cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8221020
title: RIBFIND2 Data

description: This repository contains PDB files for the refinements of the RIBFIND2 paper.
DOI: 10.5281/zenodo.8221019
title: RIBFIND2 Data

description: This repository contains PDB files for the refinements of the RIBFIND2 paper.
DOI: 10.6084/m9.figshare.23899381
title: Supplementary Table 1 from RNF4 and USP7 cooperate in ubiquitin-regulated steps of DNA replication

description: Table containing details for RNF4 interactors from our genetic screen.
DOI: 10.6084/m9.figshare.23899381.v1
title: Supplementary Table 1 from RNF4 and USP7 cooperate in ubiquitin-regulated steps of DNA replication

description: Table containing details for RNF4 interactors from our genetic screen.
DOI: 10.6084/m9.figshare.23899384
title: Supplementary Table 2 from RNF4 and USP7 cooperate in ubiquitin-regulated steps of DNA replication

description: File containing pathway analysis details related to the genetic screen.
DOI: 10.6084/m9.figshare.23899384.v1
title: Supplementary Table 2 from RNF4 and USP7 cooperate in ubiquitin-regulated steps of DNA replication

description: File containing pathway analysis details related to the genetic screen.
DOI: 10.57680/asep.0544591
title: Mezinárodní korespondenční sítě T. G. Masaryka a vznik Československa v roce 1918 (projekt vizualizace metadat pro digitální nástroj Palladio)
title: T. G. Masaryk’s International Correspondence Networks and the Establishment of Czechoslovakia in 1918 (project metadata visualization for the digital tool Palladio)

description: Projekt vizualizace metadat specializované mapy pro digitální nástroj Palladio.
description: Project of the specialized map metadata visualization for the digital tool Palladio.
DOI: 10.6084/m9.figshare.23866113
title: Segmented olive leaf dataset

description: Dataset used to retrein mask rcnn in Detrectron 2. Used Via 2.0.8 to generate the dataset.
DOI: 10.6084/m9.figshare.22591410
title: Insulin resistance in patients with cancer: a systematic review and meta-analysis

description: Insulin resistance is a critical cause of metabolic dysfunctions. Metabolic dysfunction is common in patients with cancer and is associated with higher cancer recurrence rates and reduced overall survival. Yet, insulin resistance is rarely considered in the clinic and thus it is uncertain how frequently this condition occurs in patients with cancer. To address this knowledge gap, we performed a systematic review and a meta-analysis guided by the Preferred Items for Systematic Review and Meta-Analyses (PRISMA) statement. We included studies assessing insulin resistance in patients with various cancer diagnoses, using the gold-standard hyperinsulinemic–euglycemic clamp method. Studies eligible for inclusion were as follows: (1) included cancer patients older than 18 years of age; (2) included an age-matched control group consisting of individuals without cancer or other types of neoplasms; (3) measured insulin sensitivity using the hyperinsulinemic–euglycemic clamp method. We searched the databases MEDLINE, Embase, and Cochrane Central Register of Controlled Trials for articles published from database inception through March 2023 with no language restriction, supplemented by backward and forward citation searching. Bias was assessed using funnel plot. Fifteen studies satisfied the criteria. The mean insulin-stimulated rate of glucose disposal (Rd) was 7.5 mg/kg/min in control subjects (<i>n</i> = 154), and 4.7 mg/kg/min in patients with a cancer diagnosis (<i>n</i> = 187). Thus, the Rd mean difference was −2.61 mg/kg/min [95% confidence interval, −3.04; −2.19], <i>p</i>&lt;.01). Heterogeneity among the included studies was insignificant (<i>p</i>=.24). These findings suggest that patients with a cancer diagnosis are markedly insulin resistant. As metabolic dysfunction in patients with cancer associates with increased recurrence and reduced overall survival, future studies should address if ameliorating insulin resistance in this population can improve these outcomes thereby improving patient care.Key pointsMetabolic dysfunction increases cancer recurrence rates and reduces survival for patients with cancer.Insulin resistance is a critical cause of metabolic dysfunctions.To date, no comprehensive compilation of research investigating insulin resistance in cancer patients has been produced.In this meta-analysis, we found that patients with various cancers were markedly insulin-resistant. Metabolic dysfunction increases cancer recurrence rates and reduces survival for patients with cancer. Insulin resistance is a critical cause of metabolic dysfunctions. To date, no comprehensive compilation of research investigating insulin resistance in cancer patients has been produced. In this meta-analysis, we found that patients with various cancers were markedly insulin-resistant.
DOI: 10.6084/m9.figshare.22677308
title: Are education and cohabitation associated with health-related quality of life and self-management during breast cancer follow-up? A longitudinal study

