cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.k3ypj2
title: Occurrence Download

description: A dataset containing 240 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aloidendron ramosissimum"
 ]
}

 The dataset includes 240 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030209-251025141854904/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.29037187
title: Interstitial lung disease recurrence on chemotherapy rechallenge in breast cancer: a nationwide Japanese database

description: The present study assessed the incidence of drug-induced interstitial lung disease (ILD) recurrence among breast cancer patients who underwent rechallenge with cancer-directed therapy. Japanese insurance claims data and the Diagnosis Procedure Combination database (2009–2022) involving 81,601 patients were analyzed to evaluate 1,042 breast cancer patients who developed ILD. Of these, 566 patients underwent cancer-directed therapy rechallenge, and 42.1% of them were re-challenged with the same therapeutic regimen that caused the initial ILD. ILD recurrence was observed in 18.9% of the patients, with a median recurrence time of 40 days. The drugs most commonly causing ILD were cytotoxic agents, and those most frequently used for rechallenge were cytotoxic agents.   A notable ILD recurrence rate was observed in breast cancer patients after a cancer-directed therapy rechallenge, highlighting the need for cautious treatment planning and personalised strategies to balance cancer control while mitigating ILD risk. This article discusses a study that researched a lung condition known as interstitial lung disease (ILD) in individuals with breast cancer who were treated again with cancer-directed therapy after recovering from ILD. ILD involves inflammation and damage to the lungs and can be a serious side effect of cancer treatment. We analyzed data from Japanese health insurance claims and hospital records from 2009 to 2022, of 81,601 patients with breast cancer, 1,042 developed ILD that required treatment with steroids. Of the 1,042 patients, 566 underwent cancer-directed therapy again after their initial ILD episode. The findings showed that approximately 19% of these patients experienced ILD recurrence, typically approximately 40 days after they had started cancer-directed therapy again. The most common rechallenge therapy for these patients was cytotoxic drugs, which are powerful and used to kill cancer cells. The results of this study highlight the risk of ILD recurrence in patients with breast cancer who undergo cancer-directed therapy again. This insight is crucial for doctors and patients when deciding on cancer treatments, especially after a patient has already had ILD. This demonstrates the importance of careful planning and personalized treatment strategies to manage the risk of ILD while attempting to effectively control cancer. This study helps in understanding the trade-off between treating cancer to protect patients while not causing serious side effects such as ILD.
DOI: 10.6084/m9.figshare.29037187.v1
title: Interstitial lung disease recurrence on chemotherapy rechallenge in breast cancer: a nationwide Japanese database

description: The present study assessed the incidence of drug-induced interstitial lung disease (ILD) recurrence among breast cancer patients who underwent rechallenge with cancer-directed therapy. Japanese insurance claims data and the Diagnosis Procedure Combination database (2009–2022) involving 81,601 patients were analyzed to evaluate 1,042 breast cancer patients who developed ILD. Of these, 566 patients underwent cancer-directed therapy rechallenge, and 42.1% of them were re-challenged with the same therapeutic regimen that caused the initial ILD. ILD recurrence was observed in 18.9% of the patients, with a median recurrence time of 40 days. The drugs most commonly causing ILD were cytotoxic agents, and those most frequently used for rechallenge were cytotoxic agents.   A notable ILD recurrence rate was observed in breast cancer patients after a cancer-directed therapy rechallenge, highlighting the need for cautious treatment planning and personalised strategies to balance cancer control while mitigating ILD risk. This article discusses a study that researched a lung condition known as interstitial lung disease (ILD) in individuals with breast cancer who were treated again with cancer-directed therapy after recovering from ILD. ILD involves inflammation and damage to the lungs and can be a serious side effect of cancer treatment. We analyzed data from Japanese health insurance claims and hospital records from 2009 to 2022, of 81,601 patients with breast cancer, 1,042 developed ILD that required treatment with steroids. Of the 1,042 patients, 566 underwent cancer-directed therapy again after their initial ILD episode. The findings showed that approximately 19% of these patients experienced ILD recurrence, typically approximately 40 days after they had started cancer-directed therapy again. The most common rechallenge therapy for these patients was cytotoxic drugs, which are powerful and used to kill cancer cells. The results of this study highlight the risk of ILD recurrence in patients with breast cancer who undergo cancer-directed therapy again. This insight is crucial for doctors and patients when deciding on cancer treatments, especially after a patient has already had ILD. This demonstrates the importance of careful planning and personalized treatment strategies to manage the risk of ILD while attempting to effectively control cancer. This study helps in understanding the trade-off between treating cancer to protect patients while not causing serious side effects such as ILD.
DOI: 10.6084/m9.figshare.28684119
title: Systematic literature review of the epidemiology of neurotrophic tyrosine receptor kinase positive solid tumor sites

