cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5008808
title: Supplementary Material for: Noninvasive Prenatal Detection of Trisomy 21 by Targeted Semiconductor Sequencing: A Technical Feasibility Study

description: <b><i>Objective:</i></b> To develop an alternate noninvasive prenatal testing method for the assessment of trisomy 21 (T21) using a targeted semiconductor sequencing approach. <b><i>Methods:</i></b> A customized AmpliSeq panel was designed with 1,067 primer pairs targeting specific regions on chromosomes 21, 18, 13, and others. A total of 235 samples, including 30 affected with T21, were sequenced with an Ion Torrent Proton sequencer, and a method was developed for assessing the probability of fetal aneuploidy via derivation of a risk score. <b><i>Results:</i></b> Application of the derived risk score yields a bimodal distribution, with the affected samples clustering near 1.0 and the unaffected near 0. For a risk score cutoff of 0.345, above which all would be considered at “high risk,” all 30 T21-positive pregnancies were correctly predicted to be affected, and 199 of the 205 non-T21 samples were correctly predicted. The average hands-on time spent on library preparation and sequencing was 19 h in total, and the average number of reads of sequence obtained was 3.75 million per sample. <b><i>Conclusion:</i></b> With the described targeted sequencing approach on the semiconductor platform using a custom-designed library and a probabilistic statistical approach, we have demonstrated the feasibility of an alternate method of assessment for fetal T21.
DOI: 10.6084/m9.figshare.5008988.v1
title: peach.480.SNPs.vcf.tar.bz2

description: To detect the breeding footprints, we sequenced 480 peach accessions, including 52 wild relative accessions, 215 landrace accessions, and 213 improvement accessions. Using this resequencing date, we detected the genomic change during domestication and improvement.
DOI: 10.6084/m9.figshare.5008799
title: Supplementary Material for: Donor-Specific Anti-Human Leukocyte Antigens Antibodies, Acute Rejection, Renal Function, and Histology in Kidney Transplant Recipients Receiving Tacrolimus and Everolimus

description: <b><i>Background:</i></b> This analysis compared efficacy, renal function, and histology in kidney transplant recipients receiving tacrolimus (TAC) combined with everolimus (EVR) or mycophenolate (MPS). <b><i>Methods:</i></b> This was a retrospective analysis from a randomized trial in kidney transplant recipients who received a single 3 mg/kg dose of rabbit antithymocyte globulin (r-ATG), TAC, EVR, and prednisone (PRED; r-ATG/EVR, <i>n</i> = 85), basiliximab (BAS), TAC, EVR, and PRED (BAS/EVR, <i>n</i> = 102) or BAS, TAC, MPS, and PRED (BAS/MPS, <i>n</i> = 101). We evaluated the incidence of de novo donor-specific anti-human leukocyte antigens antibodies (DSA) and histology on protocol biopsies at 12 months, and the incidence of acute rejection, estimated glomerular filtration rate (eGFR) and proteinuria at 36 months. <b><i>Results:</i></b> At 12 months, there were no differences in de novo DSA (6.4 vs. 3.4 vs. 5.5%) or in subclinical inflammation (2.0 vs. 4.8 vs. 10.2%), interstitial fibrosis/tubular atrophy (57.1 vs. 58.5 vs. 53.8%) and C4d deposition (2.0 vs. 7.3 vs. 2.6%). At 36 months, there were no differences in the incidence of treatment failure (19.0 vs. 27.7 vs. 27.7%, <i>p</i> = 0.186), first biopsy-proven acute rejection (9.5 vs. 21.8 vs. 16.8%, <i>p</i> = 0.073), and urine protein/creatinine ratios (0.53 ± 1.05 vs. 0.62 ± 0.75 vs. 0.71 ± 1.24). eGFR was lower in the BAS/EVR compared to that in the BAS/MPS group (53.4 ± 20.9 vs. 50.8 ± 19.5 vs. 60.7 ± 21.2 mL/min/1.73 m<sup>2</sup>, <i>p</i> = 0.017) but comparable using a sensitive analysis (49.5 ± 23 vs. 47.5 ± 22.6 vs. 53.6 ± 27.8 mL/min/1.73 m<sup>2</sup>, <i>p</i> = 0.207). <b><i>Conclusion:</i></b> In this cohort, the use of EVR and reduced TAC concentrations were associated with comparable efficacy, renal function, and histological parameters compared to the standard-of-care immunosuppressive regimen.
DOI: 10.6084/m9.figshare.5008808.v1
title: Supplementary Material for: Noninvasive Prenatal Detection of Trisomy 21 by Targeted Semiconductor Sequencing: A Technical Feasibility Study

