bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utility of the Pectoralis Major Index in the Diagnosis of Structurally Significant Pectoralis Major Tears
Authors: ElMaraghy Amr W. , Rehsia Sacha S. , Pennings Amanda L. 
Published: December 2013

Background: Diagnosis of pectoralis major tears early in the acute phase is important for optimizing surgical repair and outcomes. However, physical examination of pectoralis major injuries can be misleading, often resulting in a potentially detrimental delay in surgical treatment. Purpose: To establish and validate a quantifiable clinical diagnostic test for structurally significant pectoralis major tears. Study Design: Cohort study (diagnosis); Level of evidence, 2. Methods: A total of 50 healthy male participants (mean age, 43.3 ± 11.9 years) with normal uninjured pectoralis major anatomy were examined. Digital photographs of all participants were taken in the “military press” starting position (90° of shoulder abduction, 90° of shoulder external rotation). The length between the ipsilateral nipple and the apex of the pectoralis major muscle curvature along the anterior axillary fold, known as the pectoralis major distance, was measured bilaterally. Two orthopaedic surgeons measured all photographs on 2 separate occasions. The pectoralis major index (PMI) was calculated as a ratio of pectoralis major distance values to establish normal values. The PMI was also calculated in a cohort of 19 male patients (mean age, 33.8 ± 6.8 years) with a pectoralis major rupture to assess the diagnostic utility of this novel quantifiable physical examination technique. Results: Mean (± standard deviation) PMI for the uninjured group was 1.0 ± 0.07. A diagnostic threshold of a PMI <0.9 resulted in a sensitivity of 79%, specificity of 98%, and overall accuracy of 93% in identifying structurally significant pectoralis major ruptures. There was no correlation between PMI and age or activity level, including participation in sports and/or weight training. The PMI technique demonstrated good to excellent intrarater reliability (intraclass correlation coefficient [ICC] = 0.82, 0.74) and interrater reliability (ICC = 0.63, 0.76). Conclusion: The PMI technique is a simple, quantifiable, and accurate clinical diagnostic test for structurally significant pectoralis major tears. Routine application of the PMI technique by clinicians may improve accurate identification of structurally significant rupture and expedite referral to a surgical specialist for optimal treatment and outcome.
Spontaneous intracerebral hemorrhage in CADASIL
Authors: Lian Lifei , Li Dujuan , Xue Zheng , Liang Qiming , Xu Feng , Kang Huicong , Liu Xiaoyan , Zhu Suiqiang 
Published: December 2013

Abstract

Background
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a rare hereditary small vascular disease and its mainly clinical manifestations are ischemic events. Spontaneous intracerebral hemorrhage (ICH) involvement in patients with CADASIL is extremely uncommon.

Case report
A 46-year-old normotensive Chinese man developed a large hematoma in the left basal ganglia after he was diagnosed with CADASIL 2 months ago, the patient did not take any antithrombotics. Susceptibility weighted imaging at pre-ICH showed multiple cerebral microbleeds (CMBs) in the bilateral basal ganglia. He experienced migraine at about 10 months post-ICH. To our knowledge, this is the first report of ICH in CADASIL patients with Arg90Cys mutation in exon 3.

Discussion and conclusions
ICH should be considered when evaluating new attacks in CADASIL patients. Thus, MRI screening for CMBs might be helpful in predicting the risk of ICH and guiding antithrombotic therapy. In addition, strict control of hypertension and cautious use of antithrombotics may be important in this context.
RNA-Seq optimization with eQTL gold standards
Authors: Ellis Shannon E , Gupta Simone , Ashar Foram N , Bader Joel S , West Andrew B , Arking Dan E 
Published: December 2013

Abstract

Background
RNA-Sequencing (RNA-Seq) experiments have been optimized for library preparation, mapping, and gene expression estimation. These methods, however, have revealed weaknesses in the next stages of analysis of differential expression, with results sensitive to systematic sample stratification or, in more extreme cases, to outliers. Further, a method to assess normalization and adjustment measures imposed on the data is lacking.

Results
To address these issues, we utilize previously published eQTLs as a novel gold standard at the center of a framework that integrates DNA genotypes and RNA-Seq data to optimize analysis and aid in the understanding of genetic variation and gene expression. After detecting sample contamination and sequencing outliers in RNA-Seq data, a set of previously published brain eQTLs was used to determine if sample outlier removal was appropriate. Improved replication of known eQTLs supported removal of these samples in downstream analyses. eQTL replication was further employed to assess normalization methods, covariate inclusion, and gene annotation. This method was validated in an independent RNA-Seq blood data set from the GTEx project and a tissue-appropriate set of eQTLs. eQTL replication in both data sets highlights the necessity of accounting for unknown covariates in RNA-Seq data analysis.

