cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1512834.v367
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1493055.v1
title: New early Miocene protoceratids (Mammalia, Artiodactyla) from Panama

description: ABSTRACTAlthough Cenozoic protoceratid artiodactyls are known from throughout North America, species referred to the Miocene protoceratine <i>Paratoceras</i> are restricted to subtropical areas of the Gulf Coast and southern Mexico and tropical areas of Panama. Newly discovered fossils from the late Arikareean Lirio Norte Local Fauna, Panama Canal basin, include partial dentitions of a protoceratid remarkably similar to those of <i>Paratoceras tedfordi</i> from Mexico, suggesting a rapid early Miocene colonization of recently emerged tropical volcanic terrains (Las Cascadas Formation). Partial lower dentitions from the overlying shallow marine to transitional Culebra Formation (early Centenario Fauna) are here referred to <i>Paratoceras orarius</i>, sp. nov., based on relatively small size, shallow mandible anterior to p3, and narrow cheek teeth. New early Hemingfordian protoceratine fossils from the upper part of the Cucaracha Formation (late Centenario Fauna) include a partial male skull and several dentitions that, together with specimens previously referred to <i>P. wardi</i> (only known from the Barstovian of Texas), are here referred to <i>Paratoceras coatesi</i>, sp. nov., based on distinctly more gracile cranial ornamentation, relatively longer nasals, a smaller and wider lower p4 (relative to m1), and more bulbous lower premolars. Results from a cladistic analysis of 15 craniodental characters coded for 11 protoceratine species suggests that <i>Paratoceras</i> is a monophyletic clade with its origin in subtropical areas of Central America, spreading into the tropics of Panama during the early Miocene (Arikareean through Hemingfordian North American Land Mammal Ages [NALMAs]), and later inhabiting subtropical areas of the Gulf Coast during the middle–late Miocene (Barstovian through Clarendonian NALMAs).SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVPhttp://zoobank.org/urn:lsid:zoobank.org:pub:31FFF397-6362-443C-A612-E9279FF122
DOI: 10.6084/m9.figshare.1493055.v3
title: New early Miocene protoceratids (Mammalia, Artiodactyla) from Panama

description: ABSTRACTAlthough Cenozoic protoceratid artiodactyls are known from throughout North America, species referred to the Miocene protoceratine <i>Paratoceras</i> are restricted to subtropical areas of the Gulf Coast and southern Mexico and tropical areas of Panama. Newly discovered fossils from the late Arikareean Lirio Norte Local Fauna, Panama Canal basin, include partial dentitions of a protoceratid remarkably similar to those of <i>Paratoceras tedfordi</i> from Mexico, suggesting a rapid early Miocene colonization of recently emerged tropical volcanic terrains (Las Cascadas Formation). Partial lower dentitions from the overlying shallow marine to transitional Culebra Formation (early Centenario Fauna) are here referred to <i>Paratoceras orarius</i>, sp. nov., based on relatively small size, shallow mandible anterior to p3, and narrow cheek teeth. New early Hemingfordian protoceratine fossils from the upper part of the Cucaracha Formation (late Centenario Fauna) include a partial male skull and several dentitions that, together with specimens previously referred to <i>P. wardi</i> (only known from the Barstovian of Texas), are here referred to <i>Paratoceras coatesi</i>, sp. nov., based on distinctly more gracile cranial ornamentation, relatively longer nasals, a smaller and wider lower p4 (relative to m1), and more bulbous lower premolars. Results from a cladistic analysis of 15 craniodental characters coded for 11 protoceratine species suggests that <i>Paratoceras</i> is a monophyletic clade with its origin in subtropical areas of Central America, spreading into the tropics of Panama during the early Miocene (Arikareean through Hemingfordian North American Land Mammal Ages [NALMAs]), and later inhabiting subtropical areas of the Gulf Coast during the middle–late Miocene (Barstovian through Clarendonian NALMAs).SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVPhttp://zoobank.org/urn:lsid:zoobank.org:pub:31FFF397-6362-443C-A612-E9279FF122
DOI: 10.6084/m9.figshare.1512834.v368
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1493055.v2
title: New early Miocene protoceratids (Mammalia, Artiodactyla) from Panama