description: <b><i>Objective:</i></b> To develop an alternate noninvasive prenatal testing method for the assessment of trisomy 21 (T21) using a targeted semiconductor sequencing approach. <b><i>Methods:</i></b> A customized AmpliSeq panel was designed with 1,067 primer pairs targeting specific regions on chromosomes 21, 18, 13, and others. A total of 235 samples, including 30 affected with T21, were sequenced with an Ion Torrent Proton sequencer, and a method was developed for assessing the probability of fetal aneuploidy via derivation of a risk score. <b><i>Results:</i></b> Application of the derived risk score yields a bimodal distribution, with the affected samples clustering near 1.0 and the unaffected near 0. For a risk score cutoff of 0.345, above which all would be considered at “high risk,” all 30 T21-positive pregnancies were correctly predicted to be affected, and 199 of the 205 non-T21 samples were correctly predicted. The average hands-on time spent on library preparation and sequencing was 19 h in total, and the average number of reads of sequence obtained was 3.75 million per sample. <b><i>Conclusion:</i></b> With the described targeted sequencing approach on the semiconductor platform using a custom-designed library and a probabilistic statistical approach, we have demonstrated the feasibility of an alternate method of assessment for fetal T21.
DOI: 10.21421/d2/gylptp
title: Heat tolerance of chickpea (Cicer arietinum L.) genotypes in thermal zone of Ethiopia, a case of Werer station

description: This database includes the research work carried out to assess the variability among chickpea genotypes for heat tolerance and high yield potential under thermal zone of Ethiopia by screening at hot spot location. The station is located at 9°20’31" N and 40°10’11" E in the Middle Awash rift valley. The elevation is at about 740 meters above sea level. The long rainy season occurring from July to September accounts for 264 mm rainfall and the short rainy season from February to April accounts 156 mm. The minimum/maximum annual temperatures is 18.9OC/38OC, while the average annual temperature is 28.4OC. Field evaluation of 18 early maturing chickpea genotypes including both Kabuli and Desi types was conducted during 2015 offseason using two planting dates of 33 January and 24th February. It involves advancing sowing date to synchronize the reproductive phase of the crop with the occurrence of higher temperature (>35OC). This method was employed to optimize planting date and to effectively identify heat tolerant germplasms. This study used measure of plant growth, yield traits and temperature prediction at different developmental stages of chickpea as tools for heat tolerance screening. Heat indices including SSI, TOL and STI were also calculated for better evaluation of genotypes for heat tolerance and some genotypes were found heat tolerant relative to others. Hence, these lines can be used in breeding program either for direct advancement based on their agronomic merit or could be used in crossing program for further manipulation.
DOI: 10.6084/m9.figshare.5008988.v2
title: peach.480.SNPs.vcf.tar.bz2

description: To detect the breeding footprints, we sequenced 480 peach accessions, including 52 wild relative accessions, 215 landrace accessions, and 213 improvement accessions. Using this resequencing date, we detected the genomic change during domestication and improvement.
DOI: 10.6084/m9.figshare.5008988.v3
title: peach.480.SNPs.vcf.tar.bz2

description: To detect the breeding footprints, we sequenced 480 peach accessions, including 52 wild relative accessions, 215 landrace accessions, and 213 improvement accessions. Using this resequencing date, we detected the genomic change during domestication and improvement.
DOI: 10.6084/m9.figshare.5008670
title: Climate Science Considerations in Indonesia's President Joko Widodo's Policy on Energy and Climate Change

