bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity
Authors: Lee Kyung-Tai , Chung Won-Hyong , Lee Sung-Yeoun , Choi Jung-Woo , Kim Jiwoong , Lim Dajeong , Lee Seunghwan , Jang Gul-Won , Kim Bumsoo , Choy Yun Ho , Liao Xiaoping , Stothard Paul , Moore Stephen S , Lee Sang-Heon , Ahn Sungmin , Kim Namshin , Kim Tae-Hun 
Published: July 2013

AbstractBackgroundHanwoo (Korean cattle), which originated from natural crossbreeding between taurine and zebu cattle, migrated to the Korean peninsula through North China. Hanwoo were raised as draft animals until the 1970s without the introduction of foreign germplasm. Since 1979, Hanwoo has been bred as beef cattle. Genetic variation was analyzed by whole-genome deep resequencing of a Hanwoo bull. The Hanwoo genome was compared to that of two other breeds, Black Angus and Holstein, and genes within regions of homozygosity were investigated to elucidate the genetic and genomic characteristics of Hanwoo.ResultsThe Hanwoo bull genome was sequenced to 45.6-fold coverage using the ABI SOLiD system. In total, 4.7 million single-nucleotide polymorphisms and 0.4 million small indels were identified by comparison with the Btau4.0 reference assembly. Of the total number of SNPs and indels, 58% and 87%, respectively, were novel. The overall genotype concordance between the SNPs and BovineSNP50 BeadChip data was 96.4%. Of 1.6 million genetic differences in Hanwoo, approximately 25,000 non-synonymous SNPs, splice-site variants, and coding indels (NS/SS/Is) were detected in 8,360 genes. Among 1,045 genes containing reliable specific NS/SS/Is in Hanwoo, 109 genes contained more than one novel damaging NS/SS/I. Of the genes containing NS/SS/Is, 610 genes were assigned as trait-associated genes. Moreover, 16, 78, and 51 regions of homozygosity (ROHs) were detected in Hanwoo, Black Angus, and Holstein, respectively. ‘Regulation of actin filament length’ was revealed as a significant gene ontology term and 25 trait-associated genes for meat quality and disease resistance were found in 753 genes that resided in the ROHs of Hanwoo. In Hanwoo, 43 genes were located in common ROHs between whole-genome resequencing and SNP chips in BTA2, 10, and 13 coincided with quantitative trait loci for meat fat traits. In addition, the common ROHs in BTA2 and 16 were in agreement between Hanwoo and Black Angus.ConclusionsWe identified 4.7 million SNPs and 0.4 million small indels by whole-genome resequencing of a Hanwoo bull. Approximately 25,000 non-synonymous SNPs, splice-site variants, and coding indels (NS/SS/Is) were detected in 8,360 genes. Additionally, we found 25 trait-associated genes for meat quality and disease resistance among 753 genes that resided in the ROHs of Hanwoo. These findings will provide useful genomic information for identifying genes or casual mutations associated with economically important traits in cattle.
Stabilized homoserine o-succinyltransferases (MetA) or L-methionine partially recovers the growth defect in Escherichia coli lacking ATP-dependent proteases or the DnaK chaperone
Authors: Mordukhova Elena A , Kim Dooil , Pan Jae-Gu 
Published: July 2013

Abstract

Background
The growth of Escherichia coli at elevated temperatures is limited due to the inherent instability of homoserine o-succinyltransferase, MetA, which is the first enzyme in the methionine biosynthesis pathway. MetA is also unstable under other stressful conditions, such as weak organic acids and oxidative stress. The MetA protein unfolds, even at 25°C, forms considerable aggregates at 37°C and completely aggregates at 44°C.

Results
We extended the MetA mutation studies using a consensus concept based on statistics and sequence database analysis to predict the point mutations resulting in increased MetA stability. In this study, four single amino acid substitutions (Q96K, I124L, I229Y and F247Y) in MetA designed according to the consensus concept and using the I-mutant2.0 modeling tool conferred accelerated growth on the E. coli strain WE at 44°C. MetA mutants that enabled E. coli growth at higher temperatures did not display increased melting temperatures (T
m
) or enhanced catalytic activity but did show improved in vivo stability at mild (37°C) and elevated (44°C) temperatures. Notably, we observed that the stabilized MetA mutants partially recovered the growth defects of E. coli mutants in which ATP-dependent proteases or the DnaK chaperone was deleted. These results suggest that the impaired growth of these E. coli mutants primarily reflect the inherent instability of MetA and, thus, the methionine supply. As further evidence, the addition of methionine recovered most of the growth defects in mutants lacking either ATP-dependent proteases or the DnaK chaperone.

