bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gut microbiota community characteristics and disease-related microorganism pattern in a population of healthy Chinese people
Authors: Zhang Wen , Li Juan , Lu Shan , Han Na , Miao Jiaojiao , Zhang Tingting , Qiang Yujun , Kong Yanhua , Wang Hong , Gao Tongxin , Liu Yuqing , Li Xiuwen , Peng Xianhui , Chen Xia , Zhao Xiaofei , Che Jie , Zhang Ling , Chen Xi , Zhang Qing , Hu Ming , Li Qun , Kan Biao 
Published: February 2019

AbstractChina’s population accounts for about 1/5th of the world’s total population. Owing to differences in environment, race, living habits, and other factors, the structure of the intestinal flora of Chinese individuals is expected to have unique features; however, this has not been thoroughly examined. Here, we collected faecal samples from healthy adults living in three cities of China and investigated their gut microbiome using metagenomics and bioinformatics technology. We found that 11 core bacterial genera were present in all of the Chinese faecal samples; moreover, several patient characteristics (age, region, body mass index, physical exercise, smoking habits, and alcoholic drink, and yogurt consumption) were found to have different effects on the gut microbiome of healthy Chinese people. We also examined the distribution patterns of disease-related microorganisms (DRMs), revealing which DRMs can potentially be used as markers for assessment of health risk. We also developed a program called “Guthealthy” for evaluating the health status associated with the microbiome and DRM pattern in the faecal samples. The microbiota data obtained in this study will provide a basis for a healthy gut microbiome composition in the Chinese population.
Epigenetic mechanisms mediate the experimental evolution of resistance against parasitic fungi in the greater wax moth Galleria mellonella
Authors: Mukherjee Krishnendu , Dubovskiy Ivan , Grizanova Ekaterina , Lehmann Rüdiger , Vilcinskas Andreas 
Published: February 2019

AbstractRecent concepts in evolutionary biology suggest that epigenetic mechanisms can translate environmental selection pressures into heritable changes in phenotype. To determine whether experimental selection for a complex trait in insects involves epigenetic modifications, we carried out a generation-spanning experiment using larvae of the greater wax moth Galleria mellonella as a model host to investigate the role of epigenetics in the heritability of resistance against the parasitic fungus Metarhizium robertsii. We investigated differences in DNA methylation, histone acetylation and microRNA (miRNA) expression between an experimentally resistant population and an unselected, susceptible line, revealing that the survival of G. mellonella larvae infected with M. robertsii correlates with tissue-specific changes in DNA methylation and histone modification and the modulation of genes encoding the corresponding enzymes. We also identified miRNAs differentially expressed between resistant and susceptible larvae and showed that these regulatory molecules target genes encoding proteinases and proteinase inhibitors, as well as genes related to cuticle composition, innate immunity and metabolism. These results support our hypothesis that epigenetic mechanisms facilitate, at least in part, the heritable manifestation of parasite resistance in insects. The reciprocal adaptations underlying host–parasite coevolution therefore extend beyond the genetic level to encompass epigenetic modifications.
Scouting for Naturally Low-Toxicity Wheat Genotypes by a Multidisciplinary Approach
Authors: Pilolli Rosa , Gadaleta Agata , Mamone Gianfranco , Nigro Domenica , De Angelis Elisabetta , Montemurro Nicola , Monaci Linda 
Published: February 2019

