cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24787278.v1
title: Supplementary Material for: A low-cost, high-fidelity simulator for transabdominal chorionic villus sampling

description: Introduction: Chorionic villus sampling (CVS) remains essential for first trimester genetic diagnosis, yet clinical volume may be insufficient to train new clinicians in the technique. Available simulation models are expensive, require animal parts or specialized resins, and cannot be stored for repeated use.

Methods: We present a model for trans-abdominal CVS (TA-CVS) which is constructed from readily-available materials costing less than $10 and can be refrigerated and re-used to train maternal fetal medicine (MFM) fellows in CVS.

Results: All three attending physicians performing TA-CVS at our institution described the model as an accurate visual and tactile simulation, prompting its integration into our fellowship curriculum. To date, two senior fellows have achieved competency on the simulator and begun to perform clinical CVS under supervision, one of whom is an author on this paper. Both fellows and attendings indicated that the simulator provided a valuable tool for repeated practice prior to clinical CVS. Simulators are now maintained on the unit and have been re-used for three months and dozens of simulated procedures each without any apparent qualitative degradation in performance.

Discussion/Conclusion: We describe a low-cost easily constructed, durable, high-fidelity simulator for TA-CVS.
DOI: 10.5281/zenodo.10355227
title: DETERMINATION OF PROFITABILITY OF AN ECONOMIC SUBJECT WITH THE HELP OF OPTIMIZATION OF FINANCIAL STATEMENTS ON THE BASIS OF INTERNATIONAL STANDARDS.
DOI: 10.5281/zenodo.10355228
title: DETERMINATION OF PROFITABILITY OF AN ECONOMIC SUBJECT WITH THE HELP OF OPTIMIZATION OF FINANCIAL STATEMENTS ON THE BASIS OF INTERNATIONAL STANDARDS.
DOI: 10.23728/b2share.41cb378f6d5542f2b6802e796845116a
title: HEAP Cervical Screening Cohort

description: The Cervical Screening Cohort enrols women screened for human papillomavirus (HPV) and cervical abnormalities within the capital region of Sweden, both from the organised screening program and the non-organised testing of cervical samples. The cohort started in 2011 and has enrolled more than 670,000 women at more than 1.2 million screening visits. Most women have contributed, on average, with two samples between 2011 and 2022. The enrolment process uses written invitations and informed consent, including an opt-out procedure. The cohort is systematically updated with individual-level data from the Swedish National Cervical Screening Registry (NKCx). Key variables include birthdate, sampling date, cytological and HPV analysis results, histopathological diagnoses (results of cervical biopsies or conisations), and screening invitations, including the invitation date. Each round of sampling and subsequent clinical follow-up is sequentially saved in the dataset, allowing for longitudinal analyses of screening results and associated results of the clinical workup. Systematic epigenomics and metagenomics analyses performed on the samples enrich the cohort data.


The cohort is ideal for longitudinal, long-term follow-up studies due to its validated documentation and registry-derived information. From the data, it is possible to penetrate important human health mechanisms. The data are available as open-access, GDPR-compliant. Samples are available after getting the required permissions. Results will help researchers understand factors that increase cancer risk and other diseases.
DOI: 10.6084/m9.figshare.24787287
title: Supplementary Material for: Twelve-months outcomes after metabolic and bariatric surgery among youths participating in a structured preparation and follow-up program – Results of the Youth with Extreme obesity Study (YES)

description: Introduction: While invasive and associated with risks, metabolic and bariatric surgery (MBS) can promote sustained weight loss and substantial health benefits in youths with extreme obesity.The path toward informed decision making for or against MBS is poorly characterized and postoperative follow-up to assess risks and benefits is inconsistent. In youths with extreme obesity we aimed to evaluate decision making toward MBS, as well as MBS outcomes and adherence with follow-up and recommendations in the setting of a structured pre- and post- MBS.
Methods: Participants were recruited in the setting of the multicenter “Youth with Extreme Obesity Study” (YES). YES is a cohort study in adolescents and young adults aged 14–24 years with obesity (BMI≥30.0 kg/m2) who were recruited at four medical centers and one job center in Germany between 2012 and 2018. Participants at two medical centers with BMI≥35kg/m2, aged 14-24 years, and interested in pursuing MBS were included in the subproject 3 “Safety and effectiveness of weight loss surgery in adolescents with severe obesity within a structured pre- and post-surgery treatment program – an observational study” that comprised a 2-months pre- and 12-months post-MBS program. 
Results: Twenty-eight of 169 youths (17%) with BMI≥35kg/m2 were interested in MBS. Twenty-six fulfilled published eligibility criteria for MBS and participated in the structured pre- MBS preparation program. Of these, 9 participants (2 female) decided against, and 17 (n=11 females) decided for MBS (sleeve gastrectomy). The 12-months follow-up rate was high (16/17 [94%]) and all participants achieved significant weight reduction (ΔBMI:-16.1±5.6 kg/m2). Eleven of 16 participants (69%) reported taking the prescribed dietary supplements in the first year after MBS, but only five of them (31%) did so daily. In contrast to the high 12-month retention rate, follow-up after completion of the structured program was low at 24-months (9/16 [56%]) and at 36-months (5/15 [36%]) respectively. 
Conclusion: Participants demonstrated active decision making for or against MBS and high adherence with the structured pre- and 12 months post- MBS program, but participation was low thereafter. These findings endorse the need for longer-term structured post-MBS programs to capture long-term outcomes and provide adequate care in this vulnerable group at the transition to adulthood.
DOI: 10.6084/m9.figshare.24787287.v1
title: Supplementary Material for: Twelve-months outcomes after metabolic and bariatric surgery among youths participating in a structured preparation and follow-up program – Results of the Youth with Extreme obesity Study (YES)

