bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of copy number variants by three detection algorithms and their association with body size in horses
Authors: Metzger Julia , Philipp Ute , Lopes Maria Susana , da Camara Machado Artur , Felicetti Michela , Silvestrelli Maurizio , Distl Ottmar 
Published: July 2013

Abstract

Background
Copy number variants (CNVs) have been shown to play an important role in genetic diversity of mammals and in the development of many complex phenotypic traits. The aim of this study was to perform a standard comparative evaluation of CNVs in horses using three different CNV detection programs and to identify genomic regions associated with body size in horses.

Results
Analysis was performed using the Illumina Equine SNP50 genotyping beadchip for 854 horses. CNVs were detected by three different algorithms, CNVPartition, PennCNV and QuantiSNP. Comparative analysis revealed 50 CNVs that affected 153 different genes mainly involved in sensory perception, signal transduction and cellular components. Genome-wide association analysis for body size showed highly significant deleted regions on ECA1, ECA8 and ECA9. Homologous regions to the detected CNVs on ECA1 and ECA9 have also been shown to be correlated with human height.

Conclusions
Comparative analysis of CNV detection algorithms was useful to increase the specificity of CNV detection but had certain limitations dependent on the detection tool. GWAS revealed genome-wide associated CNVs for body size in horses.
Defining natural species of bacteria: clear-cut genomic boundaries revealed by a turning point in nucleotide sequence divergence
Authors: Tang Le , Li Yang , Deng Xia , Johnston Randal N , Liu Gui-Rong , Liu Shu-Lin 
Published: July 2013

Abstract

Background
Bacteria are currently classified into arbitrary species, but whether they actually exist as discrete natural species was unclear. To reveal genomic features that may unambiguously group bacteria into discrete genetic clusters, we carried out systematic genomic comparisons among representative bacteria.

Results
We found that bacteria of Salmonella formed tight phylogenetic clusters separated by various genetic distances: whereas over 90% of the approximately four thousand shared genes had completely identical sequences among strains of the same lineage, the percentages dropped sharply to below 50% across the lineages, demonstrating the existence of clear-cut genetic boundaries by a steep turning point in nucleotide sequence divergence. Recombination assays supported the genetic boundary hypothesis, suggesting that genetic barriers had been formed between bacteria of even very closely related lineages. We found similar situations in bacteria of Yersinia and Staphylococcus.

Conclusions
Bacteria are genetically isolated into discrete clusters equivalent to natural species.
Novel polymerase gamma (POLG1) gene mutation in the linker domain associated with parkinsonism
Authors: Dolhun Rachel , Presant Erin M , Hedera Peter 
Published: July 2013

Abstract

Background
Mutations in the POLG1 gene have variable phenotypic presentations and a high degree of clinical suspicion is necessary for their recognition. Parkinsonism and ataxia are the most common movement disorders associated with POLG1 mutations but no phenotype-genotype correlation has been established.

Case presentation
We identified a male patient with progressive external ophthalmoplegia who also developed a progressive bradykinesia, rigidity and camptocormia in the third decade. Parkinsonism was partially responsive to dopaminegic replacement. His father and brother had reportedly similar clinical problems. Genetic analysis identified a novel mutation p.K512M in the POLG1 gene.

Conclusion
This report further expands the spectrum of POLG1-associated neurologic problems with the report of a novel mutation in the linker region of the gene, which are rarely associated with parkinsonism.
Successful reduction of hospital-acquired methicillin-resistant Staphylococcus aureus in a urology ward: a 10-year study
Authors: Tatokoro Manabu , Kihara Kazunori , Masuda Hitoshi , Ito Masaya , Yoshida Soichiro , Kijima Toshiki , Yokoyama Minato , Saito Kazutaka , Koga Fumitaka , Kawakami Satoru , Fujii Yasuhisa 
Published: July 2013

