cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1391323.v1
title: S. aureus JKD6210 plasmid sequence

description: Complete plasmid sequence for S. aureus JKD6210 as published in <em>Microbial Genomics</em> in the following article: Large tandem chromosome expansions facilitate niche adaptation during persistent infection with drug-resistant <em>Staphylococcus aureus</em> [DOI: 10.1099/mgen.0.000026].
DOI: 10.6084/m9.figshare.1391325.v1
title: S. aureus JKD6229 - annotated genome

description: Fully assembled, closed, annotated genome sequence for S. aureus solate JKD6229
DOI: 10.6084/m9.figshare.1391465.v2
title: Supplementary Table S4

description: Summary of mutations
DOI: 10.6084/m9.figshare.1391322.v1
title: S. aureus JKD6210 - annotated genome

description: Completed genome sequence and annotation for S. aureus isolate JKD6210 as published in <em>Microbial Genomics</em> in: Large tandem chromosome expansions facilitate niche adaptation during persistent infection with drug-resistant <em>Staphylococcus aureus</em> [DOI: 10.1099/mgen.0.000026].
DOI: 10.6084/m9.figshare.1391465.v1
title: Supplementary Table S4

description: Summary of mutations
DOI: 10.6084/m9.figshare.1390654
title: A new species of <i>Plioplatecarpus</i> (Mosasauridae, Plioplatecarpinae) from the Bearpaw Formation (Campanian, Upper Cretaceous) of Montana, U.S.A.

description: ABSTRACTMOR 1062 is a plioplatecarpine mosasaur that is represented by a nearly complete skull, complete cervical series, and partial dorsal vertebral column. The specimen, collected from Upper Cretaceous (Campanian) deposits of northeast Montana, exhibits a pristine level of preservation, yielding morphological details not typically observed. Phylogenetic analysis recovers MOR 1062 within an unresolved trichotomy with <i>Plioplatecarpus marshi</i> and <i>P. houzeaui</i>. However, based on the following autapomorphies, a new taxon, <i>Plioplatecarpus peckensis</i>, sp. nov., is erected to accommodate this suite of features exhibited by MOR 1062: a narrow, elongate prenarial portion of the premaxilla that is constricted at midlength; a maxilla with a nearly straight narial margin in lateral view; a short prefrontal lamina of maxilla that contributes to a very low profile of the snout immediately anterior to orbits; a suspensorial ramus of parietal that does not rotate into horizontal plane distally; nine or 10 pterygoid teeth; an otosphenoidal crest that covers the exit for cranial nerve VII in lateral view; jugular and condylar (= hypoglossal) foramina that exit separately; axial spine with a distinctly notched dorsal border; hypapophyseal peduncles on postcranial vertebrae 2–7; and hypapophyses 2–5 bearing paired, anteriorly projecting knobs.http://zoobank.org/urn:lsid:zoobank.org:pub:3F2E8116-0190-4BEB-98B2-56A767379D98SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1390651
title: The Spawning Success of Early Maturing Resident Hatchery Chinook Salmon in a Natural River System

description: Hatchery propagation of spring Chinook Salmon <i>Oncorhynchus tshawytscha</i> has been shown to increase the proportion of males maturing as minijacks (age 2) or microjacks (age 1) relative to those proportions in wild populations. However, little is known about the success of early maturing males when they spawn in the wild. A captive broodstock program for spring Chinook Salmon in the White River (a tributary of the Wenatchee River, Washington) has a high rate of early male maturity. We used genetic parentage analysis to evaluate the spawning success of anadromous males in comparison with inferred early maturing resident, hatchery-origin males that spawned naturally. Based on samples of juvenile offspring (<i>n</i> = 1,007–1,368 fish/year) and a nearly complete sample of the potential anadromous parents, we found that during 2006–2009, 26–45% of the progeny did not have a male parent in the anadromous sample. In contrast, 0–23% of the progeny did not have a female parent represented in the sample. Using grandparentage analysis, we eliminated wild resident fish as a likely source of the unsampled male parents; thus, we concluded that those male parents were most likely early maturing resident fish that had been released from the captive broodstock program. The inferred spawning success of the unsampled resident males was significantly lower than that of the anadromous males. The typical mating pattern was for an anadromous female to produce about two-thirds of her offspring with one or two anadromous males and the remaining one-third with as many as 12 or more apparently resident males. To our knowledge, this is the first study to present evidence of successful reproduction by early maturing resident, hatchery-origin Chinook Salmon in the wild. The conservation implications of this finding are complex and will depend upon the genetic basis of early maturity and its causes in hatchery settings.Received September 3, 2014; accepted January 12, 2015
DOI: 10.6084/m9.figshare.1390654.v2
title: A new species of <i>Plioplatecarpus</i> (Mosasauridae, Plioplatecarpinae) from the Bearpaw Formation (Campanian, Upper Cretaceous) of Montana, U.S.A.

