cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16621928
title: Improving empiric antibiotic prescribing in pediatric bloodstream infections: a potential application of weighted-incidence syndromic combination antibiograms (WISCA)

description: Increasing antibiotic resistance to WHO-recommended first- and second-line treatments of pediatric sepsis requires adaptation of prescribing guidelines. We discuss the potential and limitations of a weighted-incidence syndromic combination antibiogram (WISCA) as a practical tool for incorporating local microbiology data when assessing empiric coverage of commonly used antibiotics. A brief questionnaire of 18 clinically significant isolates from pediatric blood cultures (Jan-Dec 2018) was sent to a global network of pediatric hospitals in July 2019. Weighted coverage estimates of non-antipseudomonal third-generation cephalosporins (3GC) and meropenem were estimated using Monte–Carlo simulation for each site reporting &gt;100 isolates. 52 hospitals in 23 countries in 5 WHO regions responded to the questionnaire; 13 sites met the sample size requirement. The most common isolates were <i>S. aureus, Klebsiella spp</i>., <i>E. coli</i> and <i>Enterococcus</i> spp. Coverage of 3GC ranged from 39% [95%CrI: 34–43%] to 73% (two sites: [95%CrI: 65–80%]; [95%CrI: 68–86%]) and meropenem coverage ranged from 54% [95%CrI: 47–60%] to 88% [95%CrI:84–91%]. A WISCA is a data-driven, clinically intuitive tool that can be used to compare empiric antibiotic regimens for pediatric sepsis using existing large datasets. The estimates can be further refined using more complex meta-analytical methods and patient characteristics.
DOI: 10.6084/m9.figshare.19197025
title: Axin2-lineage cells contribute to neonatal tendon regeneration

description: Tendon injuries are a challenging clinical problem with few treatment options. Identifying the molecular regulators of tendon is required for the development of new therapies. While the Wnt pathway is critical for the maintenance and differentiation of many tissues, the role of Wnt signaling in tendon cell biology remains largely unexplored. The effects of Wnt activation were tested <i>in vitro</i> using neonatal tendon-derived cells cultured in 2D and 3D conditions. The inducible Axin2CreERT2 was then used to label Axin2+ cells <i>in vivo</i> and cells were traced during neonatal tendon regeneration. We showed that activation of Wnt signaling results in proliferation of neonatal tendon cells. While tendon marker expression was inhibited by Wnt activation under 2D conditions, <i>Scx</i> expression was not affected under 3D uniaxial tension, suggesting that the microenvironment contextualizes tendon cell response to Wnt signaling. Using an <i>in vivo</i> model of neonatal tendon regeneration, we further showed that Wnt signaling cells comprise a subpopulation of tenocyte and epitenon cells that proliferate after injury and are recruited during regeneration. Collectively, these studies suggest that Wnt signaling may play a role in tendon cell proliferation, differentiation, and regeneration.
DOI: 10.6084/m9.figshare.19197025.v1
title: Axin2-lineage cells contribute to neonatal tendon regeneration

description: Tendon injuries are a challenging clinical problem with few treatment options. Identifying the molecular regulators of tendon is required for the development of new therapies. While the Wnt pathway is critical for the maintenance and differentiation of many tissues, the role of Wnt signaling in tendon cell biology remains largely unexplored. The effects of Wnt activation were tested <i>in vitro</i> using neonatal tendon-derived cells cultured in 2D and 3D conditions. The inducible Axin2CreERT2 was then used to label Axin2+ cells <i>in vivo</i> and cells were traced during neonatal tendon regeneration. We showed that activation of Wnt signaling results in proliferation of neonatal tendon cells. While tendon marker expression was inhibited by Wnt activation under 2D conditions, <i>Scx</i> expression was not affected under 3D uniaxial tension, suggesting that the microenvironment contextualizes tendon cell response to Wnt signaling. Using an <i>in vivo</i> model of neonatal tendon regeneration, we further showed that Wnt signaling cells comprise a subpopulation of tenocyte and epitenon cells that proliferate after injury and are recruited during regeneration. Collectively, these studies suggest that Wnt signaling may play a role in tendon cell proliferation, differentiation, and regeneration.
DOI: 10.5281/zenodo.6949284
title: Four Reference Quality Genome Assemblies of Pyrenophora teres f. maculata: A Resource for Studying the Barley Spot Form Net Blotch Interaction

