cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1568464
title: Interaction of meropenem with ‘N’ and ‘B’ isoforms of human serum albumin: a spectroscopic and molecular docking study

description: Carbapenems are used to control the outbreak of β-lactamases expressing bacteria. The effectiveness of drugs is influenced by its interaction with human serum albumin (HSA). Strong binding of carbapenems to HSA may lead to decreased bioavailability of the drug. The non-optimal drug dosage will provide a positive selection pressure on bacteria to develop resistance. Here, we investigated the interaction between meropenem and HSA at physiological pH 7.5 (N-isoform HSA) and non-physiological pH 9.2 (B-isoform HSA). Results showed that meropenem quenches the fluorescence of both ‘N’ and ‘B’ isoforms of HSA (Δ<i>G</i> 4 M<sup>−1</sup>). Electrostatic interactions and van der Waal interactions along with H-bonds stabilized the complex of meropenem with ‘N’ and ‘B’ isoforms of HSA, respectively. Molecular docking results revealed that meropenem binds to HSA near Sudlow’s site II (subdomain IIIA) close to Trp-214 with a contribution of a few residues of subdomain IIA. CD spectroscopy showed a change in the conformation of both the isoforms of HSA upon meropenem binding. The catalytic efficiency of HSA (only N-isoform) on p-nitrophenyl acetate was increased primarily due to a decrease in <i>K</i><sub>m</sub> and an increase in <i>k</i><sub>cat</sub> values. This study provides an insight into the molecular basis of interaction between meropenem and HSA.
DOI: 10.6084/m9.figshare.1568461
title: Taxonomic revision of <i>Plesiofuro mingshuica</i> from the Lower Triassic of northern Gansu, China, and the relationships of early neopterygian clades

description: ABSTRACTThe ray-finned fish <i>Plesiofuro mingshuica</i> from the Triassic non-marine deposits of northern Gansu Province, China, was previously misidentified as a caturid halecomorph. This erroneous taxonomic assignment contributed to the misinterpretation of the age of the <i>Plesiofuro</i>-bearing fossil beds as Early Jurassic. Here, we provide a taxonomic revision of this problematic taxon based on a comparative study including over 500 new specimens. The revised description of <i>Plesiofuro</i> accommodates significant changes to the reconstruction of the snout, skull roof, cheek, circumorbital, and operculogular series, as well as the lower jaw. Results of a cladistic analysis incorporating these new data place <i>Plesiofuro</i> as a stem-group neopterygian. Additionally, phylogenetic results show that both ‘Perleidiformes’ and ‘Peltopleuriformes’ are paraphyletic, encompassing several independent stem-neopterygian subclades. As such, this study sheds new light on one of the least resolved areas of osteichthyan phylogeny: the so-called ‘subholosteans’ of the neopterygian total group. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVPCitation for this article: Xu, G.-H., K.-Q. Gao, and M. I. Coates. 2015. Taxonomic revision of <i>Plesiofuro mingshuica</i> from the Lower Triassic of northern Gansu, China, and the relationships of early neopterygian clades. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2014.1001515.
DOI: 10.6084/m9.figshare.1568464.v2
title: Interaction of meropenem with ‘N’ and ‘B’ isoforms of human serum albumin: a spectroscopic and molecular docking study

description: Carbapenems are used to control the outbreak of β-lactamases expressing bacteria. The effectiveness of drugs is influenced by its interaction with human serum albumin (HSA). Strong binding of carbapenems to HSA may lead to decreased bioavailability of the drug. The non-optimal drug dosage will provide a positive selection pressure on bacteria to develop resistance. Here, we investigated the interaction between meropenem and HSA at physiological pH 7.5 (N-isoform HSA) and non-physiological pH 9.2 (B-isoform HSA). Results showed that meropenem quenches the fluorescence of both ‘N’ and ‘B’ isoforms of HSA (Δ<i>G</i> 4 M<sup>−1</sup>). Electrostatic interactions and van der Waal interactions along with H-bonds stabilized the complex of meropenem with ‘N’ and ‘B’ isoforms of HSA, respectively. Molecular docking results revealed that meropenem binds to HSA near Sudlow’s site II (subdomain IIIA) close to Trp-214 with a contribution of a few residues of subdomain IIA. CD spectroscopy showed a change in the conformation of both the isoforms of HSA upon meropenem binding. The catalytic efficiency of HSA (only N-isoform) on p-nitrophenyl acetate was increased primarily due to a decrease in <i>K</i><sub>m</sub> and an increase in <i>k</i><sub>cat</sub> values. This study provides an insight into the molecular basis of interaction between meropenem and HSA.
DOI: 10.6084/m9.figshare.1568465.v1
title: Geochemical and Microbiological Studies of Nitrous Oxide Variations within the New NEEM Greenland Ice Core during the Last Glacial Period

