cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5311090
title: Dataset for: Tracking of unfamiliar odors is facilitated by signal amplification through anoctamin 2 chloride channels in mouse olfactory receptor neurons

description: Many animals follow odor trails to find food, nesting sites or mates, and they require only faint olfactory cues to do so. The performance of a tracking dog, for instance, poses the question on how the animal is able to distinguish a target odor from the complex chemical background around the trail. Current concepts of odor perception suggest that animals memorize each odor as an olfactory object, a percept that enables fast recognition of the odor and the interpretation of its valence. An open question still is how this learning process operates efficiently at the low odor concentrations that typically prevail when animals inspect an odor trail. To understand olfactory processing under these conditions, we studied the role of an amplification mechanism that boosts signal transduction at low stimulus intensities, a process mediated by calcium-gated anoctamin 2 chloride channels. Genetically altered Ano2-/- mice, which lack these channels, display an impaired cue-tracking behavior at low odor concentrations when challenged with an unfamiliar, but not with a familiar, odor. Moreover, recordings from the olfactory epithelium revealed that odor coding lacks sensitivity and temporal resolution in anoctamin 2-deficient mice. Our results demonstrate that the detection of an unfamiliar, weak odor, as well as its memorization as an olfactory object, require signal amplification in olfactory receptor neurons. This process may underlie the phenomenal tracking abilities of animals that follow odor trails.
DOI: 10.6084/m9.figshare.5311096.v1
title: Dataset for: Male apoE*3-Leiden.CETP – mice on high-fat high-cholesterol diet exhibit a biphasic dyslipidemic response, mimicking the changes in plasma lipids observed through life in men.

description: The physiological adaptations resulting in the development of the metabolic syndrome in man occur over a time span of several decades. This combined with the prohibitive financial cost and ethical concerns to measure key metabolic parameters repeatedly in subjects for the major part of their life span, makes that comprehensive longitudinal human data sets are virtually non-existent. While experimental mice are often used, little is known whether this species is in fact an adequate model to better understand the mechanisms that drive the metabolic syndrome in man. We took up the challenge to study the response of male apoE*3-Leiden.CETP mice (with a humanized lipid profile) to a high-fat high-cholesterol diet for six months. Study parameters include body weight, food intake, plasma and liver lipids, hepatic transcriptome, VLDL – triglyceride production and importantly the use of stable isotopes to measure hepatic de novo lipogenesis, gluconeogenesis, and biliary/fecal sterol secretion to assess metabolic fluxes. The key observations include 1) high inter-individual variation, 2) a largely unaffected hepatic transcriptome at 2, 3 and 6 months, 3) a biphasic response curve of the main metabolic features over time, and 4) maximum insulin resistance preceding dyslipidemia. The biphasic response in plasma triglyceride and total cholesterol appears to mimic that of men in cross-sectional studies. Combined, these observations suggest that studies such as these can help to delineate the causes of metabolic derangements in patients suffering from metabolic syndrome.
DOI: 10.6084/m9.figshare.5311090.v1
title: Dataset for: Tracking of unfamiliar odors is facilitated by signal amplification through anoctamin 2 chloride channels in mouse olfactory receptor neurons

description: Many animals follow odor trails to find food, nesting sites or mates, and they require only faint olfactory cues to do so. The performance of a tracking dog, for instance, poses the question on how the animal is able to distinguish a target odor from the complex chemical background around the trail. Current concepts of odor perception suggest that animals memorize each odor as an olfactory object, a percept that enables fast recognition of the odor and the interpretation of its valence. An open question still is how this learning process operates efficiently at the low odor concentrations that typically prevail when animals inspect an odor trail. To understand olfactory processing under these conditions, we studied the role of an amplification mechanism that boosts signal transduction at low stimulus intensities, a process mediated by calcium-gated anoctamin 2 chloride channels. Genetically altered Ano2-/- mice, which lack these channels, display an impaired cue-tracking behavior at low odor concentrations when challenged with an unfamiliar, but not with a familiar, odor. Moreover, recordings from the olfactory epithelium revealed that odor coding lacks sensitivity and temporal resolution in anoctamin 2-deficient mice. Our results demonstrate that the detection of an unfamiliar, weak odor, as well as its memorization as an olfactory object, require signal amplification in olfactory receptor neurons. This process may underlie the phenomenal tracking abilities of animals that follow odor trails.
DOI: 10.6084/m9.figshare.5311093.v1
title: Dataset for: Phagocytosis and Inflammation: Exploring the effects of the components of E-cigarette vapour on macrophages.

