cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/8dyncfg3y8.1
title: Blood alternative splicing biomarker for infectious disease. Zhang et al.

description: Assays detecting blood transcriptome changes are being intensely studied for infectious disease diagnosis. Blood-based RNA alternative splicing events, which have not been well-characterized in pathogen infection, have potential normalization and assay platform stability advantages compared to gene expression for diagnosis. Here, we present a computational framework for developing robust alternative splicing diagnostic biomarkers. The framework analyzes patient whole-blood RNA sequencing (RNA-seq) data to identify and optimize alternative splicing biomarkers for diagnosing infectious disease. Leveraging a large prospective cohort of SARS-CoV-2 infection, we identify a major splicing program switch upon viral infection. Functional analysis reveals significant enrichment of differential splicing events in immune-specific protein domains and genes. Using test whole-blood RNA-seq data from an independent cohort, we demonstrate the superiority of alternative splicing biomarkers for SARS-CoV-2 diagnosis compared to six reported transcriptome signatures. We then optimize a subset of alternative splicing-based biomarkers to develop microfluidic PCR diagnostic assays for SARS-CoV-2 diagnosis. This assay achieves nearly perfect test accuracy (61/62=98.4%; positive percent agreement=96.7%, negative percent agreement=100%) using a naive principal component classifier, which was significantly more accurate than a gene expression PCR assay tested in the same cohort. Therefore, our RNA splicing computational framework enables a promising avenue for host response diagnosis of infection.
DOI: 10.17632/ms3365kb5p.1
title: A1-A4 (DHB vs 13C6-DHB) and B1-B20 (MALDI matrix screening)

description: Mass Spectrometry Imaging datasets of control mouse control sections prepared with DHB and 13C6-DHB (A1-A4) or different MALDI matrices (B1-B20) (Refer to original publication for further details).

General Metadata:
Mus musculus
Brain
TM sprayer
100 μm
100-1000
9.4T Solarix FTICR (Bruker)
Positive/Profile
DOI: 10.17632/gwx6t2mdwf.1
title: Prevalence of Escherichia coli Isolated from Oropharynx and Trachea of Clinically Sick Poultry and Antimicrobial Resistance Pattern of the Strains Isolated

description: Table 1: An overview of samples collected from 100 clinically sick chickens and isolation frequency of E. coli from their oropharyngeal and cloacal swab samples 
Table 2: Antibiotic resistance profiles of the E. coli isolates tested by Bauer-Kirby method
Table 3: Detection of oxytetracycline resistance genes from the resistant isolates
Table 4: Unconditional associations between isolation of E. coli from tracheal samples of poultry suffering from different clinical illness and the variables recorded during the collection of samples 
Table 5: Unconditional associations between isolation of E. coli from oropharyngeal samples of poultry suffering from different clinical illness and the variables recorded during the collection of samples 
Table 6: Unconditional associations between isolation of Escherichia coli from both tracheal and oropharyngeal samples of poultry suffering from different clinical illness and the variables recorded during the collection of samples 
Table 7: Multivariable logistic regression (initial model) for assessing the variables independently associated with the isolation of Escherichia coli from oropharyngeal samples of poultry suffering from different clinical illness 
Table 8: Concentrations and diffusion zone breakpoints for resistance against antibiotics standard for E. coli isolates (CLSI, 2011)
Table 9: Primers used to test tetracycline resistance genes
Figure 1: Map showing the locations of the areas from where the samples were referred
Figure 2: PCR products showing the tetA gene-sized amplicon (502 bp) of a representative number of isolates resistant to oxytetracycline
Figure 3: PCR products-band showing of the tetB gene-sized amplicon (930 bp) of a representative number of isolates resistant to oxytetracycline
Figure 4: PCR products-band showing of the tetC gene-sized amplicon (888 bp) of two isolates resistant to oxytetracycline
DOI: 10.17632/gwhrg7tcfp.1
title: Understanding ecosystem pressures, condition and marine macroinvertebrate ecosystem services in seagrasses and mangroves in a digital age: Case of Inhambane Bay, Mozambique

