cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19166357.v1
title: Highly specific functional equivalence of XN-HPC for optimum CD34+ cell count in harvested allogeneic bone marrow stem cell products

description: To establish a reliable XN-HPC cutoff, for an effective CD34 + cell count of ≥2 × 10<sup>6</sup>cells/kg of the recipient’s body weight, in harvested bone marrow products in allogenic transplantation. The study was carried out in two phases. In retrospective Phase 1, data from 47 donors were analyzed. Sysmex analyzer XN-20 and BD FACS Calibur were employed to process XN-HPC and CD34 + cell enumeration, respectively. To make the two variables comparable, both XN-HPC and CD34 + cell counts were reported as the number of cells/kg of the recipient’s body weight. Spearman’s rank correlation coefficient was calculated for CD34 + cells and XN-HPC, followed by the calculation of the receiver operating characteristic (ROC) curve to identify the XN-HPC value which could effectively predict the cutoff of ≥2 × 10<sup>6</sup> CD34 + cells/kg of the recipient’s body weight. In Phase 2, the computed XN-HPC cutoff was validated in a prospective set of 53 donors by obtaining the positive and negative predictive values. Statistically significant correlation was obtained between XN-HPC and CD34 + cell count with Spearman’s rho of 0.54 (<i>p</i>-value &lt;0.001). The optimal XN-HPC cutoff, for the required CD34 + ve cell count of ≥2 × 10<sup>6</sup> cells/kg of the recipient’s body weight, was calculated to be ≥2.80×10<sup>6</sup> cells/kg of the recipient’s body weight with the specificity and sensitivity of 100% and 31%, respectively. The ROC curve demonstrated the area under the curve to be 0.74. Phase 2 validation revealed 100% PPV. For harvested bone marrow products with XN-HPC of ≥2.80×10<sup>6</sup> cell/kg of the recipient’s body weight, CD34 + cell enumeration by flow cytometry can safely be disposed of.
DOI: 10.6084/m9.figshare.21731213
title: Comparison of Molecular International Prognostic Scoring System (M-IPSS) and Revised International Prognostic Scoring System (R-IPSS) in Thai patients with myelodysplastic neoplasms

description: Risk stratification is essential for treatment decision in myelodysplastic neoplasms (MDS). Molecular international prognostic scoring system (M-IPSS) has been recently developed combining somatic mutations and clinical information being used in the revised international prognostic scoring system (R-IPSS). We aimed to explore the performances of M-IPSS and R-IPSS in Thai patients with MDS. MDS patients were stratified into risk categories using R-IPSS and M-IPSS scores. The performance of both models were evaluated for prognostic prediction. One hundred and sixty-two MDS patients were recruited from the multicenter study. Survival analysis revealed that both R-IPSS and M-IPSS were good prediction models with the Concordance Index (C-index) of 0.71 (95% Confidence interval [CI] 0.64–0.78) and 0.75 (95% CI 0.69–0.80), respectively (<i>p</i> = 0.22). Comparing the two, 13 of 162 (8%) cases were re-staged between lower and higher risks which would have affected treatment decisions. Our study showed that R-IPSS score can be used for risk stratification in most Thai patients. A prediction model using somatic mutations specifically in Asian patients should be formulated in the future.
DOI: 10.6084/m9.figshare.21731213.v2
title: Comparison of Molecular International Prognostic Scoring System (M-IPSS) and Revised International Prognostic Scoring System (R-IPSS) in Thai patients with myelodysplastic neoplasms

description: Risk stratification is essential for treatment decision in myelodysplastic neoplasms (MDS). Molecular international prognostic scoring system (M-IPSS) has been recently developed combining somatic mutations and clinical information being used in the revised international prognostic scoring system (R-IPSS). We aimed to explore the performances of M-IPSS and R-IPSS in Thai patients with MDS. MDS patients were stratified into risk categories using R-IPSS and M-IPSS scores. The performance of both models were evaluated for prognostic prediction. One hundred and sixty-two MDS patients were recruited from the multicenter study. Survival analysis revealed that both R-IPSS and M-IPSS were good prediction models with the Concordance Index (C-index) of 0.71 (95% Confidence interval [CI] 0.64–0.78) and 0.75 (95% CI 0.69–0.80), respectively (<i>p</i> = 0.22). Comparing the two, 13 of 162 (8%) cases were re-staged between lower and higher risks which would have affected treatment decisions. Our study showed that R-IPSS score can be used for risk stratification in most Thai patients. A prediction model using somatic mutations specifically in Asian patients should be formulated in the future.
DOI: 10.6084/m9.figshare.19749969
title: Bendamustine treatment of haematological malignancies: significant risks of opportunistic viral, fungal and bacterial infections

