cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3408022.v1
title: Aberrant DNA methylation of WNT pathway genes in the development and progression of CIMP-negative colorectal cancer

description: The WNT signaling pathway has an essential role in colorectal carcinogenesis and progression, which involves a cascade of genetic and epigenetic changes. We aimed to analyze DNA methylation affecting the WNT pathway genes in colorectal carcinogenesis in promoter and gene body regions using whole methylome analysis in 9 colorectal cancer, 15 adenoma, and 6 normal tumor adjacent tissue (NAT) samples by methyl capture sequencing. Functional methylation was confirmed on 5-aza-2′-deoxycytidine-treated colorectal cancer cell line datasets. In parallel with the DNA methylation analysis, mutations of WNT pathway genes (<i>APC</i>, β-catenin/<i>CTNNB1</i>) were analyzed by 454 sequencing on GS Junior platform. Most differentially methylated CpG sites were localized in gene body regions (95% of WNT pathway genes). In the promoter regions, 33 of the 160 analyzed WNT pathway genes were differentially methylated in colorectal cancer vs. normal, including hypermethylated <i>AXIN2, CHP1, PRICKLE1, SFRP1, SFRP2, SOX17</i>, and hypomethylated <i>CACYBP, CTNNB1, MYC</i>; 44 genes in adenoma vs. NAT; and 41 genes in colorectal cancer vs. adenoma comparisons. Hypermethylation of <i>AXIN2, DKK1, VANGL1</i>, and <i>WNT5A</i> gene promoters was higher, while those of <i>SOX17, PRICKLE1, DAAM2</i>, and <i>MYC</i> was lower in colon carcinoma compared to adenoma. Inverse correlation between expression and methylation was confirmed in 23 genes, including <i>APC, CHP1, PRICKLE1, PSEN1</i>, and <i>SFRP1</i>. Differential methylation affected both canonical and noncanonical WNT pathway genes in colorectal normal-adenoma-carcinoma sequence. Aberrant DNA methylation appears already in adenomas as an early event of colorectal carcinogenesis.
DOI: 10.6084/m9.figshare.3408004
title: Bayesian networks to identify statistical dependencies. A case study of Spanish university students’ habits

description: <i>Objective</i>: The present study sought to discover the relationships among different features characterizing Spanish university students’ habits through a Bayesian network (BN). The set of features with the strongest influence in specific features can be determined. <i>Methods</i>: A BN was built from a dataset composed of 13 relevant features, determining the dependencies and conditional independencies from empirical data in a multivariate context. The structure was learned with the <i>bnlearn</i> package in R language introducing prior knowledge, and the parameters were obtained with Netica software. Three reasoning patterns were considered to make inferences: <i>intercausal, evidential</i>, and <i>causal</i> reasoning. <i>Results</i>: BN determined the different relationships. Through inference several conclusions were achieved, for instance a high probability value of physical activity in low state was obtained when active peers were instantiated to none state, self-rated fitness to fair state, bmi to normal weight, sitting time to moderate, age to 22–25, and gender to woman state. <i>Conclusions</i>: Bayesian networks may help to characterize Spanish University students’ habits.
DOI: 10.6084/m9.figshare.3408004.v1
title: Bayesian networks to identify statistical dependencies. A case study of Spanish university students’ habits

description: <i>Objective</i>: The present study sought to discover the relationships among different features characterizing Spanish university students’ habits through a Bayesian network (BN). The set of features with the strongest influence in specific features can be determined. <i>Methods</i>: A BN was built from a dataset composed of 13 relevant features, determining the dependencies and conditional independencies from empirical data in a multivariate context. The structure was learned with the <i>bnlearn</i> package in R language introducing prior knowledge, and the parameters were obtained with Netica software. Three reasoning patterns were considered to make inferences: <i>intercausal, evidential</i>, and <i>causal</i> reasoning. <i>Results</i>: BN determined the different relationships. Through inference several conclusions were achieved, for instance a high probability value of physical activity in low state was obtained when active peers were instantiated to none state, self-rated fitness to fair state, bmi to normal weight, sitting time to moderate, age to 22–25, and gender to woman state. <i>Conclusions</i>: Bayesian networks may help to characterize Spanish University students’ habits.
DOI: 10.6084/m9.figshare.3407998
title: Role and expression of <i>cry1</i> in the adductor muscle of the oyster <i>Crassostrea gigas</i> during daily and tidal valve activity rhythms

description: Cryptochromes are flavin- and pterin-containing photoreceptors of the cryptochrome/photolyase family. They play critical roles in organisms, among are which light-dependent and light-independent roles in biological rhythms. The present work aimed at describing a cryptochrome gene in the oyster <i>Crassostrea gigas</i> by (i) a characterization and phylogenetic analysis and (ii) by studying its expression in the relationship to rhythmic valve behavior in different entrainment regimes. Cryptochrome expression was focused on the adductor muscle of the oyster, the effector of the valve behavior. The results suggest involvement of <i>Cgcry1</i> in oyster rhythmicity as a sensor of environmental zeitgebers, associated with circadian rhythms and potentially to tidal activity. The characterized gene belongs to type 1 cryptochrome/insect-type cry. Additionally, <i>Cgcry1</i> presented a daily oscillation under L:D entrainment, which disappeared in constant darkness. Transcript expression of <i>Cgcry1</i> also oscillated at tidal frequency under tidal entrainment and in constant darkness. Finally, exposure of tidally entrained oysters to saxitoxin (STX)-producing alga <i>Alexandrium minutum</i> induced a dose effect response in oysters by first altering <i>Cgcry1</i> expression and then the behavior of oysters with increasing concentrations of toxins. This study initiates the characterization of the molecular clock in the oyster <i>C. gigas</i> and its interactions with environmental zeitgebers.
DOI: 10.6084/m9.figshare.3407998.v1
title: Role and expression of <i>cry1</i> in the adductor muscle of the oyster <i>Crassostrea gigas</i> during daily and tidal valve activity rhythms

description: Cryptochromes are flavin- and pterin-containing photoreceptors of the cryptochrome/photolyase family. They play critical roles in organisms, among are which light-dependent and light-independent roles in biological rhythms. The present work aimed at describing a cryptochrome gene in the oyster <i>Crassostrea gigas</i> by (i) a characterization and phylogenetic analysis and (ii) by studying its expression in the relationship to rhythmic valve behavior in different entrainment regimes. Cryptochrome expression was focused on the adductor muscle of the oyster, the effector of the valve behavior. The results suggest involvement of <i>Cgcry1</i> in oyster rhythmicity as a sensor of environmental zeitgebers, associated with circadian rhythms and potentially to tidal activity. The characterized gene belongs to type 1 cryptochrome/insect-type cry. Additionally, <i>Cgcry1</i> presented a daily oscillation under L:D entrainment, which disappeared in constant darkness. Transcript expression of <i>Cgcry1</i> also oscillated at tidal frequency under tidal entrainment and in constant darkness. Finally, exposure of tidally entrained oysters to saxitoxin (STX)-producing alga <i>Alexandrium minutum</i> induced a dose effect response in oysters by first altering <i>Cgcry1</i> expression and then the behavior of oysters with increasing concentrations of toxins. This study initiates the characterization of the molecular clock in the oyster <i>C. gigas</i> and its interactions with environmental zeitgebers.
DOI: 10.6084/m9.figshare.3407977
title: Multicomponent diffusion in aluminosilicate garnet: coupling effects due to charge compensation

description: Three kinds of multicomponent diffusion effects, arising from three distinct physical mechanisms, are evident in stranded diffusion profiles at the rims of partially resorbed garnets from the contact aureole of the Makhavinekh Lake Pluton, northern Labrador. Profiles that display a subtle maximum in Ca concentration are explained by the prevailing ideal mean-field theory of multicomponent diffusion, but models implementing that theory cannot replicate inverted profiles for Li and internal maxima for Nd, Sm, and Eu. The anomalous profiles are quantitatively reproduced, however, by numerical simulations employing a model based on coupled movement of charge-compensating groups during diffusional transport of yttrium and the rare-earth elements (Y+REEs). An alkali-type charge-compensation mechanism for the heterovalent substitution of Y+REEs on dodecahedral sites in garnet produces direct charge coupling between Li<sup>+</sup> and (Y+REE)<sup>3+</sup> and leads to co-diffusion of Li<sup>+</sup>-(Y+REE)<sup>3+</sup> pairs, with the result that Li profiles closely mimic those for Y+REEs. A menzerite-type charge-compensation mechanism produces indirect charge coupling among all Y+REE components, with the result that the fluxes of low-abundance REEs become partly dependent on the fluxes of Y+REEs present in higher abundance. These findings have implications for the robustness of Li profiles in garnet as monitors of fluid–rock interaction, for geochronology based on the Sm–Nd and Lu–Hf systems, and for future experimental attempts to quantify rates of diffusion in garnet.
DOI: 10.6084/m9.figshare.3407977.v1
title: Multicomponent diffusion in aluminosilicate garnet: coupling effects due to charge compensation

description: Three kinds of multicomponent diffusion effects, arising from three distinct physical mechanisms, are evident in stranded diffusion profiles at the rims of partially resorbed garnets from the contact aureole of the Makhavinekh Lake Pluton, northern Labrador. Profiles that display a subtle maximum in Ca concentration are explained by the prevailing ideal mean-field theory of multicomponent diffusion, but models implementing that theory cannot replicate inverted profiles for Li and internal maxima for Nd, Sm, and Eu. The anomalous profiles are quantitatively reproduced, however, by numerical simulations employing a model based on coupled movement of charge-compensating groups during diffusional transport of yttrium and the rare-earth elements (Y+REEs). An alkali-type charge-compensation mechanism for the heterovalent substitution of Y+REEs on dodecahedral sites in garnet produces direct charge coupling between Li<sup>+</sup> and (Y+REE)<sup>3+</sup> and leads to co-diffusion of Li<sup>+</sup>-(Y+REE)<sup>3+</sup> pairs, with the result that Li profiles closely mimic those for Y+REEs. A menzerite-type charge-compensation mechanism produces indirect charge coupling among all Y+REE components, with the result that the fluxes of low-abundance REEs become partly dependent on the fluxes of Y+REEs present in higher abundance. These findings have implications for the robustness of Li profiles in garnet as monitors of fluid–rock interaction, for geochronology based on the Sm–Nd and Lu–Hf systems, and for future experimental attempts to quantify rates of diffusion in garnet.
DOI: 10.6084/m9.figshare.3407965
title: Landslide_inventory_final.kmz

description: Inventory of ~3000 landslides mapped out across northern California using high resolution aerial and satellite imagery in Google Earth. The inventory contains ~2000 debris slides and 1000 earthflows (both active and dormant). For each landslide an erosion rate and various geometrical parameters are given. Please see the related paper for methods behind erosion rate calculations and for further detail on mapping. The inventory is provided as a Google Earth kmz file, though shape files are available on request.
DOI: 10.6084/m9.figshare.3407962
title: Geochronology and geochemistry of volcanic rocks in the Arbasay Formation, Xinjiang Province (Northwest China): implications for the tectonic evolution of the North Tianshan

description: The extensively exposed late Carboniferous volcanic and volcaniclastic successions along the northern margin of the North Tianshan are called the Arbasay Formation. We present field-based mapping, petrography, zircon cathodoluminescence (CL) images, and U–Pb dates, as well as whole-rock geochemical data for these rocks, in order to constrain their formation age and petrogenesis, and understand the geodynamic setting. Conspicuously, the Arbasay Formation shows typical basalt–andesite–dacite–rhyolite volcanic series, and is dominated by andesites with a small amount of basalts and rhyolites based on the geological profile. U–Pb isotopic dating using the LA-ICP-MS method on zircons reveals that the volcanic rocks in the Arbasay Formation formed at 308–305 Ma, that is, late Carboniferous, rather than early Permian as previously proposed. Geochemically, the volcanic rocks mainly belong to the calc-alkaline series and have arc-like geochemical compositions. They are enriched in LREEs ((La/Yb)<sub>N</sub> = 2.9–7.5) and LILEs (K, Rb, Ba) and depleted in HFSEs (Nb, Ta, Ti). In the tectonic discrimination diagrams, the basalts mainly fall into the area of continental arc. Given our U–Pb dating results, geochemical characteristics, and the regional geological framework, we propose that the late Carboniferous volcanic rocks originated from the arc-related setting, not the intracontinental rift-related setting. They are possibly the major constituents of a continental arc that is formed with the southward subduction of the North Tianshan Oceanic lithosphere.
DOI: 10.6084/m9.figshare.3407962.v1
title: Geochronology and geochemistry of volcanic rocks in the Arbasay Formation, Xinjiang Province (Northwest China): implications for the tectonic evolution of the North Tianshan

description: The extensively exposed late Carboniferous volcanic and volcaniclastic successions along the northern margin of the North Tianshan are called the Arbasay Formation. We present field-based mapping, petrography, zircon cathodoluminescence (CL) images, and U–Pb dates, as well as whole-rock geochemical data for these rocks, in order to constrain their formation age and petrogenesis, and understand the geodynamic setting. Conspicuously, the Arbasay Formation shows typical basalt–andesite–dacite–rhyolite volcanic series, and is dominated by andesites with a small amount of basalts and rhyolites based on the geological profile. U–Pb isotopic dating using the LA-ICP-MS method on zircons reveals that the volcanic rocks in the Arbasay Formation formed at 308–305 Ma, that is, late Carboniferous, rather than early Permian as previously proposed. Geochemically, the volcanic rocks mainly belong to the calc-alkaline series and have arc-like geochemical compositions. They are enriched in LREEs ((La/Yb)<sub>N</sub> = 2.9–7.5) and LILEs (K, Rb, Ba) and depleted in HFSEs (Nb, Ta, Ti). In the tectonic discrimination diagrams, the basalts mainly fall into the area of continental arc. Given our U–Pb dating results, geochemical characteristics, and the regional geological framework, we propose that the late Carboniferous volcanic rocks originated from the arc-related setting, not the intracontinental rift-related setting. They are possibly the major constituents of a continental arc that is formed with the southward subduction of the North Tianshan Oceanic lithosphere.
DOI: 10.6084/m9.figshare.3407959
title: Test of a spreading-ridge subduction model for the origin of granitoid plutons and metavolcanic complexes in the Palaeoproterozoic Pinal forearc/subduction complex of Southern Arizona, USA

description: The Pinal terrane of southern Arizona has been characterized as a Palaeoproterozoic forearc/subduction complex (Meijer 2014). It contains granitoid plutons and metavolcanic rocks with arc affinities that have a spatial distribution reminiscent of plutons and volcanic rocks that intruded into and erupted onto the early Cenozoic forearc/subduction complex of south-central Alaska (i.e. Chugach–Prince William terrane). The magmatic rocks that intruded into and erupted onto the Alaskan forearc/subduction complex are believed to have been produced largely as a result of a spreading-ridge subduction event (SRSE) during the early Cenozoic (Bradley et al. 2003). A characteristic of these rocks is that they were emplaced in a relatively short interval of time (10–30 million years) between the arc and associated trench. In the Pinal forearc/subduction complex of southern Arizona, there are numerous plutons and several metavolcanic complexes with arc affinities scattered over a distance of approximately 300 km perpendicular to the NE–SW Palaeoproterozoic orogenic trend. If these magmatic rocks are the result of an SRSE, they should have similar emplacement ages. New zircon age data for 16 samples from metavolcanic units and granitoid plutons in the Pinal forearc/subduction complex collected over a distance of 250 km perpendicular to the orogenic trend show a narrow range of emplacement ages that average 1650 ± 20 million years. The restricted age range and the spatial distribution of the plutons and metavolcanic rocks within this forearc/subduction complex are consistent with them having originated as a result of a Palaeoproterozoic SRSE.
DOI: 10.6084/m9.figshare.3407959.v2
title: Test of a spreading-ridge subduction model for the origin of granitoid plutons and metavolcanic complexes in the Palaeoproterozoic Pinal forearc/subduction complex of Southern Arizona, USA

description: The Pinal terrane of southern Arizona has been characterized as a Palaeoproterozoic forearc/subduction complex (Meijer 2014). It contains granitoid plutons and metavolcanic rocks with arc affinities that have a spatial distribution reminiscent of plutons and volcanic rocks that intruded into and erupted onto the early Cenozoic forearc/subduction complex of south-central Alaska (i.e. Chugach–Prince William terrane). The magmatic rocks that intruded into and erupted onto the Alaskan forearc/subduction complex are believed to have been produced largely as a result of a spreading-ridge subduction event (SRSE) during the early Cenozoic (Bradley et al. 2003). A characteristic of these rocks is that they were emplaced in a relatively short interval of time (10–30 million years) between the arc and associated trench. In the Pinal forearc/subduction complex of southern Arizona, there are numerous plutons and several metavolcanic complexes with arc affinities scattered over a distance of approximately 300 km perpendicular to the NE–SW Palaeoproterozoic orogenic trend. If these magmatic rocks are the result of an SRSE, they should have similar emplacement ages. New zircon age data for 16 samples from metavolcanic units and granitoid plutons in the Pinal forearc/subduction complex collected over a distance of 250 km perpendicular to the orogenic trend show a narrow range of emplacement ages that average 1650 ± 20 million years. The restricted age range and the spatial distribution of the plutons and metavolcanic rocks within this forearc/subduction complex are consistent with them having originated as a result of a Palaeoproterozoic SRSE.
DOI: 10.6084/m9.figshare.3407959.v1
title: Test of a <b>s</b>preading-<b>r</b>idge <b>s</b>ubduction <b>m</b>odel for the <b>o</b>rigin of <b>g</b>ranitoid <b>p</b>lutons and <b>m</b>etavolcanic <b>c</b>omplexes in the Pal<b>a</b>eoproterozoic Pinal <b>f</b>orearc/<b>s</b>ubduction <b>c</b>omplex of Southern Arizona, USA