description: This study aimed to expand on existing systematic literature reviews (SLRs) by assessing the prevalence of neurotrophic tyrosine receptor kinase (NTRK) fusion-positive mutations across solid tumors in adult U.S populations. It further evaluated incidence, testing, treatment, mortality, and progression rates by tumor type, extending evidence through 2023. A SLR was conducted following Cochrane and PRISMA guidelines, with searches across Ovid Embase, Ovid MEDLINE, and Cochrane Library databases for studies published from 2013 to August 2023. Eligibility criteria included studies on NTRK fusion-positive tumors in patients aged ≥12 years. Data were extracted and assessed using the Newcastle-Ottawa Scale and JBI checklist. This SLR identified 160 studies, reporting NTRK fusion prevalence ranging from 0.03% to 0.70% across solid tumors. TRK inhibitors, particularly larotrectinib and entrectinib, were commonly used treatments. Prevalence varied significantly by cancer type, being higher in rarer cancers, such as papillary thyroid carcinoma (up to 21.4%). NTRK fusions are rare, with wide prevalence variability among cancer types. The findings highlight the need for standardized diagnostic methods and larger real-world studies to improve prevalence estimates and assess the impact of NTRK fusions on outcomes, ultimately aiding in the optimization of targeted treatments for affected patients.
DOI: 10.6084/m9.figshare.28684119.v1
title: Systematic literature review of the epidemiology of neurotrophic tyrosine receptor kinase positive solid tumor sites

description: This study aimed to expand on existing systematic literature reviews (SLRs) by assessing the prevalence of neurotrophic tyrosine receptor kinase (NTRK) fusion-positive mutations across solid tumors in adult U.S populations. It further evaluated incidence, testing, treatment, mortality, and progression rates by tumor type, extending evidence through 2023. A SLR was conducted following Cochrane and PRISMA guidelines, with searches across Ovid Embase, Ovid MEDLINE, and Cochrane Library databases for studies published from 2013 to August 2023. Eligibility criteria included studies on NTRK fusion-positive tumors in patients aged ≥12 years. Data were extracted and assessed using the Newcastle-Ottawa Scale and JBI checklist. This SLR identified 160 studies, reporting NTRK fusion prevalence ranging from 0.03% to 0.70% across solid tumors. TRK inhibitors, particularly larotrectinib and entrectinib, were commonly used treatments. Prevalence varied significantly by cancer type, being higher in rarer cancers, such as papillary thyroid carcinoma (up to 21.4%). NTRK fusions are rare, with wide prevalence variability among cancer types. The findings highlight the need for standardized diagnostic methods and larger real-world studies to improve prevalence estimates and assess the impact of NTRK fusions on outcomes, ultimately aiding in the optimization of targeted treatments for affected patients.
DOI: 10.6084/m9.figshare.28684580
title: Comparison of mTOR inhibitors combined with endocrine therapy versus that alone in breast cancer: a meta-analysis

description: This meta-analysis aims to evaluate the efficacy and safety of rapamycin (mTOR) inhibitors with endocrine therapy versus endocrine therapy alone in treating advanced or metastatic estrogen receptor/progesterone receptor (ER/PR) + breast cancer. We conducted a comprehensive search in PubMed, Web of Science, Embase, and the Cochrane Library for randomized controlled trials (RCTs) comparing mTOR inhibitors plus endocrine therapy with endocrine therapy alone up to September 2024. This analysis included 10 RCTs comprising 3,337 patients. Relative to endocrine therapy alone, the combination of mTOR inhibitors and endocrine therapy significantly improved the clinical benefit rate (RR = 1.41, <i>p</i> &lt; 0.001), overall response rate (RR = 1.40, <i>p</i> = 0.006), progression-free survival (PFS; HR = 0.67, <i>p</i> &lt; 0.001), and overall survival (OS; HR = 0.86, <i>p</i> = 0.056), although the improvement in OS was not statistically significant. Subgroup analyses indicated a more pronounced PFS advantage in patients under 65 years of age (HR = 0.55, <i>p</i> = 0.013) and those who had previously received chemotherapy (HR = 0.51, <i>p</i> = 0.001). However, the incidence of adverse events was higher in the combination therapy group, notably stomatitis (<i>p</i> &lt; 0.001), elevated aspartate aminotransferase/alanine aminotransferase (<i>p</i> = 0.04), and diarrhea (<i>p</i> = 0.01). The combination of mTOR inhibitors with endocrine therapy offers superior efficacy with manageable toxicities in patients with advanced or metastatic ER/PR+ breast cancer.
DOI: 10.6084/m9.figshare.28684580.v1
title: Comparison of mTOR inhibitors combined with endocrine therapy versus that alone in breast cancer: a meta-analysis

