cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.13145/bacdive17569.20240510.9
title: Stenotrophomonas ginsengisoli Kim et al. 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17570.20240510.9
title: Stenotrophomonas pavanii Ramos et al. 2011

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17573.20240510.9
title: Thermomonas haemolytica Busse et al. 2002

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17576.20240510.9
title: Thermomonas fusca Mergaert et al. 2003

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17577.20240510.9
title: Thermomonas hydrothermalis Alves et al. 2003

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17584.20240510.9
title: Xanthomonas campestris (Pammel 1895) Dowson 1939 emend. Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17588.20240510.9
title: Xanthomonas vasicola Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17589.20240510.9
title: Xanthomonas hyacinthi (ex Wakker 1883) Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17592.20240510.9
title: Xanthomonas vesicatoria (ex Doidge 1920) Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17593.20240510.9
title: Xanthomonas axonopodis Starr and Garcés 1950 emend. Constantin et al. 2016

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17596.20240510.9
title: Xanthomonas sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17597.20240510.9
title: Xanthomonas sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17599.20240510.9
title: Xanthomonas cynarae Trébaol et al. 2000 emend. Timilsina et al. 2019

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17600.20240510.9
title: Xanthomonas vasicola Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.26946690
title: Patient-centric microsampling for abrocitinib pharmacokinetics: multiple-analytes assay bridging using Tasso device

description: <b>Aim:</b> The feasibility of using Tasso devices (Tasso-SST<sup>®</sup> and Tasso<sup>+</sup>) collecting capillary blood samples for measuring abrocitinib and its metabolites were evaluated, and assay concordance established between capillary and venous blood samplings. <b>Methods:</b> Capillary serum and venous plasma concentrations were measured using their respective qualified and validated assays. Concentration and exposure comparisons were conducted for abrocitinib and its metabolites (M1, M2 and M4) to establish assay concordance. <b>Results:</b> The correlation coefficient between capillary serum and venous plasma concentrations were &gt;0.98 for all four analytes from three separate assays, and PK parameters (AUC<sub>last</sub> and C<sub>max</sub>) were compared and met bioequivalence criteria. <b>Conclusion:</b> These results demonstrate the feasibility of patient-centric microsampling device, such as Tasso, in future abrocitinib pediatric study. To evaluate feasibility, the Tasso serum collection microsampling devices were used parallel to venous plasma collection in abrocitinib clinical study. The serum to plasma partial validations were conducted to ensure equivalence between serum and plasma methods. Capillary serum to venous plasma concentration bridging were conducted for abrocitinib and three major metabolites (M1, M2 and M4) per currently available industry white paper. The PK exposure comparison was conducted to demonstrate similarity in concentrations data generated using the two blood collection methods (Tasso vs. traditional venous phlebotomy). Excellent concordance between the two sets of concentrations was demonstrated for all four analytes. For abrocitinib and metabolites pharmacokinetic measurement, Tasso liquid blood microsampling device is less invasive, uses lower blood volume and can be easily implemented at clinical site in pediatric study without the complication of blood-to-plasma ratio determination.
DOI: 10.6084/m9.figshare.26946690.v1
title: Patient-centric microsampling for abrocitinib pharmacokinetics: multiple-analytes assay bridging using Tasso device