description: Indonesia has continuous energy and climate policies in place to solve climate change issue. This paper will review selected highlights from President Jokowi's energy and climate policies which includes the 35000 MW project, New and Renewable Energy (NRE) initiative, fuel subsidy reform, and Indonesia's submission for COP21 Paris Agreement. The policies will be analyzed broadly and in accordance to established climate science knowledges whenever possible. Both intended and unintended consequences of the policies will be discussed.Some contradictions between energy policy, climate policy, and climate science was found. Further reliance towards coal, the inclusion of unconventional fossil fuel in NRE initiative and the lack of differentiation between land and fossil fuel carbon cycle in greenhouse gas reduction framework is inconsistent with climate change mitigation while fuel subsidy reform has to be appreciated. Consistency of the new administration is needed to keep the effective policies in place and to revise the contradictory policies for effective climate change mitigation efforts.
DOI: 10.6084/m9.figshare.5008670.v1
title: Climate Science Considerations in Indonesia's President Joko Widodo's Policy on Energy and Climate Change

description: Indonesia has continuous energy and climate policies in place to solve climate change issue. This paper will review selected highlights from President Jokowi's energy and climate policies which includes the 35000 MW project, New and Renewable Energy (NRE) initiative, fuel subsidy reform, and Indonesia's submission for COP21 Paris Agreement. The policies will be analyzed broadly and in accordance to established climate science knowledges whenever possible. Both intended and unintended consequences of the policies will be discussed.Some contradictions between energy policy, climate policy, and climate science was found. Further reliance towards coal, the inclusion of unconventional fossil fuel in NRE initiative and the lack of differentiation between land and fossil fuel carbon cycle in greenhouse gas reduction framework is inconsistent with climate change mitigation while fuel subsidy reform has to be appreciated. Consistency of the new administration is needed to keep the effective policies in place and to revise the contradictory policies for effective climate change mitigation efforts.
DOI: 10.6084/m9.figshare.5008607
title: Comparison of palbociclib in combination with letrozole or fulvestrant with endocrine therapies for advanced/metastatic breast cancer: network meta-analysis

description: <b>Background:</b> Palbociclib is the first cyclin-dependent kinase 4/6 inhibitor approved in the United States for HR+/HER2- advanced/metastatic breast cancer, in combination with letrozole as initial endocrine-based therapy in postmenopausal women or with fulvestrant in women with disease progression following endocrine therapy. We compared progression-free survival (PFS) and discontinuations due to adverse events for palbociclib combinations against other endocrine therapies using a mixed-treatment comparison meta-analysis of randomized, controlled trials. <b>Methods:</b> A systematic literature review identified relevant trials. Separate analyses were conducted for each palbociclib combination using a Bayesian approach. Treatment rankings were established using the surface under the cumulative ranking curve (SUCRA). <b>Results:</b> Sixty-five unique studies met inclusion criteria. Palbociclib plus letrozole had the highest SUCRA value (99.9%) and was associated with significantly longer PFS than all comparators in treatment-naïve patients (hazard ratios [HRs] ranged from 0.41 to 0.58). Palbociclib plus fulvestrant had the second highest SUCRA value (93.9%) and, in previously treated patients, yielded significantly longer PFS than most comparators (HRs ranged from 0.26 to 0.46); the exception was everolimus plus exemestane, with similar PFS (HR, 1.04; 95% credible interval [CrI], 0.58–1.76). Palbociclib plus fulvestrant was associated with significantly lower odds of discontinuation due to adverse events than everolimus plus exemestane (odds ratio, 0.14; 95% CrI, 0.05–0.39). <b>Conclusions:</b> The results suggest that the two palbociclib combinations yielded significantly greater PFS than endocrine therapy in treatment-naïve and previously treated patients with advanced/metastatic breast cancer. Palbociclib plus fulvestrant was associated with significantly less toxicity than everolimus plus exemestane.
DOI: 10.6084/m9.figshare.5008607.v1
title: Comparison of palbociclib in combination with letrozole or fulvestrant with endocrine therapies for advanced/metastatic breast cancer: network meta-analysis

