cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5573032
title: The timescale of early land plant evolution. 2018. Jennifer L. Morris*, Mark N. Puttick*, James Clark, Dianne Edwards, Paul Kenrick, Silvia Pressel, Charles H. Wellman, Ziheng Yang, Harald Schneider, Philip C. J. Donoghue. PNAS.

description: Alignments and input phylogenies for divergence time estimations
DOI: 10.6084/m9.figshare.5573095.v3
title: jupyter notebook to demo pyphot

description: jupyter notebook to demo pyphot
DOI: 10.6084/m9.figshare.5573029.v1
title: Dataset for: NANDROLONE-INDUCED NUCLEAR ACCUMULATION OF MYOD PROTEIN IS MEDIATED BY NUMB, A NOTCH INHIBITOR, IN C2C12 MYOBLASTS

description: Signaling via the androgen receptor (AR) stimulates myogenic progenitor differentiation. In addition, myogenic differentiation factor D (MyoD) and Numb, a Notch inhibitor, play key roles in regulating myogenic differentiation. Nandrolone, an anabolic steroid, upregulates both MyoD and Numb expression in myogenic cells. However, the molecular mechanisms by which MyoD is upregulated by nandrolone are unclear. Moreover, the potential crosstalk between nandrolone, MyoD, and Numb is not well understood. With these considerations in mind, we examined the effects of nandrolone on the expression of MyoD mRNA and protein, and determined the interactions of MyoD and Numb in the presence or absence of nandrolone in differentiating C2C12 myoblasts. Nandrolone increased MyoD mRNA and protein expression and significantly enhanced nuclear translocation of MyoD protein. The later effect of nandrolone was blunted by siRNA against Numb. Immunoprecipitation studies confirmed that Numb forms complexes with MyoD. Chromatin immunoprecipitation revealed that in the presence of nandrolone, Numb is recruited to a region of the MyH7 promotor containing the E-box to which MyoD binds. These data indicate that nandrolone-regulated MyoD activation occurs mainly through a posttranslational mechanism which promotes MyoD nuclear accumulation, and suggest that this effect of nandrolone is, at least in part, mediated by Numb.
DOI: 10.6084/m9.figshare.5573095.v2
title: jupyter notebook to demo pyphot

description: jupyter notebook to demo pyphot
DOI: 10.6084/m9.figshare.5573032.v1
title: The timescale of early land plant evolution: controlling for alterative topologies and dating strategies on divergence time estimates. 201?. Mark N. Puttick, Jennifer L. Morris, James Clark, Dianne Edwards, Paul Kenrick, Silvia Pressel, Charles H. Wellman, Ziheng Yang, Harald Schneider, Philip C. J. Donoghue

description: Alignments and input phylogenies for divergence time estimations
DOI: 10.6084/m9.figshare.5573011
title: Generation of thermostable Moloney murine leukemia virus reverse transcriptase variants using site saturation mutagenesis library and cell-free protein expression system

description: We attempted to increase the thermostability of Moloney murine leukemia virus (MMLV) reverse transcriptase (RT). The eight-site saturation mutagenesis libraries corresponding to Ala70−Arg469 in the whole MMLV RT (Thr24−Leu671), in each of which 1 out of 50 amino acid residues was replaced with other amino acid residue, were constructed. Seven-hundred and sixty eight MMLV RT clones were expressed using a cell-free protein expression system, and their thermostabilities were assessed by the temperature of thermal treatment at which they retained cDNA synthesis activity. One clone D200C was selected as the most thermostable variant. The highest temperature of thermal treatment at which D200C exhibited cDNA synthesis activity was 57ºC, which was higher than for WT (53ºC). Our results suggest that a combination of site saturation mutagenesis library and cell-free protein expression system might be useful for generation of thermostable MMLV RT in a short period of time for expression and selection. Site saturation mutagenesis library of MMLV RT was constructed and expressed using cell-free protein expression system.
DOI: 10.6084/m9.figshare.5573011.v1
title: Generation of thermostable Moloney murine leukemia virus reverse transcriptase variants using site saturation mutagenesis library and cell-free protein expression system

