bluuebunny/crossref_metadata_2025_split huggingface dataset:
Facile Discovery of a Diverse Panel of Anti-Ebola Virus Antibodies by Immune Repertoire Mining
Authors: Wang Bo , Kluwe Christien A. , Lungu Oana I. , DeKosky Brandon J. , Kerr Scott A. , Johnson Erik L. , Tanno Hidetaka , Lee Chang-Han , Jung Jiwon , Rezigh Alec B. , Carroll Sean M. , Reyes Ann N. , Bentz Janelle R. , Villanueva Itamar , Altman Amy L. , Davey Robert A. , Ellington Andrew D. , Georgiou George 
Published: September 2015

AbstractThe ongoing evolution of Ebolaviruses poses significant challenges to the development of immunodiagnostics for detecting emergent viral variants. There is a critical need for the discovery of monoclonal antibodies with distinct affinities and specificities for different Ebolaviruses. We developed an efficient technology for the rapid discovery of a plethora of antigen-specific monoclonal antibodies from immunized animals by mining the VH:VL paired antibody repertoire encoded by highly expanded B cells in the draining popliteal lymph node (PLN). This approach requires neither screening nor selection for antigen-binding. Specifically we show that mouse immunization with Ebola VLPs gives rise to a highly polarized antibody repertoire in CD138+ antibody-secreting cells within the PLN. All highly expanded antibody clones (7/7 distinct clones/animal) were expressed recombinantly and shown to recognize the VLPs used for immunization. Using this approach we obtained diverse panels of antibodies including: (i) antibodies with high affinity towards GP; (ii) antibodies which bound Ebola VLP Kissidougou-C15, the strain circulating in the recent West African outbreak; (iii) non-GP binding antibodies that recognize wild type Sudan or Bundibugyo viruses that have 39% and 37% sequence divergence from Ebola virus, respectively and (iv) antibodies to the Reston virus GP for which no antibodies have been reported.
Polymorphic transitions of diborane at sub- and near-megabar pressures
Authors: Torabi Amin , Murli Chitra , Song Yang , Staroverov Viktor N. 
Published: September 2015

AbstractRecent theoretical investigations of high-pressure structures of diborane have yielded many intriguing predictions which have so far remained untested due to challenges of acquiring experimental data at extreme pressures. Here we report new pressure-induced polymorphic transformations of crystalline diborane observed between 36 and 88 GPa by in situ Raman spectroscopy and interpreted using electronic structure calculations. Two previously unknown phase transitions are identified near 42 and 57 GPa, as evidenced by significant changes in the Raman profiles. The corresponding new phases, labeled IV and V, consist of B2H6 molecules and have triclinic unit cells (P"Equation missing"), as deduced through evolutionary structure search and comparison of experimental and simulated Raman spectra. Density-functional calculations suggest that, at pressures above 110 GPa, phase V will form new molecular structures consisting of one-dimensional (BH3)n chains and will become metallic near 138 GPa. Our findings make a significant contribution to the elucidation of the structures and properties of diborane in the near-megabar pressure region.
Action mechanism of corticosteroids to aggravate Guillain-Barré syndrome
Authors: Wang Yu-Zhong , Lv Hui , Shi Qi-Guang , Fan Xu-Tao , Li Lei , Yi Wong Anna Hiu , Hao Yan-Lei , Si Chuan-Ping , Li Cui-Lan , Yuki Nobuhiro 
Published: September 2015

AbstractCorticosteroids have been proved to be ineffective for Guillain-Barré syndrome, but the mechanism remains unknown. In a rabbit model of axonal Guillain-Barré syndrome, treatment with corticosteroids significantly reduced macrophage infiltration in the spinal ventral roots and the survival rate as well as clinical improvement. On 30th day after onset, there was significantly higher frequency of axonal degeneration in the corticosteroids-treated rabbits than saline-treated rabbits. Corticosteroids may reduce the scavengers that play a crucial role for nerve regeneration, thus delay the recovery of this disease.
Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences
Authors: Wambugu Peterson W. , Brozynska Marta , Furtado Agnelo , Waters Daniel L. , Henry Robert J. 
Published: September 2015

AbstractRice is the most important crop in the world, acting as the staple food for over half of the world’s population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genomeOryzaspecies, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species,O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation.
Proton beam radiation induces DNA damage and cell apoptosis in glioma stem cells through reactive oxygen species
Authors: Alan Mitteer R. , Wang Yanling , Shah Jennifer , Gordon Sherika , Fager Marcus , Butter Param-Puneet , Jun Kim Hyun , Guardiola-Salmeron Consuelo , Carabe-Fernandez Alejandro , Fan Yi 
Published: September 2015