description: <b>Background:</b> Palbociclib is the first cyclin-dependent kinase 4/6 inhibitor approved in the United States for HR+/HER2- advanced/metastatic breast cancer, in combination with letrozole as initial endocrine-based therapy in postmenopausal women or with fulvestrant in women with disease progression following endocrine therapy. We compared progression-free survival (PFS) and discontinuations due to adverse events for palbociclib combinations against other endocrine therapies using a mixed-treatment comparison meta-analysis of randomized, controlled trials. <b>Methods:</b> A systematic literature review identified relevant trials. Separate analyses were conducted for each palbociclib combination using a Bayesian approach. Treatment rankings were established using the surface under the cumulative ranking curve (SUCRA). <b>Results:</b> Sixty-five unique studies met inclusion criteria. Palbociclib plus letrozole had the highest SUCRA value (99.9%) and was associated with significantly longer PFS than all comparators in treatment-naïve patients (hazard ratios [HRs] ranged from 0.41 to 0.58). Palbociclib plus fulvestrant had the second highest SUCRA value (93.9%) and, in previously treated patients, yielded significantly longer PFS than most comparators (HRs ranged from 0.26 to 0.46); the exception was everolimus plus exemestane, with similar PFS (HR, 1.04; 95% credible interval [CrI], 0.58–1.76). Palbociclib plus fulvestrant was associated with significantly lower odds of discontinuation due to adverse events than everolimus plus exemestane (odds ratio, 0.14; 95% CrI, 0.05–0.39). <b>Conclusions:</b> The results suggest that the two palbociclib combinations yielded significantly greater PFS than endocrine therapy in treatment-naïve and previously treated patients with advanced/metastatic breast cancer. Palbociclib plus fulvestrant was associated with significantly less toxicity than everolimus plus exemestane.
DOI: 10.6084/m9.figshare.5008577
title: Table S6 from A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination

description: A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68-Myr <i>Tyrannosaurus rex</i> fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr <i>Brachylophosaurus canadensis</i> fossil were reported which has remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, <i>Struthio camelus</i>. The resulting LC–MS/MS data were found to match all of the proposed sequences for both the original <i>Tyrannosaurus</i> and <i>Brachylophosaurus</i> studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated.
DOI: 10.6084/m9.figshare.5008574
title: Table S4 from A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination

description: A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68-Myr <i>Tyrannosaurus rex</i> fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr <i>Brachylophosaurus canadensis</i> fossil were reported which has remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, <i>Struthio camelus</i>. The resulting LC–MS/MS data were found to match all of the proposed sequences for both the original <i>Tyrannosaurus</i> and <i>Brachylophosaurus</i> studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated.
DOI: 10.6084/m9.figshare.5008577.v1
title: Table S6 from A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination

description: A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68-Myr <i>Tyrannosaurus rex</i> fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr <i>Brachylophosaurus canadensis</i> fossil were reported which has remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, <i>Struthio camelus</i>. The resulting LC–MS/MS data were found to match all of the proposed sequences for both the original <i>Tyrannosaurus</i> and <i>Brachylophosaurus</i> studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated.
DOI: 10.6084/m9.figshare.5008568
title: Table S2 from A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination

description: A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68-Myr <i>Tyrannosaurus rex</i> fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr <i>Brachylophosaurus canadensis</i> fossil were reported which has remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, <i>Struthio camelus</i>. The resulting LC–MS/MS data were found to match all of the proposed sequences for both the original <i>Tyrannosaurus</i> and <i>Brachylophosaurus</i> studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated.
DOI: 10.6084/m9.figshare.5008574.v1
title: Table S4 from A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination

description: A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68-Myr <i>Tyrannosaurus rex</i> fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr <i>Brachylophosaurus canadensis</i> fossil were reported which has remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, <i>Struthio camelus</i>. The resulting LC–MS/MS data were found to match all of the proposed sequences for both the original <i>Tyrannosaurus</i> and <i>Brachylophosaurus</i> studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated.