cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15390905
title: Supplementary data for the manuscript, "Comprehensive Assessment of Physiochemical Metrics for the Clustering of Adaptive Immune Repertoires"

description: These files are a compilation of publicly available immune repertoire data and simulated immune repertoires used in the manuscript  "Comprehensive Assessment of Physiochemical Metrics for the Clustering of Adaptive Immune Repertoires" by Alexander Girgis et al.  In addition, data from the BLOCKS database (Henikoff and Henikoff, 1992) and AAIndex (Kawashima and Kanehisa, 2000) which are used in ths manuscript are included for convenience. Lastly, we include selected analysis scripts and code to clarify our methodology for the interested reader. The manuscript will be linked upon publication. 
description: A continued challenge in the analysis of adaptive immune receptor repertoires (AIRRs) is the prediction of antigen reactivity from primary sequence data. Many algorithms infer antigen-specific responses by measuring sequence similarity between receptors. Similarity is often scored using tools for protein alignment such as the BLOSUM matrices. However, these metrics were designed to identify homology in genomic proteins, not VDJ-recombined immune receptors. Comparison of these metrics against other approaches is underexplored. We sought to make physiochemical-based alternatives which may improve performance.  We evaluated the impact of these metrics by clustering 383 simulated and biological repertoires using traditional and physiochemical-based scoring matrices. While physiochemical and traditional scoring had similar efficacy, the membership of antigen-specific clusters varied.  Lastly, we inferred antigen-specific immune responses in pancreatic cancer and rheumatoid arthritis. Results varied depending on the matrix used, emphasizing a poor consensus among methods. Despite equivocal performance, physiochemical metrics can increase the interpretability of clustered data. These results suggest that analysts must carefully consider characteristics of sequence similarity measures to apply the most appropriate methods to their data. We facilitate further exploration of scoring metrics by centralizing AIRR clustering and physiochemical sequence characterization in a software tool called Homolig (Homol-Ig) associated with our analyses.
DOI: 10.5066/p138opd2
title: Macoma Clam Prey Identified by DNA Metabarcoding, 2018 and 2019, Alaska

description: This dataset describes sequence data derived from 18S ribosomal and ribulose bisphosphate carboxylase (rbcL) DNA. Stomach contents from 190 Macoma calcarea clams were examined for this study. Clams were collected from the Bering Sea and Chukchi Sea, Alaska in 2018 and 2019 using benthic van Veen grabs.
DOI: 10.15468/dl.x7gtnt
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "StateProvince is Tamaulipas",
 "TaxonKey is Loricariidae"
 ]
}

 The dataset includes 10 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026922-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fcezwq
title: Occurrence Download

description: A dataset containing 673950 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2025-04-17",
 "EventDate is less than or equal to 2025-05-17",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 673950 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026912-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mev8e3
title: Occurrence Download

description: A dataset containing 14476 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Digitalización y Sistematización de las Colecciones Biológicas Nacionales del Instituto de Biología, UNAM (vertebrados)",
 "OccurrenceStatus is Present",
 "PublishingOrg is ff90b050-c256-11db-b71b-b8a03c50a862",
 "TaxonKey is Squamata"
 ]
}

 The dataset includes 14476 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026923-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28150900
title: Genetic testing results of retinal dystrophies in a diverse population: impact of race and ethnicity

description: Due to the recent advent of gene-targeted retinal therapies, the clinical value of high-yield genetic testing for inherited retinal dystrophies (IRDs) has increased considerably. However, diagnostic yield is limited by the reported patient populations in allele frequency databases. This study aimed to determine the effect of race and ethnicity on diagnostic yield in IRDs. Retrospective review of individuals with suspected IRD based on clinical findings or diagnosis of associated syndrome who underwent genetic testing between 2009 and 2021. Self-reported race and ethnicity, ophthalmic examination findings, ERG results, and genetic testing findings were collected and analyzed. In 93 individuals (90 families) with suspected IRD, the diagnostic yield was 72% (67 individuals). The rate of diagnostic yield was not significantly associated with family history, associated syndromes, age at testing, ERG results, or ophthalmic exam findings. Further, higher rates of positive diagnostic yield were not associated with more recent genetic testing. There was a trend toward differences in diagnostic yield between races (77% White, 65% Other, 64% Asian, 50% Black) and ratio of pathogenic/likely pathogenic (P/LP) variants to variants of unknown significance (46%:54% White, 36%:64% Other, 31%:69% Asian, 30%:70% Black). Current genetic testing for IRDs trends toward higher diagnostic yield and identification of P/LP variants in patients identifying as White compared to other races. In order to prevent negative impacts on access to gene-targeted trials and treatments for non-White patients, wider genetic testing in diverse populations is required to create comprehensive catalogs of gene variants associated with IRDs.
DOI: 10.6084/m9.figshare.28150900.v1
title: Genetic testing results of retinal dystrophies in a diverse population: impact of race and ethnicity