description: Introduction: While invasive and associated with risks, metabolic and bariatric surgery (MBS) can promote sustained weight loss and substantial health benefits in youths with extreme obesity.The path toward informed decision making for or against MBS is poorly characterized and postoperative follow-up to assess risks and benefits is inconsistent. In youths with extreme obesity we aimed to evaluate decision making toward MBS, as well as MBS outcomes and adherence with follow-up and recommendations in the setting of a structured pre- and post- MBS.
Methods: Participants were recruited in the setting of the multicenter “Youth with Extreme Obesity Study” (YES). YES is a cohort study in adolescents and young adults aged 14–24 years with obesity (BMI≥30.0 kg/m2) who were recruited at four medical centers and one job center in Germany between 2012 and 2018. Participants at two medical centers with BMI≥35kg/m2, aged 14-24 years, and interested in pursuing MBS were included in the subproject 3 “Safety and effectiveness of weight loss surgery in adolescents with severe obesity within a structured pre- and post-surgery treatment program – an observational study” that comprised a 2-months pre- and 12-months post-MBS program. 
Results: Twenty-eight of 169 youths (17%) with BMI≥35kg/m2 were interested in MBS. Twenty-six fulfilled published eligibility criteria for MBS and participated in the structured pre- MBS preparation program. Of these, 9 participants (2 female) decided against, and 17 (n=11 females) decided for MBS (sleeve gastrectomy). The 12-months follow-up rate was high (16/17 [94%]) and all participants achieved significant weight reduction (ΔBMI:-16.1±5.6 kg/m2). Eleven of 16 participants (69%) reported taking the prescribed dietary supplements in the first year after MBS, but only five of them (31%) did so daily. In contrast to the high 12-month retention rate, follow-up after completion of the structured program was low at 24-months (9/16 [56%]) and at 36-months (5/15 [36%]) respectively. 
Conclusion: Participants demonstrated active decision making for or against MBS and high adherence with the structured pre- and 12 months post- MBS program, but participation was low thereafter. These findings endorse the need for longer-term structured post-MBS programs to capture long-term outcomes and provide adequate care in this vulnerable group at the transition to adulthood.
DOI: 10.5281/zenodo.10246017
title: PyPSA-PL: Sectorally-integrated modelling of the Polish energy system until 2040

description: This record contains all the scripts and data from the PyPSA-PL modelling exercise that supported the report:

Kubiczek, P., Smoleń, M., Żelisko, W. (2023). Polska prawie bezemisyjna. Cztery scenariusze transformacji energetycznej do 2040 r. Instrat Policy Paper 06/2023. https://www.instrat.pl/polska-2040
The record structure is based on the PyPSA-PL repository https://github.com/instrat-pl/pypsa-pl (v2.1).
DOI: 10.5281/zenodo.10246018
title: PyPSA-PL: Sectorally-integrated modelling of the Polish energy system until 2040

description: This record contains all the scripts and data from the PyPSA-PL modelling exercise that supported the report:

