cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0363482
title: KCTD8 gene and brain growth in adverse intrauterine environment: a genome-wide association study

description: The most dramatic growth of the human brain occurs in utero and during the first 2 years of postnatal life. Genesis of the cerebral cortex involves cell proliferation, migration, and apoptosis, all of which may be influenced by prenatal environment. Here, we show that variation in KCTD8 (potassium channel tetramerization domain 8) is associated with brain size in female adolescents (rs716890, P = 5.40 × 10(-09)). Furthermore, we found that the KCTD8 locus interacts with prenatal exposure to maternal cigarette smoking vis-à-vis cortical area and cortical folding: In exposed girls only, the KCTD8 locus explains up to 21% of variance. Using head circumference as a proxy of brain size at 7 years of age, we have replicated this gene-environment interaction in an independent sample. We speculate that KCTD8 might modulate adverse effects of smoking during pregnancy on brain development via apoptosis triggered by low intracellular levels of potassium, possibly reducing the number of progenitor cells.
DOI: 10.14288/1.0363483
title: ‘‘Guilt by Association’’ Is the Exception Rather Than the Rule in Gene Networks

description: Gene networks are commonly interpreted as encoding functional information in their connections. An extensively validated principle called guilt by association states that genes which are associated or interacting are more likely to share function. Guilt by association provides the central top-down principle for analyzing gene networks in functional terms or assessing their quality in encoding functional information. In this work, we show that functional information within gene networks is typically concentrated in only a very few interactions whose properties cannot be reliably related to the rest of the network. In effect, the apparent encoding of function within networks has been largely driven by outliers whose behaviour cannot even be generalized to individual genes, let alone to the network at large. While experimentalist-driven analysis of interactions may use prior expert knowledge to focus on the small fraction of critically important data, large-scale computational analyses have typically assumed that high-performance cross-validation in a network is due to a generalizable encoding of function. Because we find that gene function is not systemically encoded in networks, but dependent on specific and critical interactions, we conclude it is necessary to focus on the details of how networks encode function and what information computational analyses use to extract functional meaning. We explore a number of consequences of this and find that network structure itself provides clues as to which connections are critical and that systemic properties, such as scale-free-like behaviour, do not map onto the functional connectivity within networks.
DOI: 10.14288/1.0363905
title: Using text mining to link journal articles to neuroanatomical databases

description: The electronic linking of neuroscience information, including data embedded in the primary literature, would permit powerful queries and analyses driven by structured databases. This task would be facilitated by automated procedures that can identify biological concepts in journals. Here we apply an approach for automatically mapping formal identifiers of neuroanatomical regions to text found in journal abstracts, applying it to a large body of abstracts from the Journal of Comparative Neurology (JCN). The analyses yield over 100,000 brain region mentions, which we map to 8,225 brain region concepts in multiple organisms. Based on the analysis of a manually annotated corpus, we estimate mentions are mapped at 95% precision and 63% recall. Our results provide insights into the patterns of publication on brain regions and species of study in JCN but also point to important challenges in the standardization of neuroanatomical nomenclatures. We find that many terms in the formal terminologies never appear in a JCN abstract, and, conversely, many terms that authors use are not reflected in the terminologies. To improve the terminologies, we deposited 136 unrecognized brain regions into the Neuroscience Lexicon (NeuroLex). The training data, terminologies, normalizations, evaluations, and annotated journal abstracts are freely available at http://www.chibi.ubc.ca/WhiteText/.
DOI: 10.14288/1.0363992
title: Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text