description: We attempted to increase the thermostability of Moloney murine leukemia virus (MMLV) reverse transcriptase (RT). The eight-site saturation mutagenesis libraries corresponding to Ala70−Arg469 in the whole MMLV RT (Thr24−Leu671), in each of which 1 out of 50 amino acid residues was replaced with other amino acid residue, were constructed. Seven-hundred and sixty eight MMLV RT clones were expressed using a cell-free protein expression system, and their thermostabilities were assessed by the temperature of thermal treatment at which they retained cDNA synthesis activity. One clone D200C was selected as the most thermostable variant. The highest temperature of thermal treatment at which D200C exhibited cDNA synthesis activity was 57ºC, which was higher than for WT (53ºC). Our results suggest that a combination of site saturation mutagenesis library and cell-free protein expression system might be useful for generation of thermostable MMLV RT in a short period of time for expression and selection. Site saturation mutagenesis library of MMLV RT was constructed and expressed using cell-free protein expression system.
DOI: 10.6084/m9.figshare.5572993
title: Dataset for: Oleoylethanolamide-induced anorexia in rats is associated with locomotor impairment

description: The endogenous peroxisome proliferator-activated receptor alpha (PPAR-α) agonist Oleoylethanolamide (OEA) inhibits eating in rodents, mainly by delaying the onset of meals. The underlying mechanisms of OEA-induced anorexia, however, remain unclear. Animals treated with high OEA doses were shown to display signs of discomfort and impaired locomotion. Therefore, we first examined whether the impaired locomotion may contribute to OEA’s anorectic effect. Second, it is controversial whether abdominal vagal afferents are necessary for OEA’s anorectic effect. Thus, we explored alternative peripheral neural pathways mediating IP OEA’s anorectic effect by performing a celiac-superior mesenteric ganglionectomy (CGX) or a subdiaphragmatic vagal deafferentation (SDA) alone or in combination. Exogenously administered OEA at a commonly used dose (10mg/kg BW, IP) concurrently reduced food intake and compromised locomotor activity. Attempts to dissociate both phenomena using the dopamine D2/D3 receptor agonist Quinpirole (1 mg/kg BW, SC) failed because Quinpirole antagonized both, OEA-induced locomotor impairment and delay in eating onset. CGX attenuated the prolongation of the latency to eat by IP OEA, but neither SDA nor CGX prevented IP OEA-induced locomotor impairment. Our results indicate that IP OEA’s anorectic effect may be secondary to impaired locomotion rather than due to physiological satiety. They further confirm that vagal afferents do not mediate exogenous OEA’s anorectic effects, but suggest a role for spinal afferents in addition to an alternative, non-neuronal signaling route.
DOI: 10.6084/m9.figshare.5573032.v2
title: The timescale of early land plant evolution. 2018. Mark N. Puttick, Jennifer L. Morris, James Clark, Dianne Edwards, Paul Kenrick, Silvia Pressel, Charles H. Wellman, Ziheng Yang, Harald Schneider, Philip C. J. Donoghue. Proceedings of the National Academy of Sciences of the United States of America.

description: Alignments and input phylogenies for divergence time estimations
DOI: 10.6084/m9.figshare.5572993.v1
title: Dataset for: Oleoylethanolamide-induced anorexia in rats is associated with locomotor impairment

