bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome
Authors: Brooks Brandon , Olm Matthew R. , Firek Brian A. , Baker Robyn , Thomas Brian C. , Morowitz Michael J. , Banfield Jillian F. 
Published: November 2017

AbstractPreterm infants exhibit different microbiome colonization patterns relative to full-term infants, and it is speculated that the hospital room environment may contribute to infant microbiome development. Here, we present a genome-resolved metagenomic study of microbial genotypes from the gastrointestinal tracts of infants and from the neonatal intensive care unit (NICU) room environment. Some strains detected in hospitalized infants also occur in sinks and on surfaces, and belong to species such as Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa, and Klebsiella pneumoniae, which are frequently implicated in nosocomial infection and preterm infant gut colonization. Of the 15 K. pneumoniae strains detected in the study, four were detected in both infant gut and room samples. Time series experiments showed that nearly all strains associated with infant gut colonization can be detected in the room after, and often before, detection in the gut. Thus, we conclude that a component of premature infant gut colonization is the cycle of microbial exchange between the room and the occupant.
Alpha-synuclein facilitates to form short unconventional microtubules that have a unique function in the axonal transport
Authors: Toba Shiori , Jin Mingyue , Yamada Masami , Kumamoto Kanako , Matsumoto Sakiko , Yasunaga Takuo , Fukunaga Yuko , Miyazawa Atsuo , Fujita Sakiko , Itoh Kyoko , Fushiki Shinji , Kojima Hiroaki , Wanibuchi Hideki , Arai Yoshiyuki , Nagai Takeharu , Hirotsune Shinji 
Published: November 2017

AbstractAlthough α-synuclein (αSyn) has been linked to Parkinson’s disease (PD), the mechanisms underlying the causative role in PD remain unclear. We previously proposed a model for a transportable microtubule (tMT), in which dynein is anchored to a short tMT by LIS1 followed by the kinesin-dependent anterograde transport; however the mechanisms that produce tMTs have not been determined. Our in vitro investigations of microtubule (MT) dynamics revealed that αSyn facilitates the formation of short MTs and preferentially binds to MTs carrying 14 protofilaments (pfs). Live-cell imaging showed that αSyn co-transported with dynein and mobile βIII-tubulin fragments in the anterograde transport. Furthermore, bi-directional axonal transports are severely affected in αSyn and γSyn depleted dorsal root ganglion neurons. SR-PALM analyses further revealed the fibrous co-localization of αSyn, dynein and βIII-tubulin in axons. More importantly, 14-pfs MTs have been found in rat femoral nerve tissue, and they increased approximately 19 fold the control in quantify upon nerve ligation, indicating the unconventional MTs are mobile. Our findings indicate that αSyn facilitates to form short, mobile tMTs that play an important role in the axonal transport. This unexpected and intriguing discovery related to axonal transport provides new insight on the pathogenesis of PD.
Integrated Proteomic and Metabolomic prediction of Term Preeclampsia
Authors: Bahado-Singh Ray , Poon Liona C. , Yilmaz Ali , Syngelaki Argyro , Turkoglu Onur , Kumar Praveen , Kirma Joseph , Allos Matthew , Accurti Veronica , Li Jiansheng , Zhao Peng , Graham Stewart F. , Cool David R. , Nicolaides Kypros 
Published: November 2017

AbstractTerm preeclampsia (tPE), ≥37 weeks, is the most common form of PE and the most difficult to predict. Little is known about its pathogenesis. This study aims to elucidate the pathogenesis and assess early prediction of tPE using serial integrated metabolomic and proteomic systems biology approaches. Serial first- (11–14 weeks) and third-trimester (30–34 weeks) serum samples were analyzed using targeted metabolomic (1H NMR and DI-LC-MS/MS) and proteomic (MALDI-TOF/TOF-MS) platforms. We analyzed 35 tPE cases and 63 controls. Serial first- (sphingomyelin C18:1 and urea) and third-trimester (hexose and citrate) metabolite screening predicted tPE with an area under the receiver operating characteristic curve (AUC) (95% CI) = 0.817 (0.732–0.902) and a sensitivity of 81.6% and specificity of 71.0%. Serial first [TATA box binding protein-associated factor (TBP)] and third-trimester [Testis-expressed sequence 15 protein (TEX15)] protein biomarkers highly accurately predicted tPE with an AUC (95% CI) of 0.987 (0.961–1.000), sensitivity 100% and specificity 98.4%. Integrated pathway over-representation analysis combining metabolomic and proteomic data revealed significant alterations in signal transduction, G protein coupled receptors, serotonin and glycosaminoglycan metabolisms among others. This is the first report of serial integrated and combined metabolomic and proteomic analysis of tPE. High predictive accuracy and potentially important pathogenic information were achieved.
Hippocampal MRS and subfield volumetry at 7T detects dysfunction not specific to seizure focus
Authors: Voets Natalie L. , Hodgetts Carl J. , Sen Arjune , Adcock Jane E. , Emir Uzay 
Published: November 2017

