bluuebunny/crossref_metadata_2025_split huggingface dataset:
EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs)
Authors: Liao Jian-You , Yang Bing , Zhang Yu-Chan , Wang Xiao-Juan , Ye Yushan , Peng Jing-Wen , Yang Zhi-Zhi , He Jie-Hua , Zhang Yin , Hu KaiShun , Lin De-Chen , Yin Dong 
Published: July 2019

ABSTRACTRNA binding proteins (RBPs) are a large protein family that plays important roles at almost all levels of gene regulation through interacting with RNAs, and contributes to numerous biological processes. However, the complete list of eukaryotic RBPs including human is still unavailable. In this study, we systematically identified RBPs in 162 eukaryotic species based on both computational analysis of RNA binding domains (RBDs) and large-scale RNA binding proteomic (RBPome) data, and established a comprehensive eukaryotic RBP database, EuRBPDB (http://EuRBPDB.syshospital.org:8081). We identified a total of 311,571 RBPs with RBDs and 3,639 non-canonical RBPs without known RBDs. EuRBPDB provides detailed annotations for each RBP, including basic information and functional annotation. Moreover, we systematically investigated RBPs in the context of cancer biology based on published literatures and large-scale omics data. To facilitate the exploration of the clinical relevance of RBPs, we additionally designed a cancer web interface to systematically and interactively display the biological features of RBPs in various types of cancers. EuRBPDB has a user-friendly web interface with browse and search functions, as well as data downloading function. We expect that EuRBPDB will be a widely-used resource and platform for the RNA biology community.
Temporal integration of narrative information in a hippocampal amnesic patient
Authors: Zuo Xiaoye , Honey Christopher J. , Barense Morgan D. , Crombie Davide , Norman Kenneth A. , Hasson Uri , Chen Janice 
Published: July 2019

AbstractDefault network regions appear to integrate information over time windows of 30 seconds or more during narrative listening. Does this long-timescale capability require the hippocampus? Amnesic behavior suggests that the hippocampus may not be needed for online processing when input is continuous and semantically rich: amnesics can participate in conversations and tell stories spanning minutes, and when tested immediately on recently heard prose their performance is relatively preserved. We hypothesized that default network regions can integrate the semantically coherent information of a narrative across long time windows, even in the absence of the hippocampus. To test this prediction, we measured BOLD activity in the brain of a hippocampal amnesic patient (D. A.) and healthy control participants while they listened to a seven-minute narrative. The narrative was played either in its intact form, or as a paragraph-scrambled version, which has been previously shown to interfere with the long-range temporal dependencies in default network activity. In the intact story condition, D. A.’s moment-by-moment BOLD activity spatial patterns were similar to those of controls in low-level auditory cortex as well as in some high-level default network regions (including lateral and medial posterior parietal cortex). Moreover, as in controls, D. A.’s response patterns in medial and lateral posterior parietal cortex were disrupted when paragraphs of the story were presented in a shuffled order, suggesting that activity in these areas did depend on information from 30 seconds or more in the past. Together, these results suggest that some default network cortical areas can integrate information across long timescales, even in the absence of the hippocampus.
Identification of porcine RUNX1 as an LPS-dependent gene expression regulator in PBMCs by Super deepSAGE sequencing of multiple tissues
Authors: Huang Tinghua , Yang Min , Dong Kaihui , Xu Mingjiang , Liu Jinhui , Chen Zhi , Zhu Shijia , Chen Wang , Yin Jun , Jin Kai , Deng Yu , Guan Zhou , Huang Xiali , Yang Jun , Han Rongxun , Yao Min 
Published: July 2019

