cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8332643
title: Extracts of bilberry (<i>Vaccinium myrtillus</i> L.) fruits improve liver steatosis and injury in mice by preventing lipid accumulation and cell death

description: Bilberry has been reported to have anti-oxidant and anti-inflammatory properties. We studied the effect of bilberry (<i>Vaccinium myrtillus</i> L.) fruits extracts (BEs) on the pathogenesis caused by lipid accumulation in fatty liver and non-alcoholic steatohepatitis (NASH). 5 μg/ml of BEs was enough to suppress lipid accumulation in the fatty liver model of the mouse hepatic AML12 cells. BEs increased cell viability and anti-oxidant capacity, presumably by activating (phosphorylating) Akt/STAT3 and inducing MnSOD/catalase. BEs also significantly reduced Rubicon and induced p62/SQSTM1, possibly contributing to reduce cellular lipids (lipophagy). When the mice were fed supplemented with BEs (5% or 10%, w/w), hepatic steatosis, injury, and hypercholesterolemia/hyperglycemia were significantly improved. Furthermore, histological and cytokine studies indicated that BEs possibly suppress hepatic inflammation (hepatitis) and fibrosis. Therefore, BEs improved liver steatosis and injury, and potentially suppress fibrosis by suppressing inflammatory response, which therefore may prevent the progression of fatty liver to NASH. Bilberry fruits extracts suppressed hepatocyte injury caused by early fat accumulation. Therefore, bilberry is expected to be a liver-friendly food.
DOI: 10.25375/uct.8332652.v1
title: Impact of nanoparticle-support interactions in co3o4/al2o3 catalysts for the preferential oxidation of carbon monoxide: Raw data for Nyathi et al., ACS Catal., 2019 (10.1021/acscatal.9b00685)

description: Impact of nanoparticle-support interactions in co3o4/al2o3 catalysts for the preferential oxidation of carbon monoxide. Raw data related to an article by Nyathi <i>et al</i>., <i>ACS Catal.</i>, 2019 (10.1021/acscatal.9b00685) for public access which can potentially be used, for example, for re-plotting of certain figures for inclusion in journal review articles or any other ethical research purposes. Note the data can be re-published with special permission from the American Chemical Society.
DOI: 10.6084/m9.figshare.8332643.v1
title: Extracts of bilberry (<i>Vaccinium myrtillus</i> L.) fruits improve liver steatosis and injury in mice by preventing lipid accumulation and cell death

description: Bilberry has been reported to have anti-oxidant and anti-inflammatory properties. We studied the effect of bilberry (<i>Vaccinium myrtillus</i> L.) fruits extracts (BEs) on the pathogenesis caused by lipid accumulation in fatty liver and non-alcoholic steatohepatitis (NASH). 5 μg/ml of BEs was enough to suppress lipid accumulation in the fatty liver model of the mouse hepatic AML12 cells. BEs increased cell viability and anti-oxidant capacity, presumably by activating (phosphorylating) Akt/STAT3 and inducing MnSOD/catalase. BEs also significantly reduced Rubicon and induced p62/SQSTM1, possibly contributing to reduce cellular lipids (lipophagy). When the mice were fed supplemented with BEs (5% or 10%, w/w), hepatic steatosis, injury, and hypercholesterolemia/hyperglycemia were significantly improved. Furthermore, histological and cytokine studies indicated that BEs possibly suppress hepatic inflammation (hepatitis) and fibrosis. Therefore, BEs improved liver steatosis and injury, and potentially suppress fibrosis by suppressing inflammatory response, which therefore may prevent the progression of fatty liver to NASH. Bilberry fruits extracts suppressed hepatocyte injury caused by early fat accumulation. Therefore, bilberry is expected to be a liver-friendly food.
DOI: 10.7483/opendata.cms.xbtd.nkd3
title: /SingleMu/Run2011B-12Oct2013-v1/AOD
DOI: 10.6084/m9.figshare.8332613
title: Source data used to create graphs

description: these tables were used to create graphs regarding aiptasia response to heat stress and relationship between gene expression to gene accessibility.
DOI: 10.6084/m9.figshare.8332586
title: pipeline_config_rsfc_weight_loss.yml

description: The Configurable Pipeline for the Analysis of <em>Connectomes</em> (C-PAC) pipeline configuration file depicting the preprocessing procedure.<br>
DOI: 10.6084/m9.figshare.8332586.v1
title: pipeline_config_rsfc_weight_loss.yml

