cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14339423
title: Is the capture of invertebrate prey by the aquatic carnivorous plant <i>Utricularia australis</i> selective?

description: <i>Utricularia</i> (bladderwort) trap contents have frequently been used to define its diet, but there is a scarcity of information on prey availability. Yet making comparisons between trap contents and outside communities could help define feeding strategies of these fascinating carnivorous plants. This study focuses on <i>U. australis</i>, the most common aquatic bladderwort in central Italy, with data of inside- and outside-trap communities from 23 sites. The feeding strategy of <i>U. australis</i> is highly dependent on prey availability and size; the prey has to be large enough to stimulate trap triggering, yet small enough to be taken up through the trap door unimpeded. In addition, the prey has to be moderately motile but not dispersive. The trap contents were generally a mixture of species taken up by active and spontaneous trap firing. Stimulation of a heavy epiphytic growth by <i>Utricularia</i> resulted in higher entrapment of epiphyte-grazing taxa resulting in a positive feedback loop. The comparative data here also suggest that prey digestion is a rapid enough process that keeps up with the seasonal succession of the outside community. The trapped community (or the diet) of <i>U. australis</i> seems to derive by the contribution of all these factors.
DOI: 10.6084/m9.figshare.14339423.v1
title: Is the capture of invertebrate prey by the aquatic carnivorous plant <i>Utricularia australis</i> selective?

description: <i>Utricularia</i> (bladderwort) trap contents have frequently been used to define its diet, but there is a scarcity of information on prey availability. Yet making comparisons between trap contents and outside communities could help define feeding strategies of these fascinating carnivorous plants. This study focuses on <i>U. australis</i>, the most common aquatic bladderwort in central Italy, with data of inside- and outside-trap communities from 23 sites. The feeding strategy of <i>U. australis</i> is highly dependent on prey availability and size; the prey has to be large enough to stimulate trap triggering, yet small enough to be taken up through the trap door unimpeded. In addition, the prey has to be moderately motile but not dispersive. The trap contents were generally a mixture of species taken up by active and spontaneous trap firing. Stimulation of a heavy epiphytic growth by <i>Utricularia</i> resulted in higher entrapment of epiphyte-grazing taxa resulting in a positive feedback loop. The comparative data here also suggest that prey digestion is a rapid enough process that keeps up with the seasonal succession of the outside community. The trapped community (or the diet) of <i>U. australis</i> seems to derive by the contribution of all these factors.
DOI: 10.6084/m9.figshare.13979584
title: PD-L1 and IDO1 are potential targets for treatment in patients with primary diffuse large B-cell lymphoma of the CNS

description: Programmed cell death 1 (PD-1) and its ligands PD-L1 and PD-L2, as well as Indoleamine 2,3-deoxygenase (IDO1) can be expressed both by tumor and microenvironmental cells and are crucial for tumor immune escape. We aimed to evaluate the role of PD-1, its ligands and IDO1 in a cohort of patients with primary diffuse large B-cell lymphoma of the CNS (PCNSL). Tissue microarrays (TMAs) were constructed in 45 PCNSL cases. RNA extraction from whole tissue sections and RNA sequencing were successfully performed in 33 cases. Immunohistochemical stainings for PD-1, PD-L1/paired box protein 5 (PAX-5), PD-L2/PAX-5 and IDO1, and Epstein-Barr virus encoding RNA (EBER) <i>in situ</i> hybridization were analyzed. High proportions of PD-L1 and PD-L2 positive tumor cells were observed in 11% and 9% of cases, respectively. High proportions of PD-L1 and PD-L2 positive leukocytes were observed in 55% and 51% of cases, respectively. RNA sequencing revealed that gene expression of <i>IDO1</i> was high in patients with high proportion of PD-L1 positive leukocytes (<i>p</i> = .01). Protein expression of IDO1 in leukocytes was detected in 14/45 cases, in 79% of these cases a high proportion of PD-L1 positive leukocytes was observed. Gene expression of <i>IDO1</i> was high in EBER-positive cases (<i>p</i> = .0009) and protein expression of IDO1 was detected in five of six EBER-positive cases. Our study shows a significant association between gene and protein expression of IDO1 and protein expression of PD-L1 in the tumor microenvironment of PCNSL, possibly of importance for prediction of response to immunotherapies.
DOI: 10.6084/m9.figshare.13979584.v1
title: PD-L1 and IDO1 are potential targets for treatment in patients with primary diffuse large B-cell lymphoma of the CNS

