bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rehumanizing the homeless: Altered BOLD response following contact with an extreme outgroup
Authors: Kirk P. A. , Cohen A. O. , Sinnott-Armstrong W. , Harris L.T. 
Published: November 2018

AbstractDehumanized perception strips people of their humanity by ignoring their mental states. Evidence has accumulated to suggest many individuals do not spontaneously attribute mental states towards certain social groups, such as the homeless, and drug-addicted (Fiske et al., 2002, Harris & Fiske, 2006; 2007; 2011). These groups tend to elicit differential BOLD signal within areas associated with social cognition. To investigate the versatility of this response, two experiments were conducted: a mixed design study (20 participants); and a repeated-measures design (11 participants). These investigated the malleability of social cognition following a contact intervention with the homeless. Both experiments had participants make emotional judgements toward eight different social groups whilst under fMRI. The two studies found mixed evidence, demonstrating altered response to homeless people in regions such as the mPFC, Insula, IPL, and MTG following social contact. This lends some support to the use of contact as an effective intervention.
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
Authors: Kang Kyo Bin , Ernst Madeleine , van der Hooft Justin J. J. , da Silva Ricardo R. , Park Junha , Medema Marnix H. , Sung Sang Hyun , Dorrestein Pieter C. 
Published: November 2018

SUMMARYPlants produce a myriad of specialized metabolites to overcome their sessile habit and combat biotic as well as abiotic stresses. Evolution has shaped specialized metabolite diversity, which drives many other aspects of plant biodiversity. However, until recently, large-scale studies investigating specialized metabolite diversity in an evolutionary context have been limited by the impossibility to identify chemical structures of hundreds to thousands of compounds in a time-feasible manner. Here, we introduce a workflow for large-scale, semi-automated annotation of specialized metabolites, and apply it for over 1000 metabolites of the cosmopolitan plant family Rhamnaceae. We enhance the putative annotation coverage dramatically, from 2.5 % based on spectral library matches alone to 42.6 % of total MS/MS molecular features extending annotations from well-known plant compound classes into the dark plant metabolomics matter. To gain insights in substructural diversity within the plant family, we also extract patterns of co-occurring fragments and neutral losses, so-called Mass2Motifs, from the dataset; for example, only the Ziziphoid clade developed the triterpenoid biosynthetic pathway, whereas the Rhamnoid clade predominantly developed diversity in flavonoid glycosides, including 7-O-methyltransferase activity. Our workflow provides the foundations towards the automated, high-throughput chemical identification of massive metabolite spaces, and we expect it to revolutionize our understanding of plant chemoevolutionary mechanisms.
The functional brain favours segregated modular connectivity at old age unless targeted by neurodegeneration
Authors: Peraza Luis R , O’Brien John T , Blamire Andrew , Kaiser Marcus , Taylor John-Paul 
Published: November 2018

AbstractBrain’s modular connectivity gives this organ resilience and adaptability. The ageing process alters the human brain, leading to modifications to its organised modularity and these changes are further accentuated by neurodegeneration, leading to disorganisation. To understand this further, we analysed modular variability—heterogeneity of modules—and modular dissociation—detachment from segregated connectivity—in two ageing cohorts and a mixed cohort of neurodegenerative diseases. Our results revealed that the brain follows a universal pattern of modular variability that matches highly active and metacognitive brain regions: the association cortices. We also proved that in ageing the brain moves towards a modular segregated structure despite presenting with increased modular heterogeneity—modules in older adults are not only segregated but their shape and size are more variable than in young adults. In the presence of neurodegeneration, the brain maintains its segregated connectivity globally but not locally; the modular brain shows patterns of differentiated pathology.
Inhibition of the 60S ribosome biogenesis GTPase LSG1 causes endoplasmic reticular disruption and cellular senescence
Authors: Pantazi Asimina , Quintanilla Andrea , Hari Priya , Tarrats Nuria , Parasyraki Eleftheria , Dix Flora Lucy , Patel Jaiyogesh , Chandra Tamir , Acosta Juan Carlos , Finch Andrew John 
Published: November 2018