AbstractGenome-wide identification of gene expression regulators may facilitate our understanding of the transcriptome constructed by gene expression profiling experiment. These regulators may be selected as targets for genetic manipulations in farm animals. In this study, we developed a gene expression profile of 76,000+ unique transcripts for 224 porcine samples from 28 normal tissues collected from 32 animals using Super deepSAGE (serial analysis of gene expression by deep sequencing) technology. Excellent sequencing depth has been achieved for each multiplexed library, and principal component analysis showed that duplicated samples from the same tissues cluster together, demonstrating the high quality of the Super deepSAGE data. Comparison with previous research indicated that our results not only have excellent reproducibility but also have greatly extended the coverage of the sample types as well as the number of genes. Clustering analysis discovered ten groups of genes showing distinct expression patterns among those samples. Binding motif over representative analysis identified 41 regulators responsible for the regulation of these gene clusters. Finally, we demonstrate a potential application of this dataset to infectious and immune research by identifying an LPS-dependent transcription factor, runt-related transcription factor 1 (RUNX1), in peripheral blood mononuclear cells (PBMCs). The selected genes are specifically responsible for the transcription of toll-like receptor 2 (TLR2), lymphocyte-specific protein tyrosine kinase (LCK), vav1 oncogene (VAV1), and other 32 genes. These genes belong to the T and B cell signaling pathways, making them potential novel targets for the diagnostic and therapy of bacterial infections and other immune disorders.
Development of vascular myogenic responses in zebrafish
Authors: Bahrami Nabila , Childs Sarah J. 
Published: July 2019

ABSTRACTThe vascular system is placed under enormous stress at the onset of cardiac contractility and blood flow. Nascent blood vessel tubes initially consist of a thin endothelial wall and rapidly acquire support from mural cells (pericytes and vascular smooth muscle cells; vSMCs). Following their association with vessels, mural cells acquire vasoactive ability (contraction and relaxation). However, we have little information as to when this vasoactivity first develops, and the extent to which each mural cell type contributes to vascular tone regulation during development. For the first time in an in vivo system, we highlight the dynamic changes in mural cell vasoactivity during development. We assess mural cell vasoactivity in the early zebrafish cerebral vasculature in response to pharmacological agents. We determine that pericyte-covered vessels constrict and dilate at 4 days post fertilization (dpf) but not at 6 dpf. The prostaglandin EP4 receptor contributes to pericyte-covered vessel dilation at 4 dpf. In contrast, vSMC-covered vessels constrict but do not dilate at 4 dpf. At 6 dpf, vSMC-covered vessels continue to constrict but only dilate from a pre-constricted state. Using genetic ablation, we demonstrate that mural cell contraction and relaxation is an active response by pericytes and vSMCs. Thus, we show that both pericytes and vSMCs have the ability to regulate cerebral vascular tone but at different stages of development. Pericytes are involved in regulating vessel diameters prior to the maturation of the vSMCs. Once vSMCs mature, pericytes are no longer active, and only vSMCs regulate vascular tone in the developing embryonic brain of zebrafish. The onset of vasoactivity of vSMCs corresponds to the development of increased neuronal activity and neurovascular coupling.
Overlapping attentional networks yield divergent behavioral predictions across tasks: Neuromarkers for diffuse and focused attention?
Authors: Wu Esther X.W. , Liaw Gwenisha J. , Goh Rui Zhe , Chia Tiffany T.Y. , Chee Alisia M.J. , Obana Takashi , Rosenberg Monica D. , Yeo B.T. Thomas , Asplund Christopher L. 
Published: July 2019

