cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5522/04/19175153
title: Culture-Free Enumeration of Mycobacterium tuberculosis in Mouse Tissues Using the Molecular Bacterial Load Assay for Preclinical Drug Development: Source Data

description: The turnaround times for phenotypic tests used to monitor the bacterial load of <i>Mycobacterium tuberculosis</i>, in both clinical and preclinical studies, are delayed by the organism’s slow growth in culture media. The existence of differentially culturable populations of <i>M.</i> <i>tuberculosis</i> may result in an underestimate of the true number. Moreover, culture methods are susceptible to contamination resulting in loss of critical data points. We report the adaptation of our robust, culture-free assay utilising 16S ribosomal RNA, developed for sputum, to enumerate the number of bacteria present in animal tissues as a tool to improve the read-outs in preclinical drug efficacy studies. Initial assay adaptation was performed using naïve mouse lungs spiked with known quantities of <i>M. tuberculosis</i> and an internal RNA control. Tissues were homogenised, total RNA extracted, and enumeration performed using RT-qPCR. We then evaluated the utility of the assay, in comparison to bacterial counts estimated using growth assays on solid and liquid media, to accurately inform bacterial load in tissues from <i>M. tuberculosis</i>-infected mice before and during treatment with a panel of drug combinations. When tested on lung tissues derived from infected mice, the MBL assay produced comparable results to the bacterial counts in solid culture (colony forming units: CFU). Notably, under specific drug treatments, the MBL assay was able to detect a significantly higher number of <i>M. tuberculosis</i> compared to CFU, likely indicating the presence of bacteria that were unable to produce colonies in solid-based culture. Additionally, growth recovery in liquid media using the most probable number (MPN) assay was able to account for the discrepancy between the MBL assay and CFU number, suggesting that the MBL assay detects differentially culturable sub-populations of <i>M. tuberculosis</i>. The MBL can enumerate the bacterial load in animal tissues in real time without the need to wait for extended periods for cultures to grow. The readout correlates well with CFUs. Importantly, we have shown that the MBL is able to measure specific populations of bacteria not cultured on solid agar. The adaptation of this assay for preclinical studies has the potential to decrease the readout time of data acquisition from animal experiments and could represent a valuable tool for tuberculosis drug discovery and development.<br> This dataset contains all the data that were collected as part of this project. These data include the cycle thresholds (Cq) from real time quantitative PCR reactions of the internal control RNA and the <i>M. tuberculosis</i>-specific 16S rRNA derived either from spiked naïve mouse tissues or infected animals with <i>M. tuberculosis</i>. Molecular bacterial load values are compared with Colony Forming Units from solid agar-based plates and Most Probable Number counts using liquid-based media.
DOI: 10.5522/04/19175153.v2
title: Culture-Free Enumeration of Mycobacterium tuberculosis in Mouse Tissues Using the Molecular Bacterial Load Assay for Preclinical Drug Development: Source Data