description: Oncologist-led follow-up after breast cancer (BC) is increasingly replaced with less intensive follow-up based on higher self-management, which may overburden the less resourceful patients. We examined whether socioeconomic factors measured recently after the implementation of a new follow-up program for BC patients were associated with health-related quality of life (HRQoL) and self-management 12 months later. Between January and August 2017, we invited 1773 patients in Region Zealand, Denmark, to participate in baseline and 12 months follow-up questionnaires. The patients had surgery for low- and intermediate risk BC 1–10 years prior to the survey, and they had recently been allocated to the new follow-up program of either patient-initiated follow-up, or in-person or telephone follow-up with a nurse, based on patients’ preferences. We examined associations between socioeconomic factors (education and cohabitation) at baseline and two outcomes: HRQoL (EORTC QLQ-C30 and QLQ-BR23) and self-management factors (health care provider, confidence in follow-up, contact at symptoms of concern, and self-efficacy) at 12 months follow-up. Sensitivity analyses were performed according to time since diagnosis (≤ 5 &gt; 5 years). Furthermore, we investigated whether treatment and self-management factors modified the associations. A total of 987 patients were included in the analyses. We found no statistically significant associations between socioeconomic factors and HRQoL, except in patients ≤ 5 years from diagnosis. For self-management patients with short education were more likely to report that they had not experience relevant symptoms of concern compared to those with medium/long education (OR 1.75 95% CI: 1.04; 2.95). We found no clear patterns indicating that treatment or self-management factors modified the associations between socioeconomics’ and HRQoL. Overall socioeconomic factors did not influence HRQoL and self-management factors except for experiencing and reporting relevant symptoms of concern. Socioeconomic factors may, however, influence HRQoL in patients within five years of diagnosis.
DOI: 10.6084/m9.figshare.22677308.v3
title: Are education and cohabitation associated with health-related quality of life and self-management during breast cancer follow-up? A longitudinal study

description: Oncologist-led follow-up after breast cancer (BC) is increasingly replaced with less intensive follow-up based on higher self-management, which may overburden the less resourceful patients. We examined whether socioeconomic factors measured recently after the implementation of a new follow-up program for BC patients were associated with health-related quality of life (HRQoL) and self-management 12 months later. Between January and August 2017, we invited 1773 patients in Region Zealand, Denmark, to participate in baseline and 12 months follow-up questionnaires. The patients had surgery for low- and intermediate risk BC 1–10 years prior to the survey, and they had recently been allocated to the new follow-up program of either patient-initiated follow-up, or in-person or telephone follow-up with a nurse, based on patients’ preferences. We examined associations between socioeconomic factors (education and cohabitation) at baseline and two outcomes: HRQoL (EORTC QLQ-C30 and QLQ-BR23) and self-management factors (health care provider, confidence in follow-up, contact at symptoms of concern, and self-efficacy) at 12 months follow-up. Sensitivity analyses were performed according to time since diagnosis (≤ 5 &gt; 5 years). Furthermore, we investigated whether treatment and self-management factors modified the associations. A total of 987 patients were included in the analyses. We found no statistically significant associations between socioeconomic factors and HRQoL, except in patients ≤ 5 years from diagnosis. For self-management patients with short education were more likely to report that they had not experience relevant symptoms of concern compared to those with medium/long education (OR 1.75 95% CI: 1.04; 2.95). We found no clear patterns indicating that treatment or self-management factors modified the associations between socioeconomics’ and HRQoL. Overall socioeconomic factors did not influence HRQoL and self-management factors except for experiencing and reporting relevant symptoms of concern. Socioeconomic factors may, however, influence HRQoL in patients within five years of diagnosis.
DOI: 10.6084/m9.figshare.22953557
title: Transitioning from conventional photon therapy to proton therapy for primary brain tumors

