cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7117544.v1
title: Thy1-jRGECO1a transgenic mouse lines confocal microscopy data

description: <b><i>Thy1 </i></b><b>transgenic mice expressing the red fluorescent calcium indicator jRGECO1a for neuronal population imaging <i>in vivo</i></b> Hod Dana<sup>1,2</sup>, Ondrej Novak<sup>1,3</sup>, Michael Guardado-Montesino<sup>1</sup>, James W. Fransen<sup>4</sup>Amy Hu<sup>1</sup>, Bart G. Borghuis<sup>4</sup>, Caiying Guo<sup>1</sup>, Douglas S. Kim<sup>1</sup>, Karel Svoboda<sup>1</sup> <sup>1 </sup><em>Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA </em><em><sup>2 </sup></em><em>Present address: Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH </em><em><sup>3 </sup></em><em>Department of Auditory Neuroscience, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic</em><sup>4 </sup>Department of Anatomical Sciences and Neurobiology, University of Louisville School of Medicine, Louisville, KY<em> </em><em> </em><em>Supplementary Images:</em><em>High-resolution confocal images for mouse lines GP8.20, GP8.31, GP8.58, GP8.62.</em>For details see Dana et al Plos One, 2018
DOI: 10.6084/m9.figshare.7117628.v3
title: Observations on Random Sampling Reduction Algorithms

description: Abstract:Development of efficient solvers of the (approximated) shortest vector problem over lattices is an important research area because the security of lattice-based schemes is based on the hardness of the shortest vector problem. Random sampling reduction is an approach to construct efficient solvers of the shortest vector problem by combining lattice basis reduction and sampling of short lattice vectors. In this talk, we show our observations on random sampling reduction algorithms, and recently proposed our probabilistic analysis framework (IACR ePrint 2018/815).<br><br>Note:This is revised version to fix several typos.To make the slide easier to read, three correlation heatmaps are uploaded separately.<br>
DOI: 10.6084/m9.figshare.7117628
title: Observations on Random Sampling Reduction Algorithms

description: Abstract:Development of efficient solvers of the (approximated) shortest vector problem over lattices is an important research area because the security of lattice-based schemes is based on the hardness of the shortest vector problem. (Random) sampling reduction is an approach to construct efficient solvers of the shortest vector problem by combining lattice basis reduction and sampling of short lattice vectors. In this talk, we show our observations on random sampling reduction algorithms, and recently proposed our probabilistic analysis framework (IACR ePrint 2018/815).<br><br>Note:This is revised version to fix several typos.To make the slide easier to read, three correlation heatmaps are uploaded separately.<br>
DOI: 10.6084/m9.figshare.7117463
title: Van Eijk, Boekhoud et al. Supplemental (R1)

description: Supplemental material for a manuscript under revision
DOI: 10.6084/m9.figshare.7117463.v1
title: Van Eijk, Boekhoud et al. Supplemental (R1)

description: Supplemental material for a manuscript under revision
DOI: 10.6084/m9.figshare.7117439
title: Data

description: Mass loss was monitored using a precision weighing balance.Top surface temperature was measured using a thermal (IR) camera.Bottom surface and ambient temperature was monitored using a T-type thermocouple.Relative humidity in the ambient was measured using HIH-3000 Honeywell sensor.IR images were analyzed using a software SMARTVIEW (FLUKE).<br>
DOI: 10.17045/sthlmuni.7117430
title: NrdJm phylogeny

description: <b></b>All NrdJm sequences from NCBI’s RefSeq database were downloaded from RNRdb (http://rnrdb.pfitmap.org) and clustered with USEARCH (Edgar 2010) at 90% sequence identity to reduce redundancy. Non full-length sequences and sequences of dubious quality were manually removed, before aligning all 363 sequences with ProbCons (Do et al. 2005). Trustworthy alignment positions were selected with the BMGE algorithm (Criscuolo and Gribaldo 2010) using the BLOSUM30 substitution matrix, ending up with 363 well-aligned positions forming 350 distinct alignment patterns. RAxML version 8.2.4 (Stamatakis 2014) was used to estimate a phylogeny, using the PROTGAMMAAUTO model, rapid bootstrapping with the autoMRE bootstopping followed by a full maximum likelihood tree search.<br>The file is viewable with Dendroscope (Huson et al. 2007).<br>v2: Addition of Lactobacillus leichmannii sequence.<br>
DOI: 10.17045/sthlmuni.7117430.v2
title: NrdJm phylogeny