AbstractUltra high-field 7T MRI offers sensitivity to localize hippocampal pathology in temporal lobe epilepsy (TLE), but has rarely been evaluated in patients with normal-appearing clinical MRI. We applied multimodal 7T MRI to assess if focal subfield atrophy and deviations in brain metabolites characterize epileptic hippocampi. Twelve pre-surgical TLE patients (7 MRI-negative) and age-matched healthy volunteers were scanned at 7T. Hippocampal subfields were manually segmented from 600μm isotropic resolution susceptibility-weighted images. Hippocampal metabolite spectra were acquired to determine absolute concentrations of glutamate, glutamine, myo-inositol, NAA, creatine and choline. We performed case-controls analyses, using permutation testing, to identify abnormalities in hippocampal imaging measures in individual patients, for evaluation against clinical evidence of seizure lateralisation and neuropsychological memory test scores. Volume analyses identified hippocampal subfield atrophy in 9/12 patients (75%), commonly affecting CA3. 7/8 patients had altered metabolite concentrations, most showing reduced glutamine levels (62.5%). However, neither volume nor metabolite deviations consistently lateralized the epileptogenic hippocampus. Rather, lower subiculum volumes and glutamine concentrations correlated with impaired verbal memory performance. Hippocampal subfield and metabolic abnormalities detected at 7T appear to reflect pathophysiological processes beyond epileptogenesis. Despite limited diagnostic contributions, these markers show promise to help elucidate mnemonic processing in TLE.
Inhibition of the inflammatory response to stress by targeting interaction between PKR and its cellular activator PACT
Authors: Dabo Stephanie , Maillard Patrick , Collados Rodriguez Milagros , Hansen Marianne Doré , Mazouz Sabrina , Bigot Donna-Joe , Tible Marion , Janvier Geneviève , Helynck Olivier , Cassonnet Patricia , Jacob Yves , Bellalou Jacques , Gatignol Anne , Patel Rekha C. , Hugon Jacques , Munier-Lehmann Hélène , Meurs Eliane F. 
Published: November 2017

AbstractPKR is a cellular kinase involved in the regulation of the integrative stress response (ISR) and pro-inflammatory pathways. Two N-terminal dsRNA Binding Domains (DRBD) are required for activation of PKR, by interaction with either dsRNA or PACT, another cellular DRBD-containing protein. A role for PKR and PACT in inflammatory processes linked to neurodegenerative diseases has been proposed and raised interest for pharmacological PKR inhibitors. However, the role of PKR in inflammation is subject to controversy. We identified the flavonoid luteolin as an inhibitor of the PKR/PACT interaction at the level of their DRBDs using high-throughput screening of chemical libraries by homogeneous time-resolved fluorescence. This was further validated using NanoLuc-Based Protein Complementation Assay. Luteolin inhibits PKR phosphorylation, the ISR and the induction of pro-inflammatory cytokines in human THP1 macrophages submitted to oxidative stress and toll-like receptor (TLR) agonist. Similarly, luteolin inhibits induction of pro-inflammatory cytokines in murine microglial macrophages. In contrast, luteolin increased activation of the inflammasome, in a PKR-independent manner. Collectively, these data delineate the importance of PKR in the inflammation process to the ISR and induction of pro-inflammatory cytokines. Pharmacological inhibitors of PKR should be used in combination with drugs targeting directly the inflammasome.
Asymmetrical bipolar nanosecond electric pulse widths modify bipolar cancellation
Authors: Valdez Chris M. , Barnes Ronald A. , Roth Caleb C. , Moen Erick K. , Throckmorton Graham A. , Ibey Bennett L. 
Published: November 2017