description: Programmed cell death 1 (PD-1) and its ligands PD-L1 and PD-L2, as well as Indoleamine 2,3-deoxygenase (IDO1) can be expressed both by tumor and microenvironmental cells and are crucial for tumor immune escape. We aimed to evaluate the role of PD-1, its ligands and IDO1 in a cohort of patients with primary diffuse large B-cell lymphoma of the CNS (PCNSL). Tissue microarrays (TMAs) were constructed in 45 PCNSL cases. RNA extraction from whole tissue sections and RNA sequencing were successfully performed in 33 cases. Immunohistochemical stainings for PD-1, PD-L1/paired box protein 5 (PAX-5), PD-L2/PAX-5 and IDO1, and Epstein-Barr virus encoding RNA (EBER) <i>in situ</i> hybridization were analyzed. High proportions of PD-L1 and PD-L2 positive tumor cells were observed in 11% and 9% of cases, respectively. High proportions of PD-L1 and PD-L2 positive leukocytes were observed in 55% and 51% of cases, respectively. RNA sequencing revealed that gene expression of <i>IDO1</i> was high in patients with high proportion of PD-L1 positive leukocytes (<i>p</i> = .01). Protein expression of IDO1 in leukocytes was detected in 14/45 cases, in 79% of these cases a high proportion of PD-L1 positive leukocytes was observed. Gene expression of <i>IDO1</i> was high in EBER-positive cases (<i>p</i> = .0009) and protein expression of IDO1 was detected in five of six EBER-positive cases. Our study shows a significant association between gene and protein expression of IDO1 and protein expression of PD-L1 in the tumor microenvironment of PCNSL, possibly of importance for prediction of response to immunotherapies.
DOI: 10.6084/m9.figshare.14141907
title: The PROMova study comparing active and passive use of patient-reported outcome measures in ovarian cancer follow-up: effect on patient-perceived involvement, satisfaction with care, and usefulness

description: Patients with ovarian cancer often experience substantial health problems and side effects resulting in reduced quality of life (QoL). Different models of using patient-reported outcome measures (PROMs) during follow-up may improve the quality of care. This national, multicenter observational study investigated the effect of active use of PROMs on patient-perceived involvement, satisfaction with care, unmet needs, and QoL during follow-up of ovarian cancer. Ovarian cancer patients were recruited at the end of primary treatment at eight centers in Denmark. During 18 months of follow-up patients repeatedly completed European Organization for Research and Treatment of Cancer (EORTC) questionnaires covering health related QoL and symptoms. At the sites using PROMs actively (ACT), the clinician had access to an overview of the patient's scores during the clinical encounter. Clinicians using PROMs passively were alerted in case of severe development of symptoms. Following each encounter, patients evaluated their health service experience by completing the CollaboRATE scale of involvement in decision making, the Patient Experience Questionnaire, and ad hoc questions covering patient-perceived usefulness of the PROMs. A total of 223 patients were enrolled, i.e., 168 (75.3%) at five sites using ACT and 53 (23.8%) at three sites using them passively. We found no statistically significant difference in involvement in the decision making, satisfaction with care, unmet needs, and QoL between the two groups. The majority of patients found it useful to complete the PROMs, although it did not seem to significantly support them in raising issues with the oncologist. Active use of PROMs did not improve patients’ experience of involvement in follow-up care as compared to passive use.
DOI: 10.6084/m9.figshare.13651548.v1
title: Prognostic role of TLR4 and TLR2 in hepatocellular carcinoma

description: Prognostic role of TLR4 and TLR2 in hepatocellular carcinoma
DOI: 10.6084/m9.figshare.14141907.v1
title: The PROMova study comparing active and passive use of patient-reported outcome measures in ovarian cancer follow-up: effect on patient-perceived involvement, satisfaction with care, and usefulness

