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opencc-by-4.0Feb 2021View details →

Aseptic Meningitis: Case Definition Pictorial Algorithm

This post contains the Pictorial Algorithm for Aseptic Meningitis. They are included in the case definition companion guides, which contain resources and tools specific to events that have a published Brighton Collaboration case definition.

opencc-by-4.0Mar 2021View details →

Acute Disseminated Encephalomyelitis (ADEM): Case Definition Pictorial Algorithm

This post contains the Pictorial Algorithm for Acute Disseminated Encephalomyelitis (ADEM). They are included in the case definition companion guides, which contain resources and tools specific to events that have a published Brighton Collaboration case definition.

opencc-by-4.0Feb 2021View details →

Thrombocytopenia: Case Definition Pictorial Algorithm

This post contains the Pictorial Algorithm for Thrombocytopenia. They are included in the case definition companion guides, which contain resources and tools specific to events that have a published Brighton Collaboration case definition.

Outcome of severe COVID-19: spotlight on fatigue, fatiguability, multidomain complaints and pattern of cognitive deficits in a case series without prior brain dysfunction and without COVID-19-related stroke and/or cardiac arrest

Outcome of severe COVID-19: spotlight on fatigue, fatiguability, multidomain complaints and pattern of cognitive deficits in a case series without prior brain dysfunction and without COVID-19-related stroke and/or cardiac arrest Valérie Beaud1, Sonia Crottaz-Herbette1, Vincent Dunet2, Jean-François Knebel1, Pierre-Alexandre Bart3, Stephanie Clarke1 1 Service of Neuropsychology and Neurorehabilitation, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland 2 Service of Diagnostic and Interventional Radiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland 3 Service of Internal Medicine, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland ABSTRACT Background: Cognitive deficits were often reported during the acute and post-acute stages of severe COVID-19 and were often, but not always, associated with signs of brain damage. Population-wide surveys highlighted the need for investigations into the nature, the severity and the evolution of cognitive, behavioural and psychiatric deficits. Case presentation: We report the outcome at 12 months after severe COVID-19 involving intensive care unit stay and mechanical ventilation in six patients. None of the patients had history of prior brain dysfunction and none sustained stroke and/or cardiac arrest during COVID-19. A pervading mental and physical fatigue was consistently reported as well as numerous multidomain complaints, which affect to some extend everyday life, and for some of the patients a mental fatiguability, a certain degree of neurobehavioural (apathy) and/or psychiatric (anxiety) dysfunction. Standardized neuropsychological tests revealed for 4 of the 6 patients the occurrence relatively isolated of cognitive dysfunction or performance at the lower limit of the norm in some, but not all attentional, executive and/or working memory tests. Somatic scales highlighted the presence of dyspnoea, muscle weakness, olfactory disorder and/or minor sleep problems in some but not all patients. Conclusion: Fatigue, fatiguability, multidomain complaints, which affect to some extend everyday life, cognitive dysfunction or performance at the lower limit of the norm and a certain degree of neurobehavioural and/or psychiatric and/or somatic dysfunction can occur in the aftermath of severe COVID-19 even in the absence of neurological antecedents or of COVID-19-related stroke and/or cardiac arrest.

Supporting dataset: Towards the Optimal Representation of Sub-Grid Heterogeneity in Land Surface Models - Upper Colorado River Basin study case

Supporting files for the manuscript "Towards the Optimal Representation of Sub-Grid Heterogeneity in Land Surface Models - Upper Colorado River Basin study case." The dataset contains the ESCF derived from the original 800 HydroBlocks simulations used to train/test the random forest models (RFM) to compute the annual mean ESCFs for soil moisture content, sensible heat, latent heat, and runoff, as well as the obtained RFM to compute the resulting number of tiles for a given configuration over the study domain. Besides, the dataset includes the ESCFs for the quasi-fully distributed simulation (QFD) and the input data layers required to run HydroBlocks simulations over the study domain.

opencc-by-4.0Aug 2022View details →

BioExcel Use Case 1: collection of output data from molecular dynamics simulation