AbstractCellular senescence is triggered by diverse stimuli and is characterised by long-term growth arrest and secretion of cytokines and chemokines (termed the SASP - senescence-associated secretory phenotype). Senescence can be organismally beneficial as it can prevent the propagation of damaged or mutated clones and stimulate their clearance by immune cells. However, it has recently become clear that senescence also contributes to the pathophysiology of aging through the accumulation of damaged cells within tissues. Here we describe that inhibition of the reaction catalysed by LSG1, a GTPase involved in the biogenesis of the 60S ribosomal subunit, leads to a robust induction of cellular senescence. Perhaps surprisingly, this was not due to ribosome depletion or translational insufficiency, but rather through perturbation of endoplasmic reticulum (ER) homeostasis and a dramatic upregulation of the cholesterol biosynthesis pathway. This cholesterol/ER signature is shared with several other forms of senescence and contributes to the cell cycle arrest in oncogene-induced senescence (OIS). Furthermore, targetting of LSG1 resulted in amplification of the cholesterol/ER signature and restoration of a robust cellular senescence response in transformed cells, suggesting potential therapeutic uses of LSG1 inhibition.
Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates
Authors: Galata Valentina , Laczny Cédric C. , Backes Christina , Hemmrich-Stanisak Georg , Schmolke Susanne , Franke Andre , Meese Eckart , Herrmann Mathias , Müller Lutz von , Plum Achim , Müller Rolf , Stähler Cord , Posch Andreas E. , Keller Andreas 
Published: November 2018

AbstractEmerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly sequenced whole genomes) and culture-based resistance profiles (10,991 of 11,087 isolates were comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns could be observed including increasing resistance rates forAcinetobacter baumanniito carbapenems and forEscherichia colito fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species such as conserved essential genes and known resistance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene-drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into a resource, GEAR-base, available for academic research use free of charge athttps://gear-base.com.
Persistence of Fusarium oxysporum f. sp. fragariae in soil through asymptomatic colonization of rotation crops
Authors: Henry Peter M. , Pastrana Ana M. , Leveau Johan H.J. , Gordon Thomas R. 
Published: November 2018

ABSTRACTAsymptomatic plant colonization is hypothesized to enhance persistence of pathogenic forms of Fusarium oxysporum in the absence of a susceptible host. However, a correlation between pathogen populations on living plant tissues and soilborne populations after tillage has not been demonstrated. Living and dead tissues of broccoli, lettuce, spinach, wheat, cilantro, raspberry, and strawberry plants inoculated with Fusarium oxysporum f. sp. fragariae (the cause of Fusarium wilt of strawberry) were assayed to quantify the incidence of infection and extent of colonization by this pathogen. All crops could be infected by F. oxysporum f. sp. fragariae, but the extent of colonization varied between plant species. Pathogen population densities on non-living crown tissues incorporated into the soil matrix were typically greater than those observed on living tissues. Crop-dependent differences in the inoculum density of F. oxysporum f. sp. fragariae in soil were only observed after decomposition of crop residue. Forty-four weeks after plants were incorporated into the soil, F. oxysporum f. sp. fragariae soil population densities were positively correlated with population densities on plant tissue fragments recovered at the same timepoint. Results indicate that asymptomatic colonization can have a significant, long-term impact on soilborne populations of Fusarium wilt pathogens. Cultural practices, such as crop rotation, should be leveraged to favor pathogen population decline by planting hosts that do not support extensive population growth on living or decomposing tissues.
ReQTL – an allele-level measure of variation-expression genomic relationships
Authors: Spurr Liam , Alomran Nawaf , Słowiński Piotr , Li Muzi , Bousounis Pavlos , Zhang Qianqian , Sein Justin , Crandall Keith A. , Tsaneva-Atanasova Krasimira , Horvath Anelia 
Published: November 2018