description: Deep polar ice cores provide atmospheric records of nitrous oxide (N<sub>2</sub>O) and other trace gases reflecting climate history along with a parallel archive of microbial cells transported with mineral dust, marine and volcanic aerosols from around the globe. Our interdisciplinary study of 32 samples from different depths of the recently drilled NEEM Greenland ice core addressed the question whether the identified microorganisms were capable of post-depositional biological production of N<sub>2</sub>O in-situ. We used high-resolution geochemical and microbiological approaches to examine the N<sub>2</sub>O concentrations, the quantitative distributions of dust, Ca<sup>+2</sup>, NH<sub>4</sub><sup>+</sup> and NO<sub>3</sub><sup>−</sup> ions related to N cycle pathways, the microbial abundance and diversity at specific NEEM core depths from 1758 m to 1867.8 m. Results showed varying concentrations of N<sub>2</sub>O (220–271.5 ppb). Microbial abundance fluctuated between 3.3×10<sup>4</sup> and 3.3×10<sup>6</sup> cells mL<sup>−1</sup> in direct correlation with dust and Ca<sup>2+</sup> concentrations with higher cell numbers deposited during colder periods. The average values of NH<sub>4</sub><sup>+</sup> and NO<sub>3</sub><sup>−</sup> indicated that substrates were available for the microorganisms capable of utilizing them. PCR amplification of selected functional genes involved in bacterial and archaeal nitrification and denitrification was not successful.Sanger and Illumina MiSeq sequence analyses of SSU rRNA genes showed variable representation of A<i>lpha-, Beta- and Gammaproteobacteria, Firmicutes, Actinobacteria</i>, chloroplasts and fungi. The metabolic potential of the dominant genera of <i>Proteobacteria</i> and <i>Firmicutes</i> as possible N<sub>2</sub>O producers suggested that denitrification activity may have led to in-situ production and accumulation of N<sub>2</sub>O.
DOI: 10.6084/m9.figshare.1568464.v1
title: Interaction of Meropenem with ‘N’ and ‘B’ Isoforms of Human Serum Albumin: a Spectroscopic and Molecular Docking Study

description: Carbapenems are used to control the outbreak of β-lactamases expressing bacteria. The effectiveness of drugs is influenced by its interaction with human serum albumin (HSA). Strong binding of carbapenems to HSA may lead to decreased bioavailability of the drug. The non-optimal drug dosage will provide a positive selection pressure on bacteria to develop resistance. Here, we investigated the interaction between meropenem and HSA at physiological pH 7.5 (N isoform HSA) and non-physiological pH 9.2 (B isoform HSA). Results showed that meropenem quenches the fluorescence of both ‘N’ and ‘B’ isoforms of HSA (Δ<i>G</i>&lt;0 and binding constant ~ 10<sup>4</sup> M<sup>−1</sup>). Electrostatic interactions and van der Waal interactions along with H-bonds stabilized the complex of meropenem with ‘N’ and ‘B’ isoforms of HSA, respectively. Molecular docking results revealed that meropenem binds to HSA near Sudlow’s site II (subdomain IIIA) close to Trp-214 with a contribution of a few residues of subdomain IIA. CD spectroscopy showed a change in the conformation of both the isoforms of HSA upon meropenem binding. The catalytic efficiency of HSA (only N-isoform) on p-nitrophenyl acetate was increased primarily due to a decrease in <i>K</i><sub>m</sub> and an increase in <i>k</i><sub>cat</sub> values. This study provides an insight into the molecular basis of interaction between meropenem and HSA.
DOI: 10.6084/m9.figshare.1568465.v3
title: Geochemical and Microbiological Studies of Nitrous Oxide Variations within the New NEEM Greenland Ice Core during the Last Glacial Period