description: ABSTRACTAlthough Cenozoic protoceratid artiodactyls are known from throughout North America, species referred to the Miocene protoceratine <i>Paratoceras</i> are restricted to subtropical areas of the Gulf Coast and southern Mexico and tropical areas of Panama. Newly discovered fossils from the late Arikareean Lirio Norte Local Fauna, Panama Canal basin, include partial dentitions of a protoceratid remarkably similar to those of <i>Paratoceras tedfordi</i> from Mexico, suggesting a rapid early Miocene colonization of recently emerged tropical volcanic terrains (Las Cascadas Formation). Partial lower dentitions from the overlying shallow marine to transitional Culebra Formation (early Centenario Fauna) are here referred to <i>Paratoceras orarius</i>, sp. nov., based on relatively small size, shallow mandible anterior to p3, and narrow cheek teeth. New early Hemingfordian protoceratine fossils from the upper part of the Cucaracha Formation (late Centenario Fauna) include a partial male skull and several dentitions that, together with specimens previously referred to <i>P. wardi</i> (only known from the Barstovian of Texas), are here referred to <i>Paratoceras coatesi</i>, sp. nov., based on distinctly more gracile cranial ornamentation, relatively longer nasals, a smaller and wider lower p4 (relative to m1), and more bulbous lower premolars. Results from a cladistic analysis of 15 craniodental characters coded for 11 protoceratine species suggests that <i>Paratoceras</i> is a monophyletic clade with its origin in subtropical areas of Central America, spreading into the tropics of Panama during the early Miocene (Arikareean through Hemingfordian North American Land Mammal Ages [NALMAs]), and later inhabiting subtropical areas of the Gulf Coast during the middle–late Miocene (Barstovian through Clarendonian NALMAs).SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVPhttp://zoobank.org/urn:lsid:zoobank.org:pub:31FFF397-6362-443C-A612-E9279FF122
DOI: 10.6084/m9.figshare.1512834.v369
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1512834.v371
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1493048
title: Baited remote underwater video system (BRUVs) survey of chondrichthyan diversity in False Bay, South Africa

description: Global declines in chondrichthyan populations necessitate evidence‑based planning for their conservation. False Bay, in south‑west South Africa, has a high diversity of marine biota, with Atlantic and Indian Ocean influences, but its chondrichthyan fauna is poorly described ecologically. False Bay has a long fishing history and supports various harvesting methods, including shark‑directed fishing. This is the first baited remote underwater video system (BRUVs) survey of the relative abundance, diversity and seasonal distribution of chondrichthyans in False Bay. Nineteen species from 11 families were recorded across 185 sites at between 4 and 49 m depth. Diversity was greatest in summer, on reefs and in shallow water. Endemic scyliorhinids, especially <i>Haploblepharus edwardsii</i>, dominated everywhere, in summer and winter. Habitat and season were key predictors of species composition, and a significant interaction between depth and season indicated migration patterns for <i>Mustelus mustelus</i>. By avoiding the selectivity associated with catch records, BRUVs data are superior to fishery‑dependent catch‑per‑unit‑effort data to monitor chondrichthyan diversity and abundance. Baited remote underwater video systems access greater depths and more habitats than previously surveyed in False Bay and avoid taxonomic lumping typical of catch records in the region, making them more efficient than other methods of surveying chondrichthyan diversity.
DOI: 10.6084/m9.figshare.1512834.v370
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1493048.v1
title: Baited remote underwater video system (BRUVs) survey of chondrichthyan diversity in False Bay, South Africa

description: Global declines in chondrichthyan populations necessitate evidence‑based planning for their conservation. False Bay, in south‑west South Africa, has a high diversity of marine biota, with Atlantic and Indian Ocean influences, but its chondrichthyan fauna is poorly described ecologically. False Bay has a long fishing history and supports various harvesting methods, including shark‑directed fishing. This is the first baited remote underwater video system (BRUVs) survey of the relative abundance, diversity and seasonal distribution of chondrichthyans in False Bay. Nineteen species from 11 families were recorded across 185 sites at between 4 and 49 m depth. Diversity was greatest in summer, on reefs and in shallow water. Endemic scyliorhinids, especially <i>Haploblepharus edwardsii</i>, dominated everywhere, in summer and winter. Habitat and season were key predictors of species composition, and a significant interaction between depth and season indicated migration patterns for <i>Mustelus mustelus</i>. By avoiding the selectivity associated with catch records, BRUVs data are superior to fishery‑dependent catch‑per‑unit‑effort data to monitor chondrichthyan diversity and abundance. Baited remote underwater video systems access greater depths and more habitats than previously surveyed in False Bay and avoid taxonomic lumping typical of catch records in the region, making them more efficient than other methods of surveying chondrichthyan diversity.
DOI: 10.6084/m9.figshare.1493045
title: Lessons learned from the parallel universe of consumer electronics: Making Computer Aided Drug Design work on the platforms of the future

description: Poster presented at the Gordon Research Conference: Computer Aided Drug Design 2015, describing a range of chemistry functionality that has been made to work on mobile apps. Each of these workflows involved removing a variety of barriers to adoption, both technical and sociological. The result is a strong platform for chemical informatics in drug discovery that has been tailored to the extremely high user experience required for the realm of consumer electronics. This is interesting not only for mobile apps, but also modern desktop or web applications, as customer expectations continue to rise to match those of other industries.
DOI: 10.6084/m9.figshare.1493050.v1
title: Cross-cancer profiling of molecular alterations within the human autophagy interaction network

