bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein–Sol: a web tool for predicting protein solubility from sequence
Authors: Hebditch Max , Carballo-Amador M Alejandro , Charonis Spyros , Curtis Robin , Warwicker Jim 
Published: May 2017

Abstract

Motivation
Protein solubility is an important property in industrial and therapeutic applications. Prediction is a challenge, despite a growing understanding of the relevant physicochemical properties.

Results
Protein–Sol is a web server for predicting protein solubility. Using available data for Escherichia coli protein solubility in a cell-free expression system, 35 sequence-based properties are calculated. Feature weights are determined from separation of low and high solubility subsets. The model returns a predicted solubility and an indication of the features which deviate most from average values. Two other properties are profiled in windowed calculation along the sequence: fold propensity, and net segment charge. The utility of these additional features is demonstrated with the example of thioredoxin.

Availability and implementation
The Protein–Sol webserver is available at http://protein-sol.manchester.ac.uk.
Electromagnetic interior transmission eigenvalue problem for inhomogeneous media containing obstacles and its applications to near cloaking
Authors: Li Xiaofei , Li Jingzhi , Liu Hongyu , Wang Yuliang 
Published: May 2017

Abstract
This article is concerned with the invisibility cloaking in electromagnetic wave scattering from a new perspective. We are especially interested in achieving the invisibility cloaking by completely regular and isotropic mediums. Our study is based on an interior transmission eigenvalue problem. We propose a cloaking scheme that takes a three-layer structure including a cloaked region, a lossy layer and a cloaking shell. The target medium in the cloaked region can be arbitrary but regular, whereas the mediums in the lossy layer and the cloaking shell are both regular and isotropic. We establish that there exists an infinite set of incident waves such that the cloaking device is nearly invisible under the corresponding wave interrogation. The set of waves is generated from the Maxwell–Herglotz approximation of the associated interior transmission eigenfunctions. We provide the mathematical design of the cloaking device and sharply quantify the cloaking performance.
Natural and artificial spectral edges in exoplanets
Authors: Lingam Manasvi , Loeb Abraham 
Published: May 2017

Abstract
Technological civilizations may rely upon large-scale photovoltaic arrays to harness energy from their host star. Photovoltaic materials, such as silicon, possess distinctive spectral features, including an ‘artificial edge' that is characteristically shifted in wavelength shortwards of the ‘red edge' of vegetation. Future observations of reflected light from exoplanets would be able to detect both natural and artificial edges photometrically, if a significant fraction of the planet's surface is covered by vegetation or photovoltaic arrays, respectively. The stellar energy thus tapped can be utilized for terraforming activities by transferring heat and light from the day side to the night side on tidally locked exoplanets, thereby producing detectable artefacts.
Methotrexate as effective and safe choice for the treatment of rheumatoid arthritis
Authors: Kumar Vivek , Prakash Jaya , Kumar Ajai , Tripathy Baishnab C. , Gupta Varsha , Khan Mohammad Yahiya 
Published: May 2017

Background:
Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease. For controlling the disease activity, various therapeutic modalities are used. Each of them have advantages and limitations. This study analyzes effectiveness and toxicity of methotrexate (MTX) on liver and lipid functions in selected RA patients and controls.

Methods:
This study included samples of patients with RA who were on MTX therapy and had long-term follow-up. The control and patient samples were used for analysis of lipid parameters, inflammatory markers as erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP), essential mineral accumulation, and liver and kidney function test.

Results:
Hemoglobin was reduced in RA patients; however, ESR, CRP and pain on the visual analog scale were significantly higher as compared to controls. Their alanine aminotransferase, aspartate aminotransferase and uric acid were within normal ranges. Serum magnesium was significantly reduced in RA patients. They showed higher values for zinc, phosphorous, and copper. They had borderline dyslipidemia.