description: The Configurable Pipeline for the Analysis of <em>Connectomes</em> (C-PAC) pipeline configuration file depicting the preprocessing procedure.<br>
DOI: 10.6084/m9.figshare.8332613.v2
title: Source data used to create graphs

description: these tables were used to create graphs regarding aiptasia response to heat stress and relationship between gene expression to gene accessibility.
DOI: 10.6084/m9.figshare.8332613.v1
title: Source data used to create graphs

description: these tables were used to create graphs regarding aiptasia response to heat stress and relationship between gene expression to gene accessibility.
DOI: 10.6084/m9.figshare.8332481
title: Serum osteocalcin predicts HTO-ROD in KTRs

description: <b>Serum osteocalcin predicts HTO-ROD in KTRs</b>
DOI: 10.6084/m9.figshare.8332556
title: The genus <i>Patriarchus</i> Ameghino, 1889 (Mammalia, Notoungulata, Typotheria), from the Santa Cruz Formation, Santa Cruz Province, Argentina

description: In 1889, Florentino Ameghino erected <i>Patriarchus palmidens</i>, based on a specimen from a western outcrop of the Santa Cruz Formation (early Miocene) and associated it with the ‘Notohippidian stage’. Later, Ameghino added seven other species to the genus from eastern localities of the same formation. Since 1900, <i>Patriarchus</i> has been considered to be a junior synonym of <i>Protypotherium</i>. Here, we present a systematic revision and recognize the genus <i>Patriarchus</i> as monospecific, with <i>Pa. palmidens</i> characterized by i1–c mesiodistally expanded, labially convex, and similar in size; i1–c with a short lingual sulcus that does not extend to the base of the teeth and ‘V’-shaped in occlusal view; p1 labially and lingually bilobate, with trigonid larger than talonid; and i1–p1 in a continuous series without overlapping. Five of the remaining species are recognized as belonging to <i>Protypotherium</i>. Therefore, <i>Patriarchus</i> is presently monospecific (<i>Pa. palmidens</i>) and restricted to the western region of Santa Cruz Province, particularly to the Río Bote locality. <i>Patriarchus</i> is included for the first time in a cladistic analysis to discover its phylogenetic relationships within the Interatheriidae. It is nested within the most derived Interatheriinae and is recovered as the sister group of the Laventan <i>Miocochilius</i>; this clade is, in turn, the sister group of <i>Cochilius</i> plus <i>Interatherium</i>. These results support the hypothesis that the origin of the Miocene Interatheriines was a single evolutionary event.
DOI: 10.6084/m9.figshare.8332556.v1
title: The genus <i>Patriarchus</i> Ameghino, 1889 (Mammalia, Notoungulata, Typotheria), from the Santa Cruz Formation, Santa Cruz Province, Argentina

description: In 1889, Florentino Ameghino erected <i>Patriarchus palmidens</i>, based on a specimen from a western outcrop of the Santa Cruz Formation (early Miocene) and associated it with the ‘Notohippidian stage’. Later, Ameghino added seven other species to the genus from eastern localities of the same formation. Since 1900, <i>Patriarchus</i> has been considered to be a junior synonym of <i>Protypotherium</i>. Here, we present a systematic revision and recognize the genus <i>Patriarchus</i> as monospecific, with <i>Pa. palmidens</i> characterized by i1–c mesiodistally expanded, labially convex, and similar in size; i1–c with a short lingual sulcus that does not extend to the base of the teeth and ‘V’-shaped in occlusal view; p1 labially and lingually bilobate, with trigonid larger than talonid; and i1–p1 in a continuous series without overlapping. Five of the remaining species are recognized as belonging to <i>Protypotherium</i>. Therefore, <i>Patriarchus</i> is presently monospecific (<i>Pa. palmidens</i>) and restricted to the western region of Santa Cruz Province, particularly to the Río Bote locality. <i>Patriarchus</i> is included for the first time in a cladistic analysis to discover its phylogenetic relationships within the Interatheriidae. It is nested within the most derived Interatheriinae and is recovered as the sister group of the Laventan <i>Miocochilius</i>; this clade is, in turn, the sister group of <i>Cochilius</i> plus <i>Interatherium</i>. These results support the hypothesis that the origin of the Miocene Interatheriines was a single evolutionary event.
DOI: 10.6084/m9.figshare.8332478
title: Can trophectoderm RNA analysis predict human blastocyst competency?

