bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implication for alphavirus host-cell entry and assembly indicated by a 3.5Å resolution cryo-EM structure
Authors: Chen Lihong , Wang Ming , Zhu Dongjie , Sun Zhenzhao , Ma Jun , Wang Jinglin , Kong Lingfei , Wang Shida , Liu Zaisi , Wei Lili , He Yuwen , Wang Jingfei , Zhang Xinzheng 
Published: December 2018

AbstractAlphaviruses are enveloped RNA viruses that contain several human pathogens. Due to intrinsic heterogeneity of alphavirus particles, a high resolution structure of the virion is currently lacking. Here we provide a 3.5 Å cryo-EM structure of Sindbis virus, using block based reconstruction method that overcomes the heterogeneity problem. Our structural analysis identifies a number of conserved residues that play pivotal roles in the virus life cycle. We identify a hydrophobic pocket in the subdomain D of E2 protein that is stabilized by an unknown pocket factor near the viral membrane. Residues in the pocket are conserved in different alphaviruses. The pocket strengthens the interactions of the E1/E2 heterodimer and may facilitate virus assembly. Our study provides structural insights into alphaviruses that may inform the design of drugs and vaccines.
Spike-timing-dependent plasticity learning of coincidence detection with passively integrated memristive circuits
Authors: Prezioso M. , Mahmoodi M. R. , Bayat F. Merrikh , Nili H. , Kim H. , Vincent A. , Strukov D. B. 
Published: December 2018

AbstractSpiking neural networks, the most realistic artificial representation of biological nervous systems, are promising due to their inherent local training rules that enable low-overhead online learning, and energy-efficient information encoding. Their downside is more demanding functionality of the artificial synapses, notably including spike-timing-dependent plasticity, which makes their compact efficient hardware implementation challenging with conventional device technologies. Recent work showed that memristors are excellent candidates for artificial synapses, although reports of even simple neuromorphic systems are still very rare. In this study, we experimentally demonstrate coincidence detection using a spiking neural network, implemented with passively integrated metal-oxide memristive synapses connected to an analogue leaky-integrate-and-fire silicon neuron. By employing spike-timing-dependent plasticity learning, the network is able to robustly detect the coincidence by selectively increasing the synaptic efficacies corresponding to the synchronized inputs. Not surprisingly, our results indicate that device-to-device variation is the main challenge towards realization of more complex spiking networks.
miR-122 removal in the liver activates imprinted microRNAs and enables more effective microRNA-mediated gene repression
Authors: Valdmanis Paul N. , Kim Hak Kyun , Chu Kirk , Zhang Feijie , Xu Jianpeng , Munding Elizabeth M. , Shen Jia , Kay Mark A. 
Published: December 2018

AbstractmiR-122 is a highly expressed liver microRNA that is activated perinatally and aids in regulating cholesterol metabolism and promoting terminal differentiation of hepatocytes. Disrupting expression of miR-122 can re-activate embryo-expressed adult-silenced genes, ultimately leading to the development of hepatocellular carcinoma (HCC). Here we interrogate the liver transcriptome at various time points after genomic excision of miR-122 to determine the cellular consequences leading to oncogenesis. Loss of miR-122 leads to specific and progressive increases in expression of imprinted clusters of microRNAs and mRNA transcripts at the Igf2 and Dlk1-Dio3 loci that could be curbed by re-introduction of exogenous miR-122. mRNA targets of other abundant hepatic microRNAs are functionally repressed leading to widespread hepatic transcriptional de-regulation. Together, this reveals a transcriptomic framework for the hepatic response to loss of miR-122 and the outcome on other microRNAs and their cognate gene targets.
Hierarchical quantum classifiers
Authors: Grant Edward , Benedetti Marcello , Cao Shuxiang , Hallam Andrew , Lockhart Joshua , Stojevic Vid , Green Andrew G. , Severini Simone 
Published: December 2018