description: E-cigarettes are perceived as harmless; however, evidence of their safety is lacking. New data suggests E-cigarettes discharge a range of compounds capable of physiological damage to users. We previously established that cigarette smoke caused defective alveolar macrophage phagocytosis. The present study compared the effect E-cigarette of components; E-liquid flavours, nicotine, vegetable glycerine, and propylene glycol on phagocytosis, pro-inflammatory cytokine secretion, and phagocytic recognition molecule expression using differentiated THP-1 macrophages. Similar to CSE, phagocytosis of NTHi bacteria was significantly decreased by E-liquid flavouring (11.65-15.75%) vs. control (27.01%). Nicotine also decreased phagocytosis (15.26%). E-liquid, nicotine, and E-liquid + nicotine reduced phagocytic recognition molecules; SR-A1 and TLR-2. IL-8 secretion increased with flavour and nicotine, while TNFα, IL-1β, IL-6, MIP-1α, MIP-1β, and MCP-1 decreased after exposure to most flavours and nicotine. PG, VG, or PG:VG mix also induced a decrease in MIP-1α and MIP-1β. We conclude that E-cigarettes can cause macrophage phagocytic dysfunction, expression of phagocytic recognition receptors and cytokine secretion pathways. As such, E-cigarettes should be treated with caution by users, especially those who are non-smokers.
DOI: 10.6084/m9.figshare.5311087
title: Dataset for: Plasmalogen homeostasis: regulation of plasmalogen biosynthesis and its physiological consequence in mammals

description: Plasmalogens, mostly ethanolamine-containing alkenyl ether phospholipids, are a major sub-class of glycerophospholipids. Plasmalogen synthesis is initiated in peroxisomes and completed in endoplasmic reticulum. The absence of plasmalogens in several organs of peroxisome biogenesis-defective patients suggests that<i> de novo</i> synthesis of plasmalogens plays a pivotal role in the plasmalogen homeostasis in tissues. Plasmalogen synthesis is regulated by modulating the stability of fatty acyl-CoA reductase 1 on peroxisomal membrane, a rate-limiting enzyme in plasmalogen synthesis, by sensing plasmalogens in the inner leaflet of plasma membranes. Dysregulation of plasmalogen homeostasis impairs cholesterol biosynthesis by altering the stability of squalene monooxygenase, a key enzyme in the cholesterol biosynthesis, implying physiological consequences of plasmalogen homeostasis in cholesterol metabolism in cells and organs such as liver.
DOI: 10.6084/m9.figshare.5311105.v1
title: Dataset for: Recurrence-associated gene signature optimizes recurrence free survival prediction of colorectal cancer

description: High throughput gene expression profiling has showed great promise in providing insight into molecular mechanisms. Metastasis-related mRNAs may potentially enrich genes with the ability to predict cancer recurrence，therefore we attempted to build a recurrence-associated gene signature to improve prognostic prediction of colorectal cancer (CRC). We identified 2848 differentially expressed mRNAs by analyzing CRC tissues with or without metastasis. For the selection of prognostic genes, a LASSO Cox regression model was employed. Using this method, a 13-mRNA signature was identified and then validated in two independent Gene Expression Omnibus (GEO) cohorts. This classifier could successfully discriminate the high-risk patients in discovery cohort (HR = 5.27, 95%CI= 2.30-12.08, P &lt; 0.0001). Analysis in two independent cohorts yielded consistent results (GSE14333: HR=4.55, 95%CI=2.18 – 9.508, P&lt;0.0001) (GSE33113: HR=3.26, 95%CI=2.16 – 9.16, P=0.0176). Further analysis revealed that the prognostic value of this signature was independent of tumor stage, postoperative chemotherapy and somatic mutation. Receiver operating characteristic (ROC) analysis showed that the area under receiver operating characteristic curve (AUC) of this signature was 0.8861 and 0.8157 in the discovery and validation cohort, respectively. A nomogram was constructed for clinicians, which did well in the calibration plots. Furthermore, this 13-mRNA signature outperformed other known gene signatures, including oncotypeDX colon cancer assay. Single-sample gene-set enrichment analysis (ssGSEA) revealed that a group of pathways related to drug resistance, cancer metastasis and stemness were significantly enriched in the high-risk patients. In conclusion, this 13-mRNA signature may be a useful tool for prognostic evaluation and will facilitate personalized management of CRC patients.
DOI: 10.6084/m9.figshare.5311048
title: The Ewens-Watterson test for neutrality at 7 microsatellite loci in Spodoptera exigua