Kubiczek, P., Smoleń, M., Żelisko, W. (2023). Polska prawie bezemisyjna. Cztery scenariusze transformacji energetycznej do 2040 r. Instrat Policy Paper 06/2023. https://www.instrat.pl/polska-2040
The record structure is based on the PyPSA-PL repository https://github.com/instrat-pl/pypsa-pl (v2.1).
DOI: 10.6084/m9.figshare.24787293
title: Supplementary Material for: Twelve-months outcomes after metabolic and bariatric surgery among youths participating in a structured preparation and follow-up program – Results of the Youth with Extreme obesity Study (YES)

description: Introduction: While invasive and associated with risks, metabolic and bariatric surgery (MBS) can promote sustained weight loss and substantial health benefits in youths with extreme obesity.The path toward informed decision making for or against MBS is poorly characterized and postoperative follow-up to assess risks and benefits is inconsistent. In youths with extreme obesity we aimed to evaluate decision making toward MBS, as well as MBS outcomes and adherence with follow-up and recommendations in the setting of a structured pre- and post- MBS.
Methods: Participants were recruited in the setting of the multicenter “Youth with Extreme Obesity Study” (YES). YES is a cohort study in adolescents and young adults aged 14–24 years with obesity (BMI≥30.0 kg/m2) who were recruited at four medical centers and one job center in Germany between 2012 and 2018. Participants at two medical centers with BMI≥35kg/m2, aged 14-24 years, and interested in pursuing MBS were included in the subproject 3 “Safety and effectiveness of weight loss surgery in adolescents with severe obesity within a structured pre- and post-surgery treatment program – an observational study” that comprised a 2-months pre- and 12-months post-MBS program. 
Results: Twenty-eight of 169 youths (17%) with BMI≥35kg/m2 were interested in MBS. Twenty-six fulfilled published eligibility criteria for MBS and participated in the structured pre- MBS preparation program. Of these, 9 participants (2 female) decided against, and 17 (n=11 females) decided for MBS (sleeve gastrectomy). The 12-months follow-up rate was high (16/17 [94%]) and all participants achieved significant weight reduction (ΔBMI:-16.1±5.6 kg/m2). Eleven of 16 participants (69%) reported taking the prescribed dietary supplements in the first year after MBS, but only five of them (31%) did so daily. In contrast to the high 12-month retention rate, follow-up after completion of the structured program was low at 24-months (9/16 [56%]) and at 36-months (5/15 [36%]) respectively. 
Conclusion: Participants demonstrated active decision making for or against MBS and high adherence with the structured pre- and 12 months post- MBS program, but participation was low thereafter. These findings endorse the need for longer-term structured post-MBS programs to capture long-term outcomes and provide adequate care in this vulnerable group at the transition to adulthood.
DOI: 10.6084/m9.figshare.24787293.v1
title: Supplementary Material for: Twelve-months outcomes after metabolic and bariatric surgery among youths participating in a structured preparation and follow-up program – Results of the Youth with Extreme obesity Study (YES)

description: Introduction: While invasive and associated with risks, metabolic and bariatric surgery (MBS) can promote sustained weight loss and substantial health benefits in youths with extreme obesity.The path toward informed decision making for or against MBS is poorly characterized and postoperative follow-up to assess risks and benefits is inconsistent. In youths with extreme obesity we aimed to evaluate decision making toward MBS, as well as MBS outcomes and adherence with follow-up and recommendations in the setting of a structured pre- and post- MBS.
Methods: Participants were recruited in the setting of the multicenter “Youth with Extreme Obesity Study” (YES). YES is a cohort study in adolescents and young adults aged 14–24 years with obesity (BMI≥30.0 kg/m2) who were recruited at four medical centers and one job center in Germany between 2012 and 2018. Participants at two medical centers with BMI≥35kg/m2, aged 14-24 years, and interested in pursuing MBS were included in the subproject 3 “Safety and effectiveness of weight loss surgery in adolescents with severe obesity within a structured pre- and post-surgery treatment program – an observational study” that comprised a 2-months pre- and 12-months post-MBS program. 
Results: Twenty-eight of 169 youths (17%) with BMI≥35kg/m2 were interested in MBS. Twenty-six fulfilled published eligibility criteria for MBS and participated in the structured pre- MBS preparation program. Of these, 9 participants (2 female) decided against, and 17 (n=11 females) decided for MBS (sleeve gastrectomy). The 12-months follow-up rate was high (16/17 [94%]) and all participants achieved significant weight reduction (ΔBMI:-16.1±5.6 kg/m2). Eleven of 16 participants (69%) reported taking the prescribed dietary supplements in the first year after MBS, but only five of them (31%) did so daily. In contrast to the high 12-month retention rate, follow-up after completion of the structured program was low at 24-months (9/16 [56%]) and at 36-months (5/15 [36%]) respectively. 
Conclusion: Participants demonstrated active decision making for or against MBS and high adherence with the structured pre- and 12 months post- MBS program, but participation was low thereafter. These findings endorse the need for longer-term structured post-MBS programs to capture long-term outcomes and provide adequate care in this vulnerable group at the transition to adulthood.
DOI: 10.5281/zenodo.10287541
title: Spatiotemporal profiling defines persistence and resistance dynamics during targeted treatment of melanoma

