bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transient potassium channels augment degeneracy in hippocampal active dendritic spectral tuning
Authors: Rathour Rahul Kumar , Malik Ruchi , Narayanan Rishikesh 
Published: April 2016

AbstractHippocampal pyramidal neurons express an intraneuronal map of spectral tuning mediated by hyperpolarization-activated cyclic-nucleotide-gated nonspecific-cation channels. Modeling studies have predicted a critical regulatory role for A-type potassium (KA) channels towards augmenting functional robustness of this map. To test this, we performed patch-clamp recordings from soma and dendrites of rat hippocampal pyramidal neurons, and measured spectral tuning before and after blocking KA channels using two structurally distinct pharmacological agents. Consistent with computational predictions, we found that blocking KA channels resulted in a significant reduction in resonance frequency and significant increases in input resistance, impedance amplitude and action-potential firing frequency across the somato-apical trunk. Furthermore, across all measured locations, blocking KA channels enhanced temporal summation of postsynaptic potentials and critically altered the impedance phase profile, resulting in a significant reduction in total inductive phase. Finally, pair-wise correlations between intraneuronal percentage changes (after blocking KA channels) in different measurements were mostly weak, suggesting differential regulation of different physiological properties by KA channels. Our results unveil a pivotal role for fast transient channels in regulating theta-frequency spectral tuning and intrinsic phase response, and suggest that degeneracy with reference to several coexisting functional maps is mediated by cross-channel interactions across the active dendritic arbor.
Diarrhoea in the critically ill is common, associated with poor outcome and rarely due to Clostridium difficile
Authors: Tirlapur Nikhil , Puthucheary Zudin A. , Cooper Jackie A. , Sanders Julie , Coen Pietro G. , Moonesinghe S. Ramani , Wilson A. Peter , Mythen Michael G. , Montgomery Hugh E. 
Published: April 2016

AbstractDiarrhoea is common in Intensive Care Unit (ICU) patients, with a reported prevalence of 15–38%. Many factors may cause diarrhoea, including Clostridium difficile, drugs (e.g. laxatives, antibiotics) and enteral feeds. Diarrhoea impacts on patient dignity, increases nursing workload and healthcare costs and exacerbates morbidity through dermal injury, impaired enteral uptake and subsequent fluid imbalance. We analysed a cohort of 9331 consecutive patients admitted to a mixed general intensive care unit to establish the prevalence of diarrhoea in intensive care unit patients and its relationship with infective aetiology and clinical outcomes. We provide evidence that diarrhoea is common (12.9% (1207/9331) prevalence) in critically ill patients, independently associated with increased intensive care unit length of stay (mean (standard error) 14.8 (0.26) vs 3.2 (0.09) days, p < 0.001) and mortality (22.0% (265/1207) vs 8.7% (705/8124), p < 0.001; adjusted hazard ratio 1.99 (95% CI 1.70–2.32), p < 0.001) compared to patients without diarrhoea even after adjusting for potential confounding factors and infrequently caused by infective aetiology (112/1207 (9.2%)) such as Clostridium difficile (97/1048 (9.3%) tested) or virological causes (9/172 (5.7%) tested). Our findings suggest non-infective causes of diarrhoea in ICU predominate and pathophysiology of diarrhoea in critically ill patients warrants further investigation.
Genome-wide profiles of methylation, microRNAs, and gene expression in chemoresistant breast cancer
Authors: He Dong-Xu , Gu Feng , Gao Fei , Hao Jun-jun , Gong Desheng , Gu Xiao-Ting , Mao Ai-Qin , Jin Jian , Fu Li , Ma Xin 
Published: April 2016