description: &lt;p&gt;Motivation: Automated annotation of neuroanatomical connectivity statements from the neuroscience literature would enable accessible and large-scale connectivity resources. Unfortunately, the connectivity findings are not formally encoded and occur as natural language text. This hinders aggregation, indexing, searching and integration of the reports. We annotated a set of 1377 abstracts for connectivity relations to facilitate automated extraction of connectivity relationships from neuroscience literature. We tested several baseline measures based on co-occurrence and lexical rules. We compare results from seven machine learning methods adapted from the protein interaction extraction domain that employ part-of-speech, dependency and syntax features.&lt;p&gt; &lt;p&gt;Results: Co-occurrence based methods provided high recall with weak precision. The shallow linguistic kernel recalled 70.1% of the sentence-level connectivity statements at 50.3% precision. Owing to its speed and simplicity, we applied the shallow linguistic kernel to a large set of new abstracts. To evaluate the results, we compared 2688 extracted connections with the Brain Architecture Management System (an existing database of rat connectivity). The extracted connections were connected in the Brain Architecture Management System at a rate of 63.5%, compared with 51.1% for co-occurring brain region pairs. We found that precision increases with the recency and frequency of the extracted relationships.&lt;p&gt;
DOI: 10.6073/pasta/25b4c17c2c53892d09721299d1a070cb
title: Zooplankton collected with a 2-m, 700-um net towed from surface to 120 m, aboard Palmer Station Antarctica LTER annual cruises off the western Antarctic peninsula, 2009 - 2024.

description: Zooplankton are a morphologically and taxonomically diverse group of animals. Many zooplankton feed on phytoplankton and thus provide a link between primary producers and higher trophic levels. Zooplankton density and biovolume were determined at grid stations on the annual LTER cruises along the western Antarctic Peninsula (WAP). Annual cruises take place between late December to early February, except for the NBP21-13 cruise, which was November and December. Typically, zooplankton were collected with a 2x2 meter, 700um mesh net fitted with a flow meter and towed obliquely to 120m. Zooplankton distributions vary spatially due to water column characteristics, which affect their predators' distributions. As climate change continues to affect the WAP, the relative abundance of the various zooplankton components can also be expected to change.
DOI: 10.14288/1.0377456
title: Crescent Beach data

description: As part of the project that led to the excavation of the Crescent Beach site in 1989-90, three sites had their artifacts classified using the same system. These are the collections from the 1989-90 excavations at Crescent Beach, the 1949-50 excavations at Whalen Farm and the 1948 excavations at the Locarno Beach site. The description and illustrations of the artifact classes are found in Chapter V of The Crescent Beach site and the place of the Locarno Beach phase (edited by R.G. Matson) available at: https://circle.ubc.ca/handle/2429/39218. The individual artifacts have their provenience, classification and metric measurements given in the Crescent Beach Artifacts databases. Three separate files in DBaseIII format, one for each site, are described in the Codebook for the Crescent Beach artifacts. In Chapter XII of the Crescent Beach monograph, a number of Locarno Beach culture or related components are compared using multivariate techniqes. In the Site Codebook the Excel file that tabulates the 26 assemblages and 55 artifact classes used is described.
DOI: 10.14288/1.0314344
title: Effects of social housing on reversal learning and fearfulness in dairy calves

description: Early life social deprivation can cause cognitive deficits, behavioural abnormalities, and anxiety in rodents and primates. This study investigated its effects on dairy calves. First single-housed calves were compared to calves reared in a complex social group in their ability to learn a discrimination reversal. In the second experiment, individual calves were compared with those raised in pairs from 6 d, in pairs from 42 d, and complex group from early life. Both reversal learning and anxiety (fear of novel objects) was assessed. The results, showing learning deficits and elevated anxiety in single-housed calves, and intermediate learning abilities in late paired calves, are reported in a paper under revision for PLOS One. The data provided give individual IDs, treatment (level of social housing), dates training and testing occurred, success or failure at reversal learning and number of sessions taken to reach the learning criterion, latencies to touch the novel object or a human handler, counts of other fear-related behaviours during the test (e.g. retreats), and notes on relevant health information, etc.
DOI: 10.14288/1.0319863
title: BC Transit Routes for Victoria, Whistler, Pemberton Local and Commuter, Squamish Commuter, Kelowna and Kamloops, 21 March 2013

