bluuebunny/crossref_metadata_2025_split huggingface dataset:
Marine medaka ATP-binding cassette (ABC) superfamily and new insight into teleost Abch nomenclature
Authors: Jeong Chang-Bum , Kim Bo-Mi , Kang Hye-Min , Choi Ik-Young , Rhee Jae-Sung , Lee Jae-Seong 
Published: October 2015

AbstractThe ABC gene family is recognized as one of the largest gene families in all kingdoms of life. Although many genes involved in the ABC superfamily have been annotated from several fish species, information on large sets of the ABC superfamily and their evolutionary characterization are still unclear. In the marine medaka Oryzias melastigma, 50 ABC transporters were identified with bioinformatics-aided in silico analyses and their full-length cDNA sequences were characterized. Phylogenetic analysis revealed that they could be classified into the eight subfamilies (A–H) that include all members of all ABC subfamilies. Interestingly, several teleosts’ Abcg members were closely clustered with Abch members in a distinctive clade. The abch gene was also observed in the coelacanth and the spotted gar, suggesting that this gene was retained from a bilaterian ancestor and that a gene loss event recently occurred in the tetrapod lineage. In teleosts, the nomenclature of previously annotated abcg genes should be considered carefully, as they form a distinctive clade with the marine medaka abch subfamily and other teleost abch genes, but not with the members of the Abcg subfamily.
Conserved phosphorylation sites in the activation loop of the Arabidopsis phytosulfokine receptor PSKR1 differentially affect kinase and receptor activity
Authors: Hartmann Jens , Linke Dennis , Bönniger Christine , Tholey Andreas , Sauter Margret 
Published: October 2015

PSK (phytosulfokine) is a plant peptide hormone perceived by a leucine-rich repeat receptor kinase. Phosphosite mapping of epitope-tagged PSKR1 (phytosulfokine receptor 1) from Arabidopsis thaliana plants identified Ser696 and Ser698 in the JM (juxtamembrane) region and probably Ser886 and/or Ser893 in the AL (activation loop) as in planta phosphorylation sites. In vitro-expressed kinase was autophosphorylated at Ser717 in the JM, and at Ser733, Thr752, Ser783, Ser864, Ser911, Ser958 and Thr998 in the kinase domain. The LC–ESI–MS/MS spectra provided support that up to three sites (Thr890, Ser893 and Thr894) in the AL were likely to be phosphorylated in vitro. These sites are evolutionarily highly conserved in PSK receptors, indicative of a conserved function. Site-directed mutagenesis of the four conserved residues in the activation segment, Thr890, Ser893, Thr894 and Thr899, differentially altered kinase activity in vitro and growth-promoting activity in planta. The T899A and the quadruple-mutated TSTT-A (T890A/S893A/T894A/T899A) mutants were both kinase-inactive, but PSKR1(T899A) retained growth-promoting activity. The T890A and S893A/T894A substitutions diminished kinase activity and growth promotion. We hypothesize that phosphorylation within the AL activates kinase activity and receptor function in a gradual and distinctive manner that may be a means to modulate the PSK response.
Polarisation rotation Bragg grating with high diffraction efficiency using Si waveguide top surface groove grating
Authors: Okayama H. , Onawa Y. , Shimura D. , Yaegashi H. , Sasaki H. 
Published: October 2015

Polarisation‐independent Bragg grating wavelength filter with high diffraction efficiency using silicon waveguide is reported. An antisymmetric grating structure with groove at the top surface of the waveguide is used to generate the polarisation rotation Bragg diffraction. The concept was verified by simulation. Polarisation‐independent bandpass filter consisting of 3 dB coupler and polarisation rotation Bragg diffraction was experimentally demonstrated.
Myocardial NF-κB activation is essential for zebrafish heart regeneration
Authors: Karra Ravi , Knecht Anne K. , Kikuchi Kazu , Poss Kenneth D. 
Published: October 2015

Significance
Heart failure occurs when the heart cannot pump enough blood to meet the body’s demands. The heart most often weakens through the loss of muscle cells, called cardiomyocytes. Heart failure is a devastating disease, and one possible cure is to replace the lost cardiomyocytes through regeneration. Unlike humans, zebrafish can efficiently regenerate their hearts after injury. Interestingly, zebrafish heart cells are similar to human heart cells at the molecular level. Understanding how zebrafish can regenerate cardiac tissue can help identify regenerative therapies for humans. Here, we find that NF-κB signaling is a link between the injury response and the regenerative program in zebrafish.
Identity and the developmental origins of fusion: an exploratory approach / La identidad y los orígenes de la fusión en el desarrollo: un enfoque exploratorio
Authors: Gaviria Elena , Ferreira Carolina , Martínez Mercedes , Whitehouse Harvey 
Published: October 2015