AbstractCancer chemoresistance is regulated by complex genetic and epigenetic networks. In this study, the features of gene expression, methylation, and microRNA (miRNA) expression were investigated with high-throughput sequencing in human breast cancer MCF-7 cells resistant to adriamycin (MCF-7/ADM) and paclitaxel (MCF-7/PTX). We found that: ① both of the chemoresistant cell lines had similar, massive changes in gene expression, methylation, and miRNA expression versus chemosensitive controls. ② Pairwise integration of the data highlighted sets of genes that were regulated by either methylation or miRNAs, and sets of miRNAs whose expression was controlled by DNA methylation in chemoresistant cells. ③ By combining the three sets of high-throughput data, we obtained a list of genes whose expression was regulated by both methylation and miRNAs in chemoresistant cells; ④ Expression of these genes was then validated in clinical breast cancer samples to generate a 17-gene signature that showed good predictive and prognostic power in triple-negative breast cancer patients receiving anthracycline-taxane-based neoadjuvant chemotherapy. In conclusion, our results have generated a new workflow for the integrated analysis of the effects of miRNAs and methylation on gene expression during the development of chemoresistance.
Breakdown of the Migdal approximation at Lifshitz transitions with giant zero-point motion in the H3S superconductor
Authors: Jarlborg Thomas , Bianconi Antonio 
Published: April 2016

AbstractWhile 203 K high temperature superconductivity in H3S has been interpreted by BCS theory in the dirty limit here we focus on the effects of hydrogen zero-point-motion and the multiband electronic structure relevant for multigap superconductivity near Lifshitz transitions. We describe how the topology of the Fermi surfaces evolves with pressure giving different Lifshitz-transitions. A neck-disrupting Lifshitz-transition (type 2) occurs where the van Hove singularity, vHs, crosses the chemical potential at 210 GPa and new small 2D Fermi surface portions appear with slow Fermi velocity where the Migdal-approximation becomes questionable. We show that the neglected hydrogen zero-point motion ZPM, plays a key role at Lifshitz transitions. It induces an energy shift of about 600 meV of the vHs. The other Lifshitz-transition (of type 1) for the appearing of a new Fermi surface occurs at 130 GPa where new Fermi surfaces appear at the Γ point of the Brillouin zone here the Migdal-approximation breaks down and the zero-point-motion induces large fluctuations. The maximum Tc = 203 K occurs at 160 GPa where EF/ω0 = 1 in the small Fermi surface pocket at Γ. A Feshbach-like resonance between a possible BEC-BCS condensate at Γ and the BCS condensate in different k-space spots is proposed.
The neglected nano-specific toxicity of ZnO nanoparticles in the yeast Saccharomyces cerevisiae
Authors: Zhang Weicheng , Bao Shaopan , Fang Tao 
Published: April 2016

AbstractNanoparticles (NPs) with unique physicochemical properties induce nano-specific (excess) toxicity in organisms compared with their bulk counterparts. Evaluation and consideration of nano-specific toxicity are meaningful for the safe design and environmental risk assessment of NPs. However, ZnO NPs have been reported to lack excess toxicity for diverse organisms. In the present study, the nano-specific toxicity of ZnO NPs was evaluated in the yeast Saccharomyces cerevisiae. Nano-specific toxicity of ZnO NPs was not observed in the wild type yeast. However, the ZnO NPs induced very similar nano-specific toxicities in the three mutants with comparable log Te(particle) values (0.64 vs 0.65 vs 0.62), suggesting that the mutants were more sensitive and specific for the NPs’ nano-specific toxicity. The toxic effects in the yeast were slightly attributable to dissolved zinc ions from the ZnO (nano or bulk) particles. Oxidative damage and mechanical damage contributed to the toxic effect of the ZnO particles. The mechanism of mechanical damage is proposed to be an inherent characteristic underlying the nano-specific toxicity in the mutants. The log Te(particle) was a useful parameter for evaluation of NPs nano-specific toxicity, whereas log Te(ion) efficiently determined the NPs toxicity associated with released ions.
Theoretical Investigations of Optical Origins of Fluorescent Graphene Quantum Dots
Authors: Wang Jingang , Cao Shuo , Ding Yong , Ma Fengcai , Lu Wengang , Sun Mengtao 
Published: April 2016

AbstractThe optical properties of graphene quantum dots (GQDs) were investigated theoretically. We focused on the photoinduced charge transfer and electron-hole coherence of single-layer graphene in the electronic transitions in the visible regions. Surface functionalization with donor or acceptor groups produced a red shift in the absorption spectrum, and electrons and holes were highly delocalized. The recombination of excited, well-separated electron-hole (e–h) pairs can result in enhanced fluorescence. This fluorescence enhancement by surface functionalization occurs because of the decreased symmetry of the graphene resulting from the roughened structure of the surface-functionalized GQDs.
PAK5 is auto-activated by a central domain that promotes kinase oligomerization
Authors: Tabanifar Bahareh , Zhao Zhuoshen , Manser Ed 
Published: April 2016

