cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3083629
title: Characterization of conserved arginine residues on Cdt1 that affect licensing activity and interaction with Geminin or Mcm complex

description: All organisms ensure once and only once replication during S phase through a process called replication licensing. Cdt1 is a key component and crucial loading factor of Mcm complex, which is a central component for the eukaryotic replicative helicase. In higher eukaryotes, timely inhibition of Cdt1 by Geminin is essential to prevent rereplication. Here, we address the mechanism of DNA licensing using purified Cdt1, Mcm and Geminin proteins in combination with replication in <i>Xenopus</i> egg extracts. We mutagenized the 223th arginine of mouse Cdt1 (mCdt1) to cysteine or serine (R-S or R-C, respectively) and 342nd and 346th arginines constituting an arginine finger-like structure to alanine (RR-AA). The RR-AA mutant of Cdt1 could not only rescue the DNA replication activity in Cdt1-depleted extracts but also its specific activity for DNA replication and licensing was significantly increased compared to the wild-type protein. In contrast, the R223 mutants were partially defective in rescue of DNA replication and licensing. Biochemical analyses of these mutant Cdt1 proteins indicated that the RR-AA mutation disabled its functional interaction with Geminin, while R223 mutations resulted in ablation in interaction with the Mcm2∼7 complex. Intriguingly, the R223 mutants are more susceptible to the phosphorylation-induced inactivation or chromatin dissociation. Our results show that conserved arginine residues play critical roles in interaction with Geminin and Mcm that are crucial for proper conformation of the complexes and its licensing activity.
DOI: 10.6084/m9.figshare.3083629.v1
title: Characterization of conserved arginine residues on Cdt1 that affect licensing activity and interaction with Geminin or Mcm complex

description: All organisms ensure once and only once replication during S phase through a process called replication licensing. Cdt1 is a key component and crucial loading factor of Mcm complex, which is a central component for the eukaryotic replicative helicase. In higher eukaryotes, timely inhibition of Cdt1 by Geminin is essential to prevent rereplication. Here, we address the mechanism of DNA licensing using purified Cdt1, Mcm and Geminin proteins in combination with replication in <i>Xenopus</i> egg extracts. We mutagenized the 223th arginine of mouse Cdt1 (mCdt1) to cysteine or serine (R-S or R-C, respectively) and 342nd and 346th arginines constituting an arginine finger-like structure to alanine (RR-AA). The RR-AA mutant of Cdt1 could not only rescue the DNA replication activity in Cdt1-depleted extracts but also its specific activity for DNA replication and licensing was significantly increased compared to the wild-type protein. In contrast, the R223 mutants were partially defective in rescue of DNA replication and licensing. Biochemical analyses of these mutant Cdt1 proteins indicated that the RR-AA mutation disabled its functional interaction with Geminin, while R223 mutations resulted in ablation in interaction with the Mcm2∼7 complex. Intriguingly, the R223 mutants are more susceptible to the phosphorylation-induced inactivation or chromatin dissociation. Our results show that conserved arginine residues play critical roles in interaction with Geminin and Mcm that are crucial for proper conformation of the complexes and its licensing activity.
DOI: 10.6084/m9.figshare.3083641.v2
title: Data of Paper "DAD with hash"

description: Experiment data including scenario 1 and 2, 30-days network traffic.
DOI: 10.6084/m9.figshare.3083635.v1
title: PTSD data of ASL.rar

description: PASL data for PTSD
DOI: 10.6084/m9.figshare.3083641.v1
title: PONE-D-15-44316-data.rar

description: Experiment data including scenario 1 and 2, 30-days network traffic.
DOI: 10.6084/m9.figshare.3083644.v1
title: New Rhinocerotidae from the Kisingiri localities (lower Miocene of Western Kenya)