MotivationBy testing for association of DNA genotypes with gene expression levels, expression quantitative trait locus (eQTL) analyses have been instrumental in understanding how thousands of single nucleotide variants (SNVs) may affect gene expression. As compared to DNA genotypes, RNA genetic variation represents a phenotypic trait that reflects the actual allele content of the studied system. RNA genetic variation can be measured at expressed genome regions, and differs from the DNA genotype in sites subjected to regulatory forces. Therefore, assessment of correlation between RNA genetic variation and gene expression can reveal regulatory genomic relationships in addition to eQTLs.ResultsWe introduce ReQTL, an eQTL modification which substitutes the DNA allele count for the variant allele frequency (VAF) at expressed SNV loci in the transcriptome. We exemplify the method on sets of RNA-sequencing data from human tissues obtained though the Genotype-Tissue Expression Project (GTEx) and demonstrate that ReQTL analyses show consistently high performance and sufficient power to identify both previously known and novel molecular associations. The majority of the SNVs implicated in significant cis-ReQTLs identified by our analysis were previously reported as significant cis-eQTL loci. Notably, trans ReQTL loci in our data were substantially enriched in RNA-editing sites. In summary, ReQTL analyses are computationally feasible and do not require matched DNA data, hence they have a high potential to facilitate the discovery of novel molecular interactions through exploration of the increasingly accessible RNA-sequencing datasets.Availability and implementationSample scripts used in our ReQTL analyses are available with the Supplementary Material (ReQTL_sample_code).Contacthorvatha@gwu.edu or lfspurr@gwmail.gwu.eduSupplementary InformationRe_QTL_Supplementary_Data.zip
A multi-species repository of social networks
Authors: Sah Pratha , Méndez José David , Bansal Shweta 
Published: November 2018

AbstractSocial network analysis is an invaluable tool to understand the patterns, evolution, and consequences of sociality. Comparative studies over the spectrum of sociality across taxonomic groups are particularly valuable. Such studies however require quantitative information on social interactions across multiple species which is not easily available. We introduce the Animal Social Network Repository (ASNR) as the first multi-taxonomic repository that collates more than 650 social networks from 47 species, including those of mammals, reptiles, fish, birds, and insects. The repository was created by consolidating social network datasets from the literature on wild and captive animals into a consistent and easy-to-use network data format. The repository is archived at https://bansallab.github.io/asnr/. ASNR has tremendous research potential, including testing hypotheses in the fields of animal ecology, social behavior, epidemiology and evolutionary biology.
In for a penny, in for a pound: Examining motivated memory through the lens of retrieved context models
Authors: Talmi Deborah , Kavaliauskaite Deimante , Daw Nathaniel D. 
Published: November 2018

AbstractWhen people encounter items that they believe will help them gain reward, they later remember them better than others. A recent model of emotional memory, the emotional Context Maintenance and Retrieval model (eCMR), predicts that these effects would be stronger when stimuli that predict high and low reward can compete with each other both during encoding and retrieval. We tested this prediction in two experiments. Participants were promised £1 for remembering some pictures, but only a few pence for remembering others. Their recall of the content of the pictures they saw was tested after one minute and in Experiment 2, also after 24 hours. Memory at immediate test showed effects of list composition. Recall of stimuli that predicted high reward was greater than of stimuli that predicted lower reward, but only when high- and low-reward items were studied and recalled together, not when they were studied and recalled separately. More high-reward items in mixed lists were forgotten over a 24-hour retention interval compared to items studied in other conditions, but reward did not modulate the forgetting rate, a null effect which should be replicated in a larger sample. These results confirm eCMR’s predictions, although further research is required to compare that model against alternatives.
BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper
Authors: Guidi Giulia , Ellis Marquita , Rokhsar Daniel , Yelick Katherine , Buluç Aydın 
Published: November 2018