description: Deep polar ice cores provide atmospheric records of nitrous oxide (N<sub>2</sub>O) and other trace gases reflecting climate history along with a parallel archive of microbial cells transported with mineral dust, marine and volcanic aerosols from around the globe. Our interdisciplinary study of 32 samples from different depths of the recently drilled NEEM Greenland ice core addressed the question whether the identified microorganisms were capable of post-depositional biological production of N<sub>2</sub>O in situ. We used high-resolution geochemical and microbiological approaches to examine the N<sub>2</sub>O concentrations, the quantitative distributions of dust, Ca<sup>+2</sup>, NH<sub>4</sub><sup>+</sup> and NO<sub>3</sub><sup>−</sup> ions related to N cycle pathways, the microbial abundance and diversity at specific NEEM core depths from 1758 m to 1867.8 m. Results showed varying concentrations of N<sub>2</sub>O (220–271.5 ppb). Microbial abundance fluctuated between 3.3 × 10<sup>4</sup> and 3.3 × 10<sup>6</sup> cells mL<sup>−1</sup> in direct correlation with dust and Ca<sup>2+</sup> concentrations with higher cell numbers deposited during colder periods. The average values of NH<sub>4</sub><sup>+</sup> and NO<sub>3</sub><sup>−</sup> indicated that substrates were available for the microorganisms capable of utilizing them. PCR amplification of selected functional genes involved in bacterial and archaeal nitrification and denitrification was not successful. Sanger and Illumina MiSeq sequence analyses of SSU rRNA genes showed variable representation of A<i>lpha-, Beta- and Gammaproteobacteria, Firmicutes, Actinobacteria</i>, chloroplasts and fungi. The metabolic potential of the dominant genera of <i>Proteobacteria</i> and <i>Firmicutes</i> as possible N<sub>2</sub>O producers suggested that denitrification activity may have led to in-situ production and accumulation of N<sub>2</sub>O.
DOI: 10.6084/m9.figshare.1568465.v2
title: Geochemical and Microbiological Studies of Nitrous Oxide Variations within the New NEEM Greenland Ice Core During the Last Glacial Period

description: Deep polar ice cores provide atmospheric records of nitrous oxide (N<sub>2</sub>O) and other trace gases reflecting climate history along with a parallel archive of microbial cells transported with mineral dust, marine and volcanic aerosols from around the globe. Our interdisciplinary study of 32 samples from different depths of the recently drilled NEEM Greenland ice core addressed the question whether the identified microorganisms were capable of post-depositional biological production of N<sub>2</sub>O in situ. We used high-resolution geochemical and microbiological approaches to examine the N<sub>2</sub>O concentrations, the quantitative distributions of dust, Ca<sup>+2</sup>, NH<sub>4</sub><sup>+</sup> and NO<sub>3</sub><sup>−</sup> ions related to N cycle pathways, the microbial abundance and diversity at specific NEEM core depths from 1758 m to 1867.8 m. Results showed varying concentrations of N<sub>2</sub>O (220–271.5 ppb). Microbial abundance fluctuated between 3.3 × 10<sup>4</sup> and 3.3 × 10<sup>6</sup> cells mL<sup>−1</sup> in direct correlation with dust and Ca<sup>2+</sup> concentrations with higher cell numbers deposited during colder periods. The average values of NH<sub>4</sub><sup>+</sup> and NO<sub>3</sub><sup>−</sup> indicated that substrates were available for the microorganisms capable of utilizing them. PCR amplification of selected functional genes involved in bacterial and archaeal nitrification and denitrification was not successful. Sanger and Illumina MiSeq sequence analyses of SSU rRNA genes showed variable representation of A<i>lpha-, Beta- and Gammaproteobacteria, Firmicutes, Actinobacteria</i>, chloroplasts and fungi. The metabolic potential of the dominant genera of <i>Proteobacteria</i> and <i>Firmicutes</i> as possible N<sub>2</sub>O producers suggested that denitrification activity may have led to in-situ production and accumulation of N<sub>2</sub>O.
DOI: 10.6084/m9.figshare.1568459
title: Hair follicle and interfollicular epidermal stem cells make varying contributions to wound regeneration

description: Upon wounding, multiple stem cell populations in the hair follicle (HF) and interfollicular epidermis (IFE) converge at the site of injury. Although these cells can contribute permanently to the regenerating epithelium, it remains unclear whether these contributions vary among cells originating from diverse compartments in the skin. By comparing the fates of several keratinocyte lineages, we observed here an initial decrease in both HF- and IFE-derived cells within the transient acanthotic layers of the regenerating epithelium. At the same time, the relative abundance of early-arriving IFE-derived cells specifically in the wound basal layer declined as later-arriving HF-derived cells entered the site of injury. Although laggard bulge-derived cells were typically constrained at the regenerative periphery, these cells persisted in the wound basal layer. Finally, suppressing Notch enabled IFE-derived cells to out-compete HF-derived cells. Taken together, these findings indicate that IFE-, HF- and bulge-derived cells make distinct contributions to regeneration over time. Furthermore, we speculate that extrinsic, non-genetic factors such as spatial constraint, distance from the wound, and basal versus suprabasal position may largely determine whether a cell ultimately persists.
DOI: 10.6084/m9.figshare.1568458
title: Atrial fibrillation in amyloidotic cardiomyopathy: prevalence, incidence, risk factors and prognostic role