description: Bendamustine is a standard treatment for low-grade B-cell lymphomas, and considered safe in clinical trials. Its safety in routine practice might be different. We retrospectively analyzed the infection complications in an unselected cohort of patients treated with bendamustine over a nine-year period. Patients were regularly monitored for blood counts and cytomegalovirus (CMV) reactivation by antigen assay and polymerase chain reaction. They received granulocyte colony stimulating factor for neutropenia, and routine anti-pneumocystis and optional anti-fungal prophylaxis. There were 179 men and 127 women at a median age of 61.5 (20–90) years, 52% receiving bendamustine for relapsed/refractory disease. Malignancies included low-grade B-cell lymphomas (54%), myeloma (10%), T-cell lymphomas (11%), Hodgkin lymphoma (2%) and other lymphoid neoplasms (23%). Most patients had good performance status (Eastern Cooperative Oncology Group score: 0–1, 72%). CMV reactivation occurred in 58 patients (19%) at a median age of 68 (39–85) years. Univariate analysis showed CMV reactivation to be significantly associated with elevated lactate dehydrogenase (<i>P</i> = 0.045), decreased albumin (<i>P</i> = 0.003) and older age (reactivation versus no reactivation: 66.3 ± 11.4 versus 59.4 ± 14.5 years, <i>P</i> = 0.0016). Age remained the only significant risk on multivariate analysis. CMV reactivation resulted in retinitis (<i>N</i> = 4), ependymitis/ventriculitis (<i>N</i> = 1) and duodenitis/colitis (<i>N</i> = 1). Invasive fungal disease occurred in five patients (candidemia, <i>N</i> = 2; aspergillosis <i>N</i> = 1; cryptococcemia, <i>N</i> = 1; scedosporiosis, <i>N</i>–1). Nineteen patients had culture positive septicaemia. Our observations showed that even with a vigorous anti-infective strategy, bendamustine treatment was still associated with significant risks of bacterial and opportunistic viral and fungal infections.
DOI: 10.6084/m9.figshare.19749969.v1
title: Bendamustine treatment of haematological malignancies: significant risks of opportunistic viral, fungal and bacterial infections

description: Bendamustine is a standard treatment for low-grade B-cell lymphomas, and considered safe in clinical trials. Its safety in routine practice might be different. We retrospectively analyzed the infection complications in an unselected cohort of patients treated with bendamustine over a nine-year period. Patients were regularly monitored for blood counts and cytomegalovirus (CMV) reactivation by antigen assay and polymerase chain reaction. They received granulocyte colony stimulating factor for neutropenia, and routine anti-pneumocystis and optional anti-fungal prophylaxis. There were 179 men and 127 women at a median age of 61.5 (20–90) years, 52% receiving bendamustine for relapsed/refractory disease. Malignancies included low-grade B-cell lymphomas (54%), myeloma (10%), T-cell lymphomas (11%), Hodgkin lymphoma (2%) and other lymphoid neoplasms (23%). Most patients had good performance status (Eastern Cooperative Oncology Group score: 0–1, 72%). CMV reactivation occurred in 58 patients (19%) at a median age of 68 (39–85) years. Univariate analysis showed CMV reactivation to be significantly associated with elevated lactate dehydrogenase (<i>P</i> = 0.045), decreased albumin (<i>P</i> = 0.003) and older age (reactivation versus no reactivation: 66.3 ± 11.4 versus 59.4 ± 14.5 years, <i>P</i> = 0.0016). Age remained the only significant risk on multivariate analysis. CMV reactivation resulted in retinitis (<i>N</i> = 4), ependymitis/ventriculitis (<i>N</i> = 1) and duodenitis/colitis (<i>N</i> = 1). Invasive fungal disease occurred in five patients (candidemia, <i>N</i> = 2; aspergillosis <i>N</i> = 1; cryptococcemia, <i>N</i> = 1; scedosporiosis, <i>N</i>–1). Nineteen patients had culture positive septicaemia. Our observations showed that even with a vigorous anti-infective strategy, bendamustine treatment was still associated with significant risks of bacterial and opportunistic viral and fungal infections.
DOI: 10.6084/m9.figshare.19586563
title: Gene expression profiles and cytokine environments determine the in vitro proliferation and expansion capacities of human hematopoietic stem and progenitor cells