Conclusions
A collection of stable single-residue mutated MetA enzymes were constructed and investigated as background for engineering the stabilized mutants. In summary, the mutations in a single gene, metA, reframe the window of growth temperature in both normal and mutant E. coli strains.
Different culture media affect growth characteristics, surface marker distribution and chondrogenic differentiation of human bone marrow-derived mesenchymal stromal cells
Authors: Hagmann Sebastien , Moradi Babak , Frank Sebastian , Dreher Thomas , Kämmerer Peer Wolfgang , Richter Wiltrud , Gotterbarm Tobias 
Published: July 2013

AbstractBackgroundBone marrow-derived mesenchymal stromal cells (BM-MSCs) play an important role in modern tissue engineering, while distinct variations of culture media compositions and supplements have been reported. Because MSCs are heterogeneous regarding their regenerative potential and their surface markers, these parameters were compared in four widely used culture media compositions.MethodsMSCs were isolated from bone marrow and expanded in four established cell culture media. MSC yield/1000 MNCs, passage time and growth index were observed. In P4, typical MSC surface markers were analysed by fluorescence cytometry. Additionally, chondrogenic, adipogenic and osteogenic differentiation potential were evaluated.ResultsGrowth index and P0 cell yield varied importantly between the media. The different expansion media had a significant influence on the expression of CD10, CD90, CD105, CD140b CD146 and STRO-1. While no significant differences were observed regarding osteogenic and adipogenic differentiation, chondrogenic differentiation was superior in medium A as reflected by GAG/DNA content.ConclusionsThe choice of expansion medium can have a significant influence on growth, differentiation potential and surface marker expression of mesenchymal stromal cells, which is of fundamental importance for tissue engineering procedures.
A randomized controlled trial to assess the efficacy and cost-effectiveness of urinary catheters with silver alloy coating in spinal cord injured patients: trial protocol
Authors: Bonfill Xavier , Rigau David , Jáuregui-Abrisqueta María Luisa , Barrera Chacón Juana María , Salvador de la Barrera Sebastián , Alemán-Sánchez Carolina María , Bea-Muñoz Manuel , Moraleda Pérez Susana , Borau Duran Albert , Espinosa Quirós Juan Ramón , Ledesma Romano Luís , Esteban Fuertes Manuel , Araya Ignacio , Martínez-Zapata Ma José 
Published: July 2013

AbstractBackgroundPatients with non-acute spinal cord injury that carry indwelling urinary catheters have an increased risk of urinary tract infection (UTIs). Antiseptic Silver Alloy-Coated Silicone Urinary Catheters seems to be a promising intervention to reduce UTIs; however, actual evidence cannot be extrapolated to spinal cord injured patients. The aim of this trial is to make a comparison between the use of antiseptic silver alloy-coated silicone urinary catheters and the use of standard urinary catheters in spinal cord injured patients to prevent UTIs.Methods/DesignThe study will consist in an open, randomized, multicentre, and parallel clinical trial with blinded assessment. The study will include 742 spinal cord injured patients who require at least seven days of urethral catheterization as a method of bladder voiding. Participants will be online centrally randomized and allocated to one of the two study arms (silver alloy-coated or standard catheters). Catheters will be used for a maximum period of 30 days or removed earlier if the clinician considers it necessary. The main outcome will be the incidence of UTIs by the time of catheter removal or at day 30 after catheterization, the event that occurs first. Intention-to-treat analysis will be performed, as well as a primary analysis of all patients.DiscussionThe aim of this study is to assess whether silver alloy-coated silicone urinary catheters improve ITUs in spinal cord injured patients. ESCALE is intended to be the first study to evaluate the efficacy of the silver alloy-coated catheters in spinal cord injured patients.Trial registrationNCT01803919
Compound 49b protects against blast-induced retinal injury
Authors: Jiang Youde , Liu Li , Pagadala Jayaprakash , Miller Duane D , Steinle Jena J 
Published: July 2013

Abstract

Aim
To determine whether Compound 49b, a novel beta-adrenergic receptor agonist, can prevent increased inflammation and apoptosis in mice after exposure to ocular blast.