Conclusion
As each RNA-Seq experiment is unique with its own experiment-specific limitations, we offer an easily-implementable method that uses the replication of known eQTLs to guide each step in one’s data analysis pipeline. In the two data sets presented herein, we highlight not only the necessity of careful outlier detection but also the need to account for unknown covariates in RNA-Seq experiments.
Genome wide association studies for body conformation traits in the Chinese Holstein cattle population
Authors: Wu Xiaoping , Fang Ming , Liu Lin , Wang Sheng , Liu Jianfeng , Ding Xiangdong , Zhang Shengli , Zhang Qin , Zhang Yuan , Qiao Lv , Lund Mogens Sandø , Su Guosheng , Sun Dongxiao 
Published: December 2013

AbstractBackgroundGenome-wide association study (GWAS) is a powerful tool for revealing the genetic basis of quantitative traits. However, studies using GWAS for conformation traits of cattle is comparatively less. This study aims to use GWAS to find the candidates genes for body conformation traits.ResultsThe Illumina BovineSNP50 BeadChip was used to identify single nucleotide polymorphisms (SNPs) that are associated with body conformation traits. A least absolute shrinkage and selection operator (LASSO) was applied to detect multiple SNPs simultaneously for 29 body conformation traits with 1,314 Chinese Holstein cattle and 52,166 SNPs. Totally, 59 genome-wide significant SNPs associated with 26 conformation traits were detected by genome-wide association analysis; five SNPs were within previously reported QTL regions (Animal Quantitative Trait Loci (QTL) database) and 11 were very close to the reported SNPs. Twenty-two SNPs were located within annotated gene regions, while the remainder were 0.6–826 kb away from known genes. Some of the genes had clear biological functions related to conformation traits. By combining information about the previously reported QTL regions and the biological functions of the genes, we identifiedDARC,GAS1,MTPN, HTR2A,ZNF521,PDIA6, andTMEM130as the most promising candidate genes for capacity and body depth, chest width, foot angle, angularity, rear leg side view, teat length, and animal size traits, respectively. We also found four SNPs that affected four pairs of traits, and the genetic correlation between each pair of traits ranged from 0.35 to 0.86, suggesting that these SNPs may have a pleiotropic effect on each pair of traits.ConclusionsA total of 59 significant SNPs associated with 26 conformation traits were identified in the Chinese Holstein population. Six promising candidate genes were suggested, and four SNPs showed genetic correlation for four pairs of traits.
The role of acupoint stimulation as an adjunct therapy for lung cancer: a systematic review and meta-analysis
Authors: Chen Hai-Yong , Li Shi-Guang , Cho William CS , Zhang Zhang-Jin 
Published: December 2013

Abstract

Background
Lung cancer is the leading cause of death in cancer patients. Clinical studies showed that a variety of acupoint stimulations have been extensively used for lung cancer patients, including needle insertion, injection with herbal extraction, plaster application, and moxibustion. However, the role of acupoint stimulation in lung cancer treatment was not fully reviewed.

Methods
In the present study, we conducted a systematic review and meta-analysis on the role of acupoint stimulation in lung cancer treatment by electronic and manual searching in seven databases, including Ovid (Ovid MEDLINE, AMED, CAB Abstracts, EMBASE), EBSCOhost research databases (Academic Search premier, MEDLINE, CIHAHL Plus), PreQuest (British Nursing Index, ProQuest Medical Library, ProQuest Dissertations & Theses A&I, PsycINFO), and ISI web of knowledge (Web of Science, BIOSIS Citation Index, Biological Abstracts, Chinese Science Citation Database), CNKI, Wanfang Data, and CQVIP.

Results
Our study showed that acupoint stimulation has strong immunomodulatory effect for lung cancer patients as demonstrated by the significant increase of IL-2, T cell subtypes (CD3+ and CD4+, but not CD8+ cells), and natural killer cells. Further analysis revealed that acupoint stimulation remarkably alleviates the conventional therapy-induced bone marrow suppression (hemoglobin, platelet, and WBC reduction) in lung cancer patients, as well as decreases nausea and vomiting. The pooled studies also showed that acupoint stimulation can improve Karnofsky performance status, immediate tumor response, quality of life (EORCT-QLQ-C30), and pain control of cancer patients.

