bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Memristors for Robust Local Learning of Hardware Restricted Boltzmann Machines
Authors: Ernoult Maxence , Grollier Julie , Querlioz Damien 
Published: February 2019

AbstractOne of the biggest stakes in nanoelectronics today is to meet the needs of Artificial Intelligence by designing hardware neural networks which, by fusing computation and memory, process and learn from data with limited energy. For this purpose, memristive devices are excellent candidates to emulate synapses. A challenge, however, is to map existing learning algorithms onto a chip: for a physical implementation, a learning rule should ideally be tolerant to the typical intrinsic imperfections of such memristive devices, and local. Restricted Boltzmann Machines (RBM), for their local learning rule and inherent tolerance to stochasticity, comply with both of these constraints and constitute a highly attractive algorithm towards achieving memristor-based Deep Learning. On simulation grounds, this work gives insights into designing simple memristive devices programming protocols to train on chip Boltzmann Machines. Among other RBM-based neural networks, we advocate using a Discriminative RBM, with two hardware-oriented adaptations. We propose a pulse width selection scheme based on the sign of two successive weight updates, and show that it removes the constraint to precisely tune the initial programming pulse width as a hyperparameter. We also propose to evaluate the weight update requested by the algorithm across several samples and stochastic realizations. We show that this strategy brings a partial immunity against the most severe memristive device imperfections such as the non-linearity and the stochasticity of the conductance updates, as well as device-to-device variability.
Finding an Optimal Corneal Xenograft Using Comparative Analysis of Corneal Matrix Proteins Across Species
Authors: Sharifi R. , Yang Y. , Adibnia Y. , Dohlman C. H. , Chodosh J. , Gonzalez-Andrades M. 
Published: February 2019

AbstractNumerous animal species have been proposed as sources of corneal tissue for obtaining decellularized xenografts. The selection of an appropriate animal model must take into consideration the differences in the composition and structure of corneal proteins between humans and other animal species in order to minimize immune response and improve outcome of the xenotransplant. Here, we compared the amino-acid sequences of 16 proteins present in the corneal stromal matrix of 14 different animal species using Basic Local Alignment Search Tool, and calculated a similarity score compared to the respective human sequence. Primary amino acid structures, isoelectric point and grand average of hydropathy (GRAVY) values of the 7 most abundant proteins (i.e. collagen α-1 (I), α-1 (VI), α-2 (I) and α-3 (VI), as well as decorin, lumican, and keratocan) were also extracted and compared to those of human. The pig had the highest similarity score (91.8%). All species showed a lower proline content compared to human. Isoelectric point of pig (7.1) was the closest to the human. Most species have higher GRAVY values compared to human except horse. Our results suggest that porcine cornea has a higher relative suitability for corneal transplantation into humans compared to other studied species.
Preoperative platelet-to-lymphocyte ratio and neutrophil-to-lymphocyte ratio as predictors of clinical outcome in patients with gallbladder cancer
Authors: Zhu Sha , Yang Jing , Cui Xiwei , Zhao Yunuo , Tao Zhihang , Xia Fan , Chen Linyan , Huang Juan , Ma Xuelei 
Published: February 2019

AbstractSome inflammatory biomarkers are associated with the post-surgical prognosis in cancer patients. However, their clinical importance in gallbladder cancer has rarely been explored. The aim of this study is to assess the efficacy of surgical intervention and the effectiveness of preoperative test on neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR) and monocyte-to-lymphocyte ratio (MLR) for predicting the prognosis in gallbladder cancer patients. In this study, a total of 255 gallbladder cancer patients were retrospectively selected. For each patient, we recorded his/her treatment algorithm (with or without surgery) and their preoperative inflammatory biomarkers, as well as their detailed survival information for 5 years. A total of 216 patients received surgical intervention and the other 39 chose conservative treatment. The median survival time was 4.6 months for non-surgical group (P < 0.001), and 12.2 months for surgical intervention group. Among the surgical group, ROC analysis showed the AUC of NLR, PLR and MLR were 0.675 (95% CI: 0.600 to 0.751, P < 0.001), 0.599 (95% CI: 0.520 to 0.677, P = 0.017) and 0.607 (95% CI: 0.529 to 0.686, P = 0.009), respectively. In conclusion, surgical intervention did improve the overall survival, and elevated NLR and MLR before surgery are associated with shorter OS of GBC patients.
The genetic Creutzfeldt-Jakob disease with E200K mutation: analysis of clinical, genetic and laboratory features of 30 Chinese patients
Authors: Gao Li-Ping , Shi Qi , Xiao Kang , Wang Jing , Zhou Wei , Chen Cao , Dong Xiao-Ping 
Published: February 2019

