bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Simple, Robust and Efficient Computational Method for n-Octanol/Water Partition Coefficients of Substituted Aromatic Drugs
Authors: Bahmani Asrin , Saaidpour Saadi , Rostami Amin 
Published: July 2017

AbstractIn this paper, multiple linear regression (MLR) was used to build quantitative structure property relationship (QSPR) of n-octanol-water partition coefficient (logPo/w) of 195 substituted aromatic drugs. The molecular descriptors were calculated for each compound by the VLifeMDS. By applying genetic algorithm/multiple linear regressions (GA/MLR) the most relevant descriptors were selected to build a QSPR model. The robustness of the model was characterized by the statistical validation and applicability domain (AD). The prediction results from MLR are in good agreement with the experimental values. The R2and Q2LOOfor MLR are 0.9433, 0.9341. The AD of the model was analyzed based on the Williams plot. The effects of different selected descriptors are described.
Gilgamesh is required for the maintenance of germline stem cells in Drosophila testis
Authors: Chen Dongsheng , Zhu Xiangxiang , Zhou Lijuan , Wang Jian , Tao Xiaoqian , Wang Shuang , Sun Fuling , Kan Xianzhao , Han Zhengqi , Gu Yuelin 
Published: July 2017

AbstractEmerging evidence supports that stem cells are regulated by both intrinsic and extrinsic mechanisms. However, factors that determine the fate of stem cells remain incompletely understood. The Drosophila testis provides an exclusive powerful model in searching for potential important regulatory factors and their underlying mechanisms for controlling the fate of germline stem cells (GSCs). In this study, we have found that Drosophila gilgamesh (gish), which encodes a homologue of human CK1-γ (casein kinase 1-gamma), is required intrinsically for GSC maintenance. Our genetic analyses indicate gish is not required for Dpp/Gbb signaling silencing of bam and is dispensable for Dpp/Gbb signaling-dependent Dad expression. Finally, we show that overexpression of gish fail to dramatically increase the number of GSCs. These findings demonstrate that gish controls the fate of GSCs in Drosophila testis by a novel Dpp/Gbb signaling-independent pathway.
Surges in trematode prevalence linked to centennial-scale flooding events in the Adriatic
Authors: Scarponi Daniele , Azzarone Michele , Kowalewski Michał , Huntley John Warren 
Published: July 2017

AbstractThe forecasts of increasing global temperature and sea level rise have led to concern about the response of parasites to anthropogenic climate change. Whereas ecological studies of parasite response to environmental shifts are necessarily limited to short time scales, the fossil record can potentially provide a quantitative archive of long-term ecological responses to past climate transitions. Here, we document multi-centennial scale changes in prevalence of trematodes infesting the bivalve host Abra segmentum through multiple sea-level fluctuations preserved in brackish Holocene deposits of the Po Plain, Italy. Prevalence values were significantly elevated (p < 0.01) in samples associated with flooding surfaces, yet the temporal trends of parasite prevalence and host shell length, cannot be explained by Waltherian facies change, host availability, salinity, diversity, turnover, or community structure. The observed surges in parasite prevalence during past flooding events indicate that the ongoing global warming and sea-level rise will lead to significant intensification of trematode parasitism, suppressed fecundity of common benthic organisms, and negative impacts on marine ecosystems, ecosystem services, and, eventually, to human well-being.
Recent Warming and Cooling in the Antarctic Peninsula Region has Rapid and Large Effects on Lichen Vegetation
Authors: Sancho Leopoldo G. , Pintado Ana , Navarro Francisco , Ramos Miguel , De Pablo Miguel Angel , Blanquer Jose Manuel , Raggio Jose , Valladares Fernando , Green Thomas George Allan 
Published: July 2017