Identity fusion involves a visceral feeling of oneness with a group, despite personal and social selves remaining differentiated. Previous research on identity fusion has focused on samples of adults and adolescents. The present studies aim at exploring how and when identity fusion develops in childhood. Our first goal was to find out to what extent personal and social identities must be developed for fusion to become possible. We conducted two exploratory studies where school-age children (six to 12 years old) participated in either focus group sessions or individual interviews. Our results show that although children are able to feel strongly connected with a group and express willingness to make significant personal sacrifices for the group, they fail to show fusion as it is found in adults, since their personal identity is not fully developed yet. Instead, these findings suggest the existence of a prior feeling that we called ‘protofusion’, the core of which is the strength of the relational ties with the members of the group.
A novel bi-level meta-analysis approach: applied to biological pathway analysis
Authors: Nguyen Tin , Tagett Rebecca , Donato Michele , Mitrea Cristina , Draghici Sorin 
Published: October 2015

Abstract
Motivation: The accumulation of high-throughput data in public repositories creates a pressing need for integrative analysis of multiple datasets from independent experiments. However, study heterogeneity, study bias, outliers and the lack of power of available methods present real challenge in integrating genomic data. One practical drawback of many P-value-based meta-analysis methods, including Fisher’s, Stouffer’s, minP and maxP, is that they are sensitive to outliers. Another drawback is that, because they perform just one statistical test for each individual experiment, they may not fully exploit the potentially large number of samples within each study.
Results: We propose a novel bi-level meta-analysis approach that employs the additive method and the Central Limit Theorem within each individual experiment and also across multiple experiments. We prove that the bi-level framework is robust against bias, less sensitive to outliers than other methods, and more sensitive to small changes in signal. For comparative analysis, we demonstrate that the intra-experiment analysis has more power than the equivalent statistical test performed on a single large experiment. For pathway analysis, we compare the proposed framework versus classical meta-analysis approaches (Fisher’s, Stouffer’s and the additive method) as well as against a dedicated pathway meta-analysis package (MetaPath), using 1252 samples from 21 datasets related to three human diseases, acute myeloid leukemia (9 datasets), type II diabetes (5 datasets) and Alzheimer’s disease (7 datasets). Our framework outperforms its competitors to correctly identify pathways relevant to the phenotypes. The framework is sufficiently general to be applied to any type of statistical meta-analysis.
Availability and implementation: The R scripts are available on demand from the authors.
Contact: sorin@wayne.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
3DRobot: automated generation of diverse and well-packed protein structure decoys
Authors: Deng Haiyou , Jia Ya , Zhang Yang 
Published: October 2015

Abstract
Motivation: Computationally generated non-native protein structure conformations (or decoys) are often used for designing protein folding simulation methods and force fields. However, almost all the decoy sets currently used in literature suffer from uneven root mean square deviation (RMSD) distribution with bias to non-protein like hydrogen-bonding and compactness patterns. Meanwhile, most protein decoy sets are pre-calculated and there is a lack of methods for automated generation of high-quality decoys for any target proteins.
Results: We developed a new algorithm, 3DRobot, to create protein structure decoys by free fragment assembly with enhanced hydrogen-bonding and compactness interactions. The method was benchmarked with three widely used decoy sets from ab initio folding and comparative modeling simulations. The decoys generated by 3DRobot are shown to have significantly enhanced diversity and evenness with a continuous distribution in the RMSD space. The new energy terms introduced in 3DRobot improve the hydrogen-bonding network and compactness of decoys, which eliminates the possibility of native structure recognition by trivial potentials. Algorithms that can automatically create such diverse and well-packed non-native conformations from any protein structure should have a broad impact on the development of advanced protein force field and folding simulation methods.
Availiablity and implementation: http://zhanglab.ccmb.med.umich.edu/3DRobot/
Contact: jiay@phy.ccnu.edu.cn; zhng@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The Occurrence of Iron-Deficiency Anemia in Children with Type 1 Diabetes
Authors: Wójciak Rafał W. , Mojs Ewa , Stanisławska-Kubiak Maia 
Published: October 2015