AbstractA bipolar (BP) nanosecond electric pulse (nsEP) exposure generates reduced calcium influx compared to a unipolar (UP) nsEP. This attenuated physiological response from a BP nsEP exposure is termed “bipolar cancellation” (BPC). The predominant BP nsEP parameters that induce BPC consist of a positive polarity (↑) front pulse followed by the delivery of a negative polarity (↓) back pulse of equal voltage and width; thereby the duration is twice a UP nsEP exposure. We tested these BPC parameters, and discovered that a BP nsEP with symmetrical pulse widths is not required to generate BPC. For example, our data revealed the physiological response initiated by a ↑900 nsEP exposure can be cancelled by a second pulse that is a third of its duration. However, we observed a complete loss of BPC from a ↑300 nsEP followed by a ↓900 nsEP exposure. Spatiotemporal analysis revealed these asymmetrical BP nsEP exposures generate distinct local YO-PRO®-1 uptake patterns across the plasma membrane. From these findings, we generated a conceptual model that suggests BPC is a phenomenon balanced by localized charging and discharging events across the membrane.
Differential prognostic value of MYC immunohistochemistry in subtypes of papillary renal cell carcinoma
Authors: Bellut Julia , Bertz Simone , Nolte Elke , Stöhr Christine , Polifka Iris , Lieb Verena , Herrmann Edwin , Jung Rudolf , Hartmann Arndt , Wullich Bernd , Taubert Helge , Wach Sven 
Published: November 2017

AbstractThe histomorphological subtyping of papillary renal cell carcinomas (pRCCs) has improved the predictions of patients’ long-term survival. Based on our previous results, we hypothesized that the MYC proto-oncogene would show differential expression in pRCC subtypes. Using a multi-institutional cohort of 204 pRCC patients we assessed the additional value of the immunohistochemical markers MYC, MINA53, and Ki67 in predicting patient’s long-term survival. The clinical endpoints were overall survival (OS) and cancer-specific survival (CSS). Nomograms were constructed to predict each patient’s risk of death (OS). The incorporation of the MYC staining patterns allowed the stratification of pRCC type 1 patients into better and worse prognostic groups. None of the patients with pRCC type 1 tumors and favorable MYC staining patterns died from tumor-related causes. This prognostic value was independent of the patient’s age at surgery, the pathological tumor stage and presence of lymph node invasion. we could show that the immunohistochemical assessment of MYC and the histomorphological subtyping of pRCC stratifies pRCC type 1 tumors with regard to OS and CSS. The determination of the histomorphologic pRCC subtype in combination with the MYC immunohistochemical staining patterns allows a more accurate prediction of patients’ individual risk of death.
Topology-commanded optical properties of bistable electric-field-induced torons in cholesteric bubble domains
Authors: Varanytsia Andrii , Posnjak Gregor , Mur Urban , Joshi Vinay , Darrah Kelsey , Muševič Igor , Čopar Simon , Chien Liang-Chy 
Published: November 2017

AbstractNowadays, complicated topological defects enable many experimental manipulations and configurational simulations of active soft matter for optical and photonic applications. Investigation of topological defects in soft anisotropic materials enables one to better understand three-dimensional orientation fields in cholesteric liquid crystals. Here, we describe optical properties of bistable bubble domain (BD) texture torons in a thin layer of cholesteric liquid crystal (CLC), frustrated by homeotropic anchoring conditions, and reliably switchable by a random process. The control of macroscopic optical density and diffraction efficiency of the BD texture is demonstrated by a selection of a confinement ratio of the CLC. Experimentally reconstructed CLC director profile reveals the topology of BD torons allowing consideration of naturally occurring BD texture for applications in optical and photonic devices, which are bistably switchable between active and transparent optical states.
Remotely Triggered Locomotion of Hydrogel Mag-bots in Confined Spaces
Authors: Shen Tong , Font Marti Garriga , Jung Sukwon , Gabriel Millicent L. , Stoykovich Mark P. , Vernerey Franck J. 
Published: November 2017

AbstractIn this study, soft hydrogel crawlers with remote magnetic-responsive motility in confined spaces have been developed. Inspired by the motion of maggots, the hydrogel crawlers can reversibly contract and elongate their body controlled by repeatedly switching on/off an alternating magnetic field. Based on the cyclic deformation, the hydrogel crawlers can move peristaltically in a confined space that is coated with asymmetric micro-patterns. The dependence of the hydrogel motility on the pattern structures and lubrication is characterized using experimental measurements. Such a hydrogel system pioneers the study of active motile systems in porous media and has the potential to impact the fields of targeted drug delivery and active actuators.
Determination of Asphaltene Critical Nanoaggregate Concentration Region Using Ultrasound Velocity Measurements
Authors: Svalova Aleksandra , Parker Nicholas G. , Povey Malcolm J. W. , Abbott Geoffrey D. 
Published: November 2017

