cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4506158.v2
title: Genetic diversity and relationship of Indian Muscovy duck populations

description: Assessment of genetic diversity within and between populations is a prerequisite for sustainable utilization of domestic species. The domestic Muscovy duck (<i>Cairina moschata</i>) is an economically important species around the world for its unique meat taste and low-caloric content. It is one of the important domestic species in India as it ensures food security to the rural sectors. In this study, we have analyzed the genetic diversity and relationship of four Muscovy duck populations collected from different states (Assam, Mizoram, Odisha and Kerala) of India using mtDNA cytochrome b and nuclear DNA CYP2U1 genes. The results showed low genetic diversity among populations for both the genes. Kerala population showed significant genetic differences from the other three populations. The median joining network of cytochrome <i>b</i> gene suggested that the domestic Muscovy ducks present in India are the product of a single domestication event and probably introduced to India several years ago, as reported elsewhere. This study has also showed the suitability of nuclear DNA CYP2U1 gene in genetic diversity analysis.
DOI: 10.6084/m9.figshare.3968913.v1
title: Phylogenetic relationships of <i>D. rudis</i> (Bedriaga, 1886) and <i>D. bithynica</i>(Mehely, 1909) based on microsatellite and mitochondrial DNA in Turkey

description: The spiny-tailed lizard of the genus <i>Darevskia</i> have a series of taxonomic revisions, but still their phylogenetic relationships remain uncertain. In the present study, we have assessed taxonomic relationships among <i>Darevskia bithynica</i> and <i>Darevskia rudis</i> populations through estimation of phylogenetic relationships among 96 specimens using microsatellite DNA (<i>Du215</i>, <i>Du281</i>, <i>Du323</i> and <i>Du418</i> loci) and 53 specimens using mtDNA (16S rRNA and cytb) from main populations in Turkey. Although <i>D. b. bithynica</i> and <i>D. r. mirabilis</i> were separated based on the PCoA analysis at low level from other <i>D. rudis</i> and <i>D. bithynica</i> populations, the distance values of Nei's genetic distance, Nei's unbiased genetic distance, Fst and Linear Fst were not high among taxa in microsatellite DNA. On the other hand, our phylogenetic analyses (NJ, ML, MP and BI) did not separate <i>D. rudis</i> and <i>D. bithynica</i> populations. Finally, most of the topologically identical trees of phylogenetic analyses and microsatellite results showed that the extant populations of <i>D. rudis</i> and <i>D. bithynica</i> were found to be polytomy. Based on our molecular phylogenetic study, <i>D. rudis</i> complex is still ongoing revisions.
DOI: 10.6084/m9.figshare.4506158
title: Genetic diversity and relationship of Indian Muscovy duck populations

description: Assessment of genetic diversity within and between populations is a prerequisite for sustainable utilization of domestic species. The domestic Muscovy duck (<i>Cairina moschata</i>) is an economically important species around the world for its unique meat taste and low-caloric content. It is one of the important domestic species in India as it ensures food security to the rural sectors. In this study, we have analyzed the genetic diversity and relationship of four Muscovy duck populations collected from different states (Assam, Mizoram, Odisha and Kerala) of India using mtDNA cytochrome b and nuclear DNA CYP2U1 genes. The results showed low genetic diversity among populations for both the genes. Kerala population showed significant genetic differences from the other three populations. The median joining network of cytochrome <i>b</i> gene suggested that the domestic Muscovy ducks present in India are the product of a single domestication event and probably introduced to India several years ago, as reported elsewhere. This study has also showed the suitability of nuclear DNA CYP2U1 gene in genetic diversity analysis.
DOI: 10.6084/m9.figshare.4506158.v1
title: Genetic diversity and relationship of Indian Muscovy duck populations

description: Assessment of genetic diversity within and between populations is a prerequisite for sustainable utilization of domestic species. The domestic Muscovy duck (<i>Cairina moschata</i>) is an economically important species around the world for its unique meat taste and low-caloric content. It is one of the important domestic species in India as it ensures food security to the rural sectors. In this study, we have analyzed the genetic diversity and relationship of four Muscovy duck populations collected from different states (Assam, Mizoram, Odisha and Kerala) of India using mtDNA cytochrome b and nuclear DNA CYP2U1 genes. The results showed low genetic diversity among populations for both the genes. Kerala population showed significant genetic differences from the other three populations. The median joining network of cytochrome <i>b</i> gene suggested that the domestic Muscovy ducks present in India are the product of a single domestication event and probably introduced to India several years ago, as reported elsewhere. This study has also showed the suitability of nuclear DNA CYP2U1 gene in genetic diversity analysis.
DOI: 10.6084/m9.figshare.4592629.v2
title: Back from the dead! Resurrection and revalidation of the Indian endemic snake genus <i>Wallophis</i> Werner, 1929 (Squamata: Colubridae) insights from molecular data

