence that both may have a common pathophysiology. Objective: The objective of this study was to conduct a literature review aiming to show theories and hypotheses that justify a single pathophysiology for ED and LUTS/BPH. Methods: A search in Medline using the keywords of the Medical Subject Headings (MESH) ‘erectile dysfunction’ and ‘lower urinary tract symptoms’ in all fields of the database up to 15 December 2012. This search found 198 relevant articles that were analyzed. Results: The data and articles were divided according to the type of evidence found. There are strong epidemiological data showing that LUTS/BPH is a risk factor for developing ED. Several experimental models demonstrated partial obstruction of the bladder in animals causes voiding disorders as well as a negative impact on erectile function of the operated animals. The increased adrenergic tonus in animals leads to prostate growth and urodynamic conditions similar to those found in men with LUTS and ED. Arteriosclerosis may lead to loss of vesical complacency, urinary tract obstruction and fibrosis of the cavernous bodies. The use of phosphodiesterase type 5 inhibitors (PDE-5i) and/or alpha-adrenergic blockers to treat ED and LUTS/BPH reinforces the hypothesis that, at least in some patients, both clinical pictures may have the same pathophysiology.
Unplanned urology readmissions in a district general hospital: are we meeting the standard?
Authors: Raslan M , Floyd Ms , Itam S , Mukherjee R , Irwin Pp , Maddineni Sb 
Published: May 2013

Background Recent changes in practice standards and remuneration to UK Trusts have been refined to penalise institutions for patient readmission within 30 days of discharge. The purpose of this study was to determine if the target rate of less than 6.5% was attained within the setting of a district general hospital (DGH) and also to comment on readmission trends. Materials and methods A retrospective study was performed over 12 months examining all unplanned readmissions to hospital 30 days following discharge from Urology. Elective as well as emergency cases were audited. Results A total of 4124 patients were treated and discharged by the department over 12 months. One hundred and eighty-four (4.4%) patients were readmitted: 93 (51%) patients following acute presentations and 91 (49%) following elective procedures. The commonest causes for unplanned readmission were haematuria, 29 cases (16%), acute urinary retention, 28 cases (15%) and ureteric colic, 25 cases (14%). Readmission rates following flexible cystoscopy and TRUS biopsy were 1% and 3%, respectively. Only six of 70 patients (9%) were readmitted following TURP. Five (3%) of the 184 readmissions required a second procedure. Conclusion Our department met the predetermined standard in achieving an unplanned readmission rate of less than 6.5%. This study also highlighted the need for discharge policies for common acute presentations.
Adult T-cell leukemia cells overexpress Wnt5a and promote osteoclast differentiation
Authors: Bellon Marcia , Ko Nga Ling , Lee Min-Jung , Yao Yuan , Waldmann Thomas A. , Trepel Jane B. , Nicot Christophe 
Published: May 2013

Key PointsProfiling of the Wnt/β-catenin pathway reveals overexpression of Wnt5a, LEF-1 and TCF-1 in ATL patient cells. ATL cells overexpress Wnt5a, which enhances osteoclastogenesis and may contribute to the osteolytic bone lesions and hypercalcemia.
Genome-wide association study of antibody response to Newcastle disease virus in chicken
Authors: Luo Chenglong , Qu Hao , Ma Jie , Wang Jie , Li Chunyu , Yang Chunfen , Hu Xiaoxiang , Li Ning , Shu Dingming 
Published: May 2013

