bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of PUF60 in Transcriptional and Post-transcriptional Regulation of Hepatitis B Virus Pregenomic RNA Expression
Authors: Sun Suofeng , Nakashima Kenji , Ito Masahiko , Li Yuan , Chida Takeshi , Takahashi Hirotaka , Watashi Koichi , Sawasaki Tatsuya , Wakita Takaji , Suzuki Tetsuro 
Published: October 2017

AbstractHere we identified PUF60, a splicing factor and a U2 small nuclear ribonucleoprotein auxiliary factor, as a versatile regulator of transcriptional and post-transcriptional steps in expression of hepatitis B virus (HBV) 3.5 kb, precore plus pregenomic RNA. We demonstrate that PUF60 is involved in: 1) up-regulation of core promoter activity through its interaction with transcription factor TCF7L2, 2) promotion of 3.5 kb RNA degradation and 3) suppression of 3.5 kb RNA splicing. When the 1.24-fold HBV genome was introduced into cells with the PUF60-expression plasmid, the 3.5 kb RNA level was higher at days 1–2 post-transfection but declined thereafter in PUF60-expressing cells compared to viral replication control cells. Deletion analyses showed that the second and first RNA recognition motifs (RRMs) within PUF60 are responsible for core promoter activation and RNA degradation, respectively. Expression of PUF60 mutant deleting the first RRM led to higher HBV production. To our knowledge, this is the first to identify a host factor involved in not only positively regulating viral gene expression but also negative regulation of the same viral life cycle. Functional linkage between transcriptional and post-transcriptional controls during viral replication might be involved in mechanisms for intracellular antiviral defense and viral persistence.
Clinicopathological and molecular characteristics of synchronous gastric adenocarcinoma and gastrointestinal stromal tumors
Authors: Luo Jun-Ming , Cao Fa-Long , Meng Chen , Lin Li-Jun , Ma Si-Qing , Peng Shao-Hua , Gao Hong-Ling , Javidiparsijani Sara , Wang Gui-Rong , Zhang Meng-Lan , Xin Jian-Guo , Wang Yi-Chun , Zhang Shu-Kun 
Published: October 2017

AbstractSynchronous gastric tumors that consist of both gastrointestinal stromal tumor (GIST) and adenocarcinoma are rare. We studied the clinicopathological and molecular characteristics of six cases containing both gastric adenocarcinoma and GIST. By means of immunohistochemical analysis, all GIST cells expressed CD117, CD34 and Dog1 in all six synchronous gastric adenocarcinomas with GIST, and in GIST alone. Sequencing analysis demonstrated that exon 11 c-kit mutations were present in two of six synchronous tumors and four of five GISTs. One of the two exon 11 c-kit mutations in synchronous adenocarcinomas with GISTs was an uncommon mutation of CTT > CCA at amino acid 576, and the other was a GTT deletion at amino acid 560. The mutation was a homozygous A > G mutation in exon 12 (amino acid 567) of PDGFR-α. We concluded that the exon 11 mutations were the most important in both cases of synchronous gastric adenocarcinoma with GIST and GIST alone. The mutation rate was higher in GIST alone than in synchronous adenocarcinoma with GIST.
HIV-infected macrophages and microglia that survive acute infection become viral reservoirs by a mechanism involving Bim
Authors: Castellano Paul , Prevedel Lisa , Eugenin Eliseo A. 
Published: October 2017

AbstractWhile HIV kills most of the cells it infects, a small number of infected cells survive and become latent viral reservoirs, posing a significant barrier to HIV eradication. However, the mechanism by which immune cells resist HIV-induced apoptosis is still incompletely understood. Here, we demonstrate that while acute HIV infection of human microglia/macrophages results in massive apoptosis, a small population of HIV-infected cells survive infection, silence viral replication, and can reactivate viral production upon specific treatments. We also found that HIV fusion inhibitors intended for use as antiretroviral therapies extended the survival of HIV-infected macrophages. Analysis of the pro- and anti-apoptotic pathways indicated no significant changes in Bcl-2, Mcl-1, Bak, Bax or caspase activation, suggesting that HIV blocks a very early step of apoptosis. Interestingly, Bim, a highly pro-apoptotic negative regulator of Bcl-2, was upregulated and recruited into the mitochondria in latently HIV-infected macrophages bothin vitroandin vivo. Together, these results demonstrate that macrophages/microglia act as HIV reservoirs and utilize a novel mechanism to prevent HIV-induced apoptosis. Furthermore, they also suggest that Bim recruitment to mitochondria could be used as a biomarker of viral reservoirsin vivo.
Multiobjective differential evolution-based multifactor dimensionality reduction for detecting gene–gene interactions
Authors: Yang Cheng-Hong , Chuang Li-Yeh , Lin Yu-Da 
Published: October 2017