description: <b></b>All NrdJm sequences from NCBI’s RefSeq database were downloaded from RNRdb (http://rnrdb.pfitmap.org) and clustered with USEARCH (Edgar 2010) at 90% sequence identity to reduce redundancy. Non full-length sequences and sequences of dubious quality were manually removed, before aligning all 363 sequences with ProbCons (Do et al. 2005). Trustworthy alignment positions were selected with the BMGE algorithm (Criscuolo and Gribaldo 2010) using the BLOSUM30 substitution matrix, ending up with 363 well-aligned positions forming 350 distinct alignment patterns. RAxML version 8.2.4 (Stamatakis 2014) was used to estimate a phylogeny, using the PROTGAMMAAUTO model, rapid bootstrapping with the autoMRE bootstopping followed by a full maximum likelihood tree search.<br>The file is viewable with Dendroscope (Huson et al. 2007).<br>v2: Addition of Lactobacillus leichmannii sequence.<br>
DOI: 10.17045/sthlmuni.7117430.v1
title: NrdJm phylogeny

description: <b></b>All NrdJm sequences from NCBI’s RefSeq database were downloaded from RNRdb (http://rnrdb.pfitmap.org) and clustered with USEARCH (Edgar 2010) at 90% sequence identity to reduce redundancy. Non full-length sequences and sequences of dubious quality were manually removed, before aligning all 363 sequences with ProbCons (Do et al. 2005). Trustworthy alignment positions were selected with the BMGE algorithm (Criscuolo and Gribaldo 2010) using the BLOSUM30 substitution matrix, ending up with 363 well-aligned positions forming 350 distinct alignment patterns. RAxML version 8.2.4 (Stamatakis 2014) was used to estimate a phylogeny, using the PROTGAMMAAUTO model, rapid bootstrapping with the autoMRE bootstopping followed by a full maximum likelihood tree search.<br>The file is viewable with Dendroscope (Huson et al. 2007).<br>
DOI: 10.6084/m9.figshare.7117385.v1
title: Bwt fluctuation_Supplemental Table-JCEM.docx

description: ContextBody-weight fluctuation (weight cycling) has been found to be associated with higher mortality and cardiovascular events in patients with coronary artery disease. However, there are very limited data regarding the relationship between body-weight fluctuation and health-related outcomes in the general population.MethodsWe examined whether body-weight fluctuation can associate incident diabetes mellitus and cardiovascular events, and mortality in a Korean population from the Korean Genome and Epidemiology Study. The intra-individual fluctuations of body weight were calculated by average successive variability (ASV), and health-related outcomes were collected every 2 years for 16 years in 3,678 participants.ResultsParticipants with a high ASV of body weight were more obese and had higher blood pressure and HbA1c levels at baseline than those with a low ASV of body weight. A one-unit increase in ASV of body weight was associated with increase in mortality (HR 1.46, 95% CI 1.32-1.62, P &lt; 0.001). However, the association between the ASV of body weight and incident diabetes mellitus seemed to be influenced by baseline body mass index (BMI); negative effect in subjects with BMI &lt; 25 kg/m2 (HR 1.36, 95% CI 1.11-1.65, P = 0.003) and protective effect in those with BMI ≥ 25 kg/m2 (HR 0.76, 95% CI 0.60-0.95, P = 0.014). There was no association between the ASV of body weight and cardiovascular event. ConclusionBody-weight fluctuation was associated with mortality. In addition, the effect of body-weight fluctuation on incident diabetes mellitus depended on the presence of obesity at baseline.
DOI: 10.6084/m9.figshare.7117199
title: A cancer associated somatic mutation in LC3B attenuates its binding to E1-like ATG7 protein and subsequent lipidation