AbstractThe Antarctic Peninsula has had a globally large increase in mean annual temperature from the 1951 to 1998 followed by a decline that still continues. The challenge is now to unveil whether these recent, complex and somewhat unexpected climatic changes are biologically relevant. We were able to do this by determining the growth of six lichen species on recently deglaciated surfaces over the last 24 years. Between 1991 and 2002, when mean summer temperature (MST) rose by 0.42 °C, five of the six species responded with increased growth. MST declined by 0.58 °C between 2002 and 2015 with most species showing a fall in growth rate and two of which showed a collapse with the loss of large individuals due to a combination of increased snow fall and longer snow cover duration. Increased precipitation can, counter-intuitively, have major negative effects when it falls as snow at cooler temperatures. The recent Antarctic cooling is having easily detectable and deleterious impacts on slow growing and highly stress-tolerant crustose lichens, which are comparable in extent and dynamics, and reverses the gains observed over the previous decades of exceptional warming.
Evolutionarily conserved BIL4 suppresses the degradation of brassinosteroid receptor BRI1 and regulates cell elongation
Authors: Yamagami Ayumi , Saito Chieko , Nakazawa Miki , Fujioka Shozo , Uemura Tomohiro , Matsui Minami , Sakuta Masaaki , Shinozaki Kazuo , Osada Hiroyuki , Nakano Akihiko , Asami Tadao , Nakano Takeshi 
Published: July 2017

AbstractBrassinosteroids (BRs), plant steroid hormones, play important roles in plant cell elongation and differentiation. To investigate the mechanisms of BR signaling, we previously used the BR biosynthesis inhibitor Brz as a chemical biology tool and identified the Brz-insensitive-long hypocotyl4 mutant (bil4). Although the BIL4 gene encodes a seven-transmembrane-domain protein that is evolutionarily conserved in plants and animals, the molecular function of BIL4 in BR signaling has not been elucidated. Here, we demonstrate that BIL4 is expressed in early elongating cells and regulates cell elongation in Arabidopsis. BIL4 also activates BR signaling and interacts with the BR receptor brassinosteroid insensitive 1 (BRI1) in endosomes. BIL4 deficiency increases the localization of BRI1 in the vacuoles. Our results demonstrate that BIL4 regulates cell elongation and BR signaling via the regulation of BRI1 localization.
Altered hippocampal volume and functional connectivity in males with Internet gaming disorder comparing to those with alcohol use disorder
Authors: Yoon Eun Jin , Choi Jung-Seok , Kim Heejung , Sohn Bo Kyung , Jung Hee Yeon , Lee Jun-Young , Kim Dai-Jin , Park Sun-Won , Kim Yu Kyeong 
Published: July 2017

AbstractInternet gaming disorder (IGD) has been conceptualized as a behavioral addiction and shares clinical, neuropsychological, and personality characteristics with alcohol use disorder (AUD), but IGD dose not entail brain exposure to toxic agents, which renders it different from AUD. To achieve a clear understanding of the neurobiological features of IGD, we aimed to identify morphological and functional changes in IGD and compare them with those in AUD. Individuals with IGD showed larger volume in the hippocampus/amygdala and precuneus than healthy controls (HCs). The volume in the hippocampus positively correlated with the symptom severity of IGD. Moreover, functional connectivity analysis with the hippocampus/amygdala cluster revealed that the left ventromedial prefrontal cortex showed stronger functional connectivity in individuals with IGD compared to those with AUD. In contrast, individuals with AUD exhibited the smaller cerebellar volume and thinner medial frontal cortex than HCs. The volume in the cerebellum correlated with impaired working memory function as well as duration of illness in AUD group. Findings suggested that altered volume and functional connectivity in the hippocampus/amygdala in IGD might be associated with abnormally enhanced memory process of gaming-related cues, while abnormal cortical changes and cognitive impairments in AUD might be associated with neurotoxic effects of alcohol.
Physiological stress-induced corticosterone increases heme uptake via KLF4-HCP1 signaling pathway in hippocampus neurons
Authors: Li Hongxia , Zhang Caixia , Shen Hui , Shen Zhilei , Wu Lusha , Mo Fengfeng , Li Min 
Published: July 2017