description: BC Transit routes for Victoria, Whistler, Pemberton Local and Commuter, Squamish Commuter, Kelowna and Kamloops. The routes were created from the Google transit feed (GTFS) and ArcGIS Network Analyst. As no route shape information was available from the feed, the shape of the route was extrapolated from the road network and layout of transit stops. The transit routes were not verified as no maps are available. Although routes were calculated as carefully as possible, this data set carries no guarantee of accuracy beyond the information included in the Google transit feed.
DOI: 10.14288/1.0363481
title: FTO, obesity and the adolescent brain

description: Genetic variations in fat mass- and obesity (FTO)-associated gene, a well-replicated gene locus of obesity, appear to be associated also with reduced regional brain volumes in elderly. Here, we examined whether FTO is associated with total brain volume in adolescence, thus exploring possible developmental effects of FTO. We studied a population-based sample of 598 adolescents recruited from the French Canadian founder population in whom we measured brain volume by magnetic resonance imaging. Total fat mass was assessed with bioimpedance and body mass index was determined with anthropometry. Genotype-phenotype associations were tested with Merlin under an additive model. We found that the G allele of FTO (rs9930333) was associated with higher total body fat [TBF (P = 0.002) and lower brain volume (P = 0.005)]. The same allele was also associated with higher lean body mass (P = 0.03) and no difference in height (P = 0.99). Principal component analysis identified a shared inverse variance between the brain volume and TBF, which was associated with FTO at P = 5.5 × 10(-6). These results were replicated in two independent samples of 413 and 718 adolescents, and in a meta-analysis of all three samples (n = 1729 adolescents), FTO was associated with this shared inverse variance at P = 1.3 × 10(-9). Co-expression networks analysis supported the possibility that the underlying FTO effects may occur during embryogenesis. In conclusion, FTO is associated with shared inverse variance between body adiposity and brain volume, suggesting that this gene may exert inverse effects on adipose and brain tissues. Given the completion of the overall brain growth in early childhood, these effects may have their origins during early development.
DOI: 10.14288/1.0363484
title: Genome-wide expression profiling of schizophrenia using a large combined cohort

description: Numerous studies have examined gene expression profiles in post-mortem human brain samples from individuals with schizophrenia compared to healthy controls, to gain insight into the molecular mechanisms of the disease. While some findings have been replicated across studies,there is a general lack of consensus of which genes or pathways are affected. It has been unclear if these differences are due to the underlying cohorts, or methodological considerations. Here we present the most comprehensive analysis to date of expression patterns in the prefrontal cortex of schizophrenic compared to unaffected controls. Using data from seven independent studies, we assembled a data set of 153 affected and 153 control individuals. Remarkably, we identified expression differences in the brains of schizophrenics that are validated by up to seven laboratories using independent cohorts. Our combined analysis revealed a signature of 39 probes that are up-regulated in schizophrenia and 86 down-regulated. Some of these genes were previously identified in studies that were not included in our analysis, while others are novel to our analysis. In particular, we observe gene expression changes associated with various aspects of neuronal communication, and alterations of processes affected as a consequence of changes in synaptic functioning. A gene network analysis predicted previously unidentified functional relationships among the signature genes. Our results provide evidence for a common underlying expression signature in this heterogeneous disorder.
DOI: 10.14288/1.0363896
title: Neuron-enriched gene expression patterns are regionally anti-correlated with oligodendrocyte-enriched patterns in the adult mouse and human brain