description: Updated draft genome assembly (FASTA) and annotation (GFF) for the <em>P. teres </em>f.<em> maculata </em>isolate FGOB10Ptm-1.
DOI: 10.5281/zenodo.6949283
title: Four Reference Quality Genome Assemblies of Pyrenophora teres f. maculata: A Resource for Studying the Barley Spot Form Net Blotch Interaction

description: Updated draft genome assembly (FASTA) and annotation (GFF) for the <em>P. teres </em>f.<em> maculata </em>isolate FGOB10Ptm-1.
DOI: 10.17632/rjyvdyrj6y.1
title: TROPICAL SPRUE: DIAGNOSTIC CHALLENGES OF AN OLD DISEASE BUT UNDERRECOGNIZED. A TUNISIAN CASE REPORT

description: A tunisian case report of a latent Tropical sprue presented by a visitor of an endemic area 
Tropical sprue (TS) is a post-infective disease of the small bowel characterized by a malabsorption syndrome affecting tropics inhabitants and visitors. Diagnosis of TS remain challenging since it can be confused with common diarrheal diseases, especially in non-endemic areas.
After ruling out other causes of chronic dirrhea, improvement after an optimal management combining rehydration, replacement of micronutrient, folate and vitamin B12 deficiencies as well as a prolonged antibiotic course supports the diagnosis of TS.
DOI: 10.5281/zenodo.5841954
title: Vascular lesions and brain atrophy in Alzheimer's, vascular and mixed dementia: an optimized 3T MRI protocol reveals distinctive radiological profiles

description: <strong>Background</strong> Behavioral and psychological symptoms of dementia (BPSD) are a distressful condition. We aimed to investigate the BPSD distribution in subjects with cognitive impairment, and the potential correlations between BPSD and neurodegeneration in terms of cerebrospinal fluid (CSF) tau and brain atrophy. <strong>Methods</strong> Seventy-six subjects received a diagnosis of Alzheimer’s (AD=32), vascular (VD=26) or mixed (MD=18) dementia according to Hachinski scale and NINCDS-ADRDA criteria. Three independent raters assessed the brain images acquired according to a high resolution 3T MRI protocol (including 3D FLAIR, T1, SWI and 2D coronal T2 sequences) with semiquantitative scales for vascular lesions (periventricular and deep white matter lesions, PVL and DWML, deep grey matter lesions, DGML, enlarged perivascular spaces, PVS, and microbleeds, MB) and brain atrophy (medial temporal atrophy, MTA, posterior atrophy, PA, global cortical atrophy-frontal, GCA-F, and Evans’ index). The inter-rater agreement was assessed with the intraclass correlation coefficient (ICC). <strong>Results</strong> Raters reached a good-to-excellent agreement for all scales (ICC ranging 0.78-0.96). A greater number of PVL (p&lt;0.001), DWML (p&lt;0.001), DGML (p=0.010) and PVS (p=0.001) was observed in VD compared to AD, while MD showed a significant greater number of PVL (p=0.001), DWML (p=0.002), DGML (p=0.018) and deep and juxtacortical MB (p=0.006 and p&lt;0.001, respectively). No significant difference was observed in scores of cortical atrophy scales and Evans’ index among the three groups. <strong>Conclusion</strong> The use of a high-resolution 3T MRI protocol, including SWI, allowed a reliable and time-saving assessment of vascular lesions and atrophy using dedicated visual scales. Our findings confirm that white and grey matter lesions are the predominant abnormalities in both vascular and mixed dementia, whereas juxtacortical microbleeds predominate in mixed dementia, suggesting that cerebral amyloid angiopathy could be the main underlying pathology.
DOI: 10.5281/zenodo.5841953
title: Vascular lesions and brain atrophy in Alzheimer's, vascular and mixed dementia: an optimized 3T MRI protocol reveals distinctive radiological profiles