AbstractBackgroundTo eradicate hospital-acquired methicillin-resistantStaphylococcus aureus(MRSA) using a stepwise infection control strategy that includes an avoidance of antimicrobial prophylaxis (AMP) based on surgical wound classification and an improvement in operative procedures in gasless single-port urologic surgery.MethodsThe study was conducted at an 801-bed university hospital. Since 2001, in the urology ward, we have introduced the stepwise infection control strategy. In 2007, surveillance cultures for MRSA in all urological patients were commenced. The annual incidence of MRSA was calculated as a total number of newly identified MRSA cases per 1,000 patient days. Trend analysis was performed using a Poisson regression.ResultsOver the study period, 139,866 patients, including 10,201 urology patients, were admitted to our hospital. Of these patients, 3,719 patients, including 134 ones in the urology ward, were diagnosed with MRSA throughout the entire hospital. Although the incidence of MRSA increased throughout the entire hospital (p= 0.002), it decreased significantly in the urology ward (p< 0.0001). Of the 134 cases, 45 (33.6%) were classified as “imported,” and 89 (66.4%) as “acquired.” In the urology ward, the incidence of acquired MRSA decreased significantly over time (p< 0.0001), whereas the incidence of imported MRSA did not change over time (p= 0.66). A significant decrease (p< 0.0001) in the incidence of clinically significant MRSA infection over time was found.ConclusionsStepwise infection control strategy that includes a reduction or avoidance of antimicrobial prophylaxis in minimally invasive surgery can contribute to a reduction in hospital-acquired MRSA.Trial registrationCurrent study has approved by the institutional ethical review board (No.1141).
Saturated fatty acid palmitate-induced insulin resistance is accompanied with myotube loss and the impaired expression of health benefit myokine genes in C2C12 myotubes
Authors: Yang Ming , Wei Dandan , Mo Chunfen , Zhang Jie , Wang Xu , Han Xiaojuan , Wang Zhe , Xiao Hengyi 
Published: July 2013

Abstract

Background
Excessive circular fatty acid, particlarly saturated fatty acid, can result in insulin resistance in skeletal muscle, but other adverse effects of fatty acid accumulation in myocytes remain unclear.

Methods
Differentiated C2C12 myotubes were used. The effects of palmitate on cell viability, glucose uptake, gene expression and myotube loss were evaluated by MTT assay, 2NBDG uptake, qRT-PCR, Western Blot and crystal staining-based myotube counting, respectively. In some expreiments, oleate was administrated, or the inhibitors of signaling pathways were applied.

Results
Palmitate-induced cellular insulin resistance was clarified by the reduced Akt phosphorylation, glucose uptake and Glut4 expression. Palmitate-caused myotube loss was clearly observed under microscope and proved by myotube counting and expression analysis of myotube marker genes. Moreover, palmitate-induced transcriptional suppression of three health benefit myokine genes (FNDC5, CTRP15 and FGF21) was found, and the different involvement of p38 and PI3K in the transcription of these genes was noticed.

Conclusions
Palmitate-induced insulin resistance accompanys myotube loss and the impaired expression of FNDC5, CTRP15 and FGF21genes in C2C12 myotubes. These results provide novel evidence indicating the negative role of high concentration of palmitate in myotubes.
Proteomic analysis of the inhibitory effect of epigallocatechin gallate on lipid accumulation in human HepG2 cells
Authors: Liu Zhonghua , Li Qin , Huang Jianan , Liang Qionglin , Yan Yujun , Lin Haiyan , Xiao Wenjun , Lin Yong , Zhang Sheng , Tan Bin , Luo Guoan 
Published: July 2013

Abstract

Background
(−)-Epigallocatechin-3-gallate (EGCG), the most abundant catechin found in green tea, effectively reduces body weight and tissue and blood lipid accumulation. To explore the mechanism by which EGCG inhibits cellular lipid accumulation in free fatty acid (FFA) induced HepG2 cell culture, we investigated the proteome change of FFA-induced HepG2 cells exposed to EGCG using two-dimensional gel electrophoresis and mass spectrometry.

Results
In this study, 36 protein spots showed a significant change in intensity by more than 1.5-fold from the control group to the FFA group and from the FFA group to the FFA + EGCG group. Among them, 24 spots were excised from gels and identified by LC-MS/MS. In total, 18 proteins were successfully identified. All identified proteins were involved in lipid metabolism, glycometabolism, antioxidant defense, respiration, cytoskeleton organization, signal transduction, DNA repair, mRNA processing, iron storage, or were chaperone proteins. This indicated that these physiological processes may play roles in the mechanism of inhibition of lipid accumulation by EGCG in FFA-induced HepG2 cells. Western blotting analysis was used to verify the expression levels of differentially expressed proteins, which agree with the proteomic results.