description: Abstract: An important goal in neuroscience is to understand gene expression patterns in the brain. The recent availability of comprehensive and detailed expression atlases for mouse and human creates opportunities to discover global patterns and perform cross-species comparisons. Recently we reported that the major source of variation in gene transcript expression in the adult normal mouse brain can be parsimoniously explained as reflecting regional variation in glia to neuron ratios, and is correlated with degree of connectivity and location in the brain along the anterior-posterior axis. Here we extend this investigation to two gene expression assays of adult normal human brains that consisted of over 300 brain region samples, and perform comparative analyses of brain-wide expression patterns to the mouse. We performed principal components analysis (PCA) on the regional gene expression of the adult human brain to identify the expression pattern that has the largest variance. As in the mouse, we observed that the first principal component is composed of two anti-correlated patterns enriched in oligodendrocyte and neuron markers respectively. However, we also observed interesting discordant patterns between the two species. For example, a few mouse neuron markers show expression patterns that are more correlated with the human oligodendrocyte-enriched pattern and vice-versa. In conclusion, our work provides insights into human brain function and evolution by probing global relationships between regional cell type marker expression patterns in the human and mouse brain.
DOI: 10.14288/1.0363907
title: Assessing identity, redundancy and confounds in Gene Ontology annotations over time

description: &lt;p&gt;MOTIVATION:&lt;p&gt; &lt;p&gt;The Gene Ontology (GO) is heavily used in systems biology, but the potential for redundancy, confounds with other data sources and problems with stability over time have been little explored.&lt;p&gt; &lt;p&gt;RESULTS:&lt;p&gt; &lt;p&gt;We report that GO annotations are stable over short periods, with 3% of genes not being most semantically similar to themselves between monthly GO editions. However, we find that genes can alter their 'functional identity' over time, with 20% of genes not matching to themselves (by semantic similarity) after 2 years. We further find that annotation bias in GO, in which some genes are more characterized than others, has declined in yeast, but generally increased in humans. Finally, we discovered that many entries in protein interaction databases are owing to the same published reports that are used for GO annotations, with 66% of assessed GO groups exhibiting this confound. We provide a case study to illustrate how this information can be used in analyses of gene sets and networks. &lt;p&gt; &lt;p&gt;AVAILABILITY:&lt;p&gt; &lt;p&gt;Data available at http://chibi.ubc.ca/assessGO.&lt;p&gt;
DOI: 10.14288/1.0319865
title: UBC Library Space Use Observation Study

description: &lt;p&gt;During the sample week (Mar 31-Apr 6 2014) UBC Library staff counted the number of users in publicly available study space in the two largest UBC Vancouver library branches, Irving K. Barber Learning Centre and Koerner Library. Counts took place twice daily, beginning around 10am and 2pm each day* and recording information about seating type, location, and activity.&lt;/p&gt; &lt;p&gt; The study was planned by Jeremy Buhler, Julie Mitchell, and Trish Rosseel. &lt;/p&gt; &lt;p&gt; Please contact Jeremy Buhler at jeremy.buhler@ubc.ca if you have questions. &lt;/p&gt;
DOI: 10.14288/1.0319852
title: Bologna Sant'Orsola Maternity Clinic Database, 1880-1940

description: The variables contained in the data sets are primarily concerned with perinatal outcomes and maternal health.The types of fields are wide-ranging but are primarily concerned with infant birth, maternal health, and socioeconomic status.
DOI: 10.14288/1.0390957
title: Data for: The effects of social environment on standing behavior and the development of claw horn lesions

