cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26188/23294693.v1
title: Upper Limb Forward-reaching Data from Non-disabled Human Subjects

description: This dataset captures the upper limb and trunk movement kinematics, as well as surface electromyography (sEMG) data from 7 upper-arm muscles, of 10 non-disabled human subjects. The data was collected during forward-reaching actions toward 9 spatial locations in the parasagittal plane. The dataset can be used to analyze human movement patterns and develop algorithms for the control of movement in assistive robotic devices, such as powered prostheses. The experiment was conducted in a virtual reality (VR) environment using a head-mounted display (HMD). The spatial locations of the targets are designed to elicit specific upper limb joint displacements. The kinematics recorded include shoulder, scapular, and trunk movements. The muscles monitored include biceps brachii short/long head, triceps brachii lateral/long head, and anterior/middle/posterior deltoid. <br> For more details please refer to the GitHub repository with the link in the Related Material.
DOI: 10.5281/zenodo.8004388
title: MR to Ultrasound Registration for Prostate Challenge - Dataset

description: Multimodal image registration between pre-operative and intra-operative imaging enables the fusion of clinically important information during many surgical and interventional tasks. The registration of magnetic resonance imaging (MRI) and transrectal ultrasound (TRUS) images assists prostate biopsy and focal therapy, arguably having transformed prostate cancer patient care to a less invasive and more localized diagnostic, monitoring and treatment pathway. Though, even with great progress having been made by the community in the past two decades, challenges remain in this application. First, paired MRI and TRUS data from a sizable patient cohort are not routinely stored in clinical practice, and publicly-accessible data is scarce and low-quality. Second, annotating anatomical and pathological landmarks on both images - critical in representing corresponding locations for validation - requires expert domain knowledge and experience from multiple disciplines including urology, radiology and pathology. In addition to its prevalence-warranted clinical importance, this is also a unique application that saw a wide range of registration algorithms proposed and housed intriguing debates such as rigid-versus-nonrigid and FLE-versus-TRE. Both feature- and intensity-based classical methods and unsupervised or segmentation-driven learning methods have been innovated with some most technically interesting approaches in the field such as biomechanical regularisation and statistical motion modelling. The mu-Reg challenge aims to provide well-curated, yet real-world clinical data, with more than a hundred paired MR and TRUS images, annotated carefully by researchers and clinicians with more than 15 years of experience working with this application. The outcome of the challenge includes one of the first multimodal imaging data, facilitated with expert annotations for validation, for benchmarking advancement in registration methodology, as well as for future research in managing the most common non-skin cancer in men. --- <strong>The training and validation data may be used within the research remit of this challenge and in further research-related publications. The training and validation data are not to be used commercially. However, if the desired use is unclear, the organizers ask that those accessing the data refrain from further use or distribution outside of this challenge.</strong> --- Challenge information is accessible at: https://muregpro.github.io/
DOI: 10.6084/m9.figshare.23295002
title: Supplementary Material for: Cognitive Activities, Lifestyle Factors and Risk of Cognitive Impairment, With an Analysis of the Apolipoprotein Epsilon 4 Genotype