Methods
Eyes of C57/BL6 mice were exposed to a blast of air from a paintball gun at 26 psi (≈0.18 MPa). Eyes were collected 4 hours, 24 hours, and 72 hours after blast exposure. In a subset of mice, Compound 49b eyedrops (1 mM) were applied within 4 hours, 24 hours, or 72 hours of the blast. Three days after blast exposure, all mice were sacrificed. One eye was used to measure levels of retinal proteins (TNFα, IL-1β, Bax, BcL-xL, caspase 3, and cytochrome C). The other eye was used for TUNEL labeling of apoptotic cells, which were co-labeled with NeuN to stain for retinal ganglion cells.

Results
We found that ocular exposure to 26 psi air pressure led to a significant increase in levels of apoptotic and inflammatory mediators within 4 hours, which lasted throughout the period investigated. When Compound 49b was applied within 4 hours or 24 hours of blast injury, levels of apoptotic and inflammatory mediators were significantly reduced. Application of Compound 49b within 72 hours of blast injury reduced levels of inflammatory mediators, but not to untreated levels.

Conclusions
Ocular blast injury produces a significant increase in levels of key inflammatory and apoptotic markers in the retina as early as 4 hours after blast exposure. These levels are significantly reduced if a beta-adrenergic receptor agonist is applied within 24 hours of blast exposure. Data suggest that local application of beta-adrenergic receptor agonists may be beneficial to reduce inflammation and apoptosis.
Possible association between common variants of the phenylalanine hydroxylase (PAH) gene and memory performance in healthy adults
Authors: Teraishi Toshiya , Sasayama Daimei , Hori Hiroaki , Yamamoto Noriko , Fujii Takashi , Matsuo Junko , Nagashima Anna , Kinoshita Yukiko , Hattori Kotaro , Ota Miho , Fujii Sayaka , Kunugi Hiroshi 
Published: July 2013

Abstract

Background
Phenylalanine hydroxylase (PAH) is the enzyme that metabolizes phenylalanine, an essential amino acid required for catecholamine synthesis. Rare mutations in PAH are causal to phenylketonuria (PKU), an autosomal recessive disease characterized by neuropsychiatric symptoms including intellectual disability. We examined whether there is an association between common single nucleotide polymorphisms (SNPs) of PAH and memory performance in the Japanese population.

Methods
Subjects were 599 healthy adults (166 males and 433 females; mean age 43.8 ± 15.5 years). The Wechsler Memory Scale-Revised (WMS-R) was administered to all participants to assess memory performance. Genotyping was performed for 6 selected tagging SNPs of PAH (rs1722387, rs3817446, rs1718301, rs2037639, rs10860936 and rs11111419).

Results
Analyses of covariance controlling for sex and education years, indicated a significant association between a SNP (rs2037639) and age-corrected verbal memory index of WMS-R (nominal p = 0.0013) which remained significant after correction for multiple testing ( p = 0.0013 < 0.0017 = 0.05/30tests). Individuals with the GG genotype showed a significantly lower mean verbal memory score, compared with those individuals carrying the AA/AG genotype (106.0 ± 16.0 vs. 111.7 ± 13.4; p = 0.00099). A haplotype block containing two markers of rs2037639 and rs10860936 was associated with verbal memory index (permutation global p = 0.0091).