AbstractAttention is a critical cognitive function, allowing humans to select, enhance, and sustain focus on information of behavioral relevance. Attention contains dissociable neural and psychological components. Nevertheless, some brain networks support multiple attentional functions. Connectome-based Predictive Models (CPM), which associate individual differences in task performance with functional connectivity patterns, provide a compelling example. A sustained attention network model (saCPM) successfully predicted performance for selective attention, inhibitory control, and reading recall tasks. Here we constructed a visual attentional blink (VAB) model (vabCPM), comparing its performance predictions and network edges associated with successful and unsuccessful behavior to the saCPM’s. In the VAB, attention devoted to a target often causes a subsequent item to be missed. Although frequently attributed to attentional limitations, VAB deficits may attenuate when participants are distracted or deploy attention diffusely. Participants (n=73; 24 males) underwent fMRI while performing the VAB task and while resting. Outside the scanner, they completed other cognitive tasks over several days. A vabCPM constructed from these data successfully predicted VAB performance. Strikingly, the network edges that predicted better VAB performance (positive edges) predicted worse selective and sustained attention performance, and vice versa. Predictions from the saCPM mirrored these results, with the network’s negative edges predicting better VAB performance. Furthermore, the vabCPM’s positive edges significantly overlapped with the saCPM’s negative edges, and vice versa. We conclude that these partially overlapping networks each have general attentional functions. They may indicate an individual’s propensity to diffusely deploy attention, predicting better performance for some tasks and worse for others.Significance statementA longstanding question in psychology and neuroscience is whether we have general capacities or domain-specific ones. For such general capacities, what is the common function? Here we addressed these questions using the attentional blink (AB) task and neuroimaging. Individuals searched for two items in a stream of distracting items; the second item was often missed when it closely followed the first. How often the second item was missed varied across individuals, which was reflected in attention networks. Curiously, the networks’ pattern of function that was good for the AB was bad for other tasks, and vice versa. We propose that these networks may represent not a general attentional ability, but rather the tendency to attend in a less focused manner.
Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer
Authors: Dreyer Stephan B. , Upstill-Goddard Rosie , Paulus-Hock Viola , Paris Clara , Lampraki Eirini-Maria , Dray Eloise , Serrels Bryan , Caligiuri Giuseppina , Rebus Selma , Brunton Holly , Cunningham Richard , Nourse Craig , Bailey Ulla-Maja , Jones Marc , Moran-Jones Kim , Wright Derek W. , Duthie Fraser , Oien Karin , Evers Lisa , McKay Colin J. , McGregor Grant A. , Gulati Aditi , Brough Rachel , Bajrami Ilirjana , Pettitt Stephan , Dziubinski Michele L. , Candido Juliana , Balkwill Frances , Barry Simon T. , Grützmann Robert , Rahib Lola ,   Glasgow Precision Oncology Laboratory,   Australian Pancreatic Cancer Genome Initiative, Johns Amber , Pajic Marina , Froeling Fieke E. M. , Beer Phillip , Musgrove Elizabeth A. , Petersen Gloria M. , Ashworth Alan , Frame Margaret C. , Crawford Howard C. , Simeone Diane M. , Lord Chris , Mukhopadhyay Debabrata , Pilarsky Christian , Cooke Susanna L. , Jamieson Nigel B. , Morton Jennifer P. , Sansom Owen J. , Bailey Peter J. , Biankin Andrew V. , Chang David K. 
Published: July 2019

ABSTRACTContinuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. We interrogated the transcriptome, genome, proteome and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting the DNA damage response (DDR) and replication stress. We show that patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, co-segregates with response to platinum and PARP inhibitor therapy in vitro and in vivo. We generated a novel signature of replication stress with potential clinical utility in predicting response to ATR and WEE1 inhibitor treatment. Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR proficient PC, and post-platinum therapy.Abstract FigureSTATEMENT OF SIGNIFICANCEWe define therapeutic strategies that target subgroups of PC using novel signatures of DNA damage response deficiency and replication stress. This potentially offers patients with DNA repair defects therapeutic options outside standard of care platinum chemotherapy and is being tested in clinical trials on the Precision-Panc platform.
Association of maternal prenatal psychological stressors and distress with maternal and early infant faecal bacterial profile
Authors: Naudé Petrus J.W. , Claassen-Weitz Shantelle , Gardner-Lubbe Sugnet , Botha Gerrit , Kaba Mamadou , Zar Heather J. , Nicol Mark P. , Stein Dan J. 
Published: July 2019