The Use Case aims to address all the challenges related to antibody design through an integrative approach combining the core BioExcel software comprising of GROMACS, HADDOCK and PMX. The folder  contains the GROMACS output files (xtc and pdb file). Molecular Dynamics simulations have been performed with GROMACS version 2020 and CHARMM36 force field. The input files and scripts of the final protocol are publicly available on BioExcel GitHub https://github.com/bioexcel/BioExcel-UseCase1. The Use Case 1 protocol was presented at the BioExcel Summer School on Biomolecular Simulation in 2021 (see <a href="https://doi.org/10.5281/zenodo.7009238">https://doi.org/10.5281/zenodo.7009238</a> or <a href="https://youtu.be/_TDKfKX4kwM">https://youtu.be/_TDKfKX4kwM</a>)

opencc-zeroAug 2022View details →

Data for: Social-ecological vulnerability of fishing communities to climate change: a U.S. West Coast case study

Climate change is already impacting coastal communities, and ongoing and future shifts in fisheries species productivity from climate change have implications for the livelihoods and cultures of coastal communities. Harvested marine species in the California Current Large Marine Ecosystem support U.S. West Coast communities economically, socially, and culturally. Ecological vulnerability assessments exist for individual species in the California Current but ecological and human vulnerability are linked and vulnerability is expected to vary by community. Here, we present automatable, reproducible methods for assessing the vulnerability of U.S. West Coast fishing-dependent communities to climate change within a social-ecological vulnerability framework. We first assessed the ecological risk of marine resources, on which fishing communities rely, to 50 years of climate change projections. We then combined this with the adaptive capacity of fishing communities, based on social indicators, to assess the potential ability of communities to cope with future changes. Specific communities (particularly in Washington state) were determined to be at risk to climate change mainly due to economic reliance on at risk marine fisheries species, like salmon, hake, or sea urchins. But, due to higher social adaptive capacity, these communities were often not found to be the most vulnerable overall. Conversely, certain communities that were not the most at risk, ecologically and economically, ranked in the category of highly vulnerable communities due to low adaptive capacity based on social indicators (particularly in Southern California). Certain communities were both ecologically at risk due to catch composition and socially vulnerable (low adaptive capacity) leading to the highest tier of vulnerability. The integration of climatic, ecological, economic, and societal data reveals that factors underlying vulnerability are variable across fishing communities on the U.S West Coast, and suggests the need to develop a variety of well-aligned strategies to adapt to the ecological impacts of climate change.

opencc-zeroAug 2022View details →

Effectiveness of seasonal malaria chemoprevention administered in a mass campaign in the Kedougou region of Senegal in 2016: a Case-control study

Context Seasonal malaria chemoprevention (SMC) with Sulfadoxine-Pyrimethamine plus Amodiaquine (SPAQ) is a malaria prevention strategy recommended since 2012 by the World Health Organization (WHO) for children under 5 years of age. In Senegal, the scaling up of the SMC has started since 2013 in the south-eastern regions of the country with an extension of the target to 10 years old children. The scaling up of SMC requires a regular evaluation of the strategy as recommended by the WHO. This study was conducted to evaluate the effectiveness of SMC. Methodology A case-control study was conducted in some villages of the health districts of Saraya and Kedougou in the Kedougou region from July to December 2016. A "case" was a sick child, aged 3 months to 10 years, seen in consultation and with a positive RDT. The "control" was a child of the same age group with a negative RDT and living in the same compound as the case or in a neighbouring compound. Each case was matched with two controls. Exposure to SMC was assessed by interviewing the mothers/caretakers and by checking the SMC administration card. Results A total of 492 children, including 164 cases and 328 controls, were recruited for our study. Their mean ages were 5.32 (+/- 2.15) and 4.44 (+/-2.25) years for the cases and the controls respectively. Male children predominated in both cases (55.49%) and controls (51.22%) (p=0.18). Net ownership was 85.80% among cases and 90.85% among controls (p=0.053). The proportion of controls who received SMC was higher than that of cases (98.17% vs 85.98%; (p=1.10-7)). The protective effectiveness of SMC was 89% (IC 95% = 84–93%) (OR=0.11). Conclusion SMC is therefore an effective strategy in the control of malaria in children. Case-control studies are a good approach for monitoring the efficacy of drugs administered during SMC.