AbstractQuantum circuits with hierarchical structure have been used to perform binary classification of classical data encoded in a quantum state. We demonstrate that more expressive circuits in the same family achieve better accuracy and can be used to classify highly entangled quantum states, for which there is no known efficient classical method. We compare performance for several different parameterizations on two classical machine learning datasets, Iris and MNIST, and on a synthetic dataset of quantum states. Finally, we demonstrate that performance is robust to noise and deploy an Iris dataset classifier on the ibmqx4 quantum computer.
Serum alkaline phosphatase relates to cardiovascular risk markers in children with high calcium-phosphorus product
Authors: Xargay-Torrent Sílvia , Espuña-Capote Núria , Montesinos-Costa Mercè , Prats-Puig Anna , Carreras-Badosa Gemma , Díaz-Roldán Ferran , De Zegher Francis , Ibáñez Lourdes , Bassols Judit , López-Bermejo Abel 
Published: December 2018

AbstractAlthough alkaline phosphatase (ALP) correlates with cardiovascular risk in adults, there are no studies in children. We evaluated the association between serum ALP levels, calcium-phosphorus product (Ca*P) and cardiovascular risk markers in healthy children. Children aged 7.9 ± 1.4 (n = 379) were recruited in this cross-sectional study. The main outcome measures were systolic and diastolic blood pressure (SBP and DBP) and carotid intima-media thickness (cIMT). Additional assessments were body-mass index (BMI), waist circumference, homeostatic model assessment of insulin resistance (HOMA-IR) and fasting lipids, ALP, serum calcium, phosphorus and Ca*P. ALP was directly correlated with BMI (p < 0.0001), waist circumference (p < 0.0001), SBP (p < 0.0001), cIMT (p = 0.005), HOMA-IR (p < 0.0001), and fasting triglycerides (p = 0.0001). Among them, in children with Ca*P values above the median the associations were BMI (r = 0.231; p = 0.001), waist (r = 0.252; p < 0.0001), SBP (r = 0.324; p < 0.0001), cIMT (r = 0.248; p = 0.001) and HOMA-IR (r = 0.291; p < 0.0001)]. ALP independently associated with SBP (β = 0.290, p < 0.001) and cIMT (β = 0.179, p = 0.013) in children with higher Ca*P, after adjusting for confounding variables. Circulating ALP is associated with a more adverse cardiovascular profile in children with higher Ca*P. We suggest that serum ALP and Ca*P levels could contribute to the assessment of risk for cardiovascular disease in children.
Nanopore-based detection and characterization of yam viruses
Authors: Filloux Denis , Fernandez Emmanuel , Loire Etienne , Claude Lisa , Galzi Serge , Candresse Thierry , Winter Stephan , Jeeva M. L. , Makeshkumar T. , Martin Darren P. , Roumagnac Philippe 
Published: December 2018

AbstractWe here assessed the capability of the MinION sequencing approach to detect and characterize viruses infecting a water yam plant. This sequencing platform consistently revealed the presence of several plant virus species, including Dioscorea bacilliform virus, Yam mild mosaic virus and Yam chlorotic necrosis virus. A potentially novel ampelovirus was also detected by a complimentary Illumina sequencing approach. The full-length genome sequence of yam chlorotic necrosis virus was determined using Sanger sequencing, which enabled determination of the coverage and sequencing accuracy of the MinION technology. Whereas the total mean sequencing error rate of yam chlorotic necrosis virus-related MinION reads was 11.25%, we show that the consensus sequence obtained either by de novo assembly or after mapping the MinION reads on the virus genomic sequence was >99.8% identical with the Sanger-derived reference sequence. From the perspective of potential plant disease diagnostic applications of MinION sequencing, these degrees of sequencing accuracy demonstrate that the MinION approach can be used to both reliably detect and accurately sequence nearly full-length positive-sense single-strand polyadenylated RNA plant virus genomes.
Photonic topological phases in dispersive metamaterials
Authors: Yu You-Zhong , Chern Ruey-Lin 
Published: December 2018

AbstractWe analyze the photonic topological phases in dispersive metamaterials which satisfy the degenerate condition at a reference frequency. The electromagnetic duality allows for the hybrid modes to be decoupled and described by the spin-orbit Hamiltonians with pseudospin 1, which result in nonzero spin Chern numbers that characterize the topological phases. In particular, the combined Hamiltonian of the hybrid modes complies with a fermionic-like pseudo time-reversal symmetry that ensures the Kramers degeneracy, leading to the topological protection of helical edge states. The transverse spin generated by the evanescent surface waves is perpendicular to the wave vector, which exhibits the spin-momentum locking as in the surface states for three-dimensional topological insulators. The topological properties of the helical edge states are further illustrated with the robust transport of a pair of counterpropagating surface waves with opposite polarization handedness at an irregular boundary of the metamaterial.
Antisense oligonucleotides targeting angiotensinogen: insights from animal studies
Authors: Wu Chia-Hua , Wang Ya , Ma Murong , Mullick Adam E. , Crooke Rosanne M. , Graham Mark J. , Daugherty Alan , Lu Hong S. 
Published: December 2018