description: The endogenous peroxisome proliferator-activated receptor alpha (PPAR-α) agonist Oleoylethanolamide (OEA) inhibits eating in rodents, mainly by delaying the onset of meals. The underlying mechanisms of OEA-induced anorexia, however, remain unclear. Animals treated with high OEA doses were shown to display signs of discomfort and impaired locomotion. Therefore, we first examined whether the impaired locomotion may contribute to OEA’s anorectic effect. Second, it is controversial whether abdominal vagal afferents are necessary for OEA’s anorectic effect. Thus, we explored alternative peripheral neural pathways mediating IP OEA’s anorectic effect by performing a celiac-superior mesenteric ganglionectomy (CGX) or a subdiaphragmatic vagal deafferentation (SDA) alone or in combination. Exogenously administered OEA at a commonly used dose (10mg/kg BW, IP) concurrently reduced food intake and compromised locomotor activity. Attempts to dissociate both phenomena using the dopamine D2/D3 receptor agonist Quinpirole (1 mg/kg BW, SC) failed because Quinpirole antagonized both, OEA-induced locomotor impairment and delay in eating onset. CGX attenuated the prolongation of the latency to eat by IP OEA, but neither SDA nor CGX prevented IP OEA-induced locomotor impairment. Our results indicate that IP OEA’s anorectic effect may be secondary to impaired locomotion rather than due to physiological satiety. They further confirm that vagal afferents do not mediate exogenous OEA’s anorectic effects, but suggest a role for spinal afferents in addition to an alternative, non-neuronal signaling route.
DOI: 10.6084/m9.figshare.5573032.v3
title: The timescale of early land plant evolution. 2018. Jennifer L. Morris, Mark N. Puttick, James Clark, Dianne Edwards, Paul Kenrick, Silvia Pressel, Charles H. Wellman, Ziheng Yang, Harald Schneider, Philip C. J. Donoghue. PNAS.

description: Alignments and input phylogenies for divergence time estimations
DOI: 10.6084/m9.figshare.5572981
title: Endometriosis and gestational diabetes mellitus risk: a systematic review and meta-analysis

description: <b>Objective:</b> To perform a systematic review and meta-analysis regarding endometriosis and the risk of gestational diabetes mellitus (GDM). <b>Methods:</b> We carried out a search of the following databases: Medline, Embase, Web of Science, Cochrane Library, Scopus, Scielo, Clinicaltrials.gov, the UK Clinical Trials Gateway, and the Australian New Zealand Clinical Trials Registry, from inception through April 28 2017, without language restrictions, in order to evaluate the effect of endometriosis over GDM risk, in women with and without endometriosis. Odds ratios (ORs) and their 95% confidence intervals (CIs) or mean differences (MDs) were calculated as effects. Methodological quality of evidence was assessed with the Newcastle–Ottawa Scale, and heterogeneity among studies with the <i>I</i><sup>2</sup> statistic. Random-effects models were used for meta-analyses, and publication bias was assessed with Egger’s test. <b>Results:</b> We identified 12 studies (10 cohort and two case control studies) with a total of 48,762 pregnancies, including 3,461 with endometriosis. Endometriosis had no significant effect on GDM risk (OR =1.14; 95% CI: 0.86, 1.51; <i>p</i> = .35, <i>I</i><sup>2</sup> = 56%, Egger’s test <i>p</i> = .45). Secondary outcomes (gestational age at delivery, birthweight, and Neonatal Intensive Care Unit admission) were statistically similar in women with and without endometriosis. <b>Conclusions:</b> Better-designed studies are needed to confirm our results.
DOI: 10.6084/m9.figshare.5572984
title: Call types of Bigg’s killer whales (<i>Orcinus orca</i>) in western Alaska: using vocal dialects to assess population structure

