bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomass accumulation during reed encroachment reduces efficiency of restoration of Baltic coastal grasslands
Authors: Sammul Marek , Kauer Karin , Köster Tiina 
Published: November 2011

AbstractQuestionTo what extent is restoration of vegetation in coastal grasslands delayed by accumulation of nutrients after abandonment of traditional management and subsequent reed encroachment? How does nutrient flow in the plant–soil system react to reintroduction of grazing?LocationCoast of Baltic Sea, western Estonia.MethodsAbandoned, continuously managed and restored coastal meadows were selected in four different study regions and their vegetation composition sampled. Nitrogen, P, K, Na, Ca and Mg concentrations and C/N ratios were determined in both vegetation and soil. Differences between management groups were evaluated.ResultsComparison among different management groups revealed several differences in both relative and total amount of nutrients in soil and vegetation. Most soil properties of restored sites were similar to those in abandoned sites. Carbon stock in the soil profile doubled after abandonment, total N concentration in the top soil layer increased while plant available P concentration decreased. The phytomass and chemical composition of phytomass rapidly changed back to a ‘normal’ level after restoration. Species composition remained different, but species typical of coastal grasslands were present in restored sites. There was a strong site specificity in the results.ConclusionsRe‐establishment of grazing had a rapid impact on plant biomass of coastal grasslands. Species composition responded more slowly, but target species returned relatively quickly. Slow recovery of soil properties, however, means that the results of restoration may be fragile and return of tall‐growth vegetation is very probable if managent intensity declines. Long restoration periods should be planned to reach pre‐abandonment environmental conditions when using non‐destructive restoration methods.
Efficacy of human chorionic gonadotropin to induce ovulation in the mare, when associated with a single dose of dexamethasone administered at breeding time
Authors: BUCCA S. , CARLI A. 
Published: November 2011

SummaryReasons for performing study: Human chorionic gonadotropin (hCG) and dexamethasone have a role in the reproductive management protocols of mares susceptible to persistent mating‐induced endometritis (PMIE). However, it is possible that there is interference between these 2 drugs.Objectives: The objective of this retrospective study was to determine the efficacy of hCG to induce ovulation in mares treated with dexamethasone at breeding time.Methods: Medical records from 152 mares and 223 cycles were analysed. In 113 cycles, mares susceptible to PMIE were treated with 1500 iu hCG and a single dose of 50 mg dexamethasone, 110 cycles were used as controls and subsequent ovulation was assessed ultrasonographically and compared.Results: Dexamethasone did not inhibit ovulation in mares susceptible to PMIE.Conclusions and potential relevance: Multiple administrations of dexamethasone to mares in early oestrus have induced ovulation failure. However, a single dose of dexamethasone, administered at breeding time, has been used as an effective modulator of PMIE in susceptible mares and does not interfere with efficacy of hCG to induce ovulation.
Sporting activity following colic surgery in horses: A retrospective study
Authors: CHRISTOPHERSEN M. T. , TNIBAR A. , PIHL T. H. , ANDERSEN P. H. , EKSTRØM C. T. 
Published: November 2011