Conclusions
From the proteomic analysis, we hypothesized that EGCG reduced cellular lipid accumulation in FFA-induced HepG2 cells through the activation of AMP-activated protein kinase (AMPK) resulting from the generation of reactive oxygen species (ROS). The induction of ROS may be a result of EGCG regulation of the antioxidant defense system. Activation of AMPK shifted some FFA toward oxidation, away from lipid and triglyceride storage, and suppressed hepatic gluconeogenesis. The findings of this study improve our understanding of the molecular mechanisms of inhibition of lipid accumulation by EGCG in HepG2 cells.
High sensitivity of middle-wavelength infrared photodetectors based on an individual InSb nanowire
Authors: Kuo Cheng-Hsiang , Wu Jyh-Ming , Lin Su-Jien , Chang Wen-Chih 
Published: July 2013

Abstract
Single-crystal indium antimony (InSb) nanowire was fabricated into middle-infrared photodetectors based on a metal–semiconductor-metal (M-S-M) structure. The InSb nanowires were synthesized using an electrochemical method at room temperature. The characteristics of the FET reveal an electron concentration of 3.6 × 1017 cm−3 and an electron mobility of 215.25 cm2 V−1 s−1. The photodetectors exhibit good photoconductive performance, excellent stability, reproducibility, superior responsivity (8.4 × 104 A W−1), and quantum efficiency (1.96 × 106%). These superior properties are attributed to the high surface-to-volume ratio and single-crystal 1D nanostructure of photodetectors that significantly reduce the scattering, trapping, and the transit time between the electrodes during the transport process. Furthermore, the M-S-M structure can effectively enhance space charge effect by the formation of the Schottky contacts, which significantly assists with the electron injection and photocurrent gain.
Joint subcarrier and power allocation for physical layer security in cooperative OFDMA networks
Authors: Wang An , Chen Jin , Cai Yueming , Cai Chunxiao , Yang Wendong , Cheng Yunpeng 
Published: July 2013

Abstract
In this paper, a joint subcarrier and power allocation algorithm is proposed to improve the physical layer security in cooperative orthogonal frequency division multiple access (OFDMA) networks, where several source-destination pairs and one untrusted relay are involved. The relay is friendly and intends to help these pairs to enhance their communications. However, it may be overheard by a malicious eavesdropper at the same time. To optimize the joint subcarrier and power allocation with low complexity, we divide the optimization problem into two simpler subproblems. Firstly, the subcarriers are assigned to the source-destination pairs by employing the dual approach under the assumption that the relay power is equally allocated to all the subcarriers. Then, the relay power is allocated to the subcarriers based on the alternative ascending clock auction mechanism. In addition, we prove that the two subproblems can converge after a finite number of iterations. We also find that the proposed auction is cheat-proof and, thus, can avoid the cheating behaviors in the auction process. Numerical results demonstrate that our proposed algorithm can effectively improve the system sum secrecy rate, and the convergence performance is also desirable.
Intracerebroventricular administration of lipopolysaccharide induces indoleamine-2,3-dioxygenase-dependent depression-like behaviors
Authors: Lawson Marcus A , Parrott Jennifer M , McCusker Robert H , Dantzer Robert , Kelley Keith W , O’Connor Jason C 
Published: July 2013

Abstract

Background
Activation of the tryptophan degrading enzyme indoleamine-2,3-dioxygenase 1 (IDO1) is associated with the development of behavioral signs of depression. Systemic immune challenge induces IDO1 in both the periphery and the brain, leading to increased circulating and brain concentrations of kynurenines. However, whether IDO1 activity within the brain is necessary for the manifestation of depression-like behavior of mice following a central immune challenge remains to be elucidated.

Methods
We investigated the role of brain IDO1 in mediating depression-like behavior of mice in response to intracerebroventricular injection of saline or lipopolysaccharide (LPS, 10 ng).

Results
LPS increased the duration of immobility in the tail suspension test and decreased preference for a sucrose solution. These effects were associated with an activation of central but not peripheral IDO1, as LPS increased brain kynurenine but had no effect on plasma concentrations of kynurenine. Interestingly, genetic deletion or pharmacological inhibition of IDO1, using 1-methyl-tryptophan, abrogated the reduction in sucrose preference induced by intracerebroventricular LPS. 1-Methyl-tryptophan also blocked the LPS-induced increase in duration of immobility during the tail suspension test.