description: Patients with ovarian cancer often experience substantial health problems and side effects resulting in reduced quality of life (QoL). Different models of using patient-reported outcome measures (PROMs) during follow-up may improve the quality of care. This national, multicenter observational study investigated the effect of active use of PROMs on patient-perceived involvement, satisfaction with care, unmet needs, and QoL during follow-up of ovarian cancer. Ovarian cancer patients were recruited at the end of primary treatment at eight centers in Denmark. During 18 months of follow-up patients repeatedly completed European Organization for Research and Treatment of Cancer (EORTC) questionnaires covering health related QoL and symptoms. At the sites using PROMs actively (ACT), the clinician had access to an overview of the patient's scores during the clinical encounter. Clinicians using PROMs passively were alerted in case of severe development of symptoms. Following each encounter, patients evaluated their health service experience by completing the CollaboRATE scale of involvement in decision making, the Patient Experience Questionnaire, and ad hoc questions covering patient-perceived usefulness of the PROMs. A total of 223 patients were enrolled, i.e., 168 (75.3%) at five sites using ACT and 53 (23.8%) at three sites using them passively. We found no statistically significant difference in involvement in the decision making, satisfaction with care, unmet needs, and QoL between the two groups. The majority of patients found it useful to complete the PROMs, although it did not seem to significantly support them in raising issues with the oncologist. Active use of PROMs did not improve patients’ experience of involvement in follow-up care as compared to passive use.
DOI: 10.6084/m9.figshare.13637306
title: Identification of a novel resistance mechanism in venetoclax treatment and its prediction in chronic lymphocytic leukemia

description: The Bcl-2 inhibitor venetoclax has been recently introduced into the treatment of chronic lymphocytic leukemia. Venetoclax is a highly effective drug, however acquired resistance may make long-term treatment challenging. In our study, we present potential novel resistance mechanisms and prognostic markers that are potentially able to predict the early appearance of the resistance. Repeated complete blood counts, flow cytometric measurements, and physical examinations were performed during the patient follow-up. Clinical and laboratory parameters showed that the patient developed clinical resistance to venetoclax on day 450 of therapy. Resistance mutation analysis (D103Y) and apoptosis arrays from samples at the time of resistance were done. We were able to identify the resistance mutations just a very low variant allele frequency level from the resistant samples. Furthermore we detected increased Bcl-2 expression in peripheral blood (PB), and XIAP overexpression in bone marrow (BM) that could lead to venetoclax resistance. We examined the immunophenotype of CLL cells and recognized that while the expression of CD86 did not change until day 270 of the treatment, since then its expression steadily increased. Moreover, we compared the expression of CD86 in the resistant PB and BM samples and did not find a notable difference between the compartments. Our results imply that CLL cells may try to avoid the apoptotic effect of venetoclax through increased CD86 expression by activating antiapoptotic mechanisms. Confirmatory experiments are still required to unequivocally prove that CD86 is a prognostic marker, however, its predictive property during the venetoclax treatment is promising.
DOI: 10.6084/m9.figshare.13637306.v1
title: Identification of a novel resistance mechanism in venetoclax treatment and its prediction in chronic lymphocytic leukemia

description: The Bcl-2 inhibitor venetoclax has been recently introduced into the treatment of chronic lymphocytic leukemia. Venetoclax is a highly effective drug, however acquired resistance may make long-term treatment challenging. In our study, we present potential novel resistance mechanisms and prognostic markers that are potentially able to predict the early appearance of the resistance. Repeated complete blood counts, flow cytometric measurements, and physical examinations were performed during the patient follow-up. Clinical and laboratory parameters showed that the patient developed clinical resistance to venetoclax on day 450 of therapy. Resistance mutation analysis (D103Y) and apoptosis arrays from samples at the time of resistance were done. We were able to identify the resistance mutations just a very low variant allele frequency level from the resistant samples. Furthermore we detected increased Bcl-2 expression in peripheral blood (PB), and XIAP overexpression in bone marrow (BM) that could lead to venetoclax resistance. We examined the immunophenotype of CLL cells and recognized that while the expression of CD86 did not change until day 270 of the treatment, since then its expression steadily increased. Moreover, we compared the expression of CD86 in the resistant PB and BM samples and did not find a notable difference between the compartments. Our results imply that CLL cells may try to avoid the apoptotic effect of venetoclax through increased CD86 expression by activating antiapoptotic mechanisms. Confirmatory experiments are still required to unequivocally prove that CD86 is a prognostic marker, however, its predictive property during the venetoclax treatment is promising.
DOI: 10.6084/m9.figshare.13503107.v2
title: Characteristics and outcomes of participants in colorectal cancer biomarker trials versus a real-world cohort