description: We describe new material of Rhinocerotidae recently collected in western Kenya. A skull from Karungu is one of the best-preserved Miocene skulls in Africa. It differs substantially from that of <i>Rusingaceros leakeyi</i>, the only other relatively well-known rhino from this region and age, in its degree of brachycephaly, possession of a deep nasal notch, and long nasal bones that probably carried a horn of moderate size. Miocene African rhinos are still too poorly known to resolve their phylogenetic relationships, but we tentatively assign this skull to a new species of <i>Victoriaceros</i>, a genus whose type species comes from the younger site of Maboko, although the Karungu skull has a much smaller nasal horn. A parsimony analysis resolves them as sister species within the Elasmotheriini, close to the other African genera <i>Turkanatherium</i> and <i>Chilotheridium</i>, but we consider this result debatable, as <i>Victoriaceros</i> differs considerably from them. Still, they might all be descended from European forms. A partial skull from Gumba is assigned to the Aceratheriini, making it one of the earliest representatives of this group and suggesting that the origin of this tribe could be African. http://zoobank.org/urn:lsid:zoobank.org:pub:2B1E8135-CCD4-43EB-826B-6DF7176DC74E SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Geraads, D., T. Lehmann, D. J. Peppe, and K. P. McNulty. 2016. New Rhinocerotidae from the Kisingiri localities (lower Miocene of western Kenya). Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1103247.
DOI: 10.6084/m9.figshare.3083617
title: The SUMO deconjugating peptidase Smt4 contributes to the mechanism required for transition from sister chromatid arm cohesion to sister chromatid pericentromere separation

description: The pericentromere chromatin protrudes orthogonally from the sister-sister chromosome arm axis. Pericentric protrusions are organized in a series of loops with the centromere at the apex, maximizing its ability to interact with stochastically growing and shortening kinetochore microtubules. Each pericentromere loop is ∼50 kb in size and is organized further into secondary loops that are displaced from the primary spindle axis. Cohesin and condensin are integral to mechanisms of loop formation and generating resistance to outward forces from kinesin motors and anti-parallel spindle microtubules. A major unanswered question is how the boundary between chromosome arms and the pericentromere is established and maintained. We used sister chromatid separation and dynamics of LacO arrays distal to the pericentromere to address this issue. Perturbation of chromatin spring components results in 2 distinct phenotypes. In cohesin and condensin mutants sister pericentric LacO arrays separate a defined distance independent of spindle length. In the absence of Smt4, a peptidase that removes SUMO modifications from proteins, pericentric LacO arrays separate in proportion to spindle length increase. Deletion of Smt4, unlike depletion of cohesin and condensin, causes stretching of both proximal and distal pericentromere LacO arrays. The data suggest that the sumoylation state of chromatin topology adjusters, including cohesin, condensin, and topoisomerase II in the pericentromere, contribute to chromatin spring properties as well as the sister cohesion boundary.
DOI: 10.6084/m9.figshare.3083635.v2
title: PTSD data of ASL

description: PASL data for PTSD
DOI: 10.6084/m9.figshare.3083617.v1
title: The SUMO deconjugating peptidase Smt4 contributes to the mechanism required for transition from sister chromatid arm cohesion to sister chromatid pericentromere separation

description: The pericentromere chromatin protrudes orthogonally from the sister-sister chromosome arm axis. Pericentric protrusions are organized in a series of loops with the centromere at the apex, maximizing its ability to interact with stochastically growing and shortening kinetochore microtubules. Each pericentromere loop is ∼50 kb in size and is organized further into secondary loops that are displaced from the primary spindle axis. Cohesin and condensin are integral to mechanisms of loop formation and generating resistance to outward forces from kinesin motors and anti-parallel spindle microtubules. A major unanswered question is how the boundary between chromosome arms and the pericentromere is established and maintained. We used sister chromatid separation and dynamics of LacO arrays distal to the pericentromere to address this issue. Perturbation of chromatin spring components results in 2 distinct phenotypes. In cohesin and condensin mutants sister pericentric LacO arrays separate a defined distance independent of spindle length. In the absence of Smt4, a peptidase that removes SUMO modifications from proteins, pericentric LacO arrays separate in proportion to spindle length increase. Deletion of Smt4, unlike depletion of cohesin and condensin, causes stretching of both proximal and distal pericentromere LacO arrays. The data suggest that the sumoylation state of chromatin topology adjusters, including cohesin, condensin, and topoisomerase II in the pericentromere, contribute to chromatin spring properties as well as the sister cohesion boundary.
DOI: 10.6084/m9.figshare.3083635.v3
title: PTSD data of ASL

description: PASL data for PTSD
DOI: 10.6084/m9.figshare.3083584
title: Worldwide withdrawal of medicinal products because of adverse drug reactions: a systematic review and analysis