description: ABSTRACTMOR 1062 is a plioplatecarpine mosasaur that is represented by a nearly complete skull, complete cervical series, and partial dorsal vertebral column. The specimen, collected from Upper Cretaceous (Campanian) deposits of northeast Montana, exhibits a pristine level of preservation, yielding morphological details not typically observed. Phylogenetic analysis recovers MOR 1062 within an unresolved trichotomy with <i>Plioplatecarpus marshi</i> and <i>P. houzeaui</i>. However, based on the following autapomorphies, a new taxon, <i>Plioplatecarpus peckensis</i>, sp. nov., is erected to accommodate this suite of features exhibited by MOR 1062: a narrow, elongate prenarial portion of the premaxilla that is constricted at midlength; a maxilla with a nearly straight narial margin in lateral view; a short prefrontal lamina of maxilla that contributes to a very low profile of the snout immediately anterior to orbits; a suspensorial ramus of parietal that does not rotate into horizontal plane distally; nine or 10 pterygoid teeth; an otosphenoidal crest that covers the exit for cranial nerve VII in lateral view; jugular and condylar (= hypoglossal) foramina that exit separately; axial spine with a distinctly notched dorsal border; hypapophyseal peduncles on postcranial vertebrae 2–7; and hypapophyses 2–5 bearing paired, anteriorly projecting knobs.http://zoobank.org/urn:lsid:zoobank.org:pub:3F2E8116-0190-4BEB-98B2-56A767379D98SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1390654.v1
title: A new species of <i>Plioplatecarpus</i> (Mosasauridae, Plioplatecarpinae) from the Bearpaw Formation (Campanian, Upper Cretaceous) of Montana, U.S.A.

description: ABSTRACTMOR 1062 is a plioplatecarpine mosasaur that is represented by a nearly complete skull, complete cervical series, and partial dorsal vertebral column. The specimen, collected from Upper Cretaceous (Campanian) deposits of northeast Montana, exhibits a pristine level of preservation, yielding morphological details not typically observed. Phylogenetic analysis recovers MOR 1062 within an unresolved trichotomy with <i>Plioplatecarpus marshi</i> and <i>P. houzeaui</i>. However, based on the following autapomorphies, a new taxon, <i>Plioplatecarpus peckensis</i>, sp. nov., is erected to accommodate this suite of features exhibited by MOR 1062: a narrow, elongate prenarial portion of the premaxilla that is constricted at midlength; a maxilla with a nearly straight narial margin in lateral view; a short prefrontal lamina of maxilla that contributes to a very low profile of the snout immediately anterior to orbits; a suspensorial ramus of parietal that does not rotate into horizontal plane distally; nine or 10 pterygoid teeth; an otosphenoidal crest that covers the exit for cranial nerve VII in lateral view; jugular and condylar (= hypoglossal) foramina that exit separately; axial spine with a distinctly notched dorsal border; hypapophyseal peduncles on postcranial vertebrae 2–7; and hypapophyses 2–5 bearing paired, anteriorly projecting knobs.http://zoobank.org/urn:lsid:zoobank.org:pub:3F2E8116-0190-4BEB-98B2-56A767379D98SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1390650
title: Ultrastructural relationship of the phagophore with surrounding organelles

