cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20131655
title: Supplementary Material for: Immature Brain Cortical Neurons Have Low Transcriptional Competence to Activate Antiviral Defences and Control RNA Virus Infections

description: Virus infections of the central nervous system (CNS) cause important diseases of humans and animals. As in other tissues, innate antiviral responses mediated by type I interferons (IFNs) are crucially important in controlling CNS virus infections. The maturity of neuronal populations is an established critical factor determining the outcome of CNS virus infection. Using primary cultures of mouse cortical neurons, we investigated the relationships between neuronal maturation, type I IFN responses, and the outcome of Semliki Forest virus infection. The virus replicated better, infected more cells, and produced higher titres of infectious viruses in immature neurons. Complete transcriptome analysis demonstrated that resting immature neurons have low transcriptional competence to mount antiviral responses. They had no detectable transcription of the genes <i>Ddx58</i> and <i>Ifih1</i>, which encode key RNA virus cytoplasmic sensors RIG-I and MDA5, and very low expression of genes encoding key regulators of associated signalling pathways. Upon infection, immature neurons failed to mount an antiviral response as evidenced by their failure to produce chemokines, IFNs, and other cytokines. Treatment of immature neurons with exogenous IFNβ prior to infection resulted in antiviral responses and lower levels of virus replication and infectious virus production. In contrast, resting mature neurons generated a robust antiviral response. This was augmented by pretreatment with IFNβ. Infection of mature neurons derived from IFNAR<sup>−/−</sup> mice did not make an antiviral response and replicated virus to high levels.
DOI: 10.6084/m9.figshare.20271921
title: Supplementary Material for: Association between transcription factor 7-like 2 C/T polymorphism and diabetic retinopathy risk: a meta-analysis

description: Background: Previous studies have suggested a close association between transcription factor 7-like 2 (TCF7L2) polymorphisms and diabetic retinopathy (DR) susceptibility. However, the published results were inconsistent. This meta-analysis was conducted to review and examine the relationship between TCF7L2 rs7903146 C/T polymorphism and DR risk. Materials and methods: Online databases were searched and the related studies were identified in this meta-analysis. Odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were calculated to examine the statistical power. Moreover, heterogeneity test, sensitivity accumulative analysis and publication bias were conducted to measure the statistical effect. Result: 6 studies involving 12,982 subjects were included in this meta-analysis to assess the association between rs7903146 C/T polymorphism and DR susceptibility. The synthetic results indicated that the mutation of rs7903146 C/T polymorphism maybe accompany with an increased risk for DR (T vs. C: OR=1.26, 95%CI=1.00-1.60, P=0.05, I2=83.5%; TT vs. CC: OR=1.79 95%CI=1.12-2.86, P=0.02, I2=80.2%; TT vs. CC+CT: OR=1.62, 95%CI=1.38-1.92, P&lt;0.01, I2=32.3%). Moreover, the subgroup analysis also demonstrated an increasing risk for DR with T mutations in Caucasian descendants. Conclusion: The current evidences meta-analysis suggested that the TCF7L2 rs7903146 C/T polymorphism might be play an important role in DR susceptibility.
DOI: 10.6084/m9.figshare.21118969
title: Supplementary Material for: Chronic Pain and Psychiatric Conditions

description: Chronic pain is a common condition with high socioeconomic and public health burden. A wide range of psychiatric conditions are often comorbid with chronic pain and chronic pain conditions, negatively impacting successful treatment of either condition. The psychiatric condition receiving most attention in the past with regards to chronic pain comorbidity has been major depressive disorder, despite the fact that many other psychiatric conditions also demonstrate epidemiological and genetic overlap with chronic pain. Further understanding potential mechanisms involved in psychiatric and chronic pain comorbidity could lead to new treatment strategies both for each type of disorder in isolation, and in scenarios of comorbidity. This article provides an overview of relationships between DSM-5 psychiatric diagnoses and chronic pain, with particular focus on PTSD, ADHD and BPD, disorders which are less commonly studied in conjunction with chronic pain. We also discuss potential mechanisms that may drive comorbidity, and present new findings on the genetic overlap of chronic pain and ADHD, and chronic pain and BPD.
DOI: 10.6084/m9.figshare.21550911
title: Supplementary Material for: GSK3β Inhibition Prevents Macrophage Reprogramming by High-Dose Methotrexate

description: Methotrexate (MTX) is an antifolate drug used as a chemotherapeutic agent for acute lymphoblastic leukemia, where MTX improves patients’ prognosis. Macrophage reprogramming is being increasingly assessed as an antitumor therapeutic strategy. However, and although MTX limits the pathogenic action of macrophages in chronic inflammatory diseases, its effects on tumor-promoting macrophages have not been previously explored. We now report that MTX shapes the transcriptional and functional profile of M-CSF-dependent human macrophages, whose transcriptome is highly enriched in the gene signature that defines pathogenic tumor-associated macrophages (“large TAM”). Specifically, MTX prompted the acquisition of the gene signature of antitumoral “small TAM” and skewed macrophages toward an IL-6<sup>high</sup> IFNβ1<sup>high</sup> IL-10<sup>low</sup> phenotype upon subsequent stimulation. Mechanistically, the MTX-induced macrophage reprogramming effect correlated with a reduction of the M-CSF receptor CSF1R expression and function, as well as a diminished expression of MAF and MAFB transcription factors, primary determinants of pro-tumoral macrophages whose transcriptional activity is dependent on GSK3β. Indeed, the ability of MTX to transcriptionally reprogram macrophages toward an antitumoral phenotype was abrogated by inhibition of GSK3β. Globally, our results establish MTX as a macrophage reprogramming drug and indicate that its ability to modulate macrophage polarization may also underlie its therapeutic benefits. Since GSK3β inhibition abrogates the reprogramming action of MTX, our results suggest that the GSK3β-MAFB/MAF axis constitutes a target for the macrophage-centered antitumor strategies.
DOI: 10.57745/p64gu4
title: PM-N38-12-R2.bam
DOI: 10.57745/pesbld
title: PM-N38-12-R3.bam
DOI: 10.57745/jugnzy
title: PM-N38-16-R1.bam
DOI: 10.57745/umg3sv
title: PM-N38-16-R2.bam
DOI: 10.57745/0euxyr
title: PM-N38-16-R3.bam
DOI: 10.57745/mgsgxv
title: PM-R23-12-R1.bam
DOI: 10.57745/otecub
title: PM-R23-12-R2.bam
DOI: 10.57745/wyswm7
title: PM-R23-12-R3.bam
DOI: 10.57745/pltigy
title: PM-R23-16-R1.bam
DOI: 10.57745/tyi3d3
title: PM-R23-16-R2.bam
DOI: 10.57745/xcu8z9
title: PM-R23-16-R3.bam
DOI: 10.6073/pasta/06c6b9983a5f0a44349e027a002f5040
title: SBC LTER: Beach: Time series of abundance of birds and stranded kelp on selected beaches, ongoing since 2008

description: Dataset contains the distribution, abundance and seasonal occurrence of birds, humans, dogs, and of freshly stranded giant kelp (Macrocystis pyrifera) plants and holdfasts present during monthly low-tide (&lt;= 2.5 ft) weekday surveys of standard 1 km long transects on selected sandy beaches of the mainland coast of the Santa Barbara Channel. The abundance of humans, dogs, marine mammals and dead or oiled wildlife is also recorded during each survey. Sampling began in 2008 and is ongoing. See Methods for more information.
DOI: 10.6073/pasta/cd4cf864efecd69891dfe1d73b9ac9c3
title: SBC LTER: Reef: Kelp Forest Community Dynamics: Invertebrate and algal density

description: These data describe the abundance and size of a select group of about 50 species of benthic invertebrates and understory algae in fixed plots (either 1mx1m or 20mx1m) along permanent transects. These data are part of SBCLTER?s kelp forest monitoring program to track long-term patterns in species abundance and diversity of reef-associated organisms in the Santa Barbara Channel, California, USA. The sampling locations in this dataset are at nine reef sites along the mainland coast of the Santa Barbara Channel and at two sites on the north side of Santa Cruz Island. These sites reflect several oceanographic regimes in the channel and vary in distance from sources of terrestrial runoff. Sampling began in 2000, and these data are updated annually.
DOI: 10.17632/z78zz7mv7h.2
title: Data for speciation of ROG emissions from residential combustion