description: Proton radiation therapy (PT) has become a treatment option alongside photon therapy (XRT) for lower-grade gliomas (LGG). In this single-institution retrospective study, we investigate the patient characteristics and treatment outcomes, including pseudo-progression (PsP), for LGG patients selected for PT. Adult patients with grade 2–3 glioma consecutively treated with radiotherapy (RT) from May 2012 to December 2019 were retrospectively included in this cohort study. Tumor characteristics and treatment data were collected. The groups treated with PT and XRT were compared regarding treatment characteristics, side effects, occurrence of PsP, and survival outcomes. PsP was defined as new or growing lesions followed by either decrease or stabilization during a 12 month-period with no treatment. Out of 143 patients meeting the inclusion criteria, 44 were treated with PT, 98 with XRT and one with mixed PT + XRT. The patients receiving PT were younger, had a lower tumor grade, more oligodendrogliomas and received a lower mean brain and brainstem dose. PsP was observed in 21 out of 126 patients, with no difference between XRT and PT (<i>p</i> = .38). The rate of fatigue in immediate connection to RT (zero to three months after) was higher for XRT than for PT (<i>p</i> = .016). The PT patients had a significantly better PFS and OS than the XRT patients (<i>p</i> = .025 and .035), but in multivariate analysis radiation modality was non-significant. Higher average dose to both brain and brainstem was associated with inferior PFS and OS (<i>p</i> &lt; .001). Median follow-up time were 69 months and 26 months for XRT and PT patients, respectively. Contrary to previous studies, there was no difference in risk of PsP for XRT and PT. PT was associated with lower rates of fatigue &lt;3 months after RT. The superior survival outcomes for PT indicates that the patients with the best prognosis were referred to PT.
DOI: 10.6084/m9.figshare.22657047
title: Effect of docetaxel added to bicalutamide in Hormone-Naïve non-metastatic prostate cancer with rising PSA, a randomized clinical trial (SPCG-14)

description: Historically, endocrine therapy was used in a range of scenarios in patients with rising PSA, both as a treatment for locally advanced non-metastatic prostate cancer and PSA recurrence following curative intended therapy. In the present study the objective was to investigate if chemotherapy added to endocrine therapy could improve progression-free survival (PFS). Patients with hormone-naïve, non-metastatic prostate cancer and rising prostate-specific antigen (PSA), enrolled from Sweden, Denmark, the Netherlands, and Finland, were randomized to long-term bicalutamide (150 mg daily) or plus docetaxel (75 mg/m<sup>2</sup>, q3w, 8–10 cycles) without prednisone, after stratification for the site, prior local therapy or not, and PSA doubling time. The primary endpoint was 5-year PFS analyzed with a stratified Cox proportional hazards regression model on intention to treat basis. Between 2009 and 2018, a total of 348 patients were randomized; 315 patients had PSA relapse after radical treatment, 33 patients had no prior local therapy. Median follow-up was 4.9 years (IQR 4.0–5.1). Adding docetaxel improved PFS (HR 0.68, 95% CI 0.50–0.93; <i>p</i> = 0.015). Docetaxel showed an advantage for patients with PSA relapse after prior local therapy (HR 0.67, 95% CI 0.49–0.94; <i>p</i> = 0.019). One event of neutropenic infection/fever occurred in 27% of the patients receiving docetaxel. Limitations were slow recruitment, lack of enrolling patients without radical local treatment, and too short follow-up for evaluation of overall survival in patients with PSA relapse. Docetaxel improved PFS in patients starting bicalutamide due to PSA relapse after local therapy or localized disease without local therapy. Confirmatory studies of the efficacy of docetaxel in the setting of PSA-only relapse in addition to endocrine therapies may be justified if longer follow-up will show increased metastatic-free survival.
DOI: 10.6084/m9.figshare.22677308.v2
title: Are education and cohabitation associated with health-related quality of life and self-management during breast cancer follow-up? A longitudinal study