description: Phagophore nucleates from a subdomain of the endoplasmic reticulum (ER) termed the omegasome and also makes contact with other organelles such as mitochondria, Golgi complex, plasma membrane and recycling endosomes during its formation. We have used serial block face scanning electron microscopy (SB-EM) and electron tomography (ET) to image phagophore biogenesis in 3 dimensions and to determine the relationship between the phagophore and surrounding organelles at high resolution. ET was performed to confirm whether membrane contact sites (MCSs) are evident between the phagophore and those surrounding organelles. In addition to the known contacts with the ER, we identified MCSs between the phagophore and membranes from putative ER exit sites, late endosomes or lysosomes, the Golgi complex and mitochondria. We also show that one phagophore can have simultaneous MCSs with more than one organelle. Future membrane flux experiments are needed to determine whether membrane contacts also signify lipid translocation.
DOI: 10.6084/m9.figshare.1390651.v2
title: The Spawning Success of Early Maturing Resident Hatchery Chinook Salmon in a Natural River System

description: Hatchery propagation of spring Chinook Salmon <i>Oncorhynchus tshawytscha</i> has been shown to increase the proportion of males maturing as minijacks (age 2) or microjacks (age 1) relative to those proportions in wild populations. However, little is known about the success of early maturing males when they spawn in the wild. A captive broodstock program for spring Chinook Salmon in the White River (a tributary of the Wenatchee River, Washington) has a high rate of early male maturity. We used genetic parentage analysis to evaluate the spawning success of anadromous males in comparison with inferred early maturing resident, hatchery-origin males that spawned naturally. Based on samples of juvenile offspring (<i>n</i> = 1,007–1,368 fish/year) and a nearly complete sample of the potential anadromous parents, we found that during 2006–2009, 26–45% of the progeny did not have a male parent in the anadromous sample. In contrast, 0–23% of the progeny did not have a female parent represented in the sample. Using grandparentage analysis, we eliminated wild resident fish as a likely source of the unsampled male parents; thus, we concluded that those male parents were most likely early maturing resident fish that had been released from the captive broodstock program. The inferred spawning success of the unsampled resident males was significantly lower than that of the anadromous males. The typical mating pattern was for an anadromous female to produce about two-thirds of her offspring with one or two anadromous males and the remaining one-third with as many as 12 or more apparently resident males. To our knowledge, this is the first study to present evidence of successful reproduction by early maturing resident, hatchery-origin Chinook Salmon in the wild. The conservation implications of this finding are complex and will depend upon the genetic basis of early maturity and its causes in hatchery settings.Received September 3, 2014; accepted January 12, 2015
DOI: 10.6084/m9.figshare.1390651.v1
title: The Spawning Success of Early Maturing Resident Hatchery Chinook Salmon in a Natural River System

description: Hatchery propagation of spring Chinook Salmon <i>Oncorhynchus tshawytscha</i> has been shown to increase the proportion of males maturing as minijacks (age 2) or microjacks (age 1) relative to those proportions in wild populations. However, little is known about the success of early maturing males when they spawn in the wild. A captive broodstock program for spring Chinook Salmon in the White River (a tributary of the Wenatchee River, Washington) has a high rate of early male maturity. We used genetic parentage analysis to evaluate the spawning success of anadromous males in comparison with inferred early maturing resident, hatchery-origin males that spawned naturally. Based on samples of juvenile offspring (<i>n</i> = 1,007–1,368 fish/year) and a nearly complete sample of the potential anadromous parents, we found that during 2006–2009, 26–45% of the progeny did not have a male parent in the anadromous sample. In contrast, 0–23% of the progeny did not have a female parent represented in the sample. Using grandparentage analysis, we eliminated wild resident fish as a likely source of the unsampled male parents; thus, we concluded that those male parents were most likely early maturing resident fish that had been released from the captive broodstock program. The inferred spawning success of the unsampled resident males was significantly lower than that of the anadromous males. The typical mating pattern was for an anadromous female to produce about two-thirds of her offspring with one or two anadromous males and the remaining one-third with as many as 12 or more apparently resident males. To our knowledge, this is the first study to present evidence of successful reproduction by early maturing resident, hatchery-origin Chinook Salmon in the wild. The conservation implications of this finding are complex and will depend upon the genetic basis of early maturity and its causes in hatchery settings.Received September 3, 2014; accepted January 12, 2015
DOI: 10.6084/m9.figshare.1390649
title: Induction and adaptation of chaperone-assisted selective autophagy CASA in response to resistance exercise in human skeletal muscle