description: Processed data:
inferCNV_output_WM4237.zip, inferCNV_output_WM4007.zip - InferCNV-derived CNV profiles for 12 Visium samples of model WM4237 or WM4007.
ad_all_human_clustered_cnv_WM4237.h5ad, ad_all_human_clustered_cnv_WM4007.h5ad - AnnData object containing integration, dimensionality reduction and clustering of the inferCNV-derived CNV profiles for 12 Visium samples of model WM4237 or WM4007.
ad_all_human_clustered_im_st_WM4237.h5ad, ad_all_human_clustered_im_st_WM4007.h5ad - AnnData object containing integration, dimensionality reduction and clustering of imaging and nuclear morphometric features (output of STQ pipeline) for 12 Visium samples of model WM4237 or WM4007. "_im" for imaging, "_st" for Visium.
ad_all_human_clustered_im_ad_WM4237_m.h5ad, ad_all_human_clustered_im_ad_WM4007_m.h5ad - AnnData object containing integration, dimensionality reduction and clustering of imaging and nuclear morphometric features (output of STQ pipeline) for additional H&E slides (non-Visium) of model WM4237 or WM4007. "_im" for imaging, "_m" for Macenko normalization of the H&E slides with STQ.
ids_WM4237_AD.txt, ids_WM4007_AD.txt, ids_WM4237_ST.txt, ids_WM4237_ST.txt - list of identifiers of all samples (tissue sections).
ad_all_human_clustered_st_WM4237.h5ad, ad_all_human_clustered_st_WM4007.h5ad -  AnnData object containing integration, dimensionality reduction and clustering of RNA profiles for 12 Visium samples of model WM4237 or WM4007.
CNV_burden_WM4237.csv, CNV_burden_WM4007.csv -  Per-spot values of InferCNV-derived CNV burden for samples of models WM4237 or WM4007.
ad_all_scaled_filtered_st_WM4237.h5ad, ad_all_scaled_filtered_st_WM4007.h5ad -  AnnData objects containing concatenated and pre-processed samples of WM4237 or WM4007.
WM4237_3_AD_m-Imaging-STQ.zip, WM4007_3_AD_m-Imaging-STQ.zip - Imaging portion of STQ pipeline output derived from additional (non-Visium) H&E-stained tissue sections of model WM4237 or WM4007.
WM4237_ST-Imaging-STQ.tar.gz, WM4007_ST-Imaging-STQ.tar.gz -  Imaging portion of STQ pipeline output derived from Visium H&E-stained tissue sections of model WM4237 or WM4007.
WM4237-ST-downstream-output.tar.gz, WM4007-ST-downstream-output.tar.gz - ST-downstream-processing pipeline output for Visium samples of model WM4237 or WM4007.
WM4237-STQ-sequencing.tar.gz, WM4007-STQ-sequencing.tar.gz - RNA sequencing portion of STQ pipeline output derived from Visium samples of model WM4237 or WM4007.
rna-pseudotime-ordered.zip -  Pseudotime ordering of RNA profiles of spots for each time point (T0, T1, T2, T3, T4, TC) for samples of models WM4237 and WM4007.
DOI: 10.6084/m9.figshare.24787296
title: Snow leopard numt hits

description: Numt sequences identified in a snow leopard nuclear genome.
DOI: 10.6084/m9.figshare.24787335
title: Supplementary Material for: Abrocitinib Provides Rapid and Sustained Improvement in Skin Pain and Is Associated With Improved Quality of Life Outcomes in Adult and Adolescent Patients With Moderate-to-Severe Atopic Dermatitis