description: We have systematically identified medicinal products withdrawn worldwide because of adverse drug reactions, assessed the level of evidence used for making the withdrawal decisions, and explored the patterns of withdrawals over time. We searched PubMed, the WHO database of withdrawn products, and selected texts. We included products that were withdrawn after launch from 1950 onwards, excluding non-human and over-the-counter medicines. We assessed the levels of evidence on which withdrawals were based using the Oxford Center for Evidence Based Medicine Levels of Evidence. Of 353 medicinal products withdrawn from any country, only 40 were withdrawn worldwide. Anecdotal reports were cited as evidence for withdrawal in 30 (75%) and deaths occurred in 27 (68%). Hepatic, cardiac, and nervous system toxicity accounted for over 60% of withdrawals. In 28 cases, the first withdrawal was initiated by the manufacturer. The median interval between the first report of an adverse drug reaction that led to withdrawal and the first withdrawal was 1 year (range 0–43 years). Worldwide withdrawals occurred within 1 year after the first withdrawal in any country. In conclusion, the time it takes for drugs to be withdrawn worldwide after reports of adverse drug reactions has shortened over time. However, there are inconsistencies in current withdrawal procedures when adverse drug reactions are suspected. A uniform method for establishing worldwide withdrawal of approved medicinal products when adverse drug reactions are suspected should be developed, to facilitate global withdrawals. Rapid synthesis of the evidence on harms should be a priority when serious adverse reactions are suspected.
DOI: 10.6084/m9.figshare.3083584.v1
title: Worldwide withdrawal of medicinal products because of adverse drug reactions: a systematic review and analysis

description: We have systematically identified medicinal products withdrawn worldwide because of adverse drug reactions, assessed the level of evidence used for making the withdrawal decisions, and explored the patterns of withdrawals over time. We searched PubMed, the WHO database of withdrawn products, and selected texts. We included products that were withdrawn after launch from 1950 onwards, excluding non-human and over-the-counter medicines. We assessed the levels of evidence on which withdrawals were based using the Oxford Center for Evidence Based Medicine Levels of Evidence. Of 353 medicinal products withdrawn from any country, only 40 were withdrawn worldwide. Anecdotal reports were cited as evidence for withdrawal in 30 (75%) and deaths occurred in 27 (68%). Hepatic, cardiac, and nervous system toxicity accounted for over 60% of withdrawals. In 28 cases, the first withdrawal was initiated by the manufacturer. The median interval between the first report of an adverse drug reaction that led to withdrawal and the first withdrawal was 1 year (range 0–43 years). Worldwide withdrawals occurred within 1 year after the first withdrawal in any country. In conclusion, the time it takes for drugs to be withdrawn worldwide after reports of adverse drug reactions has shortened over time. However, there are inconsistencies in current withdrawal procedures when adverse drug reactions are suspected. A uniform method for establishing worldwide withdrawal of approved medicinal products when adverse drug reactions are suspected should be developed, to facilitate global withdrawals. Rapid synthesis of the evidence on harms should be a priority when serious adverse reactions are suspected.
DOI: 10.6084/m9.figshare.3083635.v5
title: PTSD data of ASL

description: PASL data for PTSD
DOI: 10.6084/m9.figshare.3083485
title: Enhancing_pubic_participatin_in_EIA_in_China.docx.pdf

description: This dissertation was designed for investing current implementation of public participation wihtin EIA system in China. The study found that the development of Public Participation in China is advanced while the implementation is poor and many third parties have less opportunities to access EIA process.
DOI: 10.6084/m9.figshare.3083524
title: GMG final report for distribution.pdf

description: Report from a 2013 U.S. National Science Foundation Workshop on Geomicrobiology and Microbial Geochemistry
DOI: 10.6084/m9.figshare.3083554
title: Opposing Effects of Different Soil Organic Matter Fractions on Crop Yields, Ecol Appl 2016, Data

description: Data on maize crop yields, soil organic matter fractions, and microbial enzymes from farms in Western Kenya.
DOI: 10.6084/m9.figshare.3083524.v1
title: GMG final report for distribution.pdf

description: Report from a 2013 U.S. National Science Foundation Workshop on Geomicrobiology and Microbial Geochemistry
DOI: 10.6084/m9.figshare.3083635.v6
title: PTSD data of ASL