SummaryReasons for performing study: There is a paucity of studies addressing sporting activity and horse owners' satisfaction after horses have undergone colic surgery.Objectives: To determine 1) survival rate after colic surgery, 2) prevalence of horses returning to, or starting, sporting activities and 3) assess the owners' satisfaction regarding colic surgery.Methods: Cases that underwent exploratory celiotomy for colic between January 2005 and August 2010 were reviewed. All horses that had one or more celiotomies and were discharged after colic surgery were included in a telephone questionnaire survey. Only horses that survived at least 6 months after colic surgery were included in the sporting activity analysis. Data extracted from the records included case details, intra‐operative diagnosis and surgical treatment. Information from a telephone questionnaire included the horses' post surgical details (horse alive or subjected to euthanasia, post operative complications, pre‐ and post surgical use, return to sporting activity, sporting performance, behavioural changes, management changes and recommendation by owner for colic surgery). A logistic regression model was used for the statistical analysis of post hospitalisation performance and an ordinal regression model used for analysis of post colic complications and of owner's recommendation of surgery. A Kaplan‐Meier survival curve was computed to show survival of horses discharged after colic surgery.Results: The survival rates (%) at 6, 12, 24, 36, 48 and 60 months were 95.3, 86.6, 80.9, 76.9, 62.1 and 57.6, respectively. A large majority of horses (86.1%) resumed or started sporting activities after colic surgery. The proportion of horses that the owners believed to achieve the same or better performance after surgery was 83.5%. In 89.9% of the cases, owners stated that they would recommend colic surgery.Conclusions: Horses discharged after colic surgery had a high long‐term survival rate. A high prevalence of horses resumed or started sporting activities with a high proportion of horses at their presurgical performance level. The large majority of owners of discharged horses were satisfied with colic surgery performed on their horses.
Dynamic respiratory videoendoscopy in ridden sport horses: Effect of head flexion, riding and airway inflammation in 129 cases
Authors: VAN ERCK E. 
Published: November 2011

SummaryReasons for performing study:Dynamic upper airway obstruction (UAO) is a cause of respiratory noise and sometimes poor performance in sport horses. Riding, head flexion and airway inflammation may impact upper respiratory tract stability during exercise.Objectives:To evaluate upper airway mechanical behaviour in ridden sport horses using overground endoscopy and the effect of head flexion, rider intervention and underlying airway inflammation on the pharynx and larynx.Methods:Resting and exercising videoendoscopic recordings during ridden exercise were obtained in 129 sport horses referred mainly for respiratory noise, poor performance or routine evaluation. The rider modified poll flexion and way of riding during the test and associated changes in UAO were recorded. Presence of upper and lower airway inflammation was also assessed.Results:Dynamic UAO was diagnosed in 91% (64/70) of the horses referred for respiratory noise and in 71% (29/41) of horses referred for poor performance. Pharyngeal instability was the most frequently diagnosed problem. However, differences were observed between dressage horses and showjumpers. Rider interaction and head flexion exacerbated upper airway instability and promoted the occurrence of complex UAO. Both lower airway inflammation and pharyngeal lymphoid hyperplasia were associated with pharyngeal instability, but not with any other UAO.Conclusions:Rider intervention during ridden exercise (i.e. the various movements a horse might be asked to perform) influences upper airway morphology and function and, in cases of upper airway dynamic obstruction, can contribute to increasing laryngeal and/or pharyngeal instability in sport horses.Potential relevance:As these are changes that would not usually be seen with treadmill videoendoscopy, ridden videoendoscopy should be the preferred method for evaluation of the upper airway in sport horses.
Genome Sequencing Reveals a Phage in Helicobacter pylori
Authors: Lehours Philippe , Vale Filipa F. , Bjursell Magnus K. , Melefors Ojar , Advani Reza , Glavas Steve , Guegueniat Julia , Gontier Etienne , Lacomme Sabrina , Alves Matos António , Menard Armelle , Mégraud Francis , Engstrand Lars , Andersson Anders F. 
Published: November 2011