description: Due to the recent advent of gene-targeted retinal therapies, the clinical value of high-yield genetic testing for inherited retinal dystrophies (IRDs) has increased considerably. However, diagnostic yield is limited by the reported patient populations in allele frequency databases. This study aimed to determine the effect of race and ethnicity on diagnostic yield in IRDs. Retrospective review of individuals with suspected IRD based on clinical findings or diagnosis of associated syndrome who underwent genetic testing between 2009 and 2021. Self-reported race and ethnicity, ophthalmic examination findings, ERG results, and genetic testing findings were collected and analyzed. In 93 individuals (90 families) with suspected IRD, the diagnostic yield was 72% (67 individuals). The rate of diagnostic yield was not significantly associated with family history, associated syndromes, age at testing, ERG results, or ophthalmic exam findings. Further, higher rates of positive diagnostic yield were not associated with more recent genetic testing. There was a trend toward differences in diagnostic yield between races (77% White, 65% Other, 64% Asian, 50% Black) and ratio of pathogenic/likely pathogenic (P/LP) variants to variants of unknown significance (46%:54% White, 36%:64% Other, 31%:69% Asian, 30%:70% Black). Current genetic testing for IRDs trends toward higher diagnostic yield and identification of P/LP variants in patients identifying as White compared to other races. In order to prevent negative impacts on access to gene-targeted trials and treatments for non-White patients, wider genetic testing in diverse populations is required to create comprehensive catalogs of gene variants associated with IRDs.
DOI: 10.6084/m9.figshare.28381058
title: Nationwide incidence and survival of retinoblastoma in the USA between 1996 and 2018: a review of 5730 cases

description: Retinoblastoma is the most common intraocular cancer in children, with significant variations in incidence and Survival. This study sought to evaluate nationwide retinoblastoma incidences and survival rates in the United States from 1996 to 2018. We extracted data from the North American Association of Central Cancer Registries (NACCR) and the National Program of Cancer Registries between 1996 and 2018. Cases were stratified by sex, age, race, Hispanic origin, urban or rural origin, stage of the disease, and state of residence and compared by laterality. We applied SEER*Stat version 8.4.0.1 software for age-adjusted incidence rates (AAIR) and annual average per cent change (AAPC) and JoinPoint version 4.9.1.0 software to assess incidence trends. Survival trends were evaluated with JPSurv online software. The study comprised 5730 patients with a crude incidence rate (CIR) of 0.89 per million. The incidence declined from 29.6 per million in the first year of life to 16.5 in the second year. The CIR for unilateral and bilateral diseases were 0.61 and 0.27, respectively. Males had a slightly higher and significant crude incidence of 0.93 versus 0.86 for females. Hispanics had the highest rate of 1.48 in general. Treatment data revealed chemotherapy usage in 39% of unilateral and 78% of bilateral patients. The 5-year cumulative relative Survival did not significantly differ between unilateral (96.8%) and bilateral (97.0%) patients. A slight but significant annual decline in CIR was observed, with a trend toward an increase in the percentage of patients diagnosed in the first year of life. This study indicated an overall decrease in incidence but a slight increase in early diagnosis. Findings underscore the need for consistent surveillance, early detection strategies, and personalized care to improve patient outcomes. The changes in the Survival in the unilateral disease require further investigations and mitigation strategies.
DOI: 10.6084/m9.figshare.28381058.v1
title: Nationwide incidence and survival of retinoblastoma in the USA between 1996 and 2018: a review of 5730 cases

