cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1494590.v7
title: Activation of new replication foci under conditions of replication stress

description: DNA damage, binding of drugs to DNA or a shortage of nucleotides can decrease the rate or completely halt the progress of replication forks. Although the global rate of replication decreases, mammalian cells can respond to replication stress by activating new replication origins. We demonstrate that a moderate level of stress induced by inhibitors of topoisomerase I, commencing in early, mid or late S-phase, induces activation of new sites of replication located within or in the immediate vicinity of the original replication factories; only in early S some of these new sites are also activated at a distance greater than 300 nm. Under high stress levels very few new replication sites are activated; such sites are located within the original replication regions. There is a large variation in cellular response to stress – while in some cells the number of replication sites increases even threefold, it decreases almost twofold in other cells. Replication stress results in a loss of PCNA from replication factories and a twofold increase in nuclear volume. These observations suggest that activation of new replication origins from the pool of dormant origins within replication cluster under conditions of mild stress is generally restricted to the original replication clusters (factories) active at a time of stress initiation, while activation of distant origins and new replication factories is suppressed.
DOI: 10.6084/m9.figshare.1494600.v17
title: ImpactMapper (outdated version)

description: Please get the newest version from the link below.
DOI: 10.6084/m9.figshare.1512834.v358
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.v359
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.v360
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.v361
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.v362
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.1493798
title: Cretaceous angiosperm pollen from the Kachaike Formation, south-western Santa Cruz Province, Argentina

description: Thirty-three angiosperm pollen species are here reported from mid-Cretaceous deposits of the Kachaike Formation, Austral Basin, southern Argentina. <i>Clavatipollenites</i> is the most abundant angiosperm genus, with six well-defined morphological groups recognised on the basis of their reticulum morphology and sculpture. Pollen of eudicots are scarce, represented by tricolpate (<i>Psilatricolpites</i> spp. and <i>Tricolpites</i> spp.), tricolporoidate and tricolporate morphotypes (<i>Dryadopollis</i> spp.). Increasing complexity in the aperture structure is seen throughout the sequence; tricolpate and tricolporoidate forms are recorded in almost all samples, while tricolporate pollen grains are restricted to the middle and upper levels of the unit. The high species richness and abundance of monocolpate-ulcerate angiosperm related to monocots or magnoliids <i>sensu lato</i> recorded in the unit is comparable to that previously recognised in other assemblages from the early and middle Albian of the southern (e.g. Australia) and northern hemispheres (e.g. Western Portuguese basin, Europe). The recorded increase in the number of angiosperm species towards the middle and upper parts of the Kachaike Formation, with the presence of monocolpate, tricolpate, tricolporoidate and tricolporate pollen, suggests an early-early middle Albian age for these parts of the unit, in agreement with the early Albian age proposed for its basal levels on the basis of dinoflagellates.
DOI: 10.6084/m9.figshare.1512834.v363
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.1493798.v1
title: Cretaceous angiosperm pollen from the Kachaike Formation, south-western Santa Cruz Province, Argentina

description: Thirty-three angiosperm pollen species are here reported from mid-Cretaceous deposits of the Kachaike Formation, Austral Basin, southern Argentina. <i>Clavatipollenites</i> is the most abundant angiosperm genus, with six well-defined morphological groups recognised on the basis of their reticulum morphology and sculpture. Pollen of eudicots are scarce, represented by tricolpate (<i>Psilatricolpites</i> spp. and <i>Tricolpites</i> spp.), tricolporoidate and tricolporate morphotypes (<i>Dryadopollis</i> spp.). Increasing complexity in the aperture structure is seen throughout the sequence; tricolpate and tricolporoidate forms are recorded in almost all samples, while tricolporate pollen grains are restricted to the middle and upper levels of the unit. The high species richness and abundance of monocolpate-ulcerate angiosperm related to monocots or magnoliids <i>sensu lato</i> recorded in the unit is comparable to that previously recognised in other assemblages from the early and middle Albian of the southern (e.g. Australia) and northern hemispheres (e.g. Western Portuguese basin, Europe). The recorded increase in the number of angiosperm species towards the middle and upper parts of the Kachaike Formation, with the presence of monocolpate, tricolpate, tricolporoidate and tricolporate pollen, suggests an early-early middle Albian age for these parts of the unit, in agreement with the early Albian age proposed for its basal levels on the basis of dinoflagellates.
DOI: 10.6084/m9.figshare.1512834.v364
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.1493058
title: Targeting the cell wall of <i>Mycobacterium tuberculosis</i>: a molecular modeling investigation of the interaction of imipenem and meropenem with <i>L</i>,<i>D</i>-transpeptidase 2