AbstractBackgroundFindings from animal studies indicate that the early gut bacteriome is a potential mechanism linking maternal prenatal stress with health trajectories in offspring. However, clinical studies are scarce and the associations of maternal psychological profiles with the early infant faecal bacteriome is unknown. This study aimed to investigate the associations of prenatal stressors and distress with early infant faecal bacterial profiles in a South African birth cohort study.MethodsAssociations between prenatal symptoms of depression, distress, intimate partner violence (IPV) and posttraumatic stress-disorder (PTSD) and faecal bacterial profiles were evaluated in meconium and subsequent stool specimens from 84 mothers and 101 infants at birth, and longitudinally from a subset of 69 and 36 infants at 4–12 and 20–28 weeks of age, respectively in a South African birth cohort study.ResultsInfants born to mothers exposed to high levels of IPV had significantly higher proportions of unclassified genera within the family Enterobacteriaceae detected at birth; higher proportions of the genus Weissella at 4-12 weeks; and increased proportions of genera within the family Enterobacteriaceae over time (birth to 28 weeks of life). Faecal specimens from mothers exposed to IPV had higher proportions of the family Lactobacillaceae and lower proportions of Peptostreptococcaceae at birth. Maternal psychological distress was associated with decreased proportions of the family Veillonellaceae in infants at 20-28 weeks and a slower decline in Gammaproteobacteria over time. No changes in beta diversity were apparent for maternal or infant faecal bacterial profiles in relation to any of the prenatal measures for psychological adversities.ConclusionIPV during pregnancy is associated with altered bacterial profiles in infant and maternal faecal bacteria. These findings may provide insights in the involvement of the gut bacteria linking maternal psychological adversity and the maturing infant brain.
The intra-genus and inter-species quorum-sensing autoinducers exert distinct control overVibrio choleraebiofilm formation and dispersal
Authors: Bridges Andrew A. , Bassler Bonnie L. 
Published: July 2019

AbstractVibrio choleraepossesses multiple quorum-sensing systems that control virulence and biofilm formation among other traits. At low cell densities, when quorum-sensing autoinducers are absent,V. choleraeforms biofilms. At high cell densities, when autoinducers have accumulated, biofilm formation is repressed and dispersal occurs. Here, we focus on the roles of two well-characterized quorum-sensing autoinducers that function in parallel. One autoinducer, called CAI-1, is used to measurevibrioabundance, and the other autoinducer, called AI-2, is a broadly-made universal autoinducer that is presumed to enableV. choleraeto assess the total bacterial cell density of the vicinal community. The twoV. choleraeautoinducers funnel information into a shared signal relay pathway. This feature of the quorum-sensing system architecture has made it difficult to understand how specific information can be extracted from each autoinducer, how the autoinducers might drive distinct output behaviors, and in turn, how the bacteria use quorum sensing to distinguish self from other in bacterial communities. We develop a live-cell biofilm formation and dispersal assay that allows examination of the individual and combined roles of the two autoinducers in controllingV. choleraebehavior. We show that the quorum-sensing system works as a coincidence detector in which both autoinducers must be present simultaneously for repression of biofilm formation to occur. Within that context, the CAI-1 quorum-sensing pathway is activated when only a fewV. choleraecells are present, whereas the AI-2 pathway is activated only at much higher cell density. The consequence of this asymmetry is that exogenous sources of AI-2, but not CAI-1, contribute to satisfying the coincidence detector to repress biofilm formation and promote dispersal. We propose thatV. choleraeuses CAI-1 to verify that some of its kin are present before committing to the high-cell-density quorum-sensing mode, but it is, in fact, the universal autoinducer AI-2, that sets the pace of theV. choleraequorum-sensing program. This first report of unique roles for the differentV. choleraeautoinducers suggests that detection of self fosters a distinct outcome from detection of other.
Sub-atomic resolution crystal structures reveal conserved geometric outliers at functional sites
Authors: Laulumaa Saara , Kursula Petri 
Published: July 2019