Objective A higher risk for iron deficiency, which can lead to anemia, has been noticed in children with early stages of type 1 diabetes. Anemia in diabetes is not uncommon and thus may contribute to disease complications. The aim of the study was to determine the influence of type 1 diabetes incidence on the manifestation of iron-deficiency anemia. Materials and Methods The study included 100 children with type 1 diabetes, aged 6 to 17 years. The diagnosis of type 1 diabetes in all patients was made on the basis of clinical symptoms and, at a later stage, on the basis of the occurrence of islet cell autoantibodies. The patients were divided into groups according to the duration of the disease: those with newly diagnosed type 1 diabetes (ND), those who have the disease for 1 to 3 years (FMD), those who have it for 4 to 6 years (SMD), and those who have it for more than 6 years (LD). Morphological parameters of blood have been measured by means of the flame atomic absorption spectrometry method: red blood cells (RBC), hemoglobin (HGB), acetylated HGB, hematocrit (HCT), RBC volume (mean corpuscular volume [MCV]), HGB mass in RBC (mean corpuscular HGB [MCH]), mean HGB content in RBC (MCH concentration), and serum iron concentration. Results In the ND children, significantly lower concentrations of HCT and HGB as well as the amount of RBC and MCV have been shown, in comparison with the children who have type 1 diabetes longer: for HGB, compared with the FMD children; for HCT, compared with the SMD and LD children; for RBC, compared with the LD children; and for MCV, compared with the SMD children. Some significant inverse correlation has been observed in the MCH concentration in comparison with the children who have type 1 diabetes for more than 1 year. It has been shown that, when compared with the FMD, SMD, and LD children, more ND children are characterized by the coexistence of at least 3 reduced values of the morphological blood parameters associated with iron-deficiency anemia (26%, 17%, 7%, and 3%, respectively). At the same time, it has been found that the mean iron concentration in the blood serum of the ND group is significantly lower than that of the SMD and LD groups. Conclusions The incidence of anemia in the early stages of the disease justifies conducting the screening in all children with type 1 diabetes and taking appropriate preventive measures toward the patients at risk for iron-deficiency anemia.
The Role of Serum Soluble Urokinase-Type Plasminogen Activator Receptor in Stable Chronic Obstructive Pulmonary Disease
Authors: Can Ümmügülsüm , Güzelant Asuman , Yerlikaya Fatma Hümeyra , Yosunkaya Şebnem 
Published: October 2015

Background Chronic obstructive pulmonary disease (COPD) results from an abnormal inflammatory response of the lungs to noxious particles or gases. Serum soluble urokinase-type plasminogen activator receptor (suPAR) is a glycoprotein secreted during infections and inflammation. The main goal of this study was to evaluate the serum suPAR level in stable COPD patients compared with a control group. Methods Forty-six stable COPD patients and 41 control subjects were included in the study. Blood samples were collected from 46 stable COPD patients (40 men, 6 women; mean [SD] age, 55.92 [7.91] years; the forced expiratory volume in 1 second, 45.32% [19.1%] of predicted). Forty-one healthy subjects were selected as control subjects and were matched to COPD patients with respect to age and body mass index. Serum suPAR and plasma fibrinogen levels were measured in stable COPD patients and control subjects. Results Serum suPAR levels of the COPD patients were significantly higher than those of the control subjects (4.94 [2.79] and 2.40 [2.01] ng/mL, respectively; P < 0.001). Plasma fibrinogen levels of the COPD patients were significantly higher than those of the control subjects (406.77 [172.6] and 336.53 [96.1] g/L, respectively; P < 0.05). Conclusions Our study indicated that serum suPAR may play an important role in the inflammatory process of COPD, and this increase may be particularly large for patients in Global Initiative for Chronic Obstructive Lung Disease stages III and IV. Serum suPAR and plasma fibrinogen level measurements may be useful for the evaluation of stable COPD.
Age and Ethnicity in Cirrhosis
Authors: Sajja Krishna C. , Mohan Desh P. , Rockey Don C. 
Published: October 2015