AbstractAsphaltenes constitute the heaviest, most polar and aromatic fraction of petroleum crucial to the formation of highly-stable water-in-crude oil emulsions. The latter occur during crude oil production as well as spills and cause difficulties to efficient remediation practice. It is thought that in nanoaggregate form, asphaltenes create elastic layers around water droplets enhancing stability of the emulsion matrix. Ultrasonic characterisation is a high-resolution non-invasive tool in colloidal analysis shown to successfully identify asphaltene nanoaggregation in toluene. The high sensitivity of acoustic velocity to molecular rearrangements and ease in implementation renders it an attractive method to study asphaltene phase properties. Currently, aggregation is thought to correspond to an intersection of two concentration-ultrasonic velocity regressions. Our measurements indicate a variation in the proximity of nanoaggregation which is not accounted for by present models. We attribute this uncertainty to physico-chemical heterogeneity of the asphaltene fraction driven by variation in molecular size and propose a critical nanoaggregation region. We treated asphaltenes from North and South American crude oils with ruthenium ion catalysed oxidation to characterize their n-alkyl appendages attached to aromatic cores. Principal component analysis was performed to investigate the coupling between asphaltene structures and velocity measurements and their impact on aggregation.
Beliefs about Others’ Abilities Alter Learning from Observation
Authors: Selbing Ida , Olsson Andreas 
Published: November 2017

AbstractLearning what is dangerous by observing others can be safer and more efficient than individual learning. The efficiency of observational learning depends on how observational information is used, something we propose depends on our beliefs’ about others. Here, we investigated how described and actual abilities of another individual (a demonstrator) influenced performance and psychophysiology during learning of an observational avoidance task. Participants were divided into two groups. In each group there were two demonstrators who were described as either high (Described-High group) or low (Described-Low group) in their ability to learn the task. In both groups, one demonstrator had a high ability (Actual-High) and the other had a low ability (Actual-Low) to learn. Participants performed worse in the Described-Low compared to the Described-High group. Pupil dilation, and behavioral data in combination with reinforcement learning modeling, suggested that the described ability influenced performance by affecting the level of attention towards the observational information. Skin conductance responses and pupil dilation provided us with a separate measure of learning in addition to choice behavior.
The electron-phonon interaction at deep Bi
2
Te3-semiconductor interfaces from Brillouin light scattering
Authors: Wiesner M. , Trzaskowska A. , Mroz B. , Charpentier S. , Wang S. , Song Y. , Lombardi F. , Lucignano P. , Benedek G. , Campi D. , Bernasconi M. , Guinea F. , Tagliacozzo A. 
Published: November 2017

AbstractIt is shown that the electron-phonon interaction at a conducting interface between a topological insulator thin film and a semiconductor substrate can be directly probed by means of high-resolution Brillouin light scattering (BLS). The observation of Kohn anomalies in the surface phonon dispersion curves of a 50 nm thick Bi2Te3 film on GaAs, besides demonstrating important electron-phonon coupling effects in the GHz frequency domain, shows that information on deep interface electrons can be obtained by tuning the penetration depth of optically-generated surface phonons so as to selectively probe the interface region, as in a sort of quantum sonar.
Polarization of the Majorana quasiparticles in the Rashba chain
Authors: Maśka Maciej M. , Domański Tadeusz 
Published: November 2017

AbstractWe demonstrate that the selective equal–spin Andreev reflection (SESAR) spectroscopy can be used in STM experiments to distinguish the zero–energy Majorana quasiparticles from the ordinary fermionic states of the Rashba chain. Such technique, designed for probing the p–wave superconductivity, could be applied to the intersite pairing of equal–spin electrons in the chain of magnetic Fe atoms deposited on the superconducting Pb substrate. Our calculations of the effective pairing amplitude for individual spin components imply the magnetically polarized Andreev conductance, which can be used to ‘filter’ the Majorana quasiparticles from the ordinary in–gap states, although the pure spin current (i.e., perfect polarization) is impossible.
Genome-wide analysis of circular RNAs in prenatal and postnatal pituitary glands of sheep
Authors: Li Cunyuan , Li Xiaoyue , Ma Qiman , Zhang Xiangyu , Cao Yang , Yao Yang , You Shuang , Wang Dawei , Quan Renzhe , Hou Xiaoxu , Liu Zhijin , Zhan Qianqian , Liu Li , Zhang Mengdan , Yu Shuting , Ni Wei , Hu Shengwei 
Published: November 2017