AbstractGlioblastoma multiforme (GBM) is among the most lethal of human malignancies. Most GBM tumors are refractory to cytotoxic therapies. Glioma stem cells (GSCs) significantly contribute to GBM progression and post-treatment tumor relapse, therefore serving as a key therapeutic target; however, GSCs are resistant to conventional radiation therapy. Proton therapy is one of the newer cancer treatment modalities and its effects on GSCs function remain unclear. Here, by utilizing patient-derived GSCs, we show that proton radiation generates greater cytotoxicity in GSCs than x-ray photon radiation. Compared with photon radiation, proton beam irradiation induces more single and double strand DNA breaks, less H2AX phosphorylation, increased Chk2 phosphorylation and reduced cell cycle recovery from G2 arrest, leading to caspase-3 activation, PARP cleavage and cell apoptosis. Furthermore, proton radiation generates a large quantity of reactive oxygen species (ROS), which is required for DNA damage, cell cycle redistribution, apoptosis and cytotoxicity. Together, these findings indicate that proton radiation has a higher efficacy in treating GSCs than photon radiation. Our data reveal a ROS-dependent mechanism by which proton radiation induces DNA damage and cell apoptosis in GSCs. Thus, proton therapy may be more efficient than conventional x-ray photon therapy for eliminating GSCs in GBM patients.
Latent virus infection upregulates CD40 expression facilitating enhanced autoimmunity in a model of multiple sclerosis
Authors: Casiraghi Costanza , Citlali Márquez Ana , Shanina Iryna , Horwitz Marc Steven 
Published: September 2015

AbstractEpstein-Barr virus (EBV) has been identified as a putative environmental trigger of multiple sclerosis (MS) by multiple groups working worldwide. Previously, we reported that when experimental autoimmune encephalomyelitis (EAE) was induced in mice latently infected with murine γ-herpesvirus 68 (γHV-68), the murine homolog to EBV, a disease more reminiscent of MS developed. Specifically, MS-like lesions developed in the brain that included equal numbers of IFN-γ producing CD4+ and CD8+ T cells and demyelination, none of which is observed in MOG induced EAE. Herein, we demonstrate that this enhanced disease was dependent on the γHV-68 latent life cycle and was associated with STAT1 and CD40 upregulation on uninfected dendritic cells. Importantly, we also show that, during viral latency, the frequency of regulatory T cells is reduced via a CD40 dependent mechanism and this contributes towards a strong T helper 1 response that resolves in severe EAE disease pathology. Latent γ-herpesvirus infection established a long-lasting impact that enhances subsequent adaptive autoimmune responses.
GSTP1 and GSTO1 single nucleotide polymorphisms and the response of bladder cancer patients to intravesical chemotherapy
Authors: Deng Xiaheng , Yang Xiao , Cheng Yidong , Liu Xuzhong , Li Xiao , Zhao Ruizhe , Qin Chao , Lu Qiang , Yin Changjun 
Published: September 2015

AbstractSNPs may restrict cell detoxification activity and be a potential risk factor for cancer chemosensitivity. We evaluated the predictive value of these polymorphisms on the sensitivity of bladder cancer patients to epirubicin and mitomycin chemotherapy instillation as well as their toxicities. SNPs were analyzed by TaqMan genotyping assays in 130 patients treated with epirubicin and 114 patients treated with mitomycin. Recurrence-free survival (RFS) was estimated by the Kaplan-Meier method and hazard ratios (HRs) and 95% confidence intervals (CIs) of the HRs were derived from multivariate Cox proportional hazard models. GSTP1 rs1695 and GSTO1 rs4925 were also associated with RFS in the epirubicin group. Patients carrying the GSTP1 AG+GG and GSTO1 AC+AA genotypes had an unfavorable RFS. Patients with the GSTP1 AA and GSTO1 CC genotypes had a reduced risk of recurrence after the instillation of epirubicin. In addition, patients with the GSTP1 rs1695 AA genotype had an increased risk of irritative voiding symptoms; while patients with the GSTO1 rs4925 CC genotype had a decreased risk of hematuria. Our results suggest that GSTP1 and GSTO1 polymorphisms are associated with epirubicin treatment outcomes as well as with epirubicin-related toxicity.
Metamaterial Absorber for Electromagnetic Waves in Periodic Water Droplets
Authors: Yoo Young Joon , Ju Sanghyun , Park Sang Yoon , Ju Kim Young , Bong Jihye , Lim Taekyung , Kim Ki Won , Rhee Joo Yull , Lee YoungPak 
Published: September 2015

