cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21336/gen.c4k3-4j06
title: ACTRIS Cloud Remote Sensing Data during the COVID-19 pandemic

description: This dataset contains ACTRIS/Cloudnet cloud profilling observations obtained from 12 stations during the January- May 2020 period. The data are archived and accessible from the cloud profiling database hosted by the Finnish Meteorological Institute (FMI) (https://cloudnet.fmi.fi).
DOI: 10.6084/m9.figshare.13065986.v19
title: Gastric cancer lymph node data set

description: This is a dataset of pathological lymph nodes for gastric cancer. It can be used to test a gastric cancer lymph node metastasis detection model proposed in "Predicting gastric cancer outcome from resected lymph node histopathology images using deep learning".<br>
DOI: 10.5281/zenodo.4303823
title: Gluten content in products

description: Evaluation of gluten content in various, also cereal, products.
DOI: 10.5281/zenodo.4303822
title: Gluten content in products

description: Evaluation of gluten content in various, also cereal, products.
DOI: 10.5281/zenodo.4303796
title: Supplyment of Paper

description: This is the supplyment data for our paper.
DOI: 10.5281/zenodo.4303795
title: Supplyment of Paper

description: This is the supplyment data for our paper.
DOI: 10.17632/fhww2x8yy6.2
title: Diagnosis of gamma/delta mycosis fungoides requires longitudinal clinical observation

description: ST1: Abbreviations: mo, months; HTN, hypertension; C, Caucasian; LE, lower extremity; UE, upper extremity; CR, complete remission; PR, partial response; AWD, alive with disease; DOD, died of disease; IFN, Interferon-α-2a; Bex, bexarotene; Gem, gemcitabine; PUVA, psoralen (P) and ultraviolet A (UVA); NB-UVB, narrow band-ultraviolet B; BMT, bone marrow transplant. TNMB classifications and disease stages were based on the 2007 staging guidelines defined by the International Society of Cutaneous Lymphomas and the European Organisation for Research and Treatment of Cancer Cutaneous Lymphoma Task Force. ST2: lymphoid cells as positive if &gt; 50% of cells showed staining, focally positive if 10-50% (+/-) of cells showed staining, and negative if &lt;10% of cells showed staining. For CD2, CD5, and CD7, results were defined as preserved expression if &gt;50% of cells were positive, and partial/subtotal loss of expression if &lt;50% (+/-) of cells were positive. Molecular pathology results of T-cell receptor (TCR) gene rearrangement, including TCRγ and TCR𝛽 were a part of the routine workup and were retrieved from the medical records. The first row of Case 4 refers to the plaques and the second row to the tumours. EBER, EBV-encoded RNA; GB, granzyme B; TIA-1, T-cell intracellular antigen-1; TCR, T-cell receptor. SF1: A-B) Case 1 presenting with a ~ 5 cm confluent reddish-brown annular patch with overlying scale on the right lower abdomen and right flank. C-F) Case 2 initial cutaneous lesions exhibiting variable sized reddish brown annular patches and plaques with overlying scale to the trunk and left axillary region. F) Case 2 demonstrating stage progression with a dark red multi-lobed tumours with overlying scale involving the right nasal sidewall. G-H) Case 3 initially demonstrating erythematous scaly patches and plaques symmetrically on the trunk and proximal lower extremities and. I-J) Case 4 initially manifesting erythematous scaly patches and plaques on the trunk and upper extremities (E), and subsequently developing ulcerating tumours on the right plantar SF2: A) H&E reveals an atypical lymphoid infiltrate within the epidermis and reactive superficial dermal infiltrate. The epidermotropic lymphoma cells are small-to-medium size with perinuclear halos and hyperchromatic nuclei. Intraepidermal T-cells are negative for CD4 (B), CD8 (C), and Beta-F1 (D). Reactive superficial dermal infiltrate stains positive for Beta-F1 and CD4. Epidermotropic lymphoid cells strongly express TCR-δ (E) and cytotoxic marker TIA (F). G) H&E, atypical lymphoid infiltrate indistinguishable from that or early-stage MF and 2019 biopsy. A reactive superficial dermal infiltrate is noted. H) Epidermotropic lymphoid cells are positive for T-cell marker, CD3, show scant CD4 expression (I) and negative CD8 expression (J).
DOI: 10.17632/rwbyk5hprm.1
title: Autistic traits as a potential confounding factor in the relationship between schizotypy and conspiracy beliefs

