bluuebunny/crossref_metadata_2025_split huggingface dataset:
Attenuation of Na/K-ATPase Mediated Oxidant Amplification with pNaKtide Ameliorates Experimental Uremic Cardiomyopathy
Authors: Liu Jiang , Tian Jiang , Chaudhry Muhammad , Maxwell Kyle , Yan Yanling , Wang Xiaoliang , Shah Preeya T. , Khawaja Asad A. , Martin Rebecca , Robinette Tylor J. , El-Hamdani Adee , Dodrill Michael W. , Sodhi Komal , Drummond Christopher A. , Haller Steven T. , Kennedy David J. , Abraham Nader G. , Xie Zijian , Shapiro Joseph I. 
Published: October 2016

AbstractWe have previously reported that the sodium potassium adenosine triphosphatase (Na/K-ATPase) can effect the amplification of reactive oxygen species. In this study, we examined whether attenuation of oxidant stress by antagonism of Na/K-ATPase oxidant amplification might ameliorate experimental uremic cardiomyopathy induced by partial nephrectomy (PNx). PNx induced the development of cardiac morphological and biochemical changes consistent with human uremic cardiomyopathy. Both inhibition of Na/K-ATPase oxidant amplification with pNaKtide and induction of heme oxygenase-1 (HO-1) with cobalt protoporphyrin (CoPP) markedly attenuated the development of phenotypical features of uremic cardiomyopathy. In a reversal study, administration of pNaKtide after the induction of uremic cardiomyopathy reversed many of the phenotypical features. Attenuation of Na/K-ATPase oxidant amplification may be a potential strategy for clinical therapy of this disorder.
Tunable Resonators for Nonlinear Modal Interactions
Authors: Ramini Abdallah H. , Hajjaj Amal Z. , Younis Mohammad I. 
Published: October 2016

AbstractUnderstanding the various mechanisms of nonlinear mode coupling in micro and nano resonators has become an imminent necessity for their successful implementation in practical applications. However, consistent, repeatable, and flexible experimental procedures to produce nonlinear mode coupling are lacking, and hence research into well-controlled experimental conditions is crucial. Here, we demonstrate well-controlled and repeatable experiments to study nonlinear mode coupling among micro and nano beam resonators. Such experimental approach can be applied to other micro and nano structures to help study their nonlinear interactions and exploit them for higher sensitive and less noisy responses. Using electrothermal tuning and electrostatic excitation, we demonstrate three different kinds of nonlinear interactions among the first and third bending modes of vibrations of slightly curved beams (arches): two-one internal resonance, three-one internal resonance, and mode veering (near crossing). The experimental procedure is repeatable, highly flexible, do not require special or precise fabrication, and is conducted in air and at room temperature. This approach can be applied to other micro and nano structures, which come naturally curved due to fabrication imperfections, such as CNTs, and hence lays the foundation to deeply investigate the nonlinear mode coupling in these structures in a consistent way.
Electrodynamic study of YIG filters and resonators
Authors: Krupka Jerzy , Salski Bartlomiej , Kopyt Pawel , Gwarek Wojciech 
Published: October 2016

AbstractNumerical solutions of coupled Maxwell and Landau-Lifshitz-Gilbert equations for a magnetized yttrium iron garnet (YIG) sphere acting as a one-stage filter are presented. The filter is analysed using finite-difference time-domain technique. Contrary to the state of the art, the study shows that the maximum electromagnetic power transmission through the YIG filter occurs at the frequency of the magnetic plasmon resonance with the effective permeability of the gyromagnetic medium μr ≈ −2, and not at a ferromagnetic resonance frequency. Such a new understanding of the YIG filter operation, makes it one of the most commonly used single-negative plasmonic metamaterials. The frequency of maximum transmission is also found to weakly depend on the size of the YIG sphere. An analytic electromagnetic analysis of resonances in a YIG sphere is performed for circularly polarized electromagnetic fields. The YIG sphere is situated in a free space and in a large spherical cavity. The study demonstrates that both volume resonances and magnetic plasmon resonances can be solutions of the same transcendental equations.
Characterization of a very rare case of living ewe-buck hybrid using classical and molecular cytogenetics
Authors: Pauciullo Alfredo , Knorr Christoph , Perucatti Angela , Iannuzzi Alessandra , Iannuzzi Leopoldo , Erhardt Georg 
Published: October 2016