description: Introduction: Cognitive stimulating activities and a healthy lifestyle are associated with less cognitive impairment. However, whether the association is varied by Apolipoprotein epsilon 4 (APOE ε4) allele carrier status remains inconclusive. We aimed to investigate whether the association of cognitively stimulating activities and a healthy lifestyle with the risk of cognitive impairment varied by APOE ε4 allele carrier status. Methods: A case-control study was conducted for adults aged 60 years and above. Six province administrative units (Beijing, Shanghai, Hubei, Sichuan, Guangxi, and Yunnan) were included using stratified multi-stage cluster sampling. A total of 1300 individuals were identified with cognitive impairment (cases) at enrollment and were matched 1:2 on sex, age (±2 years), and residential district with controls who were cognitively normal at the time of the evaluation. We used a standardized questionnaire to collect information on cognitive stimulating activities, lifestyle factors, demographics, and comorbidity. Cognitive stimulating activities included reading books or newspapers, playing cards or mahjong, using the Internet, socializing with neighbors, and community activities. Lifestyle factors included smoking, alcohol drinking, daily tea drinking, and regular exercise. We used logistic regression to assess the interaction between cognitive stimulating activities, lifestyle factors, and APOE ε4 allele carrier status (yes/no) on the risk of cognitive impairment. We tested for additive interaction by estimating relative excess risk (RERI) due to interaction and multiplicative interaction employing the P value of the interaction term of each lifestyle factor and APOE ε4 into the model. Results: Four cognitive stimulating activities were associated with less cognitive impairment regardless of APOE ε4 status. Using the Internet (odds ratio [OR] 0.53, 95% confidence interval [CI], 0.30-0.95), daily tea drinking (OR 0.79; 95% CI, 0.63-0.98), and regular exercise (OR 0.78; 95% CI, 0.65-0.94) were associated with less cognitive impairment only in non-carriers. Multiplicative and additive interactions were found between community activities and APOE ε4 carrier status (Multiplicative P value=.03; RERI 0.738, 95% CI, 0.201-1.275). Conclusion: The associations between cognitive activities and cognitive impairment were robust regardless of the APOE ε4 carrier status, while the associations between lifestyle factors and cognitive impairment varied by APOE ε4 carrier status.
DOI: 10.5281/zenodo.7957277
title: Dataset: Green light during incubation: effects on hatching characteristics in brown and white laying hens

description: Dataset used for the paper "Green light during incubation: effects on hatching characteristics in brown and white laying hens".<br> <br> Abstract: Providing light during incubation is being investigated as a method to improve welfare in later life in poultry. This incubation method would more closely approximate chicken natural environment compared to the current incubation in darkness. Previous studies showed promising results of light during incubation on broiler welfare, but little is known about effects of light during incubation on laying hens. Especially, information about its effects on hatching characteristics (hatch time, hatchability, chick quality, body weight and embryonic age of death) is scarce and requires investigation in both white and brown egg layers. In the current study, Dekalb White (DW) and ISA Brown (ISA) eggs were incubated in complete darkness (dark) or in a light:dark cycle of 12L:12D throughout incubation (light), resulting in four treatment groups: DW-dark, DW-light, ISA-dark, and ISA-light. In the light treatments, green LEDs of 520nm wavelength were used, at an intensity of 400 lux. First, light transmission through the eggshell was measured through 27 eggs. Then, an analysis of the effects of light during incubation on hatching characteristics was performed on 711 chicks in two consecutive experimental rounds. Light transmission was higher through white eggshells than through brown eggshells (N = 27, p &lt; 0.001). Light during incubation had no effects on hatching characteristics (N = 711, p ≥ 0.1). Despite the difference of light transmission through eggshell between hybrids, there was no interaction between incubation treatment and hybrid on hatching characteristics (N = 471, p ≥ 0.06). Hatch time was longer and navel quality was better in DW than in ISA, while body weight and embryonic age of death were lower in DW than in ISA (all p &lt; 0.001). Males and females had similar chick quality scores except for the beak quality, which was better for males (N = 486, p = 0.003). To conclude, green light during incubation did not negatively affect hatching characteristics in either DW nor ISA laying hen hybrids. Future research should therefore focus on its potential benefits for laying hen welfare.
DOI: 10.5281/zenodo.7957278
title: Dataset: Green light during incubation: effects on hatching characteristics in brown and white laying hens