PAKs (p21 activated kinases) are an important class of Rho effectors. These contain a Cdc42–Rac1 interaction and binding (CRIB) domain and a flanking auto-inhibitory domain (AID) which binds the C-terminal catalytic domain. The group II kinases PAK4 and PAK5 are considered significant therapeutic targets in cancer. Among human cancer cell lines we tested, PAK5 protein levels are much lower than those of PAK4, even in NCI-H446 which has the highest PAK5 mRNA expression. Although these two kinases are evolutionarily and structurally related, it has never been established why PAK4 is inactive whereas PAK5 has high basal activity. The AID of PAK5 is functionally indistinguishable from that of PAK4, pointing to other regions being responsible for higher activity of PAK5. Gel filtration indicates PAK4 is a monomer but PAK5 is dimeric. The central region of PAK5 (residues 109–420) is shown here to promote self-association, and an elevated activity, but has no effect on activation loop Ser602 phosphorylation. These residues allow PAK5 to form characteristic puncta in cells, and removing sequences involved in oligomerization suppresses kinase activity. Our model suggests PAK5 self-association interferes with AID binding to the catalytic domain, thus maintaining its high activity. Further, our model explains the observation that PAK5 (1–180) inhibits PAK5 in vitro.
Identifying cell-specific microRNA transcriptional start sites
Authors: Hua Xu , Chen Luxiao , Wang Jin , Li Jie , Wingender Edgar 
Published: April 2016

Abstract
Motivation: Identification of microRNA (miRNA) transcriptional start sites (TSSs) is crucial to understand the transcriptional regulation of miRNA. As miRNA expression is highly cell specific, an automatic and systematic method that could identify miRNA TSSs accurately and cell specifically is in urgent requirement.
Results: A workflow to identify the TSSs of miRNAs was built by integrating the data of H3K4me3 and DNase I hypersensitive sites as well as combining the conservation level and sequence feature. By applying the workflow to the data for 54 cell lines from the ENCODE project, we successfully identified TSSs for 663 intragenic miRNAs and 620 intergenic miRNAs, which cover 84.2% (1283/1523) of all miRNAs recorded in miRBase 18. For these cell lines, we found 4042 alternative TSSs for intragenic miRNAs and 3186 alternative TSSs for intergenic miRNAs. Our method achieved a better performance than the previous non-cell-specific methods on miRNA TSSs. The cell-specific method developed by Georgakilas et al. gives 158 TSSs of higher accuracy in two cell lines, benefitting from the employment of deep-sequencing technique. In contrast, our method provided a much higher number of miRNA TSSs (7228) for a broader range of cell lines without the limitation of costly deep-sequencing data, thus being more applicable for various experimental cases. Analysis showed that upstream promoters at − 2 kb to − 200 bp of TSS are more conserved for independently transcribed miRNAs, while for miRNAs transcribed with host genes, their core promoters (−200 bp to 200 bp of TSS) are significantly conserved.
Availability and implementation: Predicted miRNA TSSs and promoters can be downloaded from supplementary files.
Contact: jwang@nju.edu.cn or jlee@nju.edu.cn or edgar.wingender@bioinf.med.uni-goettingen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Romulus: robust multi-state identification
of transcription factor binding sites from
DNase-seq data
Authors: Jankowski Aleksander , Tiuryn Jerzy , Prabhakar Shyam 
Published: April 2016