ABSTRACTHelicobacter pylorichronically infects the gastric mucosa in more than half of the human population; in a subset of this population, its presence is associated with development of severe disease, such as gastric cancer. Genomic analysis of several strains has revealed an extensiveH. pyloripan-genome, likely to grow as more genomes are sampled. Here we describe the draft genome sequence (63 contigs; 26× mean coverage) ofH. pyloristrain B45, isolated from a patient with gastric mucosa-associated lymphoid tissue (MALT) lymphoma. The major finding was a 24.6-kb prophage integrated in the bacterial genome. The prophage shares most of its genes (22/27) with prophage region II ofHelicobacter acinonychisstrain Sheeba. After UV treatment of liquid cultures, circular DNA carrying the prophage integrase gene could be detected, and intracellular tailed phage-like particles were observed inH. pyloricells by transmission electron microscopy, indicating that phage production can be induced from the prophage. PCR amplification and sequencing of the integrase gene from 341H. pyloristrains from different geographic regions revealed a high prevalence of the prophage (21.4%). Phylogenetic reconstruction showed four distinct clusters in the integrase gene, three of which tended to be specific for geographic regions. Our study implies that phages may play important roles in the ecology and evolution ofH. pylori.IMPORTANCEHelicobacter pylorichronically infects the gastric mucosa in more than half of the human population, and while most of the infected individuals do not develop disease,H. pyloriinfection doubles the risk of developing gastric cancer. An abundance and diversity of viruses (phages) infect microbial populations in most environments and are important mediators of microbial diversity. Our finding of a 24.6-kb prophage integrated inside anH. pylorigenome and the observation of circular integrase gene-containing DNA and phage-like particles inside cells upon UV treatment demonstrate that we have discovered a viableH. pyloriphage. The additional finding of integrase genes in a large proportion of screened isolates of diverse geographic origins indicates that the prevalence of prophages may have been underestimated inH. pylori. Since phages are important drivers of microbial evolution, the discovery should be important for understanding and predicting genetic diversity inH. pylori.
Identification of Cancer Patients with Lynch Syndrome: Clinically Significant Discordances and Problems in Tissue-Based Mismatch Repair Testing
Authors: Bartley Angela N. , Luthra Rajyalakshmi , Saraiya Devki S. , Urbauer Diana L. , Broaddus Russell R. 
Published: November 2011

Abstract
Tissue-based microsatellite instability (MSI) analysis and immunohistochemistry for DNA mismatch repair proteins are accepted screening tools to evaluate patients with cancer for Lynch syndrome. These laboratory analyses are thus important tools in cancer prevention. Quality assurance review was conducted to identify test discordances and problems. These results were then analyzed in conjunction with genetic testing outcomes. Six hundred and forty-six consecutive tumors from 2002 to 2010 were examined. MSI-low tumors were excluded so that 591 tumors comprised the final analyses. Discordance was defined as a discrepancy between immunohistochemical and MSI analysis. Problem was defined as indeterminate or questionable immunohistochemical or MSI results. All results and clinical and family histories were centrally reviewed by two pathologists and one genetics counselor. Discordances and problems were identified in 23 of 591 (3.9%) of the tumors. Twelve of 102 MSI-high carcinomas (11.8%) and one of 489 microsatellite stable tumors had discordant immunohistochemistry. Of these 13 tumors, 11 were from patients who had personal and/or family cancer histories concerning for a germline mismatch repair gene mutation. In addition to discordances, 10 tumors with problematic immunohistochemical profiles were identified. Accurate evaluation of MSI was possible in all tumors. In summary, concordance between immunohistochemistry and MSI was high, particularly for tumors that are microsatellite stable. Greater frequency of test discordance was identified in the tumors that were MSI-high. Thus, a major consequence of the use of immunohistochemistry by itself as a screen is the failure to identify colorectal and endometrial cancer patients who likely have Lynch syndrome. Cancer Prev Res; 5(2); 320–7. ©2011 AACR.
Organ Specificity of the Bladder Carcinogen 4-Aminobiphenyl in Inducing DNA Damage and Mutation in Mice
Authors: Yoon Jae-In , Kim Sang-In , Tommasi Stella , Besaratinia Ahmad 
Published: November 2011