AbstractBackgroundSince the first outbreak in Indonesia in 1926, Newcastle disease has become one of the most common and contagious bird diseases throughout the world. To date, enhancing host antibody response by vaccination remains the most efficient strategy to control outbreaks of Newcastle disease. Antibody response plays an important role in host resistance to Newcastle disease, and selection for antibody response can effectively improve disease resistance in chickens. However, the molecular basis of the variation in antibody response to Newcastle disease virus (NDV) is not clear. The aim of this study was to detect genes modulating antibody response to NDV by a genome-wide association study (GWAS) in chickens.ResultsTo identify genes or chromosomal regions associated with antibody response to NDV after immunization, a GWAS was performed using 39,833 SNP markers in a chicken F2resource population derived from a cross between two broiler lines that differed in their resistance. Two SNP effects reached 5% Bonferroni genome-wide significance (P<1.26×10-6). These two SNPs,rs15354805andrs15355555, were both on chicken (Gallus gallus) chromosome 1 and spanned approximately 600 Kb, from 100.4 Mb to 101.0 Mb.Rs15354805is in intron 7 of the chickenRoundabout,axon guidance receptor,homolog 2(ROBO2) gene, andrs15355555is located about 243 Kb upstream ofROBO2.Rs15354805explained 5% of the phenotypic variation in antibody response to NDV, post immunization, in chickens.Rs15355555had a similar effect asrs15354805because of its linkage disequilibrium withrs15354805(r2=0.98).ConclusionThe region at about 100 Mb from the proximal end of chicken chromosome 1, including theROBO1andROBO2genes, has a strong effect on the antibody response to the NDV in chickens. This study paves the way for further research on the host immune response to NDV.
Transcriptional analysis of oligosaccharide utilization by Bifidobacterium lactisBl-04
Authors: Andersen Joakim M , Barrangou Rodolphe , Hachem Maher Abou , Lahtinen Sampo J , Goh Yong Jun , Svensson Birte , Klaenhammer Todd R 
Published: May 2013

Abstract

Background
Probiotic bifidobacteria in combination with prebiotic carbohydrates have documented positive effects on human health regarding gastrointestinal disorders and improved immunity, however the selective routes of uptake remain unknown for most candidate prebiotics. The differential transcriptomes of Bifidobacterium animalis subsp. lactis Bl-04, induced by 11 potential prebiotic oligosaccharides were analyzed to identify the genetic loci involved in the uptake and catabolism of α- and β-linked hexoses, and β-xylosides.

Results
The overall transcriptome was modulated dependent on the type of glycoside (galactosides, glucosides or xylosides) utilized. Carbohydrate transporters of the major facilitator superfamily (induced by gentiobiose and β-galacto-oligosaccharides (GOS)) and ATP-binding cassette (ABC) transporters (upregulated by cellobiose, GOS, isomaltose, maltotriose, melibiose, panose, raffinose, stachyose, xylobiose and β-xylo-oligosaccharides) were differentially upregulated, together with glycoside hydrolases from families 1, 2, 13, 36, 42, 43 and 77. Sequence analysis of the identified solute-binding proteins that determine the specificity of ABC transporters revealed similarities in the breadth and selectivity of prebiotic utilization by bifidobacteria.

Conclusion
This study identified the differential gene expression for utilization of potential prebiotics highlighting the extensive capabilities of Bifidobacterium lactis Bl-04 to utilize oligosaccharides. Results provide insights into the ability of this probiotic microbe to utilize indigestible carbohydrates in the human gastrointestinal tract.
Discovering putative prion sequences in complete proteomes using probabilistic representations of Q/N-rich domains
Authors: Espinosa Angarica Vladimir , Ventura Salvador , Sancho Javier 
Published: May 2013

Abstract

Background
Prion proteins conform a special class among amyloids due to their ability to transmit aggregative folds. Prions are known to act as infectious agents in neurodegenerative diseases in animals, or as key elements in transcription and translation processes in yeast. It has been suggested that prions contain specific sequential domains with distinctive amino acid composition and physicochemical properties that allow them to control the switch between soluble and β-sheet aggregated states. Those prion-forming domains are low complexity segments enriched in glutamine/asparagine and depleted in charged residues and prolines. Different predictive methods have been developed to discover novel prions by either assessing the compositional bias of these stretches or estimating the propensity of protein sequences to form amyloid aggregates. However, the available algorithms hitherto lack a thorough statistical calibration against large sequence databases, which makes them unable to accurately predict prions without retrieving a large number of false positives.