Abstract
Motivation: Computational prediction of transcription factor (TF) binding sites in the genome remains a challenging task. Here, we present Romulus, a novel computational method for identifying individual TF binding sites from genome sequence information and cell-type–specific experimental data, such as DNase-seq. It combines the strengths of previous approaches, and improves robustness by reducing the number of free parameters in the model by an order of magnitude.
Results: We show that Romulus significantly outperforms existing methods across three sources of DNase-seq data, by assessing the performance of these tools against ChIP-seq profiles. The difference was particularly significant when applied to binding site prediction for low-information-content motifs. Our method is capable of inferring multiple binding modes for a single TF, which differ in their DNase I cut profile. Finally, using the model learned by Romulus and ChIP-seq data, we introduce Binding in Closed Chromatin (BCC) as a quantitative measure of TF pioneer factor activity. Uniquely, our measure quantifies a defining feature of pioneer factors, namely their ability to bind closed chromatin.
Availability and Implementation: Romulus is freely available as an R package at http://github.com/ajank/Romulus .
Contact: ajank@mimuw.edu.pl
Supplementary information: Supplementary data are available at Bioinformatics online.
Development of polymer–fullerene solar cells
Authors: Zhang Fengling , Inganäs Olle , Zhou Yinhua , Vandewal Koen 
Published: April 2016

Abstract
Global efforts and synergetic interdisciplinary collaborations on solution-processed bulk-heterojunction polymer solar cells (PSCs or OPVs) made power conversion efficiencies over 10% possible. The rapid progress of the field is credited to the synthesis of a large number of novel polymers with specially tunable optoelectronic properties, a better control over the nano-morphology of photoactive blend layers, the introduction of various effective interfacial layers, new device architectures and a deeper understanding of device physics. We will review the pioneering materials for polymer–fullerene solar cells and trace the progress of concepts driving their development. We discuss the evolution of morphology control, interfacial layers and device structures fully exploring the potential of photoactive materials. In order to guide a further increase in power conversion efficiency of OPV, the current understanding of the process of free charge carrier generation and the origin of the photovoltage is summarized followed by a perspective on how to overcome the limitations for industrializing PSCs.
First-principles design of spintronics materials
Authors: Li Xingxing , Yang Jinlong 
Published: April 2016

Abstract
Spintronics is one of the most promising next generation information technology, which uses the spins of electrons as information carriers and possesses potential advantages of speeding up data processing, high circuit integration density, and low energy consumption. However, spintronics faces a number of challenges, including spin generation and injection, long distance spin transport, and manipulation and detection of spin orientation. In solving these issues, new concepts and spintronics materials were proposed one after another, such as half metals, spin gapless semiconductors, and bipolar magnetic semiconductors. Topological insulators can also be viewed as a special class of spintronics materials, with their surface states used for pure spin generation and transportation. In designing these spintronics materials, first-principles calculations play a very important role. This article attempts to give a brief review of the basic principles and theoretical design of these materials. Meanwhile, we also give some attentions to the antiferromagnetic spintronics, which is mainly based on antiferromagnets and has aroused much interest in recent years.
An effective selection method for low-mass active black holes and first spectroscopic identification
Authors: Morokuma Tomoki , Tominaga Nozomu , Tanaka Masaomi , Yasuda Naoki , Furusawa Hisanori , Taniguchi Yuki , Kato Takahiro , Jiang Ji-an , Nagao Tohru , Kuncarayakti Hanindyo , Morokuma-Matsui Kana , Ikeda Hiroyuki , Blinnikov Sergei , Nomoto Ken'ichi , Kokubo Mitsuru , Doi Mamoru 
Published: April 2016

Abstract
We present a new method for effectively selecting objects which may be low-mass active black holes (BHs) at galaxy centers using high-cadence optical imaging data, and our first spectroscopic identification of an active 2.7 × 106 M⊙ BH at z = 0.164. This active BH was originally selected due to its rapid optical variability, from a few hours to a day, based on Subaru Hyper Suprime-Cam g-band imaging data taken with a 1 hr cadence. Broad and narrow Hα lines and many other emission ones are detected in our optical spectra taken with Subaru FOCAS, and the BH mass is measured via the broad Hα emission line width (1880 km s−1) and luminosity (4.2 × 1040 erg s−1) after careful correction to the atmospheric absorption around 7580–7720 Å. We measure the Eddington ratio and find it to be as low as 0.05, considerably smaller than those in a previous SDSS sample with similar BH mass and redshift, which indicates one of the special potentials of our Subaru survey. The g − r color and morphology of the extended component indicate that the host galaxy is a star-forming galaxy. We also show the effectiveness of our variability selection for low-mass active BHs.
PRECL: A new method for interferometry imaging from closure phase
Authors: Ikeda Shiro , Tazaki Fumie , Akiyama Kazunori , Hada Kazuhiro , Honma Mareki 
Published: April 2016