AbstractRecent advances in long-read sequencing enable the characterization of genome structure and its intra- and inter-species variation at a resolution that was previously impossible. Detecting overlaps between reads is integral to many long-read genomics pipelines, such as de novo genome assembly. While longer reads simplify genome assembly and improve the contiguity of the reconstruction, current long-read technologies come with high error rates. We present Berkeley Long-Read to Long-Read Aligner and Overlapper (BELLA), a novel algorithm for computing overlaps and alignments via sparse matrix-matrix multiplication that balances the goals of recall and precision, performing well on both.We present a probabilistic model that demonstrates the feasibility of using short k-mers for detecting candidate overlaps. We then introduce a notion of reliable k-mers based on our probabilistic model. Combining reliable k-mers with our binning mechanism eliminates both the k-mer set explosion that would otherwise occur with highly erroneous reads and the spurious overlaps from k-mers originating in repetitive regions. Finally, we present a new method based on Chernoff bounds for separating true overlaps from false positives using a combination of alignment techniques and probabilistic modeling. Our methodologies aim at maximizing the balance between precision and recall. On both real and synthetic data, BELLA performs amongst the best in terms of F1 score, showing performance stability which is often missing for competitor software. BELLA’s F1 score is consistently within 1.7% of the top entry. Notably, we show improved de novo assembly results on synthetic data when coupling BELLA with the Miniasm assembler.
Longitudinal dentate nuclei iron concentration and atrophy in Friedreich ataxia: IMAGE-FRDA
Authors: Ward Phillip G. D. , Harding Ian H , Close Thomas G. , Corben Louise A , Delatycki Martin B , Storey Elsdon , Georgiou-Karistianis Nellie , Egan Gary F 
Published: November 2018

AbstractBackgroundFriedreich ataxia is a recessively inherited, progressive neurological disease characterised by impaired mitochondrial iron metabolism. The dentate nuclei of the cerebellum are characteristic sites of neurodegeneration in the disease, but little is known of the longitudinal progression of pathology in these structures.MethodsUsing in vivo magnetic resonance imaging, including quantitative susceptibility mapping, we investigated changes in iron concentration and volume in the dentate nuclei in individuals with Friedreich ataxia (n=20) and healthy controls (n=18) over a two-year period.ResultsThe longitudinal rate of iron concentration was significantly elevated bilaterally in participants with Friedreich ataxia relative to healthy controls. Atrophy rates did not differ significantly between groups. Change in iron concentration and atrophy both correlated with baseline disease severity or duration, indicating sensitivity of these measures to disease stage. Moreover, atrophy was maximal in individuals early in the disease course, while the rate of iron concentration increased with disease progression.ConclusionsProgressive dentate nuclei pathology is evident in vivo in Friedreich ataxia, and the rates of change of iron concentration and atrophy in these structures are sensitive to the disease stage. The findings are consistent with an increased rate of iron concentration and atrophy early in the disease, followed by iron accumulation and stable volume in later stages. This pattern suggests that iron dysregulation persists after loss of the vulnerable neurons in the dentate. The significant changes observed over a two-year period highlights the utility of quantitative susceptibility mapping as a longitudinal biomarker and staging tool.
Soil nutrient adequacy for optimal cassava growth, implications on cyanogenic glucoside production: a case of konzo-affected Mtwara region, Tanzania
Authors: Imakumbili Matema L.E. , Semu Ernest , Semoka Johnson M.R. , Abass Adebayo , Mkamilo Geoffrey 
Published: November 2018

