cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3118519
title: ABCE1 is essential for S phase progression in human cells

description: ABCE1 is a highly conserved protein universally present in eukaryotes and archaea, which is crucial for the viability of different organisms. First identified as RNase L inhibitor, ABCE1 is currently recognized as an essential translation factor involved in several stages of eukaryotic translation and ribosome biogenesis. The nature of vital functions of ABCE1, however, remains unexplained. Here, we study the role of ABCE1 in human cell proliferation and its possible connection to translation. We show that ABCE1 depletion by siRNA results in a decreased rate of cell growth due to accumulation of cells in S phase, which is accompanied by inefficient DNA synthesis and reduced histone mRNA and protein levels. We infer that in addition to the role in general translation, ABCE1 is involved in histone biosynthesis and DNA replication and therefore is essential for normal S phase progression. In addition, we analyze whether ABCE1 is implicated in transcript-specific translation via its association with the eIF3 complex subunits known to control the synthesis of cell proliferation-related proteins. The expression levels of a few such targets regulated by eIF3A, however, were not consistently affected by ABCE1 depletion.
DOI: 10.6084/m9.figshare.3118528.v1
title: Combining Functional Data Registration and Factor Analysis

description: We extend the definition of functional data registration to encompass a larger class of registration models. In contrast to traditional registration models, we allow for registered functions that have more than one primary direction of variation. The proposed Bayesian hierarchical model simultaneously registers the observed functions and estimates the two primary factors that characterize variation in the registered functions. Each registered function is assumed to be predominantly composed of a linear combination of these two primary factors, and the function-specific weights for each observation are estimated within the registration model. We show how these estimated weights can easily be used to classify functions after registration using both simulated data and a juggling data set.
DOI: 10.6084/m9.figshare.3118519.v1
title: ABCE1 is essential for S phase progression in human cells

description: ABCE1 is a highly conserved protein universally present in eukaryotes and archaea, which is crucial for the viability of different organisms. First identified as RNase L inhibitor, ABCE1 is currently recognized as an essential translation factor involved in several stages of eukaryotic translation and ribosome biogenesis. The nature of vital functions of ABCE1, however, remains unexplained. Here, we study the role of ABCE1 in human cell proliferation and its possible connection to translation. We show that ABCE1 depletion by siRNA results in a decreased rate of cell growth due to accumulation of cells in S phase, which is accompanied by inefficient DNA synthesis and reduced histone mRNA and protein levels. We infer that in addition to the role in general translation, ABCE1 is involved in histone biosynthesis and DNA replication and therefore is essential for normal S phase progression. In addition, we analyze whether ABCE1 is implicated in transcript-specific translation via its association with the eIF3 complex subunits known to control the synthesis of cell proliferation-related proteins. The expression levels of a few such targets regulated by eIF3A, however, were not consistently affected by ABCE1 depletion.
DOI: 10.6084/m9.figshare.3118504
title: Sexual dimorphism in activation of placental autophagy in obese women with evidence for fetal programming from a placenta-specific mouse model

description: The incidence of maternal obesity and its co-morbidities (diabetes, cardiovascular disease) continues to increase at an alarming rate, with major public health implications. In utero exposure to maternal obesity has been associated with development of cardiovascular and metabolic diseases in the offspring as a result of developmental programming. The placenta regulates maternal-fetal metabolism and shows significant changes in its function with maternal obesity. Autophagy is a cell-survival process, which is responsible for the degradation of damaged organelles and misfolded proteins. Here we show an activation of autophagosomal formation and autophagosome-lysosome fusion in placentas of males but not females from overweight (OW) and obese (OB) women vs. normal weight (NW) women. However, total autophagic activity in these placentas appeared to be decreased as it showed an increase in SQSTM1/p62 and a decrease in lysosomal biogenesis. A mouse model with a targeted deletion of the essential autophagy gene <i>Atg7</i> in placental tissue showed significant placental abnormalities comparable to those seen in human placenta with maternal obesity. These included a decrease in expression of mitochondrial genes and antioxidants, and decreased lysosomal biogenesis. Strikingly, the knockout mice were developmentally programmed as they showed an increased sensitivity to high-fat diet-induced obesity, hyperglycemia, hyperinsulinemia, increased adiposity, and cardiac remodeling. In summary, our results indicate a sexual dimorphism in placental autophagy in response to maternal obesity. We also show that autophagy plays an important role in placental function and that inhibition of placental autophagy programs the offspring to obesity, and to metabolic and cardiovascular diseases.
DOI: 10.6084/m9.figshare.3118504.v2
title: Sexual dimorphism in activation of placental autophagy in obese women with evidence for fetal programming from a placenta-specific mouse model