description: This meta-analysis aims to evaluate the efficacy and safety of rapamycin (mTOR) inhibitors with endocrine therapy versus endocrine therapy alone in treating advanced or metastatic estrogen receptor/progesterone receptor (ER/PR) + breast cancer. We conducted a comprehensive search in PubMed, Web of Science, Embase, and the Cochrane Library for randomized controlled trials (RCTs) comparing mTOR inhibitors plus endocrine therapy with endocrine therapy alone up to September 2024. This analysis included 10 RCTs comprising 3,337 patients. Relative to endocrine therapy alone, the combination of mTOR inhibitors and endocrine therapy significantly improved the clinical benefit rate (RR = 1.41, <i>p</i> &lt; 0.001), overall response rate (RR = 1.40, <i>p</i> = 0.006), progression-free survival (PFS; HR = 0.67, <i>p</i> &lt; 0.001), and overall survival (OS; HR = 0.86, <i>p</i> = 0.056), although the improvement in OS was not statistically significant. Subgroup analyses indicated a more pronounced PFS advantage in patients under 65 years of age (HR = 0.55, <i>p</i> = 0.013) and those who had previously received chemotherapy (HR = 0.51, <i>p</i> = 0.001). However, the incidence of adverse events was higher in the combination therapy group, notably stomatitis (<i>p</i> &lt; 0.001), elevated aspartate aminotransferase/alanine aminotransferase (<i>p</i> = 0.04), and diarrhea (<i>p</i> = 0.01). The combination of mTOR inhibitors with endocrine therapy offers superior efficacy with manageable toxicities in patients with advanced or metastatic ER/PR+ breast cancer.
DOI: 10.6084/m9.figshare.28776475.v1
title: Cost-effective shallow genome-wide sequencing for profiling plasma cfDNA signatures to enhance lung cancer detection

description: Lung cancer (LC) screening via low-dose computed tomography (LDCT) faces challenges including high false-positive rates and low patient compliance. Circulating tumor DNA (ctDNA)-based tests offer a minimally invasive alternative but are limited by high costs and low sensitivity, particularly in early-stage detection. This study introduces a cost-effective, shallow genome-wide sequencing approach for LC detection by profiling multiple cell-free DNA (cfDNA) signatures. We developed a multimodal cfDNA assay with shallow sequencing coverage (0.5×) that integrates fragmentomic, nucleosome, end-motif, and copy number alteration analyses. A machine-learning model trained on a discovery cohort (99 LC patients, 168 healthy controls) and validated on an independent cohort (58 LC patients, 71 controls) demonstrated robust performance. The ensemble model exhibited outstanding performance, achieving an AUC of 0.97 and a specificity of 92% in both the discovery and validation cohorts, with sensitivities of 94% and 90%, respectively. Notably, it outperformed hotspot mutation-based assays and the multi-cancer SPOT-MAS assay in sensitivity across all LC stages. This assay provides a cost-effective, accurate, and minimally invasive method for LC detection, addressing the limitations of current screening methods. It represents a promising complementary tool to improve early detection and patient outcomes in LC. Lung cancer screening can be expensive and sometimes gives false positives, leading to unnecessary worry and extra tests. Many people also skip screening because it is inconvenient. A simple blood test could be a better option, but current ones are costly and not always accurate for early detection. In this study, researchers developed an affordable blood test that looks at tiny fragments of DNA in the blood. They used machine learning to train the test on samples from lung cancer patients and healthy people, then its accuracy was checked on a separate group. The test correctly detected lung cancer in 90% of cases and ruled out healthy individuals with 92% accuracy. It outperformed existing tests and could become an easy and effective way to catch lung cancer early, helping more people get treated in time.
DOI: 10.6084/m9.figshare.28911747
title: ELAINE 3: phase 3 study of lasofoxifene plus abemaciclib to treat ER+/HER2-, <i>ESR1</i>-mutated, metastatic breast cancer