description: <b>Aim:</b> The feasibility of using Tasso devices (Tasso-SST<sup>®</sup> and Tasso<sup>+</sup>) collecting capillary blood samples for measuring abrocitinib and its metabolites were evaluated, and assay concordance established between capillary and venous blood samplings. <b>Methods:</b> Capillary serum and venous plasma concentrations were measured using their respective qualified and validated assays. Concentration and exposure comparisons were conducted for abrocitinib and its metabolites (M1, M2 and M4) to establish assay concordance. <b>Results:</b> The correlation coefficient between capillary serum and venous plasma concentrations were &gt;0.98 for all four analytes from three separate assays, and PK parameters (AUC<sub>last</sub> and C<sub>max</sub>) were compared and met bioequivalence criteria. <b>Conclusion:</b> These results demonstrate the feasibility of patient-centric microsampling device, such as Tasso, in future abrocitinib pediatric study. To evaluate feasibility, the Tasso serum collection microsampling devices were used parallel to venous plasma collection in abrocitinib clinical study. The serum to plasma partial validations were conducted to ensure equivalence between serum and plasma methods. Capillary serum to venous plasma concentration bridging were conducted for abrocitinib and three major metabolites (M1, M2 and M4) per currently available industry white paper. The PK exposure comparison was conducted to demonstrate similarity in concentrations data generated using the two blood collection methods (Tasso vs. traditional venous phlebotomy). Excellent concordance between the two sets of concentrations was demonstrated for all four analytes. For abrocitinib and metabolites pharmacokinetic measurement, Tasso liquid blood microsampling device is less invasive, uses lower blood volume and can be easily implemented at clinical site in pediatric study without the complication of blood-to-plasma ratio determination.
DOI: 10.13145/bacdive17602.20240510.9
title: Xanthomonas arboricola Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17604.20240510.9
title: Xanthomonas arboricola Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17605.20240510.9
title: Xanthomonas bromi Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17606.20240510.9
title: Xanthomonas cassavae (ex Wiehe and Dowson 1953) Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17607.20240510.9
title: Xanthomonas codiaei Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17608.20240510.9
title: Xanthomonas cucurbitae (ex Bryan 1926) Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.26166976
title: Robust Matrix Completion with Heavy-Tailed Noise

description: This article studies noisy low-rank matrix completion in the presence of heavy-tailed and possibly asymmetric noise, where we aim to estimate an underlying low-rank matrix given a set of highly incomplete noisy entries. Though the matrix completion problem has attracted much attention in the past decade, there is still lack of theoretical understanding when the observations are contaminated by heavy-tailed noises. Prior theory falls short of explaining the empirical results and is unable to capture the optimal dependence of the estimation error on the noise level. In this article, we adopt an adaptive Huber loss to accommodate heavy-tailed noise, which is robust against large and possibly asymmetric errors when the parameter in the Huber loss function is carefully designed to balance the Huberization biases and robustness to outliers. Then, we propose an efficient nonconvex algorithm via a balanced low-rank Burer-Monteiro matrix factorization and gradient descent with robust spectral initialization. We prove that under merely a bounded second-moment condition on the error distributions, rather than the sub-Gaussian assumption, the Euclidean errors of the iterates generated by the proposed algorithm decrease geometrically fast until achieving a minimax-optimal statistical estimation error, which has the same order as that in the sub-Gaussian case. The key technique behind this significant advancement is a powerful leave-one-out analysis framework. The theoretical results are corroborated by our numerical studies. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.13145/bacdive17609.20240510.9
title: Xanthomonas pisi (ex Goto and Okabe 1958) Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17610.20240510.9
title: Xanthomonas sacchari Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.26166976.v1
title: Robust Matrix Completion with Heavy-tailed Noise

description: This paper studies noisy low-rank matrix completion in the presence of heavy-tailed and possibly asymmetric noise, where we aim to estimate an underlying low-rank matrix given a set of highly incomplete noisy entries. Though the matrix completion problem has attracted much attention in the past decade, there is still lack of theoretical understanding when the observations are contaminated by heavy-tailed noises. Prior theory falls short of explaining the empirical results and is unable to capture the optimal dependence of the estimation error on the noise level. In this paper, we adopt an adaptive Huber loss to accommodate heavy-tailed noise, which is robust against large and possibly asymmetric errors when the parameter in the Huber loss function is carefully designed to balance the Huberization biases and robustness to outliers. Then, we propose an efficient nonconvex algorithm via a balanced low-rank Burer-Monteiro matrix factorization and gradient descent with robust spectral initialization. We prove that under merely a bounded second-moment condition on the error distributions, rather than the sub-Gaussian assumption, the Euclidean errors of the iterates generated by the proposed algorithm decrease geometrically fast until achieving a minimax-optimal statistical estimation error, which has the same order as that in the sub-Gaussian case. The key technique behind this significant advancement is a powerful leave-one-out analysis framework. The theoretical results are corroborated by our numerical studies.
DOI: 10.13145/bacdive17611.20240510.9
title: Xanthomonas theicola Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17612.20240510.9
title: Xanthomonas translucens (ex Jones et al. 1917) Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17613.20240510.9
title: Xanthomonas euvesicatoria Jones et al. 2006 emend. Constantin et al. 2016