description: <i>Background</i>: Although atrial fibrillation (AF) is a known complication of amyloidotic cardiomyopathy (AC), a precise pathophysiological and prognostic characterization is not available. We therefore aimed to assess prevalence, incidence, risk factors and prognostic significance of AF in light-chain (AL), hereditary transthyretin-related (m-ATTR) and non-mutant transthyretin-related (wt-ATTR) AC. <i>Methods</i>: Retrospective study of 262 patients with AC (123 AL, 94 m-ATTR, 45 wt-ATTR) from a single center. <i>Results</i>: AF prevalence was 15% (AL 9%, m-ATTR 11%, wt-ATTR 40%). During a median follow-up of 1.2 years 11 patients developed AF (2.1% person-years). Age, heart failure (HF), left ventricular (LV) ejection fraction, renal involvement, left atrial size and right atrial pressure were independently associated with AF. AF was associated with incident HF but not with increased mortality. All AF patients were prescribed warfarin and none suffered thromboembolic events. <i>Conclusions</i>: In AC the prevalence of AF varies widely according to etiology with a mean value of 15% that reaches 40% in wt-ATTR amyloidosis. Age, HF, LV ejection fraction, left atrial size and right atrial pressure were the main independent risk factors, while wall thickness and etiology were not the main independent risk factors. AF does not seem to impact all-cause mortality but was strongly associated with prevalent and incident HF.
DOI: 10.6084/m9.figshare.1568461.v2
title: Taxonomic revision of <i>Plesiofuro mingshuica</i> from the Lower Triassic of northern Gansu, China, and the relationships of early neopterygian clades

description: ABSTRACTThe ray-finned fish <i>Plesiofuro mingshuica</i> from the Triassic non-marine deposits of northern Gansu Province, China, was previously misidentified as a caturid halecomorph. This erroneous taxonomic assignment contributed to the misinterpretation of the age of the <i>Plesiofuro</i>-bearing fossil beds as Early Jurassic. Here, we provide a taxonomic revision of this problematic taxon based on a comparative study including over 500 new specimens. The revised description of <i>Plesiofuro</i> accommodates significant changes to the reconstruction of the snout, skull roof, cheek, circumorbital, and operculogular series, as well as the lower jaw. Results of a cladistic analysis incorporating these new data place <i>Plesiofuro</i> as a stem-group neopterygian. Additionally, phylogenetic results show that both ‘Perleidiformes’ and ‘Peltopleuriformes’ are paraphyletic, encompassing several independent stem-neopterygian subclades. As such, this study sheds new light on one of the least resolved areas of osteichthyan phylogeny: the so-called ‘subholosteans’ of the neopterygian total group. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVPCitation for this article: Xu, G.-H., K.-Q. Gao, and M. I. Coates. 2015. Taxonomic revision of <i>Plesiofuro mingshuica</i> from the Lower Triassic of northern Gansu, China, and the relationships of early neopterygian clades. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2014.1001515.
DOI: 10.6084/m9.figshare.1568461.v1
title: Taxonomic revision of <i>Plesiofuro mingshuica</i> from the Lower Triassic of northern Gansu, China, and the relationships of early neopterygian clades

description: ABSTRACTThe ray-finned fish <i>Plesiofuro mingshuica</i> from the Triassic non-marine deposits of northern Gansu Province, China, was previously misidentified as a caturid halecomorph. This erroneous taxonomic assignment contributed to the misinterpretation of the age of the <i>Plesiofuro</i>-bearing fossil beds as Early Jurassic. Here, we provide a taxonomic revision of this problematic taxon based on a comparative study including over 500 new specimens. The revised description of <i>Plesiofuro</i> accommodates significant changes to the reconstruction of the snout, skull roof, cheek, circumorbital, and operculogular series, as well as the lower jaw. Results of a cladistic analysis incorporating these new data place <i>Plesiofuro</i> as a stem-group neopterygian. Additionally, phylogenetic results show that both ‘Perleidiformes’ and ‘Peltopleuriformes’ are paraphyletic, encompassing several independent stem-neopterygian subclades. As such, this study sheds new light on one of the least resolved areas of osteichthyan phylogeny: the so-called ‘subholosteans’ of the neopterygian total group. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1568458.v2
title: Atrial fibrillation in amyloidotic cardiomyopathy: prevalence, incidence, risk factors and prognostic role