Abstract
Angiotensinogen (AGT) is the unique substrate of all angiotensin peptides. We review the recent preclinical research of AGT antisense oligonucleotides (ASOs), a rapidly evolving therapeutic approach. The scope of the research findings not only opens doors for potentially new therapeutics of hypertension and many other diseases, but also provides insights into understanding critical physiological and pathophysiological roles mediated by AGT.
Age Effects on Concurrent Speech Segregation by Onset Asynchrony
Authors: Stuckenberg Maria V. , Nayak Chaitra V. , Meyer Bernd T. , Völker Christoph , Hohmann Volker , Bendixen Alexandra 
Published: December 2018

Purpose
For elderly listeners, it is more challenging to listen to 1 voice surrounded by other voices than for young listeners. This could be caused by a reduced ability to use acoustic cues—such as slight differences in onset time—for the segregation of concurrent speech signals. Here, we study whether the ability to benefit from onset asynchrony differs between young (18–33 years) and elderly (55–74 years) listeners.

Method

We investigated young (normal hearing,
N
= 20) and elderly (mildly hearing impaired,
N
= 26) listeners' ability to segregate 2 vowels with onset asynchronies ranging from 20 to 100 ms. Behavioral measures were complemented by a specific event-related brain potential component, the object-related negativity, indicating the perception of 2 distinct auditory objects.

Results
Elderly listeners' behavioral performance (identification accuracy of the 2 vowels) was considerably poorer than young listeners'. However, both age groups showed the same amount of improvement with increasing onset asynchrony. Object-related negativity amplitude also increased similarly in both age groups.

Conclusion
Both age groups benefit to a similar extent from onset asynchrony as a cue for concurrent speech segregation during active (behavioral measurement) and during passive (electroencephalographic measurement) listening.
Gaia Data Release 2
Authors: Marrese P. M. , Marinoni S. , Fabrizio M. , Altavilla G. 
Published: December 2018

Context. Although the Gaia catalogue on its own is a very powerful tool, it is the combination of this high-accuracy archive with other archives that will truly open up amazing possibilities for astronomical research. The advanced interoperation of archives is based on cross-matching, leaving the user with the feeling of working with one single data archive. The data retrieval should work not only across data archives but also across wavelength domains. The first step for a seamless access to the data is the computation of the cross-match between Gaia and external surveys.
Aims. We describe the adopted algorithms and results of the pre-computed cross-match of the Gaia Data Release 2 (DR2) catalogue with dense surveys (Pan-STARRS1 DR1, 2MASS, SDSS DR9, GSC 2.3, URAT-1, allWISE, PPMXL, and APASS DR9) and sparse catalogues (HIPPARCOS2, Tycho-2, and RAVE 5).
Methods. A new algorithm is developed specifically for sparse catalogues. Improvements and changes with respect to the algorithm adopted for DR1 are described in detail.
Results. The outputs of the cross-match are part of the official Gaia DR2 catalogue. The global analysis of the cross-match results is also presented.
« Médecine 4.0 »
Authors: Wolf Bernhard , Scholze Christian 
Published: December 2018

Les progrès électroniques des cent dernières années ont apporté d’énormes contributions à la recherche médicale et au développement de nouveaux procédés thérapeutiques. Au cours des dernières années notamment, il a été démontré que les capteurs intelligents, avec des interfaces radio appropriées, permettront bientôt de relier entre eux les processus diagnostiques et thérapeutiques en médecine - il sera ainsi possible de développer de toutes nouvelles formes de traitements [1]. Cette nouvelle « médecine 4.0 » a fait l’objet d’un premier article de la série, dans lequel étaient présentés les progrès acquis grâce à la fusion de la technologie des micro-capteurs, de la microélectronique et des technologies de l’information et de la communication, en détaillant particulièrement le cas de la chimiothérapie personnalisée. L’objet de ce nouvel article est de présenter davantage d’applications pratiques de ces nouvelles méthodes thérapeutiques.
Justification of method of continuous measurements of position of sides of surface mine
Authors: Ilyukhin D A , Ivanik S A , Pevnev A S 
Published: December 2018