AbstractGenetic Creutzfeldt-Jakob disease (gCJD) with E200K mutation is one of the common subtypes of human genetic prion diseases worldwide. In this study, we systematically analyzed 30 Chinese E200K gCJD cases for their epidemiological, clinical, laboratory and genetic features. The patients came from 12 different provinces, majority in northern part of China. The onset age varied from 42 to 71 year-old (y), with the median of was 57 y. The CYP4X1 gene rs9793471 SNP was tested. Only one patient’s rs9793471 genotype was GA and the others’ were AA. The gender ratio (M: F) was 1:1.73 (11:19). The foremost symptoms and clinical progression of Chinese E200K gCJD patients were quite similar as sporadic CJD cases. Only a few cases (4/30) recalled clearly disease related family history. 74.1% (20/27), 86.7% (26/30) and 50.0% (13/26) of the cases were CSF 14-3-3 positive, sCJD associated abnormalities on MRI and special PSWC on EEG, respectively. The median clinical duration was 9 months (varying from 2 to 26 months). All 30 Chinese E200K gCJD patients were M129M and E219E homozygous. 21 members from 3 families conducted PRNP sequencing and 16 asymptomatic carriers of E200K mutation with M129M and E219E homozygous were identified. This is the largest study on E200K gCJD patients in China, which would benefit to the knowledge of E200K gCJD.
Suppressing the NHEJ pathway by DNA-PKcs inhibitor NU7026 prevents degradation of HBV cccDNA cleaved by CRISPR/Cas9
Authors: Kostyushev Dmitry , Kostyusheva Anastasiya , Brezgin Sergey , Zarifyan Dmitry , Utkina Anastasiya , Goptar Irina , Chulanov Vladimir 
Published: February 2019

AbstractChronic hepatitis B is a severe liver disease caused by hepatitis B virus (HBV) infection. Covalently closed circular DNA (cccDNA), a super-spiralized, double-stranded form of the HBV genome, is the major determinant of viral persistence. CRISPR/Cas9 nucleases have been recently shown to introduce double-stranded DNA breaks into HBV cccDNA. The inflicted damage results predominantly in erroneous repair of cccDNA by non-homologous end-joining (NHEJ). NHEJ has been suggested to enhance anti-HBV activity of CRISPR/Cas9 and increase cccDNA mutation. In this study, we assessed anti-HBV activity of CRISPR/Cas9 and cccDNA repair outcomes in an altered NHEJ/HR environment. NU7026, a strong inhibitor of NHEJ, prevented CRISPR/Cas9-mediated degradation of cccDNA and resulted in frequent on-target deletions. We conclude that CRISPR/Cas9 is a highly effective tool to degrade cccDNA and first demonstrate that inhibiting NHEJ impairs cccDNA degradation.
Niraparib activates interferon signaling and potentiates anti-PD-1 antibody efficacy in tumor models
Authors: Wang Zebin , Sun Kaiming , Xiao Yonghong , Feng Bin , Mikule Keith , Ma XiaoYan , Feng Ningping , Vellano Christopher P. , Federico Lorenzo , Marszalek Joseph R. , Mills Gordon B. , Hanke Jeffrey , Ramaswamy Sridhar , Wang Jing 
Published: February 2019

AbstractPARP inhibitors have been proven clinically efficacious in platinum-responsive ovarian cancer regardless of BRCA1/2 status and in breast cancers with germline BRCA1/2 mutation. However, resistance to PARP inhibitors may preexist or evolve during treatment in many cancer types and may be overcome by combining PARP inhibitors with other therapies, such as immune checkpoint inhibitors, which confer durable responses and are rapidly becoming the standard of care for multiple tumor types. This study investigated the therapeutic potential of combining niraparib, a highly selective PARP1/2 inhibitor, with anti-PD-1 immune checkpoint inhibitors in preclinical tumor models. Our results indicate that niraparib treatment increases the activity of the type I (alpha) and type II (gamma) interferon pathways and enhances the infiltration of CD8+ cells and CD4+ cells in tumors. When coadministered in immunocompetent models, the combination of niraparib and anti-PD-1 demonstrated synergistic antitumor activities in both BRCA-proficient and BRCA-deficient tumors. Interestingly, mice with tumors cured by niraparib monotherapy completely rejected tumor growth upon rechallenge with the same tumor cell line, suggesting the potential establishment of immune memory in animals treated with niraparib monotherapy. Taken together, our findings uncovered immunomodulatory effects of niraparib that may sensitize tumors to immune checkpoint blockade therapies.
Development of a suicide index model in general adolescents using the South Korea 2012–2016 national representative survey data
Authors: Lee Jinhee , Jang Ho , Kim Jongkoo , Min Seongho 
Published: February 2019