Results
Here we present a computational strategy to predict putative prion-forming proteins in complete proteomes using probabilistic representations of prionogenic glutamine/asparagine rich regions. After benchmarking our predictive model against large sets of non-prionic sequences, we were able to filter out known prions with high precision and accuracy, generating prediction sets with few false positives. The algorithm was used to scan all the proteomes annotated in public databases for the presence of putative prion proteins. We analyzed the presence of putative prion proteins in all taxa, from viruses and archaea to plants and higher eukaryotes, and found that most organisms encode evolutionarily unrelated proteins with susceptibility to behave as prions.

Conclusions
To our knowledge, this is the first wide-ranging study aiming to predict prion domains in complete proteomes. Approaches of this kind could be of great importance to identify potential targets for further experimental testing and to try to reach a deeper understanding of prions’ functional and regulatory mechanisms.
Characterization of human plasma-derived exosomal RNAs by deep sequencing
Authors: Huang Xiaoyi , Yuan Tiezheng , Tschannen Michael , Sun Zhifu , Jacob Howard , Du Meijun , Liang Meihua , Dittmar Rachel L , Liu Yong , Liang Mingyu , Kohli Manish , Thibodeau Stephen N , Boardman Lisa , Wang Liang 
Published: May 2013

Abstract

Background
Exosomes, endosome-derived membrane microvesicles, contain specific RNA transcripts that are thought to be involved in cell-cell communication. These RNA transcripts have great potential as disease biomarkers. To characterize exosomal RNA profiles systemically, we performed RNA sequencing analysis using three human plasma samples and evaluated the efficacies of small RNA library preparation protocols from three manufacturers. In all we evaluated 14 libraries (7 replicates).

Results
From the 14 size-selected sequencing libraries, we obtained a total of 101.8 million raw single-end reads, an average of about 7.27 million reads per library. Sequence analysis showed that there was a diverse collection of the exosomal RNA species among which microRNAs (miRNAs) were the most abundant, making up over 42.32% of all raw reads and 76.20% of all mappable reads. At the current read depth, 593 miRNAs were detectable. The five most common miRNAs (miR-99a-5p, miR-128, miR-124-3p, miR-22-3p, and miR-99b-5p) collectively accounted for 48.99% of all mappable miRNA sequences. MiRNA target gene enrichment analysis suggested that the highly abundant miRNAs may play an important role in biological functions such as protein phosphorylation, RNA splicing, chromosomal abnormality, and angiogenesis. From the unknown RNA sequences, we predicted 185 potential miRNA candidates. Furthermore, we detected significant fractions of other RNA species including ribosomal RNA (9.16% of all mappable counts), long non-coding RNA (3.36%), piwi-interacting RNA (1.31%), transfer RNA (1.24%), small nuclear RNA (0.18%), and small nucleolar RNA (0.01%); fragments of coding sequence (1.36%), 5′ untranslated region (0.21%), and 3′ untranslated region (0.54%) were also present. In addition to the RNA composition of the libraries, we found that the three tested commercial kits generated a sufficient number of DNA fragments for sequencing but each had significant bias toward capturing specific RNAs.

Conclusions
This study demonstrated that a wide variety of RNA species are embedded in the circulating vesicles. To our knowledge, this is the first report that applied deep sequencing to discover and characterize profiles of plasma-derived exosomal RNAs. Further characterization of these extracellular RNAs in diverse human populations will provide reference profiles and open new doors for the development of blood-based biomarkers for human diseases.
Sequencing platform and library preparation choices impact viral metagenomes
Authors: Solonenko Sergei A , Ignacio-Espinoza J César , Alberti Adriana , Cruaud Corinne , Hallam Steven , Konstantinidis Kostas , Tyson Gene , Wincker Patrick , Sullivan Matthew B 
Published: May 2013

