bluuebunny/crossref_metadata_2025_split huggingface dataset:
Smartphone-Based Accurate Analysis of Retinal Vasculature towards Point-of-Care Diagnostics
Authors: Xu Xiayu , Ding Wenxiang , Wang Xuemin , Cao Ruofan , Zhang Maiye , Lv Peilin , Xu Feng 
Published: October 2016

AbstractRetinal vasculature analysis is important for the early diagnostics of various eye and systemic diseases, making it a potentially useful biomarker, especially for resource-limited regions and countries. Here we developed a smartphone-based retinal image analysis system for point-of-care diagnostics that is able to load a fundus image, segment retinal vessels, analyze individual vessel width, and store or uplink results. The proposed system was not only evaluated on widely used public databases and compared with the state-of-the-art methods, but also validated on clinical images directly acquired with a smartphone. An Android app is also developed to facilitate on-site application of the proposed methods. Both visual assessment and quantitative assessment showed that the proposed methods achieved comparable results to the state-of-the-art methods that require high-standard workstations. The proposed system holds great potential for the early diagnostics of various diseases, such as diabetic retinopathy, for resource-limited regions and countries.
The pioneering role of PRDM9 indel mutations in tarsier evolution
Authors: Heerschop Sacha , Zischler Hans , Merker Stefan , Perwitasari-Farajallah Dyah , Driller Christine 
Published: October 2016

AbstractPRDM9 is currently the sole speciation gene found in vertebrates causing hybrid sterility probably due to incompatible alleles. Its role in defining the double strand break loci during the meiotic prophase I is crucial for proper chromosome segregation. Therefore, the rapid turnover of the loci determining zinc finger array seems to be causative for incompatibilities. We here investigated the zinc finger domain-containing exon of PRDM9 in 23 tarsiers. Tarsiers, the most basal extant haplorhine primates, exhibit two frameshifting indels at the 5′-end of the array. The first mutation event interrupts the reading frame and function while the second compensates both. The fixation of this allele variant in tarsiers led to hypothesize that de- and reactivation of the zinc finger domain drove the speciation in early haplorhine or tarsiiform primates. Moreover, the high allelic diversity within Tarsius points to multiple effects of genetic drift reflecting their phylogeographic history since the Miocene.
Microbial Degradation of Cellular Kinases Impairs Innate Immune Signaling and Paracrine TNFα Responses
Authors: Barth Kenneth , Genco Caroline Attardo 
Published: October 2016

AbstractThe NFκB and MAPK signaling pathways are critical components of innate immunity that orchestrate appropriate immune responses to control and eradicate pathogens. Their activation results in the induction of proinflammatory mediators, such as TNFα a potent bioactive molecule commonly secreted by recruited inflammatory cells, allowing for paracrine signaling at the site of an infection. In this study we identified a novel mechanism by which the opportunistic pathogen Porphyromonas gingivalis dampens innate immune responses by disruption of kinase signaling and degradation of inflammatory mediators. The intracellular immune kinases RIPK1, TAK1, and AKT were selectively degraded by the P. gingivalis lysine-specific gingipain (Kgp) in human endothelial cells, which correlated with dysregulated innate immune signaling. Kgp was also observed to attenuate endothelial responsiveness to TNFα, resulting in a reduction in signal flux through AKT, ERK and NFκB pathways, as well as a decrease in downstream proinflammatory mRNA induction of cytokines, chemokines and adhesion molecules. A deficiency in Kgp activity negated decreases to host cell kinase protein levels and responsiveness to TNFα. Given the essential role of kinase signaling in immune responses, these findings highlight a unique mechanism of pathogen-induced immune dysregulation through inhibition of cell activation, paracrine signaling, and dampened cellular proinflammatory responses.
A crucial role for spatial distribution in bacterial quorum sensing
Authors: Gao Meng , Zheng Huizhen , Ren Ying , Lou Ruyun , Wu Fan , Yu Weiting , Liu Xiudong , Ma Xiaojun 
Published: October 2016