description: This is the data set associated with the submission "Autistic traits as a potential confounding factor in the relationship between schizotypy and conspiracy beliefs".
DOI: 10.17632/rgnr6srkkh.1
title: Data for: Redox architecture at the Devonian–Carboniferous transition in South China and its implications for the biotic crisis

description: Isotope geochemical data
DOI: 10.17632/sdkg5xfvkx.1
title: MOLECULAR-CELL-D-20-01167_Revised Manuscript 12-2-2020

description: Supporting data for revised manuscript MOLECULAR-CELL-D-20-01167, Sadras et al.
DOI: 10.17632/nrvwdyysv9.1
title: Bank credit, micro finance and female ownership

description: We utilise firm level data from Enterprise surveys from the World Bank (see http://www.enterprisesurveys.org). These surveys encompass a representative random sample of firms with data collected across the world by using the same core questionnaire and the same sampling method. Surveys use a stratified random sampling technique. Our study sample includes unlisted firms from 22 countries in 2017 and 2018. Overall, we find some evidence for the existence of a gender gap in the credit market. Our finding supports the argument that, in this context, microfinance is an effective tool for promoting women's empowerment.
DOI: 10.17632/dwy8tmvywm.1
title: Data from eukaryote-conserved histone post-translational modification landscape in Giardia duodenalis revealed by mass spectrometry

description: Diarrheal disease caused by Giardia duodenalis is highly prevalent, causing over 200 million cases globally each year. The processes that drive parasite virulence, host immune evasion and transmission involve coordinated gene expression and have been linked to epigenetic regulation. Epigenetic regulatory systems are eukaryote-conserved, including in deep branching excavates such as Giardia, with several studies already implicating histone post-translational modifications (PTMs) in regulation of its pathogenesis and life cycle. However, further insights into Giardia chromatin dynamics have been hindered by a lack of site-specific knowledge of histone modifications. Using mass spectrometry, we have provided the first known molecular map of histone methylation, acetylation and phosphorylation modifications in Giardia core histones. We have identified over 50 previously unreported histone modifications including sites with established roles in epigenetic regulation, and co-occurring modifications indicative of PTM crosstalk. These demonstrate conserved histone modifications in Giardia which are equivalent to many other eukaryotes, and suggest that similar epigenetic mechanisms are in place in this parasite. Further, we used sequence, domain and structural homology to annotate putative histone enzyme networks in Giardia, highlighting representative chromatin modifiers which appear sufficient for identified sites, particularly those from H3 and H4 variants. This study is to our knowledge the first and most comprehensive, complete and accurate view of Giardia histone PTMs to date, and a substantial step towards understanding their associations in parasite development and virulence.
DOI: 10.17632/8b7v9rdjwt.3
title: JSLE and healthy control metabolomics
DOI: 10.5519/9x0wq4pn
title: List of publications with NHM fossil sponges

description: The NHM Porifera Collection contains almost 3000 referenced individuals as hand specimens and thin sections. From these, more than 2000 are figured and the rest are cited in more than 140 bibliographic references, inlcuding numerus types
DOI: 10.17632/t5ryx5mk2k.1
title: Transcriptome analysis of Pedobacter lusitanus NL19 grown in TSB and PC culture media

description: We report the application of RNA-seq metodology to analyze the differentially expressed genes (DEGs) of Pedobacter lusitanus NL19 grown in two different culture media, TSB and PC, characterized to contain high and low concentration of peptone from casein (PC), respectively. Broth with higher concentrations of PC has been previously associated with the abolishment of antibiotic production by P. lusitanus NL19. RNA-seq results showed that P. lusitanus NL19 grown in TSB and in PC generated 22 783 626 and 43 625 972 sequence reads, respectively. For gene expression analysis, 96,67% and 96,53% of the total fragments obtained for TSB and PC, respectively, were successfully mapped against P. lusitanus NL19 reference genome which allowed the identification of a total of 261 DEGs. More specifically, 108 genes were upregulated when NL19 was grown in TSB compared with its growth in PC, whereas 153 were downregulated. The biological function of most of these DEGs (53,7%) could not be predicted. For the others, genes involved in molecular functions and encoding cellular components were mostly upregulated and genes encoding biological processes were mostly downregulated. In general this study provided some insights on the main cellular pathways that are shaped in the presence of different concentrations of PC in P. lusitanus NL19, showing that high concentrations of PC strongly downregulates the de novo biosynthesis of biotin and the transcription of genes required for pedopeptin’s production, including a L-Dap biosynthetic operon. On the other hand, it increases the transcription of MFS efflux pumps and iron-uptake systems.
DOI: 10.17632/352fgv8x99.1
title: Kychygina et al.