AbstractIron overload has attracted much attention because of its adverse effect in increasing the risk of developing several neurodegenerative disorders. Under various pathologic conditions, a lot of heme are released. The aggregation of heme is more neurotoxic than that of iron released from the heme breakdown. Our previous studies demonstrated that psychological stress (PS) is a risk factor of cerebral iron metabolism disorders, thus causing iron accumulation in rat brains. In the present study, we found PS could increase heme uptake via heme carrier protein 1 (HCP1) in rat brains. We demonstrated that Glucocorticoid (GC), which is largely secreted under stress, could up-regulate HCP1 expression, thus promoting heme uptake in neurons. We also ascertained that HCP1 expression can be induced by GC through a transcription factor, Krüppel-like factor 4 (KLF4). These results may gain new insights into the etiology of heme uptake and iron accumulation in PS rats, and find new therapeutic targets of iron accumulation in Parkinson’s disease or Alzheimer’s disease.
Minimum Winfree loop determines self-sustained oscillations in excitable Erdös-Rényi random networks
Authors: Qian Yu , Cui Xiaohua , Zheng Zhigang 
Published: July 2017

AbstractThe investigation of self-sustained oscillations in excitable complex networks is very important in understanding various activities in brain systems, among which the exploration of the key determinants of oscillations is a challenging task. In this paper, by investigating the influence of system parameters on self-sustained oscillations in excitable Erdös-Rényi random networks (EERRNs), the minimum Winfree loop (MWL) is revealed to be the key factor in determining the emergence of collective oscillations. Specifically, the one-to-one correspondence between the optimal connection probability (OCP) and the MWL length is exposed. Moreover, many important quantities such as the lower critical connection probability (LCCP), the OCP, and the upper critical connection probability (UCCP) are determined by the MWL. Most importantly, they can be approximately predicted by the network structure analysis, which have been verified in numerical simulations. Our results will be of great importance to help us in understanding the key factors in determining persistent activities in biological systems.
Integrative analyses of translatome and transcriptome reveal important translational controls in brown and white adipose regulated by microRNAs
Authors: Reid David W. , Xu Dan , Chen Peng , Yang Hongyuan , Sun Lei 
Published: July 2017

AbstractThe epidemic of obesity and diabetes has markedly spurred the research interest in adipocyte biology. Brown adipocytes are specialized for energy expenditure and of therapeutic interest for treatment of metabolic diseases, but how brown adipocytes are distinguished from white adipocytes at the level of translational regulation remains poorly understood. To systemically determine the translational control of gene expression in adipose tissue, we performed ribosome profiling and RNA-seq in parallel to depict the translatome and transcriptome changes during primary brown and white adipogenesis, and between brown and white adipose tissue. The most prominent layer of translational regulation was the increased translation efficiency of genes encoding mitochondria components in brown adipocytes relative to white. Systemic analysis of the regulatory interactions between microRNAs and their targets revealed that microRNAs were more active in repressing targets’ mRNA abundance and translation in brown fat. Together, our data comprehensively delineated a landscape integrating transcriptome and translatome in adipose tissue.
Neural oscillations associated with auditory duration maintenance in working memory
Authors: Yu Xiaolin , Chen Youguo , Qiu Junjie , Li Xiang , Huang Xiting 
Published: July 2017

AbstractThe neural representation of auditory duration remains unknown. Here, we used electroencephalogram (EEG) recordings to investigate neural oscillations during the maintenance of auditory duration in working memory (WM). EEG analyses indicated that the auditory duration length was not associated with changes in the theta band amplitude, whereas the alpha band amplitudes during 3-s and 4-s auditory duration conditions were lower than during the 1-s and 2-s conditions. Moreover, the alpha band amplitude and accuracy were positively correlated in the 2-s duration condition. We also found that the neural representation of auditory duration is segmented, with a critical threshold point of approximately 2 s, which is shorter than that for visual duration (3 s). The results emphasised the involvement of the alpha band in auditory duration maintenance in WM. Our study’s findings indicate that different internal representations of auditory durations are maintained in WM below and above 2 s from the perspective of electrophysiology. Additionally, the critical threshold point is related to the sensory modality of duration.
Localization of damage in the human leg muscles induced by downhill running
Authors: Maeo Sumiaki , Ando Yukino , Kanehisa Hiroaki , Kawakami Yasuo 
Published: July 2017