description: A systematic review of the literature showed that trophectoderm biopsy could assist in the selection of healthy embryos for uterine transfer without affecting implantation rates. However, previous studies attempting to establish the relationship between trophectoderm gene expression profiles and implantation competency using either microarrays or RNA sequencing strategies, were not sufficiently optimized to handle the exceptionally low RNA inputs available from biopsied material. In this pilot study, we report that differential gene expression in human trophectoderm biopsies assayed by an ultra-sensitive next generation RNA sequencing strategy could predict blastocyst implantation competence. RNA expression profiles from isolated human trophectoderm cells were analysed with established clinical pregnancy being the primary endpoint. Following RNA sequencing, a total of 47 transcripts were found to be significantly differentially expressed between the trophectoderm cells from successfully implanted (competent) versus unsuccessful (incompetent) blastocysts. Of these, 36 transcripts were significantly down-regulated in the incompetent blastocysts, including Hydroxysteroid 17-Beta Dehydrogenase 1 (<i>HSD17B1</i>) and Cytochrome P450 Family 11 Subfamily A Member 1 (<i>CYP11A1</i>), while the remaining 11 transcripts were significantly up-regulated, including <i>BCL2</i> Antagonist/Killer 1 (<i>BAK1</i>) and KH Domain Containing 1 Pseudogene 1 (<i>KHDC1P1</i>) of which the latter was always detected in the incompetent and absent in all competent blastocysts. Ontological analysis of differentially expressed RNAs revealed pathways involved in steroidogenic processes with high confidence. Novel differentially expressed transcripts were also noted by reference to a de novo sequence assembly. The selection of the blastocyst with the best potential to support full-term pregnancy following single embryo transfer could reduce the need for multiple treatment cycles and embryo transfers. The main limitation was the low sample size (N = 8). Despite this shortcoming, the pilot suggests that trophectoderm biopsy could assist with the selection of healthy embryos for embryo transfer. A larger cohort of samples is needed to confirm these findings. <b>Abbreviations:</b> AMA: advanced maternal age; ART: assisted reproductive technology; CP: clinical pregnancy; DE: differential expression; FDR: false discovery rate; IVF: in vitro fertilization; LD PCR: long distance PCR; qRT-PCR: quantitative real-time PCR; SET: single embryo transfer; TE: trophectoderm
DOI: 10.6084/m9.figshare.8332478.v1
title: Can trophectoderm RNA analysis predict human blastocyst competency?

description: A systematic review of the literature showed that trophectoderm biopsy could assist in the selection of healthy embryos for uterine transfer without affecting implantation rates. However, previous studies attempting to establish the relationship between trophectoderm gene expression profiles and implantation competency using either microarrays or RNA sequencing strategies, were not sufficiently optimized to handle the exceptionally low RNA inputs available from biopsied material. In this pilot study, we report that differential gene expression in human trophectoderm biopsies assayed by an ultra-sensitive next generation RNA sequencing strategy could predict blastocyst implantation competence. RNA expression profiles from isolated human trophectoderm cells were analysed with established clinical pregnancy being the primary endpoint. Following RNA sequencing, a total of 47 transcripts were found to be significantly differentially expressed between the trophectoderm cells from successfully implanted (competent) versus unsuccessful (incompetent) blastocysts. Of these, 36 transcripts were significantly down-regulated in the incompetent blastocysts, including Hydroxysteroid 17-Beta Dehydrogenase 1 (<i>HSD17B1</i>) and Cytochrome P450 Family 11 Subfamily A Member 1 (<i>CYP11A1</i>), while the remaining 11 transcripts were significantly up-regulated, including <i>BCL2</i> Antagonist/Killer 1 (<i>BAK1</i>) and KH Domain Containing 1 Pseudogene 1 (<i>KHDC1P1</i>) of which the latter was always detected in the incompetent and absent in all competent blastocysts. Ontological analysis of differentially expressed RNAs revealed pathways involved in steroidogenic processes with high confidence. Novel differentially expressed transcripts were also noted by reference to a de novo sequence assembly. The selection of the blastocyst with the best potential to support full-term pregnancy following single embryo transfer could reduce the need for multiple treatment cycles and embryo transfers. The main limitation was the low sample size (N = 8). Despite this shortcoming, the pilot suggests that trophectoderm biopsy could assist with the selection of healthy embryos for embryo transfer. A larger cohort of samples is needed to confirm these findings. <b>Abbreviations:</b> AMA: advanced maternal age; ART: assisted reproductive technology; CP: clinical pregnancy; DE: differential expression; FDR: false discovery rate; IVF: in vitro fertilization; LD PCR: long distance PCR; qRT-PCR: quantitative real-time PCR; SET: single embryo transfer; TE: trophectoderm
DOI: 10.6084/m9.figshare.8332481.v1
title: NTX-ROD statistics.xls

description: <b>Serum osteocalcin in KTRs with HTO</b>
DOI: 10.7483/opendata.cms.cjyu.omf5
title: /Tau/Run2011B-12Oct2013-v1/AOD
DOI: 10.6084/m9.figshare.8332481.v3
title: Renal osteodystrophy and biomarkers in KTX

description: <b>Serum osteocalcin predicts HTO-ROD in KTRs</b>
DOI: 10.25375/uct.8332436
title: RSOS Response time of an avian prey to a simulated hawk attack is slower in darker conditions, but is independent of hawk colour morph

description: Manuscript published in the Royal Society Open Science:<br>Nebel, C., Sumasgutner, P., Pajot, A. and Amar A. Response times of an avian prey to a simulated hawk attack is slower in darker conditions, but is independent of hawk colour morph<br>Abstract:To avoid predation, many species rely on vision to detect predators and initiate an escape response. The ability to detect predators may be lower in darker light conditions or with darker backgrounds. For birds, however, this has never been experimentally tested. We test the hypothesis that the response time of avian prey (feral pigeon <i>Columbia livia f. domestica</i>) to a simulated hawk attack (taxidermy mounted colour-polymorphic black sparrowhawk <i>Accipiter melanoleucus</i>) will differ depending on light levels or background colour. We predict that response will be slower under darker conditions, which would translate into higher predation risk. The speed of response of prey in relation to light level or background colour may also interact with the colour of the predator, and this idea underpins a key hypothesis proposed for the maintenance of different colour morphs in polymorphic raptors. We therefore test whether speed of reaction is influenced by the morph of the hawk (dark/light) in combination with light conditions (dull/bright), or background colours (black/white). We predict slowest responses to morphs under conditions that less contrast with the plumage of the hawk (e.g. light morph under bright light or white background). In support of our first hypothesis, pigeons reacted slower under duller light and with a black background. However, we found no support for the second hypothesis, with response times observed between the hawk morphs being irrespective of light levels or background colour. Our findings experimentally confirm that birds detect avian predators less efficiently under darker conditions. These conditions, for example, might occur during early mornings or in dense forests, which could lead to changes in anti-predator behaviours. However, our results provide no support that different morphs may be maintained in a population due to differential selective advantages linked to improved hunting efficiencies in different conditions due to crypsis.
DOI: 10.25375/uct.8332436.v2
title: RSOS Response time of an avian prey to a simulated hawk attack is slower in darker conditions, but is independent of hawk colour morph

description: Manuscript published in the Royal Society Open Science:<br>Nebel, C., Sumasgutner, P., Pajot, A. and Amar A. Response times of an avian prey to a simulated hawk attack is slower in darker conditions, but is independent of hawk colour morph<br>Abstract:To avoid predation, many species rely on vision to detect predators and initiate an escape response. The ability to detect predators may be lower in darker light conditions or with darker backgrounds. For birds, however, this has never been experimentally tested. We test the hypothesis that the response time of avian prey (feral pigeon <i>Columbia livia f. domestica</i>) to a simulated hawk attack (taxidermy mounted colour-polymorphic black sparrowhawk <i>Accipiter melanoleucus</i>) will differ depending on light levels or background colour. We predict that response will be slower under darker conditions, which would translate into higher predation risk. The speed of response of prey in relation to light level or background colour may also interact with the colour of the predator, and this idea underpins a key hypothesis proposed for the maintenance of different colour morphs in polymorphic raptors. We therefore test whether speed of reaction is influenced by the morph of the hawk (dark/light) in combination with light conditions (dull/bright), or background colours (black/white). We predict slowest responses to morphs under conditions that less contrast with the plumage of the hawk (e.g. light morph under bright light or white background). In support of our first hypothesis, pigeons reacted slower under duller light and with a black background. However, we found no support for the second hypothesis, with response times observed between the hawk morphs being irrespective of light levels or background colour. Our findings experimentally confirm that birds detect avian predators less efficiently under darker conditions. These conditions, for example, might occur during early mornings or in dense forests, which could lead to changes in anti-predator behaviours. However, our results provide no support that different morphs may be maintained in a population due to differential selective advantages linked to improved hunting efficiencies in different conditions due to crypsis.
DOI: 10.6084/m9.figshare.8332430
title: Supplementary Material for: Heart Rate Monitoring in Newborn Babies: A Systematic Review