AbstractPerfect metamaterial absorber (PMA) can intercept electromagnetic wave harmful for body in Wi-Fi, cell phones and home appliances that we are daily using and provide stealth function that military fighter, tank and warship can avoid radar detection. We reported new concept of water droplet-based PMA absorbing perfectly electromagnetic wave with water, an eco-friendly material which is very plentiful on the earth. If arranging water droplets with particular height and diameter on material surface through the wettability of material surface, meta-properties absorbing electromagnetic wave perfectly in GHz wide-band were shown. It was possible to control absorption ratio and absorption wavelength band of electromagnetic wave according to the shape of water droplet–height and diameter– and apply to various flexible and/or transparent substrates such as plastic, glass and paper. In addition, this research examined how electromagnetic wave can be well absorbed in water droplets with low electrical conductivity unlike metal-based metamaterials inquiring highly electrical conductivity. Those results are judged to lead broad applications to variously civilian and military products in the future by providing perfect absorber of broadband in all products including transparent and bendable materials.
Rapid heterogeneous assembly of multiple magma reservoirs prior to Yellowstone supereruptions
Authors: Wotzlaw Jörn-Frederik , Bindeman Ilya N. , Stern Richard A. , D’Abzac Francois-Xavier , Schaltegger Urs 
Published: September 2015

AbstractLarge-volume caldera-forming eruptions of silicic magmas are an important feature of continental volcanism. The timescales and mechanisms of assembly of the magma reservoirs that feed such eruptions as well as the durations and physical conditions of upper-crustal storage remain highly debated topics in volcanology. Here we explore a comprehensive data set of isotopic (O, Hf) and chemical proxies in precisely U-Pb dated zircon crystals from all caldera-forming eruptions of Yellowstone supervolcano. Analysed zircons record rapid assembly of multiple magma reservoirs by repeated injections of isotopically heterogeneous magma batches and short pre-eruption storage times of 103 to 104 years. Decoupled oxygen-hafnium isotope systematics suggest a complex source for these magmas involving variable amounts of differentiated mantle-derived melt, Archean crust and hydrothermally altered shallow-crustal rocks. These data demonstrate that complex magma reservoirs with multiple sub-chambers are a common feature of rift- and hotspot related supervolcanoes. The short duration of reservoir assembly documents rapid crustal remelting and two to three orders of magnitude higher magma production rates beneath Yellowstone compared to continental arc volcanoes. The short pre-eruption storage times further suggest that the detection of voluminous reservoirs of eruptible magma beneath active supervolcanoes may only be possible prior to an impending eruption.
Reveel: large-scale population genotyping using low-coverage sequencing data
Authors: Huang Lin , Wang Bo , Chen Ruitang , Bercovici Sivan , Batzoglou Serafim 
Published: September 2015

Abstract
Motivation: Population low-coverage whole-genome sequencing is rapidly emerging as a prominent approach for discovering genomic variation and genotyping a cohort. This approach combines substantially lower cost than full-coverage sequencing with whole-genome discovery of low-allele frequency variants, to an extent that is not possible with array genotyping or exome sequencing. However, a challenging computational problem arises of jointly discovering variants and genotyping the entire cohort. Variant discovery and genotyping are relatively straightforward tasks on a single individual that has been sequenced at high coverage, because the inference decomposes into the independent genotyping of each genomic position for which a sufficient number of confidently mapped reads are available. However, in low-coverage population sequencing, the joint inference requires leveraging the complex linkage disequilibrium (LD) patterns in the cohort to compensate for sparse and missing data in each individual. The potentially massive computation time for such inference, as well as the missing data that confound low-frequency allele discovery, need to be overcome for this approach to become practical.
Results: Here, we present Reveel, a novel method for single nucleotide variant calling and genotyping of large cohorts that have been sequenced at low coverage. Reveel introduces a novel technique for leveraging LD that deviates from previous Markov-based models, and which is aimed at computational efficiency as well as accuracy in capturing LD patterns present in rare haplotypes. We evaluate Reveel’s performance through extensive simulations as well as real data from the 1000 Genomes Project, and show that it achieves higher accuracy in low-frequency allele discovery and substantially lower computation cost than previous state-of-the-art methods.
Availability and implementation: http://reveel.stanford.edu/.
Contact: serafim@cs.stanford.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Protest and Institutional Change
Authors: Aleman Jose 
Published: September 2015

Abstract
This article studies how social protest contributes to institutional reforms in both new and established democracies. It evaluates the effects of social protest on changes in the protection of workers’ rights, women’s political rights, and the ability of other branches of government to constrain chief executives. Three important findings emerge in this regard: (1) strikes promote workers’ rights, (2) general strikes advance women’s political rights in the presence of an independent judiciary, and (3) antigovernment demonstrations constrain executives, while riots empower them when the government is cohesive. Regarding the mechanisms behind these changes, the analysis reveals that whereas the effects of strikes on workers’ rights are not institutionally mediated, general strikes can affect women’s political rights indirectly through the institution of an independent judiciary. Antigovernment demonstrations and riots can likewise affect executive constraints indirectly, through the behavior of actors in other branches of government.
Altered Mitochondrial Dynamics Contributes to Propofol-induced Cell Death in Human Stem Cell–derived Neurons
Authors: Twaroski Danielle M. , Yan Yasheng , Zaja Ivan , Clark Eric , Bosnjak Zeljko J. , Bai Xiaowen 
Published: September 2015