description: The monotypic colubrid snake genus <i>Wallophis</i> is revalidated and rediagnosed. Partial sequence for nuclear gene Oocyte maturation factor Mos (c-<i>mos</i>), mitochondrial Nicotinamide adenine dinucleotide dehydrogenase subunit 4 (<i>ND4</i>) and cytochrome b (cyt <i>b</i>) were used to assess phylogenetic relationship. <i>Wallophis brachyura</i> type species for the genus was found to be a member of the Western Palearctic clade of Colubrinae and is recovered as a sister taxa to <i>Wallaceophis gujaratensis</i>. <i>Wallophis</i> differs from <i>Wallaceophis</i> in an uncorrected pairwise p-distance of 17% for mitochondrial <i>ND4</i> gene. <i>Wallaceophis gujaratensis</i> was described in three different spellings in the literature hence we here propose <i>Wallaceophis gujaratensis</i> as the correct spelling for the species based on provisions in the article 24.2.3. of the International Code for Zoological Nomenclature.
DOI: 10.34740/kaggle/dsv/2662035
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.6084/m9.figshare.11955882
title: Can a machine-learning model improve the prediction of nodal stage after a positive sentinel lymph node biopsy in breast cancer?

description: <b>Background:</b> The current standard for evaluating axillary nodal burden in clinically node negative breast cancer is sentinel lymph node biopsy (SLNB). However, the accuracy of SLNB to detect nodal stage N2-3 remains debatable. Nomograms can help the decision-making process between axillary treatment options. The aim of this study was to create a new model to predict the nodal stage N2-3 after a positive SLNB using machine learning methods that are rarely seen in nomogram development. <b>Material and methods:</b> Primary breast cancer patients who underwent SLNB and axillary lymph node dissection (ALND) between 2012 and 2017 formed cohorts for nomogram development (training cohort, <i>N</i> = 460) and for nomogram validation (validation cohort, <i>N</i> = 70). A machine learning method known as the gradient boosted trees model (XGBoost) was used to determine the variables associated with nodal stage N2-3 and to create a predictive model. Multivariate logistic regression analysis was used for comparison. <b>Results:</b> The best combination of variables associated with nodal stage N2-3 in XGBoost modeling included tumor size, histological type, multifocality, lymphovascular invasion, percentage of ER positive cells, number of positive sentinel lymph nodes (SLN) and number of positive SLNs multiplied by tumor size. Indicating discrimination, AUC values for the training cohort and the validation cohort were 0.80 (95%CI 0.71–0.89) and 0.80 (95%CI 0.65–0.92) in the XGBoost model and 0.85 (95%CI 0.77–0.93) and 0.75 (95%CI 0.58–0.89) in the logistic regression model, respectively. <b>Conclusions:</b> This machine learning model was able to maintain its discrimination in the validation cohort better than the logistic regression model. This indicates advantages in employing modern artificial intelligence techniques into nomogram development. The nomogram could be used to help identify nodal stage N2-3 in early breast cancer and to select appropriate treatments for patients.
DOI: 10.6084/m9.figshare.11955882.v2
title: Can a machine-learning model improve the prediction of nodal stage after a positive sentinel lymph node biopsy in breast cancer?