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17614.20240510.9
title: Xanthomonas perforans Jones et al. 2006

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17615.20240510.9
title: Xanthomonas cynarae Trébaol et al. 2000 emend. Timilsina et al. 2019

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17616.20240510.9
title: Xanthomonas hortorum Vauterin et al. 1995

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.26495940
title: Probability of Causation with Sample Selection: A Reanalysis of the Impacts of <i>Jóvenes en Acción</i> on Formality

description: This article identifies the probability of causation when there is sample selection. We show that the probability of causation is partially identified for individuals who are always observed regardless of treatment status and derive sharp bounds under three increasingly restrictive sets of assumptions. The first set imposes an exogenous treatment and a monotone sample selection mechanism. To tighten these bounds, the second set also imposes the monotone treatment response assumption, while the third set additionally imposes a stochastic dominance assumption. Finally, we use experimental data from the Colombian job training program <i>Jóvenes en Acción</i> to empirically illustrate our approach’s usefulness. We find that, among always-employed women, at least 10.2% and at most 13.4% transitioned to the formal labor market because of the program. However, our 90%-confidence region does not reject the null hypothesis that the lower bound is equal to zero.
DOI: 10.6084/m9.figshare.26495940.v1
title: Probability of Causation with Sample Selection: A Reanalysis of the Impacts of <i>Jóvenes en Acción</i> on Formality

description: This article identifies the probability of causation when there is sample selection. We show that the probability of causation is partially identified for individuals who are always observed regardless of treatment status and derive sharp bounds under three increasingly restrictive sets of assumptions. The first set imposes an exogenous treatment and a monotone sample selection mechanism. To tighten these bounds, the second set also imposes the monotone treatment response assumption, while the third set additionally imposes a stochastic dominance assumption. Finally, we use experimental data from the Colombian job training program <i>Jóvenes en Acción</i> to empirically illustrate our approach’s usefulness. We find that, among always-employed women, at least 10.2% and at most 13.4% transitioned to the formal labor market because of the program. However, our 90%-confidence region does not reject the null hypothesis that the lower bound is equal to zero.
DOI: 10.13145/bacdive17622.20240510.9
title: Xylella fastidiosa Wells et al. 1987

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17623.20240510.9
title: Wohlfahrtiimonas chitiniclastica Tóth et al. 2008

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.27061791
title: Novel buffer for long-term preservation of DNA in biological material at room temperature