description: The restrictive eligibility criteria of therapy-focused cancer clinical trials can limit the external validity of the results. The characteristics and survival outcomes of patients enrolled in stand-alone biomarker studies have yet to be explored. We examined the characteristics of patients enrolled in a series of biomarker studies in stage II and III colorectal cancer (CRC) and of the broader patient population from which the study cohorts were recruited. We examined three distinct trial scenarios: a retrospective cohort study (RCS) where archival tissue samples were analyzed, a prospective observational study (POS) where blood samples were collected but patients received standard treatment and a randomized clinical trial (RCT) where biomarker analysis could inform clinical care. Clinical data for each study time period were extracted from a prospective registry. For all CRC patients (<i>n</i> = 4033) in this study, the median age was 70 years and 54% were ECOG 0. For patients in the RCS (<i>n</i> = 450), POS (<i>n</i> = 284) and RCT (<i>n</i> = 230), the median age was 72, 65 and 64 years, with 45%, 74% and 79% being ECOG 0. For the POS and RCT, 33% and 36% of all patients with the relevant disease stage were enrolled over the study recruitment period. Survival outcomes were similar for patients in the RCS and POS. RCT outcome data are not available. As for therapy-based trials, enrollment in prospective biomarker studies may be selective, despite relatively broad eligibility criteria. Characteristics and recruitment were similar for POS and RCT patients, indicating study complexity may not necessarily limit patient recruitment. For the prospective biomarker study cohorts examined, the selective recruitment did not significantly impact survival outcomes, suggesting potential for high external validity.
DOI: 10.6084/m9.figshare.13503107
title: Characteristics and outcomes of participants in colorectal cancer biomarker trials versus a real-world cohort

description: The restrictive eligibility criteria of therapy-focused cancer clinical trials can limit the external validity of the results. The characteristics and survival outcomes of patients enrolled in stand-alone biomarker studies have yet to be explored. We examined the characteristics of patients enrolled in a series of biomarker studies in stage II and III colorectal cancer (CRC) and of the broader patient population from which the study cohorts were recruited. We examined three distinct trial scenarios: a retrospective cohort study (RCS) where archival tissue samples were analyzed, a prospective observational study (POS) where blood samples were collected but patients received standard treatment and a randomized clinical trial (RCT) where biomarker analysis could inform clinical care. Clinical data for each study time period were extracted from a prospective registry. For all CRC patients (<i>n</i> = 4033) in this study, the median age was 70 years and 54% were ECOG 0. For patients in the RCS (<i>n</i> = 450), POS (<i>n</i> = 284) and RCT (<i>n</i> = 230), the median age was 72, 65 and 64 years, with 45%, 74% and 79% being ECOG 0. For the POS and RCT, 33% and 36% of all patients with the relevant disease stage were enrolled over the study recruitment period. Survival outcomes were similar for patients in the RCS and POS. RCT outcome data are not available. As for therapy-based trials, enrollment in prospective biomarker studies may be selective, despite relatively broad eligibility criteria. Characteristics and recruitment were similar for POS and RCT patients, indicating study complexity may not necessarily limit patient recruitment. For the prospective biomarker study cohorts examined, the selective recruitment did not significantly impact survival outcomes, suggesting potential for high external validity.
DOI: 10.6084/m9.figshare.13503107.v1
title: Characteristics and outcomes of participants in colorectal cancer biomarker trials versus a real-world cohort