description: Chaperone-assisted selective autophagy (CASA) is a tension-induced degradation pathway essential for muscle maintenance. Impairment of CASA causes childhood muscle dystrophy and cardiomyopathy. However, the importance of CASA for muscle function in healthy individuals has remained elusive so far. Here we describe the impact of strength training on CASA in a group of healthy and moderately trained men. We show that strenuous resistance exercise causes an acute induction of CASA in affected muscles to degrade mechanically damaged cytoskeleton proteins. Moreover, repeated resistance exercise during 4 wk of training led to an increased expression of CASA components. In human skeletal muscle, CASA apparently acts as a central adaptation mechanism that responds to acute physical exercise and to repeated mechanical stimulation.
DOI: 10.6084/m9.figshare.1390650.v2
title: Ultrastructural relationship of the phagophore with surrounding organelles

description: Phagophore nucleates from a subdomain of the endoplasmic reticulum (ER) termed the omegasome and also makes contact with other organelles such as mitochondria, Golgi complex, plasma membrane and recycling endosomes during its formation. We have used serial block face scanning electron microscopy (SB-EM) and electron tomography (ET) to image phagophore biogenesis in 3 dimensions and to determine the relationship between the phagophore and surrounding organelles at high resolution. ET was performed to confirm whether membrane contact sites (MCSs) are evident between the phagophore and those surrounding organelles. In addition to the known contacts with the ER, we identified MCSs between the phagophore and membranes from putative ER exit sites, late endosomes or lysosomes, the Golgi complex and mitochondria. We also show that one phagophore can have simultaneous MCSs with more than one organelle. Future membrane flux experiments are needed to determine whether membrane contacts also signify lipid translocation.
DOI: 10.6084/m9.figshare.1390633
title: Gaussian Job Archive for C6H6Br8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1390634
title: Gaussian Job Archive for C6H6Br4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1390634.v1
title: Gaussian Job Archive for C6H6Br4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1390650.v1
title: Ultrastructural relationship of the phagophore with surrounding organelles

description: Phagophore nucleates from a subdomain of the endoplasmic reticulum (ER) termed the omegasome and also makes contact with other organelles such as mitochondria, Golgi complex, plasma membrane and recycling endosomes during its formation. We have used serial block face scanning electron microscopy (SB-EM) and electron tomography (ET) to image phagophore biogenesis in 3 dimensions and to determine the relationship between the phagophore and surrounding organelles at high resolution. ET was performed to confirm whether membrane contact sites (MCSs) are evident between the phagophore and those surrounding organelles. In addition to the known contacts with the ER, we identified MCSs between the phagophore and membranes from putative ER exit sites, late endosomes or lysosomes, the Golgi complex and mitochondria. We also show that one phagophore can have simultaneous MCSs with more than one organelle. Future membrane flux experiments are needed to determine whether membrane contacts also signify lipid translocation.
DOI: 10.6084/m9.figshare.1390633.v1
title: Gaussian Job Archive for C6H6Br8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1390649.v2
title: Induction and adaptation of chaperone-assisted selective autophagy CASA in response to resistance exercise in human skeletal muscle