description: <i>Background</i>: Although atrial fibrillation (AF) is a known complication of amyloidotic cardiomyopathy (AC), a precise pathophysiological and prognostic characterization is not available. We therefore aimed to assess prevalence, incidence, risk factors and prognostic significance of AF in light-chain (AL), hereditary transthyretin-related (m-ATTR) and non-mutant transthyretin-related (wt-ATTR) AC. <i>Methods</i>: Retrospective study of 262 patients with AC (123 AL, 94 m-ATTR, 45 wt-ATTR) from a single center. <i>Results</i>: AF prevalence was 15% (AL 9%, m-ATTR 11%, wt-ATTR 40%). During a median follow-up of 1.2 years 11 patients developed AF (2.1% person-years). Age, heart failure (HF), left ventricular (LV) ejection fraction, renal involvement, left atrial size and right atrial pressure were independently associated with AF. AF was associated with incident HF but not with increased mortality. All AF patients were prescribed warfarin and none suffered thromboembolic events. <i>Conclusions</i>: In AC the prevalence of AF varies widely according to etiology with a mean value of 15% that reaches 40% in wt-ATTR amyloidosis. Age, HF, LV ejection fraction, left atrial size and right atrial pressure were the main independent risk factors, while wall thickness and etiology were not the main independent risk factors. AF does not seem to impact all-cause mortality but was strongly associated with prevalent and incident HF.
DOI: 10.6084/m9.figshare.1568459.v2
title: Hair follicle and interfollicular epidermal stem cells make varying contributions to wound regeneration

description: Upon wounding, multiple stem cell populations in the hair follicle (HF) and interfollicular epidermis (IFE) converge at the site of injury. Although these cells can contribute permanently to the regenerating epithelium, it remains unclear whether these contributions vary among cells originating from diverse compartments in the skin. By comparing the fates of several keratinocyte lineages, we observed here an initial decrease in both HF- and IFE-derived cells within the transient acanthotic layers of the regenerating epithelium. At the same time, the relative abundance of early-arriving IFE-derived cells specifically in the wound basal layer declined as later-arriving HF-derived cells entered the site of injury. Although laggard bulge-derived cells were typically constrained at the regenerative periphery, these cells persisted in the wound basal layer. Finally, suppressing Notch enabled IFE-derived cells to out-compete HF-derived cells. Taken together, these findings indicate that IFE-, HF- and bulge-derived cells make distinct contributions to regeneration over time. Furthermore, we speculate that extrinsic, non-genetic factors such as spatial constraint, distance from the wound, and basal versus suprabasal position may largely determine whether a cell ultimately persists.
DOI: 10.6084/m9.figshare.1568458.v1
title: Atrial fibrillation in amyloidotic cardiomyopathy: prevalence, incidence, risk factors and prognostic role

description: <i>Background</i>: Although atrial fibrillation (AF) is a known complication of amyloidotic cardiomyopathy (AC), a precise pathophysiological and prognostic characterization is not available. We therefore aimed to assess prevalence, incidence, risk factors and prognostic significance of AF in light-chain (AL), hereditary transthyretin-related (m-ATTR) and non-mutant transthyretin-related (wt-ATTR) AC.<i>Methods</i>: Retrospective study of 262 patients with AC (123 AL, 94 m-ATTR, 45 wt-ATTR) from a single center.<i>Results</i>: AF prevalence was 15% (AL 9%, m-ATTR 11%, wt-ATTR 40%). During a median follow-up of 1.2 years 11 patients developed AF (2.1% person-years). Age, heart failure (HF), left ventricular (LV) ejection fraction, renal involvement, left atrial size and right atrial pressure were independently associated with AF. AF was associated with incident HF but not with increased mortality. All AF patients were prescribed warfarin and none suffered thromboembolic events.<i>Conclusions</i>: In AC the prevalence of AF varies widely according to etiology with a mean value of 15% that reaches 40% in wt-ATTR amyloidosis. Age, HF, LV ejection fraction, left atrial size and right atrial pressure were the main independent risk factors, while wall thickness and etiology were not the main independent risk factors. AF does not seem to impact all-cause mortality but was strongly associated with prevalent and incident HF.