opencc-zeroSep 2022View details →

Modeling the demography of species providing extended parental care: A capture-recapture approach with a case study on Polar Bears (Ursus maritimus)

1. In species providing extended parental care, one or both parents care for altricial young over a period including more than one breeding season. We expect large parental investment and long-term dependency within family units to cause high variability in life trajectories among individuals with complex consequences at the population level. So far, models for estimating demographic parameters in free-ranging animal populations mostly ignore extended parental care, thereby limiting our understanding of its consequences on parents and offspring life histories. 2. We designed a capture-recapture multi-event model for studying the demography of species providing extended parental care. It handles statistical multiple-year dependency among individual demographic parameters grouped within family units, variable litter size, and uncertainty on the timing at offspring independence. It allows for the evaluation of trade-offs among demographic parameters, the influence of past reproductive history on the caring parent's survival status, breeding probability and litter size probability, while accounting for imperfect detection of family units. We assess the model performance using simulated data, and illustrate its use with a long-term dataset collected on the Svalbard polar bears (Ursus maritimus). 3. Our model performed well in terms of bias and mean square error and in estimating demographic parameters in all simulated scenarios, both when offspring departure probability from the family unit occurred at a constant rate or varied during the field season depending on the date of capture. For the polar bear case study, we provide estimates of adult and dependent offspring survival rates, breeding probability and litter size probability. Results showed that the outcome of the previous reproduction influenced breeding probability. 4. Overall, our results show the importance of accounting for i) the multiple-year statistical dependency within family units, ii) uncertainty on the timing at offspring independence, and iii) past reproductive history of the caring parent. If ignored, estimates obtained for breeding probability, litter size, and survival can be biased. This is of interest in terms of conservation because species providing extended parental care are often long-living mammals vulnerable or threatened with extinction.

opencc-zeroSep 2022View details →

Data from: Exploring conflicts in whole genome phylogenetics: A case study within Manakins (Aves: Pipridae)

Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to investigating biological sources of phylogenetic incongruence, it is also important to reduce noise in the phylogenomic dataset by using an appropriate filtering approach that addresses gene tree estimation errors. We present the results of a case study in manakins, focusing on the very difficult clade comprising the genera Antilophia and Chiroxiphia. Previous studies suggest that Antilophia is nested within Chiroxiphia, though relationships among Antilophia+Chiroxiphia species have been highly unstable. We extracted more than 11,000 loci (ultra-conserved elements and introns) from whole genomes and conducted analyses using concatenation and multi-species coalescent methods. Topologies resulting from analyses using all loci differed depending on the data type and analytical method, with two clades (Antilophia+Chiroxiphia and Manacus+Pipra+Machaeopterus) in the manakin tree showing incongruent results. We hypothesized that gene trees that conflicted with a long coalescent branch (e.g., the branch uniting Antilophia+Chiroxiphia) might be enriched for cases of gene tree estimation error, so we conducted analyses that either constrained those gene trees to include monophyly of Antilophia+Chiroxiphia or excluded these loci. While constraining trees reduced some incongruence, excluding the trees led to completely congruent species trees, regardless of the data type or model of sequence evolution used. We found that a suite of gene metrics (most importantly the number of informative sites and likelihood of intralocus recombination) collectively explained the loci that resulted in non-monophyly of Antilophia+Chiroxiphia. We also found evidence for introgression that may have contributed to the discordant topologies we observe in Antilophia+Chiroxiphia and led to deviations from expectations given the multi-species coalescent model. Our study highlights the importance of identifying factors that can obscure phylogenetic signal when dealing with recalcitrant phylogenetic problems, such as gene tree estimation error, incomplete lineage sorting and reticulation events.