description: Marine macroinvertebrates (MMI) sustain high biodiversity, ecosystem functioning and multiple ecosystem services (ES), but they can be impacted by the pressures exerted on ecosystems and their condition. We assessed ecosystem pressures (habitat conversion, overexploitation and climate change) and condition (environmental quality and ecosystem attributes), and MMI ES (provisioning, regulation and maintenance, and cultural) in seagrasses and mangroves of the Inhambane bay (INB), Mozambique, using digital data from satellite, biodiversity platforms, natural history collections databases, scientific literature and fisheries national reports. The study revealed that both, seagrass and mangrove extents of the INB have increased significantly since 2016. The surface partial pressure CO2 and sea surface height above sea level (i.e., sea level anomalies), and surface pH have significantly increased and decreased respectively.  While sea surface temperature showed no significant annual variation, there was an increasing trend. Out of the seven environmental quality variables which showed a decline in concentrations (except PO4 increasing), only silicate, PO4 and phytoplankton concentrations in the bay showed significant annual varying trends. The biological condition of the bay shows that seagrasses present higher species richness and occurrences than mangroves. The MMI ES included the temporal assessment of food (provisioning); water quality regulation, hydrological flux, climate regulation, MMI as decomposition precursors, and habitat modification (regulation and maintenance); and recreation, stewardship and sense of belonging, scientific and traditional knowledge, and formal and informal education and training (cultural). MMI production has increased significantly, which parallels rising fishing efforts and indicates overexploitation that needs urgent attention. MMI regulation and maintenance, and cultural ES did not show significant trends overtime and they were probably underestimated due to data gaps. Notwithstanding, the study provided relevant data that can support future regulation and maintenance as well as cultural ES assessments and suggests a relation to the establishment of marine protected areas and MMI biodiversity. Conserving MMI and enhancing their ‘traditional’ use is key to their sustainable use. The results of this study contribute to the baseline information of the pressures and changes in condition of the INB which are potentially threatening to the MMI ES. It also revealed unexplored services of MMI in the INB, hence this study can be used to address issues on the unexplored MMI ES which can promote local economy.
DOI: 10.17632/hb74mbvrg9.1
title: Supplements for article "Blood profile and thyroid cancer"

description: Supplement 3. The blood biomarker list.
Supplement 4. The heatmap of all included variables.  Abbreviation: NA, not applicable.
Supplement 5. The results of biomarker difference using the Student t-test and the Mann–Whitney U-test.
DOI: 10.17632/n2bvxb9z7f.1
title:  A HD-Zip transcription factor specifies fates of multicellular trichomes via dosage-dependent mechanisms in tomato. Wu, etal, 2022.

description: The raw data of blot in this study (A HD-Zip transcription factor specifies fates of multicellular trichomes via dosage-dependent mechanisms in tomato).
DOI: 10.17632/tcc7hftfdy.1
title: Bifidobacterium infantis and 2’-Fucosyllactose supplementation in early life may have potential long-term benefits on gut microbiota, intestinal development, and immune function in mice

description: Bifidobacterium infantis and 2’-Fucosyllactose supplementation in early life may have potential long-term benefits on gut microbiota, intestinal development, and immune function in mice
DOI: 10.17632/gd4hc7ym7r.1
title: Fintech research: systematic mapping, classification, and future direction.

description: The data of primary studies for the paper: Fintech research: systematic mapping, classification, and future direction.
DOI: 10.17632/gd4hc7ym7r.2
title: Fintech research: systematic mapping, classification, and future direction.

description: The data of primary studies for the paper: Fintech research: systematic mapping, classification, and future direction.
DOI: 10.17632/b4sktt33bt.2
title: Content Analysis of Engineering College Library Website

description: Few are bibliometrics and few are survey based articles
DOI: 10.17632/7vpbj9m58j.1
title: Current and legacy effects of neighborhood communities on plant growth and aboveground herbivory

description: In a long-term grassland experiment (the experimental design can be found in van Der Putten et al., 2000; Bezemer et al., 2006 and Veen et al., 2018 ), we examined the relative importance of the current and legacy above- and belowground effects of plant communities on the growth and aboveground herbivore damage on a focal plant, Leucanthemum vulgare. Focal plants were planted into tubes with soil collected from different plant communities and placed back into these plant communities. Weekly, plant growth and damage were recorded and after 12 weeks plant biomass was measured. Sheet1: vegetation and soil characteristics of 15 plots in 2003; Sheet 2: Plant community composition data of 15 plots in 2003; Sheet 3: The focal plant dry biomass (shoot, root, and total dry mass). Sheet 4: Aboveground herbivory of focal plants.
DOI: 10.17632/prnhy5zt8m.1
title: Dimensional distribution and localization of amphiboles within human AECs

description: Dataset related to the paper "Dimensional distribution and localization of amphiboles within human alveolar epithelial cells"
DOI: 10.17632/bbnzj5np6z.1
title: This is the data and scripts for: The potential of biological control against Heterobasidion root rot is not realized in practical forestry

description: The raw data of stumps can be found in Data/Stump_data.xlsx Where: "Site" is site number, "Stump": Is the stump number, "Infection_area": Is the infected area, "No_colonies": Is the number of Heterobasidion colonies on the stump, "Coverage": Is the coverage of P. gigantea, "Area": Is the stump area.