description: The interplay between intrinsic and extrinsic elements involved in the physiology of hematopoietic cells is not completely understood. In the present study, we analyzed the transcriptional profiles of human cord blood-derived hematopoietic stem cells (HSCs), as well as myeloid (MPCs) and erythroid (EPCs) progenitors, and assessed their proliferation and expansion kinetics in vitro. All cell populations were obtained by cell-sorting, and were cultured in liquid cultures supplemented with different cytokine combinations. Their gene expression profiles were determined by RNA microarrays right after cell-sorting, before culture. HSCs showed the highest proliferation and expansion capacities in culture, and were found to be more closely related, in transcriptional terms, to MPCs than to EPCs. This correlated with the fact that after 30 days, only cultures initiated with HSCs and MPCs were sustained. Expression of cell cycle and cell division-related genes was enriched in EPCs. Such cells showed significantly higher proliferation than MPCs, however, their expansion potential was reduced, so that cultures initiated with EPCs declined after 15 days and became exhausted by day 30. Proliferation and expansion of HSCs and EPCs were higher in the presence of a cytokine combination that favors erythropoiesis, whereas the growth of MPCs was higher under a cytokine combination that favors myelopoiesis. This study shows a correlation between the transcriptional profiles of HSCs, MPCs, and EPCs, and their respective in vitro growth under particular culture conditions. These results may be relevant in the development of ex vivo systems for the expansion of hematopoietic cells for clinical application.
DOI: 10.6084/m9.figshare.19586563.v1
title: Gene expression profiles and cytokine environments determine the in vitro proliferation and expansion capacities of human hematopoietic stem and progenitor cells

description: The interplay between intrinsic and extrinsic elements involved in the physiology of hematopoietic cells is not completely understood. In the present study, we analyzed the transcriptional profiles of human cord blood-derived hematopoietic stem cells (HSCs), as well as myeloid (MPCs) and erythroid (EPCs) progenitors, and assessed their proliferation and expansion kinetics in vitro. All cell populations were obtained by cell-sorting, and were cultured in liquid cultures supplemented with different cytokine combinations. Their gene expression profiles were determined by RNA microarrays right after cell-sorting, before culture. HSCs showed the highest proliferation and expansion capacities in culture, and were found to be more closely related, in transcriptional terms, to MPCs than to EPCs. This correlated with the fact that after 30 days, only cultures initiated with HSCs and MPCs were sustained. Expression of cell cycle and cell division-related genes was enriched in EPCs. Such cells showed significantly higher proliferation than MPCs, however, their expansion potential was reduced, so that cultures initiated with EPCs declined after 15 days and became exhausted by day 30. Proliferation and expansion of HSCs and EPCs were higher in the presence of a cytokine combination that favors erythropoiesis, whereas the growth of MPCs was higher under a cytokine combination that favors myelopoiesis. This study shows a correlation between the transcriptional profiles of HSCs, MPCs, and EPCs, and their respective in vitro growth under particular culture conditions. These results may be relevant in the development of ex vivo systems for the expansion of hematopoietic cells for clinical application.
DOI: 10.6084/m9.figshare.17694830
title: Efficacy and safety of adding gemtuzumab ozogamicin to conventional chemotherapy for adult acute myeloid leukemia: a systematic review and meta-analysis