AbstractFor short-wavelength VLBI observations, it is difficult to measure the phase of the visibility function accurately. The closure phases are reliable measurements under this situation, though it is not sufficient to retrieve all of the phase information. We propose a new method, phase retrieval from closure phase (PRECL). PRECL estimates all the visibility phases only from the closure phases. Combining PRECL with a sparse modeling method we have already proposed, the imaging process of VLBI does not rely on a dirty image or self-calibration. The proposed method is tested numerically and the results are promising.
A modified Bernese periacetabular osteotomy suitable for less experienced surgeons and underequipped hospitals
Authors: Emara Khaled M. , Ghafar KhaledAbd E.L. , Diab Ramy Ahmed , Tawfik Noha 
Published: April 2016

Background:
The classic Bernese periacetabular osteotomy is technically demanding, requires special surgical instruments, and requires increased radiation exposure during the procedure. We describe a modified technique for this osteotomy that is easier and requires no special surgical instruments and only minimal intraoperative radiation exposure.

Methods:
Twenty patients with acetabular dysplasia underwent our modified technique through a posterior hip approach that included a trochanteric osteotomy and superior pubic ramus osteotomy through a limited anterior approach. The osteotomy cuts were performed under direct vision.

Results:
The change in the acetabular inclination ranged from 5 to 19 degrees; the change in anterior and lateral center edge angles ranged from 14 to 42 degrees and 20 to 38 degrees, respectively. The procedure provided medial translation of the hip center with an average change of 6 mm. Clinical outcome analysis showed pain relief and improved hip function in 17 patients with improvement in the Harris Hip Score ranging from 15-25 points. Three patients did not show improvement of hip function, with sciatic nerve injury occurring in one patient, which recovered spontaneously after 6 wk, and delayed union of the trochanteric osteotomy in two patients.

Conclusions:
Our technique of performing periacetabular osteotomy through a posterior hip approach and limited anterior approach carries some disadvantages to the patient (risks of injury to the blood supply of the femoral head, heterotopic ossification, and complications of trochanteric osteotomy), but it is an easier technique that does not require special surgical instruments, and minimizes the need for intraoperative fluoroscopy, making it suitable for under-equipped centers and for the less experienced surgeons.
Complications in diabetic patients undergoing revision total joint arthroplasty
Authors: Mazoch Mathew , Barnes C. Lowry , Cooper Kasa 
Published: April 2016

Background:
The risks of complications in individuals with diabetes undergoing primary total joint arthroplasty are well discussed in the literature; however, little is written about their risks with revision procedures. This study evaluates complications surrounding revision arthroplasty in diabetics compared with controls.

Methods:
Six hundred and thirty-five patients underwent revision total hip and knee surgery since 2004. Sixty-five diabetics who underwent revision arthroplasty were compared to 65 matched controls. Demographics, comorbidities, and hemoglobin A1c (HgbA1c) levels were analyzed in comparison to complications encountered.

Results:
Of the 635 revision arthroplasty patients sampled, 10.2% (65/635) of patients had both diabetes and HgbA1c levels drawn. Thirty (46%) diabetic patients experienced 58 complications and required 25 additional procedures. Twenty-three (35%) controls experienced 35 complications and had 22 additional procedures. HgbA1c levels were a median (quartiles) of 5.90 (5.60–6.40) among diabetics without a complication, compared to 6.55 (6.10–7.20) among diabetics with at least one complication (P=0.0006). The number of complications was also strongly correlated with patient’s HbA1c (Spearman’s rho=0.417; P=0.0009). Diabetic patients had a higher complication rate and number of complications than controls. Diabetic patients were at higher risk of developing infections (18.4% vs. 4.6%; P=0.025), periprosthetic fractures (9.2% vs. 0%; P=0.028), and more severe rare complications (P=0.0029).

Conclusions:
The study suggests that diabetics with better glycemic control tend to have fewer complications. Diabetics undergoing revision arthroplasty appear to be at a higher risk of developing infections, periprosthetic fractures, and rare events than nondiabetics.