Background Cirrhosis is diagnosed in patients of all ages and is the end result of many different diseases. The aim of this study was to characterize clinical and ethnic features of adult patients who were admitted to the hospital at different (young/old) ages and examine associations between age and ethnicity within these groups. Methods In this retrospective analysis of a diverse cohort of 2017 patients with a clinical diagnosis of cirrhosis between January 2001 and December 2011, we focused on age, ethnicity, and outcome of patients with cirrhosis. Results We identified 219 patients younger than the age of 40 years, including 87 (11%) of 802 white, 31 (6%) of 550 African American, and 89 (16%) of 550 Hispanic patients ( P < 0.001). Ethnicity and causes of cirrhosis were found to have a significant correlation with age. Overall, Hispanic and white patients together were more than twice as likely to be diagnosed with cirrhosis at an age younger than 40 years compared with African American patients ( P < 0.001). Autoimmune hepatitis caused cirrhosis at a younger age regardless of ethnicity ( P < 0.001), whereas cryptogenic/nonalcoholic fatty liver disease/nonalcoholic steatohepatitis was more likely identified at an older age ( P = 0.008). African American patients with cirrhosis due to either alcohol or hepatitis C virus were older than Hispanic ( P < 0.001 and P = 0.003, respectively) and white patients ( P < 0.001 and P < 0.001, respectively) at presentation. Finally, younger patients admitted with cirrhosis had a higher in-hospital mortality rate ( P < 0.001). Conclusions The data suggest an association between ethnicity and age of cirrhosis diagnosis, both overall and in patients with certain cirrhosis etiologies. This work raises the possibility of an ethnic and/or genetic basis for cirrhosis.
Association of Methylenetetrahydrofolate Reductase Gene C677T Polymorphism with Multiple Sclerosis in Turkish Patients
Authors: Cevik Betul , Yigit Serbulent , Karakus Nevin , Aksoy Durdane , Kurt Semiha , Ates Omer 
Published: October 2015

Background and Aim Multiple sclerosis (MS) is a chronic neurodegenerative autoimmune disease of the central nervous system. Genetic risk factors are known to contribute to the etiology of MS. Methylenetetrahydrofolate reductase (MTHFR) gene C677T polymorphism has been associated with susceptibility to various autoimmune diseases. The aim of this study was to investigate a possible association between the MTHFR gene C677T polymorphism and MS in Turkish patients. Methods The study included 130 MS patients and 150 group-matched controls. Genomic DNA was isolated and genotyped using polymerase chain reaction–based restriction fragment length polymorphism assay for the MTHFR gene exon C677T polymorphism. Results The genotype and allele frequencies of C677T polymorphism showed statistically significant differences between MS patients and controls ( P = 0.002 and P = 0.002; odds ratio, 1.79; 95% confidence interval, 1.23-2.63, respectively). A significant association was observed when the patients were compared with the controls according to CC genotype versus CT + TT genotypes ( P = 0.0005; odds ratio, 2.35; 95% confidence interval, 1.45-3.82). There were no statistically significant association between MTHFR gene C677T polymorphism and baseline clinical and demographical characteristics of MS patients. Conclusions These results showed that T allele of C677T polymorphism was associated with MS susceptibility in Turkish population.
The Syndrome of a Large Drop in Hematocrit in Hospitalized Patients: Clinical Features and Gastrointestinal Bleeding Outcomes
Authors: Ong Bryan , Rockey Don C. 
Published: October 2015

Background Hemoglobin/hematocrit decreases in hospitalized patients without evidence of obvious gastrointestinal (GI) bleeding are common and often attributed to GI lesions. We hypothesized that inpatients with hematocrit declines without clinically overt GI bleeding have distinct clinical features and hence aimed to evaluate this clinical syndrome. Methods We evaluated consecutive GI consults for patients with a decrease (drop) in hematocrit. Patients with documented prior GI bleeding, melena, hematochezia, hematemesis, and melenemesis were excluded. Hematocrit drops were calculated from preconsult zenith and nadir values and identified as acute (within 7 days), intermediate (7–30 days), or remote (beyond 30 days) on the basis of the shortest time to a hematocrit drop of at least 6%. Results We identified 101 patients having hematocrit drops without clinical evidence of GI bleeding. Seventy-six patients (75%) had an acute drop in hematocrit with a mean decline of 9.5%, whereas the 25 patients with an intermediate or remote drop in hematocrit had a mean decline of 12.5%. Endoscopic evaluation was performed in 55 patients. Five patients (5%) had a lesion consistent with GI bleeding; identified lesions included ischemic colitis, duodenal ulcer, esophageal varices, and postsphincterotomy ulcer. In the remaining 96 patients, a clinical explanation for the hematocrit drop was identified in 56 patients (58%), most commonly attributed to sepsis/shock, volume shifts, and postprocedure bleeding. Conclusions Hematocrit drops without visible GI bleeding were uncommonly caused by bleeding intestinal lesions, contrary to current dogma. Non-GI explanations for hematocrit drops were often identified, although the cause of hematocrit drop remained unexplained in many patients.
Low Vitamin D Level and Impact on Severity and Recurrence of Clostridium difficile Infections
Authors: Abdelfatah Mohamed , Nayfe Rabih , Moftakhar Bahar , Nijim Ala , El Zoghbi Maysaa , Donskey Curtis J. , Kandil Hossam , Watkins Richard R. 
Published: October 2015