AbstractSuicide is a leading cause of death among adolescents and a major public health concern. Here we developed a risk stratification model for adolescent suicide attempts using sociodemographic characteristics, risk behaviours and psychological variables. Participants were 247,222 subjects in the Korea Youth Risk Behavior Web-based Survey (KYRBS). We developed a suicide index based on the suicide risk estimated in the generalized linear model and proposed the risk stratification model using the R language to measure the probability of suicide attempt among adolescents. Among the study population, the annual rate of suicide attempt was approximately 4%. The model provided good prediction for suicide attempt (AUC = 0.85). The important univariate risk factors for the outcome were dimensional measures of age, sex, breakfast consumption, experience of violence, sleep duration, perceived stress, feeling of sadness, current cigarette smoking, current alcohol drinking, perceived general health, perceived academic record, household economic status and living with biological or adoptive parents. Our suicide index model allowed the identification of adolescents who are at a high risk for suicide. This tool may promote the prevention of adolescent suicide and can be particularly useful in everyday settings where it is difficult to contact mental health professionals immediately.
Screening of endogenous strong promoters for enhanced production of medium-chain-length polyhydroxyalkanoates in Pseudomonas mendocina NK-01
Authors: Zhao Fengjie , Liu Xiangsheng , Kong Annie , Zhao Yuxin , Fan Xu , Ma Ting , Gao Weixia , Wang Shufang , Yang Chao 
Published: February 2019

AbstractPolyhydroxyalkanoate (PHA) can be produced by microorganisms from renewable resources and is regarded as a promising bioplastic to replace petroleum-based plastics. Pseudomonas mendocina NK-01 is a medium-chain-length PHA (mcl-PHA)-producing strain and its whole-genome sequence is currently available. The yield of mcl-PHA in P. mendocina NK-01 is expected to be improved by applying a promoter engineering strategy. However, a limited number of well-characterized promoters has greatly restricted the application of promoter engineering for increasing the yield of mcl-PHA in P. mendocina NK-01. In this work, 10 endogenous promoters from P. mendocina NK-01 were identified based on RNA-seq and promoter prediction results. Subsequently, 10 putative promoters were characterized for their strength through the expression of a reporter gene gfp. As a result, five strong promoters designated as P4, P6, P9, P16 and P25 were identified based on transcriptional level and GFP fluorescence intensity measurements. To evaluate whether the screened promoters can be used to enhance transcription of PHA synthase gene (phaC), the three promoters P4, P6 and P16 were separately integrated into upstream of the phaC operon in the genome of P. mendocina NK-01, resulting in the recombinant strains NKU-4C1, NKU-6C1 and NKU-16C1. As expected, the transcriptional levels of phaC1 and phaC2 in the recombinant strains were increased as shown by real-time quantitative RT-PCR. The phaZ gene encoding PHA depolymerase was further deleted to construct the recombinant strains NKU-∆phaZ-4C1, NKU-∆phaZ-6C1 and NKU-∆phaZ-16C1. The results from shake-flask fermentation indicated that the mcl-PHA titer of recombinant strain NKU-∆phaZ-16C1 was increased from 17 to 23 wt% compared with strain NKU-∆phaZ. This work provides a feasible method to discover strong promoters in P. mendocina NK-01 and highlights the potential of the screened endogenous strong promoters for metabolic engineering of P. mendocina NK-01 to increase the yield of mcl-PHA.
A functional connectome phenotyping dataset including cognitive state and personality measures
Authors: Mendes Natacha , Oligschläger Sabine , Lauckner Mark E. , Golchert Johannes , Huntenburg Julia M. , Falkiewicz Marcel , Ellamil Melissa , Krause Sarah , Baczkowski Blazej M. , Cozatl Roberto , Osoianu Anastasia , Kumral Deniz , Pool Jared , Golz Laura , Dreyer Maria , Haueis Philipp , Jost Rebecca , Kramarenko Yelyzaveta , Engen Haakon , Ohrnberger Katharina , Gorgolewski Krzysztof J. , Farrugia Nicolas , Babayan Anahit , Reiter Andrea , Schaare H. Lina , Reinelt Janis , Röbbig Josefin , Uhlig Marie , Erbey Miray , Gaebler Michael , Smallwood Jonathan , Villringer Arno , Margulies Daniel S. 
Published: February 2019