AbstractQuorum sensing (QS) is a process that enables bacteria to communicate using secreted signaling molecules, and then makes a population of bacteria to regulate gene expression collectively and control behavior on a community-wide scale. Theoretical studies of efficiency sensing have suggested that both mass-transfer performance in the local environment and the spatial distribution of cells are key factors affecting QS. Here, an experimental model based on hydrogel microcapsules with a three-dimensional structure was established to investigate the influence of the spatial distribution of cells on bacterial QS. Vibrio harveyi cells formed different spatial distributions in the microcapsules, i.e., they formed cell aggregates with different structures and sizes. The cell aggregates displayed stronger QS than did unaggregated cells even when equal numbers of cells were present. Large aggregates (LA) of cells, with a size of approximately 25 μm, restricted many more autoinducers (AIs) than did small aggregates (SA), with a size of approximately 10 μm, thus demonstrating that aggregate size significantly affects QS. These findings provide a powerful demonstration of the fact that the spatial distribution of cells plays a crucial role in bacterial QS.
One-Pot Approach to Prepare Organo-silica Hybrid Capillary Monolithic Column with Intact Mesoporous Silica Nanoparticle as Building Block
Authors: Liu Shengju , Peng Jiaxi , Liu Zheyi , Liu Zhongshan , Zhang Hongyan , Wu Ren’an 
Published: October 2016

AbstractA facile “one-pot” approach to prepare organo-silica hybrid capillary monolithic column with intact mesoporous silica nanoparticle (IMSN) as crosslinker and building block was described. An IMSN crosslinked octadecyl-silica hybrid capillary monolithic column (IMSN-C18 monolithic column) was successfully prepared, and the effects of fabrication conditions (e.g. concentration of intact mesoporous silica nanoparticle, polycondensation temperature, content of vinyltrimethoxysilane and stearyl methacrylate) on the structures of the IMSN-C18 monolithic column were studied in detail. The IMSN-C18 hybrid monolithic column possessed uniform morphology, good mechanical and pH stability (pH 1.1–11), which was applied to the separations of alkyl benzenes, polycyclic aromatic hydrocarbons (PAHs), as well as proteins. The minimum plate height of 10.5 μm (corresponding to 95000 N m−1) for butylbenzene and high reproducibility were achieved. The analysis of tryptic digest of bovine serum albumin (BSA) was carried out on the IMSN-C18 monolithic column by cLC coupled mass spectrometry (cLC-MS/MS), with the protein sequence coverage of 87.5% for BSA, demonstrating its potential application in proteomics.
Prediction of phosphothreonine sites in human proteins by fusing different features
Authors: Zhao Ya-Wei , Lai Hong-Yan , Tang Hua , Chen Wei , Lin Hao 
Published: October 2016

AbstractPhosphorylation is one of the most important protein post-translation modifications. With the rapid development of high-throughput mass spectrometry, phosphorylation site data is rapidly accumulating, which provides us an opportunity to systematically investigate and predict phosphorylation in proteins. The phosphorylation of threonine is the addition of a phosphoryl group to its polar side chains group. In this work, we statistically analyzed the distribution of the different properties including position conservation, secondary structure, accessibility and some other physicochemical properties of the residues surrounding the phosphothreonine site and non-phosphothreonine site. We found that the distributions of those features are non-symmetrical. Based on the distribution of properties, we developed a new model by using optimal window size strategy and feature selection technique. The cross-validated results show that the area under receiver operating characteristic curve reaches to 0.847, suggesting that our model may play a complementary role to other existing methods for predicting phosphothreonine site in proteins.
Impact of the Ile105Val Polymorphism of the Glutathione S-transferase P1 (GSTP1) Gene on Obesity and Markers of Cardiometabolic Risk in Young Adult Population
Authors: Chielle E. , Trott A. , da Silva Rosa B. , Casarin J. , Fortuna P. , da Cruz I. , Moretto M. , Moresco R. 
Published: October 2016