Conclusions:
MTX was found to be safe and effective for treatment of RA. The liver function test of RA patients was normal. They had disturbances in mineral accumulation, suggesting the requirement of mineral evaluation and supplementation especially of magnesium in RA patients. The treatment was beneficial in reducing inflammation and reducing the activity of the disease. The treatment was also beneficial for lipid parameters reducing the risk of cardiovascular disease. The study supports MTX as the good choice for treatment of RA.
Are cephalomedullary interlocking screws superior to standard interlocking screws in subtrochanteric femoral fractures with an intact lesser trochanter?
Authors: Konopka Geoffrey , Ritchey Andrew , Ambrose Catherine G. , Galpin Matthew , Munz John W. , Achor Timothy S. , Choo Andrew , Gary Joshua L. 
Published: May 2017

Background:
Subtrochanteric femoral fractures often are treated with cephalomedullary nails, but standard intramedullary nails may be sufficient to treat many subtrochanteric femoral fractures. We hypothesized that standard intramedullary nailing of subtrochanteric femoral fractures with an intact lesser trochanter is not inferior to cephalomedullary nailing.

Methods:
We performed a retrospective analysis of patients treated with an intramedullary device for a proximal femoral fracture within 5 cm of the lesser trochanter between January 1, 2011 and December 31, 2013. We compared standard and cephalomedullary nails with regards to fracture union, nonunion, and alignment. Exclusion criteria included comminution involving the lesser trochanter, intertrochanteric fractures, use of a plate, or pathologic fractures.

Results:
Fifty patients with 52 subtrochanteric femoral fractures met the inclusion criteria, with 39 men and 11 women. Thirteen fractures were treated with a standard, locked intramedullary nail, of which nine had adequate follow-up (69%). All nine fractures healed uneventfully. Thirty-nine fractures were treated with a cephalomedullary nail in 38 patients, of which 30 had adequate follow-up (77%). There were two nonunions that required revision surgery (5%) in the cephalomedullary group. There was no statistically significant difference between the two groups with respect to fracture union, nonunion, or revision surgery (P=0.59 Fisher Exact Test).

Conclusions:
Subtrochanteric femoral fractures with an intact lesser trochanter can be successfully treated with standard locking nails. This study is underpowered to determine if standard locking or cephalomedullary locking is superior to the other, but all failures occurred in the cephalomedullary group.
Female exposure to endocrine disrupting chemicals and fecundity: a review
Authors: Mínguez-Alarcón Lidia , Gaskins Audrey J. 
Published: May 2017

Purpose of review
Endocrine disrupting chemicals (EDCs) have been known for their ability to interfere with aspects of hormone action resulting in adverse health consequences among animals and humans; however, the effects of EDCs on human fecundity have shown inconsistent findings. This review summarizes the most recent epidemiologic literature from humans on the potential effects of female exposure to nonpersistent EDCs, specifically bisphenol A (BPA), phthalates, parabens, and triclosan, on fecundity, measured by markers of reproductive hormones, markers of ovulation or ovarian reserve, IVF outcomes, and time-to-pregnancy.

Recent findings
Although the epidemiologic literature on this topic is growing, the evidence supporting an association between female urinary concentrations of BPA, phthalates, parabens and triclosan, and fecundity remains unclear. The heterogeneous results could be due to methodological differences in recruitment populations (fertile vs. subfertile), study designs (prospective vs. retrospective), assessment of exposure (including differences in the number and timing of urine samples and differences in the analytical methods used to assess the urinary concentrations), residual confounding due to diet or other lifestyle factors, and coexposures to other chemicals.

Summary
At present, there is limited evidence to conclude that female exposure to nonpersistent EDCs affect fecundity in humans. Further studies focusing on exposure to mixtures of EDCs are needed.
Outbreaks of nontuberculous mycobacteria
Authors: Sood Geeta , Parrish Nikki 
Published: May 2017

Purpose of review
The purpose of this review is to summarize the emerging literature on nontuberculous mycobacteria outbreaks in healthcare settings. As our ability to identify mycobacterial species develops, we are better able to recognize epidemiologic connections and better understand the prevalence and importance of these outbreaks and pseudo-outbreaks in healthcare settings.

Recent findings
The number of outbreaks related to nontuberculous outbreaks is increasing because of heightened awareness and better diagnostic tests for species level identification of mycobacteria. Outbreaks in healthcare settings have been related to cardiac surgery, plastic surgery, including medical tourism, colonized humidifiers and heater–cooler devices, imperfect disinfection, and hospital water sources. Mycobacteria have a predilection to form biofilms, are resistant to disinfection and are prevalent in hospital water systems. Patients with structural lung disease like cystic fibrosis patients are at particularly high risk for mycobacterial infection. It has been thought that acquisition in this patient population is from common environmental exposure; however, there is increasing evidence that transmission in this patient population can occur through either direct or indirect patient-to-patient spread.