description: Retinoblastoma is the most common intraocular cancer in children, with significant variations in incidence and Survival. This study sought to evaluate nationwide retinoblastoma incidences and survival rates in the United States from 1996 to 2018. We extracted data from the North American Association of Central Cancer Registries (NACCR) and the National Program of Cancer Registries between 1996 and 2018. Cases were stratified by sex, age, race, Hispanic origin, urban or rural origin, stage of the disease, and state of residence and compared by laterality. We applied SEER*Stat version 8.4.0.1 software for age-adjusted incidence rates (AAIR) and annual average per cent change (AAPC) and JoinPoint version 4.9.1.0 software to assess incidence trends. Survival trends were evaluated with JPSurv online software. The study comprised 5730 patients with a crude incidence rate (CIR) of 0.89 per million. The incidence declined from 29.6 per million in the first year of life to 16.5 in the second year. The CIR for unilateral and bilateral diseases were 0.61 and 0.27, respectively. Males had a slightly higher and significant crude incidence of 0.93 versus 0.86 for females. Hispanics had the highest rate of 1.48 in general. Treatment data revealed chemotherapy usage in 39% of unilateral and 78% of bilateral patients. The 5-year cumulative relative Survival did not significantly differ between unilateral (96.8%) and bilateral (97.0%) patients. A slight but significant annual decline in CIR was observed, with a trend toward an increase in the percentage of patients diagnosed in the first year of life. This study indicated an overall decrease in incidence but a slight increase in early diagnosis. Findings underscore the need for consistent surveillance, early detection strategies, and personalized care to improve patient outcomes. The changes in the Survival in the unilateral disease require further investigations and mitigation strategies.
DOI: 10.6084/m9.figshare.28141411
title: Association between gene polymorphisms and glaucoma susceptibility among Africans: a systematic review and meta-analysis

description: This study sought to analyze the effect of allele mutations and gene functions specific to glaucoma susceptibility among Africans. Potentially relevant studies were retrieved from major bibliographic databases (PubMed, Scopus, and Web of Science). Data were extracted and study-specific estimates were meta-analyzed using various models to obtain pooled results. A total of 11 studies were included in the study. The studies included a total of 3,191 cases with glaucoma and 3,013 controls across all variants. There is no association between the E396E variants of the myocilin (MYOC) gene and an increased likelihood of susceptibility to POAG (OR: 0.91 [95% CI 0.42 to 1.97]). The R141L variant of the Lysyl Oxidase Like 1 (LOXL1) gene is associated with an approximately 3-fold increased likelihood of susceptibility to exfoliative syndrome/exfoliative glaucoma (XFS/XFG) (OR: 2.68 [95% CI 0.04 to 198.94]). There is no association between the G153D variant of the LOXL1 gene and an increased likelihood of susceptibility to XFS/XFG (OR: 0.42 [95% CI 0.02 to 7.65]). The rs59892895*C variant of the Amyloid Beta Precursor Protein Binding Family B Member 2 (APBB2) is associated with a 34% increased likelihood of susceptibility to POAG (OR: 1.34 [95% CI 1.13 to 1.58]). Although progress has been made in understanding the genetic basis of the pathogenesis of glaucoma, several gene mutations related to glaucoma pathogenesis in Africans are yet to be discovered, especially those associated with the pathogenesis of POAG, the most prevalent glaucoma subtype in Africa.
DOI: 10.6084/m9.figshare.28141411.v1
title: Association between gene polymorphisms and glaucoma susceptibility among Africans: a systematic review and meta-analysis

description: This study sought to analyze the effect of allele mutations and gene functions specific to glaucoma susceptibility among Africans. Potentially relevant studies were retrieved from major bibliographic databases (PubMed, Scopus, and Web of Science). Data were extracted and study-specific estimates were meta-analyzed using various models to obtain pooled results. A total of 11 studies were included in the study. The studies included a total of 3,191 cases with glaucoma and 3,013 controls across all variants. There is no association between the E396E variants of the myocilin (MYOC) gene and an increased likelihood of susceptibility to POAG (OR: 0.91 [95% CI 0.42 to 1.97]). The R141L variant of the Lysyl Oxidase Like 1 (LOXL1) gene is associated with an approximately 3-fold increased likelihood of susceptibility to exfoliative syndrome/exfoliative glaucoma (XFS/XFG) (OR: 2.68 [95% CI 0.04 to 198.94]). There is no association between the G153D variant of the LOXL1 gene and an increased likelihood of susceptibility to XFS/XFG (OR: 0.42 [95% CI 0.02 to 7.65]). The rs59892895*C variant of the Amyloid Beta Precursor Protein Binding Family B Member 2 (APBB2) is associated with a 34% increased likelihood of susceptibility to POAG (OR: 1.34 [95% CI 1.13 to 1.58]). Although progress has been made in understanding the genetic basis of the pathogenesis of glaucoma, several gene mutations related to glaucoma pathogenesis in Africans are yet to be discovered, especially those associated with the pathogenesis of POAG, the most prevalent glaucoma subtype in Africa.
DOI: 10.6084/m9.figshare.28284327.v1
title: Whole genome sequencing of 10 families with optic disc drusen