description: Bigg’s killer whales (<i>Orcinus orca;</i> i.e. ‘transient’ ecotype), as apex predators, are important to the dynamics of marine ecosystems, but little is known about their population structure in western Alaska. Currently, all Bigg’s killer whales in western Alaska are ascribed to a single broad stock for management under the US Marine Mammal Protection Act. However, recent nuclear microsatellite and mitochondrial DNA analyses indicate that this stock is likely comprised of genetically distinct sub-populations. In accordance with what is known about killer whale vocal dialects in other locations, we used the spatial distribution of group-specific call types to investigate the population structure of Bigg’s killer whales in this part of Alaska. Digital audio recordings were collected from 33 Bigg’s killer whale encounters throughout the Aleutian and Pribilof Islands in the summers of 2001–2007 and 2009–2010. Recorded calls were qualitatively classified into discrete types and then quantitatively described using 12 structural and time-frequency measures. Resulting call categories were validated using a random forest approach. A total of 36 call types and subtypes were identified across the entire study area, and regional patterns of call type use revealed three distinct dialects which correspond to proposed genetic delineations. Our results suggest that there are at least three acoustically and genetically distinct sub-populations in western Alaska, and we present an initial catalogue for this area describing the regional vocal repertoires of Bigg’s killer whale call types.
DOI: 10.6084/m9.figshare.5572984.v1
title: Call types of Bigg’s killer whales (<i>Orcinus orca</i>) in western Alaska: using vocal dialects to assess population structure

description: Bigg’s killer whales (<i>Orcinus orca;</i> i.e. ‘transient’ ecotype), as apex predators, are important to the dynamics of marine ecosystems, but little is known about their population structure in western Alaska. Currently, all Bigg’s killer whales in western Alaska are ascribed to a single broad stock for management under the US Marine Mammal Protection Act. However, recent nuclear microsatellite and mitochondrial DNA analyses indicate that this stock is likely comprised of genetically distinct sub-populations. In accordance with what is known about killer whale vocal dialects in other locations, we used the spatial distribution of group-specific call types to investigate the population structure of Bigg’s killer whales in this part of Alaska. Digital audio recordings were collected from 33 Bigg’s killer whale encounters throughout the Aleutian and Pribilof Islands in the summers of 2001–2007 and 2009–2010. Recorded calls were qualitatively classified into discrete types and then quantitatively described using 12 structural and time-frequency measures. Resulting call categories were validated using a random forest approach. A total of 36 call types and subtypes were identified across the entire study area, and regional patterns of call type use revealed three distinct dialects which correspond to proposed genetic delineations. Our results suggest that there are at least three acoustically and genetically distinct sub-populations in western Alaska, and we present an initial catalogue for this area describing the regional vocal repertoires of Bigg’s killer whale call types.
DOI: 10.6084/m9.figshare.5572966
title: Growth and Poverty Revisited from a Multidimensional Perspective

description: The actual impact of economic growth on poverty reduction is of fundamental importance to the development agenda. This paper offers new empirical evidence on growth and poverty measured from a multidimensional perspective using the global Multidimensional Poverty Index. Results from a First Difference Estimator Model suggest that while economic growth reduces multidimensional poverty, this impact is well below a one-to-one relationship and lower than the impact of growth on income poverty. Results from a cross-section model additionally suggest that countries with higher levels of exports, higher share of industry and services and higher control of corruption have lower multidimensional poverty.
DOI: 10.6084/m9.figshare.5572963
title: The Effects of Ethnic Chinese Minority on Vietnam’s Regional Economic Development in the Post-Vietnam War Period

description: This paper examines the impact of the Hoa, an ethnically Chinese, economically dominant minority, on regional economic development in Vietnam. To address the endogeneity of the geographical distribution of the Hoa, we use an important historical episode: the rapid deterioration in Sino-Vietnamese diplomatic relationship that led many ethnic Chinese to flee abroad, particularly to the refugee camps in the Guangxi province of China, in 1979. We find that the effects of proximity to the refugee camps on the share of ethnic Chinese in 1989 were more pronounced for provinces that had a larger presence of the ethnic Chinese population in 1979. We also find strong correlations between the 1989 share of ethnic Chinese (instrumented) and contemporary indicators of economic performance. The results suggest that the ethnic Chinese minority had positive economic impacts on Vietnam’s regional economies and that the post-Vietnam War exodus of ethnic Chinese was likely to have had long-term negative economic impacts.
DOI: 10.6084/m9.figshare.5572966.v1
title: Growth and Poverty Revisited from a Multidimensional Perspective