Summary
Mycobacteria outbreaks in healthcare settings have been underrecognized. As we identify additional clusters of infection with better diagnostic tools and heightened awareness, we will likely need better infection control practices to prevent infections in healthcare settings.
Noninvasive Thermometry in High-Intensity Focused Ultrasound Ablation
Authors: Zhou Yufeng 
Published: May 2017

AbstractHigh-intensity focused ultrasound (HIFU) is emerging as an effective and promising treatment modality for the formation of coagulative necrosis inside the cancer/tumor noninvasively. To guarantee the efficacy and efficiency of HIFU ablation, the temperature field and consequent thermal dose should be monitored accurately in a high temporal and spatial resolution in real time. However, because of the significant variations of the tissue properties and deep penetration of HIFU beam, especially in the abdominal application, noninvasive thermometry is a very challenging topic, which may hamper the wide acceptance of HIFU by physicians worldwide. In this article, currently available thermometry techniques are reviewed, and their translation from hyperthermia range to the higher temperature for irreversible lesion production is discussed. With the technology improvement and/or development of new approaches, the performance of noninvasive thermometry may meet the clinical requirements.
Effect of Fc-γ Receptor Polymorphism on Rituximab-Mediated B Cell Depletion in ABO-Incompatible Adult Living Donor Liver Transplantation
Authors: Sakai Hiroshi , Tanaka Yuka , Tazawa Hirofumi , Shimizu Seiichi , Verma Sapana , Ohira Masahiro , Tahara Hiroyuki , Ide Kentaro , Ishiyama Kohei , Kobayashi Tsuyoshi , Onoe Takashi , Ohdan Hideki 
Published: May 2017

Background
The affinity of IgG Fc receptor (FcγR) for rituximab, an anti-CD20 IgG1, differs based on single-nucleotide polymorphisms (SNPs) in FcγRs. This study aimed to explore the effect of such SNPs on clinical response to rituximab and outcomes in patients of ABO-incompatible (ABOi) living donor liver transplantation (LDLT).

Methods
SNPs of FCGR2A[131H/R] and FCGR3A[158F/V], alleles encoding FcγR, were identified in 20 patients desensitized with rituximab before ABOi LDLT. The effect of these SNPs on B cell elimination and outcomes was analyzed in the patients.

Results
The isoform encoded by FCGR2A[131H/H] had a higher affinity for IgG1, and accordingly, the effects of rituximab on B cells were more profound in individuals with FCGR2A[131H/H] than in individuals with FCGR2A[131H/R or R/R]. Specifically, the time to B-cell reappearance in the peripheral blood was significantly delayed, and total serum IgM levels were significantly lower early after LDLT in individuals with FCGR2A[131H/H], even though these SNPs did not significantly affect the reduction of antiblood group A/B antibodies. The incidence of blood stream infection was also significantly higher in individuals with FCGR2A[131H/H], and this SNP was associated with poor prognosis. Despite no significant effect of FCGR3A[158F/V] on survival after ABOi liver grafts, the incidence of infection was significantly higher in individuals with FCGR3A[158F/V or F/F] than in individuals with FCGR3A[158V/V].

Conclusions
Our findings indicate FCGR SNPs influence the effect of rituximab on B-cell depletion and are possibly predisposing factors for infectious complications after ABOi LDLT. This study will be a good foundation for further studies on larger cohorts.
Association between a functional polymorphism rs10830963 inmelatonin receptor 1Band risk of gestational diabetes mellitus: an updated meta-analysis
Authors: Xiangyuan Yu , Qianqian Wang , Linyuan Qin , Lingxiang Peng , Zaiming Chen , Xiumei Qin , Yuchun Wang , Qingfeng Shi , Hongping Yu 
Published: May 2017