description: Cells used in RT experiment: Ctrl (non-transduced HDF) - black RT profiles Lamin A (HDF EGFP-Lamin A) - grey RT profiles Progerin (HDF EGFP-Progerin) - red RT profiles
DOI: 10.17632/x22n4y8s33.2
title: Phase Separation-mediated Condensation of Whirlin-Myo15-Eps8 Stereocilia Tip Complex

description: Raw imaging data for Lin et al Phase Separation-mediated Condensation of Whirlin-Myo15-Eps8 Stereocilia Tip Complex.
DOI: 10.17632/5phjgcvtjh.1
title: Malvan Marine Sanctuary coral and benthic cover data

description: Percent composition data of dominant benthic characteristics of the Malvan Marine Sanctuary
DOI: 10.17632/yymcmw4hhm.1
title: GC data of volatile organic compounds during enzymolysis and other data

description: The data includes three parts: 1. Formula of E-tongue standard solution. This was used to track the changes of taste by E-tongue. 2. Free amino acids content and composition in different samples. This was used to compare the enzymatic hydrolysis results of three enzymes. 3. GC data of volatile organic compounds during enzymolysis of three enzymes. This was used for flavor analysis during enzymolysis.
DOI: 10.17632/kfprktxj2y.1
title: Mangrove soil organic carbon in Red River Delta, Vietnam

description: mangrove soil organic carbon (SOC) contents in the Red River Delta, Vietnam, and remote sensing datasets derived from Sentinel-1, Sentinel-2, and ALOS-2 PALSAR-2 in a total of 85 soil cores.
DOI: 10.5519/qd.z1dt57fr
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.6084/m9.figshare.13325360
title: Supplementary Material for: Mucosa-Associated Microbiota in Patients with Irritable Bowel Syndrome: A Comparison of Subtypes

description: <b><i>Background:</i></b> Most studies on gut microbiome of irritable bowel syndrome (IBS) have focused on fecal microbiota, instead of mucosa-associated microbiota (MAM). <b><i>Aims:</i></b> The aim of this study wasto investigate the MAM in IBS patients including the difference in subtypes of IBS, namely, diarrhea-predominant IBS (IBS-D) and constipation-predominant IBS (IBS-C). <b><i>Methods:</i></b> Endoscopic brush samples were taken from terminal ileum and sigmoid colon of patients with IBS (17 IBS-D patients and 7 IBS-C patients) and 10 healthy controls. The MAM of samples was profiled by 16S rRNA gene amplicon sequencing. Potential changes in the MAM at the functional level were evaluated using PICRUSt software and the KEGG database. <b><i>Results:</i></b> There were no differences <i>in MAM composition between terminal</i> ileum and sigmoid colon according to β-diversity based on the UniFrac distance. In view of α-diversity, Shannon (evenness) but not Chao1 (richness) or observed operational taxonomic units tended to be lower in sigmoid colon MAM of IBS-C and IBS-D than the control group. The abundance of 4 genera in the sigmoid colon and 7 genera in the terminal ileum was significantly different among the 3 groups. Linear discriminant analysis effect size (LEfSe) showed that the genera of <i>Ruminococcus</i>, <i>Akkermansia</i>, <i>Butyrivibrio</i>, <i>Methylobacterium</i>, and <i>Microbacterium</i> and the family Erysipelotrichaceae were significantly higher in the IBS-C group, and the abundance of the genera <i>Streptococcus</i>, <i>Acidaminococcus</i>, <i>Butyricicoccus</i>, and <i>Parvimonas</i> was significantly higher in the IBS-D group. In addition, the proportion of genes responsible for the secretion system and LPS biosynthesis was significantly higher and that for methane metabolism, lysine biosynthesis, and enzyme families was significantly lower in the IBS-D group than in the IBS-C group. <b><i>Conclusion:</i></b> Dysbiosis pattern and the function of the microbiome seem to be different among subtypes of IBS, and MAM may play a crucial role in IBS symptom generation.
DOI: 10.6084/m9.figshare.13325360.v1
title: Supplementary Material for: Mucosa-Associated Microbiota in Patients with Irritable Bowel Syndrome: A Comparison of Subtypes