description: Macroautophagy/autophagy is a conserved catabolic process that maintains cellular homeostasis under basal growth and stress conditions. In cancer, autophagy can either prevent or promote tumor growth, at early or advanced stages, respectively. We screened public databases to identify autophagy-related somatic mutations in cancer, using a computational approach to identify cancer mutational target sites, employing exact statistics. The top significant hit was a missense mutation (Y113C) in the MAP1LC3B/LC3B (microtubule associated protein 1 light chain 3 beta) protein, which occurred at a significant frequency in cancer, and was detected in early stages in primary tumors of patients with known tumor lineage. The mutation reduced the formation of GFP-LC3B puncta and attenuated LC3B lipidation during Torin1-induced autophagy. Its effect on the direct physical interaction of LC3B with each of the 4 proteins that control its maturation or lipidation was tested by applying a protein-fragment complementation assay and co-immunoprecipitation experiments. Interactions with ATG4A and ATG4B proteases were reduced, yet without perturbing the cleavage of mutant LC3B. Most importantly, the mutation significantly reduced the interaction with the E1-like enzyme ATG7, but not the direct interaction with the E2-like enzyme ATG3, suggesting a selective perturbation in the binding of LC3B to some of its partner proteins. Structure analysis and molecular dynamics simulations of LC3B protein and its mutant suggest that the mutation changes the conformation of a loop that has several contact sites with ATG4B and the ATG7 homodimer. We suggest that this loss-of-function mutation, which attenuates autophagy, may promote early stages of cancer development.
DOI: 10.6084/m9.figshare.7117196
title: A nuclear membrane-derived structure associated with Atg8 is involved in the sequestration of selective cargo, the Cvt complex, during autophagosome formation in yeast

description: Macroautophagy (hereafter autophagy) is a conserved intracellular degradation mechanism required for cell survival. A double-membrane structure, the phagophore, is generated to sequester cytosolic cargos destined for degradation in the vacuole. The mechanism involved in the biogenesis of the phagophore is still an open question. We focused on 4 autophagy-related (Atg) proteins (Atg2, Atg9, Atg14, and Atg18), which are involved in the formation of the phagophore in order to gain a more complete understanding of the membrane dynamics that occur during formation of the autophagosome. The corresponding mutants, while defective in autophagy, nonetheless generate the membrane-bound form of Atg8, allowing us to use this protein as a marker for the nascent autophagosome precursor membrane. Using electron microscopy (EM), we discovered in these <i>atg</i> mutants a novel single-membrane structure (~120 to 150 nm in size). Electron tomography revealed that this structure originates from a part of the nuclear membrane, and we have named it the alphasome. Our data suggest that the alphasome is associated with Atg8, and sequesters selective cargo, the Cvt complex, during autophagy. <b>Abbreviations:</b> 3D: three-dimensional; AB: autophagic body; AP: autophagosome; Atg: autophagy-related; Cvt: cytoplasm-to-vacuole targeting; EM: electron microscopy; IEM: immunoelectron microscopy; L: lipid droplet; N: nucleus; NM: nuclear membrane; PAS: phagophore assembly site; PE: phosphatidylethanolamine; prApe1: precursor aminopeptidase I; rER: rough endoplasmic reticulum; TEM: transmission electron microscopy; V: vacuole; VLP: virus-like particle;
DOI: 10.6084/m9.figshare.7117199.v1
title: A cancer associated somatic mutation in LC3B attenuates its binding to E1-like ATG7 protein and subsequent lipidation

description: Macroautophagy/autophagy is a conserved catabolic process that maintains cellular homeostasis under basal growth and stress conditions. In cancer, autophagy can either prevent or promote tumor growth, at early or advanced stages, respectively. We screened public databases to identify autophagy-related somatic mutations in cancer, using a computational approach to identify cancer mutational target sites, employing exact statistics. The top significant hit was a missense mutation (Y113C) in the MAP1LC3B/LC3B (microtubule associated protein 1 light chain 3 beta) protein, which occurred at a significant frequency in cancer, and was detected in early stages in primary tumors of patients with known tumor lineage. The mutation reduced the formation of GFP-LC3B puncta and attenuated LC3B lipidation during Torin1-induced autophagy. Its effect on the direct physical interaction of LC3B with each of the 4 proteins that control its maturation or lipidation was tested by applying a protein-fragment complementation assay and co-immunoprecipitation experiments. Interactions with ATG4A and ATG4B proteases were reduced, yet without perturbing the cleavage of mutant LC3B. Most importantly, the mutation significantly reduced the interaction with the E1-like enzyme ATG7, but not the direct interaction with the E2-like enzyme ATG3, suggesting a selective perturbation in the binding of LC3B to some of its partner proteins. Structure analysis and molecular dynamics simulations of LC3B protein and its mutant suggest that the mutation changes the conformation of a loop that has several contact sites with ATG4B and the ATG7 homodimer. We suggest that this loss-of-function mutation, which attenuates autophagy, may promote early stages of cancer development.
DOI: 10.6084/m9.figshare.7117196.v1
title: A nuclear membrane-derived structure associated with Atg8 is involved in the sequestration of selective cargo, the Cvt complex, during autophagosome formation in yeast

