bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examination and Treatment of Hamstring Related Injuries
Authors: Sherry Marc 
Published: December 2011

Context: There is a wide spectrum of hamstring-related injuries that can occur in the athlete. Accurate diagnosis is imperative to prevent delayed return to sport, injury recurrence, and accurate clinical decision making regarding the most efficacious treatment. Evidence Acquisition: This review highlights current evidence related to the diagnosis and treatment of hamstring-related injuries in athletes. Data sources were limited to peer-reviewed publications indexed in MEDLINE from 1988 through May 2011. Results: An accurate diagnostic process for athletes with posterior thigh–related complaints should include a detailed and discriminative history, followed by a thorough clinical examination. Diagnostic imaging should be utilized when considering hamstring avulsion or ischial apophyseal avulsion. Diagnostic imaging may also be needed to further define the cause of referred posterior thigh pain. Conclusions: Differentiating acute hamstring strains, hamstring tendon avulsions, ischial apophyseal avulsions, proximal hamstring tendinopathies, and referred posterior thigh pain is critical in determining the most appropriate treatment and expediting safe return to play.
Anterior Cruciate Ligament Injury Prevention Training in Female Athletes
Authors: Noyes Frank R. , Barber Westin Sue D. 
Published: December 2011

Context: Many anterior cruciate ligament (ACL) injury prevention training programs have been published, but few have assessed the effects of training on both ACL injury rates and athletic performance tests. Objective: To determine if ACL injury prevention programs have a positive influence on both injury rates and athletic performance tests in female athletes. Data sources: In August 2011, a search was conducted (1995–August 2011) of the PubMed, Science Direct, and CINAHL databases. Study selection: Selected studies determined the effect of ACL intervention training programs on ACL incidence rates (determined by athlete-exposures) and athletic performance tests, such as isokinetic strength, vertical jump height, speed, agility, and dynamic balance. Because no single article contained both criteria, investigations were cross-referenced to obtain data on both factors from the same training programs. Data extraction: The authors reviewed the selected studies for cohort population numbers, age, sports, duration of study, program components, duration of training, number of athlete-exposures, ACL injury incidence rates, and results of athletic performance tests. Results: Initially, 57 studies were identified that described 42 ACL injury prevention training programs. Of these, 17 studies that investigated 5 programs met the inclusion criteria. Two programs significantly reduced ACL injury rates and improved athletic performance tests: Sportsmetrics and the Prevent Injury and Enhance Performance program (PEP). Sportsmetrics produced significant increases in lower extremity and abdominal strength, vertical jump height, estimated maximal aerobic power, speed, and agility. Prevent Injury and Enhance Performance significantly improved isokinetic knee flexion strength but did not improve vertical jump height, speed, or agility. The other 3 programs (Myklebust, the “11,” and Knee Ligament Injury Prevention) did not improve both ACL injury rates and athletic performance tests. Conclusions: Only the Sportsmetrics and PEP ACL intervention training programs had a positive influence on injury reduction and athletic performance tests.
sPLA2-V inhibits EPCR anticoagulant and antiapoptotic properties by accommodating lysophosphatidylcholine or PAF in the hydrophobic groove
Authors: López-Sagaseta Jacinto , Puy Cristina , Tamayo Ibai , Allende Mikel , Cerveró Jorge , Velasco Susana E. , Esmon Charles T. , Montes Ramón , Hermida José 
Published: December 2011