description: <b>Background:</b> The current standard for evaluating axillary nodal burden in clinically node negative breast cancer is sentinel lymph node biopsy (SLNB). However, the accuracy of SLNB to detect nodal stage N2-3 remains debatable. Nomograms can help the decision-making process between axillary treatment options. The aim of this study was to create a new model to predict the nodal stage N2-3 after a positive SLNB using machine learning methods that are rarely seen in nomogram development. <b>Material and methods:</b> Primary breast cancer patients who underwent SLNB and axillary lymph node dissection (ALND) between 2012 and 2017 formed cohorts for nomogram development (training cohort, <i>N</i> = 460) and for nomogram validation (validation cohort, <i>N</i> = 70). A machine learning method known as the gradient boosted trees model (XGBoost) was used to determine the variables associated with nodal stage N2-3 and to create a predictive model. Multivariate logistic regression analysis was used for comparison. <b>Results:</b> The best combination of variables associated with nodal stage N2-3 in XGBoost modeling included tumor size, histological type, multifocality, lymphovascular invasion, percentage of ER positive cells, number of positive sentinel lymph nodes (SLN) and number of positive SLNs multiplied by tumor size. Indicating discrimination, AUC values for the training cohort and the validation cohort were 0.80 (95%CI 0.71–0.89) and 0.80 (95%CI 0.65–0.92) in the XGBoost model and 0.85 (95%CI 0.77–0.93) and 0.75 (95%CI 0.58–0.89) in the logistic regression model, respectively. <b>Conclusions:</b> This machine learning model was able to maintain its discrimination in the validation cohort better than the logistic regression model. This indicates advantages in employing modern artificial intelligence techniques into nomogram development. The nomogram could be used to help identify nodal stage N2-3 in early breast cancer and to select appropriate treatments for patients.
DOI: 10.6084/m9.figshare.11826969
title: Influence of pretreatment with everolimus or sunitinib on the subacute hematotoxicity of <sup>177</sup>Lu-DOTATATE PRRT

description: <b>Background:</b> Peptide receptor radionuclide therapy (PRRT) is a validated treatment for somatostatin receptor overexpressing neuroendocrine tumors (NETs). The NETTER-1 trial demonstrated a pronounced positive effect on progression-free-survival compared to high dose somatostatin analogs (SSAs), with a strong tendency toward overall survival benefit. Our aim was to investigate the influence of pretreatment with everolimus and/or sunitinib on subacute hematotoxicity of PRRT. To assess the influence of prior treatment with everolimus/sunitinib might be of clinical relevance due to the link between short-term hematotoxicity and increased incidence of late hematotoxicity. <b>Material and methods:</b> Our single-center retrospective study enrolled all patients treated with <sup>177</sup>Lu-DOTATATE PRRT (1–4 cycles of 7.4 GBq), between November 2013 and July 2018. Patients were assigned to two groups according to their pretreatment: no targeted agents (<i>N</i> = 41), or targeted agents (everolimus, sunitinib or both; <i>N</i> = 41). The end point was subacute hematotoxicity, defined as the nadir value between the first administration until 3 months after the last administration, using the CTCAE 4.03 classification. The impact of splenectomy was also explored. <b>Results:</b> Eighty percent of patients had a primary gastroenteropancreatic NET. No statistically significant differences in severe subacute hematotoxicity were seen in the pretreated group vs. the naive group for hemoglobin (grade 3/4: 12% vs. 22%), neither for leucocytes (grade 3/4: 10% vs. 7%), neutrophils (grade 3/4: 5% vs. 7%), lymphocytes (grade 3/4: 49% vs. 37%) and platelets (grade 3/4: 15% vs. 15%). Furthermore, we observed significantly lower toxicity for total white blood cells, lymphocytes and platelets in the subgroup that had splenectomy (<i>N</i> = 12). Limitations of this study include the potential bias in lack of use of targeted agents in patients more susceptible to toxicity, and the limited number of patients and events. <b>Conclusions:</b> In a patient cohort with NET pretreated with everolimus and/or sunitinib, we could not demonstrate a significant effect of prior/pretreatment with everolimus and/or sunitinib on the subacute hematotoxicity of <sup>177</sup>Lu-DOTATATE PRRT.
DOI: 10.6084/m9.figshare.11826969.v2
title: Influence of pretreatment with everolimus or sunitinib on the subacute hematotoxicity of <sup>177</sup>Lu-DOTATATE PRRT