Abstract
As a result of full-scale surveys of parameters of open mining facilities, a set of discrete values is basically obtained. The geomechanical state of the ledges of the sides of the pit and dumps can not be fully represented without obtaining objective information about the dynamics of the deformation regime of the observed object. This information is necessary throughout the life of the quarry, in order to ensure its trouble-free operation. Thus, effective monitoring of the ledges of the sides of quarries and dumps is a necessary part of the mining safety system for the enterprise, and also allows checking the correctness of the previously adopted design solutions for setting the sides and ledges of the quarry to a stationary position. This paper presents a measurement technique that allows obtaining continuous data in real time to ensure the safety of work.
A Preliminary Clinical Trial Comparing Split Treatments to the Face and Hand With Autologous Fat Grafting and Platelet-Rich Plasma (PRP): A 3D, IRB-Approved Study
Authors: Sasaki Gordon H 
Published: December 2018

Abstract

Background
Numerous methodologies have been suggested to enhance fat graft survival, but few long-term studies are available.

Objectives
The authors of this institutional review board-approved study investigated the safety and efficacy of utilizing platelet-rich plasma (PRP).

Methods
Each of 10 patients received equal volumes of syringe-harvested, centrifuged fat to opposing midfaces with a lateral submuscular aponeurotic system-plication or no face lift and hands that were combined with equal volumes of either concentrated PRP or normal saline. Comparable assessments of fat retention/baseline values by 3D Vectra Analysis, VISIA, and Cortex facial skin analyses were performed. Clinical results were judged on a visual analogue scale.

Results
The average percent change in mean volume assessments at the fat/PRP sites from baseline values, as profiled by 3D Vectra Analysis, demonstrated a higher, but statistically nonsignificant value over 1 year than the percent value changes at the fat/normal saline sites in the opposing face or hand. Three independent evaluators were able to assess volume restorations to the malar fat pad, naso-jugal groove, and nasolabial fold as well as to intermetacarpal hollowness with reduction of visible veins and tendons in the anterior midface and hands with both treatments. No adverse events were observed over the year-long study. Perioperative edema, erythema, bruising, and tenderness lasted up to 1 to 2 weeks at most.

Conclusions
Autologous fat grafting continues to be a safe and effective adjunct in facial and hand aesthetic surgery. This study will require more patients and longer follow-up periods to determine whether PRP has a potential role to increase fat graft retention in aesthetic patients.

Level of Evidence: 3
Implementation of a Stirling number estimator enables direct calculation of population genetics tests for large sequence datasets
Authors: Chen Swaine L 
Published: December 2018

Abstract

Motivation
Stirling numbers enter into the calculation of several population genetics statistics, including Fu’s Fs. However, as alignments become large (≥50 sequences), the Stirling numbers required rapidly exceed the standard floating point range. Another recursive method for calculating Fu’s Fs suffers from floating point underflow issues.

Results
I implemented an estimator for Stirling numbers that has the advantage of being uniformly applicable to the full parameter range for Stirling numbers. I used this to create a hybrid Fu’s Fs calculator that accounts for floating point underflow. My new algorithm is hundreds of times faster than the recursive method. This algorithm now enables accurate calculation of statistics such as Fu’s Fs for very large alignments.

Availability and implementation
An R implementation is available at http://github.com/swainechen/hfufs.

Supplementary information
Supplementary data are available at Bioinformatics online.
CASMAP: detection of statistically significant combinations of SNPs in association mapping
Authors: Llinares-López Felipe , Papaxanthos Laetitia , Roqueiro Damian , Bodenham Dean , Borgwardt Karsten 
Published: December 2018

Abstract

Summary
Combinatorial association mapping aims to assess the statistical association of higher-order interactions of genetic markers with a phenotype of interest. This article presents combinatorial association mapping (CASMAP), a software package that leverages recent advances in significant pattern mining to overcome the statistical and computational challenges that have hindered combinatorial association mapping. CASMAP can be used to perform region-based association studies and to detect higher-order epistatic interactions of genetic variants. Most importantly, unlike other existing significant pattern mining-based tools, CASMAP allows for the correction of categorical covariates such as age or gender, making it suitable for genome-wide association studies.

