cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5008559
title: Table S5 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.5008553
title: Table S1 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.5008559.v1
title: Table S5 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.v1
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.5008553.v1
title: Table S1 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.5008547
title: Table S3 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.5008547.v1
title: Table S3 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.5008445
title: ESM 1 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?

description: <b>GPS locations of lionfish abundance survey locations around Utila, Honduras</b>.
DOI: 10.6084/m9.figshare.5008439
title: ESM 1 Table - Details on pictures and visits from Behaviour of free ranging wild boar towards their dead fellows: potential implications for the transmission of African swine fever

description: The behaviour of free ranging wild boar (<i>Sus scrofa</i>) towards carcasses of their conspecifics potentially infected with African swine fever (ASF) may significantly influence the course of an ASF epidemic. This study aims to better understand the behaviour of wild boar towards their dead fellows. Thirty-two wild boar carcasses on nine study sites in northeast Germany were monitored under field conditions by photo-trapping from October 2015 until October 2016. During this period, a total of 122 160 pictures were taken, thereof 16 111 pictures from wild boar. In both winter and summer, wild boar seemed to be particularly interested in the soil next to and underneath the carcasses. About one third of the visits of wild boar lead to direct contact with dead conspecifics. The contacts consisted mostly in sniffing and poking on the carcass. Under the given ecological and climatic conditions, there was no evidence for intra-species scavenging. However, piglets were observed several times chewing bare bones once skeletonization of the carcasses was complete. It must be assumed that all these types of contact may represent a risk for transmission. Both the high tenacity of ASF virus and the long time wild boar carcasses can remain in the environment, allow the persistence of the virus for several months or even years. We therefore consider the rapid detection and removal (or destruction on the spot) of contaminated carcasses as an important control measure against ASF in wild boar.
DOI: 10.6084/m9.figshare.5008445.v1
title: ESM 1 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?

description: <b>GPS locations of lionfish abundance survey locations around Utila, Honduras</b>.
DOI: 10.6084/m9.figshare.5008439.v1
title: ESM 1 Table - Details on pictures and visits from Behaviour of free ranging wild boar towards their dead fellows: potential implications for the transmission of African swine fever

description: The behaviour of free ranging wild boar (<i>Sus scrofa</i>) towards carcasses of their conspecifics potentially infected with African swine fever (ASF) may significantly influence the course of an ASF epidemic. This study aims to better understand the behaviour of wild boar towards their dead fellows. Thirty-two wild boar carcasses on nine study sites in northeast Germany were monitored under field conditions by photo-trapping from October 2015 until October 2016. During this period, a total of 122 160 pictures were taken, thereof 16 111 pictures from wild boar. In both winter and summer, wild boar seemed to be particularly interested in the soil next to and underneath the carcasses. About one third of the visits of wild boar lead to direct contact with dead conspecifics. The contacts consisted mostly in sniffing and poking on the carcass. Under the given ecological and climatic conditions, there was no evidence for intra-species scavenging. However, piglets were observed several times chewing bare bones once skeletonization of the carcasses was complete. It must be assumed that all these types of contact may represent a risk for transmission. Both the high tenacity of ASF virus and the long time wild boar carcasses can remain in the environment, allow the persistence of the virus for several months or even years. We therefore consider the rapid detection and removal (or destruction on the spot) of contaminated carcasses as an important control measure against ASF in wild boar.
DOI: 10.6084/m9.figshare.5008388
title: Sample information from <i>Wolbachia</i>-induced meiotic drive and feminization is associated with an independent occurrence of selective mitochondrial sweep in a butterfly