Abstract
Aromatic amines are a widespread class of environmental contaminants present in various occupational settings and tobacco smoke. Exposure to aromatic amines is a major risk factor for bladder cancer development. The etiologic involvement of aromatic amines in the genesis of bladder cancer is attributable to their ability to form DNA adducts, which upon eluding repair and causing mispairing during replication, may initiate mutagenesis. We have investigated the induction of DNA adducts in relation to mutagenesis in bladder and various nontarget organs of transgenic Big Blue mice treated weekly (i.p.) with a representative aromatic amine compound, 4-aminobiphenyl (4-ABP), for six weeks, followed by a six-week recovery period. We show an organ-specificity of 4-ABP in inducing repair-resistant DNA adducts in bladder, kidney, and liver of carcinogen-treated animals, which accords with the bioactivation pathway of this chemical in the respective organs. In confirmation, we show a predominant and sustained mutagenic effect of 4-ABP in bladder, and much weaker but significant mutagenicity of 4-ABP in the kidney and liver of carcinogen-treated mice, as reflected by the elevation of background cII mutant frequency in the respective organs. The spectrum of mutations produced in bladder of 4-ABP–treated mice matches the known mutagenic properties of 4-ABP–DNA adducts, as verified by the preponderance of induced mutations occurring at G:C base pairs (82.9%), with the vast majority being G:C→T:A transversions (47.1%). Our data support a possible etiologic role of 4-ABP in bladder carcinogenesis and provide a mechanistic view on how DNA adduct–driven mutagenesis, specifically targeted to bladder urothelium, may account for organ-specific tumorigenicity of this chemical. Cancer Prev Res; 5(2); 299–308. ©2011 AACR.
Trapped Core Formation within a Shoaling Nonlinear Internal Wave
Authors: Lien Ren-Chieh , D’Asaro Eric A. , Henyey Frank , Chang Ming-Huei , Tang Tswen-Yung , Yang Yiing-Jang 
Published: November 2011

Abstract
Large-amplitude (100–200 m) nonlinear internal waves (NLIWs) were observed on the continental slope in the northern South China Sea nearly diurnally during the spring tide. The evolution of one NLIW as it propagated up the continental slope is described. The NLIW arrived at the slope as a nearly steady-state solitary depression wave. As it propagated up the slope, the wave propagation speed C decreased dramatically from 2 to 1.3 m s−1, while the maximum along-wave current speed Umax remained constant at 2 m s−1. As Umax exceeded C, the NLIW reached its breaking limit and formed a subsurface trapped core with closed streamlines in the coordinate frame of the propagating wave. The trapped core consisted of two counter-rotating vortices feeding a jet within the core. It was highly turbulent with 10–50-m density overturnings caused by the vortices acting on the background stratification, with an estimated turbulent kinetic energy dissipation rate of O(10−4) W kg−1 and an eddy diffusivity of O(10−1) m2 s−1. The core mixed continually with the surrounding water and created a wake of mixed water, observed as an isopycnal salinity anomaly. As the trapped core formed, the NLIW became unsteady and dissipative and broke into a large primary wave and a smaller wave. Although shoaling alone can lead to wave fission, the authors hypothesize that the wave breaking and the trapped core evolution may further trigger the fission process. These processes of wave fission and dissipation continued so that the NLIW evolved from a single deep-water solitary wave as it approached the continental slope into a train of smaller waves on the Dongsha Plateau. Observed properties, including wave width, amplitude, and propagation speed, are reasonably predicted by a fully nonlinear steady-state internal wave model, with better agreement in the deeper water. The agreement of observed and modeled propagation speed is improved when a reasonable vertical profile of background current is included in the model.
Parameterization of the Sedimentation of Raindrops with Finite Maximum Diameter
Authors: Ziemer Corinna , Wacker Ulrike 
Published: November 2011