AbstractCircular RNAs (circRNAs) are a class of animal non-coding RNAs and play an impor-tant role in animal growth and development. However, the expression and function of circRNAs in the pituitary gland of sheep are unclear. Transcriptome profiling of circRNAs in the pituitary gland of sheep may enable us to understand their biological functions. In the present study, we identified 10,226 circRNAs from RNA-seq data in the pituitary gland of prenatal and postnatal sheep. Reverse transcription PCR and DNA sequencing analysis confirmed the presence of several circRNAs. Real-time RT-PCR analysis showed that sheep circRNAs are resistant to RNase R digestion and are expressed in prenatal and postnatal pituitary glands. GO and KEGG enrichment analysis showed that host genes of differentially expressed circRNAs are involved in the regulation of hormone secretion as well as in several pathways related to these processes. We determined that numerous circRNAs interact with pituitary-specific miRNAs that are involved in the biologic functions of the pituitary gland. Moreover, several circRNAs contain at least one IRES element and open reading frame, indicating their potential to encode proteins. Our study provides comprehensive expression profiles of circRNAs in the pituitary gland, thereby offering a valuable resource for circRNA biology in sheep.
Free-running Sn precipitates: an efficient phase separation mechanism for metastable Ge1−xSnx epilayers
Authors: Groiss Heiko , Glaser Martin , Schatzl Magdalena , Brehm Moritz , Gerthsen Dagmar , Roth Dietmar , Bauer Peter , Schäffler Friedrich 
Published: November 2017

AbstractThe revival of interest in Ge1−xSnx alloys with x ≥ 10% is mainly owed to the recent demonstration of optical gain in this group-IV heterosystem. Yet, Ge and Sn are immiscible over about 98% of the composition range, which renders epilayers based on this material system inherently metastable. Here, we address the temperature stability of pseudomorphic Ge1−xSnx films grown by molecular beam epitaxy. Both the growth temperature dependence and the influence of post-growth annealing steps were investigated. In either case we observe that the decomposition of epilayers with Sn concentrations of around 10% sets in above ≈230 °C, the eutectic temperature of the Ge/Sn system. Time-resolved in-situ annealing experiments in a scanning electron microscope reveal the crucial role of liquid Sn precipitates in this phase separation process. Driven by a gradient of the chemical potential, the Sn droplets move on the surface along preferential crystallographic directions, thereby taking up Sn and Ge from the strained Ge1−xSnx layer. While Sn-uptake increases the volume of the melt, single-crystalline Ge becomes re-deposited by a liquid-phase epitaxial process at the trailing edge of the droplet. This process makes phase separation of metastable GeSn layers particularly efficient at rather low temperatures.
Resident Microbiome Disruption with Antibiotics Enhances Virulence of a Colonizing Pathogen
Authors: Thomason Courtney A. , Mullen Nathan , Belden Lisa K. , May Meghan , Hawley Dana M. 
Published: November 2017

AbstractThere is growing evidence that symbiotic microbes play key roles in host defense, but less is known about how symbiotic microbes mediate pathogen-induced damage to hosts. Here, we use a natural wildlife disease system, house finches and the conjunctival bacterial pathogen Mycoplasma gallisepticum (MG), to experimentally examine the impact of the ocular microbiome on host damage and pathogen virulence factors during infection. We disrupted the ocular bacterial community of healthy finches using an antibiotic that MG is intrinsically resistant to, then inoculated antibiotic- and sham-treated birds with MG. House finches with antibiotic-disrupted ocular microbiomes had more severe MG-induced conjunctival inflammation than birds with unaltered microbiomes, even after accounting for differences in conjunctival MG load. Furthermore, MG cultures from finches with disrupted microbiomes had increased sialidase enzyme and cytadherence activity, traits associated with enhanced virulence in Mycoplasmas, relative to isolates from sham-treated birds. Variation in sialidase activity and cytadherence among isolates was tightly linked with degree of tissue inflammation in hosts, supporting the consideration of these traits as virulence factors in this system. Overall, our results suggest that microbial dysbiosis can result in enhanced virulence of colonizing pathogens, with critical implications for the health of wildlife, domestic animals, and humans.