Background Clostridium difficile infection (CDI) has recently markedly increased, incurring greater health care–associated costs and hospitalizations especially in vitamin D deficient patients. Accordingly, the aim of this study was to evaluate the relationship between low vitamin D levels and the severity and recurrence of CDI. Methods A retrospective case-control study evaluated patients hospitalized between 2007 and 2013 with CDI and a positive C. difficile toxin assay. Severe complicated CDI was defined based on (1) laboratory or radiological criteria correlated clinically and (2) sepsis requiring intensive care unit admission. Recurrent CDI (RCDI) was defined as a new episode of diarrhea occurring within 90 days of resolution of the initial episode for at least 10 days after discontinuing therapy and confirmed by positive stool C. difficile toxin assay or polymerase chain reaction. Patients were divided into 4 groups based on vitamin D level (ng/mL): severely deficient (<10), insufficient (10-19.9), predeficient (20-29.9), and control group (≥30). Results Two hundred seventy-one patients were diagnosed with CDI, of which 48 had RCDI distributed as 5 (12.5%), 15 (16.1%), 10 (15.6%), and 13 (17.5%) patients in each of the aforementioned groups, respectively ( P= 0.55). Severe complicated CDI was identified in 7 (17.5%), 17 (18.2%), 9 (14%), and 3 (4%) patients, respectively ( P = 0.04). Thirty-day mortality was 1 of 40, 1 of 93, 2 of 64, and 2 of 74 patients, respectively ( P = 0.43). Conclusions Normal vitamin D level has a protective effect against severe CDI, and low vitamin D is associated with greater severity of CDI but not with an increased risk of RCDI or 30-day mortality.
The Effect of Exercise on Lipid Profiles and Inflammatory Markers in Lean Male Adolescents: A Prospective Interventional Study
Authors: Huang Chun-Jui , Kwok Chin-Fai , Chou Chung-Hsing , Chou Yu-Ching , Ho Low-Tone , Shih Kuang-Chung 
Published: October 2015

Background Physical activity improves body composition and inflammatory markers in obese individuals, but little is known about the nonobese population. Objective The aim of this study was to investigate associations between exercise and inflammatory cytokines in lean male adolescents in Taiwan. Methods This interventional study enrolled a total of 79 normal body weight male adolescents [mean age, 16.8 (1.0) years] from the Army Academy of Taiwan. Body composition and inflammatory markers were measured at baseline and upon completion of a 12-week exercise intervention program. Results Subjects’ postintervention anthropometric measures, including waist circumference [74.6 (5.2) → 72.6 (5.2) cm], hip circumference [92.3 (4.1) → 89.9 (5.0) cm], body fat mass [10.2 (3.2) → 8.2 (3.2) kg], and body fat percentage [15.8% (4.2) → 12.6 (4.5)%] declined significantly compared to preintervention (all P < 0.001), as did systolic blood pressure ( P = 0.002) and mean blood pressure ( P = 0.020). Postintervention body height and free fat mass increased significantly (both P < 0.001). Subjects’ postintervention lipids including total cholesterol, low-density lipoprotein, high-density lipoprotein, and triglycerides increased significantly (all P < 0.001). Inflammatory markers including adiponectin [14.32 (6.68) → 31.31 (30.53) μg/mL, P < 0.001], interleukin 6 [2.15 (4.81) → 2.86 (6.37) pg/mL, P = 0.005], and C-reactive protein [1.00 (2.57) → 2.30 (4.17) μg/mL, P < 0.001] increased significantly postintervention, but not leptin. Conclusions Exercise training significantly improves body composition and anti-inflammatory adiponectin levels in lean male adolescents.