description: Background: Skin pain in atopic dermatitis (AD) increases with disease severity and is associated with substantial quality of life (QoL) burden. 
Objectives: To evaluate abrocitinib efficacy on skin pain and QoL in adults and adolescents with moderate-to-severe AD.
Methods: This post hoc analysis included data with abrocitinib administered as monotherapy (pooled phase 2b [NCT02780167] and phase 3 JADE MONO-1 [NCT03349060] and MONO-2 [NCT03575871]) or in combination with topical therapy (phase 3 JADE COMPARE [NCT03720470] and JADE TEEN [NCT03796676]). Patients received oral, once-daily abrocitinib 200 mg, abrocitinib 100 mg, or placebo for 12 or 16 weeks (JADE COMPARE). Skin pain was rated using the Pruritus and Symptoms Assessment for Atopic Dermatitis (PSAAD) skin pain Numerical Rating Scale (NRS) item (“How painful was your skin over the past 24 hours?”) on a scale from 0 (not painful) to 10 (extremely painful). Itch (Peak Pruritus NRS) and QoL (Dermatology Life Quality Index or Children’s Dermatology Life Quality Index) were assessed. Least squares mean (LSM) change from baseline was analyzed using mixed effects repeated measures modeling.
Results: A total of 1822 patients (monotherapy pool, n=942; JADE COMPARE, n=595; JADE TEEN; n=285) were analyzed. LSM change from baseline in PSAAD skin pain score was significantly greater with abrocitinib versus placebo from week 2 through week 12 or 16 across all 3 study populations and occurred in a dose-dependent manner. A greater proportion of patients achieved a ≥4-point improvement from baseline in PSAAD skin pain score with abrocitinib (200 mg and 100 mg) versus placebo in the monotherapy pool (56% and 38% vs 12%; week 12), JADE COMPARE (72% and 52% vs 26%; week 16), and JADE TEEN (51% and 60% vs 31%; week 12). Additionally, a greater proportion of patients achieved a stringent threshold of skin pain improvement (PSAAD skin pain score &lt;2) with abrocitinib versus placebo. Adults and adolescents who achieved a ≥4-point improvement in skin pain reported greater QoL improvement than those who did not achieve a ≥4-point improvement. A positive correlation (≥0.3) was observed between skin pain and QoL and separately between skin pain and itch across the 3 study populations.
Conclusion: Abrocitinib as monotherapy or in combination with topical therapy improved skin pain and was associated with improved QoL in both adults and adolescents with moderate-to-severe AD across all evaluated studies.
DOI: 10.6084/m9.figshare.24787335.v1
title: Supplementary Material for: Abrocitinib Provides Rapid and Sustained Improvement in Skin Pain and Is Associated With Improved Quality of Life Outcomes in Adult and Adolescent Patients With Moderate-to-Severe Atopic Dermatitis

description: Background: Skin pain in atopic dermatitis (AD) increases with disease severity and is associated with substantial quality of life (QoL) burden. 
Objectives: To evaluate abrocitinib efficacy on skin pain and QoL in adults and adolescents with moderate-to-severe AD.
Methods: This post hoc analysis included data with abrocitinib administered as monotherapy (pooled phase 2b [NCT02780167] and phase 3 JADE MONO-1 [NCT03349060] and MONO-2 [NCT03575871]) or in combination with topical therapy (phase 3 JADE COMPARE [NCT03720470] and JADE TEEN [NCT03796676]). Patients received oral, once-daily abrocitinib 200 mg, abrocitinib 100 mg, or placebo for 12 or 16 weeks (JADE COMPARE). Skin pain was rated using the Pruritus and Symptoms Assessment for Atopic Dermatitis (PSAAD) skin pain Numerical Rating Scale (NRS) item (“How painful was your skin over the past 24 hours?”) on a scale from 0 (not painful) to 10 (extremely painful). Itch (Peak Pruritus NRS) and QoL (Dermatology Life Quality Index or Children’s Dermatology Life Quality Index) were assessed. Least squares mean (LSM) change from baseline was analyzed using mixed effects repeated measures modeling.
Results: A total of 1822 patients (monotherapy pool, n=942; JADE COMPARE, n=595; JADE TEEN; n=285) were analyzed. LSM change from baseline in PSAAD skin pain score was significantly greater with abrocitinib versus placebo from week 2 through week 12 or 16 across all 3 study populations and occurred in a dose-dependent manner. A greater proportion of patients achieved a ≥4-point improvement from baseline in PSAAD skin pain score with abrocitinib (200 mg and 100 mg) versus placebo in the monotherapy pool (56% and 38% vs 12%; week 12), JADE COMPARE (72% and 52% vs 26%; week 16), and JADE TEEN (51% and 60% vs 31%; week 12). Additionally, a greater proportion of patients achieved a stringent threshold of skin pain improvement (PSAAD skin pain score &lt;2) with abrocitinib versus placebo. Adults and adolescents who achieved a ≥4-point improvement in skin pain reported greater QoL improvement than those who did not achieve a ≥4-point improvement. A positive correlation (≥0.3) was observed between skin pain and QoL and separately between skin pain and itch across the 3 study populations.
Conclusion: Abrocitinib as monotherapy or in combination with topical therapy improved skin pain and was associated with improved QoL in both adults and adolescents with moderate-to-severe AD across all evaluated studies.