description: <strong>Background</strong> Behavioral and psychological symptoms of dementia (BPSD) are a distressful condition. We aimed to investigate the BPSD distribution in subjects with cognitive impairment, and the potential correlations between BPSD and neurodegeneration in terms of cerebrospinal fluid (CSF) tau and brain atrophy. <strong>Methods</strong> Seventy-six subjects received a diagnosis of Alzheimer’s (AD=32), vascular (VD=26) or mixed (MD=18) dementia according to Hachinski scale and NINCDS-ADRDA criteria. Three independent raters assessed the brain images acquired according to a high resolution 3T MRI protocol (including 3D FLAIR, T1, SWI and 2D coronal T2 sequences) with semiquantitative scales for vascular lesions (periventricular and deep white matter lesions, PVL and DWML, deep grey matter lesions, DGML, enlarged perivascular spaces, PVS, and microbleeds, MB) and brain atrophy (medial temporal atrophy, MTA, posterior atrophy, PA, global cortical atrophy-frontal, GCA-F, and Evans’ index). The inter-rater agreement was assessed with the intraclass correlation coefficient (ICC). <strong>Results</strong> Raters reached a good-to-excellent agreement for all scales (ICC ranging 0.78-0.96). A greater number of PVL (p&lt;0.001), DWML (p&lt;0.001), DGML (p=0.010) and PVS (p=0.001) was observed in VD compared to AD, while MD showed a significant greater number of PVL (p=0.001), DWML (p=0.002), DGML (p=0.018) and deep and juxtacortical MB (p=0.006 and p&lt;0.001, respectively). No significant difference was observed in scores of cortical atrophy scales and Evans’ index among the three groups. <strong>Conclusion</strong> The use of a high-resolution 3T MRI protocol, including SWI, allowed a reliable and time-saving assessment of vascular lesions and atrophy using dedicated visual scales. Our findings confirm that white and grey matter lesions are the predominant abnormalities in both vascular and mixed dementia, whereas juxtacortical microbleeds predominate in mixed dementia, suggesting that cerebral amyloid angiopathy could be the main underlying pathology.
DOI: 10.17632/pc4mb3h8hz.2
title: Multi-Label Retinal Diseases (MuReD) Dataset

description: Abstract:
Early detection of retinal diseases is one of the most important means of preventing partial or permanent blindness in patients. One of the major stumbling blocks for manual retinal examination is the lack of a sufficient number of qualified medical personnel per capita to diagnose diseases. Computer-aided diagnosis systems (CAD) have proven to be very effective in helping physicians reduce the time taken to make a diagnosis and minimize variability in image interpretation. Still, they are not flexible enough to accommodate the simultaneous presence of multiple retinal diseases, which is a common situation in real-world applications. In the past years, few datasets that focus on the classification of numerous retinal pathologies present at the same time, i.e., multi-label classification have been proposed, but there are some shared problems with all of them, such as a narrow range of pathologies to classify, high level of class imbalance, low amount of samples for the underrepresented labels, no assurance in image quality, among others. All these problems hinder the performance of any model trained with these datasets, which leads to poor robustness, lack of generalization, and reduced trustability in its predictions.
To address these problems, we constructed the Multi-Label Retinal Diseases (MuReD) dataset, using images collected from three different state-of-the-art sources, i.e., ARIA, STARE, and RFMiD datasets, and performing a sequence of post-processing steps to ensure the quality of the images, a wide range of diseases to classify, and a sufficient number of samples per disease label.
The MuReD dataset consists of 2208 images with 20 different labels, with varying image quality and resolution. At the same time, ensuring a minimal degree of quality in the data, with a sufficient number of samples per label. To the best of our knowledge, the MuReD dataset, is the only publicly available dataset that applies a sequence of post-processing steps to ensure the quality of the images, the variety of pathologies, and the number of samples per label, resulting in increased data quality and a significant reduction of the class imbalance present in the publicly available datasets.
It is envisaged that the MuReD dataset will enable the creation of more robust, general, and trustable models for the automatic detection and classification of retinal diseases.

Files Description:
1. The file "train_data.csv" contains the images from the training set, along with the 20 different labels.
2. The file "val_data.csv" contains the images from the validation set, along with the 20 different labels.
3. The folder "images" contains all the images that compose the MuReD dataset.

The images come in two different formats, i.e., .tiff and .png.
There is no single image resolution. Given that the images come from different sources, resolution can vary from 520x520 to 3400x2800 depending on the source of the image.
DOI: 10.17632/5gb24nwk7y.1
title: Supplementary Material for Disruptive Solutions on Requirement Engineering for Agile Software Development: A tertiary study

description: This repository delivers the supplementary material for the paper: Disruptive Solutions on Requirement Engineering for Agile Software Development: A tertiary study.