Abstract

Background
Microbes drive the biogeochemistry that fuels the planet. Microbial viruses modulate their hosts directly through mortality and horizontal gene transfer, and indirectly by re-programming host metabolisms during infection. However, our ability to study these virus-host interactions is limited by methods that are low-throughput and heavily reliant upon the subset of organisms that are in culture. One way forward are culture-independent metagenomic approaches, but these novel methods are rarely rigorously tested, especially for studies of environmental viruses, air microbiomes, extreme environment microbiology and other areas with constrained sample amounts. Here we perform replicated experiments to evaluate Roche 454, Illumina HiSeq, and Ion Torrent PGM sequencing and library preparation protocols on virus metagenomes generated from as little as 10pg of DNA.

Results
Using %G + C content to compare metagenomes, we find that (i) metagenomes are highly replicable, (ii) some treatment effects are minimal, e.g., sequencing technology choice has 6-fold less impact than varying input DNA amount, and (iii) when restricted to a limited DNA concentration (<1μg), changing the amount of amplification produces little variation. These trends were also observed when examining the metagenomes for gene function and assembly performance, although the latter more closely aligned to sequencing effort and read length than preparation steps tested. Among Illumina library preparation options, transposon-based libraries diverged from all others and adaptor ligation was a critical step for optimizing sequencing yields.

Conclusions
These data guide researchers in generating systematic, comparative datasets to understand complex ecosystems, and suggest that neither varied amplification nor sequencing platforms will deter such efforts.
Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction
Authors: Beneventi Magda Aparecida , da Silva Orzenil Bonfim , de Sá Maria Eugênia Lisei , Firmino Alexandre Augusto Pereira , de Amorim Regina Maria Santos , Albuquerque Érika Valéria Saliba , da Silva Maria Cristina Mattar , da Silva Joseane Padilha , Campos Magnólia de Araújo , Lopes Marcus José Conceição , Togawa Roberto Coiti , Pappas Georgios Joanis , Grossi–de–Sa Maria Fatima 
Published: May 2013

Abstract

Background
Root-knot nematodes (RKN– Meloidogyne genus) present extensive challenges to soybean crop. The soybean line (PI 595099) is known to be resistant against specific strains and races of nematode species, thus its differential gene expression analysis can lead to a comprehensive gene expression profiling in the incompatible soybean-RKN interaction. Even though many disease resistance genes have been studied, little has been reported about phytohormone crosstalk on modulation of ROS signaling during soybean-RKN interaction.

Results
Using 454 technology to explore the common aspects of resistance reaction during both parasitism and resistance phases it was verified that hormone, carbohydrate metabolism and stress related genes were consistently expressed at high levels in infected roots as compared to mock control. Most noteworthy genes include those encoding glycosyltransferases, peroxidases, auxin-responsive proteins and gibberellin-regulated genes. Our data analysis suggests the key role of glycosyltransferases, auxins and components of gibberellin signal transduction, biosynthesis and deactivation pathways in the resistance reaction and their participation in jasmonate signaling and redox homeostasis in mediating aspects of plant growth and responses to biotic stress.

Conclusions
Based on this study we suggest a reasonable model regarding to the complex mechanisms of crosstalk between plant hormones, mainly gibberellins and auxins, which can be crucial to modulate the levels of ROS in the resistance reaction to nematode invasion. The model also includes recent findings concerning to the participation of DELLA-like proteins and ROS signaling controlling plant immune or stress responses. Furthermore, this study provides a dataset of potential candidate genes involved in both nematode parasitism and resistance, which can be tested further for their role in this biological process using functional genomics approaches.
Comparing the effects of isoflurane and pentobarbital on the responses of cutaneous mechanoreceptive afferents
Authors: Cheng Ju-Wen , Weber Alison I , Bensmaia Sliman J 
Published: May 2013