AbstractThe endothelial protein C receptor (EPCR) plays an important role in cardiovascular disease by binding protein C/activated protein C (APC). EPCR structure contains a hydrophobic groove filled with an unknown phospholipid needed to perform its function. It has not been established whether lipid exchange takes place in EPCR as a regulatory mechanism of its activity. Our objective was to identify this phospholipid and to explore the possibility of lipid exchange as a regulatory mechanism of EPCR activity driven by the endothelially expressed secretory group V phospholipase A2 (sPLA2-V). We identified phosphatidylcholine (PCh) as the major phospholipid bound to human soluble EPCR (sEPCR). PCh in EPCR could be exchanged for lysophosphatidylcholine (lysoPCh) and platelet activating factor (PAF). Remarkably, lysoPCh and PAF impaired the protein C binding ability of sEPCR. Inhibition of sPLA2-V, responsible for lysoPCh and PAF generation, improved APC binding to endothelial cells. EPCR-dependent protein C activation and APC antiapoptotic effect were thus significantly enhanced. In contrast, endothelial cell supplementation with sPLA2-V inhibited both APC generation and its antiapoptotic effects. We conclude that APC generation and function can be modulated by changes in phospholipid occupancy of its endothelial cell receptor.
Partial plasma cell differentiation as a mechanism of lost major histocompatibility complex class II expression in diffuse large B-cell lymphoma
Authors: Wilkinson Sarah T. , Vanpatten Kristie A. , Fernandez Diane R. , Brunhoeber Patrick , Garsha Karl E. , Glinsmann-Gibson Betty J. , Grogan Thomas M. , Teruya-Feldstein Julie , Rimsza Lisa M. 
Published: December 2011

AbstractLoss of major histocompatibility complex class II (MHC II) expression is associated with poor patient outcome in diffuse large B-cell lymphoma (DLBCL). As MHC II molecules are lost with plasmacytic differentiation in normal cells, we asked whether MHC II loss in DLBCL is associated with an altered differentiation state. We used gene expression profiling, quantum dots, and immunohistochemistry to study the relationship between MHC II and plasma cell markers in DLBCL and plasmablastic lymphoma (PBL). Results demonstrate that MHC II(−) DLBCL immunophenotypically overlap with PBL and demonstrate an inverse correlation between MHC II and plasma cell markers MUM1, PRDM1/Blimp1, and XBP1s. In addition, MHC II expression is significantly higher in germinal center-DLBCL than activated B cell-DLBCL. A minor subset of cases with an unusual pattern of mislocalized punctate MHC II staining and intermediate levels of mRNA is also described. Finally, we show that PBL is negative for MHC II. The results imply a spectrum of MHC II expression that is more frequently diminished in tumors derived from B cells at the later stages of differentiation (with complete loss in PBL). Our observations provide a possible unifying concept that may contribute to the poor outcome reported in all MHC II(−) B-cell tumors.
MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites
Authors: Kotera Masaaki , Tokimatsu Toshiaki , Kanehisa Minoru , Goto Susumu 
Published: December 2011

Abstract

Background
In contrast to the increasing number of the successful genome projects, there still remain many orphan metabolites for which their synthesis processes are unknown. Metabolites, including these orphan metabolites, can be classified into groups that share the same core substructures, originated from the same biosynthetic pathways. It is known that many metabolites are synthesized by adding up building blocks to existing metabolites. Therefore, it is proposed that, for any given group of metabolites, finding the core substructure and the branched substructures can help predict their biosynthetic pathway. There already have been many reports on the multiple graph alignment techniques to find the conserved chemical substructures in relatively small molecules. However, they are optimized for ligand binding and are not suitable for metabolomic studies.

Results
We developed an efficient multiple graph alignment method named as MUCHA (Multiple Chemical Alignment), specialized for finding metabolic building blocks. This method showed the strength in finding metabolic building blocks with preserving the relative positions among the substructures, which is not achieved by simply applying the frequent graph mining techniques. Compared with the combined pairwise alignments, this proposed MUCHA method generally reduced computational costs with improving the quality of the alignment.