Conclusions
Acupoint stimulation is found to be effective in lung cancer treatment, further confirmatory evaluation via large scale randomized trials is warranted.
A preliminary analysis of the effect of the new rural cooperative medical scheme on inpatient care at a county hospital
Authors: Ye Chiyu , Duan Shengnan , Wu Yuan , Hu Huimei , Liu Xiaofang , You Hua , Wang Linghao , Bogg Lennart , Dong Hengjin 
Published: December 2013

Abstract

Background
China in 2009 committed to reach universal health coverage by promoting three forms of health insurance; NCMS for the rural population, UEBMI for formally employed urban residents and URBMI for other urban residents. NCMS has expanded to near universal coverage in rural China since launching in 2003. The objective of this study aimed to assess the effect of NCMS on inpatient care utilization from 2003 to 2012 at Longyou county hospital, Zhejiang province.

Methods
The research was conducted at Longyou county, Zhejiang province. All registered inpatient admissions from January 1, 2003, to June 30, 2012, were included in the study. The PLSQL Developer software was used to select the interesting variables in the hospital information database and saved in an Excel 2003 file. The interesting variables included the patients’ general information (name, gender, age, payment method), discharge diagnosis, length of hospital stay, and expenditure (total expenditure and out-of-pocket payment). Two common diseases (coronary arteriosclerotic disease and pneumonia) were selected as tracer conditions.

Results
292,400 rural residents were enrolled in the Longyou county NCMS by 2011, 95.4% of the eligible population. A total of 145,744 inpatient admissions were registered from 1 January 2003 to 30 June 2012. The proportion of inpatients covered by NCMS increased from 30.3% in 2004 to 54.2% in 2012 while the proportion of inpatients covered by UEBMI increased from 7.7% in 2003 to 14.7% in 2012. The average expenditure for UEBMI insured inpatients was higher than the average for NCMS insured inpatients, although the gap was narrowing. The average length of hospital stay increased every year for all inpatients, but was higher for UEBMI inpatients than for NCMS insured inpatients. For both tracer conditions the results were similar to the above findings.

Conclusions
NCMS has improved coverage height for its enrollees and resulted in increased cost of care per inpatient admission at the county hospital. However, wide differences persist between the two insurance systems in coverage height. Both systems are associated with increasing lengths of stay and rising cost per inpatient admission. We found that around 30% of inpatients were not covered by any of the two public health insurance systems, which calls for further studies.
Pancreatic-carcinoma-cell-derived pro-angiogenic factors can induce endothelial-cell differentiation of a subset of circulating CD34+ progenitors
Authors: Vizio Barbara , Biasi Fiorella , Scirelli Tiziana , Novarino Anna , Prati Adriana , Ciuffreda Libero , Montrucchio Giuseppe , Poli Giuseppe , Bellone Graziella 
Published: December 2013

Abstract

Background
CD34+ progenitor cells comprise both hematopoietic and endothelial progenitor cells. Recent studies suggest that circulating endothelial progenitor cells are recruited into the angiogenic vascular system of several cancers, including pancreatic carcinoma, and that they correlate with clinical progress. However, whether endothelial progenitor cell mobilization occurs in response to cytokine release by tumor cells is still unclear.

Methods
The chemotactic- and/or differentiating-activities of the poorly-differentiated pancreatic carcinoma cell line PT45, and of the immortal H6c7 cell line, a line of near-normal pancreatic duct epithelial cells, on endothelial progenitor cells were investigated in vitro using circulating CD34+ as model.

Results
The study showed that Vascular Endothelial Growth Factor produced by PT45 cells and, at lesser extent, by H6c7 cells, predominantly chemoattract peripheral blood CD34+ expressing the type 2 relative receptor. Addition of PT45-conditioned medium to CD34+ cells, cultured under conditions supporting myeloid cell development, diverted the differentiation of a subset of these progenitor cells into cells expressing endothelial cell markers, such as CD146, CD105, VE-cadherin and von Willebrand Factor-related antigen. Moreover, these endothelial-like cells formed capillary networks in vitro, chiefly through the release of Angiopoietin-1 by PT45 cells.