AbstractEpistasis within disease-related genes (gene–gene interactions) was determined through contingency table measures based on multifactor dimensionality reduction (MDR) using single-nucleotide polymorphisms (SNPs). Most MDR-based methods use the single contingency table measure to detect gene–gene interactions; however, some gene–gene interactions may require identification through multiple contingency table measures. In this study, a multiobjective differential evolution method (called MODEMDR) was proposed to merge the various contingency table measures based on MDR to detect significant gene–gene interactions. Two contingency table measures, namely the correct classification rate and normalized mutual information, were selected to design the fitness functions in MODEMDR. The characteristics of multiobjective optimization enable MODEMDR to use multiple measures to efficiently and synchronously detect significant gene–gene interactions within a reasonable time frame. Epistatic models with and without marginal effects under various parameter settings (heritability and minor allele frequencies) were used to assess existing methods by comparing the detection success rates of gene–gene interactions. The results of the simulation datasets show that MODEMDR is superior to existing methods. Moreover, a large dataset obtained from the Wellcome Trust Case Control Consortium was used to assess MODEMDR. MODEMDR exhibited efficiency in identifying significant gene–gene interactions in genome-wide association studies.
Human attention affects facial expressions in domestic dogs
Authors: Kaminski Juliane , Hynds Jennifer , Morris Paul , Waller Bridget M. 
Published: October 2017

AbstractMost mammalian species produce facial expressions. Historically, animal facial expressions have been considered inflexible and involuntary displays of emotional states rather than active attempts to communicate with others. In the current study, we aimed to test whether domestic dog facial expressions are subject to audience effects and/ or changes in response to an arousing stimulus (e.g. food) alone. We presented dogs with an experimental situation in which a human demonstrator was either attending to them or turned away, and varied whether she presented food or not. Dogs produced significantly more facial movements when the human was attentive than when she was not. The food, however, as a non-social but arousing stimulus, did not affect the dogs’ behaviour. The current study is therefore evidence that dogs are sensitive to the human’s attentional state when producing facial expressions, suggesting that facial expressions are not just inflexible and involuntary displays of emotional states, but rather potentially active attempts to communicate with others.
6E11, a highly selective inhibitor of Receptor-Interacting Protein Kinase 1, protects cells against cold hypoxia-reoxygenation injury
Authors: Delehouzé C. , Leverrier-Penna S. , Le Cann F. , Comte A. , Jacquard-Fevai M. , Delalande O. , Desban N. , Baratte B. , Gallais I. , Faurez F. , Bonnet M. C. , Hauteville M. , Goekjian P. G. , Thuillier R. , Favreau F. , Vandenabeele P. , Hauet T. , Dimanche-Boitrel M. T. , Bach S. 
Published: October 2017

AbstractNecroptosis is a programmed cell death pathway that has been shown to be of central pathophysiological relevance in multiple disorders (hepatitis, brain and cardiac ischemia, pancreatitis, viral infection and inflammatory diseases). Necroptosis is driven by two serine threonine kinases, RIPK1 (Receptor Interacting Protein Kinase 1) and RIPK3, and a pseudo-kinase MLKL (Mixed Lineage Kinase domain-Like) associated in a multi-protein complex called necrosome. In order to find new inhibitors for use in human therapy, a chemical library containing highly diverse chemical structures was screened using a cell-based assay. The compound 6E11, a natural product derivative, was characterized as a positive hit. Interestingly, this flavanone compound: inhibits necroptosis induced by death receptors ligands TNF-α (Tumor Necrosis Factor) or TRAIL (TNF-Related Apoptosis-Inducing Ligand); is an extremely selective inhibitor, among kinases, of human RIPK1 enzymatic activity with a nM Kd; has a non-ATP competitive mode of action and a novel putative binding site; is weakly cytotoxic towards human primary blood leukocytes or retinal pigment epithelial cells at effective concentrations; protects human aortic endothelial cells (HAEC) from cold hypoxia/reoxygenation injury more effectively than necrostatin-1 (Nec-1) and Nec-1s. Altogether, these data demonstrate that 6E11 is a novel potent small molecular inhibitor of RIPK1-driven necroptosis.
Fermi surface topology and magnetotransport in semimetallic LuSb
Authors: Pavlosiuk Orest , Kleinert Maja , Swatek Przemysław , Kaczorowski Dariusz , Wiśniewski Piotr 
Published: October 2017