AbstractP2 is a peripheral membrane protein of the vertebrate nervous system myelin sheath, having possible roles in both lipid transport and 3D molecular organization of the multilayered myelin membrane. We extended our earlier crystallographic studies on human P2 and refined its crystal structure at an ultrahigh resolution of 0.72 Å in perdeuterated form and 0.86 Å in hydrogenated form. Characteristic differences in C-H…O hydrogen bond patterns were observed between extended β strands, kinked or ending strands, and helices. Often, side-chain C-H groups engage in hydrogen bonding with backbone carbonyl moieties. The data highlight several amino acid residues with unconventional conformations, including both bent aromatic rings and twisted guanidinium groups on arginine side chains, as well as non-planar peptide bonds. In two locations, such non-ideal conformations cluster, providing proof of local functional strain. Other ultrahigh-resolution protein structures similarly contain chemical groups breaking planarity rules. For example, in SH3 domains, a conserved bent aromatic residue is observed near the ligand binding site. FABP3, belonging to the same family as P2, has several side chains and peptide bonds bent exactly as those in P2. We provide a high-resolution snapshot on non-ideal conformations of amino acid residues under local strain, possibly relevant to biological function. Geometric outliers observed in ultrahigh-resolution protein structures are real and likely relevant for ligand binding and conformational changes. Furthermore, deuteration of protein and/or solvent are promising variables in protein crystal optimization.
Biased belief updating and suboptimal choice in foraging decisions
Authors: Garrett Neil , Daw Nathaniel D. 
Published: July 2019

AbstractIn many choice scenarios, including prey, employment, and mate search, options are not encountered simultaneously and so cannot be directly compared. Deciding which ones optimally to engage, and which to forego, requires developing accurate beliefs about the overall distribution of prospects. However, the role of learning in this process – and how biases due to learning may affect choice – are poorly understood. In three experiments, we adapted a classic prey selection task from foraging theory to examine how individuals kept track of an environment’s reward rate and adjusted their choices in response to its fluctuations. In accord with qualitative predictions from optimal foraging models, participants adjusted their selectivity to the richness of the environment: becoming less selective in poorer environments and increasing acceptance of less profitable options. These preference shifts were observed not just in response to global (between block) manipulations of the offer distributions, but also to local, trial-by-trial offer variation within a block, suggesting an incremental learning rule. Further offering evidence into the learning process, these preference changes were more pronounced when the environment improved compared to when it deteriorated. All these observations were best explained by a trial-by-trial learning model in which participants estimate the overall reward rate, but with upward vs. downward changes controlled by separate learning rates. A failure to adjust expectations sufficiently when an environment becomes worse leads to suboptimal choices: options that are valuable given the environmental conditions are rejected in the false expectation that better options will materialize. These findings offer a previously unappreciated parallel in the serial choice setting of observations of asymmetric updating and resulting biased (often overoptimistic) estimates in other domains.
Open conflict as differentiation strategy in geographical indications: the Bitto Rebels case
Authors: Rinallo Diego , Pitardi Valentina 
Published: July 2019

PurposeThe purpose of this paper is to investigate how open, mediatised conflict in geographical indications (GIs) can provide the basis for differentiation strategies for heritage producers based on both functional and symbolic benefits.Design/methodology/approachLongitudinal case study based on multiple data sources, which reconstructs the history of the Bitto GIs and the conflict between the Protected Designation of Origin Bitto Consortium and a small number of heritage Bitto producers.FindingsThe paper highlights how the mediatised narration of conflict can contribute to raise consumer awareness, differentiate products and result in symbolic value creation.Research limitations/implicationsExtreme case study design purposively chosen as characterised by conditions likely to accentuate conflict.Practical implicationsThe paper develops a conceptual framework that permits to identify the potential for conflict inside GIs. It also contributes to a better understanding of the image of products protected by GIs and the role played by heritage producers. It also offers practical advice on two promotional tools, namely, trade fair participations and experiential showcases.Social implicationsThe paper offers practical advice on the safeguarding of small producers localised in cultural epicentres inside GIs.Originality/valueThe authors introduce the notions, such as competitive wars and secession, that contribute to a better understanding of centripetal/centrifugal forces inside GIs. The authors also propose a better understanding of image creation of GIs, grounded in cultural work in marketing and consumer research.