AbstractOver the last years, great efforts have been devoted to develop effective gluten detoxification strategies with a consequent detrimental alteration of the technological properties as well. Obtaining low-gluten products without affecting the rheological properties of wheat could still be considered a new challenge to face. In this investigation, we presented a comprehensive characterization of durum wheat genotypes aimed at identifying low gluten ones, which combine the potential lower toxicity/immunogenicity with conserved yield and rheological properties to encompass the perspective usability for bread or pasta making. A preliminary profiling of gluten proteins was accomplished by immunoassay-based quantification and liquid chromatography coupled to UV detection, focusing on the gliadin fraction as main responsible for immunoreactivity in celiac disease patients. In addition, data on grain protein content, grain yield per spike, dry gluten and gluten index were collected in order to provide complementary information about productivity-related traits and quali-quantitative characteristics related to wheat nutritional value and its technological properties. The whole pool of data was statistically evaluated driving to the selection of a preferred list of candidate low-toxicity genotypes that were subjected to in-vitro simulated gastroduodenal digestion and untargeted HR-MS/MS peptide identification. Finally, an in-silico risk assessment of potential toxicity for celiac disease patients was performed according to the most recent guidance provided by EFSA.
Chronic olanzapine administration causes metabolic syndrome through inflammatory cytokines in rodent models of insulin resistance
Authors: Li Huqun , Peng Shiyong , Li Shihong , Liu Shouqing , Lv Yifan , Yang Ni , Yu Liangyu , Deng Ya-Hui , Zhang Zhongjian , Fang Maosheng , Huo Yunxiang , Chen Ying , Sun Taohua , Li Weiyong 
Published: February 2019

AbstractOlanzapine is a second-generation anti-psychotic drug used to prevent neuroinflammation in patients with schizophrenia. However, the long-term administration of olanzapine leads to insulin resistance (IR); the mechanisms of this effect remains poorly understood. Using cellular and rodent models of IR induced by olanzapine, we found that chronic olanzapine treatment induces differential inflammatory cytokine reactions in peripheral adipose and the central nervous system. Long-term treatment of olanzapine caused metabolic symptoms, including IR, by markedly elevating the plasma levels of pro-inflammatory cytokines, including IL-1ß, IL-6, IL-8 and TNFα; these findings are consistent with observations from schizophrenia patients chronically treated with olanzapine. Our observations of differential inflammatory cytokine responses in white adipose tissues from the prefrontal cortex in the brain indicated cell type-specific effects of the drug. These cytokines induced IR by activating NF-kB through the suppression of IkBα. Functional blockade of the components p50/p65 of NF-kB rescued olanzapine-induced IR in NIH-3T3 L1-derived adipocytes. Our findings demonstrate that olanzapine induces inflammatory cytokine reactions in peripheral tissues without adversely affecting the central nervous system and suggest that chronic olanzapine treatment of schizophrenia patients may cause inflammation-mediated IR with minimal or no adverse effects in the brain.
PFDB: A standardized protein folding database with temperature correction
Authors: Manavalan Balachandran , Kuwajima Kunihiro , Lee Jooyoung 
Published: February 2019

AbstractWe constructed a standardized protein folding kinetics database (PFDB) in which the logarithmic rate constants of all listed proteins are calculated at the standard temperature (25 °C). A temperature correction based on the Eyring–Kramers equation was introduced for proteins whose folding kinetics were originally measured at temperatures other than 25 °C. We verified the temperature correction by comparing the logarithmic rate constants predicted and experimentally observed at 25 °C for 14 different proteins, and the results demonstrated improvement of the quality of the database. PFDB consists of 141 (89 two-state and 52 non-two-state) single-domain globular proteins, which has the largest number among the currently available databases of protein folding kinetics. PFDB is thus intended to be used as a standard for developing and testing future predictive and theoretical studies of protein folding. PFDB can be accessed from the following link: http://lee.kias.re.kr/~bala/PFDB.
Evaluation of cationic channel TRPV2 as a novel biomarker and therapeutic target in Leukemia-Implications concerning the resolution of pulmonary inflammation
Authors: Siveen Kodappully S. , Prabhu Kirti S. , Parray Aeijaz S. , Merhi Maysaloun , Arredouani Abdelilah , Chikri Mohamed , Uddin Shahab , Dermime Said , Mohammad Ramzi M. , Steinhoff Martin , Janahi Ibrahim A. , Azizi Fouad 
Published: February 2019