Conclusions
MUCHA successfully find building blocks of secondary metabolites, and has a potential to complement to other existing methods to reconstruct metabolic networks using reaction patterns.
Integrative analysis workflow for the structural and functional classification of C-type lectins
Authors: Koh Geoffrey , Low Ariana , Poh Daren , Yao Yujian , Ng Say Kong , Wong Victor Vai Tak , Vagenende Vincent , Lam Kong-Peng , Lee Dong-Yup 
Published: December 2011

Abstract

Background
It is important to understand the roles of C-type lectins in the immune system due to their ubiquity and diverse range of functions in animal cells. It has been observed that currently confirmed C-type lectins share a highly conserved domain known as the C-type carbohydrate recognition domain (CRD). Using the sequence profile of the CRD, an increasing number of putative C-type lectins have been identified. Hence, it is highly needed to develop a systematic framework that enables us to elucidate their carbohydrate (glycan) recognition function, and discover their physiological and pathological roles.

Results
Presented herein is an integrated workflow for characterizing the sequence and structural features of novel C-type lectins. Our workflow utilizes web-based queries and available software suites to annotate features that can be found on the C-type lectin, given its amino acid sequence. At the same time, it incorporates modeling and analysis of glycans - a major class of ligands that interact with C-type lectins. Thereafter, the results are analyzed together with context-specific knowledge to filter off unlikely predictions. This allows researchers to design their subsequent experiments to confirm the functions of the C-type lectins in a systematic manner.

Conclusions
The efficacy and usefulness of our proposed immunoinformatics workflow was demonstrated by applying our integrated workflow to a novel C-type lectin -CLEC17A - and we report some of its possible functions that warrants further validation through wet-lab experiments.
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information
Authors: Suzuki Shin , Yasuda Tomohiro , Shiraishi Yuichi , Miyano Satoru , Nagasaki Masao 
Published: December 2011

Abstract

Background
Structural variations (SVs) change the structure of the genome and are therefore the causes of various diseases. Next-generation sequencing allows us to obtain a multitude of sequence data, some of which can be used to infer the position of SVs.

Methods
We developed a new method and implementation named ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data – SV lengths, read lengths, and the depth of coverage of short reads – with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome. For comparison, we selected BreakDancer, CNVnator and Pindel, each of which adopts a different approach to detect SVs, e.g. discordant pair approach, depth of coverage approach and split read approach, respectively.

Results
Our method outperformed BreakDancer and CNVnator in both discovering rate and call accuracy in any type of SV. Pindel offered a similar performance as our method, but our method crucially outperformed for detecting small duplications. From our experiments, ClipCrop infer reliable SVs for the data set with more than 50 bases read lengths and 20x depth of coverage, both of which are reasonable values in current NGS data set.

Conclusions
ClipCrop can detect SVs with higher discovering rate and call accuracy than any other tool in our simulation data set.
A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information
Authors: Dai Tianli , Liu Qi , Gao Jun , Cao Zhiwei , Zhu Ruixin 
Published: December 2011

Abstract

Background
Prediction of protein-ligand binding sites is an important issue for protein function annotation and structure-based drug design. Nowadays, although many computational methods for ligand-binding prediction have been developed, there is still a demanding to improve the prediction accuracy and efficiency. In addition, most of these methods are purely geometry-based, if the prediction methods improvement could be succeeded by integrating physicochemical or sequence properties of protein-ligand binding, it may also be more helpful to address the biological question in such studies.

Results
In our study, in order to investigate the contribution of sequence conservation in binding sites prediction and to make up the insufficiencies in purely geometry based methods, a simple yet efficient protein-binding sites prediction algorithm is presented, based on the geometry-based cavity identification integrated with sequence conservation information. Our method was compared with the other three classical tools: PocketPicker, SURFNET, and PASS, and evaluated on an existing comprehensive dataset of 210 non-redundant protein-ligand complexes. The results demonstrate that our approach correctly predicted the binding sites in 59% and 75% of cases among the TOP1 candidates and TOP3 candidates in the ranking list, respectively, which performs better than those of SURFNET and PASS, and achieves generally a slight better performance with PocketPicker.