Conclusions
Our findings suggest that common genetic variations in PAH are associated with verbal memory in healthy adults. Unknown functional polymorphisms in PAH or those in other genes nearby might affect memory performance.
Traditional botanical knowledge of artisanal fishers in southern Brazil
Authors: Baptista Marcela Meneghetti , Ramos Marcelo Alves , de Albuquerque Ulysses Paulino , Coelho-de-Souza Gabriela , Ritter Mara Rejane 
Published: July 2013

AbstractBackgroundThis study characterized the botanical knowledge of artisanal fishers of the Lami community, Porto Alegre, southern Brazil based on answers to the following question: Is the local botanical knowledge of the artisanal fishers of the rural-urban district of Lami still active, even since the district’s insertion into the metropolitan region of Porto Alegre?MethodsThis region, which contains a mosaic of urban and rural areas, hosts the Lami Biological Reserve (LBR) and a community of 13 artisanal fisher families. Semi-structured interviews were conducted with 15 fishers, complemented by participatory observation techniques and free-lists; in these interviews, the species of plants used by the community and their indicated uses were identified.ResultsA total of 111 species belonging to 50 families were identified. No significant differences between the diversities of native and exotic species were found. Seven use categories were reported: medicinal (49%), human food (23.2%), fishing (12.3%), condiments (8%), firewood (5%), mystical purposes (1.45%), and animal food (0.72%). The medicinal species with the highest level of agreement regarding their main uses (AMUs) wereAloe arborescensMill., Plectranthus barbatusAndrews, Dodonaea viscosaJacq., Plectranthus ornatusCodd, Eugenia unifloraL., andFoeniculum vulgareMill. For illness and diseases, most plants were used for problems with the digestive system (20 species), followed by the respiratory system (16 species). This community possesses a wide botanical knowledge, especially of medicinal plants, comparable to observations made in other studies with fishing communities in coastal areas of the Atlantic Forest of Brazil.ConclusionsEthnobotanical studies in rural-urban areas contribute to preserving local knowledge and provide information that aids in conserving the remaining ecosystems in the region.
Analyses of chondrogenic induction of adipose mesenchymal stem cells by combined co-stimulation mediated by adenoviral gene transfer
Authors: Garza-Veloz Idalia , Romero-Diaz Viktor J , Martinez-Fierro Margarita L , Marino-Martinez Ivan A , Gonzalez-Rodriguez Manuel , Martinez-Rodriguez Herminia G , Espinoza-Juarez Marcela A , Bernal-Garza Dante A , Ortiz-Lopez Rocio , Rojas-Martinez Augusto 
Published: July 2013

Abstract
Introduction
Adipose-derived stem cells (ASCs) have the potential to differentiate into cartilage under stimulation with some reported growth and transcriptional factors, which may constitute an alternative for cartilage replacement approaches. In this study, we analyzed the in vitro chondrogenesis of ASCs transduced with adenoviral vectors encoding insulin-like growth factor-1 (IGF-1), transforming growth factor beta-1 (TGF-β1), fibroblast growth factor-2 (FGF-2), and sex-determining region Y-box 9 (SOX9) either alone or in combinations.

Methods
Aggregate cultures of characterized ovine ASCs were transduced with 100 multiplicity of infections of Ad.IGF-1, Ad.TGF-β1, Ad.FGF-2, and Ad.SOX9 alone or in combination. These were harvested at various time points for detection of cartilage-specific genes expression by quantitative real-time PCR or after 14 and 28 days for histologic and biochemical analyses detecting proteoglycans, collagens (II, I and X), and total sulfated glycosaminoglycan and collagen content, respectively.

Results
Expression analyses showed that co-expression of IGF-1 and FGF-2 resulted in higher significant expression levels of aggrecan, biglycan, cartilage matrix, proteoglycan, and collagen II (all P ≤0.001 at 28 days). Aggregates co-transduced with Ad.IGF-1/Ad.FGF-2 showed a selective expression of proteoglycans and collagen II, with limited expression of collagens I and × demonstrated by histological analyses, and had significantly greater glycosaminoglycan and collagen production than the positive control (P ≤0.001). Western blot analyses for this combination also demonstrated increased expression of collagen II, while expression of collagens I and × was undetectable and limited, respectively.