AbstractSeveral rare-earth monopnictides were shown to exhibit extreme magnetoresistance and field-induced low-temperature plateau of electrical resistivity. These features are also hallmarks of topological semimetals, thus the family is intensively explored with respect to magneto-transport properties and possible hosting Dirac fermion states. We report a comprehensive investigation of Fermi surface and electrical transport properties of LuSb, another representative of this family. At low temperatures, the magnetoresistance of LuSb was found to exceed 3000% without saturation in fields up to 9 T. Analysis of the Hall effect and the Shubnikov–de Haas oscillations revealed that the Fermi surface of this compound consists of several pockets originating from fairly compensated multi-band electronic structure, in full accordance with our first-principles calculations. Observed magnetotransport properties of LuSb can be attributed to the topology of three-dimensional Fermi surface and a compensation of electron and hole contributions.
Changes in soil properties, X-ray-mineral diffractions and infrared-functional groups in bulk soil and fractions following afforestation of farmland, Northeast China
Authors: Wang Qiong , Wang Wenjie , He Xingyuan , Zheng Qingfu , Wang Huimei , Wu Yan , Zhong Zhaoliang 
Published: October 2017

AbstractAnalysis of soil properties, the compositional traits in bulk soil and different fractions and their responses to afforestation practices may possibly facilitate clarification of the mechanisms underlying soil changes. Soil properties, the compositional functional groups and minerals were determined in the bulk soil and fractions from forests and adjacent farmlands. The afforestation of farmland could induce accumulation of soil organic carbon [SOC] (+18%) and nitrogen [N] (+4%) with pH increase (+4%), and declines in electric conductivity (−15%) and bulk density (−3%). Sand and aggregates [SA] and easily oxidized fraction [EO] mainly contributed to the SOC and N accumulation. Moreover, afforestation-induced changes were observed in O-H & N-H stretching (−26%), feldspar (+52%) and huntite crystallinity (−40%). The changes of soil properties were strongly associated with the changes in functional groups, followed by minerals. Of them, asymmetric COO- & C = O stretching & O-H bending, symmetric COO- stretching, huntite and smectite-vermiculite crystallinity were the key factors responsible for the changes of soil properties. Our findings highlight that degraded farmland afforestation could strongly affect soil properties in the bulk soil, and the changes in fractions (mainly SA and EO) as well as their changes in the compositional traits strongly supported these bulk soil changes.
Usefulness of kidney slices for functional analysis of apical reabsorptive transporters
Authors: Arakawa Hiroshi , Washio Ikumi , Matsuoka Natsumi , Kubo Hikaru , Staub Angelina Yukiko , Nakamichi Noritaka , Ishiguro Naoki , Kato Yukio , Nakanishi Takeo , Tamai Ikumi 
Published: October 2017