description: Oncologist-led follow-up after breast cancer (BC) is increasingly replaced with less intensive follow-up based on higher self-management, which may overburden the less resourceful patients. We examined whether socioeconomic factors measured recently after the implementation of a new follow-up program for BC patients were associated with health-related quality of life (HRQoL) and self-management 12 months later. Between January and August 2017, we invited 1773 patients in Region Zealand, Denmark, to participate in baseline and 12 months follow-up questionnaires. The patients had surgery for low- and intermediate risk BC 1–10 years prior to the survey, and they had recently been allocated to the new follow-up program of either patient-initiated follow-up, or in-person or telephone follow-up with a nurse, based on patients’ preferences. We examined associations between socioeconomic factors (education and cohabitation) at baseline and two outcomes: HRQoL (EORTC QLQ-C30 and QLQ-BR23) and self-management factors (health care provider, confidence in follow-up, contact at symptoms of concern, and self-efficacy) at 12 months follow-up. Sensitivity analyses were performed according to time since diagnosis (≤ 5 &gt; 5 years). Furthermore, we investigated whether treatment and self-management factors modified the associations. A total of 987 patients were included in the analyses. We found no statistically significant associations between socioeconomic factors and HRQoL, except in patients ≤ 5 years from diagnosis. For self-management patients with short education were more likely to report that they had not experience relevant symptoms of concern compared to those with medium/long education (OR 1.75 95% CI: 1.04; 2.95). We found no clear patterns indicating that treatment or self-management factors modified the associations between socioeconomics’ and HRQoL. Overall socioeconomic factors did not influence HRQoL and self-management factors except for experiencing and reporting relevant symptoms of concern. Socioeconomic factors may, however, influence HRQoL in patients within five years of diagnosis.
DOI: 10.6084/m9.figshare.22953557.v2
title: Transitioning from conventional photon therapy to proton therapy for primary brain tumors

description: Proton radiation therapy (PT) has become a treatment option alongside photon therapy (XRT) for lower-grade gliomas (LGG). In this single-institution retrospective study, we investigate the patient characteristics and treatment outcomes, including pseudo-progression (PsP), for LGG patients selected for PT. Adult patients with grade 2–3 glioma consecutively treated with radiotherapy (RT) from May 2012 to December 2019 were retrospectively included in this cohort study. Tumor characteristics and treatment data were collected. The groups treated with PT and XRT were compared regarding treatment characteristics, side effects, occurrence of PsP, and survival outcomes. PsP was defined as new or growing lesions followed by either decrease or stabilization during a 12 month-period with no treatment. Out of 143 patients meeting the inclusion criteria, 44 were treated with PT, 98 with XRT and one with mixed PT + XRT. The patients receiving PT were younger, had a lower tumor grade, more oligodendrogliomas and received a lower mean brain and brainstem dose. PsP was observed in 21 out of 126 patients, with no difference between XRT and PT (<i>p</i> = .38). The rate of fatigue in immediate connection to RT (zero to three months after) was higher for XRT than for PT (<i>p</i> = .016). The PT patients had a significantly better PFS and OS than the XRT patients (<i>p</i> = .025 and .035), but in multivariate analysis radiation modality was non-significant. Higher average dose to both brain and brainstem was associated with inferior PFS and OS (<i>p</i> &lt; .001). Median follow-up time were 69 months and 26 months for XRT and PT patients, respectively. Contrary to previous studies, there was no difference in risk of PsP for XRT and PT. PT was associated with lower rates of fatigue &lt;3 months after RT. The superior survival outcomes for PT indicates that the patients with the best prognosis were referred to PT.
DOI: 10.6084/m9.figshare.22657047.v1
title: Effect of docetaxel added to bicalutamide in Hormone-Naïve non-metastatic prostate cancer with rising PSA, a randomized clinical trial (SPCG-14)