description: <b>Introduction:</b> Compared with the 3 + 7 regimen, the addition of gemtuzumab ozogamicin (GO) has improved survival in patients with acute myeloid leukemia (AML). We conducted a systematic review and meta-analysis to examine the overall efficacy and safety of GO in combination with conventional chemotherapy regimens in patients with AML. <b>Methods:</b> We searched several databases (MEDLINE, Embase, Web of Science and Cochrane Library). Hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated for overall survival (OS) and relapse-free survival (RFS); odds ratios (ORs) with 95% CIs were calculated for the other outcomes. <b>Results:</b> Ten records involving 11 randomized controlled trials (RCTs) met the inclusion criteria. GO plus induction chemotherapy significantly increased RFS (HR: 0.84, 95% CI: 0.73–0.98), decreased the incidence of relapse (OR: 0.78, 95% CI: 0.68–0.91) and resistant disease (OR: 0.72, 95% CI: 0.61–0.84), and had no significant effect on the rate of complete remission (CR) with or without incomplete platelet recovery (OR: 1.21, 95% CI: 0.94–1.55), 30-day mortality (OR: 1.25, 95% CI: 0.99–1.57). Subgroup analysis showed significant OS benefits for patients with favorable cytogenetic (HR: 0.50, 95% CI: 0.28–0.89) or given GO at induction stage (HR: 0.91, 95% CI: 0.84–1.00). Compared with other dosing schedule groups, 3 mg/m<sup>2</sup> fractionated schedule had a greater RFS benefit (HR: 0.52, 95% CI: 0.36–0.76) and lower relapse risk (OR: 0.48, 95% CI: 0.28–0.84). <b>Conclusions:</b> Adding low-dose GO to induction or both induction and post-remission chemotherapy has considerable efficacy and unequivocal safety for newly diagnosed adult AML.
DOI: 10.6084/m9.figshare.17694830.v1
title: Efficacy and safety of adding gemtuzumab ozogamicin to conventional chemotherapy for adult acute myeloid leukemia: a systematic review and meta-analysis

description: <b>Introduction:</b> Compared with the 3 + 7 regimen, the addition of gemtuzumab ozogamicin (GO) has improved survival in patients with acute myeloid leukemia (AML). We conducted a systematic review and meta-analysis to examine the overall efficacy and safety of GO in combination with conventional chemotherapy regimens in patients with AML. <b>Methods:</b> We searched several databases (MEDLINE, Embase, Web of Science and Cochrane Library). Hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated for overall survival (OS) and relapse-free survival (RFS); odds ratios (ORs) with 95% CIs were calculated for the other outcomes. <b>Results:</b> Ten records involving 11 randomized controlled trials (RCTs) met the inclusion criteria. GO plus induction chemotherapy significantly increased RFS (HR: 0.84, 95% CI: 0.73–0.98), decreased the incidence of relapse (OR: 0.78, 95% CI: 0.68–0.91) and resistant disease (OR: 0.72, 95% CI: 0.61–0.84), and had no significant effect on the rate of complete remission (CR) with or without incomplete platelet recovery (OR: 1.21, 95% CI: 0.94–1.55), 30-day mortality (OR: 1.25, 95% CI: 0.99–1.57). Subgroup analysis showed significant OS benefits for patients with favorable cytogenetic (HR: 0.50, 95% CI: 0.28–0.89) or given GO at induction stage (HR: 0.91, 95% CI: 0.84–1.00). Compared with other dosing schedule groups, 3 mg/m<sup>2</sup> fractionated schedule had a greater RFS benefit (HR: 0.52, 95% CI: 0.36–0.76) and lower relapse risk (OR: 0.48, 95% CI: 0.28–0.84). <b>Conclusions:</b> Adding low-dose GO to induction or both induction and post-remission chemotherapy has considerable efficacy and unequivocal safety for newly diagnosed adult AML.
DOI: 10.6084/m9.figshare.20431291
title: The signature based on seven genomic instability-related genes could predict the prognosis of acute myeloid leukemia patients

description: Acute myeloid leukemia (AML) is the most common acute blood malignancy in adults. The complicated and dynamic genomic instability (GI) is the most prominent feature of AML. Our study aimed to explore the prognostic value of GI-related genes in AML patients. The mRNA data and mutation data were downloaded from the TCGA and GEO databases. Differential expression analyses were completed in limma package. GO and KEGG functional enrichment was conducted using clusterProfiler function of R. Univariate Cox and LASSO Cox regression analyses were performed to screen key genes for Risk score model construction. Nomogram was built with rms package. We identified 114 DEGs between high TMB patients and low TMB AML patients, which were significantly enriched in 429 GO terms and 13 KEGG pathways. Based on the univariate Cox and LASSO Cox regression analyses, seven optimal genes were finally applied for Risk score model construction, including SELE, LGALS1, ITGAX, TMEM200A, SLC25A21, S100A4 and CRIP1. The Risk score could reliably predict the prognosis of AML patients. Age and Risk score were both independent prognostic indicators for AML, and the Nomogram based on them could also reliably predict the OS of AML patients. A prognostic signature based on seven GI-related genes and a predictive Nomogram for AML patients are finally successfully constructed.
DOI: 10.6084/m9.figshare.20431291.v1
title: The signature based on seven genomic instability-related genes could predict the prognosis of acute myeloid leukemia patients