Conclusions
Our work has successfully indicated the importance of the sequence conservation information in binding sites prediction as well as provided a more accurate way for binding sites identification.
Effect modification of environmental factors on influenza-associated mortality: a time-series study in two Chinese cities
Authors: Yang Lin , Chen Ping Yan , He Jian Feng , Chan King Pan , Ou Chun Quan , Deng Ai Ping , Malik Peiris JS , Wong Chit Ming 
Published: December 2011

Abstract

Background
Environmental factors have been associated with transmission and survival of influenza viruses but no studies have ever explored the role of environmental factors on severity of influenza infection.

Methods
We applied a Poisson regression model to the mortality data of two Chinese metropolitan cities located within the subtropical zone, to calculate the influenza associated excess mortality risks during the periods with different levels of temperature and humidity.

Results
The results showed that high absolute humidity (measured by vapor pressure) was significantly (p < 0.05) associated with increased risks of all-cause and cardiorespiratory deaths, but not with increased risks of pneumonia and influenza deaths. The association between absolute humidity and mortality risks was found consistent among the two cities. An increasing pattern of influenza associated mortality risks was also found across the strata of low to high relative humidity, but the results were less consistent for temperature.

Conclusions
These findings highlight the need for people with chronic cardiovascular and respiratory diseases to take extra caution against influenza during hot and humid days in the subtropics and tropics.
Effects of chronic carbon monoxide exposure on fetal growth and development in mice
Authors: Venditti Carolina C , Casselman Richard , Smith Graeme N 
Published: December 2011

AbstractBackgroundCarbon monoxide (CO) is produced endogenously, and can also be acquired from many exogenous sources: ie. cigarette smoking, automobile exhaust. Although toxic at high levels, low level production or exposure lends to normal physiologic functions: smooth muscle cell relaxation, control of vascular tone, platelet aggregation, anti- inflammatory and anti-apoptotic events. In pregnancy, it is unclear at what level maternal CO exposure becomes toxic to the fetus. In this study, we hypothesized that CO would be embryotoxic, and we sought to determine at what level of chronic CO exposure in pregnancy embryo/fetotoxic effects are observed.MethodsPregnant CD1 mice were exposed to continuous levels of CO (0 to 400 ppm) from conception to gestation day 17. The effect on fetal/placental growth and development, and fetal/maternal CO concentrations were determined.ResultsMaternal and fetal CO blood concentrations ranged from 1.12- 15.6 percent carboxyhemoglobin (%COHb) and 1.0- 28.6%COHb, respectively. No significant difference was observed in placental histological morphology or in placental mass with any CO exposure. At 400 ppm CO vs. control, decreased litter size and fetal mass (p < 0.05), increased fetal early/late gestational deaths (p < 0.05), and increased CO content in the placenta and the maternal spleen, heart, liver, kidney and lung (p < 0.05) were observed.ConclusionsExposure to levels at or below 300 ppm CO throughout pregnancy has little demonstrable effect on fetal growth and development in the mouse.
Targeted sequencing library preparation by genomic DNA circularization
Authors: Myllykangas Samuel , Natsoulis Georges , Bell John M , Ji Hanlee P 
Published: December 2011

Abstract

Background
For next generation DNA sequencing, we have developed a rapid and simple approach for preparing DNA libraries of targeted DNA content. Current protocols for preparing DNA for next-generation targeted sequencing are labor-intensive, require large amounts of starting material, and are prone to artifacts that result from necessary PCR amplification of sequencing libraries. Typically, sample preparation for targeted NGS is a two-step process where (1) the desired regions are selectively captured and (2) the ends of the DNA molecules are modified to render them compatible with any given NGS sequencing platform.

Results
In this proof-of-concept study, we present an integrated approach that combines these two separate steps into one. Our method involves circularization of a specific genomic DNA molecule that directly incorporates the necessary components for conducting sequencing in a single assay and requires only one PCR amplification step. We also show that specific regions of the genome can be targeted and sequenced without any PCR amplification.