description: The incidence of maternal obesity and its co-morbidities (diabetes, cardiovascular disease) continues to increase at an alarming rate, with major public health implications. In utero exposure to maternal obesity has been associated with development of cardiovascular and metabolic diseases in the offspring as a result of developmental programming. The placenta regulates maternal-fetal metabolism and shows significant changes in its function with maternal obesity. Autophagy is a cell-survival process, which is responsible for the degradation of damaged organelles and misfolded proteins. Here we show an activation of autophagosomal formation and autophagosome-lysosome fusion in placentas of males but not females from overweight (OW) and obese (OB) women vs. normal weight (NW) women. However, total autophagic activity in these placentas appeared to be decreased as it showed an increase in SQSTM1/p62 and a decrease in lysosomal biogenesis. A mouse model with a targeted deletion of the essential autophagy gene <i>Atg7</i> in placental tissue showed significant placental abnormalities comparable to those seen in human placenta with maternal obesity. These included a decrease in expression of mitochondrial genes and antioxidants, and decreased lysosomal biogenesis. Strikingly, the knockout mice were developmentally programmed as they showed an increased sensitivity to high-fat diet-induced obesity, hyperglycemia, hyperinsulinemia, increased adiposity, and cardiac remodeling. In summary, our results indicate a sexual dimorphism in placental autophagy in response to maternal obesity. We also show that autophagy plays an important role in placental function and that inhibition of placental autophagy programs the offspring to obesity, and to metabolic and cardiovascular diseases.
DOI: 10.6084/m9.figshare.3118438
title: Raw data

description: These Excel documents contain raw data of the density and size of herbivores at the artificial structure, Cystoseira surface variation in the field experiments and in the tank experiments and salema feeding choice between Cystoseira and other common macroalgae of the infralittoral fringe.
DOI: 10.6084/m9.figshare.3118456
title: Dataset_Study_2.xlsx

description: Please refer to the following article for details:<br><i>Pro Free Will Priming Enhances "Risk-Taking" Behavior in the Iowa Gambling Task, but not in the Balloon Analogue Risk Task: Two Independent Priming Studies.</i> Yann Schrag, Alessandro Tremea, Cyril Lagger, Noé Ohana, Christine Mohr In press (2016) in PLOS ONE.
DOI: 10.6084/m9.figshare.12918146
title: New radiometric data from the South Maradi Pan-African formations, Southern Niger

description: Supplementary material 4: Raw data of Dan Issa Migmatite U-Pb
DOI: 10.6084/m9.figshare.3118414
title: Dataset_Study_1.xlsx

description: See article in PLOS ONE, in press (2016):<i>"Pro Free Will Priming Enhances “Risk-Taking” Behavior in the Iowa Gambling Task, but not in the Balloon Analogue Risk Task: Two Independent Priming Studies."</i> Yann Schrag, Alessandro Tremea, Cyril Lagger, Noé Ohana, Christine Mohr
DOI: 10.6084/m9.figshare.12918146.v1
title: New radiometric data from the South Maradi Pan-African formations, Southern Niger

description: Supplementary material 4: Raw data of Dan Issa Migmatite U-Pb
DOI: 10.6084/m9.figshare.3118438.v2
title: Raw data

description: These Excel documents contain raw data of the density and size of herbivores at the artificial structure, Cystoseira surface variation in the field experiments and in the tank experiments and salema feeding choice between Cystoseira and other common macroalgae of the infralittoral fringe.
DOI: 10.6084/m9.figshare.3118414.v1
title: Dataset_Study_1.xlsx