description: Acute myeloid leukemia (AML) is the most common acute blood malignancy in adults. The complicated and dynamic genomic instability (GI) is the most prominent feature of AML. Our study aimed to explore the prognostic value of GI-related genes in AML patients. The mRNA data and mutation data were downloaded from the TCGA and GEO databases. Differential expression analyses were completed in limma package. GO and KEGG functional enrichment was conducted using clusterProfiler function of R. Univariate Cox and LASSO Cox regression analyses were performed to screen key genes for Risk score model construction. Nomogram was built with rms package. We identified 114 DEGs between high TMB patients and low TMB AML patients, which were significantly enriched in 429 GO terms and 13 KEGG pathways. Based on the univariate Cox and LASSO Cox regression analyses, seven optimal genes were finally applied for Risk score model construction, including SELE, LGALS1, ITGAX, TMEM200A, SLC25A21, S100A4 and CRIP1. The Risk score could reliably predict the prognosis of AML patients. Age and Risk score were both independent prognostic indicators for AML, and the Nomogram based on them could also reliably predict the OS of AML patients. A prognostic signature based on seven GI-related genes and a predictive Nomogram for AML patients are finally successfully constructed.
DOI: 10.6084/m9.figshare.21831204
title: ggCaller example results

description: Output from ggCaller analysis using gene-calling and querying modes.
DOI: 10.6084/m9.figshare.21829071
title: Bentley et al 2006 CPS protein sequences

description: Manually curated protein sequences for 91 CPS loci described in Bentley et al 2006 (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0020031). Also contains individual CDS for mnaB, mnaA, fnlA and fnlB for DBG querying.
DOI: 10.6084/m9.figshare.21831369
title: Russia-Ukraine

description: This research aims to determine the mediating role of militarist and internationalist views in the relationship between the personal values of Turkish society and their attitudes toward the war.
DOI: 10.6084/m9.figshare.21831369.v1
title: Russia-Ukraine

description: This research aims to determine the mediating role of militarist and internationalist views in the relationship between the personal values of Turkish society and their attitudes toward the war.
DOI: 10.6084/m9.figshare.21829038
title: Bentley et al. 2006 CPS sequences

description: FASTA files for 91 pneumococcal capsular polysaccharide synthetic (CPS) loci from Bentley et al. 2006 (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0020031)
DOI: 10.5281/zenodo.7507721
title: The effect of element intensity that distinguishes flavour in a food packaging on the memory and perception of Peruvian millennials and centennials

description: <em>ABSTRACT</em><br> Background: Globalization has greatly facilitated access to all kinds of products and brands from different parts of the world, increasing consumer choices and, consequently, competition among packaged products. For this reason, a brand's packaging design to attract consumers must stand out among its competitors, especially if it is a new product or a new flavour. In this context, it becomes necessary to explore dimensions of packaging design that allow a high degree of differentiation. In that way, there are very efficient strategies and approaches used in the literature to perform this exploration in packagings, such as perception evaluations measured with attributes and eye-tracking technology that records direct information about visual attention on the most distinctive elements. Thus, the present study aims to determine the impact of the presentation of a new flavour on packaging by varying the intensity of the stimulus that represents it according to the Weber-Fechner law, using three main elements of the packaging: text, colour, and image.<br> Methods: The experiment exposed three groups of participants (n=30) to 3 stimuli, which were based on adding an element as the intensity of the flavour description of three products from three different food categories was intended to increase. This study used the RealEye webcam eye-tracking platform to measure attention, and a self-administered questionnaire was used to examine perception and recall. <br> Results: First, the results show that greater intensity expressed in a more significant number of visual elements facilitates flavour distinction. Second, the results reveal that perceived difficulty in flavour differentiation correlates strongly with the presence of colour and image. <br> Conclusions: Therefore, this study provides an approach to ways to optimize the intensity of flavour distinctiveness elements that may be useful, especially for less recognized brands.