description: <b>Background:</b> Peptide receptor radionuclide therapy (PRRT) is a validated treatment for somatostatin receptor overexpressing neuroendocrine tumors (NETs). The NETTER-1 trial demonstrated a pronounced positive effect on progression-free-survival compared to high dose somatostatin analogs (SSAs), with a strong tendency toward overall survival benefit. Our aim was to investigate the influence of pretreatment with everolimus and/or sunitinib on subacute hematotoxicity of PRRT. To assess the influence of prior treatment with everolimus/sunitinib might be of clinical relevance due to the link between short-term hematotoxicity and increased incidence of late hematotoxicity. <b>Material and methods:</b> Our single-center retrospective study enrolled all patients treated with <sup>177</sup>Lu-DOTATATE PRRT (1–4 cycles of 7.4 GBq), between November 2013 and July 2018. Patients were assigned to two groups according to their pretreatment: no targeted agents (<i>N</i> = 41), or targeted agents (everolimus, sunitinib or both; <i>N</i> = 41). The end point was subacute hematotoxicity, defined as the nadir value between the first administration until 3 months after the last administration, using the CTCAE 4.03 classification. The impact of splenectomy was also explored. <b>Results:</b> Eighty percent of patients had a primary gastroenteropancreatic NET. No statistically significant differences in severe subacute hematotoxicity were seen in the pretreated group vs. the naive group for hemoglobin (grade 3/4: 12% vs. 22%), neither for leucocytes (grade 3/4: 10% vs. 7%), neutrophils (grade 3/4: 5% vs. 7%), lymphocytes (grade 3/4: 49% vs. 37%) and platelets (grade 3/4: 15% vs. 15%). Furthermore, we observed significantly lower toxicity for total white blood cells, lymphocytes and platelets in the subgroup that had splenectomy (<i>N</i> = 12). Limitations of this study include the potential bias in lack of use of targeted agents in patients more susceptible to toxicity, and the limited number of patients and events. <b>Conclusions:</b> In a patient cohort with NET pretreated with everolimus and/or sunitinib, we could not demonstrate a significant effect of prior/pretreatment with everolimus and/or sunitinib on the subacute hematotoxicity of <sup>177</sup>Lu-DOTATATE PRRT.
DOI: 10.6084/m9.figshare.11925567.v2
title: Tumor-associated trypsin inhibitor (TATI) and tumor-associated trypsin-2 (TAT-2) predict outcomes in gastric cancer

description: <b>Introduction:</b> Tumor-associated trypsin inhibitor (TATI) limits serine proteases, promotes carcinogenesis in several cancers and functions as an acute-phase reactant. Tumor-associated trypsin-2 (TAT-2), a proteolytic target enzyme for TATI, can enhance invasion by promoting extracellular matrix degradation. Here, we aimed to study serum TATI and TAT-2 levels, including the TAT-2/TATI ratio, as prognostic and diagnostic biomarkers in gastric cancer. We compared the results with the plasma level of C-reactive protein (CRP). <b>Material and Methods:</b> We selected 240 individuals operated on for gastric adenocarcinoma at the Helsinki University Hospital, Finland, between 2000 and 2009. We determined the preoperative serum TAT-2, TATI and plasma CRP levels using time-resolved immunofluorometric assays using monoclonal antibodies. <b>Results:</b> The medium serum TAT-2 level was higher among gastric cancer patients [8.68 ng/ml; interquartile range (IQR) 5.93–13.2] than among benign controls (median 5.41 ng/ml; IQR 4.12–11.8; <i>p</i> = .005). Five-year survival among patients with a high serum TAT-2 was 22.9% [95% confidence interval (CI) 11.7–34.1], compared to 52.2% (95% CI 44.6–59.8; <i>p</i> p p = .037). <b>Conclusions:</b> This study shows for the first time that a high serum TAT-2 may function as a prognostic biomarker in gastric cancer and that TAT-2 levels may be elevated compared to controls. Additionally, we show that the prognosis is worse among gastric cancer patients with a high serum TATI. These biomarkers serve as prognostic factors particularly among patients with a metastatic or a locally advanced disease.
DOI: 10.6084/m9.figshare.11854743.v2
title: Implementation of contemporary chemotherapy for patients with metastatic pancreatic ductal adenocarcinoma: a population-based analysis

description: <b>Background:</b> Positive results of randomized trials led to the introduction of FOLFIRINOX in 2012 and gemcitabine with nab-paclitaxel in 2015 for patients with metastatic pancreatic ductal adenocarcinoma. It is unknown to which extent these new chemotherapeutic regimens have been implemented in clinical practice and what the impact has been on overall survival. <b>Material and methods:</b> Patients diagnosed with metastatic pancreatic ductal adenocarcinoma between 2007–2016 were included from the population-based Netherlands Cancer Registry. Multilevel logistic regression and Cox regression analyses, adjusting for patient, tumor, and hospital characteristics, were used to analyze variation of chemotherapy use. <b>Results:</b> In total, 8726 patients were included. The use of chemotherapy increased from 31% in 2007–2011 to 37% in 2012–2016 (<i>p</i> p <b>Conclusion:</b> Nationwide variation in the use of chemotherapy decreased after the implementation of FOLFIRINOX and gemcitabine with nab-paclitaxel. Still a considerable proportion of patients receives gemcitabine monotherapy. Overall survival did improve, but not clinically relevant. These results emphasize the need for a structured implementation of new chemotherapeutic regimens.
DOI: 10.6084/m9.figshare.11854743.v1
title: Implementation of contemporary chemotherapy for patients with metastatic pancreatic ductal adenocarcinoma: a population-based analysis