Conclusion
We anticipate that these rapid targeted libraries will be useful for validation of variants and may have diagnostic application.
Do we have the right models for scaling up health services to achieve the Millennium Development Goals?
Authors: Subramanian Savitha , Naimoli Joseph , Matsubayashi Toru , Peters David H 
Published: December 2011

Abstract

Background
There is widespread agreement on the need for scaling up in the health sector to achieve the Millennium Development Goals (MDGs). But many countries are not on track to reach the MDG targets. The dominant approach used by global health initiatives promotes uniform interventions and targets, assuming that specific technical interventions tested in one country can be replicated across countries to rapidly expand coverage. Yet countries scale up health services and progress against the MDGs at very different rates. Global health initiatives need to take advantage of what has been learned about scaling up.

Methods
A systematic literature review was conducted to identify conceptual models for scaling up health in developing countries, with the articles assessed according to the practical concerns of how to scale up, including the planning, monitoring and implementation approaches.

Results
We identified six conceptual models for scaling up in health based on experience with expanding pilot projects and diffusion of innovations. They place importance on paying attention to enhancing organizational, functional, and political capabilities through experimentation and adaptation of strategies in addition to increasing the coverage and range of health services. These scaling up approaches focus on fostering sustainable institutions and the constructive engagement between end users and the provider and financing organizations.

Conclusions
The current approaches to scaling up health services to reach the MDGs are overly simplistic and not working adequately. Rather than relying on blueprint planning and raising funds, an approach characteristic of current global health efforts, experience with alternative models suggests that more promising pathways involve "learning by doing" in ways that engage key stakeholders, uses data to address constraints, and incorporates results from pilot projects. Such approaches should be applied to current strategies to achieve the MDGs.
The use of paediatric artemisinin combinations in sub-Saharan Africa: a snapshot questionnaire survey of health care personnel
Authors: Agnandji Selidji T , Kurth Florian , Fernandes Jose F , Soulanoudjingar Solange S , Abossolo Beatrice P , Mombo-Ngoma Ghyslain , Basra Arti , González Raquel , Kizito Gondo , Mayengue Pembe I , Auer-Hackenberg Lorenz , Issifou Saadou , Lell Bertrand , Adegnika Ayola A , Ramharter Michael 
Published: December 2011

Abstract

Background
Paediatric drug formulations for artemisinin combination therapy (P-ACT) have been developed over the past few years and have been shown to improve the therapeutic management of young children with uncomplicated falciparum malaria. This process was however not equally paralleled by a timely adoption of P-ACT in national and international treatment recommendations. National malaria programmes in sub-Saharan Africa have not yet widely embraced this new therapeutic tool. To which extent P-ACT is used in the field in sub-Saharan Africa is not known to date.

Methods
This snapshot questionnaire survey aimed to provide an overview on the current routine practices for the availability and use of P-ACT as anti-malarial treatment for young children in sub-Saharan Africa. Health care personnel in seven countries in West-, Central, and East-Africa were invited to answer a structured questionnaire assessing use and availability of P-ACT.

Results
A total of 71 respondents including doctors, nurses and pharmacy personnel responsible for the anti-malarial treatment of young children were interviewed. P-ACT was used by 83% (95% confidence interval: 73-90%; n = 59) as first-line treatment for young children. Use of 15 different P-ACT products was reported among which only two have received WHO prequalification status and approval by a stringent registration authority. Use of a specific P-ACT product was not linked to consumer prices or availability of supporting clinical trial data, but may depend more on the marketing capacity of the manufacturer. Major differences in frequency and dosing of anti-malarial regimens with identical anti-malarial compounds and the marketing of loose combinations were recorded.

Conclusion
Paediatric ACT is widely used for the treatment of uncomplicated malaria in young children. However, the majority of P-ACT formulations in use do not meet highest international quality standards evoking concerns for patients' safety and the induction of drug resistance. Improving the quality of currently marketed P-ACT should constitute a public health priority besides their adoption into official treatment recommendations.