description: The primary aim of this prospective experimental study was to evaluate how the social environment after calving influenced standing behavior in primiparous cows. At calving, primiparous cows were mixed with familiar peers in a low-stocked pen (≤ 33% stocking density; n=22) or mixed with unknown older cows at 100% stocking density (n = 20). All study animals were mixed with older cows 3 wk after calving. Time spent standing and perching (standing with only the front feet in the stall) were measured d 1 to 3 after calving using 5 min scan sampling. To evaluate if the low-stocked treatment constituted a low-stress social environment, agonistic interactions at the feed barrier were measured for 90 min following feed delivery for a subsample of animals in both treatments (12 animals/treatment). The daily behavioral time budget, including the 90 min following milking, was examined for this subset of animals. A secondary aim was to assess if the social environment after calving was related to the risk of developing claw horn lesions later in lactation. Sole and white-line lesions were recorded at wk 6 and 12 postpartum, and animals were categorized as either having or not having at least one hemorrhage of severity ≥3 (scale 1 to 5) for each lesion type and assessment. Prolonged standing after regrouping was not observed, and standing time and time spent perching did not differ between treatments. Agonistic behaviors directed towards the focal animals occurred less frequently in the low-stocked pen compared to the control. The number and severity of sole and white-line lesions increased after calving; at wk 6 postpartum 20% of the animals in the low-stocked treatment and 50% of the animals mixed with older cows had white-line hemorrhages of severity score ≥3. In summary, under the conditions of this study social environment did not influence standing behavior, but did affect agonistic interactions and likely influenced the risk of claw horn lesions in the weeks following calving.
DOI: 10.14288/1.0314339
title: UBC Research Data Management Survey: Science and Engineering

description: In order to become better prepared to support Research Data Management (RDM) practices in sciences and engineering, UBC Library, together with the VPRI ARC, conducted a research study of all ranks of faculty members, as well as postdoctoral fellows at the Faculty of Applied Science and the Faculty of Science. This survey was conducted in Summer 2015.
DOI: 10.14288/1.0314343
title: Minding the gaps: Comparing engineering research output and library holdings at four large universities

description: This is supplementary data for the ASEE 2015 conference paper titled - "Minding the gaps: Comparing research output and library holdings in four large engineering schools"
DOI: 10.14288/1.0363908
title: Text mining for neuroanatomy using WhiteText with an updated corpus and a new web application

description: We describe the WhiteText project, and its progress towards automatically extracting statements of neuroanatomical connectivity from text. We review progress to date on the three main steps of the project: recognition of brain region mentions, standardization of brain region mentions to neuroanatomical nomenclature, and connectivity statement extraction. We further describe a new version of our manually curated corpus that adds 2,111 connectivity statements from 1,828 additional abstracts. Cross-validation classification within the new corpus replicates results on our original corpus, recalling 67% of connectivity statements at 51% precision. The resulting merged corpus provides 5,208 connectivity statements that can be used to seed species-specific connectivity matrices and to better train automated techniques. Finally, we present a new web application that allows fast interactive browsing of the over 70,000 sentences indexed by the system, as a tool for accessing the data and assisting in further curation. Software and data are freely available at http://www.chibi.ubc.ca/WhiteText/.
DOI: 10.15468/dl.xdayvw
title: Occurrence Download

description: A dataset containing 6792 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "OccurrenceStatus is Present",
 "TaxonKey is Tremarctos ornatus (F.G.Cuvier, 1825)",
 "Year 2010-2025"
 ]
}

 The dataset includes 6792 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012969-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c50z71895
title: MassIVE MSV000098919 - Proteins related to cell adhesion are downregulated in cerebrospinal fluid of patients with spinal muscular atrophy type 1 who achieved less motor improvement after nusinersen administration
title: In this longitudinal exploratory monocentric study, six children with genetic diagnosis of SMA-1 were included. Participants were infants of either gender with SMN1 homozygous gene deletion or mutation, bearing 2 or 3 copies of the SMN2 gene, aged between 1 and 6 months at symptoms onset, and between 6 and 23 months at treatment onset. Nusinersen was administered by intrathecal injection with lumbar puncture at days 0, 15, 30, 45, 60 and 180. After day 180, maintaining doses were administered every 4 months. Before applying each dose, 5 ml of CSF were drained and then, 5 ml of saline buffer with 12 mg of nusinersen per kilogram of body weight were administered. The drained CSF was immediately frozen at -80C until analysis. Samples with evident contamination with blood were discarded. Six samples of CSF were collected at different time points from each patient. The first sample was collected before administration of the first dose and labeled as t0. Next samples were collected at days 15, 30, 45, 60 and 180 and labeled as t15, t30, t45, t60 and t180 respectively.