In the following, we present the abstract of the study:

Context: Agile Software Development (ASD) is a disruptive process compared to traditional software development. Therefore, traditional Requirements Engineering (RE) forms may not be the best way to do RE for ASD (RE-ASD). Objective: Working with ASD using traditional RE ways could limit ASD's potential. Thus, it is necessary to investigate what academia and industry have done in RE to take full advantage of all of the capabilities of ASD beyond traditional RE. Method: We conducted a Tertiary Study looking for solutions for RE-ASD using the Systematic Literature Review (SLR) protocol described by Kitchenham and Charters. We then categorized the solutions into families using Targeted Coding and Constant Comparison, tools from Socio-Technical Grounded Theory (STGT). Afterward, we classified the solutions as disruptive using our model based on the Hype Level Curve concept, assessing their hype (popularity) in the software engineering community using Google Trends and Google Colab tools. Results: After executing the SLR protocol, we accepted 37 studies and encountered 136 solutions used by academia and industry for RE-ASD. We categorized these solutions into 21 solution families, six of which we classified as disruptive. Design Thinking (DT) and Artificial Intelligence (AI) were the two families of solutions that stood out the most. We also identified the type of solution (e.g., process, method, technique, tool, model, framework) and domain (academia or industry). Furthermore, we cataloged the challenges presented by the solutions. Conclusion: We concluded that only a few solutions that have been used for RE-ASD have the power to successfully challenge the mainstream Agile Software Development process by using innovation (26 out of 106). There is a gap between academia and industry regarding these disruptive solutions, and some challenges still need to be addressed in using these solutions.
The repository contains the following:
•	Dataset from the Tertiary Study:
      o	Data of the retrieved studies. It presents the classifications of the documents as 'Accepted,' 'Rejected' (with the indication of the step of the protocol the authors rejected the study), or 'Duplicated.'
      o	Data of all solutions retrieved from the accepted studies
•	Socio-Technical Grounded Theory (STGT) tools
      o	Result of the use of Targeted Coding and Constant Comparison
•	The Google Colab Notebook
      o	Code in python
      o	Results
DOI: 10.17632/whxw97nw86.2
title: Bays-damselfish

description: We conducted an observational study on the benthic community of the fringing reefs in the two major bays in Moorea, French Polynesia (Cook’s Bay and Opunohu Bay) and investigated the relationship between the presence of damselfish (Stegastes nigricans) territories and corals within the territories. We found that corals had significantly greater species richness inside of S. nigricans territories than outside. Our results support a positive effect of S. nigricans on coral diversity, potentially through indirect positive effects on many non-dominant coral species.
DOI: 10.17632/x7zb6779hf.2
title: Research data

description: reaeach data for manuscript (Bruceantin facilitates anti-PD-L1 therapy by targeting the STAT3/PD-L1 axis in glioblastoma)
DOI: 10.17632/ryfb8h9rzj.1
title: Energy modelling and carbon footprint of r-NF & NF-270-400: raw results and indicators

description: The following datasets compile the Membranes paper results and intermediate results of the paper submitted in Membranes Journal. 
-main_simulations_energy_mass.csv:  (Pot_Qi: feed flow (in m3·h-1),  Pot_n: number of elements, Pot_CF: Water recovery factor,  Perm: permeability (in L·m2·h-1·bar-1) ; Prin: feed pressure (in bar) ,  SEC: specific energy consumption (in kwh·m-3);   Vin: feed velocity (in m·s-1)  ; Rein: Reynolds number in feed flow,   Qp: product flow (in m3·h-1),  Qconc: Concentrate  flow (in m3·h-1) , Vconc: cncetrat3e flow velocity (in m·s-1) ;   Reconc: reynolds numeber in concentrate flow;  Prlosses : Pressure losses in the PV (in bar) ,  Pr_conc: Pressure at concentrate flow: in bar).
-Years_table.csv:  describes the service lifespan in which the r-NF and the NF-270 have the same CF (Pot_Qi Pot_n Pot_CF   Mix `Natural gas` Solar  Wind `Gravity driven`).
-CF_2.csv summarises the carbon footprint results in kg CO2-eq of the main processes and energy sources. the energy processes are kg CO2-eq per kwh and membranes procesess are in kg CO2-eq per module.
DOI: 10.17632/4dk842h6pg.1
title: Database of boulder transport calculation

description: The results of boulder transport calculation by tsunami and storm wave on planar and reef topography condition.
DOI: 10.17632/5z379f8jwp.1
title: The reef and planar topographic conditions 

description: In order to reveal the topography condition that tsunami and storm boulders are formed, we conducted literature review as summarised in the provided data.
DOI: 10.17632/3znw6rrwm6.1
title: LINF_300042700

description: Protein of unknown function (DUF3808)
Leishmania infantum (strain JPCM5)
DOI: 10.17632/687jbrgdj8.1
title: LINF_300042600

description: Protein of unknown function - conserved
Leishmania infantum (strain JPCM5)
DOI: 10.17632/4jvxwpdkvn.1
title: LINF_300041900

description: Protein of unknown function (DUF773)
Leishmania infantum (strain JPCM5)
DOI: 10.17632/2n56tfspww.1
title: LINF_300041800