AbstractWe investigated localization of damage within the knee extensors (KEs) and plantar flexors (PFs) induced by downhill running (DR) by using transverse relaxation time (T2)-weighted magnetic resonance imaging (MRI). Fourteen young adults performed 45-min DR (−15% slope) at their maximal tolerable velocity. At pre- and 24, 48, and 72 h post-exercise, T2-MRI was scanned and T2values for each muscle composing KEs and PFs at proximal, middle, and distal sites were calculated. Maximal isometric torque and rate of torque development (RTD: 0–30, 0–50, 0–100, 0–200 ms) were also measured. Maximal torque significantly decreased in KEs (14–17%) and PFs (6–8%) at 24–48 h post-exercise, with greater reductions for KEs. RTD in all phases, except for 0–200 ms in PFs, significantly decreased in KEs (11–42%) and PFs (13–23%) at least at one time point post-exercise. T2significantly increased at several sites (3–5%) in both muscle groups at 24 and/or 48 h post-exercise. Among the T2-increased sites, the peak effect size (Cohen’sd) regarding T2change was pronounced at proximal (1.05) and middle (1.64) vastus intermedius compared to the other sites (0.72–0.77). These results suggest that DR induces damage in both KEs and PFs, and especially affects proximal–middle sites of the vastus intermedius.
Depleted tumor suppressor miR-107 in plasma relates to tumor progression and is a novel therapeutic target in pancreatic cancer
Authors: Imamura Taisuke , Komatsu Shuhei , Ichikawa Daisuke , Miyamae Mahito , Okajima Wataru , Ohashi Takuma , Kiuchi Jun , Nishibeppu Keiji , Konishi Hirotaka , Shiozaki Atsushi , Morimura Ryo , Ikoma Hisashi , Ochiai Toshiya , Okamoto Kazuma , Taniguchi Hiroki , Otsuji Eigo 
Published: July 2017

AbstractThis study explored decreased tumor suppressor microRNA (miRNA) plasma levels in pancreatic cancer (PCa) patients to clarify their potential as novel biomarkers and therapeutic targets. We used the microRNA array-based approach to select candidates by comparing plasma levels between PCa patients and healthy volunteers. Six down-regulated miRNAs (miR-107, miR-126, miR-451, miR-145, miR-491-5p, and miR-146b-5p) were selected. Small- and large-scale analyses using samples from 100 PCa patients and 80 healthy volunteers revealed that miR-107 was the most down-regulated miRNA in PCa patients compared with healthy volunteers (P < 0.0001; area under the receiver-operating characteristic curve, 0.851). A low miR-107 plasma level was significantly associated with advanced T stage, N stage, and liver metastasis and was an independent factor predicting poor prognosis in PCa patients (P = 0.0424; hazard ratio, 2.95). miR-107 overexpression in PCa cells induced G1/S arrest with the production of p21 and inhibited cell proliferation through the transcriptional regulation of Notch2. In vivo, the restoration and maintenance of the miR-107 plasma level significantly inhibited tumor progression in mice. Depletion of the tumor suppressor miR-107 in plasma relates to tumor progression and poor outcomes. The restoration of the plasma miR-107 level might be a novel anticancer treatment strategy for PCa.
Comparative genomic analysis of Paenibacillus sp. SSG-1 and its closely related strains reveals the effect of glycometabolism on environmental adaptation
Authors: Xu Hui , Qin Shishang , Lan Yanhong , Liu Mengjia , Cao Xiyue , Qiao Dairong , Cao Yu , Cao Yi 
Published: July 2017

AbstractThe extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus. Furthermore, a large number of genes gained are associated with carbohydrate transport and metabolism. It indicates that the evolution of glycometabolism is a key factor for the environmental adaptability of Paenibacillus species. Interestingly, through horizontal gene transfer, Paenibacillus sp. SSG-1 acquired an approximately 150 kb DNA fragment and shows an agar-degrading characteristic distinct from most other non-marine bacteria. This region may be transported in bacteria as a complete unit responsible for agar degradation. Taken together, these results provide insights into the evolutionary pattern of Paenibacillus and have implications for studies on the taxonomy and functional genomics of this genus.
Nanoscale Control of Amyloid Self-Assembly Using Protein Phase Transfer by Host-Guest Chemistry
Authors: Choi Tae Su , Lee Hong Hee , Ko Young Ho , Jeong Kwang Seob , Kim Kimoon , Kim Hugh I. 
Published: July 2017