description: The Ewens-Watterson test for neutrality of microsatellite markers showed that F-value (sum of square of allelic frequency) lied outside the lower and upper limit of 95% confidence region of expected F value in 3 loci (Spe08, Spe10, Spe12) . According to results of Ewens-Watterson test for neutrality for markers, some loci were not neutral and may be linked with some selection traits. If a neutral allele statistically associated with a selected allele at another locus or genes where selection is operating significantly may be carried along and alleles cannot be separated from their genetic background. This phenomenon is known as hitchhiking. Genetic hitchhiking can be potent force in changing allelic frequency and heterozygosity (Kumar et al. 2009).
DOI: 10.6084/m9.figshare.5311087.v1
title: Dataset for: Plasmalogen homeostasis: regulation of plasmalogen biosynthesis and its physiological consequence in mammals

description: Plasmalogens, mostly ethanolamine-containing alkenyl ether phospholipids, are a major sub-class of glycerophospholipids. Plasmalogen synthesis is initiated in peroxisomes and completed in endoplasmic reticulum. The absence of plasmalogens in several organs of peroxisome biogenesis-defective patients suggests that<i> de novo</i> synthesis of plasmalogens plays a pivotal role in the plasmalogen homeostasis in tissues. Plasmalogen synthesis is regulated by modulating the stability of fatty acyl-CoA reductase 1 on peroxisomal membrane, a rate-limiting enzyme in plasmalogen synthesis, by sensing plasmalogens in the inner leaflet of plasma membranes. Dysregulation of plasmalogen homeostasis impairs cholesterol biosynthesis by altering the stability of squalene monooxygenase, a key enzyme in the cholesterol biosynthesis, implying physiological consequences of plasmalogen homeostasis in cholesterol metabolism in cells and organs such as liver.
DOI: 10.6084/m9.figshare.5311042
title: AMOVA of 7 tested geographic populations of Spodoptera exigua using 4 microsatellites loci.

description: Analysis of molecular variance (AMOVA) was performed using ARLEQUEIN version 3.11 (Excoffier et al. 2005). A two-part AMOVA analysis was conducted to check genetic divergence (FST) as a factor of variation between individuals within a given population and between populations. Molecular variance analysis showed significant variations among and within populations, 21 and 71 percent, respectively
DOI: 10.6084/m9.figshare.5311045
title: Distance genetic matrix (above diagonal) and population pairwise FST of 7 tested regions comparison by 4 microsatellites loci (below diagonal).

description: Genetic distance and pair-wise FST values between regions are shown in Table 5. The minimum genetic distance was found between the Moghan-Zarghan pair (0.116) and the maximum between the Esfahan-Sabzvar pair (0.722). Computed FST values ranged from 0.102 for the Kalposh-Miandoab to 0.349 for the Moghan-Esfahan. FST values were significant for all paired combinations (P &lt; 0.05).<br>
DOI: 10.6084/m9.figshare.5311036
title: Population-wise data on the number of individuals (Ni), total number of alleles (Na), mean number of alleles per locus (Nm), number of effective alleles (Ne), mean observed (Ho) and expected (He) heterozygosity and fixation index (F).

description: The most diverse regions (Table 3) were from Esfahan and Kalposh, showing the highest total number of alleles (TNA) and mean number of alleles (MNA). The least diverse region was Zarghan with the lowest TNA of 8, and lowest MNA of 2.000. Average observed and expected heterozygosity ranged from 0.013 to 0.137 and 0.376 to 0.573, respectively. The Esfahan and Sabzvar regions had the highest values of observed and expected heterozygosity; respectively, and the Zarghan region had the lowest values. Overall, there was good agreement between the estimates of observed average and expected heterozygosity for all regions except Zarghan that showed an overall heterozygosity deficiency.
DOI: 10.6084/m9.figshare.5311042.v1
title: AMOVA of 7 tested geographic populations of Spodoptera exigua using 7 microsatellites loci

description: Molecular variance analysis showed significant variations among and within populations, 19.91 and 70.42, respectively
DOI: 10.6084/m9.figshare.5311027
title: Locus-wise data on the number of alleles (Na), number of effective alleles (Ne), mean observed (Mean Ho) and expected (Mean He) heterozygosities, F statistics, and Hardy-Wienberg Equilibrium (HWE) obtained by analyzing seven populations of Spodoptera exigua.