description: Endocrine therapy (ET) is recommended for patients with estrogen receptor-positive (ER+) metastatic breast cancer (mBC), but most patients will develop treatment resistance, often due to mutations in the ER-α-coding gene, <i>ESR1</i>. Therapeutic options are limited for endocrine-resistant mBC, particularly following treatment with a cyclin-dependent kinase 4/6 inhibitor (CDK4/6i). Lasofoxifene had anti-tumor activity in two separate phase 2, open-label studies (ELAINE 1 and 2) when given as monotherapy or combined with abemaciclib. The phase 3, randomized ELAINE 3 trial will evaluate the efficacy and safety of lasofoxifene/abemaciclib versus fulvestrant/abemaciclib for locally advanced or metastatic, ER+/HER2- breast cancer with an <i>ESR1</i> mutation that progressed after ET-CDK4/6i treatment. Enrollment is planned for up to 500 patients to evaluate progression-free survival as the primary endpoint. <b>Clinical trial registration:</b>www.clinicaltrials.gov identifier is NCT05696626. A PDF version of this infographic is available as supplemental material.
DOI: 10.6084/m9.figshare.28911747.v1
title: ELAINE 3: phase 3 study of lasofoxifene plus abemaciclib to treat ER+/HER2-, <i>ESR1</i>-mutated, metastatic breast cancer

description: Endocrine therapy (ET) is recommended for patients with estrogen receptor-positive (ER+) metastatic breast cancer (mBC), but most patients will develop treatment resistance, often due to mutations in the ER-α-coding gene, <i>ESR1</i>. Therapeutic options are limited for endocrine-resistant mBC, particularly following treatment with a cyclin-dependent kinase 4/6 inhibitor (CDK4/6i). Lasofoxifene had anti-tumor activity in two separate phase 2, open-label studies (ELAINE 1 and 2) when given as monotherapy or combined with abemaciclib. The phase 3, randomized ELAINE 3 trial will evaluate the efficacy and safety of lasofoxifene/abemaciclib versus fulvestrant/abemaciclib for locally advanced or metastatic, ER+/HER2- breast cancer with an <i>ESR1</i> mutation that progressed after ET-CDK4/6i treatment. Enrollment is planned for up to 500 patients to evaluate progression-free survival as the primary endpoint. <b>Clinical trial registration:</b>www.clinicaltrials.gov identifier is NCT05696626. A PDF version of this infographic is available as supplemental material.
DOI: 10.6084/m9.figshare.28776475
title: Cost-effective shallow genome-wide sequencing for profiling plasma cfDNA signatures to enhance lung cancer detection

description: Lung cancer (LC) screening via low-dose computed tomography (LDCT) faces challenges including high false-positive rates and low patient compliance. Circulating tumor DNA (ctDNA)-based tests offer a minimally invasive alternative but are limited by high costs and low sensitivity, particularly in early-stage detection. This study introduces a cost-effective, shallow genome-wide sequencing approach for LC detection by profiling multiple cell-free DNA (cfDNA) signatures. We developed a multimodal cfDNA assay with shallow sequencing coverage (0.5×) that integrates fragmentomic, nucleosome, end-motif, and copy number alteration analyses. A machine-learning model trained on a discovery cohort (99 LC patients, 168 healthy controls) and validated on an independent cohort (58 LC patients, 71 controls) demonstrated robust performance. The ensemble model exhibited outstanding performance, achieving an AUC of 0.97 and a specificity of 92% in both the discovery and validation cohorts, with sensitivities of 94% and 90%, respectively. Notably, it outperformed hotspot mutation-based assays and the multi-cancer SPOT-MAS assay in sensitivity across all LC stages. This assay provides a cost-effective, accurate, and minimally invasive method for LC detection, addressing the limitations of current screening methods. It represents a promising complementary tool to improve early detection and patient outcomes in LC. Lung cancer screening can be expensive and sometimes gives false positives, leading to unnecessary worry and extra tests. Many people also skip screening because it is inconvenient. A simple blood test could be a better option, but current ones are costly and not always accurate for early detection. In this study, researchers developed an affordable blood test that looks at tiny fragments of DNA in the blood. They used machine learning to train the test on samples from lung cancer patients and healthy people, then its accuracy was checked on a separate group. The test correctly detected lung cancer in 90% of cases and ruled out healthy individuals with 92% accuracy. It outperformed existing tests and could become an easy and effective way to catch lung cancer early, helping more people get treated in time.
DOI: 10.25820/data.008106
title: Effects of bed discordance on flow, turbulence and mixing at an idealized asymmetrical confluence between two shallow streams