description: <b><i>Background:</i></b> Most studies on gut microbiome of irritable bowel syndrome (IBS) have focused on fecal microbiota, instead of mucosa-associated microbiota (MAM). <b><i>Aims:</i></b> The aim of this study wasto investigate the MAM in IBS patients including the difference in subtypes of IBS, namely, diarrhea-predominant IBS (IBS-D) and constipation-predominant IBS (IBS-C). <b><i>Methods:</i></b> Endoscopic brush samples were taken from terminal ileum and sigmoid colon of patients with IBS (17 IBS-D patients and 7 IBS-C patients) and 10 healthy controls. The MAM of samples was profiled by 16S rRNA gene amplicon sequencing. Potential changes in the MAM at the functional level were evaluated using PICRUSt software and the KEGG database. <b><i>Results:</i></b> There were no differences <i>in MAM composition between terminal</i> ileum and sigmoid colon according to β-diversity based on the UniFrac distance. In view of α-diversity, Shannon (evenness) but not Chao1 (richness) or observed operational taxonomic units tended to be lower in sigmoid colon MAM of IBS-C and IBS-D than the control group. The abundance of 4 genera in the sigmoid colon and 7 genera in the terminal ileum was significantly different among the 3 groups. Linear discriminant analysis effect size (LEfSe) showed that the genera of <i>Ruminococcus</i>, <i>Akkermansia</i>, <i>Butyrivibrio</i>, <i>Methylobacterium</i>, and <i>Microbacterium</i> and the family Erysipelotrichaceae were significantly higher in the IBS-C group, and the abundance of the genera <i>Streptococcus</i>, <i>Acidaminococcus</i>, <i>Butyricicoccus</i>, and <i>Parvimonas</i> was significantly higher in the IBS-D group. In addition, the proportion of genes responsible for the secretion system and LPS biosynthesis was significantly higher and that for methane metabolism, lysine biosynthesis, and enzyme families was significantly lower in the IBS-D group than in the IBS-C group. <b><i>Conclusion:</i></b> Dysbiosis pattern and the function of the microbiome seem to be different among subtypes of IBS, and MAM may play a crucial role in IBS symptom generation.
DOI: 10.17632/2r2r9484gp.1
title: TMEM41B is a pan-flavivirus host factor. Hoffmann et al.

description: Table S1_oligos
DOI: 10.25919/rmzw-c912
title: Parkes observations for project P1014 semester 2020APRS_06

description: The spatial distribution of neutral gas is important for understanding the interstellar medium (ISM), its evolution, and star formation. However, the distribution of Tiny Scale Atomic Structures (TSAS), especially the extremely small scale structures with spatial scales ranging from a few to hundreds of AU is largely unexplored. The formation and evolution of TSAS are still unknown. Multi-epoch observations of HI absorption against pulsars are a tested, practical observational method to probe the TSAS. Based on our observations in the 2019 APRS semester, we successfully processed baseband data and detected the HI absorption variation at over 4-months towards B1557-50. PSR B1451-68 is another ideal source to trace the TSAS because of the intervening cold gas. We thus propose one-epoch observation towards B1557-50 which should be as early in the semester as possible, and two-epoch observations towards B1451-68 to be separated by about 5 months, for monitoring the HI absorption variations and probing structures on a range of scales. This will better constrain the characteristics of variations in HI absorption, thus contribute significantly to understanding the origin of TSAS.
DOI: 10.25919/sjth-7715
title: Parkes observations for project P456 semester 2020APRS_17