AbstractBackgroundWhile pentobarbital has been used extensively in neurophysiological experiments investigating activity in peripheral nerves, it has fallen out of favor as an anesthetic because of safety concerns and is often replaced with isoflurane. However, the effects of isoflurane on the excitability of mechanoreceptive afferents have yet to be conclusively elucidated.MethodsTo fill this gap, we collected extracellular single-unit recordings of cutaneous mechanoreceptive afferents from the sciatic nerve of 21 rats during vibratory stimulation of the hindpaw. We then compared the strength and temporal structure of the afferent response measured under pentobarbital and isoflurane anesthesia.ResultsWe found that the strength and temporal structure of afferent responses were statistically equivalent whether these were evoked under isoflurane or pentobarbital.ConclusionsWe conclude that, if these two anesthetics have any effect on the responses of mechanoreceptive afferents, their effects are indistinguishable.
Novel study design to assess the utility of the copd assessment test in a primary care setting
Authors: Gruffydd-Jones Kevin , Marsden Helen , Holmes Steve , Kardos Peter , Escamilla Roger , Dal Negro Roberto , Roberts June , Nadeau Gilbert , Leather David , Jones Paul 
Published: May 2013

Abstract
The quality of a consultation provided by a physician can have a profound impact on the quality of care and patient engagement in treatment decisions. When the COPD Assessment Test (CAT) was developed, one of its aims was to aid the communication between physician and patient about the impact of COPD. We developed a novel study design to assess this in a primary care consultation.
Primary care physicians across five countries in Europe conducted videoed consultations with six standardised COPD patients (played by trained actors) which had patient-specific issues that the physician needed to identify through questioning. Half the physicians saw the patients with the completed CAT, and half without. Independent assessors scored the physicians on their ability to identify and address the patient-specific issues, review standard COPD aspects, their understanding of the case and their overall performance. This novel study design presented many challenges which needed to be addressed to achieve an acceptable level of robustness to assess the utility of the CAT. This paper discusses these challenges and the measures adopted to eliminate or minimise their impact on the study results.
Recruitment strategies and yields for the Pathobiology of Prediabetes in a Biracial Cohort: a prospective natural history study of incident dysglycemia
Authors: Ebenibo Sotonte , Edeoga Chimaroke , Ammons Ann , Egbuonu Nonso , Dagogo-Jack Samuel ,   the Pathobiology of Prediabetes in a Biracial Cohort (POP-ABC) Research Group
Published: May 2013

Abstract

Background
The Pathobiology of Prediabetes in A Biracial Cohort study is a prospective evaluation of the transition from normal to impaired glucose regulation among African American and Caucasian adults with parental type 2 diabetes. This report describes recruitment strategies and relative yields for the 376 enrolled subjects.

Methods
Recruitment occurred over 3.4 years, with clinical and metabolic assessments during 2.1-5.5 years of quarterly follow-up. The major recruitment sources were advertisements, community outreach, and clinical facilities. Advertisements included newspaper, television, radio, Internet, distributed brochures, utility bill inserts, and direct mailing. Community outreach included screening events during religious gatherings and health fairs, and referral by friends and families. The category of clinical facilities covered all subjects referred by health workers or recruited through area clinics and hospitals.

Results
57.7% of participants were African American and 42.3% were Caucasian; the mean age (± SD) was 44.2 ± 10.6 years, and ~70% were female. Advertisements yielded 52.4% of all participants, compared to 34.8% from community outreach and 12.8% from clinical facilities (P for trend < 0.0001). More Caucasians than African Americans cited advertising as the source of study information, whereas more African Americans than Caucasians cited community outreach. The accrual from clinical facilities was similar in both groups.

Conclusions
Advertisements and community outreach were robust recruitment sources for assembling a diverse longitudinal diabetes offspring cohort, but each had differential yields in African Americans and Caucasians. Thus, a multifaceted approach comprising passive and active components is needed to recruit a multiracial clinical research population.