description: ATP synthase - epsilon chain
Leishmania infantum (strain JPCM5)
DOI: 10.17632/5jy2xj563y.1
title: LINF_300041400

description: Magoh
Leishmania infantum (strain JPCM5)
DOI: 10.17632/6bfh5gvtp7.1
title: Data

description: The data which are used in this paper are here:
1- Descriptive statistics of the Dust Deposition Rate (DDR)
2- T-test for compassion between nails of 40 MS patient and 40 healthy individuals
3-Descriptive  Statistics of nail data
4- Correlation between dust heavy metals 
5-data of EF
DOI: 10.17632/3dwvf3543d.1
title: The dataset collected data on land use and carbon storage in the coastal zone of Hainan Island, China, from 1990 to 2020

description: This dataset collected data on land use and carbon storage in the coastal zone of Hainan Island, China, from 1990 to 2020, and included data on driving factors affecting land use change and other statistical data of Hainan Island. As follows:
1.	Land use data
Secondary classification distribution map of land use from 1990 to 2020 with a spatial resolution of 30×30 m and data table of land use transfer.
2.	Carbon storage data
Carbon storage per unit area Carbon storage distribution map from 1990 to 2020 and carbon storage transfer data table.
3.	Driving factors
Driving factors including DEM, slope, density, distance from town, distance from railway, distance from highway.
4.	Other data
Hainan's population, GDP and tourism Revenue.

Steps to reproduce:
The land use types in the study area were classified into seven categories: sea, cropland (paddy field and dry field), forest land (wooded land, shrub land and other forest land), grassland (high cover grassland, medium cover grassland and low cover grassland), water (rivers, reservoirs and ponds, mudflats, wetlands and lakes, etc.), built-up land (urban land, settlement and other built-up land) and unused land (sandy land and bare land, etc.), which were combined with random forest method and manual visual interpretation to obtain land use data in the study area. 
In the carbon module of the InVEST, the carbon storage of regional ecosystems was evaluated based on land use and its corresponding carbon density data.  Based on the carbon density calculation of forestland, grassland, cropland, built-up land, water area and other land types in the 2006 IPCC Guidelines for National Greenhouse Gas Inventory, this paper, combined with the climatic conditions of Hainan Province and other basic data, modified the carbon density data of different land use types in the study area, and calculated the carbon storage of the study area under in different periods.
The Digital Elevation Model (DEM) data were mainly obtained from the geospatial data cloud platform (http:www.gscloud.cn), and the slope raster data of the study area were obtained quantitatively with a spatial resolution of 30×30 m using DEM with the support of ArcGIS10.8. The main source of road data is OSM (Open Street Map, https://www.openstreetmap.org). It includes highways, national roads, urban traffic highways, high speed rail and some other roads. The data of cities, towns and rivers were mainly obtained from the Resource and Environment Science and Data Center (http://www.resdc.cn/data) and the administrative map of Hainan Province, etc. The distances from towns, rural settlements, rivers, provincial roads and rural roads were mainly calculated with the help of the Euclidean distance method.
DOI: 10.17632/jz6rsrdzg8.1
title: Data on public reference ERP-based ecosystem services in India 

description: This dataset provides information on different parameters that are useful for developing ERP systems. This dataset includes eight different parameters related to the Enterprise Resource Planning(ERP) development and identification of challenges faced by the user.
1.	ERP feedback data is important for understanding the challenges of users and improving the various parameters of ERP to increase the utilization system. We here provide comprehensive data on ERP parameters such as Data Availability and Information Quality, ERP Awareness, ERP System Quality, ERP System Security, ERP Service Quality, User Interface, and User Experience.  
2.	ERP researchers and ERP developers can use the data to better understand the user requirements, user challenges, and factors that should count while developing of ERP system.
DOI: 10.17632/pr87nccfmg.1
title: Research data for BRU

description: Research data for BRU
DOI: 10.17632/rmvshk85kr.1
title: First experience on use of Virtual Radiography Simulation software in Nigeria

description: Responses from the first users of Virtual Radiography simulation in four Nigerian universities.
DOI: 10.17632/53cwn4bnm8.1
title: LINF_310005400

description: cyclophilin 5 | CyP5 | Peptidyl-prolyl cis-trans isomerase
Leishmania infantum (strain JPCM5)
DOI: 10.17632/fxc5h2fvgm.1
title: LINF_310005100

description: Aquaglyceroporin 1 (AQP1) | aquaporin
Leishmania infantum (strain JPCM5)