description: The collection and preservation of biological material before DNA analysis is critical for inter alia biomedical research, medical diagnostics, forensics and biodiversity conservation. In this study, we evaluate an in-house formulated buffer called the Forensic DNA Laboratory-buffer (FDL-buffer) for preservation of biological material for long term at room temperature. Human saliva stored in the buffer for 8 years, human blood stored for 3 years and delicate animal tissues from the jellyfish <i>Pelagia noctiluca</i> comb jelly <i>Beroe</i> sp., stored for 4 and 6 years respectively consistently produced high-quality DNA. FDL-buffer exhibited compatibility with standard organic, salting out and spin-column extraction methods, making it versatile and applicable to a wide range of applications, including automation. DNA extractions were performed by Salting out, PCI, ZymoQuick and DNAeazy methods. DNA quantity and quality were assessed using qPCR, Qubit, gel electrophoresis, as well as Sanger sequencing, microsatellite profiling and SNPchip analysis. Preservation of DNA integrity and quality in biological samples is essential in the field of biological science, medicine and forensics. Conventional methods of storage such cold temperature and alcohol fixation can be challenging when sampling in remote destinations or with limited resources. We formulated a novel buffer referred to as the FDL-buffer offering extra-long term (&gt;5 years) preservation of DNA in biological material stored at room temperature. We validated the FDL-buffer on human saliva stored for 8 years, human blood stored for 3 years and delicate animal tissues from the jellyfish <i>Pelagia noctiluca</i> (Scyphozoa Pelagiidae) and comb jelly <i>Beroe</i> sp. (Ctenophora, Beroidae), stored without pre-treatment for 4 and 6 years, respectively. A comparative approach was employed using alternative preservation systems and DNA extraction protocols. The FDL-buffer exceeded the parallel performance of the Oragene OG-500 for preserving saliva, and effectively preserved blood samples, yielding high molecular weight DNA. Successful isolation of high-quality DNA from the marine specimens The purified DNA from the FDL-buffer consistently produced high-quality results in downstream applications, including Sanger sequencing, microsatellite fragment analysis profiling and SNPchip analysis. The FDL-buffer exhibited compatibility with standard organic and salting out extraction methods and commercial spin-column extractions. The FDL-buffer can preserve the gDNA from cells and tissues which allows these biospecimens to be transported and stored successfully without cold storage. The formulation offered a cost effective, versatile and time-saving approach for collection and long-term storage of biological material for DNA analysis.
DOI: 10.6084/m9.figshare.27061791.v1
title: Novel buffer for long-term preservation of DNA in biological material at room temperature

description: The collection and preservation of biological material before DNA analysis is critical for inter alia biomedical research, medical diagnostics, forensics and biodiversity conservation. In this study, we evaluate an in-house formulated buffer called the Forensic DNA Laboratory-buffer (FDL-buffer) for preservation of biological material for long term at room temperature. Human saliva stored in the buffer for 8 years, human blood stored for 3 years and delicate animal tissues from the jellyfish <i>Pelagia noctiluca</i> comb jelly <i>Beroe</i> sp., stored for 4 and 6 years respectively consistently produced high-quality DNA. FDL-buffer exhibited compatibility with standard organic, salting out and spin-column extraction methods, making it versatile and applicable to a wide range of applications, including automation. DNA extractions were performed by Salting out, PCI, ZymoQuick and DNAeazy methods. DNA quantity and quality were assessed using qPCR, Qubit, gel electrophoresis, as well as Sanger sequencing, microsatellite profiling and SNPchip analysis. Preservation of DNA integrity and quality in biological samples is essential in the field of biological science, medicine and forensics. Conventional methods of storage such cold temperature and alcohol fixation can be challenging when sampling in remote destinations or with limited resources. We formulated a novel buffer referred to as the FDL-buffer offering extra-long term (&gt;5 years) preservation of DNA in biological material stored at room temperature. We validated the FDL-buffer on human saliva stored for 8 years, human blood stored for 3 years and delicate animal tissues from the jellyfish <i>Pelagia noctiluca</i> (Scyphozoa Pelagiidae) and comb jelly <i>Beroe</i> sp. (Ctenophora, Beroidae), stored without pre-treatment for 4 and 6 years, respectively. A comparative approach was employed using alternative preservation systems and DNA extraction protocols. The FDL-buffer exceeded the parallel performance of the Oragene OG-500 for preserving saliva, and effectively preserved blood samples, yielding high molecular weight DNA. Successful isolation of high-quality DNA from the marine specimens The purified DNA from the FDL-buffer consistently produced high-quality results in downstream applications, including Sanger sequencing, microsatellite fragment analysis profiling and SNPchip analysis. The FDL-buffer exhibited compatibility with standard organic and salting out extraction methods and commercial spin-column extractions. The FDL-buffer can preserve the gDNA from cells and tissues which allows these biospecimens to be transported and stored successfully without cold storage. The formulation offered a cost effective, versatile and time-saving approach for collection and long-term storage of biological material for DNA analysis.
DOI: 10.13145/bacdive17624.20240510.9
title: Rudaea cellulosilytica Weon et al. 2009

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive17625.20240510.9
title: Pseudofulvimonas gallinarii Kämpfer et al. 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.