description: The Pinal terrane of southern Arizona has been characterized as a Palaeoproterozoic forearc/subduction complex (Meijer 2014). It contains granitoid plutons and metavolcanic rocks with arc affinities that have a spatial distribution reminiscent of plutons and volcanic rocks that intruded into and erupted onto the early Cenozoic forearc/subduction complex of south-central Alaska (i.e. Chugach–Prince William terrane). The magmatic rocks that intruded into and erupted onto the Alaskan forearc/subduction complex are believed to have been produced largely as a result of a spreading-ridge subduction event (SRSE) during the early Cenozoic (Bradley et al. 2003). A characteristic of these rocks is that they were emplaced in a relatively short interval of time (10–30 million years) between the arc and associated trench. In the Pinal forearc/subduction complex of southern Arizona, there are numerous plutons and several metavolcanic complexes with arc affinities scattered over a distance of approximately 300 km perpendicular to the NE–SW Palaeoproterozoic orogenic trend. If these magmatic rocks are the result of an SRSE, they should have similar emplacement ages. New zircon age data for 16 samples from metavolcanic units and granitoid plutons in the Pinal forearc/subduction complex collected over a distance of 250 km perpendicular to the orogenic trend show a narrow range of emplacement ages that average 1650 ± 20 million years. The restricted age range and the spatial distribution of the plutons and metavolcanic rocks within this forearc/subduction complex are consistent with them having originated as a result of a Palaeoproterozoic SRSE.
DOI: 10.6084/m9.figshare.3407953
title: Ethnicity is an independent predictor of IVF-ICSI outcome: a study of 5,549 cycles in Spain and India

description: <i>Aim</i>: To determine the role of ethnicity on IVF/ICSI outcomes between Indian and white Caucasian women. <i>Settings and design</i>: Retrospective cohort study. <i>Materials and methods</i>: White Caucasian and Indian women undergoing IVF/ICSI treatment cycles. Total 5549 self, non-donor, fresh IVF cycles conducted from January 2014 to March 2015, out of which, 4227 were white Caucasian and 1322 were Indian. Data were collected on baseline characteristics, IVF cycle parameters and outcomes. Ongoing pregnancy rate (OPR) was measured as main outcome. <i>Results</i>: Indian women differed significantly from white Caucasian women in baseline characteristics like age (30.6 ± 0.2 versus 37.6 ± 0.1 years; <i>p</i> 2; <i>p</i> p p p p p <i>Conclusions</i>: OPR was significantly lower among Indian ethnic group following IVF/ICSI suggest that ethnicity, like age, is a major and an independent predictor of IVF outcome.
DOI: 10.6084/m9.figshare.3407953.v1
title: Ethnicity is an independent predictor of IVF-ICSI outcome: a study of 5,549 cycles in Spain and India

description: <i>Aim</i>: To determine the role of ethnicity on IVF/ICSI outcomes between Indian and white Caucasian women. <i>Settings and design</i>: Retrospective cohort study. <i>Materials and methods</i>: White Caucasian and Indian women undergoing IVF/ICSI treatment cycles. Total 5549 self, non-donor, fresh IVF cycles conducted from January 2014 to March 2015, out of which, 4227 were white Caucasian and 1322 were Indian. Data were collected on baseline characteristics, IVF cycle parameters and outcomes. Ongoing pregnancy rate (OPR) was measured as main outcome. <i>Results</i>: Indian women differed significantly from white Caucasian women in baseline characteristics like age (30.6 ± 0.2 versus 37.6 ± 0.1 years; <i>p</i> 2; <i>p</i> p p p p p <i>Conclusions</i>: OPR was significantly lower among Indian ethnic group following IVF/ICSI suggest that ethnicity, like age, is a major and an independent predictor of IVF outcome.
DOI: 10.6084/m9.figshare.3407938
title: Effect of Ebola outbreak on tuberculosis care in Conakry, Guinea

description: <b>S1_TBHW_FINAL.rec. </b>This is the database about health workers before and during Ebola Outbreak in Conakry, Guinea, 2014. <b>S2_TB_EVD_PATIENTS_FINAL.dta. </b>This is the database about Tuberculosis patients before and during Ebola Outbreak in Conakry, Guinea, 2014.. <b>S3_TBSTOCK_FINAL.rec. </b>This is the database about stockouts of Tuberculosis drugs before and during Ebola Outbreak in Conakry, Guinea, 2014.. <b>S4_TBPRESUM_FINAL.rec. </b>This is the database about Tuberculosis presumptive cases before and during Ebola Outbreak in Conakry, Guinea, 2014..