description: Dataset used for the paper "Green light during incubation: effects on hatching characteristics in brown and white laying hens".<br> <br> Abstract: Providing light during incubation is being investigated as a method to improve welfare in later life in poultry. This incubation method would more closely approximate chicken natural environment compared to the current incubation in darkness. Previous studies showed promising results of light during incubation on broiler welfare, but little is known about effects of light during incubation on laying hens. Especially, information about its effects on hatching characteristics (hatch time, hatchability, chick quality, body weight and embryonic age of death) is scarce and requires investigation in both white and brown egg layers. In the current study, Dekalb White (DW) and ISA Brown (ISA) eggs were incubated in complete darkness (dark) or in a light:dark cycle of 12L:12D throughout incubation (light), resulting in four treatment groups: DW-dark, DW-light, ISA-dark, and ISA-light. In the light treatments, green LEDs of 520nm wavelength were used, at an intensity of 400 lux. First, light transmission through the eggshell was measured through 27 eggs. Then, an analysis of the effects of light during incubation on hatching characteristics was performed on 711 chicks in two consecutive experimental rounds. Light transmission was higher through white eggshells than through brown eggshells (N = 27, p &lt; 0.001). Light during incubation had no effects on hatching characteristics (N = 711, p ≥ 0.1). Despite the difference of light transmission through eggshell between hybrids, there was no interaction between incubation treatment and hybrid on hatching characteristics (N = 471, p ≥ 0.06). Hatch time was longer and navel quality was better in DW than in ISA, while body weight and embryonic age of death were lower in DW than in ISA (all p &lt; 0.001). Males and females had similar chick quality scores except for the beak quality, which was better for males (N = 486, p = 0.003). To conclude, green light during incubation did not negatively affect hatching characteristics in either DW nor ISA laying hen hybrids. Future research should therefore focus on its potential benefits for laying hen welfare.
DOI: 10.5281/zenodo.8004765
title: Dataset: Green light during incubation: effects on hatching characteristics in brown and white laying hens

description: Dataset used for the paper "Green light during incubation: effects on hatching characteristics in brown and white laying hens".<br> <br> Abstract: Providing light during incubation is being investigated as a method to improve welfare in later life in poultry. This incubation method would more closely approximate chicken natural environment compared to the current incubation in darkness. Previous studies showed promising results of light during incubation on broiler welfare, but little is known about effects of light during incubation on laying hens. Especially, information about its effects on hatching characteristics (hatch time, hatchability, chick quality, body weight and embryonic age of death) is scarce and requires investigation in both white and brown egg layers. In the current study, Dekalb White (DW) and ISA Brown (ISA) eggs were incubated in complete darkness (dark) or in a light:dark cycle of 12L:12D throughout incubation (light), resulting in four treatment groups: DW-dark, DW-light, ISA-dark, and ISA-light. In the light treatments, green LEDs of 520nm wavelength were used, at an intensity of 400 lux. First, light transmission through the eggshell was measured through 27 eggs. Then, an analysis of the effects of light during incubation on hatching characteristics was performed on 711 chicks in two consecutive experimental rounds. Light transmission was higher through white eggshells than through brown eggshells (N = 27, p &lt; 0.001). Light during incubation had no effects on hatching characteristics (N = 711, p ≥ 0.1). Despite the difference of light transmission through eggshell between hybrids, there was no interaction between incubation treatment and hybrid on hatching characteristics (N = 471, p ≥ 0.06). Hatch time was longer and navel quality was better in DW than in ISA, while body weight and embryonic age of death were lower in DW than in ISA (all p &lt; 0.001). Males and females had similar chick quality scores except for the beak quality, which was better for males (N = 486, p = 0.003). To conclude, green light during incubation did not negatively affect hatching characteristics in either DW nor ISA laying hen hybrids. Future research should therefore focus on its potential benefits for laying hen welfare.
DOI: 10.25625/2phxnc/gjgoaw
title: example_reflexive_training.py

description: :unav
DOI: 10.25625/2phxnc/6wibfx
title: monaco_preprocessing.py

description: :unav
DOI: 10.25625/2phxnc/uaya5j
title: experiment.py

description: :unav
DOI: 10.25625/2phxnc/ojulzi
title: model_util.py

description: :unav
DOI: 10.25625/2phxnc/opnyxm
title: saved_model_tester.py

description: :unav
DOI: 10.25625/2phxnc/r3cqng
title: lamb.py

description: :unav
DOI: 10.25625/2phxnc/nkb8xm
title: passage.py

description: :unav
DOI: 10.25625/2phxnc/1jqxjt
title: example_training.py

description: :unav
DOI: 10.25625/2phxnc/9untuj
title: prediction_pipeline.py

description: :unav
DOI: 10.25625/2phxnc/xxje7m
title: __init__.py

description: :unav
DOI: 10.25625/2phxnc/khmnvx
title: multi_label_classification_model.py