description: Accurate simulation of flow structures and mixing processes at open channel confluences is essential in geophysical studies, given the important role confluences play in riverine systems and riverine ecology. When two streams of equal densities but of unequal velocities and different flow directions come into contact, large-scale coherent structures are generated downstream of the confluence apex. Eddy-resolving numerical simulations have become a powerful tool to investigate these complex processes. This dataset is generated from high-precision eddy-resolving simulations, designed to advance the study of hydrodynamics and mixing at asymmetrical river confluences. The dataset comprises a series of simulated cases capturing the flow structure under varying levels of bed discordance and discharge ratios. It provides comprehensive instantaneous and time-averaged data, enabling the identification of three-dimensional flow fields and the key coherent structures.
DOI: 10.15468/dl.xdnfkt
title: Occurrence Download

description: A dataset containing 15802 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CAN.2_1",
 "Geometry POLYGON((-142.6757 47.74229,-112.19037 47.74229,-112.19037 70.24154,-142.6757 70.24154,-142.6757 47.74229))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Apidae, Megachilidae, Halictidae, Andrenidae, Colletidae, Melittidae)"
 ]
}

 The dataset includes 15802 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030210-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18419/darus-5500
title: Training dataset for AI-supported subject indexing of research data with DFG classification

description: &lt;p&gt;This is a structured JSON dataset for training and evaluating AI models for automated subject indexing of research data and linking of research data and publications. It was created for the project &lt;a href="https://wiki.bsz-bw.de/spaces/DAFDM/pages/138118716/DA-FDM"&gt;DA-FDM&lt;/a&gt; in order to train a vector based model to give automated suggestions for the topic classification of research datasets in DaRUS. In the context of this project, the DFG-classification was integrated as a controlled vocabulary in DaRUS for the Topic Classification field. DFG classes were added manually to datasets from DaRUS that were uploaded prior to the integration.&lt;/p&gt;
&lt;p&gt;This dataset includes classification tags (&lt;a href="https://w3id.org/dfgfo/2020"&gt;DFG&lt;/a&gt;, &lt;a href="https://swb.bsz-bw.de/DB=2.104/SET=1/TTL=1/START_WELCOME"&gt;GND&lt;/a&gt;, &lt;a href="https://www.wikidata.org"&gt;Wikidata&lt;/a&gt;), publication links, respective open-access information, and, if the publication is open-access, the respective full texts for datasets from DaRUS as well as &lt;a href="https://tudatalib.ulb.tu-darmstadt.de/home"&gt;TUdatalib&lt;/a&gt;.&lt;/p&gt;

&lt;p&gt;
Example object for the dataset:
&lt;pre&gt;
{
 "name": "doi:10.18419/darus-1234",
 "tags": [
 {
 "name": "dfg-fs$102-04",
 "url": "https://w3id.org/dfgfo/2020/102-04"
 },
 {
 "name": "ResearchDataSet"
 }
 ],
 "links": [
 {
 "name": "doi:10.12345/abc5678",
 "type": "publication",
 "is_open_access": true,
 "open_access_url": "https://www.asdfg.com/10.12345/abc5678",
 "text": "Extracted publication full text ..."
 }
 ]
}
&lt;/pre&gt;
&lt;/p&gt;
DOI: 10.15468/dl.nzqtpc
title: Occurrence Download

description: A dataset containing 273 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "Geometry POLYGON((80 -90,160 -90,160 30,80 30,80 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Buceros bicornis"
 ]
}

 The dataset includes 273 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030211-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.