description: 1. Residential emission ratios
2. Measurement method statistics
3. Category mass fraction
4. OHR&SOAP
5. Annual ROG emissions
6. loss & volatility & polarity
7. Deviation (flame vs whole)
DOI: 10.48786/edbt.2023.01
title: A simplified Architecture for Fast, Adaptive Compilation and Execution of SQL Queries
DOI: 10.5281/zenodo.4836157
title: RoB 2 cribsheets

description: These are the cribsheets related to the Risk of Bias assessment
DOI: 10.5517/cc3s97d
title: CCDC 112723: Experimental Crystal Structure Determination

description: Related Article: P.Erk|2002|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5683/sp2/vbpbfn
title: Replication data for: Long term monitoring of the rocky intertidal on Wizard Island in Barkley Sound

description: In 1997 the Bamfield Marine Sciences Centre established a long-term monitoring project to collect baseline data on the distribution and abundance of macroorganisms at two intertidal sites on Wizard Islet in Barkley Sound. Both sites were resampled in 2001 and 2007, and the exposed site was resampled in 2002 and 2003. In 2009, both sites were sampled again, and a Microsoft Access database was created with comparable data from previous years (1997-2007). Data is presented here for algal cover (%), sessile invertebrate cover (%), invertebrate density, and sea star density for 2009 as well as the complete Microsoft Access database. Wizard Islet (48°51’29.5”N, 125°09’31”W) is located within the Deer Group Islands in Barkley Sound and has an area of 1.73 hectares at low tide. The sheltered site (with less wave exposure) is located on a 50m stretch of fixed rocky shore on the northeast side and is characterized by Fucus and Phyllospadix (seagrass). The exposed site is located on a 50m stretch of fixed rocky shore on the southwest side and is characterized by Egregia (feather-boa kelp), goose-necked barnacles and Alaria (brown alga). Fifteen transects were randomly selected at the sheltered site (tag numbers 7, 10, 11, 12, 15, 18, 21, 26, 34, 36, 38, 40, 42, 44, 48) and the exposed site (tag numbers 1, 3, 5, 11, 15, 17, 20, 23, 25, 32, 37, 40, 44, 46, 48). Sampling was done at tidal heights of 1, 1.5, 2, 2.5, 3 and 3.5m. In 2009 tidal height of 0.5m was not sampled due to time constraints and limited low tide series. Quadrats of 25x25cm were used for percent cover of bare rock, algae, colonial and encrusting species. Quadrats of 25x25cm were also used for counts of invertebrates with the exception of seastars which were counted in 50x50cm quadrats. To maintain consistency, all quadrats were positioned to the left and above each point on the transect (when facing away from the water). Data collected by students in the Coastal Biodiversity and Conservation course taught by Dr. Brian Starzomski and Dr. Tom Okey with Teaching Assistant Christine Gruman July 27 – September 4, 2009.
DOI: 10.6073/pasta/08dd6cb668df706061bf260b183561a0
title: Plant succession and biomass dynamics following logging and burning in Watersheds 1 and 3, Andrews Experimental Forest, 1962 to Present

description: There has been long history of geomorphic, hydrological, and ecological study in the experimental watersheds of HJA, which include WS1 and WS3 and the neighboring old-growth basin, WS2. These include comparative studies of sediment yield, stream chemistry, and water flow following whole-basin logging of WS1 and patch-cut logging of WS3, and long-term studies of post-harvest forest development. The latter, initiated in 1962, are among the longest-running and most intensive studies of secondary succession in forests of North America. They are based on two types of permanent plots (understory and overstory), spatially linked to facilitate analyses of overstory-understory interactions. Plots in WS1 and WS3 occur within transects within units of the watersheds. Understory quadrats were established in 1962, prior to harvest, and have been sampled periodically since the watersheds were cut and broadcast burned. They have been used to study how species’ life histories, pre-disturbance composition, disturbance intensity, and overstory development contribute to the long-term dynamics of the understory. These are 2 m by 2 m quadrats where canopy cover, ground conditions, growth forms, species cover and biomass have been monitored. Overstory tree plots were established nearly two decades later (1979-1980) to characterize the early stages of forest development, including the recruitment (ingrowth), growth, and mortality of conifers and hardwoods. These are circular plots (radius=8.92 m) where live trees greater than or equal to 1.37 m tall are measured for diameter at breast height or basal diameter. Remeasurement of these plots occurs on 5 or 6 year intervals.
DOI: 10.6073/pasta/61cc126fc5a5a0a99b62b3aaac56f3e8
title: MCR LTER: Coral Reef: Long-term Population and Community Dynamics: Other Benthic Invertebrates, ongoing since 2005
DOI: 10.6073/pasta/cbe04a94b5f6f3859a3d9c98f5be0fc8
title: Bee species abundance and composition in three ecosystem types at the Sevilleta National Wildlife Refuge, New Mexico, USA