Conclusions
These data indicate that activation of brain IDO1 is sufficient to induce depression-like behaviors of mice in response to central LPS.
Effect of berberine on insulin resistance in women with polycystic ovary syndrome: study protocol for a randomized multicenter controlled trial
Authors: Li Yan , Ma Hongli , Zhang Yuehui , Kuang Hongying , Ng Ernest Hung Yu , Hou Lihui , Wu Xiaoke 
Published: July 2013

Abstract

Background
Insulin resistance and hyperinsulinemia play a key role in the pathogenesis of polycystic ovary syndrome (PCOS), which is characterized by hyperandrogenism, ovulatory dysfunction, and presence of polycystic ovaries on pelvic scanning. Insulin resistance is significantly associated with the long-term risks of metabolic syndrome and cardiovascular disease. Berberine has effects on insulin resistance but its use in women with PCOS has not been fully investigated. In this paper, we present a research design evaluating the effects of berberine on insulin resistance in women with PCOS.

Methods/design
This is a multicenter, randomized, placebo-controlled and double-blind trial. A total of 120 patients will be enrolled in this study and will be randomized into two groups. Berberine or placebo will be taken orally for 12 weeks. The primary outcome is the whole body insulin action assessed with the hyperinsulinemic-euglycemic clamp.

Discussion
We postulate that women with PCOS will have improved insulin resistance following berberine administration.

Trial registration
This study is registered at ClinicalTrials.gov, NCT01138930.
Potential biomarkers for predicting outcomes in CABG cardiothoracic surgeries
Authors: Preeshagul Isabel , Gharbaran Rajendra , Jeong Kyung Hwa , Abdel-Razek Ahmed , Lee Leonard Y , Elman Elie , Suh K Stephen 
Published: July 2013

Abstract
The variations in recovery time, complications, and survival among cardiac patients who have undergone coronary artery bypass graft (CABG) procedures are vast. Many formulas and theories are used to predict clinical outcome and recovery time, and current prognostic predictions are based on medical and family history, lifestyle, co-morbidities, and performance status. The identification of biomarkers that provide concrete evidence supporting clinical outcome has greatly affected the field of medicine, helping clinicians in many medicine sub-specialties to forecast clinical course. Recent studies have discovered biomarkers that may be used as predictors of cardiac patients’ status post-cardiothoracic surgery, and the applications are numerous. In this review, we assess currently available cardiac biomarkers as predictors of clinical outcome for post-operative CABG patients. Data were collected from various studies in which cardiac biomarkers were measured in pre-operative and post-operative CABG patients.
Effect of potassium deficiency on antioxidant status and cadmium toxicity in rice seedlings
Authors: Liu Chun-Hsin , Chao Yun-Yang , Kao Ching Huei 
Published: July 2013

AbstractBackgroundCadmium (Cd) is one of the most toxic heavy metals and inhibits physiological processes of plants. Potassium (K) is an essential macronutrient in plants. K deficiency and Cd stress represent two different abiotic stress conditions that occur in the field simultaneously. In this study, effects of K deficiency on antioxidant status and Cd toxicity in rice seedlings were investigated.ResultsK deficiency significantly decreased K concentration in shoots and roots. However, fresh weight and dry weight of rice seedlings were not affected by K deficiency. The activities of antioxidant enzymes (superoxide dismutase, ascorbate peroxidase, glutathione reductase, and catalase) in K-deficient leaves were higher than respective control leaves. However, K deficiency had no effect on the content of antioxidants (ascorbate and glutathione). Cd toxicity was judged by the decrease in biomass production, chlorosis, and induction of oxidative stress. Based on these criteria, we demonstrated that K deficiency protected rice seedling from Cd stress. Moreover, chlorophyll concentration was higher in K-deficient shoots and roots than their respective control shoots and roots.ConclusionsOur results indicated that K deficiency protects rice seedlings from Cd toxicity. This protective effect of K deficiency is mainly due to enhanced antioxidant enzyme activities but not inhibition of Cd uptake.
The emerging roles of Notch signaling in leukemia and stem cells
Authors: Liu Na , Zhang Jingru , Ji Chunyan 
Published: July 2013

Abstract
The Notch signaling pathway plays a critical role in maintaining the balance between cell proliferation, differentiation and apoptosis, and is a highly conserved signaling pathway that regulates normal development in a context- and dose-dependent manner. Dysregulation of Notch signaling has been suggested to be key events in a variety of hematological malignancies. Notch1 signaling appears to be the central oncogenic trigger in T cell acute lymphoblastic leukemia (T-ALL), in which the majority of human malignancies have acquired mutations that lead to constitutive activation of Notch1 signaling. However, emerging evidence unexpectedly demonstrates that Notch signaling can function as a potent tumor suppressor in other forms of leukemia. This minireview will summarize recent advances related to the roles of activated Notch signaling in human lymphocytic leukemia, myeloid leukemia, stem cells and stromal microenvironment, and we will discuss the perspectives of Notch signaling as a potential therapeutic target as well.
Computational modeling of the p7 monomer from HCV and its interaction with small molecule drugs
Authors: Wang Yi-Ting , Hsu Hao-Jen , Fischer Wolfgang B 
Published: July 2013