description: The turnaround times for phenotypic tests used to monitor the bacterial load of <i>Mycobacterium tuberculosis</i>, in both clinical and preclinical studies, are delayed by the organism’s slow growth in culture media. The existence of differentially culturable populations of <i>M.</i> <i>tuberculosis</i> may result in an underestimate of the true number. Moreover, culture methods are susceptible to contamination resulting in loss of critical data points. We report the adaptation of our robust, culture-free assay utilising 16S ribosomal RNA, developed for sputum, to enumerate the number of bacteria present in animal tissues as a tool to improve the read-outs in preclinical drug efficacy studies. Initial assay adaptation was performed using naïve mouse lungs spiked with known quantities of <i>M. tuberculosis</i> and an internal RNA control. Tissues were homogenised, total RNA extracted, and enumeration performed using RT-qPCR. We then evaluated the utility of the assay, in comparison to bacterial counts estimated using growth assays on solid and liquid media, to accurately inform bacterial load in tissues from <i>M. tuberculosis</i>-infected mice before and during treatment with a panel of drug combinations. When tested on lung tissues derived from infected mice, the MBL assay produced comparable results to the bacterial counts in solid culture (colony forming units: CFU). Notably, under specific drug treatments, the MBL assay was able to detect a significantly higher number of <i>M. tuberculosis</i> compared to CFU, likely indicating the presence of bacteria that were unable to produce colonies in solid-based culture. Additionally, growth recovery in liquid media using the most probable number (MPN) assay was able to account for the discrepancy between the MBL assay and CFU number, suggesting that the MBL assay detects differentially culturable sub-populations of <i>M. tuberculosis</i>. The MBL can enumerate the bacterial load in animal tissues in real time without the need to wait for extended periods for cultures to grow. The readout correlates well with CFUs. Importantly, we have shown that the MBL is able to measure specific populations of bacteria not cultured on solid agar. The adaptation of this assay for preclinical studies has the potential to decrease the readout time of data acquisition from animal experiments and could represent a valuable tool for tuberculosis drug discovery and development.<br> This dataset contains all the data that were collected as part of this project. These data include the cycle thresholds (Cq) from real time quantitative PCR reactions of the internal control RNA and the <i>M. tuberculosis</i>-specific 16S rRNA derived either from spiked naïve mouse tissues or infected animals with <i>M. tuberculosis</i>. Molecular bacterial load values are compared with Colony Forming Units from solid agar-based plates and Most Probable Number counts using liquid-based media.
DOI: 10.5522/04/19175153.v1
title: Culture-Free Enumeration of Mycobacterium tuberculosis in Mouse Tissues Using the Molecular Bacterial Load Assay for Preclinical Drug Development: Source Data

description: The turnaround times for phenotypic tests used to monitor the bacterial load of <i>Mycobacterium tuberculosis</i>, in both clinical and preclinical studies, are delayed by the organism’s slow growth in culture media. The existence of differentially culturable populations of <i>M.</i> <i>tuberculosis</i> may result in an underestimate of the true number. Moreover, culture methods are susceptible to contamination resulting in loss of critical data points. We report the adaptation of our robust, culture-free assay utilising 16S ribosomal RNA, developed for sputum, to enumerate the number of bacteria present in animal tissues as a tool to improve the read-outs in preclinical drug efficacy studies. Initial assay adaptation was performed using naïve mouse lungs spiked with known quantities of <i>M. tuberculosis</i> and an internal RNA control. Tissues were homogenised, total RNA extracted, and enumeration performed using RT-qPCR. We then evaluated the utility of the assay, in comparison to bacterial counts estimated using growth assays on solid and liquid media, to accurately inform bacterial load in tissues from <i>M. tuberculosis</i>-infected mice before and during treatment with a panel of drug combinations. When tested on lung tissues derived from infected mice, the MBL assay produced comparable results to the bacterial counts in solid culture (colony forming units: CFU). Notably, under specific drug treatments, the MBL assay was able to detect a significantly higher number of <i>M. tuberculosis</i> compared to CFU, likely indicating the presence of bacteria that were unable to produce colonies in solid-based culture. Additionally, growth recovery in liquid media using the most probable number (MPN) assay was able to account for the discrepancy between the MBL assay and CFU number, suggesting that the MBL assay detects differentially culturable sub-populations of <i>M. tuberculosis</i>. The MBL can enumerate the bacterial load in animal tissues in real time without the need to wait for extended periods for cultures to grow. The readout correlates well with CFUs. Importantly, we have shown that the MBL is able to measure specific populations of bacteria not cultured on solid agar. The adaptation of this assay for preclinical studies has the potential to decrease the readout time of data acquisition from animal experiments and could represent a valuable tool for tuberculosis drug discovery and development.<br> This dataset contains all the data that were collected as part of this project. These data include the cycle thresholds (Cq) from real time quantitative PCR reactions of the internal control RNA and the <i>M. tuberculosis</i>-specific 16S rRNA derived either from spiked naïve mouse tissues or infected animals with <i>M. tuberculosis</i>. Molecular bacterial load values are compared with Colony Forming Units from solid agar-based plates and Most Probable Number counts using liquid-based media.
DOI: 10.17632/sv4swfxdyj.2
title: Tracer test dataset conducted on Dinaric karst island aquifer