AbstractThe aim of the study was to investigate the association between Glutathione S-transferase P1 (GSTP1) gene polymorphism with obesity and markers of cardiometabolic risk. A cross-sectional study was carried out in individuals aged≥18 and ≤30 years. The study included 54 normal weight, 27 overweight and 68 obese volunteers. Anthropometric measurements and biochemical parameters were evaluated, the DNA was extracted from blood samples and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to measure GSTP1 Ile105Val gene polymorphism of the study participants. Also, biochemical analysis and hormone assays were carried out. A positive association between GSTP1 polymorphism and obesity was observed on subjects carrying at least one G allele (AG and GG). GG genotype was found only in the obese group. The G allele carriers presented 2.4 times higher chance of obesity when compared to those with the AA genotype. These results were independent of sex and age. We suggest that despite a study in population regional (south of Brazil), the GSTP1 gene polymorphism may play a significant role in the increase of susceptibility of obesity and contribute to identify the cardiovascular risk in young adults.
Choline and betaine ameliorate liver lipid accumulation induced by vitamin B6 deficiency in rats
Authors: Kitagawa Erina , Yamamoto Tatsuya , Fujishita Mayuko , Ota Yuki , Yamamoto Kohei , Nakagawa Tomoyuki , Hayakawa Takashi 
Published: October 2016

Abstract
We investigated the efficacy of supplementing the diet with choline or betaine in ameliorating lipid accumulation induced by vitamin B6 (B6) deficiency in rat liver. Male Wistar rats were fed a control, B6-deficient, choline-supplemented (2, 4, or 6 g choline bitartrate/kg diet) B6-deficient diet or betaine-supplemented (1, 2, or 4 g betaine anhydrous/kg diet) B6-deficient diet for 35 d; all diets contained 9 g l-methionine (Met)/kg diet. Choline or betaine supplementation attenuated liver lipid deposition and restored plasma lipid profiles to control levels. These treatments restored the disruptions in Met metabolism and the phosphatidylcholine (PC)/phosphatidylethanolamine (PE) ratio induced by B6 deficiency in liver microsomes. These results suggest that choline and betaine ameliorated liver lipid accumulation induced by B6 deficiency via recovery of Met metabolism and very low-density lipoprotein secretion by restoring the supply of PC derived from PE.
PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL
Authors: Janson Giacomo , Zhang Chengxin , Prado Maria Giulia , Paiardini Alessandro 
Published: October 2016

Abstract

Motivation
The recently released PyMod GUI integrates many of the individual steps required for protein sequence-structure analysis and homology modeling within the interactive visualization capabilities of PyMOL. Here we describe the improvements introduced into the version 2.0 of PyMod.

Results
The original code of PyMod has been completely rewritten and improved in version 2.0 to extend PyMOL with packages such as Clustal Omega, PSIPRED and CAMPO. Integration with the popular web services ESPript and WebLogo is also provided. Finally, a number of new MODELLER functionalities have also been implemented, including SALIGN, modeling of quaternary structures, DOPE scores, disulfide bond modeling and choice of heteroatoms to be included in the final model.

Availability and Implementation
PyMod 2.0 installer packages for Windows, Linux and Mac OS X and user guides are available at http://schubert.bio.uniroma1.it/pymod/index.html. The open source code of the project is hosted at https://github.com/pymodproject/pymod.
Distribution characteristics of coronal electric current density as an indicator for the occurrence of a solar flare
Authors: Kang Jihye , Magara Tetsuya , Inoue Satoshi , Kubo Yuki , Nishizuka Naoto 
Published: October 2016

Abstract
In this paper we investigate the distribution characteristics of the coronal electric current density in a flare-producing active region (AR12158; SOL2014-09-10) by reconstructing nonlinear force-free (NLFF) fields from photospheric magnetic field data. A time series of NLFF fields shows the spatial distribution and its temporal development of coronal current density in this active region. A fractal dimensional analysis shows that a concentrated coronal current forms a structure of fractal spatiality. Furthermore, the distribution function of coronal current density is featured with a double power-law profile, and the value of electric current density at the breaking point of a double power-law fitting function shows a noticeable time variation toward the onset of an X-class flare. We discuss that this quantity will be a useful indicator for the occurrence of a flare.
News Shocks in Open Economies: Evidence from Giant Oil Discoveries*
Authors: Arezki Rabah , Ramey Valerie A. , Sheng Liugang 
Published: October 2016