description: This study was designed to examine community- or population-level fluctuations in bee species at the Sevilleta National Wildlife Refuge, both intra- and inter-annually. From 2002 to 2019, passive funnel traps were used to collect bees at three sites, each representing a different ecosystem type of the southwestern U.S. (Plains grassland, Chihuahuan Desert grassland, and Chihuahuan Desert shrubland). Bees were collected during each month from March through October, and were identified to species by taxonomic experts.
DOI: 10.6073/pasta/e34b247937277b35905018f728849a10
title: North Temperate Lakes LTER: Benthic Macroinvertebrates 1981 - current

description: Macroinvertebrates are collected from selected shoreline and deep water locations in the seven primary lakes (Allequash, Big Muskellunge, Crystal, Sparkling, and Trout lakes, and unnamed lakes 27-02 [Crystal Bog], and 12-15 [Trout Bog]) in the Trout Lake area using modified Hester-Dendy samplers. Samplers are placed at fyke net and gill net locations in August and retrieved 3-4 weeks later. Macroinvertebrates are preserved in ethanol. This dataset contains counts of various groups of macroinvertebrates identified from specific samples. The majority of the identifications are at the genus level. The data table "Benthic Macroinvertebrate Codes" identifies the taxonomic group represented by each group code. Taxonomic references: Ecology and Classification of North American Freshwater Invertebrates, Edited by James H Thorp and Alan P Covich, Academic Press, Inc, 1991; Aquatic Insects of Wisconsin, William L Hilsenhoff, Natural History Museums Council, University of Wisconsin-Madison (1995). Sampling Frequency: annually Number of sites: 7
DOI: 10.6073/pasta/ed17faaca17d524a06c50a6027411cf3
title: Zooplankton density for lake samples collected near Toolik Lake Arctic LTER in the summers between 1993-2002.

description: Zooplankton density, in number per liter, was taken with a 30 cm diameter plankton net with a 335 um mesh plankton netting. All samples were collected from Toolik Lake and the lakes near the Toolik Field Station, Arctic LTER from 1993-2002. NOTE: In versions pervious to 3 the dates for 1994 and 1995 were WRONG.
DOI: 10.6073/pasta/f2d0beb83ce7ed6949364ac28df790ea
title: SBC LTER: Reef: Annual time series of biomass for kelp forest species, ongoing since 2000

description: These data are annual estimates of biomass of approximately 225 taxa of reef algae, invertebrates and fish in permanent transects at 11 kelp forest sites in the Santa Barbara Channel (2-8 transects per site). Abundance is measured annually (as percent cover or density, by size) and converted to biomass (i.e., wet mass, dry mass, decalcified dry mass, ash free dry mass) using published taxon-specific algorithms. Data collection began in summer 2000 and continues annually in summer to provide information on community structure, population dynamics and species change. The time period of data collection varied among the 11 kelp forest sites. Sampling at BULL, CARP, and NAPL began in 2000, sampling at the other 6 mainland sites (AHND, AQUE, IVEE, GOLB, ABUR, MOHK) began in 2001 (transects 3, 5, 6, 7, 8 at IVEE were added in 2011). Data collection at the two Santa Cruz Island sites (SCTW and SCDI) began in 2004. See Methods for more information. See Methods for more information.
DOI: 10.6073/pasta/f906c91e98c2a5fe752dfa0ccdc8895f
title: SBC LTER: Reef: Kelp Forest Community Dynamics: Cover of sessile organisms, Uniform Point Contact