The "Site" and "Stump corresponds to the values in the PCR datasheet.

The PCR data can be found in Data/PCR_data.xlsx Where: "Sample": Is the index for the samples, "Site" is the site number", "Stump": Is the stump number, the columns: "GH28", "GH28nest", "GH28 (redo)" and "GH28nest (redo)" are the different PCR repetitions, "Result": Is the outcome of the PCR, "Stump count": Is just a counter.

The workflow file maintains all steps needed to reproduce the result
DOI: 10.17632/jgnpbpbbx5.1
title: SVR-CLSM Code and Results for Wiesen, D., Bonilha, L., Rorden, C., Karnath, H.-O. Structural (Dis)Connectomics of spatial exploration and attention: a study of stroke patients with spatial neglect.
DOI: 10.17632/jgnpbpbbx5.2
title: SVR-CLSM Code and Results for Wiesen, D., Bonilha, L., Rorden, C., Karnath, H.-O. Disconnectomics to unravel the network underlying deficits of spatial exploration and attention.

description: SVR-CLSM Code and Results for Wiesen, D., Bonilha, L., Rorden, C., Karnath, H.-O. Disconnectomics to unravel the network underlying deficits of spatial exploration and attention.
DOI: 10.17632/4yx8vmt5fm.1
title: Survey questions and answers: a cross-sectional survey gauging the impact of COVID-19 on medical and biomedical graduates in the US and Sweden

description: Survey questions and unprocessed raw answers for two cross-sectional surveys on the impact of the COVID-19 pandemic on the education of medical and biomedical graduates based at US and Swedish universities.
This dataset relates to two manuscripts by the authors published at "BMC Medical Education" and "Biochemistry and Molecular Biology Education".
The survey was assessed by the Swedish Ethical Review Authority (Dnr 2021-00481) and the Institutional Review Board of the University of California San Diego (Project #201972XX), and found to be exempt by both. Participants provided informed consent to publication of the anonymous survey results and we followed the general principles and recommendations provided by the Helsinki Declaration and the Belmont Report. The dataset is from anonymous participants and does not contain any personally identifiable information.
DOI: 10.17632/69my4hnj2y.1
title: Exhaustive circulating tumor DNA sequencing reveals genomic landscape of Hodgkin lymphoma and facilitates ultrasensitive residual disease detection

description: Supplementary tables for manuscript: "Exhaustive circulating tumor DNA sequencing reveals genomic landscape of Hodgkin lymphoma and facilitates ultrasensitive residual disease detection"
DOI: 10.17632/cjj62tswb2.1
title: intra-specific genetic variability of African yam bean (Sphenostylis stenocarpa Hochst Ex. A. Rich) “Harms" based on rbcL gene marker

description: The data presents the rbcL gene sequences of twenty-four accessions of S. stenocarpa. Table 1 shows the passport data and country of origin of the accessions whileTable 2 explains the submitted sequences to the NCBI GenBank, the assigned GenBank numbers, matched organisms and the sequence length (bp). Single nucleotide polymorphic (SNP) of 13 variable sites are represented in Table 3 while codon usage parameters including codon bias index (CBI), scaled chi square and G+C contents of coding and non-coding position are shown in Table 4. Table 5 summarizes the codon usage and amino acid residues of the species. The estimates of genetic diversity and Maximum Likelihood of Transition/Transversion Bias are pointed out in Table 6 and 7.
DOI: 10.17632/jff3wn37m2.2
title: Dephosphorylation of the pre-initiation complex is critical for origin firing

description: Raw image files for the publication
DOI: 10.5281/zenodo.7458378
title: Particle yields configuration files for Mu2e-II target designs using Mu2e-II Offline in Geant4

description: Configuration files for the estimates of particle yields with potential Mu2e-II target designs using the Mu2e-II Offline and Geant4 MC.
description: The work is related to Fermilab LDRD "Pion-production target conceptual studies for Mu2e-II" (FNAL-LDRD-2020-020)
DOI: 10.5281/zenodo.7458377
title: Particle yields configuration files for Mu2e-II target designs using Mu2e-II Offline in Geant4

description: Configuration files for the estimates of particle yields with potential Mu2e-II target designs using the Mu2e-II Offline and Geant4 MC.
description: The work is related to Fermilab LDRD "Pion-production target conceptual studies for Mu2e-II" (FNAL-LDRD-2020-020)
DOI: 10.17632/nkmdb4n3m5.1
title: EDS Data for Duct Tape Adhesives and Tape Edge Specimens

description: These are datasets of SEM/EDS results obtained in the research project, "Analysis of Small Particles Adhering to the Edges of Duct Tape as a Means to Make Associations in a Way that is Independent of Manufactured Characteristics." The project was supported in part by Award No. 2020-MU-CX-0018 awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice. The opinions, findings, and conclusions or recommendations expressed are those of the authors and do not necessarily reflect those of the Department of Justice.