description: Tracer test was conducted by injecting Na-fluorescein into a borehole located approximately in the center of the island Vis in the Adriatic Sea (Croatia). Only 0.4 kg of dye was used as the borehole is located at the “Korita” pumping site which is the only source of fresh water on the island. Dye was recovered only at nearby boreholes, although coastal springs were monitored for two months. The dataset includes recovered dye concentrations from two boreholes with a depth of approximately 150 meters. Their coordinates and map with all sampling locations are also provided. The purpose of the tracer test was for delineating the catchment of the “Korita” pumping site and determining the maximum apparent speed of the dye, as is required by Croatian legislation. Island Vis is composed mainly of karstified carbonate rocks and belongs to the Dinaric karst region, locus typicus for karst landforms. The provided information can be used for determining the hydraulic properties of its aquifer and for research of karst in general.
Tracer test began on 22.5.2012. at 13:25 when 0.4 kg of Na-fluorescein dye (previously diluted in water) was poured into the BO-6 borehole. Immediately after that, the borehole was flushed with 10 m3 of water. On the same day, heavy rain of 88 mm/m2 fell on island Vis. Sampling points were boreholes (wells) BO-2 and BO-5, and Pizdica spring. At the beginning of the sampling period, Kamenice spring was also sampled. Since no dye was found on Pizidica and Kamenice springs, only data for boreholes are provided. BO-2 well was pumped continuously for the first ten days after dye injection. BO-5 was pumped only for sampling purposes. The frequency of sampling is shown in the provided tables, as each sample has a precise time when it was taken. All locations were sampled before dye tracer injections for determining background concentration values. GGUN-FL30 field fluorometers were used only for the detection of first dye arrival in case manual sampling wouldn`t be frequent enough. Only data for borehole BO-2 is provided as it produced positive results. The detection limit for the field fluorometer was 0.025 µg/L. Manually taken samples were brought to Croatian geological survey for laboratory analysis. There, they were analyzed on a Perkin-Elmer LS55 spectrofluorometer. All samples were treated with NaOH in order to bring pH values to 8.5. Background concentration values were subtracted from all samples. The detection limit for Na-fluorescein dye in the laboratory was 0.002 µg/L.
DOI: 10.17632/3r9bhmhz6d.2
title: Dicyphus predatory bugs pre-established on tomato plants reduce Nesiodiocoris tenuis population growth

description: Abstract
Generalist predators are increasingly used in biological pest control for greenhouse crops, as they control multiple pests and persist in crops even when prey is scarce. However, some of these predators may cause plant damage due to their omnivorous feeding behaviour. In many European regions, the omnivorous predator Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae) is considered to be a serious tomato pest, regardless of the biological control services it offers, and Integrated Pest Management (IPM) strategies are based instead on Macrolophus pygmaeus (Rambur). However, as N. tenuis may competitively displace M. pygmaeus and cause severe damage, growers often resort to pesticide use, disrupting their biological control practice. In this study, we evaluated the competitive interactions of three mirid predators, Dicyphus errans Wolff, Dicyphus bolivari Lindberg and Dicyphus cerastii Wagner, with N. tenuis. The results showed that pre-establishment of heterospecific mirid species can successfully suppress N. tenuis in the greenhouse; population growth was reduced by more than 90% compared to plants without competing predators. Further laboratory trials revealed reciprocal intraguild predation between these species in the absence of extraguild prey. Dicyphus adults predated on N. tenuis nymphs, while this was not found for M. pygmaeus. In olfactometer bioassays, N. tenuis females preferred plants previously exposed to heterospecifics but not conspecifics, suggesting that this mirid does not avoid competition. These results suggest that the three Dicyphus species could be interesting candidates for preventive releases in tomato crops due to their ability to effectively suppress N. tenuis population growth.
DOI: 10.17632/ztdpjdkx6p.3
title: Supplemental Material for: Serum testosterone levels in three-month-old boys predict  their semen quality as young adults