Abstract
Hepatitis C virus p7 protein is a 63 amino acid polytopic protein with two transmembrane domains (TMDs) and one of the prime targets for anti HCV drug development. A bio-inspired modeling pathway is used to generate plausible computational models of the two TMDs forming the monomeric protein model. A flexible region between Leu-13 and Gly-15 is identified for TMD11-32 and a region around Gly-46 to Trp-48 for TMD236-58. Mutations of the tyrosine residues in TMD236-58 into phenylalanine and serine are simulated to identify their role in shaping TMD2. Lowest energy structures of the two TMDs connected with the loop residues are used for a posing study in which small molecule drugs BIT225, amantadine, rimantadine and N N-DNJ, are identified to bind to the loop region. BIT225 is identified to interact with the backbone of the functionally important residues Arg-35 and Trp-36.
Reasons of not having breast reconstruction: a historical cohort of 1937 breast cancer patients undergoing mastectomy
Authors: Héquet Delphine , Zarca Kevin , Dolbeault Sylvie , Couturaud Benoît , Ngô Charlotte , Fourchotte Virgine , De La Rochefordière Anne , Féron Jean-Guillaume , Fitoussi Alfred , Bélichard Catherine , Reyal Fabien , Laki Fatima , Hajage David , Sigal Brigitte , Asselain Bernard , Alran Séverine ,   Institut Curie Breast Cancer Group, Roman Rouzier
Published: July 2013

AbstractBackgroundThe aims of the study were to investigate the factors associated with not having breast reconstruction following mastectomy and to assess patient satisfaction with information on reconstruction.Patients and methodsWe analysed a historical cohort of 1937 consecutive patients who underwent mastectomy at Institut Curie between January 2004 and February 2007. Their sociodemographic and clinicobiological characteristics were recorded in a prospective database. A questionnaire was sent to 10% of nonreconstructed patients.ResultsThe proportion of patients with invasive cancer was 82.7%. The rate of nonreconstruction in patients with in situ and invasive cancer was 34.6% and 74.9%, respectively. On multivariate analysis, only employment outside the home was associated with reconstruction in patients with in situ cancer (p < 0.001). In patients with invasive cancer, employment status (p < 0.001) and smoking (p = 0.045) were associated with reconstruction, while age > 50, ASA score >1, radiotherapy (p < 0.0001) and metastatic status (p = 0.018) were associated with nonreconstruction. For 80% of questionnaire responders, nonreconstruction was a personal choice, mainly for the following reasons: refusal of further surgery, acceptance of body asymmetry, risk of complications and advanced age. Information on reconstruction was entirely unsatisfactory or inadequate for 62% of patients.ConclusionBetter understanding the factors that influence decision of nonreconstruction can help us adapt the information to serve the patient’s personal needs.
High-resolution 3D shallow crustal structure in Long Beach, California: Application of ambient noise tomography on a dense seismic array
Authors: Lin Fan-Chi , Li Dunzhu , Clayton Robert W. , Hollis Dan 
Published: July 2013

Ambient noise tomography has proven to be effective in resolving shallow earth structure. We applied ambient noise tomography on a dense seismic array in Long Beach, California. The array was composed of more than 5200 stations with an average spacing close to 100 m. Three weeks of passive ambient noise were crosscorrelated between each station pair, which resulted in more than 13.5 million crosscorrelations within the area. Clear fundamental-mode Rayleigh waves were observed between 0.5 and 4 Hz, which were most sensitive to structure above 1-km depth. For each station pair, we applied frequency-time analysis to determine the phase traveltime dispersion, and, for each frequency, we applied eikonal tomography to determine the Rayleigh wave phase velocity map. The eikonal tomography accounted for ray bending by tracking the wavefront and allowed uncertainties to be estimated through statistical analysis. The compilation of phase velocity maps was then used to invert for 3D shear velocity structure. The inverted model showed clear correlation with the known geologic features such as the shallow south–north velocity dichotomy and a deeper fast anomaly associated with the Newport-Inglewood fault zone. Our results can potentially be used to complement traditional active source studies.