description: The single crystal X-ray structure of the extracellular portion of the L,D-transpeptidase (ex-Ldt<sub>Mt2</sub> – residues 120–408) enzyme was recently reported. It was observed that imipenem and meropenem inhibit activity of this enzyme, responsible for generating L,D-transpeptide linkages in the peptidoglycan layer of <i>Mycobacterium tuberculosis</i>. Imipenem is more active and isothermal titration calorimetry experiments revealed that meropenem is subjected to an entropy penalty upon binding to the enzyme. Herein, we report a molecular modeling approach to obtain a molecular view of the inhibitor/enzyme interactions. The average binding free energies for nine commercially available inhibitors were calculated using MM/GBSA and Solvation Interaction Energy (SIE) approaches and the calculated energies corresponded well with the available experimentally observed results. The method reproduces the same order of binding energies as experimentally observed for imipenem and meropenem. We have also demonstrated that SIE is a reasonably accurate and cost-effective free energy method, which can be used to predict carbapenem affinities for this enzyme. A theoretical explanation was offered for the experimental entropy penalty observed for meropenem, creating optimism that this computational model can serve as a potential computational model for other researchers in the field.
DOI: 10.6084/m9.figshare.1512834.v365
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.1493058.v1
title: Targeting the cell wall of <i>Mycobacterium tuberculosis</i>: a molecular modeling investigation of the interaction of imipenem and meropenem with <i>L</i>,<i>D</i>-transpeptidase 2

description: The single crystal X-ray structure of the extracellular portion of the L,D-transpeptidase (ex-Ldt<sub>Mt2</sub> – residues 120–408) enzyme was recently reported. It was observed that imipenem and meropenem inhibit activity of this enzyme, responsible for generating L,D-transpeptide linkages in the peptidoglycan layer of <i>Mycobacterium tuberculosis</i>. Imipenem is more active and isothermal titration calorimetry experiments revealed that meropenem is subjected to an entropy penalty upon binding to the enzyme. Herein, we report a molecular modeling approach to obtain a molecular view of the inhibitor/enzyme interactions. The average binding free energies for nine commercially available inhibitors were calculated using MM/GBSA and Solvation Interaction Energy (SIE) approaches and the calculated energies corresponded well with the available experimentally observed results. The method reproduces the same order of binding energies as experimentally observed for imipenem and meropenem. We have also demonstrated that SIE is a reasonably accurate and cost-effective free energy method, which can be used to predict carbapenem affinities for this enzyme. A theoretical explanation was offered for the experimental entropy penalty observed for meropenem, creating optimism that this computational model can serve as a potential computational model for other researchers in the field.
DOI: 10.6084/m9.figshare.1493055
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.1493054
title: Fluid Borders: Rethinking Historical Geography and Fixed Map Boundaries in Contested Regions

description: This article introduces a quantitative methodology for analyzing contested map borders. The article applies the new analytical technique to a data set of thirty maps showing Bulgaria in ca. 800 CE, a disputed state and period in medieval historiography with relevance to modern national politics and territorial claims. Based on the data set, we generate a series of new maps that make explicit the fluid medieval boundaries and general disagreement among geographers and historiographers. Our analysis begins with a simple point-in-polygon procedure to create a majority map that depicts the points included within the borders of the Bulgarian polity in sixteen or more of the maps (&gt;50 percent). The majority map is then combined with percentage maps, confidence interval map boundaries, and cluster maps. The confidence interval maps are created via a spatial bootstrapping procedure and measure the uncertainty in the majority map. The cluster maps are developed via a radial basis function and provide insight into the potential affectivity based on the cartographers' countries of origin. The final map reflects the general modern consensus of the borders of the Bulgarian polity around 800 CE. Besides its quantitative contribution to medieval and modern cartographic, historiographical, and political debates, this article has developed a widely applicable methodology for synthesizing map borders and territories in cases of cartographic disagreement.
DOI: 10.6084/m9.figshare.1512834.v366
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.1493054.v1
title: Fluid Borders: Rethinking Historical Geography and Fixed Map Boundaries in Contested Regions

description: This article introduces a quantitative methodology for analyzing contested map borders. The article applies the new analytical technique to a data set of thirty maps showing Bulgaria in ca. 800 CE, a disputed state and period in medieval historiography with relevance to modern national politics and territorial claims. Based on the data set, we generate a series of new maps that make explicit the fluid medieval boundaries and general disagreement among geographers and historiographers. Our analysis begins with a simple point-in-polygon procedure to create a majority map that depicts the points included within the borders of the Bulgarian polity in sixteen or more of the maps (&gt;50 percent). The majority map is then combined with percentage maps, confidence interval map boundaries, and cluster maps. The confidence interval maps are created via a spatial bootstrapping procedure and measure the uncertainty in the majority map. The cluster maps are developed via a radial basis function and provide insight into the potential affectivity based on the cartographers' countries of origin. The final map reflects the general modern consensus of the borders of the Bulgarian polity around 800 CE. Besides its quantitative contribution to medieval and modern cartographic, historiographical, and political debates, this article has developed a widely applicable methodology for synthesizing map borders and territories in cases of cartographic disagreement.