AbstractThe melatonin receptor 1B(MTNR1B) as a candidate gene for gestational diabetes mellitus (GDM) on the basis of its association with T2DM, β-cells function and fasting plasma glucose (FPG) level. Many studies have investigated the association betweenMTNR1Bpolymorphism rs10830963 C>G and GDM risk, but the conclusion is inconsistent. PubMed, Google Scholar and CNKI databases were searched to identify eligible studies. Pooled OR with corresponding 95% CI was used to estimate the strength of the association between rs10830963 and GDM risk using a fixed- or random-effect model. 12 eligible studies with a number of 4,782 GDM patients and 5,605 controls were included in this meta-analysis. Results indicated that the variant G allele of rs10830963 polymorphism was significantly associated with an increased risk of GDM (CG vs. CC: OR=1.23, 95%CI= 1.12–1.34,Pheterogeneity= 0.23; GG vs. CC: OR=1.74, 95%CI=1.41–2.15,Pheterogeneity= 0.002). In the stratified analysis by ethnicity, similar results were found in Asians (CG vs. CC: OR=1.15, 95%CI= 1.04–1.28,Pheterogeneity= 0.74; GG VS. CC: OR=1.48, 95%CI=1.23–1.78,Pheterogeneity= 0.08) and in Caucasians (CG vs. CC: OR=1.49, 95%CI=1.25–1.77, Pheterogeneity= 0.28; GG vs. CC: OR=2.68, 95%CI=2.03–3.54,Pheterogeneity= 0.58).
Single molecule mechanics reveal Kif15 as an active molecular ratchet with acute strain sensitivity
Authors: McHugh T. , Drechsler H. , McAinsh A. D. , Carter N. J. , Cross R. A. 
Published: May 2017

AbstractHuman Kif15 is a tetrameric kinesin-12 that contributes critically to bipolar spindle assembly in eukaryotes. Here we examine its single molecule mechanics. Under hindering loads, Kif15 steps predominantly towards microtubule plus ends, with its forestep:backstep ratio decreasing exponentially with load and stall occurring at ~6pN. Between steps, Kif15 binds stably, usually via a single head domain. By complete contrast, under assisting loads, Kif15 detaches rapidly, even in AMPPNP. Furthermore, Kif15 can autoinhibit, via an interaction requiring its C-terminus. Autoinhibited Kif15 binds microtubules nucleotide-independently, resists both hindering and assisting loads, and is further stabilized by Tpx2, which interacts with the Kif15 C-terminus. Our data reveal the mechanics of Kif15 to be extraordinarily sensitive to loading direction. When unloaded, it walks rapidly; when pulled forwards it slips and when pulled backwards it grips. We discuss the implications of this unique mechanical behaviour for the roles of Kif15 in spindle function.
Evaluation of Chromatin Accessibility in Prefrontal Cortex of Schizophrenia Cases and Controls
Authors: Bryois Julien , Garrett Melanie E , Song Lingyun , Safi Alexias , Giusti-Rodriguez Paola , Johnson Graham D , Demur Alfonso Buil , Fullard John F , Roussos Panos , Sklar Pamela , Akbarian Schahram , Haroutunian Vahram , Stockmeier Craig A , Wray Gregory A , White Kevin P , Liu Chunyu , Reddy Timothy E , Ashley-Koch Allison , Sullivan Patrick F , Crawford Gregory E 
Published: May 2017

AbstractSchizophrenia genome-wide association (GWA) studies have identified over 150 regions of the genome that are associated with disease risk, yet there is little evidence that coding mutations contribute to this disorder. To explore the mechanism of non-coding regulatory elements in schizophrenia, we performed ATAC-seq on adult prefrontal cortex brain samples from 135 individuals with schizophrenia and 137 controls, and identified 118,152 ATAC-seq peaks. These accessible chromatin regions in brain are highly enriched for SNP-heritability for schizophrenia (10.6 fold enrichment, P=2.4×10−4, second only to genomic regions conserved in Eutherian mammals) and replicated in an independent dataset (9.0 fold enrichment, P=2.7×10−4). This degree of enrichment of schizophrenia heritability was higher than in open chromatin found in 138 different cell and tissue types. Brain open chromatin regions that overlapped highly conserved regions exhibited an even higher degree of heritability enrichment, indicating that conservation can identify functional subsets within regulatory elements active in brain. However, we did not identify chromatin accessibility differences between schizophrenia cases and controls, nor did we find an interaction of chromatin QTLs with case-control status. This indicates that although causal variants map within regulatory elements, mechanisms other than differential chromatin may govern the contribution of regulatory element variation to schizophrenia risk. Our results strongly implicate gene regulatory processes involving open chromatin in the pathogenesis of schizophrenia, and suggest a strategy to understand the hundreds of common variants emerging from large genomic studies of complex brain diseases.
Reconfiguration of Dominant Coupling Modes in Mild Traumatic Brain Injury Mediated by δ-band Activity: a Resting State MEG Study
Authors: Antonakakis Marios , Dimitriadis Stavros I. , Zervakis Michalis , Papanicolaou Andrew C. , Zouridakis George 
Published: May 2017