Conclusions
The results demonstrate that pancreatic-carcinoma cells potentially attract circulating endothelial progenitor cells to the tumor site, by releasing high levels of pro-angiogenic factors such as Vascular Endothelial Growth Factor and Angiopoietin-1, and may direct the differentiation of these cell subsets of the CD34+ cell population into endothelial cells; the latter cells may become a component of the newly-formed vessels, contributing to angiogenesis-mediated tumor growth and metastasis.
LPS and TNF alpha modulate AMPA/NMDA receptor subunit expression and induce PGE2 and glutamate release in preterm fetal ovine mixed glial cultures
Authors: Weaver-Mikaere Luke , Gunn Alistair J , Mitchell Murray D , Bennet Laura , Fraser Mhoyra 
Published: December 2013

Abstract

Background
White matter injury (WMI) is the major antecedent of cerebral palsy in premature infants, and is often associated with maternal infection and the fetal inflammatory response. The current study explores the therapeutic potential of glutamate receptor blockade or cyclooxygenase-2 (COX-2) inhibition for inflammatory WMI.

Methods
Using fetal ovine derived mixed glia cultures exposed to tumour necrosis factor-α (TNF-α) or lipopolysaccharide (LPS), the expression of alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionate (AMPA) and N-methyl D-aspartate (NMDA) glutamate receptors and their contribution to inflammation mediated pre-oligodendrocyte (OL) death was evaluated. The functional significance of TNF-α and COX-2 signalling in glutamate release in association with TNF-α and LPS exposure was also assessed.

Results
AMPA and NMDA receptors were expressed in primary mixed glial cultures on developing OLs, the main cell-type present in fetal white matter at a period of high risk for WMI. We show that glutamate receptor expression and configuration are regulated by TNF-α and LPS exposure, but AMPA and NMDA blockade, either alone or in combination, did not reduce pre-OL death. Furthermore, we demonstrate that glutamate and prostaglandin E2 (PGE2) release following TNF-α or LPS are mediated by a TNF-α-COX-2 dependent mechanism.

Conclusions
Overall, these findings suggest that glial-localised glutamate receptors likely play a limited role in OL demise associated with chronic inflammation, but supports the COX-2 pathway as a potential therapeutic target for infection/inflammatory-mediated WMI.
HIV-1-associated PKA acts as a cofactor for genome reverse transcription
Authors: Giroud Charline , Chazal Nathalie , Gay Bernard , Eldin Patrick , Brun Sonia , Briant Laurence 
Published: December 2013

AbstractBackgroundHost cell proteins, including cellular kinases, are embarked into intact HIV-1 particles. We have previously shown that the Cα catalytic subunit of cAMP-dependent protein kinase is packaged within HIV-1 virions as an enzymatically active form able to phosphorylate a synthetic substratein vitro (Cartier et al. J. Biol. Chem. 278:35211 (2003)). The present study was conceived to investigate the contribution of HIV-1-associated PKA to the retroviral life cycle.ResultsNL4.3 viruses were produced from cells cultured in the presence of PKA inhibitors H89 (H89-NL4.3) or Myr-PKI (PKI-NL4.3) and analyzed for viral replication. Despite being mature and normally assembled, and containing expected levels of genomic RNA and RT enzymatic activity, such viruses showed poor infectivity. Indeed, infection generated reduced amounts of strong-strop minus strand DNA, while incoming RNA levels in target cells were unaffected. Decreased cDNA synthesis was also evidenced in intact H89-NL4.3 and PKI-NL4.3 cell free particles using endogenous reverse transcription (ERT) experiments. Moreover, similar defects were reproduced when wild type NL4.3 particles preincubated with PKA inhibitors were subjected to ERT reactions.ConclusionsAltogether, our results indicate that HIV-1-associated PKA is required for early reverse transcription of the retroviral genome both in cell free intact viruses and in target cells. Accordingly, virus-associated PKA behaves as a cofactor of an intraviral process required for optimal reverse transcription and for early post-entry events.
Exposure to vehicle emissions results in altered blood brain barrier permeability and expression of matrix metalloproteinases and tight junction proteins in mice
Authors: Oppenheim Hannah A , Lucero JoAnn , Guyot Anne-Cécile , Herbert Lindsay M , McDonald Jacob D , Mabondzo Aloïse , Lund Amie K 
Published: December 2013