description: Optic disc drusen (ODD) are believed to have a genetic predisposition, with autosomal dominant inheritance pattern with incomplete penetrance suggested through family pedigree analysis. ODD prevalence is higher in certain genetic disorders, such as pseudoxanthoma elasticum and retinitis pigmentosa. This study aimed to identify candidate genes potentially involved in the development of ODD. Family members aged 18 years or older from families with ODD were included. Participants underwent optical coherence tomography of the optic nerve head, and blood samples were collected for whole-genome sequencing using the Illumina NovaSeq 6000 platform. Single nucleotide variants were identified with the Genome Analysis Toolkit (GATK) and filtered in VarSeq using a population frequency threshold of 1%. Selected genes were classified according to ACMG guidelines. A total of 10 families were included, three of which had more than two affected members. Thirty-three variants were identified, with the following genes selected for description: <i>ABCC6, DDX50, TREX1, PLCB4, PTPRQ, LBR, RP1L1</i>, and <i>KRT3</i>. The identified candidate genes showed a wide range of functions and are associated with different disorders. Of particular interest is <i>ABCC6</i>, which normally inhibits ectopic calcification. We identified a list of candidate genes. Studies including larger ODD families are necessary to identify robust candidate genes.
DOI: 10.6084/m9.figshare.28284327
title: Whole genome sequencing of 10 families with optic disc drusen

description: Optic disc drusen (ODD) are believed to have a genetic predisposition, with autosomal dominant inheritance pattern with incomplete penetrance suggested through family pedigree analysis. ODD prevalence is higher in certain genetic disorders, such as pseudoxanthoma elasticum and retinitis pigmentosa. This study aimed to identify candidate genes potentially involved in the development of ODD. Family members aged 18 years or older from families with ODD were included. Participants underwent optical coherence tomography of the optic nerve head, and blood samples were collected for whole-genome sequencing using the Illumina NovaSeq 6000 platform. Single nucleotide variants were identified with the Genome Analysis Toolkit (GATK) and filtered in VarSeq using a population frequency threshold of 1%. Selected genes were classified according to ACMG guidelines. A total of 10 families were included, three of which had more than two affected members. Thirty-three variants were identified, with the following genes selected for description: <i>ABCC6, DDX50, TREX1, PLCB4, PTPRQ, LBR, RP1L1</i>, and <i>KRT3</i>. The identified candidate genes showed a wide range of functions and are associated with different disorders. Of particular interest is <i>ABCC6</i>, which normally inhibits ectopic calcification. We identified a list of candidate genes. Studies including larger ODD families are necessary to identify robust candidate genes.
DOI: 10.5281/zenodo.15390668
title: TABLE 1 in Description of a new species of Lasiocesa Koçak from miombo woodlands in Malawi (Lepidoptera, Lasiocampidae, Lasiocampinae, Pinarini)