description: This data repository contains the Supplemental Material from the manuscript entitled "Serum testosterone levels in three-month-old boys predict their semen quality as young adults".
DOI: 10.6084/m9.figshare.19208310
title: Flower Survey

description: For each summer transect, we recorded the number of flower units per species in a 0.25m<sup>2</sup> quadrat randomly thrown every ten meters. Flowering units were defined as in Carvell et al (2007); one flower ‘unit’ was counted as a single flower or, in the case of multiflowered stems, as an umbel, head, spike or capitulum. Flowering plants were identified to species in most cases, otherwise to the family or genus.
DOI: 10.17632/hz9pv7t2tx.3
title: Macroeconomic, institutional and financial determinants of current Account balances

description:  	Variables	Number  of Observations	Data Source
 	Dependent Variables	 	 
1	Current Account/GDP (%)	2936	WEO*
 	Macroeconomic Determinants		 
2	GDP (%)	3111	World Bank
3	Terms of Trade	2363	World Bank
4	Real Effective Exchange Rate	3132	Bruegel Think Tank
5	Trade openness (X+M)/GDP (%)	3079	World Bank
6	Average Net Crude Oil Export/GDP (%)****	2457	EIA**, World Bank
7	Government Expenditures/GDP (%)	3062	World Bank
8	Fiscal Balance/GDP (%)	2012	World Bank, OECD
9	Relative Income (US=1)	3139	World Bank
 	Demographics Determinants		 
10	Old-Age Dependency Ratio (%)	3385	World Bank
11	Youth Dependency Ratio (%)	3385	World Bank
	Macroeconomic Stability Determinant		
12	Inflation Rate (CPI)	3031	WEO*
 	Financial Determinants		 
13	Total Private Credit/GDP (%)	2945	World Bank
14	Stock Market Capitalization/GDP (%)	1984	World Bank
15	Market Turnover/GDP (%)	1957	World Bank
16	Banks Net Interest Margin (%)	1718	World Bank
 	Institutional Determinants		 
17	Size of Government Index	1492	Fraser Institute
18	Economic Freedom Summary Index	1492	Fraser Institute
19	Legal System and Property Rights Index 	1493	Fraser Institute
20	Regulation Index	1492	Fraser Institute
21	Freedom to trade internationally Index	1492	Fraser Institute
22	Political Constraint (Polcon V) Index	2942	POLCON***
23	Voice and Accountability  Index	1536	World Bank
24	Control of Corruption Index	1552	World Bank
25	Government Effectiveness Index	1552	World Bank
26	Political Stability and Absence of Violence Index	1552	World Bank
27	Regulatory Quality Index	1552	World Bank
28	Rule of Law Index	1552	World Bank
 	Human Capital Determinants		 
29	Government Education Expenditure/GDP  (%)	1785	World Bank
DOI: 10.17632/hx357jc7b2.3
title: Income traps for different income groups: An empirical investigation 

description: This data is used to investigate the income traps for different income groups by checking the stationarity of per capita income time series with breaks, if they exist. The upper and lower-middle-income traps are reviewed for 25 upper and 12 lower-middle-income countries by employing the Augmented Dickey-Fuller, Zivot- Andrews with one break, and Lee-Strazicich with two breaks test procedures over 1987-2019. Besides, by predicting their income trends, the study tests whether if five newly high-income countries Chile, Mauritius, Panama, Romania, Uruguay can close the income gap with the advanced countries. 
The empirical findings show that 18 out of 25 upper-middle-income countries and 8 out of 12 lower-middle-income countries are in the upper and lower-income trap, respectively. China is the only country that gives the hope of becoming a part of the high-income group in the following years. The findings for seven upper-middle and four lower-middle countries are ambiguous. The empirical findings of the five newly high-income countries show that Panama is on the way to catching up with the high-income group. The same ambiguity applies for Romania and Mauritius, while Uruguay and 
Chile are likely to stay at the lowest level of the high-income group that can be described as the “lowerhigh-income trap.”
DOI: 10.48370/ofd/6br6vf
title: Phlebia rufa (Pers.: Fr.) M. P. Christ., 35