description: Among four loci (Table 2), Spe09 had the highest number of alleles, whereas Spe06 had the lowest. Average observed and expected heterozygosities ranged from 0.007 to 0.172 and from 0.194 to 0.767, respectively. Locus Spe02 had the highest observed heterozygosity and locus Spe06 had the lowest observed heterozygosity. Loci Spe11 and Spe06 had the highest and lowest expected heterozygosity, respectively. The highest values of F<sub>is</sub> and F<sub>it</sub> were detected in Spe09 and the lowest on Spe02. F<sub>st </sub>values ranged from 0.123 to 0.346, detected in Spe06 and Spe02 loci, respectively. All four loci showed departures from the Hardy-Weinberg equilibrium.
DOI: 10.6084/m9.figshare.5311045.v1
title: Distance genetic matrix (above diagonal) and population pairwise FST of 7 tested regions comparison by 7 microsatellites loci (below diagonal)

description: Genetic distance and pair-wise FST values between regions are shown in Table 5. The minimum genetic distance was found between the Moghan-Miandoab pair (0.2436) and the maximum between the Moghan-Gonbad pair (0.6694). Computed FST values ranged from 0.1460 for the Kalposh-Miandoab to 0.2989 for the Zarghan-Esfahan. FST values were significant for all paired combinations (P &lt; 0.05).
DOI: 10.6084/m9.figshare.5311003
title: Characteristics of 4 microsatellites markers isolated by Kim et al (2012) used in the study

description: The propose of this study was to assess the genetic variability of seven populations of S. exigua collected from different locations of Iran by using four microsatellite markers developed by Kim et al. (2012).
DOI: 10.6084/m9.figshare.5311042.v3
title: AMOVA of 7 tested geographic populations of Spodoptera exigua using 4 microsatellites loci.

description: Analysis of molecular variance (AMOVA) was performed using ARLEQUEIN version 3.11 (Excoffier et al. 2005). A two-part AMOVA analysis was conducted to check genetic divergence (FST) as a factor of variation between individuals within a given population and between populations. Molecular variance analysis showed significant variations among and within populations, 21 and 71 percent, respectively
DOI: 10.6084/m9.figshare.5311042.v2
title: AMOVA of 7 tested geographic populations of Spodoptera exigua using 4 microsatellites loci.

description: Analysis of molecular variance (AMOVA) was performed using ARLEQUEIN version 3.11 (Excoffier et al. 2005). A two-part AMOVA analysis was conducted to check genetic divergence (FST) as a factor of variation between individuals within a given population and between populations. Molecular variance analysis showed significant variations among and within populations, 21 and 71 percent, respectively
DOI: 10.6084/m9.figshare.5310982
title: OSO Photophysiology

description: All concentrations are scaled to brine volume
DOI: 10.6084/m9.figshare.5311027.v1
title: Locus-wise data on the number of alleles (Na), number of effective alleles (Ne), mean observed (Mean Ho) and expected (Mean He) heterozygosities, F statistics, and Hardy-Wienberg Equilibrium (HWE) obtained by analyzing seven populations of Spodoptera exigua.

description: Among eight loci (Table 2), only locus Spe15 showed no scorable band, while other loci showed scorable bands for each DNA sample. Spe02 and Spe10 had the highest number of alleles, whereas Spe12 had the lowest. Average observed and expected heterozygosities ranged from 0.007 to 0.172 and from 0.193 to 0.813, respectively. Locus Spe02 had the highest observed heterozygosity and loci Spe06 and Spe09 had the lowest observed heterozygosity. Loci Spe10 and Spe06 had the highest and lowest expected heterozygosity, respectively. The highest values of F<sub>is</sub> and F<sub>it</sub> were detected in Spe09 and the lowest on Spe02. F<sub>st </sub>values ranged from 0.346 to 0.123, detected in Spe06 and Spe02 loci, respectively. Gene flow was low to moderate, from 0.470 to 1.771, were recorded respectively in Spe06 and Spe02 loci. All seven loci showed departures from the Hardy-Weinberg equilibrium.
DOI: 10.6084/m9.figshare.5310982.v1
title: OSO Photophysiology