AbstractPatients treated during leukemia face the risk of complications including pulmonary dysfunction that may result from infiltration of leukemic blast cells (LBCs) into lung parenchyma and interstitium. In LBCs, we demonstrated that transient receptor potential vanilloid type 2 channel (TRPV2), reputed for its role in inflammatory processes, exhibited oncogenic activity associated with alteration of its molecular expression profile. TRPV2 was overexpressed in LBCs compared to normal human peripheral blood mononuclear cells (PBMCs). Additionally, functional full length isoform and nonfunctional short form pore-less variant of TRPV2 protein were up-regulated and down-regulated respectively in LBCs. However, the opposite was found in PBMCs. TRPV2 silencing or pharmacological targeting by Tranilast (TL) or SKF96365 (SKF) triggered caspace-mediated apoptosis and cell cycle arrest. TL and SKF inhibited chemotactic peptide fMLP-induced response linked to TRPV2 Ca2+ activity, and down-regulated expression of surface marker CD38 involved in leukemia and lung airway inflammation. Challenging lung airway epithelial cells (AECs) with LBCs decreased (by more than 50%) transepithelial resistance (TER) denoting barrier function alteration. Importantly, TL prevented such loss in TER. Therefore, TRPV2 merits further exploration as a pharmacodynamic biomarker for leukemia patients (with pulmonary inflammation) who might be suitable for a novel [adjuvant] therapeutic strategy based on TL.
Fast NMR method to probe solvent accessibility and disordered regions in proteins
Authors: Faustino André F. , Barbosa Glauce M. , Silva Micael , Castanho Miguel A. R. B. , Da Poian Andrea T. , Cabrita Eurico J. , Santos Nuno C. , Almeida Fabio C. L. , Martins Ivo C. 
Published: February 2019

AbstractUnderstanding protein structure and dynamics, which govern key cellular processes, is crucial for basic and applied research. Intrinsically disordered protein (IDP) regions display multifunctionality via alternative transient conformations, being key players in disease mechanisms. IDP regions are abundant, namely in small viruses, allowing a large number of functions out of a small proteome. The relation between protein function and structure is thus now seen from a different perspective: as IDP regions enable transient structural arrangements, each conformer can play different roles within the cell. However, as IDP regions are hard and time-consuming to study via classical techniques (optimized for globular proteins with unique conformations), new methods are required. Here, employing the dengue virus (DENV) capsid (C) protein and the immunoglobulin-binding domain of streptococcal protein G, we describe a straightforward NMR method to differentiate the solvent accessibility of single amino acid N-H groups in structured and IDP regions. We also gain insights into DENV C flexible fold region biological activity. The method, based on minimal pH changes, uses the well-established 1H-15N HSQC pulse sequence and is easily implementable in current protein NMR routines. The data generated are simple to interpret, with this rapid approach being an useful first-choice IDPs characterization method.
Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins
Authors: Mansfield Michael James , Wentz Travis Gwynn , Zhang Sicai , Lee Elliot Jeon , Dong Min , Sharma Shashi Kant , Doxey Andrew Charles 
Published: February 2019

AbstractClostridial neurotoxins (CNTs), which include botulinum neurotoxins (BoNTs) and tetanus neurotoxin (TeNT), are the most potent toxins known to science and are the causative agents of botulism and tetanus, respectively. The evolutionary origins of CNTs and their relationships to other proteins remains an intriguing question. Here we present a large-scale bioinformatic screen for putative toxin genes in all currently available genomes. We detect a total of 311 protein sequences displaying at least partial homology to BoNTs, including 161 predicted toxin sequences that have never been characterized. We focus on a novel toxin family from Chryseobacterium piperi with homology to BoNTs. We resequenced the genome of C. piperi to confirm and further analyze the genomic context of these toxins, and also examined their potential toxicity by expression of the protease domain of one C. piperi toxin in human cells. Our analysis suggests that these C. piperi sequences encode a novel family of metalloprotease toxins that are distantly related to BoNTs with similar domain architecture. These toxins target a yet unknown class of substrates, potentially reflecting divergence in substrate specificity between the metalloprotease domains of these toxins and the related metalloprotease domain of clostridial neurotoxins.
Exciton binding energy and hydrogenic Rydberg series in layered ReS2
Authors: Jadczak J. , Kutrowska-Girzycka J. , Smoleński T. , Kossacki P. , Huang Y. S. , Bryja L. 
Published: February 2019