description: Aberrant activation or disruption of autophagy promotes tumorigenesis in various preclinical models of cancer, but whether the autophagy pathway is a target for recurrent molecular alteration in human cancer patient samples is unknown. To address this outstanding question, we surveyed 211 human autophagy-associated genes for tumor-related alterations to DNA sequence and RNA expression levels and examined their association with patient survival outcomes in multiple cancer types with sequence data from The Cancer Genome Atlas consortium. We found 3 (<i>RB1CC1/FIP200, ULK4, WDR45/WIPI4</i>) and one (<i>ATG7</i>) core autophagy genes to be under positive selection for somatic mutations in endometrial carcinoma and clear cell renal carcinoma, respectively; while 29 autophagy regulators and pathway interactors, including previously identified <i>KEAP1, NFE2L2</i> and <i>MTOR</i>, were significantly mutated in 6 of the 11 cancer types examined. Gene expression analyses revealed that <i>GABARAPL1</i> and <i>MAP1LC3C/LC3C</i> transcripts were less abundant in breast cancer and non-small cell lung cancers than in matched normal tissue controls; <i>ATG4D</i> transcripts were increased in lung squamous cell carcinoma, as were <i>ATG16L2</i> transcripts in kidney cancer. Unsupervised clustering of autophagy-associated mRNA levels in tumors stratified patient overall survival in 3 of 9 cancer types (acute myeloid leukemia, clear cell renal carcinoma, and head and neck cancer). These analyses provide the first comprehensive resource of recurrently altered autophagy-associated genes in human tumors, and highlight cancer types and subtypes where perturbed autophagy may be relevant to patient overall survival.
DOI: 10.6084/m9.figshare.1493045.v1
title: Lessons learned from the parallel universe of consumer electronics: Making Computer Aided Drug Design work on the platforms of the future

description: Poster presented at the Gordon Research Conference: Computer Aided Drug Design 2015, describing a range of chemistry functionality that has been made to work on mobile apps. Each of these workflows involved removing a variety of barriers to adoption, both technical and sociological. The result is a strong platform for chemical informatics in drug discovery that has been tailored to the extremely high user experience required for the realm of consumer electronics. This is interesting not only for mobile apps, but also modern desktop or web applications, as customer expectations continue to rise to match those of other industries.
DOI: 10.6084/m9.figshare.1493050.v2
title: Cross-cancer profiling of molecular alterations within the human autophagy interaction network

description: Aberrant activation or disruption of autophagy promotes tumorigenesis in various preclinical models of cancer, but whether the autophagy pathway is a target for recurrent molecular alteration in human cancer patient samples is unknown. To address this outstanding question, we surveyed 211 human autophagy-associated genes for tumor-related alterations to DNA sequence and RNA expression levels and examined their association with patient survival outcomes in multiple cancer types with sequence data from The Cancer Genome Atlas consortium. We found 3 (<i>RB1CC1/FIP200, ULK4, WDR45/WIPI4</i>) and one (<i>ATG7</i>) core autophagy genes to be under positive selection for somatic mutations in endometrial carcinoma and clear cell renal carcinoma, respectively, while 29 autophagy regulators and pathway interactors, including previously identified <i>KEAP1, NFE2L2,</i> and <i>MTOR</i>, were significantly mutated in 6 of the 11 cancer types examined. Gene expression analyses revealed that <i>GABARAPL1</i> and <i>MAP1LC3C/LC3C</i> transcripts were less abundant in breast cancer and non-small cell lung cancers than in matched normal tissue controls; <i>ATG4D</i> transcripts were increased in lung squamous cell carcinoma, as were <i>ATG16L2</i> transcripts in kidney cancer. Unsupervised clustering of autophagy-associated mRNA levels in tumors stratified patient overall survival in 3 of 9 cancer types (acute myeloid leukemia, clear cell renal carcinoma, and head and neck cancer). These analyses provide the first comprehensive resource of recurrently altered autophagy-associated genes in human tumors, and highlight cancer types and subtypes where perturbed autophagy may be relevant to patient overall survival.
DOI: 10.6084/m9.figshare.1493046.v1
title: Long-term live imaging reveals cytosolic immune responses of host hepatocytes against <i>Plasmodium</i> infection and parasite escape mechanisms

description: <i>Plasmodium</i> parasites are transmitted by <i>Anopheles</i> mosquitoes to the mammalian host and actively infect hepatocytes after passive transport in the bloodstream to the liver. In their target host hepatocyte, parasites reside within a parasitophorous vacuole (PV). In the present study it was shown that the parasitophorous vacuole membrane (PVM) can be targeted by autophagy marker proteins LC3, ubiquitin, and SQSTM1/p62 as well as by lysosomes in a process resembling selective autophagy. The dynamics of autophagy marker proteins in individual <i>Plasmodium berghei</i>-infected hepatocytes were followed by live imaging throughout the entire development of the parasite in the liver. Although the host cell very efficiently recognized the invading parasite in its vacuole, the majority of parasites survived this initial attack. Successful parasite development correlated with the gradual loss of all analyzed autophagy marker proteins and associated lysosomes from the PVM. However, other autophagic events like nonselective canonical autophagy in the host cell continued. This was indicated as LC3, although not labeling the PVM anymore, still localized to autophagosomes in the infected host cell. It appears that growing parasites even benefit from this form of nonselective host cell autophagy as an additional source of nutrients, as in host cells deficient for autophagy, parasite growth was retarded and could partly be rescued by the supply of additional amino acid in the medium. Importantly, mouse infections with <i>P. berghei</i> sporozoites confirmed LC3 dynamics, the positive effect of autophagy activation on parasite growth, and negative effects upon autophagy inhibition.