AbstractBackgroundTraffic-generated air pollution-exposure is associated with adverse effects in the central nervous system (CNS) in both human exposures and animal models, including neuroinflammation and neurodegeneration. While alterations in the blood brain barrier (BBB) have been implicated as a potential mechanism of air pollution-induced CNS pathologies, pathways involved have not been elucidated.ObjectivesTo determine whether inhalation exposure to mixed vehicle exhaust (MVE) mediates alterations in BBB permeability, activation of matrix metalloproteinases (MMP) -2 and −9, and altered tight junction (TJ) protein expression.MethodsApolipoprotein (Apo)E−/−and C57Bl6 mice were exposed to either MVE (100 μg/m3 PM) or filtered air (FA) for 6 hr/day for 30 days and resulting BBB permeability, expression of ROS, TJ proteins, markers of neuroinflammation, and MMP activity were assessed. Serum from study mice was applied to anin vitroBBB co-culture model and resulting alterations in transport and permeability were quantified.ResultsMVE-exposedApo E−/−mice showed increased BBB permeability, elevated ROS and increased MMP-2 and −9 activity, compared to FA controls. Additionally, cerebral vessels from MVE-exposed mice expressed decreased levels of TJ proteins, occludin and claudin-5, and increased levels of inducible nitric oxide synthase (iNOS) and interleukin (IL)-1β in the parenchyma. Serum from MVE-exposed animals also resulted in increasedin vitroBBB permeability and altered P-glycoprotein transport activity.ConclusionsThese data indicate that inhalation exposure to traffic-generated air pollutants promotes increased MMP activity and degradation of TJ proteins in the cerebral vasculature, resulting in altered BBB permeability and expression of neuroinflammatory markers.
Use of ethanol extract of Mycobacterium bovis for detection of specific antibodies in sera of farmed red deer (Cervus elaphus) with bovine tuberculosis
Authors: Wadhwa Ashutosh , Johnson Rachel E , Mackintosh Colin G , Griffin J Frank T , Waters W Ray , Bannantine John P , Eda Shigetoshi 
Published: December 2013

Abstract

Background
Bovine tuberculosis (bTB) in wildlife species poses a threat to domestic livestock in many situations. Control programs for bTB in livestock depend on testing and slaughtering the positive animals; however, the currently available diagnostic tests often have poor specificity. In our previous study, we developed a specific and sensitive enzyme linked immunosorbent assay (ELISA) for another mycobacterial disease – Johne’s disease, using surface antigens of Mycobacterium avium ssp. paratuberculosis (MAP) extracted by briefly agitating the bacilli in 80% ethanol solution. The ELISA test was named ethanol vortex ELISA (EVELISA). The objective of this study is to examine whether EVELISA technique could be used to specifically detect anti-Mycobacterium bovis (M. bovis) antibodies in the serum of M. bovis-infected farmed red deer (Cervus elaphus). We tested a total of 45 red deer serum samples, divided in 3 groups – uninfected animals (n = 15), experimentally infected with M. bovis (n = 15) and experimentally infected with MAP (n = 15).

Results
The presence of anti-M. bovis antibodies was tested using an ethanol extract of M. bovis. Without absorption of anti-MAP cross reactive antibodies, it was found that 13 out of the 15 MAP-infected animals showed high antibody binding. Using heat killed MAP as an absorbent of cross reactive antibodies, anti-M. bovis antibodies were detected in 86.7% of M. bovis-infected animals with minor false positive results caused by MAP infection.

Conclusions
The results from this study suggest that EVELISA may form a basis for a sensitive and specific test for the diagnosis of bTB in farmed red deer.
International Consortium of Rice Mutagenesis: resources and beyond
Authors: Wei Fu-Jin , Droc Gaëtan , Guiderdoni Emmanuel , Hsing Yue-ie C 
Published: December 2013

Abstract
Rice is one of the most important crops in the world. The rice community needs to cooperate and share efforts and resources so that we can understand the functions of rice genes, especially those with a role in important agronomical traits, for application in agricultural production. Mutation is a major source of genetic variation that can be used for studying gene function. We will present here the status of mutant collections affected in a random manner by physical/chemical and insertion mutageneses.
As of early September 2013, a total of 447, 919 flanking sequence tags from rice mutant libraries with T-DNA, Ac/Ds, En/Spm, Tos17, nDART/aDART insertions have been collected and publicly available. From these, 336,262 sequences are precisely positioned on the japonica rice chromosomes, and 67.5% are in gene interval. We discuss the genome coverage and preference of the insertion, issues limiting the exchange and use of the current collections, as well as new and improved resources. We propose a call to renew all mutant populations as soon as possible. We also suggest that a common web portal should be established for ordering seeds.