description: PASL data for PTSD
DOI: 10.6084/m9.figshare.3083485.v1
title: Enhancing_pubic_participatin_in_EIA_in_China.docx.pdf

description: This dissertation was designed for investing current implementation of public participation wihtin EIA system in China. The study found that the development of Public Participation in China is advanced while the implementation is poor and many third parties have less opportunities to access EIA process.
DOI: 10.6084/m9.figshare.3083416
title: Internet-based CBT for major depressive disorder

description: Data from a randomized trial of internet-based cognitive behavior therapy versus a monitored attention control for major depressive disorder in an American sample<b></b>
DOI: 10.6084/m9.figshare.3083416.v1
title: Internet-based CBT for major depressive disorder

description: Data from a randomized trial of internet-based cognitive behavior therapy versus a monitored attention control for major depressive disorder in an American sample<b></b>
DOI: 10.6084/m9.figshare.3083554.v1
title: All_Data.csv

description: Data on maize crop yields, soil organic matter fractions, and microbial enzymes from farms in Western Kenya.
DOI: 10.6084/m9.figshare.3083320
title: Euptychia oviposition and larval performance

description: Data and code for Hamm and Fordyce 2016 (Journal of Insect Science). Data are from two series of experiments conducted in Costa Rica investigating larval performance and oviposition preference on different host plants.
DOI: 10.6084/m9.figshare.3083554.v3
title: Opposing Effects of Different Soil Organic Matter Fractions on Crop Yields, Ecol Appl 2016, Data

description: Data on maize crop yields, soil organic matter fractions, and microbial enzymes from farms in Western Kenya.
DOI: 10.6084/m9.figshare.3083095
title: Experiential avoidance, coping and self-harm_Nielsen_Sayal_Townsend.sav

description: This study investigated the relationship between experiential avoidance, coping and the recency and frequency of self-harm, in a community sample. <br><br>The dataset contains self-report measures of self-harm, momentary affect, experiential avoidance and coping in response to a recent stressor.
DOI: 10.6084/m9.figshare.3083125
title: A new family of gymnodont fish (Tetraodontiformes) from the earliest Eocene of the Peri-Tethys (Kabardino-Balkaria, northern Caucasus, Russia)

description: The environmental changes that occurred during the Paleocene–Eocene transition are crucial for the interpretation of the patterns and processes of diversification of vertebrate clades. A prominent increase of the number of vertebrate families occurred between the late Paleocene and early Eocene, resulting in the appearance of many in the earliest representatives of extant lineages, including a number of marine fish groups. Tetraodontiforms are a monophyletic group of derived teleost fishes encompassing a variety of bizarre morphologies. Even though the earliest members of this order appeared in the Late Cretaceous, most of the crown lineages date back to the Eocene. One of the crown tetraodontiform groups that appeared in the fossil record during the Eocene are the gymnodonts (pufferfishes, porcupinefishes, ocean sunfishes and their allies), which include a variety of species characterized by highly modified teeth incorporated into beak-like jaws and scales usually modified into prickly spines. Herein, we describe †<i>Balkaria histiopterygia</i> gen. et sp. nov., a gymnodont fish characterized by a strikingly peculiar morphology. The single available specimen in part and counterpart documented herein was recovered from the sapropelitic deposits that originated in the northern Peri-Tethys during the transition between the Paleocene and Eocene. Today, these deposits are exposed near the village of Gerpegezh, Republic of Kabardino-Balkaria, Russia. The skeletal structure reveals an extreme mosaicism of primitive and derived characters that result in a very bizarre and unexpected morphology. †<i>Balkaria histiopterygia</i> gen. et sp. nov. is unique among the extant and other fossil gymnodont fishes by, among many other features, the huge size of its spiny-dorsal fin and the position of these spines on the top of the head. †<i>Balkaria histiopterygia</i> gen. et sp. nov. is the earliest unequivocal gymnodont fish, representing the sole member of the new family †Balkariidae. More particularly, †<i>Balkaria histiopterygia</i> gen. et sp. nov. is shown herein to be the oldest and arguably the most informative fossil of the gymnodont suborder Tetraodontoidei. The phylogenetic placement of this new taxon has been assessed based on both morphology alone and on a combination of morphological and molecular data that strongly supports the close relationship of †<i>Balkaria</i> gen. nov. to the herein restricted Tetraodontoidei. However, its position within Tetraodontoidei is unstable depending on the type of method of phylogenetic inference. Significantly younger ages, during the Late Cretaceous, are estimated for the diversification of Tetraodontiformes than in previous tip-dating analyses (Jurassic and Early Cretaceous) using the fossilized birth-death process; these new age estimates are in better agreement with the tetraodontiform fossil record. http://zoobank.org/urn:lsid:zoobank.org:pub:41764800-B0D8-4CA4-A111-5F4C4A281C37
DOI: 10.6084/m9.figshare.3083320.v1
title: Euptychia oviposition and larval performance