description: See article in PLOS ONE, in press (2016):<i>"Pro Free Will Priming Enhances “Risk-Taking” Behavior in the Iowa Gambling Task, but not in the Balloon Analogue Risk Task: Two Independent Priming Studies."</i> Yann Schrag, Alessandro Tremea, Cyril Lagger, Noé Ohana, Christine Mohr
DOI: 10.6084/m9.figshare.12918155
title: New radiometric data from the South Maradi Pan-African formations, Southern Niger

description: Supplementary material 5: Raw data of Maraka schist U-Pb
DOI: 10.6084/m9.figshare.12918155.v1
title: New radiometric data from the South Maradi Pan-African formations, Southern Niger

description: Supplementary material 5: Raw data of Maraka schist U-Pb
DOI: 10.6084/m9.figshare.3118438.v1
title: Raw data

description: These Excel documents contain raw data of the density and size of herbivores at the artificial structure, Cystoseira surface variation in the field experiments and in the tank experiments and salema feeding choice between Cystoseira and other common macroalgae of the infralittoral fringe.
DOI: 10.6084/m9.figshare.3118162
title: North American Hutterite Colonies: Geospatial Layers

description: This dataset contains two geospatial files of the Hutterite colonies in North America: a Google Earth kml file and a zipped shapefile. <br>
DOI: 10.6084/m9.figshare.3118144
title: Relationship between QT interval length and arterial stiffness in systemic lupus erythematosus (SLE): a cross-sectional case-control study

description: SPSS file containing all the clinical, analitical and complementary variables
DOI: 10.6084/m9.figshare.3118144.v1
title: Relationship between QT interval length and arterial stiffness in systemic lupus erythematosus (SLE): a cross-sectional case-control study

description: SPSS file containing all the clinical, analitical and complementary variables
DOI: 10.6084/m9.figshare.3117958
title: Physical and social factors determining quality of life for veterans with lower-limb amputation(s): a systematic review

description: <b>Purpose:</b> Most veterans live for many years after their war-related traumatic lower-limb amputation, which is why understanding which factors influence health-related quality of life (HRQoL) remains important to their long-term management. The objective of this study was to perform a review of the literature to summarize any evidence on the physical and social determinants for HRQoL in veterans with uni- or bilateral lower-limb amputation(s). <b>Method:</b> MEDLINE, EMBASE, PEDro, CINAHL, Scopus and Cochrane databases were searched systematically for eligible studies. Inclusion criteria were: traumatic lower-limb amputation(s), HRQoL outcome and veterans. Physical and social factors that influence HRQoL were extracted. <b>Results:</b> The literature search identified 2073 citations, leading to the inclusion of 10 studies in the systematic review. Physical activity level, sport participation, level of amputation, back pain, years of education, as well as duration and severity of phantom pain were found to be determining factors for HRQoL among veterans with lower-limb amputation. <b>Conclusions:</b> The identified physical and social determinants were similar to those found in civilian traumatic amputees. More high quality research designs, interventions and complex statistical analyses are warranted to identify the physical and social factors that influence the HRQoL of veteran amputees. Implications for RehabilitationRehabilitation staff should promote physical activity and participation in sport among veterans with lower-limb amputation(s).Level of amputation, back pain severity, years of education, duration of phantom pain and severity of phantom pain have been found to be determining factors for HRQoL and should be taken into consideration when planning rehabilitation programs for veterans with lower-limb amputations. Rehabilitation staff should promote physical activity and participation in sport among veterans with lower-limb amputation(s). Level of amputation, back pain severity, years of education, duration of phantom pain and severity of phantom pain have been found to be determining factors for HRQoL and should be taken into consideration when planning rehabilitation programs for veterans with lower-limb amputations.
DOI: 10.6084/m9.figshare.3117937
title: Data & Code

description: Data and code for paper "The 52 different symptoms of major depression: lack of content overlap among seven common depression scales"
DOI: 10.6084/m9.figshare.3117940
title: Unravelling cryptic species of freshwater snails (Caenogastropoda, Truncatelloidea) in the Loa River basin, Atacama Desert