Data : Planktic-benthic foraminifera ratio (%P) as a tool for the reconstruction of paleobathymetry and geohazard: A case study from Taiwan

Details of the core sites used in this study, gear used for recovery, sediment horizon analyzed, coordinates,  water depth and foraminiferal data for the size fractions of >125 µm and >63 µm (only a subset of all the sites). Study sites are divided into East Taiwan that comprises the Southern Okinawa Trough (1), Nanao-Hoping-Hateruma Basins (2), and Taitung-Hualien (3). The area of West Taiwan is consisted of the Gaoping (4), Changchun sand Ridge (5), and Henghun Ridge (6) sectors. Gear for recovery are Box core (BC); Gravity core (GC) and Grab (G). Italic numbers in TOC column (in red) are average values, italic numbers in the Laboratory column show the laboratory where the TOC and C/N were analysed, namely Geosciences-NTU (1) , Institute of Oceanography-NTU (2) and National Sun-yat sen University (3). NaN= no available data.

Seismicity modulation due to hydrological loading in a stable continental region: a case study from the Jektvik swarm sequence in Northern Norway

This folder contains earthquake catalog used in "Seismicity modulation due to hydrological loading in a stable continental region: a case study from the Jektvik swarm sequence in Northern Norway" by Shiddiqi et al. (2022) submitted to Geophysical Journal International. note: unrelocated earthquakes are marked with 999 in location errors.

Earthquake catalog for "Seismicity modulation due to hydrological loading in a stable continental region: a case study from the Jektvik swarm sequence in Northern Norway"

opencc-by-4.0Jan 2022View details →

Reproduction Package for SAS 2022 Article 'Case Study on Verification-Witness Validators: Where We Are and Where We Go'

This artifact is a reproduction package for the SAS 2022 article 'Case Study on Verification-Witness Validators: Where We Are and Where We Go'. It contains instructions, data, and scripts for reproducing our results, and the data and tables that we generated in our experiment.

opencc-zeroSep 2022View details →

Data from: Evaluating species richness using proteomic fingerprinting and DNA-barcoding – a case study on meiobenthic copepods from the Clarion Clipperton Fracture Zone

The Clarion Clipperton Fracture Zone (CCZ) is a vast deep-sea region harboring a highly diverse benthic fauna, which will be affected by potential future deep-sea mining of metal-rich polymetallic nodules. Despite the need for conservation plans and monitoring strategies in this context, the majority of taxonomic groups remains scientifically undescribed. However, molecular rapid assessment methods such as DNA-barcoding and Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) provide the potential to accelerate specimen identification and biodiversity assessment significantly in the deep-sea areas. In this study, we successfully applied both methods to investigate the diversity of meiobenthic copepods in the eastern CCZ, including the first application of MALDI-TOF MS for the identification of these deep-sea organisms. Comparing several different species delimitation tools for both datasets, we found that biodiversity values were very similar, with Pielou's Evenness varying between 0.97 and 0.99 in all datasets. Still, direct comparisons of species clusters revealed differences between all techniques and methods, which are likely caused by the high number of rare species being represented by only one specimen, despite our extensive dataset of more than 2000 specimens. Hence, we regard our study as a first approach toward setting up a reference library for mass spectrometry data of the CCZ in combination with DNA-barcodes. We conclude that proteome fingerprinting, as well as the more established DNA-barcoding, can be seen as a valuable tool for rapid biodiversity assessments in the future, even when no reference information is available.

opencc-by-4.0Jul 2022View details →

Fine-scale subpopulation detection via SNP-based unsupervised method: A case study on the 1000 Genomes Project Resources