AbstractSoils in areas affected by konzo (a cassava cyanide intoxication paralytic disorder) are predominantly infertile and probably unable to supply cassava the nutrients it needs to achieve optimal growth. The soil nutrient levels in these areas, could also be influencing cyanogenic glucoside production in cultivated cassava, however there is hardly any knowledge on this. An assessment of soil nutrient levels on cassava fields in konzo-affected areas was therefore carried out to determine their adequacy for optimal cassava growth and how this influences cassava cyanogenic glucoside production. Konzo-affected Mtwara region, in Tanzania, was used as a case study area. Correlations between total hydrogen cyanide (HCN) levels in cassava roots and various soil nutrient levels on cassava fields were carried out and relationships between cyanide intoxication and soil nutrient levels on fields from which toxic cassava roots had been harvested were also investigated. The results showed that cassava grows under conditions of severe nutrient stress in the region. Soil nutrients found to be deficient on most fields, like potassium (mean = 0.09, SD = 0.05 cmol/kg), magnesium (mean = 0.26, SD = 0.14 cmol/kg) and zinc (mean = 1.34, SD = 0.26 mg/kg), are known to reduce cyanogenic glucoside levels in cassava roots when adequate in soils. Cyanogenic glucoside levels in cassava roots however increased by high levels soil phosphorous (rs = 0.486, p = 0.026 for all varieties) and sulphur (rs = 0.593, p = 0.032 and rs = 0.714, p = 0.047; for bitter and sweet cassava varieties, respectively) on these soils. The likelihood of cassava cyanide intoxication was also increased on fields with high pH and iron levels. High levels of sulphur and phosphorus, to very high levels of iron occurred on some fields. How soil nutrient supply influences cassava cyanogenic glucoside production in the konzo-affected areas was established.
Checkpoint adaptation in repair-deficient cells drives aneuploidy and resistance to genotoxic agents
Authors: Vydzhak Olga , Bender Katharina , Klermund Julia , Busch Anke , Reimann Stefanie , Luke Brian 
Published: November 2018

AbstractHuman cancers frequently harbour mutations in DNA repair genes, rendering the use of DNA damaging agents as an effective therapeutic intervention. As therapy-resistant cells often arise, it is important to better understand the molecular pathways that drive resistance in order to facilitate the eventual targeting of such processes. We employ repair-defective diploid yeast as a model to demonstrate that, in response to genotoxic challenges, nearly all cells eventually undergo checkpoint adaptation, resulting in the generation of aneuploid cells with whole chromosome losses that have acquired resistance to the initial genotoxic challenge. We demonstrate that adaptation inhibition, either pharmacologically, or genetically, drastically reduces the occurrence of resistant cells. Additionally, the aneuploid phenotypes of the resistant cells can be specifically targeted to induce cytotoxicity. We provide evidence that TORC1 inhibition with rapamycin, in combination with DNA damaging agents, can prevent both checkpoint adaptation and the continued growth of aneuploid resistant cells.
Occupancy patterns of 208 DNA-associated proteins in a single human cell type
Authors: Partridge E. Christopher , Chhetri Surya B. , Prokop Jeremy W. , Ramaker Ryne C. , Jansen Camden S. , Goh Say-Tar , Mackiewicz Mark , Newberry Kimberly M. , Brandsmeier Laurel A. , Meadows Sarah K. , Messer C. Luke , Hardigan Andrew A. , Dean Emma C. , Jiang Shan , Savic Daniel , Mortazavi Ali , Wold Barbara J. , Myers Richard M. , Mendenhall Eric M. 
Published: November 2018

SummaryGenome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes, but only a small fraction of the >1,600 transcription factors (TFs) encoded in the human genome has been assayed. Here we present data and analyses of ChIP-seq experiments for 208 DNA-associated proteins (DAPs) in the HepG2 hepatocellular carcinoma line, spanning nearly a quarter of its expressed TFs, transcriptional co-factors, and chromatin regulator proteins. The DAP binding profiles classify into major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalog of DNA sequence motifs; 77 factors showed similar motifs to those previously described using in vivo and/or in vitro methods, and 17 yielded novel motifs. We also describe motifs corresponding to other TFs that co-enrich with the primary ChIP target. FOX family motifs are, for example, significantly enriched in ChIP-seq peaks of 37 other DAPs. We show that promoters and enhancers can be discriminated based on motif content and occupancy patterns. This large catalog reveals High Occupancy Target (HOT) regions at which many DAPs associate, although each contains motifs for only a minority of the numerous associated DAPs. These analyses provide a deeper and more complete overview of the gene regulatory networks that define this cell type.