AbstractThe dataset enables exploration of higher-order cognitive faculties, self-generated mental experience, and personality features in relation to the intrinsic functional architecture of the brain. We provide multimodal magnetic resonance imaging (MRI) data and a broad set of state and trait phenotypic assessments: mind-wandering, personality traits, and cognitive abilities. Specifically, 194 healthy participants (between 20 and 75 years of age) filled out 31 questionnaires, performed 7 tasks, and reported 4 probes of in-scanner mind-wandering. The scanning session included four 15.5-min resting-state functional MRI runs using a multiband EPI sequence and a hig h-resolution structural scan using a 3D MP2RAGE sequence. This dataset constitutes one part of the MPI-Leipzig Mind-Brain-Body database.
Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins
Authors: Blattmann Peter , Stutz Vivienne , Lizzo Giulia , Richard Joy , Gut Philipp , Aebersold Ruedi 
Published: February 2019

AbstractSequential window acquisition of all theoretical mass spectra (SWATH-MS) requires a spectral library to extract quantitative measurements from the mass spectrometry data acquired in data-independent acquisition mode (DIA). Large combined spectral libraries containing SWATH assays have been generated for humans and several other organisms, but so far no publicly available library exists for measuring the proteome of zebrafish, a rapidly emerging model system in biomedical research. Here, we present a large zebrafish SWATH spectral library to measure the abundance of 104,185 proteotypic peptides from 10,405 proteins. The library includes proteins expressed in 9 different zebrafish tissues (brain, eye, heart, intestine, liver, muscle, ovary, spleen, and testis) and provides an important new resource to quantify 40% of the protein-coding zebrafish genes. We employ this resource to quantify the proteome across brain, muscle, and liver and characterize divergent expression levels of paralogous proteins in different tissues. Data are available via ProteomeXchange (PXD010876, PXD010869) and SWATHAtlas (PASS01237).
Characterization of deep neural network features by decodability from human brain activity
Authors: Horikawa Tomoyasu , Aoki Shuntaro C. , Tsukamoto Mitsuaki , Kamitani Yukiyasu 
Published: February 2019

AbstractAchievements of near human-level performance in object recognition by deep neural networks (DNNs) have triggered a flood of comparative studies between the brain and DNNs. Using a DNN as a proxy for hierarchical visual representations, our recent study found that human brain activity patterns measured by functional magnetic resonance imaging (fMRI) can be decoded (translated) into DNN feature values given the same inputs. However, not all DNN features are equally decoded, indicating a gap between the DNN and human vision. Here, we present a dataset derived from DNN feature decoding analyses, which includes fMRI signals of five human subjects during image viewing, decoded feature values of DNNs (AlexNet and VGG19), and decoding accuracies of individual DNN features with their rankings. The decoding accuracies of individual features were highly correlated between subjects, suggesting the systematic differences between the brain and DNNs. We hope the present dataset will contribute to revealing the gap between the brain and DNNs and provide an opportunity to make use of the decoded features for further applications.
MicroRNA expression profiles across blood and different tissues in cattle
Authors: Sun Hui-Zeng , Chen Yanhong , Guan Le Luo 
Published: February 2019

AbstractMicroRNAs (miRNAs) play essential roles in regulating gene expression involved in various biological functions. The knowledge of miRNA expression profiles across different tissues in cattle is still limited. Using the miRNAs data generated from 158 samples in three studies, we characterized the miRNA expression profiles of bovine sera, exosomes and 11 different tissues. Totally 639 miRNAs were identified and 159 miRNAs were expressed in all samples. After relative log expression normalization, four miRNA expression clusters were generated: 1) sera and exosomes; 2) liver; 3) mammary gland; 4) rumen and gut tissues. The top 10 most abundant miRNAs accounted for >55% of total miRNA expression in each tissue. In addition, this study described a detailed pipeline for identification of both tissue and circulating miRNAs, and the shareable datasets can be re-used by researchers to investigate miRNA-related biological questions in cattle. In addition, a web-based repository was developed, which enables researchers to access the distribution range and raw counts number of the miRNA expression data (https://www.cattleomics.com/micrornaome).
Atomistic simulation of size‐dependent heat capacity of liquid in molecular scale confinement at different temperatures
Authors: Mahmud Rifat , Morshed A.K.M. Monjur , Paul Titan C. 
Published: February 2019