description: Species recognition in freshwater snails of the genus <i>Heleobia</i> Stimpson, 1865 in the Loa River basin is a difficult task to perform because these snails are similar in shell morphology. In this complex hydrological network, the genus comprises two endemic species, but the taxonomic status of other previously undescribed sympatric and allopatric populations is uncertain. Here we examined DNA sequences from cytochrome c oxidase subunit I (COI) gene and morphological data to investigate species boundaries along the system. Phylogenetic trees were inferred using maximum parsimony, neighbour joining, maximum likelihood and Bayesian inference methods based on samples ranging from the outlet of the Loa River on the Pacific coast to more than 4,200 m altitude in the Andes. Although not always well supported, four clades were consistently recovered in the phylogenies, one corresponding to <i>Heleobia loaensis</i> (Biese, 1947), another to <i>Heleobia opachensis</i> (Biese, 1947), and two more additional cryptic lineages. Additionally, a fifth cluster of sequences not recovered in these analyses was inferred in the BEAST analysis. Outline-based geometric morphometrics of the shell was useful to differentiate a single lineage sustaining that typological discrimination in <i>Heleobia</i> is challenging. Our results also indicate that all lineages diverged by independent non-adaptive allopatric processes during the Middle Pleistocene.
DOI: 10.6084/m9.figshare.3117937.v1
title: Data & Code

description: Data and code for paper "The 52 different symptoms of major depression: lack of content overlap among seven common depression scales"
DOI: 10.6084/m9.figshare.3117940.v1
title: Unravelling cryptic species of freshwater snails (Caenogastropoda, Truncatelloidea) in the Loa River basin, Atacama Desert

description: Species recognition in freshwater snails of the genus <i>Heleobia</i> Stimpson, 1865 in the Loa River basin is a difficult task to perform because these snails are similar in shell morphology. In this complex hydrological network, the genus comprises two endemic species, but the taxonomic status of other previously undescribed sympatric and allopatric populations is uncertain. Here we examined DNA sequences from cytochrome c oxidase subunit I (COI) gene and morphological data to investigate species boundaries along the system. Phylogenetic trees were inferred using maximum parsimony, neighbour joining, maximum likelihood and Bayesian inference methods based on samples ranging from the outlet of the Loa River on the Pacific coast to more than 4,200 m altitude in the Andes. Although not always well supported, four clades were consistently recovered in the phylogenies, one corresponding to <i>Heleobia loaensis</i> (Biese, 1947), another to <i>Heleobia opachensis</i> (Biese, 1947), and two more additional cryptic lineages. Additionally, a fifth cluster of sequences not recovered in these analyses was inferred in the BEAST analysis. Outline-based geometric morphometrics of the shell was useful to differentiate a single lineage sustaining that typological discrimination in <i>Heleobia</i> is challenging. Our results also indicate that all lineages diverged by independent non-adaptive allopatric processes during the Middle Pleistocene.
DOI: 10.6084/m9.figshare.3117958.v1
title: Physical and social factors determining quality of life for veterans with lower-limb amputation(s): a systematic review