AbstractUnlike monolayers of transition metal dichalcogenides such as MoS2,which possess high in-plane symmetry, layered ReS2exhibits reduced in-plane crystal symmetry with a distorted 1 T structure. This unique symmetry leads to anisotropic optical properties, very promising for light polarization devices. Here, we report on low temperature polarization-resolved emission and absorption measurements of excitons in ReS2from bulk to monolayer. In photoluminescence and reflectivity contrast spectra we distinguish two strongly polarized excitons X1and X2with dipole vectors along different crystal directions, which persist from bulk down to monolayer. Basing on the PL and RC spectra of bulk crystals we determine the energy of the ground and first four excited states of both excitons, which follow the usual hydrogenic Rydberg series of energy levels of 3D excitonic states (En = Ry*/n2). From the numerical fit we estimate that the energy gap is direct and equal to 1671.7 meV and binding energy of X1and X2is equal to 117.5 and 86.6 meV, respectively. In magneto-PL spectra of bulk ReS2up to B = 10 T, the energy shift of all the states is below 2 meV. On reducing the crystal thickness from bulk to monolayer the ground state experience a strong blue shift.
Gas chromatography-Mass Spectra analysis and deleterious potential of fungal based polythene-degradation products
Authors: Sangale Manisha K. , Shahnawaz Mohd. , Ade Avinash B. 
Published: February 2019

AbstractPolythene-degradation products (PE-DPs) produced due to two most efficient polythene degrading fungal isolates (Aspergillus terreus strain MANF1/WL and Aspergillus sydowii strain PNPF15/TS) after 60 days of incubation at ambient temperature with continuous shaking were analyzed by employing GC-MS method. Total 24 PE-DPs were recorded in total 4 samples i) control (pH 3.5), ii) Treatment of Aspergillus terreus strain MANF1/WL (pH 3.5), iii) control (pH 9.5) and iv) Treatment of Aspergillus sydowii strain PNP15/TS (pH 9.5). To check the deleterious status of PE-DPs using both the elite fungal isolates at in vitro level, two living systems (Sorghum and Tiger shark) were used. The percent germination rate of sorghum seeds were found unaffected with PE-DPs of both elite fungi. PE-DPs of both the fungal isolates exhibited maximum germination index at 50%. Whereas, highest elongation inhibition rate (34.75 ± 7.10) was reported with PE-DPs of Aspergillus terreus strain MANF1/WL. In case of animals system, no mortality of the Tiger sharks was documented after fifteen days of the treatment.
Disentangling locus of perceptual learning in the visual hierarchy of motion processing
Authors: Zhang Ruyuan , Tadin Duje 
Published: February 2019

AbstractVisual perceptual learning (VPL) can lead to long-lasting perceptual improvements. One of the central topics in VPL studies is the locus of plasticity in the visual processing hierarchy. Here, we tackled this question in the context of motion processing. We took advantage of an established transition from component-dependent representations at the earliest level to pattern-dependent representations at the middle-level of cortical motion processing. Two groups of participants were trained on the same motion direction identification task using either grating or plaid stimuli. A set of pre- and post-training tests was used to determine the degree of learning specificity and generalizability. This approach allowed us to disentangle contributions from different levels of processing stages to behavioral improvements. We observed a complete bi-directional transfer of learning between component and pattern stimuli that moved to the same directions, indicating learning-induced plasticity associated with intermediate levels of motion processing. Moreover, we found that motion VPL is specific to the trained stimulus direction, speed, size, and contrast, diminishing the possibility of non-sensory decision-level enhancements. Taken together, these results indicate that, at least for the type of stimuli and the task used here, motion VPL most likely alters visual computation associated with signals at the middle stage of motion processing.
The Flashed Face Distortion Effect Does Not Depend on Face-Specific Mechanisms
Authors: Balas Benjamin , Pearson Hannah 
Published: February 2019