AbstractKidney plays a key role in the elimination and reabsorption of drugs and nutrients, however in vitro methods to evaluate renal disposition are limited. In the present study, we investigated usefulness of isolated kidney slice, which had been used for transport only at basolateral membrane of tubular epithelial cells, for evaluation of apical membrane transporters. As transporters that are easy to discriminate between apical and basolateral transports, apical membrane specific and sodium-dependent transporters (SGLTs and OCTNs) and pH-dependent transporters (PEPTs) are selected. Uptake of ergothioneine, carnitine and methyl-α-D-glucopyranoside, which are substrates of apical Octn1, Octn2, and Sglt1/2, respectively, by mice kidney slices showed clear Na+ dependence and reduction by selective inhibitors. In addition, sodium dependence of ergothioneine uptake was negligible in the kidney slice from Octn1-gene deficient mice. Moreover, uptake of PepT1/2 substrate glycyl-sarcosine, was higher than that in the presence of glycyl-leucine, a non-specific Pept inhibitor. The K
m
and IC50 values for substrates and inhibitors of each transporter were mostly comparable to those obtained in transporter-transfected cells. In conclusion, it was demonstrated that kidney slices are promising tool to study transporters expressed at the apical membranes as well as basolateral membranes of kidney tubular epithelial cells.
Membrane Trafficking Modulation during Entamoeba Encystation
Authors: Herman Emily , Siegesmund Maria A. , Bottery Michael J. , van Aerle Ronny , Shather Maulood Mohammed , Caler Elisabet , Dacks Joel B. , van der Giezen Mark 
Published: October 2017

AbstractEntamoeba histolytica is an intestinal parasite that infects 50–100 million people and causes up to 55,000 deaths annually. The transmissive form of E. histolytica is the cyst, with a single infected individual passing up to 45 million cysts per day, making cyst production an attractive target for infection control. Lectins and chitin are secreted to form the cyst wall, although little is known about the underlying membrane trafficking processes supporting encystation. As E. histolytica does not readily form cysts in vitro, we assessed membrane trafficking gene expression during encystation in the closely related model Entamoeba invadens. Genes involved in secretion are up-regulated during cyst formation, as are some trans-Golgi network-to-endosome trafficking genes. Furthermore, endocytic and general trafficking genes are up-regulated in the mature cyst, potentially preserved as mRNA in preparation for excystation. Two divergent dynamin-related proteins found in Entamoeba are predominantly expressed during cyst formation. Phylogenetic analyses indicate that they are paralogous to, but quite distinct from, classical dynamins found in human, suggesting that they may be potential drug targets to block encystation. The membrane-trafficking machinery is clearly regulated during encystation, providing an additional facet to understanding this crucial parasitic process.
Quantifying Anthropogenic Stress on Groundwater Resources
Authors: Ashraf Batool , AghaKouchak Amir , Alizadeh Amin , Mousavi Baygi Mohammad , R. Moftakhari Hamed , Mirchi Ali , Anjileli Hassan , Madani Kaveh 
Published: October 2017

AbstractThis study explores a general framework for quantifying anthropogenic influences on groundwater budget based on normalized human outflow (hout) and inflow (hin). The framework is useful for sustainability assessment of groundwater systems and allows investigating the effects of different human water abstraction scenarios on the overall aquifer regime (e.g., depleted, natural flow-dominated, and human flow-dominated). We apply this approach to selected regions in the USA, Germany and Iran to evaluate the current aquifer regime. We subsequently present two scenarios of changes in human water withdrawals and return flow to the system (individually and combined). Results show that approximately one-third of the selected aquifers in the USA, and half of the selected aquifers in Iran are dominated by human activities, while the selected aquifers in Germany are natural flow-dominated. The scenario analysis results also show that reduced human withdrawals could help with regime change in some aquifers. For instance, in two of the selected USA aquifers, a decrease in anthropogenic influences by ~20% may change the condition of depleted regime to natural flow-dominated regime. We specifically highlight a trending threat to the sustainability of groundwater in northwest Iran and California, and the need for more careful assessment and monitoring practices as well as strict regulations to mitigate the negative impacts of groundwater overexploitation.
Evidence for in-gap surface states on the single phase SmB6(001) surface
Authors: Miyamachi Toshio , Suga Shigemasa , Ellguth Martin , Tusche Christian , Schneider Claus M. , Iga Fumitoshi , Komori Fumio 
Published: October 2017