description: The restrictive eligibility criteria of therapy-focused cancer clinical trials can limit the external validity of the results. The characteristics and survival outcomes of patients enrolled in stand-alone biomarker studies have yet to be explored. We examined the characteristics of patients enrolled in a series of biomarker studies in stage II and III colorectal cancer (CRC) and of the broader patient population from which the study cohorts were recruited. We examined three distinct trial scenarios: a retrospective cohort study (RCS) where archival tissue samples were analyzed, a prospective observational study (POS) where blood samples were collected but patients received standard treatment and a randomized clinical trial (RCT) where biomarker analysis could inform clinical care. Clinical data for each study time period were extracted from a prospective registry. For all CRC patients (<i>n</i> = 4033) in this study, the median age was 70 years and 54% were ECOG 0. For patients in the RCS (<i>n</i> = 450), POS (<i>n</i> = 284) and RCT (<i>n</i> = 230), the median age was 72, 65 and 64 years, with 45%, 74% and 79% being ECOG 0. For the POS and RCT, 33% and 36% of all patients with the relevant disease stage were enrolled over the study recruitment period. Survival outcomes were similar for patients in the RCS and POS. RCT outcome data are not available. As for therapy-based trials, enrollment in prospective biomarker studies may be selective, despite relatively broad eligibility criteria. Characteristics and recruitment were similar for POS and RCT patients, indicating study complexity may not necessarily limit patient recruitment. For the prospective biomarker study cohorts examined, the selective recruitment did not significantly impact survival outcomes, suggesting potential for high external validity.
DOI: 10.6084/m9.figshare.13241252
title: Delta NT-proBNP predicts cardiotoxicity in HER2-positive breast cancer patients treated with trastuzumab

description: Overall survival has improved significantly in patients with human epidermal growth receptor 2 (HER2)-positive breast cancer due to the use of the monoclonal antibody trastuzumab blocking HER2. However, patients may develop trastuzumab-induced cardiotoxicity (TIC) leading to congestive heart failure. Here we assessed whether analysing NT-proBNP and assessment of electrocardiography (ECG) could detect TIC during trastuzumab therapy. One hundred thirty-six patients undergoing adjuvant, neoadjuvant or palliative chemotherapy and HER2 blockade for HER2-positive breast cancer were prospectively assessed with echocardiography, ECG and N-terminal – pro hormone B-type natriuretic peptide (NT-proBNP) testing at baseline and at 6 and 12 months of trastuzumab therapy. TIC was defined as a left ventricular ejection fraction (LVEF) of less than 50% and a decline from baseline of ≥10 units. Six patients developed TIC under 12 months of trastuzumab therapy (incidence 4.4%). NT-proBNP increased from 198.8 ± 64.0 pg/ml to 678.7 ± 132.4 pg/ml (<i>p</i> p p p p Measuring changes in NTproBNP may be used to monitor patients for TIC under trastuzumab therapy. Patients with a cardiovascular risk profile are more at risk of developing TIC.
DOI: 10.6084/m9.figshare.13241252.v1
title: Delta NT-proBNP predicts cardiotoxicity in HER2-positive breast cancer patients treated with trastuzumab

description: Overall survival has improved significantly in patients with human epidermal growth receptor 2 (HER2)-positive breast cancer due to the use of the monoclonal antibody trastuzumab blocking HER2. However, patients may develop trastuzumab-induced cardiotoxicity (TIC) leading to congestive heart failure. Here we assessed whether analysing NT-proBNP and assessment of electrocardiography (ECG) could detect TIC during trastuzumab therapy. One hundred thirty-six patients undergoing adjuvant, neoadjuvant or palliative chemotherapy and HER2 blockade for HER2-positive breast cancer were prospectively assessed with echocardiography, ECG and N-terminal – pro hormone B-type natriuretic peptide (NT-proBNP) testing at baseline and at 6 and 12 months of trastuzumab therapy. TIC was defined as a left ventricular ejection fraction (LVEF) of less than 50% and a decline from baseline of ≥10 units. Six patients developed TIC under 12 months of trastuzumab therapy (incidence 4.4%). NT-proBNP increased from 198.8 ± 64.0 pg/ml to 678.7 ± 132.4 pg/ml (<i>p</i> p p p p Measuring changes in NTproBNP may be used to monitor patients for TIC under trastuzumab therapy. Patients with a cardiovascular risk profile are more at risk of developing TIC.
DOI: 10.6084/m9.figshare.13677523
title: Immune cell score, PD-L1 expression and prognosis in esophageal cancer

description: Immune cell score, PD-L1 expression and prognosis in esophageal cancer