AbstractDuring the last few years, rich-club (RC) organization has been studied as a possible brain-connectivity organization model for large-scale brain networks. At the same time, empirical and simulated data of neurophysiological models have demonstrated the significant role of intra-frequency and inter-frequency coupling among distinct brain areas. The current study investigates further the importance of these couplings using recordings of resting-state magnetoencephalographic activity obtained from 30 mild traumatic brain injury (mTBI) subjects and 50 healthy controls. Intra-frequency and inter-frequency coupling modes are incorporated in a single graph to detect group differences within individual rich-club subnetworks (type I networks) and networks connecting RC nodes with the rest of the nodes (type II networks). Our results show a higher probability of inter-frequency coupling for (δ−γ1), (δ−γ2), (θ−β), (θ−γ2), (α−γ2), (γ1−γ2) and intra-frequency coupling for (γ1−γ1) and (δ−δ) for both type I and type II networks in the mTBI group. Additionally, mTBI and control subjects can be correctly classified with high accuracy (98.6%), whereas a general linear regression model can effectively predict the subject group using the ratio of type I and type II coupling in the (δ, θ), (δ, β), (δ, γ1), and (δ, γ2) frequency pairs. These findings support the presence of an RC organization simultaneously with dominant frequency interactions within a single functional graph. Our results demonstrate a hyperactivation of intrinsic RC networks in mTBI subjects compared to controls, which can be seen as a plausible compensatory mechanism for alternative frequency-dependent routes of information flow in mTBI subjects.
Phenotype-driven transitions in regulatory network structure
Authors: Padi Megha , Quackenbush John 
Published: May 2017

AbstractComplex traits and diseases like human height or cancer are often not caused by a single mutation or genetic variant, but instead arise from multiple factors that together functionally perturb the underlying molecular network. Biological networks are known to be highly modular and contain dense “communities” of genes that carry out cellular processes, but these structures change between tissues, during development, and in disease. While many methods exist for inferring networks, we lack robust methods for quantifying changes in network structure. Here, we describe ALPACA (ALteredPartitionsAcrossCommunityArchitectures), a method for comparing two genome-scale networks derived from different phenotypic states to identify condition-specific modules. In simulations, ALPACA leads to more nuanced, sensitive, and robust module discovery than currently available network comparison methods. We used ALPACA to compare transcriptional networks in three contexts: angiogenic and non-angiogenic subtypes of ovarian cancer, human fibroblasts expressing transforming viral oncogenes, and sexual dimorphism in human breast tissue. In each case, ALPACA identified modules enriched for processes relevant to the phenotype. For example, modules specific to angiogenic ovarian tumors were enriched for genes associated with blood vessel development, interferon signaling, and flavonoid biosynthesis. In comparing the modular structure of networks in female and male breast tissue, we found that female breast has distinct modules enriched for genes involved in estrogen receptor and ERK signaling. The functional relevance of these new modules indicate that not only does phenotypic change correlate with network structural changes, but also that ALPACA can identify such modules in complex networks.Significance statementDistinct phenotypes are often thought of in terms of unique patterns of gene expression. But the expression levels of genes and proteins are driven by networks of interacting elements, and changes in expression are driven by changes in the structure of the associated networks. Because of the size and complexity of these networks, identifying functionally significant changes in network topology has been an ongoing challenge. We describe a new method for comparing networks derived from related conditions, such as healthy and disease tissue, and identifying emergent modules associated with the phenotypic differences between the conditions. We show that this method can find both known and previously unreported pathways involved in three contexts: ovarian cancer, tumor viruses, and breast tissue development.