description: Historically, endocrine therapy was used in a range of scenarios in patients with rising PSA, both as a treatment for locally advanced non-metastatic prostate cancer and PSA recurrence following curative intended therapy. In the present study the objective was to investigate if chemotherapy added to endocrine therapy could improve progression-free survival (PFS). Patients with hormone-naïve, non-metastatic prostate cancer and rising prostate-specific antigen (PSA), enrolled from Sweden, Denmark, the Netherlands, and Finland, were randomized to long-term bicalutamide (150 mg daily) or plus docetaxel (75 mg/m<sup>2</sup>, q3w, 8–10 cycles) without prednisone, after stratification for the site, prior local therapy or not, and PSA doubling time. The primary endpoint was 5-year PFS analyzed with a stratified Cox proportional hazards regression model on intention to treat basis. Between 2009 and 2018, a total of 348 patients were randomized; 315 patients had PSA relapse after radical treatment, 33 patients had no prior local therapy. Median follow-up was 4.9 years (IQR 4.0–5.1). Adding docetaxel improved PFS (HR 0.68, 95% CI 0.50–0.93; <i>p</i> = 0.015). Docetaxel showed an advantage for patients with PSA relapse after prior local therapy (HR 0.67, 95% CI 0.49–0.94; <i>p</i> = 0.019). One event of neutropenic infection/fever occurred in 27% of the patients receiving docetaxel. Limitations were slow recruitment, lack of enrolling patients without radical local treatment, and too short follow-up for evaluation of overall survival in patients with PSA relapse. Docetaxel improved PFS in patients starting bicalutamide due to PSA relapse after local therapy or localized disease without local therapy. Confirmatory studies of the efficacy of docetaxel in the setting of PSA-only relapse in addition to endocrine therapies may be justified if longer follow-up will show increased metastatic-free survival.
DOI: 10.6084/m9.figshare.22953557.v1
title: Transitioning from conventional photon therapy to proton therapy for primary brain tumors

description: Proton radiation therapy (PT) has become a treatment option alongside photon therapy (XRT) for lower-grade gliomas (LGG). In this single-institution retrospective study, we investigate the patient characteristics and treatment outcomes, including pseudo-progression (PsP), for LGG patients selected for PT. Adult patients with grade 2–3 glioma consecutively treated with radiotherapy (RT) from May 2012 to December 2019 were retrospectively included in this cohort study. Tumor characteristics and treatment data were collected. The groups treated with PT and XRT were compared regarding treatment characteristics, side effects, occurrence of PsP, and survival outcomes. PsP was defined as new or growing lesions followed by either decrease or stabilization during a 12 month-period with no treatment. Out of 143 patients meeting the inclusion criteria, 44 were treated with PT, 98 with XRT and one with mixed PT + XRT. The patients receiving PT were younger, had a lower tumor grade, more oligodendrogliomas and received a lower mean brain and brainstem dose. PsP was observed in 21 out of 126 patients, with no difference between XRT and PT (<i>p</i> = .38). The rate of fatigue in immediate connection to RT (zero to three months after) was higher for XRT than for PT (<i>p</i> = .016). The PT patients had a significantly better PFS and OS than the XRT patients (<i>p</i> = .025 and .035), but in multivariate analysis radiation modality was non-significant. Higher average dose to both brain and brainstem was associated with inferior PFS and OS (<i>p</i> &lt; .001). Median follow-up time were 69 months and 26 months for XRT and PT patients, respectively. Contrary to previous studies, there was no difference in risk of PsP for XRT and PT. PT was associated with lower rates of fatigue &lt;3 months after RT. The superior survival outcomes for PT indicates that the patients with the best prognosis were referred to PT.
DOI: 10.6084/m9.figshare.22708265
title: Effects on long-term survival of psychosocial group intervention in early-stage breast cancer: follow-up of a randomized controlled trial

description: The promise of prolonged survival after psychosocial interventions has long been studied, but not convincingly demonstrated. This study aims to investigate whether a psychosocial group intervention improved long-term survival in women with early-stage breast cancer and investigate differences in baseline characteristics and survival between study participants and non-participants. A total of 201 patients were randomized to two six-hour psychoeducation sessions and eight weekly sessions of group psychotherapy or care as usual. Additionally, 151 eligible patients declined to participate. Eligible patients were diagnosed and treated at Herlev Hospital, Denmark, and followed for vital status up to 18 years after their primary surgical treatment. Cox’s proportional hazard regressions were used to estimate hazard ratios (HRs) for survival. The intervention did not significantly improve survival in the intervention group compared with the control group (HR, 0.68; 95% confidence interval (CI), 0.41–1.14). Participants and non-participants differed significantly in age, cancer stage, adjuvant chemotherapy, and crude survival. When adjusted, no significant survival difference between participants and non-participants remained (HR, 0.77; 95% CI, 0.53–1.11). We could not show improved long-term survival after the psychosocial intervention. Participants survived longer than nonparticipants, but clinical and demographic characteristics, rather than study participation, seem accountable for this difference.