Conclusion
Combined overexpression of IGF-1/FGF-2 within ASCs enhances their chondrogenic differentiation inducing the expression of chondrogenic markers, suggesting that this combination is more beneficial than the other factors tested for the development of cell-based therapies for cartilage repair.
Migratory conventional dendritic cells in the induction of peripheral T cell tolerance
Authors: Broggi Achille , Zanoni Ivan , Granucci Francesca 
Published: July 2013

ABSTRACTConventional DCs are an extremely heterogeneous cell population that comprises several different subsets. A major distinction can be made between lymphoid-resident DCs that are present in the lymphoid tissues and the blood and migratory DCs that reside in the nonlymphoid tissues and migrate to the lymph nodes, both in homeostatic conditions and during the course of an infection. Migratory DCs differ from tissue to tissue but share the unique ability to transport antigens to the draining lymph nodes—in particular, tissue-restricted antigens in homeostatic conditions and microbial antigens after an infection. Recently, steady-state migratory DCs have gained much attention after the discovery of their high tolerogenic potential. The purpose of this review is to give a picture of the recent finding regarding steady-state migratory DCs with particular interest in their role in inducing T cell tolerance.
Rates and Outcomes of Follicular Lymphoma Transformation in the Immunochemotherapy Era: A Report From the University of Iowa/Mayo Clinic Specialized Program of Research Excellence Molecular Epidemiology Resource
Authors: Link Brian K. , Maurer Matthew J. , Nowakowski Grzegorz S. , Ansell Stephen M. , Macon William R. , Syrbu Sergei I. , Slager Susan L. , Thompson Carrie A. , Inwards David J. , Johnston Patrick B. , Colgan Joseph P. , Witzig Thomas E. , Habermann Thomas M. , Cerhan James R. 
Published: July 2013

Purpose This study sought to characterize transformation incidence and outcome for patients with follicular lymphoma (FL) in a prospective observational series begun after diffusion of rituximab use. Patients and Methods Patients with newly diagnosed FL were prospectively enrolled onto the University of Iowa/Mayo Clinic Specialized Program of Research Excellence Molecular Epidemiology Resource from 2002 to 2009. Patients were actively followed for re-treatment, clinical or pathologic transformation, and death. Risk of transformation was analyzed via time to transformation by using death as a competing risk. Results In all, there were 631 patients with newly diagnosed grade 1 to 3a FL who had a median age at enrollment of 60 years. At a median follow-up of 60 months (range, 11 to 110 months), 79 patients had died, and 60 patients developed transformed lymphoma, of which 51 were biopsy proven. The overall transformation rate at 5 years was 10.7%, with an estimated rate of 2% per year. Increased lactate dehydrogenase was associated with increased risk of transformation. Transformation rate at 5 years was highest in patients who were initially observed and lowest in patients who initially received rituximab monotherapy (14.4% v 3.2%; P = .021). Median overall survival following transformation was 50 months and was superior in patients with transformation greater than 18 months after FL diagnosis compared with patients with earlier transformation (5-year overall survival, 66% v 22%; P < .001). Conclusion Follicular transformation rates in the immunochemotherapy era are similar to risk of death without transformation and may be lower than reported in older series. Post-transformation prognosis is substantially better than described in older series. Initial management strategies may influence the risk of transformation.
High Procedure Volume Is Strongly Associated With Improved Survival After Lung Cancer Surgery
Authors: Lüchtenborg Margreet , Riaz Sharma P. , Coupland Victoria H. , Lim Eric , Jakobsen Erik , Krasnik Mark , Page Richard , Lind Michael J. , Peake Michael D. , Møller Henrik 
Published: July 2013

Purpose Studies have reported an association between hospital volume and survival for non–small-cell lung cancer (NSCLC). We explored this association in England, accounting for case mix and propensity to resect. Methods We analyzed data on 134,293 patients with NSCLC diagnosed in England between 2004 and 2008, of whom 12,862 (9.6%) underwent surgical resection. Hospital volume was defined according to number of patients with resected lung cancer in each hospital in each year of diagnosis. We calculated hazard ratios (HRs) for death in three predefined periods according to hospital volume, sex, age, socioeconomic deprivation, comorbidity, and propensity to resect. Results There was increased survival in hospitals performing > 150 surgical resections compared with those carrying out < 70 (HR, 0.78; 95% CI, 0.67 to 0.90; Ptrend < .01). The association between hospital volume and survival was present in all three periods of follow-up, but the magnitude of association was greatest in the early postoperative period. Conclusion High-volume hospitals have higher resection rates and perform surgery among patients who are older, have lower socioeconomic status, and have more comorbidities; despite this, they achieve better survival, most notably in the early postoperative period.