description: These data describe the cover of sessile invertebrates, understory macroalgae, and bottom substrate types as determined by a uniform point contact method. The presence of over 150 taxa of sessile invertebrates and macroalgae are recorded at 80 uniformly spaced points along permanent 40m x 2m transects. Multiple species can be recorded at any given point. Percent cover of a given species on a transect can be estimated from UPC observations as the fraction of total points at which that species was present x 100. The total percent cover of all species combined using this method can exceed 100%; however, the percent cover of any single species cannot exceed 100%. These data are part of SBC LTERs kelp forest monitoring program, which began in 2000 and was designed to track long-term patterns in species abundance and diversity of reef-associated organisms in the Santa Barbara Channel, California, USA, The sampling locations in this dataset include nine reef sites along the mainland coast of the Santa Barbara Channel and at two sites on the north side of Santa Cruz Island. These sites reflect several oceanographic regimes in the channel and vary in distance from sources of terrestrial runoff. Data collection began in 2000 and this dataset is updated annually.
DOI: 10.6084/m9.figshare.20047748
title: Supplementary Material for: Adoptively Transferred in vitro-Generated Myeloid-Derived Suppressor Cells Improve T-Cell Function and Antigen-Specific Immunity after Traumatic Lung Injury

description: Immune reactions after trauma are characterized by immediate activation of innate immunity and simultaneously downregulation of adaptive immunity leading to a misbalanced immunohomeostasis and immunosuppression of the injured host. Therefore, the susceptibility to secondary infections is strongly increased after trauma. Immune responses are regulated by a network of immune cells influencing each other and at the same time modifying their functions dependent on the inflammatory environment. Although myeloid-derived suppressor cells (MDSCs) are initially described as T-cell suppressors, their immunomodulatory capacity after trauma is mostly undefined. Therefore, in vitro-generated MDSCs were adoptively transferred into mice after blunt chest trauma (TxT). A single MDSC treatment-induced splenic T-cell expansion decreased apoptosis sensitivity and improved proliferation in the absence of T-cell exhaustion until 2 weeks after trauma. MDSC treatment had a long-lasting effect on the genomic landscape of CD4<sup>+</sup> T cells by upregulating primarily Th2-associated genes. Remarkably, immune-activating functions of MDSCs supported the ability of TxT mice to respond to post-traumatic secondary antigen challenge. Secondary insults were mimicked by immunizing MDSC-treated TxT mice with ovalbumin (OVA), followed by OVA restimulation in vitro. MDSC treatment significantly increased the frequency of OVA-specific T cells, enhanced their Th1/Th2 cytokine expression, and induced upregulation of cytolytic molecules finally improving OVA-specific cytotoxicity. Overall, we could show that therapeutic MDSC treatment after TxT improves post-traumatic T-cell functions, which might enable the traumatic host to counterbalance trauma-induced immunoparalysis.
DOI: 10.6084/m9.figshare.20159282
title: Supplementary Material for: Tollip Inhibits IL-33 Release and Inflammation in Influenza A Virus-Infected Mouse Airways

description: Respiratory influenza A virus (IAV) infection continues to pose significant challenges in healthcare of human diseases including asthma. IAV infection in mice was shown to increase IL-33, a key cytokine in driving airway inflammation in asthma, but how IL-33 is regulated during viral infection remains unclear. We previously found that a genetic mutation in Toll-interacting protein (Tollip) was linked to less airway epithelial Tollip expression, increased neutrophil chemokines, and lower lung function in asthma patients. As Tollip is involved in maintaining mitochondrial function, and mitochondrial stress may contribute to extracellular ATP release and IL-33 secretion, we hypothesized that Tollip downregulates IL-33 secretion via inhibiting ATP release during IAV infection. Wild-type and Tollip knockout (KO) mice were infected with IAV and treated with either an ATP converter apyrase or an IL-33 decoy receptor soluble ST2 (sST2). KO mice significantly lost more body weight and had increased extracellular ATP, IL-33 release, and neutrophilic inflammation. Apyrase treatment reduced extracellular ATP levels, IL-33 release, and neutrophilic inflammation in Tollip KO mice. Excessive lung neutrophilic inflammation in IAV-infected Tollip KO mice was reduced by sST2, which was coupled with less IL-33 release. Our data suggest that Tollip inhibits IAV infection, potentially by inhibiting extracellular ATP release and reducing IL-33 activation and lung inflammation. In addition, sST2 may serve as a potential therapeutic approach to mitigate respiratory viral infection in human subjects with Tollip deficiency.