The data were collected to help determine if very small particles (VSP), acquired post-manufacture and trapped in the adhesive along the edges of duct tape rolls, can discriminate among tape segments from different rolls and provide a quantitative association between segments from the same roll.

The datasets have comma separated values files (.csv) that contain data in fields generated by Thermo Fisher Scientific Explorer 4 Analyzer SEM-EDS system using the Automated Feature Analysis (AFA) program within the Thermo Fisher Scientific Corporation Perception 5 software. Analysis is performed under low vacuum conditions (0.075 torr) utilizing a 20.0 kV accelerating voltage, backscatter electron detector (BSED), working distance of approximately 9.5 mm, a spot size of approximately 56% and a magnification of 1,200X.  EDS results are based on analysis of x-rays attributable to any of the 18 elements Na, Mg, Al, Si, P, S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu and Zn. EDS Copper and Aluminum calibration checks are performed before each analytical run and during the run at the beginning of each specimen. 

Procedures described below resulted in 9 specimens for each of 30 duct tape rolls: 3 Adhesive Filler Particle specimens (3 stubs prepared from one adhesive swabbing) and 6 Tape Edge Particle specimens (left and right sides of each of the three  tape Segments). 32 process control specimens were also collected (one for each Roll during its sampling process, plus two additional specimens for make-up samplings of a fourth Segment). Adhesive specimens for Roll 103, for example, are designated as 103AFA, 103AFB and 103AFC.  Left and Right sides of Segment 2 of Roll 103 are designated, for example, as 1032L and 1032R. The Process Control Particle specimens applicable to the sampling of the 3 Segments from Roll 103 is designated, for example, as 103FC. Process Control Specimen S41FC is applicable to Tape Edge Particle Specimens 1164L, 1164R, 1284L, 1284R, 1324L and 1324R, whereas Process Control Specimen S42FC is applicable to Tape Edge Particle Specimens 1114L and 1114R.  The spreadsheets contain data on up to 5000 particles for analytical runs of up to 4 hours. For each particle there are entries under column headings as described in the attached file: Column Headings in .csv Files of Particle Datasets.
DOI: 10.5281/zenodo.7451837
title: Particle yields for Mu2e-II target designs

description: Simulated negative muon and pion yields from Mu2e-II target designs.
description: The work is related to Fermilab LDRD "Pion-production target conceptual studies for Mu2e-II" (FNAL-LDRD-2020-020)
DOI: 10.5281/zenodo.7451836
title: Particle yields for Mu2e-II target designs

description: Simulated negative muon and pion yields from Mu2e-II target designs.
description: The work is related to Fermilab LDRD "Pion-production target conceptual studies for Mu2e-II" (FNAL-LDRD-2020-020)
DOI: 10.17632/m5hzy3dbkc.1
title: Ambient noise tomography in south China using a nodal seismic array 

description: Shear wavespeed model in the upper crust in the central Nanling metallogenic belt derived from ambient noise tomography. The data set consists of the wavespeed model and the dispersion measurements:

SouthChina_Fankou_Vs.dat
1st column: Longitude in decimal degrees
2nd column: Latitude in decimal degrees
3rd column: Depth (below surface) in kilometers
4th column: Shear wavespeed
DOI: 10.17632/8jdrwtnrwv.1
title: VACUUM

description: Raw data for beam characterization measurements and plasma diagnostics
DOI: 10.17632/gtwprdjsvv.1
title: Mimickers of Monkeypox

description: Supplementary figure 1
Diseases presenting as outbreaks of blistering exanthems A) Monkeypox- pustular, targetoid, centrally crusted lesions at genital and peri-genital area B) Chickenpox- superficial ‘dewdrop on rose petal’ blisters C) Gianotti-Crosti syndrome- papulo-vesicles at knee D) Hand foot mouth disease- lesions over hands and feet E) Hand foot mouth disease- targetoid, centrally crusted and umbilicated lesions over buttocks F) Hand foot mouth disease- oral erosions.