AbstractAmyloid fibrils have recently been highlighted for their diverse applications as functional nanomaterials in modern chemistry. However, tight control to obtain a targeted fibril length with low heterogeneity has not been achieved because of the complicated nature of amyloid fibrillation. Herein, we demonstrate that fibril assemblies can be homogeneously manipulated with desired lengths from ~40 nm to ~10 μm by a phase transfer of amyloid proteins based on host-guest chemistry. We suggest that host-guest interactions with cucurbit[6]uril induce a phase transfer of amyloid proteins (human insulin, human islet amyloid polypeptide, hen egg lysozyme, and amyloid-β 1–40 & 1–42) from the soluble state to insoluble state when the amount of cucurbit[6]uril exceeds its solubility limit in solution. The phase transfer of the proteins kinetically delays the nucleation of amyloid proteins, while the nuclei formed in the early stage are homogeneously assembled to fibrils. Consequently, supramolecular assemblies of amyloid proteins with heterogeneous kinetics can be controlled by protein phase transfer based on host-guest interactions.
Monocyte adhesion to atherosclerotic matrix proteins is enhanced by Asn-Gly-Arg deamidation
Authors: Dutta Bamaprasad , Park Jung Eun , Kumar Subodh , Hao Piliang , Gallart-Palau Xavier , Serra Aida , Ren Yan , Sorokin Vitaly , Lee Chuen Neng , Ho Hee Hwa , de Kleijn Dominique , Sze Siu Kwan 
Published: July 2017

AbstractAtherosclerosis arises from leukocyte infiltration and thickening of the artery walls and constitutes a major component of vascular disease pathology, but the molecular events underpinning this process are not fully understood. Proteins containing an Asn-Gly-Arg (NGR) motif readily undergo deamidation of asparagine to generate isoDGR structures that bind to integrin αvβ3 on circulating leukocytes. Here we report the identification of isoDGR motifs in human atherosclerotic plaque components including extracellular matrix (ECM) proteins fibronectin and tenascin C, which have been strongly implicated in human atherosclerosis. We further demonstrate that deamidation of NGR motifs in fibronectin and tenascin C leads to increased adhesion of the monocytic cell line U937 and enhanced binding of primary human monocytes, except in the presence of a αvβ3-blocking antibody or the αv-selective inhibitor cilengitide. In contrast, under the same deamidating conditions monocyte-macrophages displayed only weak binding to the alternative ECM component vitronectin which lacks NGR motifs. Together, these findings confirm a critical role for isoDGR motifs in mediating leukocyte adhesion to the ECM via integrin αvβ3 and suggest that protein deamidation may promote the pathological progression of human atherosclerosis by enhancing monocyte recruitment to developing plaques.
Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites
Authors: Wang Yanan , Song Jiangning , Marquez-Lago Tatiana T. , Leier André , Li Chen , Lithgow Trevor , Webb Geoffrey I. , Shen Hong-Bin 
Published: July 2017

AbstractMatrix Metalloproteases (MMPs) are an important family of proteases that play crucial roles in key cellular and disease processes. Therefore, MMPs constitute important targets for drug design, development and delivery. Advanced proteomic technologies have identified type-specific target substrates; however, the complete repertoire of MMP substrates remains uncharacterized. Indeed, computational prediction of substrate-cleavage sites associated with MMPs is a challenging problem. This holds especially true when considering MMPs with few experimentally verified cleavage sites, such as for MMP-2, -3, -7, and -8. To fill this gap, we propose a new knowledge-transfer computational framework which effectively utilizes the hidden shared knowledge from some MMP types to enhance predictions of other, distinct target substrate-cleavage sites. Our computational framework uses support vector machines combined with transfer machine learning and feature selection. To demonstrate the value of the model, we extracted a variety of substrate sequence-derived features and compared the performance of our method using both 5-fold cross-validation and independent tests. The results show that our transfer-learning-based method provides a robust performance, which is at least comparable to traditional feature-selection methods for prediction of MMP-2, -3, -7, -8, -9 and -12 substrate-cleavage sites on independent tests. The results also demonstrate that our proposed computational framework provides a useful alternative for the characterization of sequence-level determinants of MMP-substrate specificity.