AbstractStructural and electronic properties of the SmB6(001) single-crystal surface prepared by Ar+ ion sputtering and controlled annealing are investigated by scanning tunneling microscopy. In contrast to the cases of cleaved surfaces, we observe a single phase surface with a non-reconstructed p(1 × 1) lattice on the entire surface at an optimized annealing temperature. The surface is identified as Sm-terminated on the basis of spectroscopic measurements. On a structurally uniform surface, the emergence of the in-gap state, a robust surface state against structural variation, is further confirmed inside a Kondo hybridization gap at 4.4 K by temperature and atomically-resolved spatial dependences of the differential conductance spectrum near the Fermi energy.
Zdhhc13-dependent Drp1 S-palmitoylation impacts brain bioenergetics, anxiety, coordination and motor skills
Authors: Napoli Eleonora , Song Gyu , Liu Siming , Espejo Alexsandra , Perez Carlos J. , Benavides Fernando , Giulivi Cecilia 
Published: October 2017

AbstractProteinS-palmitoylation is a reversible post-translational modification mediated by palmitoyl acyltransferase enzymes, a group of Zn2+-finger DHHC-domain-containing proteins (ZDHHC). Here, for the first time, we show that Zdhhc13 plays a key role in anxiety-related behaviors and motor function, as well as brain bioenergetics, in a mouse model (luc) carrying a spontaneousZdhhc13recessive mutation. At 3 m of age, mutant mice displayed increased sensorimotor gating, anxiety, hypoactivity, and decreased motor coordination, compared to littermate controls. Loss of Zdhhc13 in cortex and cerebellum from 3- and 24 m old hetero- and homozygous male mutant mice resulted in lower levels of Drp1S-palmitoylation accompanied by altered mitochondrial dynamics, increased glycolysis, glutaminolysis and lactic acidosis, and neurotransmitter imbalances. Employingin vivoandin vitromodels, we identified that Zdhhc13-dependent Drp1S-palmitoylation, which acting alone or in concert, enables the normal occurrence of the fission-fusion process.In vitroandin vivodirect Zdhhc13-Drp1 protein interaction was observed, confirming Drp1 as a substrate of Zdhhc13. Abnormal fission-fusion processes result in disrupted mitochondria morphology and distribution affecting not only mitochondrial ATP output but neurotransmission and integrity of synaptic structures in the brain, setting the basis for the behavioral abnormalities described in theZdhhc13-deficient mice.
Adjacent-possible ecological niche: growth of Lactobacillus species co-cultured with Escherichia coli in a synthetic minimal medium
Authors: Mizuno Kouhei , Mizuno Mamiko , Yamauchi Mio , Takemura Aya J. , Medrano Romero Veronica , Morikawa Kazuya 
Published: October 2017

AbstractIn certain conditions, members of the Lactobacillus genus are auxotrophs that have fastidious requirements for growth. Notably, Lactobacillus cannot grow in M9 medium, a minimal synthetic medium used for Escherichia coli. However, we found that some Lactobacillus strains can be grown in M9 when co-cultured with E. coli K-12. In the co-culture, L. casei proliferates exponentially, reaching cell densities of 108 CFU (colony-forming unit) ml−1 in 6 h and dominating E. coli in the late growth phase. Spent medium from E. coli grown overnight lacked this growth-promoting effect on L. casei. Similarly, the effect was not observed when the species were separated by a 0.4-µm membrane. Microscopic observations showed that L. casei are embedded in the micro-scale clusters of E. coli in the early growth phase. This study describes for the first time the ability of a Lactobacillus species to grow in minimal medium when in close proximity with co-cultured bacteria.
The Impact of parasitic loss on solar cells with plasmonic nano-textured rear reflectors
Authors: Disney Claire E. R. , Pillai Supriya , Green Martin A. 
Published: October 2017

AbstractSignificant photocurrent enhancement has been demonstrated using plasmonic light-trapping structures comprising nanostructured metallic features at the rear of the cell. These structures have conversely been identified as suffering heightened parasitic absorption into the metal at certain resonant wavelengths severely mitigating benefits of light trapping. In this study, we undertook simulations exploring the relationship between enhanced absorption into the solar cell, and parasitic losses in the metal. These simulations reveal that resonant wavelengths associated with high parasitic losses in the metal could also be associated with high absorption enhancement in the solar cell. We identify mechanisms linking these parasitic losses and absorption enhancements, but found that by ensuring correct design, the light trapping structures will have a positive impact on the overall solar cell performance. Our results clearly show that the large angle scattering provided by the plasmonic nanostructures is the reason for the enhanced absorption observed in the solar cells.