description: <b>Background:</b> Positive results of randomized trials led to the introduction of FOLFIRINOX in 2012 and gemcitabine with nab-paclitaxel in 2015 for patients with metastatic pancreatic ductal adenocarcinoma. It is unknown to which extent these new chemotherapeutic regimens have been implemented in clinical practice and what the impact has been on overall survival. <b>Material and methods:</b> Patients diagnosed with metastatic pancreatic ductal adenocarcinoma between 2007–2016 were included from the population-based Netherlands Cancer Registry. Multilevel logistic regression and Cox regression analyses, adjusting for patient, tumor, and hospital characteristics, were used to analyze variation of chemotherapy use. <b>Results:</b> In total, 8726 patients were included. The use of chemotherapy increased from 31% in 2007–2011 to 37% in 2012–2016 (<i>p</i> p <b>Conclusion:</b> Nationwide variation in the use of chemotherapy decreased after the implementation of FOLFIRINOX and gemcitabine with nab-paclitaxel. Still a considerable proportion of patients receives gemcitabine monotherapy. Overall survival did improve, but not clinically relevant. These results emphasize the need for a structured implementation of new chemotherapeutic regimens.
DOI: 10.6084/m9.figshare.11925567.v1
title: Tumor-associated trypsin inhibitor (TATI) and tumor-associated trypsin-2 (TAT-2) predict outcomes in gastric cancer

description: <b>Introduction:</b> Tumor-associated trypsin inhibitor (TATI) limits serine proteases, promotes carcinogenesis in several cancers and functions as an acute-phase reactant. Tumor-associated trypsin-2 (TAT-2), a proteolytic target enzyme for TATI, can enhance invasion by promoting extracellular matrix degradation. Here, we aimed to study serum TATI and TAT-2 levels, including the TAT-2/TATI ratio, as prognostic and diagnostic biomarkers in gastric cancer. We compared the results with the plasma level of C-reactive protein (CRP). <b>Material and Methods:</b> We selected 240 individuals operated on for gastric adenocarcinoma at the Helsinki University Hospital, Finland, between 2000 and 2009. We determined the preoperative serum TAT-2, TATI and plasma CRP levels using time-resolved immunofluorometric assays using monoclonal antibodies. <b>Results:</b> The medium serum TAT-2 level was higher among gastric cancer patients [8.68 ng/ml; interquartile range (IQR) 5.93–13.2] than among benign controls (median 5.41 ng/ml; IQR 4.12–11.8; <i>p</i> = .005). Five-year survival among patients with a high serum TAT-2 was 22.9% [95% confidence interval (CI) 11.7–34.1], compared to 52.2% (95% CI 44.6–59.8; <i>p</i> p p = .037). <b>Conclusions:</b> This study shows for the first time that a high serum TAT-2 may function as a prognostic biomarker in gastric cancer and that TAT-2 levels may be elevated compared to controls. Additionally, we show that the prognosis is worse among gastric cancer patients with a high serum TATI. These biomarkers serve as prognostic factors particularly among patients with a metastatic or a locally advanced disease.
DOI: 10.6084/m9.figshare.11854743
title: Implementation of contemporary chemotherapy for patients with metastatic pancreatic ductal adenocarcinoma: a population-based analysis

description: <b>Background:</b> Positive results of randomized trials led to the introduction of FOLFIRINOX in 2012 and gemcitabine with nab-paclitaxel in 2015 for patients with metastatic pancreatic ductal adenocarcinoma. It is unknown to which extent these new chemotherapeutic regimens have been implemented in clinical practice and what the impact has been on overall survival. <b>Material and methods:</b> Patients diagnosed with metastatic pancreatic ductal adenocarcinoma between 2007–2016 were included from the population-based Netherlands Cancer Registry. Multilevel logistic regression and Cox regression analyses, adjusting for patient, tumor, and hospital characteristics, were used to analyze variation of chemotherapy use. <b>Results:</b> In total, 8726 patients were included. The use of chemotherapy increased from 31% in 2007–2011 to 37% in 2012–2016 (<i>p</i> p <b>Conclusion:</b> Nationwide variation in the use of chemotherapy decreased after the implementation of FOLFIRINOX and gemcitabine with nab-paclitaxel. Still a considerable proportion of patients receives gemcitabine monotherapy. Overall survival did improve, but not clinically relevant. These results emphasize the need for a structured implementation of new chemotherapeutic regimens.