description: The Parkes Pulsar Timing Array (PPTA) project has three primary goals: (a) detection of gravitational waves from astronomical sources, (b) establishment of a pulsar timescale, and (c) improvement of our understanding of Solar-system dynamics. The PPTA is the oldest of three international pulsar timing groups. We have the smallest telescope and the smallest group, but the best measurements and the best results. Our bound on the strength of the incoherent gravitational wave background is the only bound which significantly constrains theoretical models. We have maintained our leading position because: we have the southern sky; we have a small but well-focussed group; we have the best-calibrated receivers; and we have been able to observe with an almost regular cadence of 15 to 20 days over a wide bandwidth. With this proposal we aim to maintain our pre-eminent position in the field. Unlike most observing proposals, this is a continuing proposal for which the observations will continue to improve bounds on ultra-low-frequency gravitational waves until they are finally detected. Continued Parkes observations will remain valuable at least until the first stage of the SKA is able to improve on our sensitivity and observing cadence. Even after the gravitational wave background is detected we will want to continue observations in support of the nascent field of gravitational wave astronomy!
DOI: 10.25919/053r-e176
title: Parkes observations for project P1021 semester 2020APRS_11

description: We propose to continue our observations of PSR J1653-45, a 951-ms pulsar in a long, 1.5-yr orbit. Binary pulsars are valuable objects of scientific study, allowing for a wide range of applications, including tests of gravity, probes of the neutron star equation of state, and fossil records of stellar evolution. Long spin-period pulsars in binary systems are generally much rarer than faster-spinning `recycled’ pulsars, and represent an under-explored region of pulsar binary evolution. In addition to its long orbital period, PSR J1653-45 also experiences extended eclipses, lasting up to half of the orbital period and whose nature is not well understood. These eclipses have also prevented the determination of an orbital or phase-connected timing solution, both vital steps in allowing for the continued study of this system. We propose a targeted, high-cadence observing campaign designed to monitor this pulsar as it transitions out of its eclipsing state. The campaign has the twin goals of both monitoring how the eclipse affects the pulsar’s emission properties, thereby revealed more about the nature of the eclipses themselves, and of extracting as much information regarding the pulsar’s orbit during its least-explored regions, thereby constrained and hopefully solving the pulsar’s orbit and ideally leading to the development of a timing solution. In both instances, we hope to gain a greater understanding of this pulsar’s properties and how it fits into this under-explored class of unrecycled pulsar binaries.
DOI: 10.25919/e20w-qe53
title: Parkes observations for project P1041 semester 2020APRS_25

description: We recently discovered five millisecond pulsars (MSPs) in the globular cluster Omega Centauri. This is the first pulsar discovery in this globular cluster. Four of these pulsars are isolated with spin periods of 4.1, 4.2, 4.6 and 6.8ms. The fifth has a spin period of 4.8ms and is in an eclipsing binary system with an orbital period of 2.1 hours. We propose to carry out a timing campaign of these new pulsars in order to study the dynamics in the core of Omega Centauri, to reveal the origin of Gamma-ray emission from the core, and to probe the ionised interstellar medium in Omega Centauri. Our proposed observations will also enable us to carry out deeper searches of pulsars in the cluster.
DOI: 10.25919/gcv7-g609
title: Parkes observations for project P885 semester 2020APRS_21

description: We propose to observe the magnetars 1E 1547.0-5408 and PSR J1622-4950 approximately weekly, to track their rotation, flux density, and polarisation, as we have long been doing through this project. The revolutionary UWL capabilities promise new opportunities to disentangle still mysterious radio emission mechanisms in magnetars. This promise is supported by the recent follow up of XTE J1810-197, again a radio magnetar after 10 years dormant, for which our observations with the UWL receiver are providing unique and tantalizing measurements of its radio spectrum and polarisation.
DOI: 10.25919/vhc1-jb37
title: Parkes observations for project P1038 semester 2020APRS_22

description: PSR~J1759-2402 is one of a small handful of pulsars which are in orbit about high mass stars. Its orbital period is 8.2 years and the orbit is highly eccentric with periastron expected in 2021 January. Although discovered at Parkes, the Lovell telescope has been monitoring the pulsar over many years. However, it's restricted bandwidth and lack of polarization capability make it unsuitable to follow the pulsar as it enters and leaves the eclipse by the companion. In contrast, the UWL on Parkes with its wide-band and excellent polarization characteristics means that we can determine scattering, polarization, dispersion measure and rotation measure changes as the pulsar enters its companion wind. We request weekly observations of the pulsar to track its progress around the orbit.