description: :unav
DOI: 10.25625/2phxnc/oiis8n
title: sitent_preprocessing.py

description: :unav
DOI: 10.25625/2phxnc/tpks9e
title: example_xai.py

description: :unav
DOI: 10.25625/2phxnc/wonypz
title: custom_dataset.py

description: :unav
DOI: 10.25625/2phxnc/1lpc8b
title: trainer.py

description: :unav
DOI: 10.25625/2phxnc/mxzayn
title: clause.py

description: :unav
DOI: 10.25625/2phxnc/nvi3wp
title: label_util.py

description: :unav
DOI: 10.25625/2phxnc/hm8cvy
title: early_stopping.py

description: :unav
DOI: 10.25625/2phxnc/d6ooon
title: lime_clause.py

description: :unav
DOI: 10.25625/2phxnc/3yfrrs
title: multi_gbert-large_monaco_epochs_20_lamb_0.0001_None_dh_0.3_da_0.0.pt

description: :unav
DOI: 10.25625/2phxnc/fzrzcs
title: requirements.txt

description: :unav
DOI: 10.25625/2phxnc/ljbqln
title: xai_graphic_generator.py

description: :unav
DOI: 10.25625/2phxnc/ffdrbn
title: anchors_wrapper.py

description: :unav
DOI: 10.25625/2phxnc/8tp2sk
title: cage_preprocessing.py

description: :unav
DOI: 10.25625/2phxnc/yi11nv
title: conllu_parser.py

description: :unav
DOI: 10.25625/2phxnc/q6iftg
title: document.py

description: :unav
DOI: 10.25625/2phxnc/la5usl
title: binary_gbert-large_monaco_epochs_20_lamb_0.0001_None_dh_0.3_da_0.0.pt

description: :unav
DOI: 10.5281/zenodo.8004812
title: Microbiota-enabled Forecast of Global Grassland pH Dynamics under Future Climate Warming Scenarios

description: Affilted dataset for analysis and scripts for modelling.
DOI: 10.5281/zenodo.8004811
title: Microbiota-enabled Forecast of Global Grassland pH Dynamics under Future Climate Warming Scenarios

description: Affilted dataset for analysis and scripts for modelling.
DOI: 10.6084/m9.figshare.20237184
title: Global patterns fo population density in birds

description: Training dataset and Population density predictions for 9089 species (Appendix S2) Reference: Santini L., Tobias J., Callaghan C., Gallego-Zamorano J., Benítez López A. 2023. Global patterns and predictors of avian population density. <em>Global Ecology and Biogeography</em>
DOI: 10.6084/m9.figshare.20237184.v1
title: Global patterns fo population density in birds

description: Training dataset and Population density predictions for 9089 species (Appendix S2) Reference: Santini L., Tobias J., Callaghan C., Gallego-Zamorano J., Benítez López A. 2023. Global patterns and predictors of avian population density. <em>Global Ecology and Biogeography</em>
DOI: 10.5281/zenodo.8004806
title: An assessment of dentist's knowledge on technological advancements in the field of maxillo-facial prosthodontics - a survey

description: its an survey conducted on practicing dentist both undergraduate and postgraduate in private clinics on technological advancements in maxillofacial prosthesis. is there any difference between the general practitioners and specialized dentists.
DOI: 10.5281/zenodo.8004805
title: An assessment of dentist's knowledge on technological advancements in the field of maxillo-facial prosthodontics - a survey

description: its an survey conducted on practicing dentist both undergraduate and postgraduate in private clinics on technological advancements in maxillofacial prosthesis. is there any difference between the general practitioners and specialized dentists.
DOI: 10.5281/zenodo.8003300
title: IN-test-subset

description: This is my first upload
DOI: 10.5281/zenodo.8003299
title: IN-test-subset

description: This is my first upload
DOI: 10.6084/m9.figshare.14371344.v1
title: Table S5.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
DOI: 10.6084/m9.figshare.14371344
title: Table S5.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.
DOI: 10.6084/m9.figshare.14371347.v1
title: Table S1.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

description: Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.