description: The actual impact of economic growth on poverty reduction is of fundamental importance to the development agenda. This paper offers new empirical evidence on growth and poverty measured from a multidimensional perspective using the global Multidimensional Poverty Index. Results from a First Difference Estimator Model suggest that while economic growth reduces multidimensional poverty, this impact is well below a one-to-one relationship and lower than the impact of growth on income poverty. Results from a cross-section model additionally suggest that countries with higher levels of exports, higher share of industry and services and higher control of corruption have lower multidimensional poverty.
DOI: 10.6084/m9.figshare.5572963.v1
title: The Effects of Ethnic Chinese Minority on Vietnam’s Regional Economic Development in the Post-Vietnam War Period

description: This paper examines the impact of the Hoa, an ethnically Chinese, economically dominant minority, on regional economic development in Vietnam. To address the endogeneity of the geographical distribution of the Hoa, we use an important historical episode: the rapid deterioration in Sino-Vietnamese diplomatic relationship that led many ethnic Chinese to flee abroad, particularly to the refugee camps in the Guangxi province of China, in 1979. We find that the effects of proximity to the refugee camps on the share of ethnic Chinese in 1989 were more pronounced for provinces that had a larger presence of the ethnic Chinese population in 1979. We also find strong correlations between the 1989 share of ethnic Chinese (instrumented) and contemporary indicators of economic performance. The results suggest that the ethnic Chinese minority had positive economic impacts on Vietnam’s regional economies and that the post-Vietnam War exodus of ethnic Chinese was likely to have had long-term negative economic impacts.
DOI: 10.6084/m9.figshare.5572957
title: Evaporation and CO<sub>2</sub> fluxes in a coastal reef: an eddy covariance approach

description: <b>Introduction:</b> We conducted season-long observations of evaporation and carbon flux at the Gulf of Aqaba coast, northern Red Sea. We used the eddy-covariance method with a two-tower setup to measure evaporation rates over land and sea and the advection between them. Using a three-dimensional mass balance approach, we calculated total evaporation as the sum of two main components in our site: horizontal advection and turbulent vertical flux, with half-hourly change of water vapor storage and horizontal flux divergence found to be negligible. <b>Outcomes:</b> Average evaporation rates were 11.4 [mm/day] from April through May (early summer) and 10.5 [mm/day] from June through August (summer). The coastal reef was a CO<sub>2</sub> sink over the period of measurements, significantly higher in June through August than in April through May. The main environmental drivers of CO<sub>2</sub> flux were humidity, water temperature, sensible heat flux, and wind speed. <b>Discussion:</b> The rates of evaporation near the shore were considerably higher than values reported in other studies typically used to represent the mean for the whole Gulf area. We found that evaporation rates computed by common bulk models approximate the mean values of evaporation but have poor representativeness of the intra-daily temporal variation of evaporation. There was a significant correlation between CO<sub>2</sub> flux and evaporation attributed to common environmental drivers of gas diffusion, turbulent fluxes, and horizontal transport. <b>Conclusion:</b> We conclude that observations of fluxes in coastal waters need to use at least a two-tower system to account for the effect of horizontal advection on the total flux.
DOI: 10.6084/m9.figshare.5572957.v1
title: Evaporation and CO<sub>2</sub> fluxes in a coastal reef: an eddy covariance approach