An enhancement of heat capacity (Cv) of nanoconfined liquid is reported using equilibrium molecular dynamics simulations using Lennard–Jones type solid–liquid molecular model. Liquid molecules are confined in between two solid surfaces with separation distance varying from 0.6 to 17.55 nm and temperature 100 K to 140 K. The obtained heat capacity of the bulk liquid is in excellent agreement with the published literature. However, in case of nanoconfined liquid, for a particular temperature and gap thickness band, a significant enhancement of heat capacity results in. For 100 K temperature and a gap thickness of 4 nm, the obtained molar heat capacity of the nanoconfined liquid is 46.45 J/mol K, i.e. the heat capacity is enhanced by 133% compared to its bulk counterpart (19.95 J/mol K). However, this broad maximum value of heat capacity shifts to a lower value at a higher temperature. At 120 and 140 K, the maximum heat capacity becomes 29.56 and 26.97 J/mol.K and the enhancement becomes 51% and 40%, respectively. The enhancement of heat capacity is attributed to the variation in density distribution, ballistic transport of thermal phonons, reduced molecular motion and a larger contribution of interfacial thermal resistance.
Strip‐based nano‐silver biocomposite construct for rapid screening of aqueous mercury
Authors: Dugyala Raju , Zahoor Gul Mir , Kumar Sriramoju Manoj , Rao Beedu Sashidhar 
Published: February 2019

A simple, rapid and a cost‐effective colorimetric method for detection of Hg2+ in an aqueous system using silver nanoparticle (AgNP) has been developed in the present study. AgNPs were synthesised using gum kondagogu (GK), a natural biopolymer that acts as both reducing and stabilising agent. The stability of GK‐AgNPs composites was determined by zeta potential and was observed to be −30.43 mV. The yellow colour spot on the nitrocellulose membrane turned colourless at Hg2+ concentration of 20 ppm in aqueous solution, which can be observed visually. By using inductively coupled plasma mass spectrometry, it was observed that as the concentration of Hg2+ increases the Ag concentration decreased. Further, scanning electron microscopy and energy‐dispersive X‐ray spectroscopy were used to confirm the morphological changes on membrane before and after treating with Hg2 +. The interference of other metal ions was also studied to validate Hg2+ specificity. This method was successfully employed to screen Hg2+ in industrial effluents. In summary, this study entails the development of a nitrocellulose membrane based mercury sensor that has practical applicability for on‐site screening of Hg2+ contamination in the aqueous system.
PSJ LDMOS with a VK dielectric layer
Authors: Wu Lijuan , Wu Yiqing , Lei Bing , Zhang Yinyan , Huang Ye , Zhu Lin 
Published: February 2019

A partial super junction lateral double‐diffused metal–oxide–semiconductor field‐effect transistor with a variable‐k dielectric layer (PSJ VK LDMOS) is proposed in this Letter. Low‐k material and PSJ are introduced into the device. PSJ provides a low‐resistance channel to reduce the specific on‐resistance (Ron,sp). Furthermore, according to an enhanced dielectric layer field, low‐k buried layer can sustain the high breakdown voltage (BV). To eliminate substrate‐assisted depletion effect and improve the lateral BV of the proposed structure, the charge compensation layer in the device adopts a variation of lateral doping technique and is combined with the N pillar in PSJ. Ultimately, the simulation results show that BV of 795.5 V and the figure of merit (FOM) of 6.1 MW cm−2 are achieved for PSJ VK LDMOS. BV and FOM are enhanced by 71.4 and 81.1%, respectively, compared with con. PSJ SOI LDMOS with the drift region length of 46.5 μm. Furthermore, Ron,sp of 103.4 mΩ cm2 is reduced by 31.2% compared with the ‘silicon limit’ at the same BV class, which breaks the ‘silicon limit’.