description: Maternally inherited <i>Wolbachia</i> endosymbionts manipulate arthropod reproduction in various ways. In the butterfly <i>Eurema mandarina</i>, a cytoplasmic incompatibility inducing <i>Wolbachia</i> strain <i>w</i>CI and the associated mtDNA haplotypes are known to originate from the sister species <i>Eurema hecabe</i>, which offered a good case study for microbe-mediated hybrid introgression. Besides <i>w</i>CI, some females with the Z0 karyotype harbour a distinct <i>Wolbachia</i> strain <i>w</i>Fem, which causes all-female production by meiotic drive and feminization. We report that a considerable proportion of <i>E. mandarina</i> females (65.7%) were infected with both <i>w</i>CI and <i>w</i>Fem (CF) on Tanegashima Island. While females singly infected with <i>w</i>CI (C) produced offspring at a 1 : 1 sex ratio, CF females produced only females. Although Z-linked sequence polymorphism showed no signs of divergence between C and CF females, mtDNA split into two discrete clades; one consisted of C females and the other CF females, both of which formed a clade with <i>E. hecabe</i> but not with uninfected <i>E. mandarina</i>. This suggests that CF matrilines also, but independently, experienced a selective sweep after hybrid introgression from <i>E. hecabe</i>. Distinct evolutionary forces were suggested to have caused C and CF matrilines to diverge, which would be irreversible because of the particular phenotype of <i>w</i>Fem.
DOI: 10.6084/m9.figshare.5008388.v1
title: Sample information from <i>Wolbachia</i>-induced meiotic drive and feminization is associated with an independent occurrence of selective mitochondrial sweep in a butterfly

description: Maternally inherited <i>Wolbachia</i> endosymbionts manipulate arthropod reproduction in various ways. In the butterfly <i>Eurema mandarina</i>, a cytoplasmic incompatibility inducing <i>Wolbachia</i> strain <i>w</i>CI and the associated mtDNA haplotypes are known to originate from the sister species <i>Eurema hecabe</i>, which offered a good case study for microbe-mediated hybrid introgression. Besides <i>w</i>CI, some females with the Z0 karyotype harbour a distinct <i>Wolbachia</i> strain <i>w</i>Fem, which causes all-female production by meiotic drive and feminization. We report that a considerable proportion of <i>E. mandarina</i> females (65.7%) were infected with both <i>w</i>CI and <i>w</i>Fem (CF) on Tanegashima Island. While females singly infected with <i>w</i>CI (C) produced offspring at a 1 : 1 sex ratio, CF females produced only females. Although Z-linked sequence polymorphism showed no signs of divergence between C and CF females, mtDNA split into two discrete clades; one consisted of C females and the other CF females, both of which formed a clade with <i>E. hecabe</i> but not with uninfected <i>E. mandarina</i>. This suggests that CF matrilines also, but independently, experienced a selective sweep after hybrid introgression from <i>E. hecabe</i>. Distinct evolutionary forces were suggested to have caused C and CF matrilines to diverge, which would be irreversible because of the particular phenotype of <i>w</i>Fem.
DOI: 10.6084/m9.figshare.5008370
title: An economic analysis of tolvaptan compared with fluid restriction among hospitalized patients with hyponatremia

description: <b>Objective</b>: The vasopressin-receptor antagonist tolvaptan is used for the treatment of hyponatremia (HN) in hospitalized patients with congestive heart failure (CHF) or syndrome of inappropriate antidiuretic hormone secretion (SIADH). The objective of this economic modeling study was to assess the potential cost and health outcomes associated with tolvaptan in comparison with fluid restriction (FR). <b>Methods</b>: A decision-analytic model was developed to estimate potential cost and health outcomes associated with tolvaptan compared with FR among hospitalized CHF and SIADH patients with severe HN (serum sodium [SS] levels &lt; 125 mEq/L). The model, which was populated with data from the published literature, assumes that response to treatment influences hospital length of stay, probability of an intensive care unit (ICU) admission, and probability of a 30-day all-cause hospital readmission. One-way and probabilistic sensitivity analyses (PSAs) assessed the influence of parameter uncertainty on model results. <b>Results</b>: Model results suggest that, among hospitalized CHF patients with severe HN, the use of tolvaptan compared with FR may lead to reductions of 7.2% and 4.6% in ICU admissions and 30-day readmissions, respectively. Compared with FR, tolvaptan may result in total cost-savings of $156 per hospitalized CHF patient. Among hospitalized SIADH patients with severe HN, the model suggested reductions of 14.6% and 5.1% in ICU admissions and 30-day readmissions, respectively. Compared with FR, tolvaptan may result in total cost-savings of $135 per hospitalized SIADH patient. PSAs found that the probabilities of net cost-savings from the use of tolvaptan compared with FR were 64% and 59% among patients with severe HN with CHF and SIADH, respectively. <b>Conclusions</b>: Decision-analytic modeling based on published data for hospitalized CHF and SIADH patients with severe HN, indicates that tolvaptan compared with FR has the potential to improve health outcomes and produce cost-savings that more than offset the cost of tolvaptan.
DOI: 10.6084/m9.figshare.5008373
title: Multiple viral infections in primary effusion lymphoma: a model of viral cooperation in lymphomagenesis