description: <b>Purpose:</b> Most veterans live for many years after their war-related traumatic lower-limb amputation, which is why understanding which factors influence health-related quality of life (HRQoL) remains important to their long-term management. The objective of this study was to perform a review of the literature to summarize any evidence on the physical and social determinants for HRQoL in veterans with uni- or bilateral lower-limb amputation(s). <b>Method:</b> MEDLINE, EMBASE, PEDro, CINAHL, Scopus and Cochrane databases were searched systematically for eligible studies. Inclusion criteria were: traumatic lower-limb amputation(s), HRQoL outcome and veterans. Physical and social factors that influence HRQoL were extracted. <b>Results:</b> The literature search identified 2073 citations, leading to the inclusion of 10 studies in the systematic review. Physical activity level, sport participation, level of amputation, back pain, years of education, as well as duration and severity of phantom pain were found to be determining factors for HRQoL among veterans with lower-limb amputation. <b>Conclusions:</b> The identified physical and social determinants were similar to those found in civilian traumatic amputees. More high quality research designs, interventions and complex statistical analyses are warranted to identify the physical and social factors that influence the HRQoL of veteran amputees. Implications for RehabilitationRehabilitation staff should promote physical activity and participation in sport among veterans with lower-limb amputation(s).Level of amputation, back pain severity, years of education, duration of phantom pain and severity of phantom pain have been found to be determining factors for HRQoL and should be taken into consideration when planning rehabilitation programs for veterans with lower-limb amputations. Rehabilitation staff should promote physical activity and participation in sport among veterans with lower-limb amputation(s). Level of amputation, back pain severity, years of education, duration of phantom pain and severity of phantom pain have been found to be determining factors for HRQoL and should be taken into consideration when planning rehabilitation programs for veterans with lower-limb amputations.
DOI: 10.6084/m9.figshare.3117796
title: DATA-PLOS-ONE.zip

description: PLOS Submission: "Analysis of Subjects' Inexperience in a Touch Screen Game: An Affective Computing Approach", Payam Parsinejad and Rifat Sipahi.<br>The folder contains the data recorded for 3 experiments (Data Sets 1--3). In Experiment 1, Data Set 1, 13 subjects, and in Data Sets 2--3, 12 subjects participated.<br><br>--bvp_data/: the blood volume pulse recoded using HR sensor for each subject participated in experiments.<br>-- sc_data/: the skin conductance recoded using SC sensor for each subject participated in experiments.--nasa_tlx_and_performance_metric.xlsx: NASA-TLX questionnaire, and subjects performance metrics (trajectory assignment)<br>IRB 11-11-19 (Northeastern University, Boston, MA)
DOI: 10.6084/m9.figshare.3117796.v1
title: DATA-PLOS-ONE.zip

description: PLOS Submission: "Analysis of Subjects' Inexperience in a Touch Screen Game: An Affective Computing Approach", Payam Parsinejad and Rifat Sipahi.<br>The folder contains the data recorded for 3 experiments (Data Sets 1--3). In Experiment 1, Data Set 1, 13 subjects, and in Data Sets 2--3, 12 subjects participated.<br><br>--bvp_data/: the blood volume pulse recoded using HR sensor for each subject participated in experiments.<br>-- sc_data/: the skin conductance recoded using SC sensor for each subject participated in experiments.--nasa_tlx_and_performance_metric.xlsx: NASA-TLX questionnaire, and subjects performance metrics (trajectory assignment)<br>IRB 11-11-19 (Northeastern University, Boston, MA)
DOI: 10.6084/m9.figshare.3117757
title: Insights into membrane translocation of the cell-penetrating peptide pVEC from molecular dynamics calculations

description: Discovery of cargo carrying cell-penetrating peptides has opened a new gate in the development of peptide-based drugs that can effectively target intracellular enzymes. Success in application and development of cell-penetrating peptides in drug design depends on understanding their translocation mechanisms. In this study, our aim was to examine the bacterial translocation mechanism of the cell-penetrating pVEC peptide (LLIILRRRIRKQAHAHSK) using steered molecular dynamics (SMD) simulations. The significance of specific residues or regions for translocation was studied by performing SMD simulations on the alanine mutants and other variants of pVEC. Residue-based analysis showed that positively charged residues contribute to adsorption to the lipid bilayer and to electrostatic interactions with the lipid bilayer as peptides are translocated. Translocation takes place in three main stages; the insertion of the N-terminus into the bilayer, the inclusion of the whole peptide inside the membrane and the exit of the N-terminus from the bilayer. These three stages mirror the three regions on pVEC; namely, the hydrophobic N-terminus, the cationic midsection, and the hydrophilic C-terminus. The N-terminal truncated pVEC, I3A, L5A, R7A mutants and scramble-pVEC make weaker interactions with the lipids during translocation highlighting the contribution of the N-terminal residues and the sequence of the structural regions to the translocation mechanism. This study provides atomistic detail about the mechanism of pVEC peptide translocation and can guide future peptide-based drug design efforts.