AbstractWhen normal faces are rapidly presented in the visual periphery, they are perceived as grotesque and distorted. This phenomenon, “The flashed-face distortion effect” (FFDE) is a powerful illusion that may reveal important properties of how faces are coded in peripheral vision. Despite the strength of the illusion (and its popularity), there has been almost no follow-up work to examine what governs the strength of the illusion or to develop a clear account of its phenomenology. Presently, our goal was to address this by manipulating aspects of facial appearance and spatial/temporal properties of the flashed-face stimulus to determine what factors modulate the illusion’s strength. In three experiments, we investigated the extent to which local contrast (operationalized by the presence or absence of makeup), image eccentricity, image size, face inversion, and presentation rate of images within the sequence each contributed to the strength of the FFDE. We found that some of these factors (eccentricity and presentation rate) mattered a great deal, while others (makeup, face inversion and image size) made little contribution to the strength of the FFDE. We discuss the implications of these results for a mechanistic account of the FFDE, and suggest several avenues for future research based on this compelling visual illusion.
Serum concentrations of IGF-I/IGF-II as biomarkers of alcohol damage during foetal development and diagnostic markers of Foetal Alcohol Syndrome
Authors: Andreu-Fernández Vicente , Bastons-Compta Adriana , Navarro-Tapia Elisabet , Sailer Sebastian , Garcia-Algar Oscar 
Published: February 2019

AbstractFoetal Alcohol Syndrome (FAS) is the most deleterious health effect derived from alcohol consumption during pregnancy and is placed at the end of the Foetal Alcohol Spectrum Disorders (FASD). Few studies have proposed potential molecular biomarkers of physical and neurological damage associated with prenatal alcohol exposure. We prospectively recruited 55 children from 8 to 12 years old, with a prenatal assessment for ethanol exposure using meconium analysis of fatty acid ethyl esters (FAEE). The control group was established for FAEE < 2 nmol/g (n = 31) and a Prenatal Ethanol Exposure (PEE) group for FAEEs > 2 nmol/g (n = 33). Moreover, 98 children adopted from Eastern European Countries (EEC) were also recruited to evaluate FASD diagnosis comprising 31 cases with complete FAS, 42 with partial FAS, 6 with ARBD and 5 with ARND. Serum values of IGF-I and IGF-II for all children recruited were determined by immunoassay. Anthropometric and neurocognitive evaluation showed severe impairments in FAS children, moderate effects in PEE and no harmful effects in the control group with no prenatal exposure to alcohol. Analysis of IGF-I and IGF-II serum concentrations revealed that FASD from EEC as well as PEE children showed significantly lower concentrations of both IGF-I and IFG-II than the control group and reference values. Moreover, Spearman correlations showed a significant effect of IGF-I on anthropometric measurements in girls, whereas IGF-II affected the neuropsychological variables in both genders. These findings validate the use of growth factors IGF-I and IGF-II as surrogate biomarkers of damage induced by prenatal exposure to ethanol and could be used in the diagnosis of foetal alcohol spectrum disorders.
Activator of G-protein signaling 8 is involved in VEGF-induced choroidal neovascularization
Authors: Hayashi Hisaki , Mamun Abdullah Al , Takeyama Masayuki , Yamamura Aya , Zako Masahiro , Yagasaki Rina , Nakahara Tsutomu , Kamei Motohiro , Sato Motohiko 
Published: February 2019

AbstractChoroidal neovascularization (CNV) is associated with age-related macular degeneration (AMD), a major cause of vision loss among elderly people. Vascular endothelial cell growth factor (VEGF) is essential for the development and progression of AMD, and VEGF signaling molecules are effective targets for the treatment of AMD. We recently reported that activator of G-protein signaling 8 (AGS8), a receptor-independent Gβγ regulator, is involved in VEGF-induced angiogenesis in cultured endothelial cells (EC); however, the role of AGS8 in CNV is not yet understood. This study aimed to explore the role of AGS8 in CNV in cultured cells, explanted choroid tissue, and laser-induced CNV in a mouse AMD model. AGS8 knockdown in cultured choroidal EC inhibited VEGF-induced VEGFR-2 phosphorylation, cell proliferation, and migration. AGS8 knockdown also downregulated cell sprouting from mouse choroidal tissue in ex vivo culture. A mouse model of laser-induced CNV, created to analyze the roles of AGS8 in vivo, demonstrated that AGS8 mRNA was significantly upregulated in choroidal lesions and AGS8 was specifically expressed in the neovasculature. Local AGS8 knockdown in intravitreal tissue significantly inhibited laser-induced AGS8 upregulation and suppressed CNV, suggesting that AGS8 knockdown in the choroid has therapeutic potential for AMD. Together, these results demonstrate that AGS8 plays critical roles in VEGF-induced CNV.