Here are the supplementary files to the paper "Fine-scale subpopulation detection via SNP-based unsupervised method: A case study on the 1000 Genomes Project Resources". The repository is organized as: <ol> <li>Supplementary information: the additional detailed information for the experiments in the paper <ul> <li>Supplementary_information_IPCAPS_Chaichoompu_v1.pdf</li> </ul> </li> <li>Real-life dataset: the 1000 genome dataset, which is referred to in the paper and is filtered with the parameters explained in the paper. Reference: https://www.internationalgenome.org/ <ul> <li>1000genomes_with_filtering.zip</li> </ul> </li> </ol>

opencc-zeroOct 2022View details →

Dataset for: On the estimation of body mass in temnospondyls: A case study using the large-bodied Eryops and Paracyclotosaurus

Temnospondyli are a morphologically varied and ecologically diverse clade of tetrapods that survived for over 200 million years. The body mass of temnospondyls is a key variable in inferring their ecological, physiological, and biomechanical attributes. However, estimating the body mass of these extinct creatures has proven difficult because the group has no extant descendants. Here we apply a wide range of body mass estimation techniques developed for tetrapods to the iconic temnospondyls Paracyclotosaurus davidi and Eryops megacephalus. These same methods are also applied to a collection of extant organisms that serve as ecological and morphological analogues. These include the giant salamanders Andrias japonicus and Andrias davidianus, the tiger salamander Ambystoma tigrinum, the California newt Taricha torosa, and the saltwater crocodile, Crocodylus porosus. We find that several methods can provide accurate mass estimations across this range of living taxa, suggesting their suitability for estimating the body masses of temnospondyls. Based on this, we estimate the mass of Paracyclotosaurus was between 159 and 365 kg, and Eryops was between 102 and 222 kg. These findings provide a basis for examining body size evolution in this clade across their entire temporal span.

opencc-by-4.0Nov 2022View details →

Legal Case Document Summarization: Extractive and Abstractive Methods and their Evaluation

This repository contains the following 3 datasets for legal document summarization : - IN-Abs : Indian Supreme Court case documents & their `abstractive' summaries, obtained from http://www.liiofindia.org/in/cases/cen/INSC/ - IN-Ext : Indian Supreme Court case documents & their `extractive' summaries, written by two law experts (A1, A2). - UK-Abs : United Kingdom (U.K.) Supreme Court case documents & their `abstractive' summaries, obtained from https://www.supremecourt.uk/decided-cases/ Please refer to the paper and the README file for more details.

opencc-zeroOct 2022View details →

Morphometry of the pedipalp patella provides new characters for species-level taxonomy in whip spiders (Arachnida, Amblypygi): A test case with description of a new species of Phrynus

Whip spiders (Amblypygi Thorell, 1883) are easily distinguished from their spider relatives (Araneae Clerck, 1757) by their raptorial pedipalps, the second pair of appendages, which are covered in spines and used to grasp and impale prey. Among other characters, the number, distribution, and size differences among the pedipalp spines continue to be important for whip spider systematics at different levels in the taxonomic hierarchy. However, traditional meristic and qualitative characters used to describe the pedipalp spines often limit their use for species-level taxonomy, as character states are invariant or overlapping. The present study employs landmark-based morphometrics to map the morphospace comprising the retrolateral surface of the pedipalp patella and its dorsal spines in a group of Neotropical whip spiders of the genus Phrynus Lamarck, 1801, all of which share an inconspicuous spine on the prolateral surface of the pedipalp tarsus, i.e., "group B" proposed by Quintero (1983). The analysis presented demonstrates that the relative pedipalp patella lengths and spine to pedipalp patella width ratios are of similar use for species diagnosis as the commonly employed relative length of leg femur I. Importantly, the analysis reveals that, beyond the traditional approach of qualitatively reporting relative pedipalp patella dorsal spine lengths (e.g., P3 > P5 > P2 > P4 > P6 > P1), the ratios between spine lengths are useful morphometric characters for species-level taxonomy in Phrynus. New morphometric ratios are provided for the species of Phrynus group B and used, together with traditional characters, to describe Phrynus guarionexi sp. nov. from the Dominican Republic. Finally, new morphological data are provided concerning the cerotegument, frontal process and prolateral surface of the pedipalp tibia in the species of group B.