AbstractThis article explores the effect of news shocks in open economies using worldwide giant oil and gas discoveries as a directly observable measure of news shocks about future output—the delay between a discovery and production is on average four to six years. We first analyze the effects of a discovery in a two-sector small open economy model with a resource sector. We then estimate the effects of giant oil and gas discoveries on a large panel of countries. Our empirical estimates are consistent with the predictions of the model. After an oil or gas discovery, the current account and saving rate decline for the first five years and then rise sharply during the ensuing years. Investment rises robustly soon after the news arrives, whereas GDP does not increase until after five years. Employment rates fall slightly and remain low for a sustained period.
Estrogen alone and health outcomes in black women by African ancestry: a secondary analyses of a randomized controlled trial
Authors: Chlebowski Rowan T. , Barrington Wendy , Aragaki Aaron K. , Manson JoAnn E. , Sarto Gloria , O'Sullivan Mary J. , Wu Daniel , Cauley Jane A. , Qi Lihong , Wallace Robert L. , Prentice Ross L. 
Published: October 2016

Abstract

Objective:
In postmenopausal black women in the Women's Health Initiative randomized trial, estrogen alone reduced breast cancers but its comprehensive influence on health outcomes in black women is unknown. Therefore, we examined this issue in the Women's Health Initiative overall and by African ancestry.

Methods:
A total of 1,616 black women with prior hysterectomy, including 1,061 with percent African ancestry determination, at 40 US centers were randomly assigned to conjugated equine estrogen (0.625 mg/d) or placebo for 7.2 years’ (median) intervention with 13 years’ cumulative follow-up. Coronary heart disease (CHD) and breast cancer were primary efficacy and safety outcomes, respectively. A global index also included stroke, colorectal cancer, hip fracture, pulmonary embolism, and death.

Results:
Black women in the estrogen-alone group compared with black women in the placebo group had fewer breast cancers (17 vs 40, hazard ratio [HR] 0.47, 95% CI 0.26-0.82). In women with more than 80% African ancestry, breast cancer HR was lower (0.32, 95% CI 0.12-0.86, trend P = 0.04 for ancestry effect). Most other outcomes including CHD, stroke, hip fracture, and the global index were null with estrogen use in black women; a global index effect was more favorable in younger black women (HR 0.65, 95% CI 0.43-0.98).

Conclusions:
In black postmenopausal women with prior hysterectomy, estrogen alone significantly reduced breast cancer incidence with no adverse influence on CHD, venous thromboembolism, or all-cause mortality. Favorable estrogen-alone global index effects in younger black women warrant further study.
Increased expression of progesterone receptor membrane component 1 is associated with aggressive phenotype and poor prognosis in ER-positive and negative breast cancer
Authors: Ruan Xiangyan , Zhang Ying , Mueck Alfred O. , Willibald Marina , Seeger Harald , Fehm Tanja , Brucker Sara , Neubauer Hans 
Published: October 2016

AbstractObjective:Expression of progesterone receptor membrane component 1 (PGRMC1) has been shown to be higher in breast cancer than normal tissue. We have previously shown that certain progestogens strongly stimulate proliferation of breast cancer cells overexpressing PGRMC1, and therefore hypothesize that PGRMC1 may play a critical role in breast cancer progression. Because little information is available if expression of PGRMC1 is also associated with worse prognosis for breast cancer patients, in this study we investigated the clinicopathologic significance of PGRMC1 expression in breast cancer tissue.Methods:Expression of PGRMC1 was analyzed by immunohistochemical staining of primary tumor tissues obtained from 69 breast cancer patients. A labeling score was developed, and results were correlated with tumor size, lymph node metastasis, and clinical outcome.Results:Overexpression of PGRMC1 is correlating with larger tumor size and lymph node metastasis. Kaplan-Meier survival curves indicate that patients with PGRMC1hightumors have poorer disease-free and overall survival independent from the estrogen receptor status than breast cancer patients with PGRMC1lowtumors.Conclusions:Our findings suggest that the expression of PGRMC1 might be useful for predicting prognosis in patients with breast cancer.
Bioavailable insulin-like growth factor-I as mediator of racial disparity in obesity-relevant breast and colorectal cancer risk among postmenopausal women
Authors: Jung Su Yon , Barrington Wendy E. , Lane Dorothy S. , Chen Chu , Chlebowski Rowan , Corbie-Smith Giselle , Hou Lifang , Zhang Zuo-Feng , Paek Min-So , Crandall Carolyn J. 
Published: October 2016

Abstract

Objective:
Bioavailable insulin-like growth factor-I (IGF-I) interacts with obesity and exogenous estrogen (E) in a racial disparity in obesity-related cancer risk, yet their interconnected pathways are not fully characterized. We investigated whether circulating bioavailable IGF-I acted as a mediator of the racial disparity in obesity-related cancers such as breast and colorectal (CR) cancers and how obesity and E use regulate this relationship.