description: TABLE 1. Data on Lasiocesa specimens and their complete barcodes (658 bp, except for LBEOA1850-12 – 634 bp) deposited in BOLD and used to compute p -distances.
Species / BINSequence pageSpecimen details and collection data (depository)L. dogma / BOLD: ABA6919GWOSW170-11♂, Cameroon, Centre, Obout Bezirk, Nkolmetet (bei Mbalmayo), 3.48961, 11.78478, 654 m, 2008-11-20, leg. M. Ochse (ZSM)GWOTB487-12♂, Ghana, Western, Ankasa National Park, 16 km east of Elubo, 1 km southeast of Nkwanta camp, Exploration Base, 5.27478, -2.64611, 103 m, 2005-04-30, leg. M. Ochse (ZSM)LBEOA1306-11♂, Liberia, Putu Range, 5.6672, -8.18694, 2010-12-20–2011-01-05, leg. Sz. Safian & E. Zakar (RMCA)LBEOA1595-11♂, Ghana, Central, Kakum Forest NP, Gyawale Forest, 5.59, 1.11833, 200 m, 2011-11-20, leg. V. Zolotuhin (CGM)L. ladislavi sp. n. / BOLD: AAY8467LBEOA117-11♀, Malawi, Northern, Rhumphi District, Nyika National Park, -10.436, 33.392, 1935 m, 2010-12-23, leg. V. Anikin (CGM)LBEOA1850-12♂, Malawi, Northern, Rumphi District, Nyika National Park, -10.72778, 33.65306, 1923 m, 2011-12-31, leg. V. Anikin (CGM)LBEOW1988-11♂, Malawi, Northern, Rumphi District, Nyika National Park, -10.72778, 33.65306, 1923 m, 2010-12-23, leg. V. Kovtunovich & P. Ustjuzhanin (CGM)
description: Published as part of Revay, Edita E., Prozorova, Tatiana A., Junnila, Amy, Yakovlev, Roman V., Saldaitis, Aidas, Volkova, Julia S., Sulak, Harald, Müller, Günter C. & Prozorov, Alexey M., 2025, Description of a new species of Lasiocesa Koçak from miombo woodlands in Malawi (Lepidoptera, Lasiocampidae, Lasiocampinae, Pinarini), pp. 322 in Zootaxa 5631 (2) on page 322, DOI: 10.11646/zootaxa.5631.2.5, http://zenodo.org/record/15370626
DOI: 10.5281/zenodo.15390670
title: TABLE 2 in Description of a new species of Lasiocesa Koçak from miombo woodlands in Malawi (Lepidoptera, Lasiocampidae, Lasiocampinae, Pinarini)

description: TABLE 2. Uncorrected pairwise distances (%) between Lasiocesa spp.
SpeciesL. dogma / BOLD: ABA6919L. ladislavi sp. n. / BOLD: AAY8467Sequence pageGWOSW 170 - 11GWOTB 487- 12LBEOA 1306 -11LBEOA1595 - 11LBEOA117 - 11LBEOA 1850 - 12LBEOW 1988 - 11GWOSW170-110.161.420.007.417.417.41GWOTB487-120.161.580.167.577.577.57LBEOA1306-111.421.581.427.107.107.10LBEOA1595-110.000.161.427.417.417.41LBEOA117-117.417.577.107.410.000.00LBEOA1850-127.417.577.107.410.000.00LBEOW1988-117.417.577.107.410.000.00
description: Published as part of Revay, Edita E., Prozorova, Tatiana A., Junnila, Amy, Yakovlev, Roman V., Saldaitis, Aidas, Volkova, Julia S., Sulak, Harald, Müller, Günter C. & Prozorov, Alexey M., 2025, Description of a new species of Lasiocesa Koçak from miombo woodlands in Malawi (Lepidoptera, Lasiocampidae, Lasiocampinae, Pinarini), pp. 323 in Zootaxa 5631 (2) on page 323, DOI: 10.11646/zootaxa.5631.2.5, http://zenodo.org/record/15370626
DOI: 10.17632/v3rkt89p4f.1
title: InBody_Scan_Dataset

description: The dataset contains detailed body composition profiling of 4,328 individuals as done by the InBody770, a certified medical body composition analyzer. The 131 records with 231 parameters cover a broad variety of physiological metrics such as total and segmental water contents, muscle contents, fat content, visceral fat area, percentages of body fat, and some important derived ratios like ECW/TBW and SMM/Weight. The data was downloaded from the internal hard disk of InBody770 directly in the standardized PDF form to offer utmost standard uniformity and accuracy for every entry. After automated conversion and cleaning steps, the data were organized into machine learning-ready format with separate sets of features: demographics, anthropometric, body composition, and metabolic risk indicators. High-resolution data offers the construction of predictive models for metabolic health risk and allows for stratified analyses based on gender, age, and BMI. Given the sheer size, granularity, and standardization of the dataset, it becomes a quintessential research instrument in support of preventive healthcare, digital biomarker discovery, and AI-assisted health risk classification.
DOI: 10.17632/rtytpmt7w8.1
title: Supplemental Material: An Alternative Method for Postoperative Scalpel Blade Removal

description: Our video shows an alternative method for postoperative scalpel blade removal that can be used in a surgical setting