Supplementary figure 2
Genital diseases which can be confused with monkeypox A) Solid papule of molluscum contagiosum at glans, which can be mistaken for a vesicle B) Umbilicated perianal papules of molluscum contagiosum in a child C) Circular and polycyclic erosions of genital herpes D) Excoriated papules of scabies at genitals, which can be mistaken for papulo-vesicles E) Multiple painless elevated and indurated primary syphilitic chancres F) Fixed drug eruption at shaft of penis presenting as painful dusky erythematous edematous plaque with a small erosion.
DOI: 10.17632/2drjzz8vpg.1
title: Supplementary Methods for Juvenile Idiopathic Arthritis in Children and Adolescents with Atopic Dermatitis: a Finnish Nationwide Registry Study

description: Supplementary Methods
DOI: 10.17632/9hksh8srdh.1
title: Execution time of double-precision and high-precision SYRk implementations on Intel Core i5-7500 and NVIDIA Turing RTX 2080

description: This dataset contains the execution time for symmetric rank-k update kernels (SYRk, BLAS Level 3) implemented using existing double-precision linear algebra software as well as multiple-precision libraries for CPU and GPU. The operation is  C = α * op(A) * op(A^T) + β * C, where α and β are scalars, C is a symmetric matrix, A is a general matrix, and op(A) is one of op(A) = A or op(A) = A^T. Here op(A) is N-by-K. Each raw file provided contains the results of three test runs in milliseconds. The complete source code for the tests can be found at https://github.com/kisupov/mpres-blas.

Common experiment settings:
• Dense, random, 1000-by-1000 matrices A and C;
• Only the upper triangular part of matrix C was used;
• Random scalars α and β;
• Measurements are in milliseconds;
• Arithmetic precision from 106 to 424 bits.

Test cases considered:
• Non transposed: op(A) = A, op(A^T) = A^T;
• Transposed: op(A) = A^T, op(A^T) = A.

Experimental environment:
• Intel Core i5 7500 processor;
• 32GB of DDR4 system memory;
• NVIDIA Turing RTX 2080 GPU (2944 CUDA Cores, Compute Capability 7.5, 8GB of GDDR6 memory);
• Ubuntu 20.04.5 LTS;
• NVIDIA Driver V455.32.00;
• CUDA Toolkit V11.1.

The following SYRk implementations are evaluated:
• OpenBLAS (OpenMP, 53 bits) – double-precision implementation for CPU using OpenBLAS (https://github.com/xianyi/OpenBLAS);
• Custom double on CPU (OpenMP, 53 bits) – custom double-precision parallel (OpenMP) implementation;
• MPFR (OpenMP) – multiple-precision parallel implementation using the GNU MPFR Library for CPU (https://www.mpfr.org/);
• cuBLAS (53 bits) – double-precision implementation for CUDA using the NVIDIA Basic Linear Algebra Subroutines library (https://docs.nvidia.com/cuda/cublas/index.html);
• Custom double on GPU (53 bits) – custom double-precision CUDA implementation;
• MPRES-BLAS – multiple-precision CUDA implementation using MPRES-BLAS library (https://github.com/kisupov/mpres-blas);
• CAMPARY – multiple-precision CUDA implementation using CAMPARY library (https://homepages.laas.fr/mmjoldes/campary/).
DOI: 10.17632/bf7crz6mvk.1
title: Data of "Effect of mindfulness-based interventions on people with prehypertension or hypertension：A systematic review and meta-analysis of randomized controlled trials"

description: The raw data were extracted from the included studies and analyzed for meta-analysis. The data show the mean and standard deviations (SD) of systolic blood pressure, diastolic blood pressure, anxiety, depression and perceived stress of intervention groups and control groups pre-intervention and post-intervetion. And tha data also show the mean change values of mean  and standard deviations.
DOI: 10.17632/bf7crz6mvk.2
title: Data of "Effect of mindfulness-based interventions on people with prehypertension or hypertension：A systematic review and meta-analysis of randomized controlled trials"

description: The raw data were extracted from the included studies and analyzed for meta-analysis. The data show the mean and standard deviations (SD) of systolic blood pressure, diastolic blood pressure, anxiety, depression and perceived stress of intervention groups and control groups pre-intervention and post-intervetion. And tha data also show the mean change values of mean  and standard deviations.
DOI: 10.17632/h9kk9cgjzk.1
title: Metastatic melanoma patients with a late complete response to immunotherapy exhibit different microbiome and dietary habits compared to early responders

description: Dietary characteristics of patients