description: All concentrations are scaled to brine volume
DOI: 10.6084/m9.figshare.5311003.v2
title: Characteristics of 4 microsatellites markers isolated by Kim et al (2012) used in the study

description: The propose of this study was to assess the genetic variability of seven populations of S. exigua collected from different locations of Iran by using four microsatellite markers developed by Kim et al. (2012).
DOI: 10.6084/m9.figshare.5311036.v1
title: Population-wise data on the number of individuals (Ni), total number of alleles (Na), mean number of alleles per locus (Nm), number of effective alleles (Ne), mean observed (Ho) and expected (He) heterozygosity and fixation index (F).

description: The most diverse regions (Table 3) were from Esfahan and Kalposh, showing the highest total number of alleles (TNA) and mean number of alleles (MNA). The least diverse region was Zarghan with the lowest TNA of 20, and lowest MNA of 2.857. Average observed and expected heterozygosity ranged from 0.075 to 0.127 and 0.483 to 0.606, respectively. The Kalposh region had the highest values of observed and expected heterozygosity, and the Zarghan region had the lowest values. Overall, there was good agreement between the estimates of observed average and expected heterozygosity for all regions except Zarghan that showed an overall heterozygosity deficiency
DOI: 10.6084/m9.figshare.5311003.v1
title: Characteristics of 8 microsatellites markers isolated by Kim et al (2012) used in the study

description: The propose of this study was to assess the genetic variability of seven populations of S. exigua collected from different locations of Iran by using eight microsatellite markers developed by Kim et al. (2012).
DOI: 10.15131/shef.data.12826076.v1
title: AI and robots in Higher Education: Eight design fictions

description: Eight design fictions that imagine the application of AI and robots to Higher Education (HE).<br>Based on a wide ranging literature review, the fictions instantiate the possibilities and controversies around AI and robots as applied in the university context, including teaching, administration and research.<br>The methods used to design this version of the fictions are described in the paper "The development of a collection of design fictions about Artificial Intelligence and robots in Higher Education" (https://doi.org/10.35542/osf.io/s2jc8) <br><br>Design fictions create a speculative space in which to raise questions about whether a particular technology is desirable, the socio-cultural assumptions built into technologies, the potential for different technologies to make different worlds, our relation to technology in general, indeed our role in making the future happen in general. <br><br>They can be used in research or teaching to elicit opinions about the future application of AI and robots to HE.<br>Fiction 1: AIDan, the teaching assistantFiction 2: FootbotballFiction 3: CriticalBot in conversationFiction 4: The intelligent campus appFiction 5: Research Management Suite TMFiction 6: Verbatim minutes of University AI project steering committee: AI implementation phase 3Fiction 7: DashboardsFiction 8: Minnie, the AI admin assistant<br>The project was funded by Society of Research into Higher Education - Research Scoping Award -SA1906. As such the fictions are the property of SRHE and deposited here by permission.<br>The research was approved by the University of Sheffield, Information School under ethics application 032657
DOI: 10.17632/hpjyhjvrvv.1
title: Computational modelling supports that Dengue virus envelope antibodies can bind to SARS-CoV-2 receptor binding sites: Is pre-exposure to dengue virus protective against COVID-19 severity?

description: Supplementary Data
DOI: 10.6084/m9.figshare.5309935
title: Data from: Dropping hints: estimating the diet of livestock in rangelands using DNA metabarcoding of faeces

description: Raw Illumina MiSeq paired-end read sequencing output in FASTQ format of 24 samples of sheep and goat feces from far western New South Wales, Australia. The reads have been de-multiplexed into 24 separate samples, with one file for each sequencing direction. Samples consist of mixed <i>rbcL</i> and ITS2 reads. Further information on each sample can be found in the key to localities spreadsheet.<br>
DOI: 10.6084/m9.figshare.5309935.v1
title: Data from: Dropping hints: estimating the diet of livestock in rangelands using DNA metabarcoding of faeces

description: Raw Illumina MiSeq paired-end read sequencing output in FASTQ format of 24 samples of sheep and goat feces from far western New South Wales, Australia. The reads have been de-multiplexed into 24 separate samples, with one file for each sequencing direction. Samples consist of mixed <i>rbcL</i> and ITS2 reads. Further information on each sample can be found in the key to localities spreadsheet.<br>