description: Data and code for Hamm and Fordyce 2016 (Journal of Insect Science). Data are from two series of experiments conducted in Costa Rica investigating larval performance and oviposition preference on different host plants.
DOI: 10.6084/m9.figshare.3083095.v1
title: Experiential avoidance, coping and self-harm_Nielsen_Sayal_Townsend.sav

description: This study investigated the relationship between experiential avoidance, coping and the recency and frequency of self-harm, in a community sample. <br><br>The dataset contains self-report measures of self-harm, momentary affect, experiential avoidance and coping in response to a recent stressor.
DOI: 10.6084/m9.figshare.3083125.v1
title: A new family of gymnodont fish (Tetraodontiformes) from the earliest Eocene of the Peri-Tethys (Kabardino-Balkaria, northern Caucasus, Russia)

description: The environmental changes that occurred during the Paleocene–Eocene transition are crucial for the interpretation of the patterns and processes of diversification of vertebrate clades. A prominent increase of the number of vertebrate families occurred between the late Paleocene and early Eocene, resulting in the appearance of many in the earliest representatives of extant lineages, including a number of marine fish groups. Tetraodontiforms are a monophyletic group of derived teleost fishes encompassing a variety of bizarre morphologies. Even though the earliest members of this order appeared in the Late Cretaceous, most of the crown lineages date back to the Eocene. One of the crown tetraodontiform groups that appeared in the fossil record during the Eocene are the gymnodonts (pufferfishes, porcupinefishes, ocean sunfishes and their allies), which include a variety of species characterized by highly modified teeth incorporated into beak-like jaws and scales usually modified into prickly spines. Herein, we describe †<i>Balkaria histiopterygia</i> gen. et sp. nov., a gymnodont fish characterized by a strikingly peculiar morphology. The single available specimen in part and counterpart documented herein was recovered from the sapropelitic deposits that originated in the northern Peri-Tethys during the transition between the Paleocene and Eocene. Today, these deposits are exposed near the village of Gerpegezh, Republic of Kabardino-Balkaria, Russia. The skeletal structure reveals an extreme mosaicism of primitive and derived characters that result in a very bizarre and unexpected morphology. †<i>Balkaria histiopterygia</i> gen. et sp. nov. is unique among the extant and other fossil gymnodont fishes by, among many other features, the huge size of its spiny-dorsal fin and the position of these spines on the top of the head. †<i>Balkaria histiopterygia</i> gen. et sp. nov. is the earliest unequivocal gymnodont fish, representing the sole member of the new family †Balkariidae. More particularly, †<i>Balkaria histiopterygia</i> gen. et sp. nov. is shown herein to be the oldest and arguably the most informative fossil of the gymnodont suborder Tetraodontoidei. The phylogenetic placement of this new taxon has been assessed based on both morphology alone and on a combination of morphological and molecular data that strongly supports the close relationship of †<i>Balkaria</i> gen. nov. to the herein restricted Tetraodontoidei. However, its position within Tetraodontoidei is unstable depending on the type of method of phylogenetic inference. Significantly younger ages, during the Late Cretaceous, are estimated for the diversification of Tetraodontiformes than in previous tip-dating analyses (Jurassic and Early Cretaceous) using the fossilized birth-death process; these new age estimates are in better agreement with the tetraodontiform fossil record. http://zoobank.org/urn:lsid:zoobank.org:pub:41764800-B0D8-4CA4-A111-5F4C4A281C37
DOI: 10.6084/m9.figshare.3082825
title: Parper network datas

description: Data are generated using the algorithm proposed by Lancichinetti A, et al. ( Physical Review E. 2008;78(4):046110)