Methods:
A total of 2,425 white and 164 African American (AA) postmenopausal women from the Women's Health Initiative Observational Study were followed from October 1, 1993 through August 29, 2014. To assess bioactive IGF-I as a mediator of race-cancer relationship, we used the Baron-Kenny method and quantitative estimation of the mediation effect.

Results:
Compared with white women, AA women had higher IGF-I levels; their higher risk of CR cancer, after accounting for IGF-I, was no longer significant. IGF-I was associated with breast and CR cancers even after controlling for race. Among viscerally obese (waist/hip ratio >0.85) and overall nonobese women (body mass index <30), IGF-I was a strong mediator, reducing the racial disparity in both cancers by 30% and 60%, respectively. In E-only users and nonusers, IGF-I explained the racial disparity in CR cancer only modestly.

Conclusions:
Bioavailable IGF-I is potentially important in racial disparities in obesity-related breast and CR cancer risk between postmenopausal AA and white women. Body fat distribution and E use may be part of the interconnected hormonal pathways related to racial difference in IGF-I levels and obesity-related cancer risk.
A Case of Child Physical Abuse With a Rolling Pin Insertion, Resulting in Bladder and Rectal Perforation
Authors: Kondolot Meda , Doganay Selim , Turan Cüneyt , Asil Hasim , Oztop Didem B. , Ozdemir Caglar 
Published: October 2016

Abstract
Visceral injuries are not uncommon in nonaccidental trauma and often require emergent operative intervention. However, sometimes it can be difficult to assess the extent of injury. In this report, we present a case of child physical abuse resulting in bladder and rectal perforations, which was initially referred to our hospital as acute abdomen with intraperitoneal free fluid on ultrasonography. An exploratory laparotomy revealed the perforations and surgical repair was performed. The patient was evaluated by the Hospital Child Protective team and it was revealed that bladder and rectum perforations were due to insertion of rolling pin into the rectum by the stepmother. The child was discharged home uneventfully with a temporary colostomy. We believe that this is the first reported case in the English literature of inflicted perforation of the rectum and bladder through insertion of a rolling pin.
Prevalence of Abuse Among Young Children With Rib Fractures
Authors: Paine Christine Weirich , Fakeye Oludolapo , Christian Cindy W. , Wood Joanne N. 
Published: October 2016

Objectives
We aimed to estimate the prevalence of abuse in young children presenting with rib fractures and to identify demographic, injury, and presentation-related characteristics that affect the probability that rib fractures are secondary to abuse.

Methods
We searched PubMed/MEDLINE and CINAHL databases for articles published in English between January 1, 1990, and June 30, 2014 on rib fracture etiology in children 5 years or younger. Two reviewers independently extracted predefined data elements and assigned quality ratings to included studies. Study-specific abuse prevalences and the sensitivities, specificities, and positive and negative likelihood ratios of patients' demographic and clinical characteristics for abuse were calculated with 95% confidence intervals.

Results
Data for 1396 children 48 months or younger with rib fractures were abstracted from 10 articles. Among infants younger than 12 months, abuse prevalence ranged from 67% to 82%, whereas children 12 to 23 and 24 to 35 months old had study-specific abuse prevalences of 29% and 28%, respectively. Age younger than 12 months was the only characteristic significantly associated with increased likelihood of abuse across multiple studies. Rib fracture location was not associated with likelihood of abuse. The retrospective design of the included studies and variations in ascertainment of cases, inclusion/exclusion criteria, and child abuse assessments prevented further meta-analysis.

Conclusions
Abuse is the most common cause of rib fractures in infants younger than 12 months. Prospective studies with standardized methods are needed to improve accuracy in determining abuse prevalence among children with rib fractures and characteristics associated with abusive rib fractures.