In common cloud microphysics parameterization models, the prognostic variables are one to three moments of the drop size distribution function. They are defined as integrals of the distribution function over a drop diameter ranging from zero to infinity. Recent works (by several authors) on a one-dimensional sedimentation problem have pointed out that there are problems with those parameterization models caused by the differing average propagation speeds of the prognostic moments. In this study, the authors propose to define the moments over a finite drop diameter range of [0, Dmax], corresponding to the limitation of drop size in nature. The ratios of the average propagation speeds are thereby also reduced. In the new model, mean particle masses above a certain threshold depending on Dmax lead to mathematical problems, which are solved by a mirroring technique. An identical, one-dimensional sedimentation problem for two moments is used to analyze the sensitivity of the results to the maximum drop diameter and to compare the proposed method with recent works. It turns out that Dmax has a systematic influence on the model’s results. A small, finite maximum drop diameter leads to a better representation of the moments and the mean drop mass when compared to the detailed microphysical model.
Risk Factors for Anterior Cruciate Ligament Injury
Authors: Smith Helen C. , Vacek Pamela , Johnson Robert J. , Slauterbeck James R. , Hashemi Javad , Shultz Sandra , Beynnon Bruce D. 
Published: November 2011

Context: Injuries to the anterior cruciate ligament (ACL) are immediately disabling and are associated with long-term consequences, such as posttraumatic osteoarthritis. It is important to have a comprehensive understanding of all possible risk factors for ACL injury to identify individuals who are at risk for future injuries and to provide an appropriate level of counseling and programs for prevention. Objective: This review, part 2 of a 2-part series, highlights what is known and still unknown regarding hormonal, genetic, cognitive function, previous injury, and extrinsic risk factors for ACL injury. Data Sources: Studies were identified from MEDLINE (1951–March 2011) using the MeSH terms anterior cruciate ligament, knee injury, and risk factors. The bibliographies of relevant articles and reviews were cross-referenced to complete the search. Study Selection: Prognostic case-control and prospective cohort study designs to evaluate risk factors for ACL injury were included in this review. Results: A total of 50 case-control and prospective cohort articles were included in parts 1 and 2. Twenty-one focused on hormonal, genetic, cognitive function, previous injury, and extrinsic risk factors. Conclusions: Several risk factors are associated with increased risk of suffering ACL injury—such as female sex, prior reconstruction of the ACL, and familial predisposition. These risk factors most likely act in combination with the anatomic factors reviewed in part 1 of this series to influence the risk of suffering ACL injury.
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling
Authors: Rousseau Mathieu , Fraser James , Ferraiuolo Maria A , Dostie Josée , Blanchette Mathieu 
Published: November 2011

Abstract

Background
Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mechanism of gene expression regulation. Chromosome Conformation Capture Carbon Copy (5C) and its variant Hi-C are techniques used to measure the interaction frequency (IF) between specific regions of the genome. Our goal is to use the IF data generated by these experiments to computationally model and analyze three-dimensional chromatin organization.

Results
We formulate a probabilistic model linking 5C/Hi-C data to physical distances and describe a Markov chain Monte Carlo (MCMC) approach called MCMC5C to generate a representative sample from the posterior distribution over structures from IF data. Structures produced from parallel MCMC runs on the same dataset demonstrate that our MCMC method mixes quickly and is able to sample from the posterior distribution of structures and find subclasses of structures. Structural properties (base looping, condensation, and local density) were defined and their distribution measured across the ensembles of structures generated. We applied these methods to a biological model of human myelomonocyte cellular differentiation and identified distinct chromatin conformation signatures (CCSs) corresponding to each of the cellular states. We also demonstrate the ability of our method to run on Hi-C data and produce a model of human chromosome 14 at 1Mb resolution that is consistent with previously observed structural properties as measured by 3D-FISH.

Conclusions
We believe that tools like MCMC5C are essential for the reliable analysis of data from the 3C-derived techniques such as 5C and Hi-C. By integrating complex, high-dimensional and noisy datasets into an easy to interpret ensemble of three-dimensional conformations, MCMC5C allows researchers to reliably interpret the result of their assay and contrast conformations under different conditions.

Availability

http://Dostielab.biochem.mcgill.ca