description: Chaperone-assisted selective autophagy (CASA) is a tension-induced degradation pathway essential for muscle maintenance. Impairment of CASA causes childhood muscle dystrophy and cardiomyopathy. However, the importance of CASA for muscle function in healthy individuals has remained elusive so far. Here we describe the impact of strength training on CASA in a group of healthy and moderately trained men. We show that strenuous resistance exercise causes an acute induction of CASA in affected muscles to degrade mechanically damaged cytoskeleton proteins. Moreover, repeated resistance exercise during 4 wk of training led to an increased expression of CASA components. In human skeletal muscle, CASA apparently acts as a central adaptation mechanism that responds to acute physical exercise and to repeated mechanical stimulation.
DOI: 10.6084/m9.figshare.1390649.v1
title: Induction and adaptation of chaperone-assisted selective autophagy CASA in response to resistance exercise in human skeletal muscle

description: Chaperone-assisted selective autophagy (CASA) is a tension-induced degradation pathway essential for muscle maintenance. Impairment of CASA causes childhood muscle dystrophy and cardiomyopathy. However, the importance of CASA for muscle function in healthy individuals has remained elusive so far. Here we describe the impact of strength training on CASA in a group of healthy and moderately trained men. We show that strenuous resistance exercise causes an acute induction of CASA in affected muscles to degrade mechanically damaged cytoskeleton proteins. Moreover, repeated resistance exercise during 4 wk of training led to an increased expression of CASA components. In human skeletal muscle, CASA apparently acts as a central adaptation mechanism that responds to acute physical exercise and to repeated mechanical stimulation.
DOI: 10.6084/m9.figshare.1390624
title: Automated Multi-Lesion Detection for Referable Diabetic Retinopathy in Indigenous Health Care

description: Diabetic Retinopathy (DR) is a complication of diabetes mellitus that affects more than one-quarter of the population with diabetes, and can lead to blindness if not discovered in time. An automated screening enables the identification of patients who need further medical attention. This study aimed to classify retinal images of Aboriginal and Torres Strait Islander peoples utilizing an automated computer-based multi-lesion eye screening program for diabetic retinopathy. The multi-lesion classifier was trained on 1,014 images from the São Paulo Eye Hospital and tested on retinal images containing no DR-related lesion, single lesions or multiple types of lesions from the Inala Aboriginal and Torres Strait Islander health care centre. The automated multi-lesion classifier has the potential to enhance the efficiency of clinical practice delivering diabetic retinopathy screening. Our program does not necessitate image samples for training from any specific ethnic group or population being assessed and is independent of image pre- or post-processing to identify retinal lesions. In this Aboriginal and Torres Strait Islander population, the program achieved 100% sensitivity and 88.9% specificity in identifying bright lesions, while detection of red lesions achieved a sensitivity of 67% and specificity of 95%. When both bright and red lesions were present, 100% sensitivity with 88.9% specificity was obtained. All results obtained with this automated screening program meet WHO standards for diabetic retinopathy screening.
DOI: 10.6084/m9.figshare.1390609
title: Homogeneity Pursuit

description: This article explores the homogeneity of coefficients in high-dimensional regression, which extends the sparsity concept and is more general and suitable for many applications. Homogeneity arises when regression coefficients corresponding to neighboring geographical regions or a similar cluster of covariates are expected to be approximately the same. Sparsity corresponds to a special case of homogeneity with a large cluster of known atom zero. In this article, we propose a new method called clustering algorithm in regression via data-driven segmentation (CARDS) to explore homogeneity. New mathematics are provided on the gain that can be achieved by exploring homogeneity. Statistical properties of two versions of CARDS are analyzed. In particular, the asymptotic normality of our proposed CARDS estimator is established, which reveals better estimation accuracy for homogeneous parameters than that without homogeneity exploration. When our methods are combined with sparsity exploration, further efficiency can be achieved beyond the exploration of sparsity alone. This provides additional insights into the power of exploring low-dimensional structures in high-dimensional regression: homogeneity and sparsity. Our results also shed lights on the properties of the fused Lasso. The newly developed method is further illustrated by simulation studies and applications to real data. Supplementary materials for this article are available online.