description: <b>Introduction</b>: Primary effusion lymphoma (PEL) is a rare B-cell lymphoid neoplasm mainly associated with HIV infection, presenting as pleural, peritoneal, and pericardial effusions. A defining property of PEL is its consistent association with Kaposi sarcoma associated herpesvirus (KSHV) infection, and, in most cases, Epstein Barr virus (EBV) co-infection. On these grounds, a review of the literature related to viral cooperation and lymphomagenesis can help to understand the complex interplay between KSHV and EBV in PEL pathogenesis. <b>Areas covered</b>: In this review, the authors highlight clinical, pathologic, genetic and proteomic features of PEL, in the context of viral cooperation in PEL lymphomagenesis. <b>Expert commentary</b>: Tumour cells are characterized by the overexpression of genes that are involved in inflammation and invasion. Coherently, PEL secretomes are enriched in proteins probably responsible for the particular tropism (cell adhesion and migration) of PEL cells. The development of PEL in HIV+ patients is multifactorial and involves a complex interplay among co-infection with oncogenic viruses (EBV and KSHV), inflammatory factors, and environmental conditions.
DOI: 10.6084/m9.figshare.5008370.v1
title: An economic analysis of tolvaptan compared with fluid restriction among hospitalized patients with hyponatremia

description: <b>Objective</b>: The vasopressin-receptor antagonist tolvaptan is used for the treatment of hyponatremia (HN) in hospitalized patients with congestive heart failure (CHF) or syndrome of inappropriate antidiuretic hormone secretion (SIADH). The objective of this economic modeling study was to assess the potential cost and health outcomes associated with tolvaptan in comparison with fluid restriction (FR). <b>Methods</b>: A decision-analytic model was developed to estimate potential cost and health outcomes associated with tolvaptan compared with FR among hospitalized CHF and SIADH patients with severe HN (serum sodium [SS] levels &lt; 125 mEq/L). The model, which was populated with data from the published literature, assumes that response to treatment influences hospital length of stay, probability of an intensive care unit (ICU) admission, and probability of a 30-day all-cause hospital readmission. One-way and probabilistic sensitivity analyses (PSAs) assessed the influence of parameter uncertainty on model results. <b>Results</b>: Model results suggest that, among hospitalized CHF patients with severe HN, the use of tolvaptan compared with FR may lead to reductions of 7.2% and 4.6% in ICU admissions and 30-day readmissions, respectively. Compared with FR, tolvaptan may result in total cost-savings of $156 per hospitalized CHF patient. Among hospitalized SIADH patients with severe HN, the model suggested reductions of 14.6% and 5.1% in ICU admissions and 30-day readmissions, respectively. Compared with FR, tolvaptan may result in total cost-savings of $135 per hospitalized SIADH patient. PSAs found that the probabilities of net cost-savings from the use of tolvaptan compared with FR were 64% and 59% among patients with severe HN with CHF and SIADH, respectively. <b>Conclusions</b>: Decision-analytic modeling based on published data for hospitalized CHF and SIADH patients with severe HN, indicates that tolvaptan compared with FR has the potential to improve health outcomes and produce cost-savings that more than offset the cost of tolvaptan.