AbstractThe natural occurrence of live hybrid offsprings between sheep and goats has been documented in literature, however all the studies have reported the mating of goats with rams, whereas the reciprocal cross was never documented. This study reports on a very rare case of interspecies hybridization occurred between a ewe (2n = 54, XX) and a buck (2n = 60, XY). The hybrid, born in a German flock under natural conditions, is characterised by an intermediate karyotype (2n = 57, XX). The CBA-banding has shown 3 metacentric and 54 acrocentric chromosomes, whereas the GTG- and RBA-banding have revealed that the autosomes involved in the hybrid combination were CHI1, 3; CHI2, 8 and CHI5, 11 corresponding to the metacentric chromosomes OAR1, OAR2 and OAR3. A tri-colour FISH using chromosome paintings and BAC probes has validated this arrangement. A further FISH analysis has been carried out to analyse the telomeres, which showed a normal structure. Nucleolus organiser-bearing chromosomes were identified as pairs OAR1p(CHI3), OAR2q(CHI2), OAR3q(CHI5), OAR4(CHI4) and OAR25(CHI28), and nuclear associations were found. Sex chromosomes were correctly arranged. The odd number of the karyotype might be responsible for a reduced fertility as consequence of the incorrect chromosomal pairing and/or segregation during the meiosis.
Membrane lipidomics in schizophrenia patients: a correlational study with clinical and cognitive manifestations
Authors: Tessier C , Sweers K , Frajerman A , Bergaoui H , Ferreri F , Delva C , Lapidus N , Lamaziere A , Roiser J P , De Hert M , Nuss P 
Published: October 2016

AbstractSchizophrenia is a severe mental condition in which several lipid abnormalities—either structural or metabolic—have been described. We tested the hypothesis that an abnormality in membrane lipid composition may contribute to aberrant dopamine signaling, and thereby symptoms and cognitive impairment, in schizophrenia (SCZ) patients. Antipsychotic-medicated and clinically stable SCZ outpatients (n=74) were compared with matched healthy subjects (HC, n=40). A lipidomic analysis was performed in red blood cell (RBC) membranes examining the major phospholipid (PL) classes and their associated fatty acids (FAs). Clinical manifestations were examined using the positive and negative syndrome scale (PANSS). Cognitive function was assessed using the Continuous Performance Test, Salience Attribution Test and Wisconsin Card Sorting Test. Sphingomyelin (SM) percentage was the lipid abnormality most robustly associated with a schizophrenia diagnosis. Two groups of patients were defined. The first group (SCZ c/SM−) is characterized by a low SM membrane content. In this group, all other PL classes, plasmalogen and key polyunsaturated FAs known to be involved in brain function, were significantly modified, identifying a very specific membrane lipid cluster. The second patient group (SCZ c/SM+) was similar to HCs in terms of RBC membrane SM composition. Compared with SCZ c/SM+, SCZ c/SM− patients were characterized by significantly more severe PANSS total, positive, disorganized/cognitive and excited psychopathology. Cognitive performance was also significantly poorer in this subgroup. These data show that a specific RBC membrane lipid cluster is associated with clinical and cognitive manifestations of dopamine dysfunction in schizophrenia patients. We speculate that this membrane lipid abnormality influences presynaptic dopamine signaling.
RGS2 expression predicts amyloid-β sensitivity, MCI and Alzheimer’s disease: genome-wide transcriptomic profiling and bioinformatics data mining
Authors: Hadar A , Milanesi E , Squassina A , Niola P , Chillotti C , Pasmanik-Chor M , Yaron O , Martásek P , Rehavi M , Weissglas-Volkov D , Shomron N , Gozes I , Gurwitz D 
Published: October 2016

AbstractAlzheimer's disease (AD) is the most frequent cause of dementia. Misfolded protein pathological hallmarks of AD are brain deposits of amyloid-β (Aβ) plaques and phosphorylated tau neurofibrillary tangles. However, doubts about the role of Aβ in AD pathology have been raised as Aβ is a common component of extracellular brain deposits found, also by in vivo imaging, in non-demented aged individuals. It has been suggested that some individuals are more prone to Aβ neurotoxicity and hence more likely to develop AD when aging brains start accumulating Aβ plaques. Here, we applied genome-wide transcriptomic profiling of lymphoblastoid cells lines (LCLs) from healthy individuals and AD patients for identifying genes that predict sensitivity to Aβ. Real-time PCR validation identified 3.78-fold lower expression of RGS2 (regulator of G-protein signaling 2; P=0.0085) in LCLs from healthy individuals exhibiting high vs low Aβ sensitivity. Furthermore, RGS2 showed 3.3-fold lower expression (P=0.0008) in AD LCLs compared with controls. Notably, RGS2 expression in AD LCLs correlated with the patients’ cognitive function. Lower RGS2 expression levels were also discovered in published expression data sets from postmortem AD brain tissues as well as in mild cognitive impairment and AD blood samples compared with controls. In conclusion, Aβ sensitivity phenotyping followed by transcriptomic profiling and published patient data mining identified reduced peripheral and brain expression levels of RGS2, a key regulator of G-protein-coupled receptor signaling and neuronal plasticity. RGS2 is suggested as a novel AD biomarker (alongside other genes) toward early AD detection and future disease modifying therapeutics.
Gesture Use in 14-Month-Old Toddlers With Hearing Loss and Their Mothers' Responses
Authors: Ambrose Sophie E. 
Published: October 2016

PurposeThis study examined the gesture use of 14-month-old toddlers with hearing loss (HL) and mothers' responses to children's early gesture use. Comparisons were made to symbolic language and to dyads in which the toddler had normal hearing (NH).MethodParticipants were 25 mother–toddler dyads in which the child had HL and a socioeconomic-status matched group of 23 mother–toddler dyads in which the child had NH. Thirty-minute mother–child interactions were video-recorded, transcribed for spoken language, sign, and gesture use, and coded for maternal responses to children's gestures. Mothers also reported on children's gestural and spoken language abilities.ResultsToddlers with HL used gesture similarly to their peers with NH, but demonstrated delays in spoken language. Spoken language and gesture were not significantly related for either group. Hearing levels were related to spoken language, but not gesture for the HL group. Maternal and child gesture were only related for signing mothers. Mothers of children with HL were more likely than their counterparts to provide no response to children's gestures.ConclusionAlthough toddlers' gesture abilities remain intact in the presence of HL, mothers were not maximally responsive to those gestures and thus should be coached to increase their provision of contingent feedback.
The Home Literacy Environment and the English Narrative Development of Spanish–English Bilingual Children
Authors: Bitetti Dana , Hammer Carol Scheffner 
Published: October 2016

PurposeThe purpose of this study was to examine the impact of the home literacy environment (HLE) on the English narrative development of Spanish–English bilingual children from low-income backgrounds.MethodLongitudinal data were collected on 81 bilingual children from preschool through 1st grade. English narrative skills were assessed in the fall and spring of each year. Microstructure measures included mean length of utterance in morphemes and number of different words. The Narrative Scoring Scheme (Heilmann, Miller, Nockerts, & Dunaway, 2010) measured macrostructure. Each fall, the children's mothers reported the frequency of literacy activities and number of children's books in the home. Growth curve modeling was used to describe the children's narrative development and the impact of the HLE over time.ResultsSignificant growth occurred for all narrative measures. The HLE did not affect microstructure growth. The frequency with which mothers read to their children had a positive impact on the growth of the children's total Narrative Scoring Scheme scores. Other aspects of the HLE, such as the frequency with which the mothers told stories, did not affect macrostructure development.ConclusionsThese results provide information about the development of English narrative abilities and demonstrate the importance of frequent book reading for the overall narrative quality of children from Spanish-speaking homes who are learning English.
Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination
Authors: Pulivarthy Sandhya R. , Lion Mattia , Kuzu Guray , Matthews Adam G. W. , Borowsky Mark L. , Morris John , Kingston Robert E. , Dennis Jonathan H. , Tolstorukov Michael Y. , Oettinger Marjorie A. 
Published: October 2016

Significance
Immunoglobulin and T-cell receptor genes are assembled in lymphoid cells from gene fragments by the process known as V(D)J recombination, which is initiated by the recombination activating gene (RAG)1/RAG2 recombinase. To ensure that recombination occurs only in the correct cell type and at the right developmental stage, multiple layers of regulation are necessary, including specific modifications of chromatin. We show that nucleosome positioning is another important factor in this regulation. Developmentally regulated changes in nucleosome positioning help to guide RAG1/RAG2 to the correct sites in recombinationally active cells. These changes occur on the scale of hundreds of kilobases, a form of regulation not typically seen in the rest of the mammalian genome.
Enhancer priming by H3K4 methyltransferase MLL4 controls cell fate transition
Authors: Wang Chaochen , Lee Ji-Eun , Lai Binbin , Macfarlan Todd S. , Xu Shiliyang , Zhuang Lenan , Liu Chengyu , Peng Weiqun , Ge Kai 
Published: October 2016

Significance
Transcriptional enhancers control cell-identity gene expression and thus determine cell identity. Enhancers are primed by histone H3K4 mono-/di-methyltransferase MLL4 before they are activated by histone H3K27 acetyltransferase p300. Here, we show that MLL4 is dispensable for cell-identity maintenance but essential for cell fate transition using several model systems including embryonic stem cell (ESC) differentiation toward somatic cells and somatic cell reprogramming into ESC-like cells. Mechanistically, MLL4 is dispensable for maintaining p300 binding on active enhancers of cell-identity genes but is required for p300 binding on enhancers activated during cell fate transition. These results indicate that, although enhancer priming by MLL4 is dispensable for cell-identity maintenance, it controls cell fate transition by orchestrating p300-mediated enhancer activation.
Aging, memory, and nonhierarchical energy landscape of spin jam
Authors: Samarakoon Anjana , Sato Taku J. , Chen Tianran , Chern Gai-Wei , Yang Junjie , Klich Israel , Sinclair Ryan , Zhou Haidong , Lee Seung-Hun 
Published: October 2016

Significance
Our bulk susceptibility and Monte Carlo simulation study of aging and memory effects in densely populated frustrated magnets (spin jam) and in a dilute magnetic alloy (spin glass) indicates a nonhierarchical landscape with a wide and nearly flat but rough bottom for the spin jam and a hierarchical rugged funnel-type landscape for the spin glass.
Disorder drives cooperative folding in a multidomain protein
Authors: Gruszka Dominika T. , Mendonça Carolina A. T. F. , Paci Emanuele , Whelan Fiona , Hawkhead Judith , Potts Jennifer R. , Clarke Jane 
Published: October 2016

Significance
Understanding the role played by disorder in biology is becoming increasingly important. Disordered proteins are central to signaling, development, initiation of transcription, and other vital cellular processes. How and why disordered proteins are used is not entirely clear, but disorder can be important in allostery, facilitate regulatory posttranslational modification, and allow rapid and specific but promiscuous binding. Here, our investigations of biofilm-promoting protein SasG illustrate that disorder can play another role. We show that the intrinsic disorder of one-half of the domains is important for imparting long-range cooperativity in folding of a large multidomain protein—allowing formation of a small local element of structure to precipitate cooperative folding of adjacent disordered domains across a length scale of ∼10 nm.
Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining
Authors: Skinnider Michael A. , Johnston Chad W. , Edgar Robyn E. , Dejong Chris A. , Merwin Nishanth J. , Rees Philip N. , Magarvey Nathan A. 
Published: October 2016

Significance
Natural products and their derivatives are essential to the treatment of many diseases. Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a class of natural products noted for their bioactivities. Genome sequencing has revealed that most natural products remain undiscovered, but the complexity and diversity of RiPPs has challenged the systematic identification of these molecules from genomic data. Here, we present an algorithm for RiPP structure prediction from prokaryotic genomes and systematically investigate the chemical space occupied by genetically encoded RiPPs. We reveal widespread biosynthesis of RiPPs by prokaryotes, identify candidates for targeted discovery, and isolate a RiPP from a rare family.
Environmental change explains cichlid adaptive radiation at Lake Malawi over the past 1.2 million years
Authors: Ivory Sarah J. , Blome Margaret W. , King John W. , McGlue Michael M. , Cole Julia E. , Cohen Andrew S. 
Published: October 2016

Significance
Tropical African lakes are well-known to house exceptionally biodiverse assemblages of fish and other aquatic fauna, which are thought to be at risk in the future. Although the modern assemblages are well-studied, direct evidence of the origin of this incredible wealth of species and the mechanisms that drive speciation are virtually unknown. We use a long sedimentary record from Lake Malawi to show that over the last 1.2 My both large-scale climatic and tectonic changes resulted in wet–dry transitions that led to extraordinary habitat variability and rapid diversification events. This work allows us to understand the environmental context of aquatic evolution in the most biodiverse tropical lake.
System crash as dynamics of complex networks
Authors: Yu Yi , Xiao Gaoxi , Zhou Jie , Wang Yubo , Wang Zhen , Kurths Jürgen , Schellnhuber Hans Joachim 
Published: October 2016

SignificanceSystem crash, as an essential part of system evolution, sometimes happens in peculiar manners: Weakened systems may survive for a surprisingly long time before suddenly meeting their final ends, whereas seemingly unbeatable giants may drastically crash to virtual nonexistence. We propose a model that describes system crash as a consequence of some relatively simple local information-based individual behaviors: Individuals leave networks according to some most straightforward assessment of current and future benefits/risks. Of note, such a simple rule may enable a single push/mistake to cause multistage-style system crash. Our study helps to make sense of the process where complex systems go into unstoppable cascading declines and provides a viewpoint of predicting the fate of some social/natural systems.
Simple dynamical models capturing the key features of the Central Pacific El Niño
Authors: Chen Nan , Majda Andrew J. 
Published: October 2016

Significance
The Central Pacific El Niño (CP El Niño) has been frequently observed in recent decades. The phenomenon is characterized by an anomalous warm sea surface temperature (SST) confined to the central Pacific and has different teleconnections from the traditional El Niño with major societal impact. Here, a simple modeling framework is developed and shown to capture the key mechanisms of the CP El Niño. In addition to the SST, other major characteristics of the CP El Niño such as the rising branch of the anomalous Walker circulation being shifted to the central Pacific and the eastern Pacific cooling with a shallow thermocline are all captured by this simple coupled model. Key features of the model are nonlinear advection of SST and effective stochastic wind bursts.
ARResT/Interrogate: an interactive immunoprofiler for IG/TR NGS data
Authors: Bystry Vojtech , Reigl Tomas , Krejci Adam , Demko Martin , Hanakova Barbora , Grioni Andrea , Knecht Henrik , Schlitt Max , Dreger Peter , Sellner Leopold , Herrmann Dietrich , Pingeon Marine , Boudjoghra Myriam , Rijntjes Jos , Pott Christiane , Langerak Anton W , Groenen Patricia J. T.A , Davi Frederic , Brüggemann Monika , Darzentas Nikos ,   EuroClonality-NGS
Published: October 2016

Abstract

Motivation
The study of immunoglobulins and T cell receptors using next-generation sequencing has finally allowed exploring immune repertoires and responses in their immense variability and complexity. Unsurprisingly, their analysis and interpretation is a highly convoluted task.

Results
We thus implemented ARResT/Interrogate, a web-based, interactive application. It can organize and filter large amounts of immunogenetic data by numerous criteria, calculate several relevant statistics, and present results in the form of multiple interconnected visualizations.

Availability and Implementation
ARResT/Interrogate is implemented primarily in R, and is freely available at http://bat.infspire.org/arrest/interrogate/

Supplementary information
Supplementary data are available at Bioinformatics online.
Safety huddles to proactively identify and address electronic health record safety
Authors: Menon Shailaja , Singh Hardeep , Giardina Traber D , Rayburn William L , Davis Brenda P , Russo Elise M , Sittig Dean F 
Published: October 2016

Objective: Methods to identify and study safety risks of electronic health records (EHRs) are underdeveloped and largely depend on limited end-user reports. “Safety huddles” have been found useful in creating a sense of collective situational awareness that increases an organization’s capacity to respond to safety concerns. We explored the use of safety huddles for identifying and learning about EHR-related safety concerns.Design: Data were obtained from daily safety huddle briefing notes recorded at a single midsized tertiary-care hospital in the United States over 1 year. Huddles were attended by key administrative, clinical, and information technology staff. We conducted a content analysis of huddle notes to identify what EHR-related safety concerns were discussed. We expanded a previously developed EHR-related error taxonomy to categorize types of EHR-related safety concerns recorded in the notes.Results: On review of daily huddle notes spanning 249 days, we identified 245 EHR-related safety concerns. For our analysis, we defined EHR technology to include a specific EHR functionality, an entire clinical software application, or the hardware system. Most concerns (41.6%) involved “EHR technology working incorrectly,” followed by 25.7% involving “EHR technology not working at all.” Concerns related to “EHR technology missing or absent” accounted for 16.7%, whereas 15.9% were linked to “user errors.”Conclusions: Safety huddles promoted discussion of several technology-related issues at the organization level and can serve as a promising technique to identify and address EHR-related safety concerns. Based on our findings, we recommend that health care organizations consider huddles as a strategy to promote understanding and improvement of EHR safety.