description: <b>Introduction:</b> We conducted season-long observations of evaporation and carbon flux at the Gulf of Aqaba coast, northern Red Sea. We used the eddy-covariance method with a two-tower setup to measure evaporation rates over land and sea and the advection between them. Using a three-dimensional mass balance approach, we calculated total evaporation as the sum of two main components in our site: horizontal advection and turbulent vertical flux, with half-hourly change of water vapor storage and horizontal flux divergence found to be negligible. <b>Outcomes:</b> Average evaporation rates were 11.4 [mm/day] from April through May (early summer) and 10.5 [mm/day] from June through August (summer). The coastal reef was a CO<sub>2</sub> sink over the period of measurements, significantly higher in June through August than in April through May. The main environmental drivers of CO<sub>2</sub> flux were humidity, water temperature, sensible heat flux, and wind speed. <b>Discussion:</b> The rates of evaporation near the shore were considerably higher than values reported in other studies typically used to represent the mean for the whole Gulf area. We found that evaporation rates computed by common bulk models approximate the mean values of evaporation but have poor representativeness of the intra-daily temporal variation of evaporation. There was a significant correlation between CO<sub>2</sub> flux and evaporation attributed to common environmental drivers of gas diffusion, turbulent fluxes, and horizontal transport. <b>Conclusion:</b> We conclude that observations of fluxes in coastal waters need to use at least a two-tower system to account for the effect of horizontal advection on the total flux.
DOI: 10.6084/m9.figshare.5572816
title: CVR dataset

description: CVR and cognition in healthy ageing<br><br>Regional CVR values calculated from ASL BOLD data, demographic and cognitive data <br>
DOI: 10.6084/m9.figshare.5572834
title: Synthetic spectra and photometry for models in the GRAMS oxygen-rich star and carbon-star grid

description: The Grid of RSG and AGB ModelS (GRAMS) is a set of radiative transfer models for circumstellar dust around low- and intermediate-mass evolved stars. These files contain the synthetic spectra and photometry for the entire oxygen-rich and carbon-star GRAMS grid in the form of a FITS array of structures. For each model photosphere, the grid contains models over a large range of dust inner shell radii and optical depths. See Sargent, Srininvasan, & Meixner (ApJ 2011 728, 93) and Srinivasan, Sargent & Meixner (A&A 2011 532, 54) for details.<br>Synthetic photometry available for the following filters:<br>MCPSU ,MCPSB ,MCPSV ,MCPSI ,2MASSJ ,2MASSH ,2MASSK ,IRAC36 ,IRAC45 ,IRAC58 ,IRAC80 ,MIPS24 ,MIPS70 ,MIPS160 ,AKARIN2 ,AKARIN3 ,AKARIN4 ,AKARIS7 ,AKARIS9W ,AKARIS11 ,AKARIL15 ,AKARIL18W ,AKARIL24 ,WISEW1 ,WISEW2 ,WISEW3 ,WISEW4 ,ISOCAMLW2 ,ISOCAMLW3 ,MIRSI_KBAND ,MIRSI4_9 ,MIRSI7_7 ,MIRSI8_7 ,MIRSI9_6 ,MIRSI10_5 ,MIRSI11_7 ,MIRSI12_28 ,MIRSI12_33 ,MIRSI18_5 ,MIRSI20_9 ,MIRSI24_5 ,GALEX_FUV ,GALEX_NUV ,SDSS_u ,SDSS_g ,SDSS_r ,SDSS_i ,SDSS_z ,MIR_NBF_1 ,MIR_NBF_2 ,MIR_NBF_3 ,MIR_NBF_4 ,MIR_NBF_5 ,MIR_NBF_6 ,MIR_NBF_7 ,MIR_NBF_8 ,MIR_NBF_9 ,MIR_NBF_10 ,MIR_NBF_11 ,MIR_NBF_12 ,MIR_NBF_13 ,MIR_NBF_14 ,MIR_NBF_15 ,MIR_NBF_16 ,MIR_NBF_17 ,MIR_NBF_18 ,MIR_NBF_19 ,MIR_NBF_20 ,MIR_NBF_21 ,MIR_NBF_22 ,MIR_NBF_23 ,Rband ,PACS70 ,PACS100 ,PACS160 ,SPIRE250 ,SPIRE350 ,SPIRE500 ,IRAS_12 ,IRAS_25 ,IRAS_60 ,IRAS_100