description: <b><i>Background:</i></b> Around 10% of newborn infants require assistance during transition after birth. Heart rate (HR) is the most important clinical indicator to evaluate the clinical status of a newborn. <b><i>Aim:</i></b> Our study aimed to review all established and novel methods to detect HR in babies giving special consideration to non-invasive techniques. <b><i>Methods:</i></b> We performed a systematic literature search on the following databases: MEDLINE, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), and CINAHL. The inclusion criteria were studies on methods to detect HR in both term and preterm infants in comparison to one of the current gold standards: pulse oximetry (PO) or electrocardiography (ECG) published in the last 15 years. Two independent reviewers screened titles and abstracts for eligibility. Data extracted in an Excel table were analysed to produce a narrative review structured around the type of monitoring, identified obstacles in use, as well as methods to overcome these limitations. <b><i>Results:</i></b> The search revealed 649 studies after duplicates were removed. Full article analysis was performed on 26 studies of which 25 met the inclusion criteria. Well established methods such as auscultation and palpation, although rapid and easily available, have been shown to be inaccurate. ECG and PO were both more precise but the delay in obtaining a reliable HR signal from birth often exceeded 1–2 min. Novel sensors offered the advantages of minimally obtrusive technologies but have limitations mainly due to movement artefact, bad sensor coupling, intermittent measurement, and poor-quality recordings. <b><i>Conclusions:</i></b> The limitations of existing methods have a potential impact on short- and long-term morbidity and mortality outcomes. The development of a technological solution to determine HR accurately and quickly in babies at birth has immense implications for further research and can guide interventions, such as placental transfusion and resuscitation.
DOI: 10.6084/m9.figshare.8332481.v4
title: Renal osteodystrophy and biomarkers in KTX

description: <b>Serum osteocalcin predicts HTO-ROD in KTRs</b>
DOI: 10.25375/uct.8332436.v1
title: RSOS_reaction time_pigeon_pulley experiment

description: Manuscript published in the Royal Society Open Science:<br>Nebel, C., Sumasgutner, P., Pajot, A. and Amar A. Response times of an avian prey to a simulated hawk attack is slower in darker conditions, but is independent of hawk colour morph<br>Abstract:To avoid predation, many species rely on vision to detect predators and initiate an escape response. The ability to detect predators may be lower in darker light conditions or with darker backgrounds. For birds, however, this has never been experimentally tested. We test the hypothesis that the response time of avian prey (feral pigeon <i>Columbia livia f. domestica</i>) to a simulated hawk attack (taxidermy mounted colour-polymorphic black sparrowhawk <i>Accipiter melanoleucus</i>) will differ depending on light levels or background colour. We predict that response will be slower under darker conditions, which would translate into higher predation risk. The speed of response of prey in relation to light level or background colour may also interact with the colour of the predator, and this idea underpins a key hypothesis proposed for the maintenance of different colour morphs in polymorphic raptors. We therefore test whether speed of reaction is influenced by the morph of the hawk (dark/light) in combination with light conditions (dull/bright), or background colours (black/white). We predict slowest responses to morphs under conditions that less contrast with the plumage of the hawk (e.g. light morph under bright light or white background). In support of our first hypothesis, pigeons reacted slower under duller light and with a black background. However, we found no support for the second hypothesis, with response times observed between the hawk morphs being irrespective of light levels or background colour. Our findings experimentally confirm that birds detect avian predators less efficiently under darker conditions. These conditions, for example, might occur during early mornings or in dense forests, which could lead to changes in anti-predator behaviours. However, our results provide no support that different morphs may be maintained in a population due to differential selective advantages linked to improved hunting efficiencies in different conditions due to crypsis.
DOI: 10.6084/m9.figshare.8332481.v5
title: Renal osteodystrophy and biomarkers in KTX

description: <b>Serum osteocalcin predicts HTO-ROD in KTRs</b>
DOI: 10.7483/opendata.cms.0kti.pbpi
title: /TauPlusX/Run2011B-12Oct2013-v1/AOD