Availability and implementation
The R and Python packages can be downloaded from our GitHub repository http://github.com/BorgwardtLab/CASMAP. The R package is also available on CRAN.

Supplementary information
Supplementary data are available at Bioinformatics online.
Comparative Immunogenicity and Safety Trial of 2 Different Schedules of Single-visit Intradermal Rabies Postexposure Vaccination
Authors: Soentjens Patrick , De Koninck Katrien , Tsoumanis Achilleas , Herssens Natacha , Van Den Bossche Dorien , Terryn Sanne , Van Gucht Steven , Van Damme Pierre , Van Herrewege Yven , Bottieau Emmanuel 
Published: December 2018

Abstract

Background
Effective and safe single-visit rabies vaccination for pre- and postexposure prophylaxis (PrEP and PEP) could substantially simplify rabies prevention and therefore increase compliance.

Methods
In a comparative trial, 303 healthy adults received a primary vaccination that consisted of 2 intradermal (ID) doses of 0.1 mL of the purified chicken embryo cell vaccine (PCEV) during a single visit. One year later, participants were randomly assigned to receive either 4 or 2 ID PEP booster doses of 0.1 mL PCEV during a single visit. The primary endpoint for immunogenicity was the percentage of participants with an adequate antibody level (>0.5 IU/mL) 7 days after the booster doses. The safety endpoint was the proportion of participants who developed adverse events (AEs) following primary and/or booster vaccination.

Results
All participants, except 1 (99.3%) in each study group, had a rabies antibody titer >0.5 IU/mL on day 7 following the booster schedules. Participants exposed to the 4-dose PEP schedule had a geometric mean titer of 20 IU/mL vs 14 IU/mL for the 2-dose PEP schedule (P = .0228). Local reactions at the injection site following PrEP and PEP were mild and transient and only seen in 14.9% and 49.6%–53% of the participants, respectively. No serious AEs were reported.

Conclusions
In healthy adults, a 2-dose (2 × 0.1 mL) single-visit ID PEP schedule was as immunologically adequate and safe as a 4-dose (4 × 0.1 mL) single-visit PEP schedule 7 to 28 months following a 2-dose (2 × 0.1 mL) single-visit ID PREP.

Clinical Trials Registration
EudraCT 2014-00183612.
The inclination to shun healthy behaviours that generate only transient benefits: the role of future clarity
Authors: Moss Simon A , Skinner Timothy C , Irons Melanie , Alexi Nektarios 
Published: December 2018

Summary
Research has not definitively ascertained the circumstances that motivate people to live a healthier lifestyle. To redress this shortfall, we report two overlapping studies that examined whether people are more inclined to value health benefits that seem enduring and fundamental rather than transient or superficial—even after controlling effort and cost. In these studies, 242 participants indicated the degree to which they implement 17 health behaviours—as well as the extent to which they perceive the benefits of these behaviours as enduring and fundamental. Furthermore, participants completed a measure that gauges future clarity. Finally, they chose which of two drugs—drugs that differ only on the longevity of effects—they prefer. Participants were more inclined to implement health behaviours that seemed to generate enduring and fundamental benefits. This effect was more pronounced in people who perceive their future as vivid and certain. Furthermore, participants tended to choose the drug that was touted as generating more enduring benefits, even after controlling cost and effort. As these results imply, to encourage healthy behaviour, health practitioners should help people clarify their future goals and then advocate behaviours that generate lasting benefits.
Regulators of Elliptic Curves
Authors: Autissier Pascal , Hindry Marc , Pazuki Fabien 
Published: December 2018

Abstract
We study the regulator of the Mordell–Weil group of elliptic curves over number fields, functions fields of characteristic 0 or function fields of characteristic $p&gt;0$. We prove a new Northcott property for the regulator of elliptic curves of rank at least 4 defined over a number field. In the function field case, we obtain that non-trivial families of elliptic curves with bounded regulators and bounded ranks are limited families. We conclude by asking new questions.