AbstractAbstract
In supratherapeutic doses, propofol increased mitochondrial fission; key proteins involved in fission were increased. Suppression of these proteins mitigated the increases in mitochondrial fission and reduced toxicity. Propofol accelerated mitochondrial permeability transition pore (mPTP) opening; blockade of fission rescued the mPTP opening time. The data indicate that propofol, when administered in supratherapeutic concentrations, may induce neurotoxicity via a mitochondria fission and mPTP pathway.

Background
Studies in developing animals have shown that anesthetic agents can lead to neuronal cell death and learning disabilities when administered early in life. Development of human embryonic stem cell–derived neurons has provided a valuable tool for understanding the effects of anesthetics on developing human neurons. Unbalanced mitochondrial fusion and fission lead to various pathological conditions including neurodegeneration. The aim of this study was to dissect the role of mitochondrial dynamics in propofol-induced neurotoxicity.

Methods
Terminal deoxynucleotidyl transferase–mediated deoxyuridine triphosphate in situ nick-end labeling staining was used to assess cell death in human embryonic stem cell–derived neurons. Mitochondrial fission was assessed using TOM20 staining and electron microscopy. Expression of mitochondrial fission-related proteins was assessed by Western blot, and confocal microscopy was used to assess opening time of the mitochondrial permeability transition pore (mPTP).

Results
Exposure to 6 h of 20 μg/ml propofol increased cell death from 3.18 ± 0.17% in the control-treated group to 9.6 ± 0.95% and led to detrimental increases in mitochondrial fission (n = 5 coverslips per group) accompanied by increased expression of activated dynamin-related protein 1 and cyclin-dependent kinase 1, key proteins responsible for mitochondrial fission. Propofol exposure also induced earlier opening of the mPTP from 118.9 ± 3.1 s in the control-treated group to 73.3 ± 1.6 s. Pretreatment of the cells with mdivi-1, a mitochondrial fission blocker rescued the propofol-induced toxicity, mitochondrial fission, and mPTP opening time (n = 75 cells per group). Inhibiting cyclin-dependent kinase 1 attenuated the increase in cell death and fission and the increase in expression of activated dynamin-related protein 1.

Conclusion
These data demonstrate for the first time that propofol-induced neurotoxicity occurs through a mitochondrial fission/mPTP-mediated pathway.
Preoperative Surgical Risk Predictions Are Not Meaningfully Improved by Including the Surgical Apgar Score
Authors: Terekhov Maxim A. , Ehrenfeld Jesse M. , Wanderer Jonathan P. 
Published: September 2015

AbstractAbstract
Both the Risk Quantification Index and Present-On-Admission Risk predicted mortality well. Adding the Surgical Apgar Score did not substantively improve predictions.

Background
Estimating surgical risk is critical for perioperative decision making and risk stratification. Current risk-adjustment measures do not integrate dynamic clinical parameters along with baseline patient characteristics, which may allow a more accurate prediction of surgical risk. The goal of this study was to determine whether the preoperative Risk Quantification Index (RQI) and Present-On-Admission Risk (POARisk) models would be improved by including the intraoperative Surgical Apgar Score (SAS).

Methods
The authors identified adult patients admitted after noncardiac surgery. The RQI and POARisk were calculated using published methodologies, and model performance was compared with and without the SAS. Relative quality was measured using Akaike and Bayesian information criteria. Calibration was compared by the Brier score. Discrimination was compared by the area under the receiver operating curves (AUROCs) using a bootstrapping procedure for bias correction.

Results
SAS alone was a statistically significant predictor of both 30-day mortality and in-hospital mortality (P < 0.0001). The RQI had excellent discrimination with an AUROC of 0.8433, which increased to 0.8529 with the addition of the SAS. The POARisk had excellent discrimination with an AUROC of 0.8608, which increased to 0.8645 by including the SAS. Similarly, overall performance and relative quality increased.

Conclusions
While AUROC values increased, the RQI and POARisk preoperative risk models were not meaningfully improved by adding intraoperative risk using the SAS. In addition to the estimated blood loss, lowest heart rate, and lowest mean arterial pressure, other dynamic clinical parameters from the patient’s intraoperative course may need to be combined with procedural risk estimate models to improve risk stratification.