description: Fungarium Makromycetes
DOI: 10.17632/pr2d4yn4dd.2
title: DSAIL Power Management Board: Powering the Raspberry Pi autonomously off the grid.

description: The files in this repository are the requirements for reproducing a power supply board to power the Raspberry Pi autonomously off-grid. The Raspberry Pi is a single board computer that runs on a complete Operating System. Its high processing capabilities and the ability to be interfaced with a lot of sensors makes it an ideal board for data collection and processing. When collecting data in the wild, away from the grid, we need to come up with ways to power the Raspberry Pi. The fact that the Raspberry   Pi is a single board computer means that care needs to be taken when powering it. At the Centre for Data Science and Artificial Intelligence, we have designed an autonomous power supply to power the Raspberry Pi in the field. The design files and software to run the system are contained in this repository. The file are divided into hardware and software. The 'Hardware' folder contains KiCad design files. The 'Software' folder contains setup instructions and programs to run the system.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             .
DOI: 10.17632/899635p4df.1
title: LINF_220022600

description: CCR4 associated factor | CAF1
Leishmania infantum (strain JPCM5)
DOI: 10.17632/7tgh5nyhnz.1
title: LINF_230005500

description: cyclophilin 11 | CYP11
Leishmania infantum (strain JPCM5)
DOI: 10.25345/c51r6n15d
title: MassIVE Reanalysis RMSV000000354.3438 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, NAALADL2 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.17632/tx765ct8sc.1
title: LINF_230005700

description: agmatinase-like protein
Leishmania infantum (strain JPCM5)
DOI: 10.17632/jp9mdbkmm2.1
title: Vibrational spectroscopy and non-parametric analysis for biodegradation evaluation: The acrylic-emulsion paint scenario

description: In this work, we utilized Raman spectroscopy, characterized by excellent lateral resolution, in capturing the degradation of paints was investigated. Six fresh and six spoilt acrylic emulsion paint samples obtained from a paint company in Lagos, Nigeria and were used for this study. They were analyzed for microbial population and types using total viable count method and analytical profile index (API20E &20NE).  Physicochemical quality markers [transmittance (TR), pH, OD600, and specific gravity (SG)] of the paints were evaluated by standard methods. Raman spectroscopy was deployed to analyze components of both fresh and spoilt paint samples. Lead (Pb) concentrations were assessed using atomic absorption spectrophotometry.
DOI: 10.17632/36kg4xvf46.1
title: Simulation data

description: Simulation dataset for data analysis
DOI: 10.17632/ywm8wnggvb.1
title: Data to 'Jaeckstein et al'

description:  RNA sequencing data comparing Eto/CL versus mock/mock mice 
 RNA sequencing data comparing P2rx4-defcient mice +/- P2RX7 nanobody
DOI: 10.25345/c5s756k8x
title: MassIVE Reanalysis RMSV000000354.3436 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RGS6 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5x05xd1t
title: MassIVE Reanalysis RMSV000000354.3439 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, HNRNPF [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.17632/x3js7s8zdv.1
title: Veganism 

description: FACTORS INFLUENCING MILLENNNIALS’ PURCHASE INTENTIONS TOWARDS VEGAN PRODUCTS IN SOUTH AFRICA.
DOI: 10.48370/ofd/siem8f
title: Phlebia rufa (Pers.: Fr.) M. P. Christ., 494

description: Fungarium Makromycetes