description: Macroautophagy (hereafter autophagy) is a conserved intracellular degradation mechanism required for cell survival. A double-membrane structure, the phagophore, is generated to sequester cytosolic cargos destined for degradation in the vacuole. The mechanism involved in the biogenesis of the phagophore is still an open question. We focused on 4 autophagy-related (Atg) proteins (Atg2, Atg9, Atg14, and Atg18), which are involved in the formation of the phagophore in order to gain a more complete understanding of the membrane dynamics that occur during formation of the autophagosome. The corresponding mutants, while defective in autophagy, nonetheless generate the membrane-bound form of Atg8, allowing us to use this protein as a marker for the nascent autophagosome precursor membrane. Using electron microscopy (EM), we discovered in these <i>atg</i> mutants a novel single-membrane structure (~120 to 150 nm in size). Electron tomography revealed that this structure originates from a part of the nuclear membrane, and we have named it the alphasome. Our data suggest that the alphasome is associated with Atg8, and sequesters selective cargo, the Cvt complex, during autophagy. <b>Abbreviations:</b> 3D: three-dimensional; AB: autophagic body; AP: autophagosome; Atg: autophagy-related; Cvt: cytoplasm-to-vacuole targeting; EM: electron microscopy; IEM: immunoelectron microscopy; L: lipid droplet; N: nucleus; NM: nuclear membrane; PAS: phagophore assembly site; PE: phosphatidylethanolamine; prApe1: precursor aminopeptidase I; rER: rough endoplasmic reticulum; TEM: transmission electron microscopy; V: vacuole; VLP: virus-like particle;
DOI: 10.6084/m9.figshare.7117178
title: DataRepository.sav

description: Handwriting data of patients with psychosis, bipolar disorder and healthy controls.
DOI: 10.6084/m9.figshare.7117193.v1
title: Amblyomin-X, a recombinant Kunitz-type inhibitor, regulates cell adhesion and migration of human tumor cells

description: In a tumor microenvironment, endothelial cell migration and angiogenesis allow cancer to spread to other organs causing metastasis. This event is regulated by proteinases that induce extracellular matrix degradation and cell-substratum detachment. In this sense, a number of molecules that are involved in cytoskeleton re-organization and intracellular signaling, including uPA its receptor uPAR as well as Rho-GTPases, have been investigated for their effects on tumor cell growth and metastasis. Along the same line, Amblyomin-X, a recombinant Kunitz-type protein, has been shown to reduce metastasis and tumor growth in <i>in vivo</i> experiments. In the present report, we provide a mechanistic insight to these antitumor effects. We demonstrate that Amblyomin-X modulates Rho-GTPases and uPAR signaling, and reduces the release of MMPs, leading to disruption of the actin cytoskeleton and decreased cell migration of tumor cell lines. Altogether, our data support a role for Amblyomin-X as a novel potential antitumor drug.
DOI: 10.25377/sussex.7117076
title: Research data for paper: 'The Role of Emergent Shared Identity in Psychosocial Support among Refugees of Conflict in Developing Countries'. Turkey data set

description: Data-set from questionnaire survey of 234 Syrian refugees in Turkey, gathered 2015. Part of Alfadhli's PhD thesis and journal publication in International Review of Social Psychology, January 2019 (Expected date of publication)<br><br><b>Abstract</b>In spite of the harsh conditions that refugees of conflicts experience for many years in exile in developing countries, there is evidence showing that refugees of conflict help each other. This study aimed to explore one possible mechanism underlying such support and sought to answer three main research questions: Do refugees share an emergent identity that facilitates support among them (similar to people affected by disasters)? Does this identity-based support have an impact on their health? If so, does this positive impact help to mitigate the negative effect of exile stressors on refugees’ health? We carried out two questionnaire surveys among Syrian refugees, first in Turkey (n = 234) and then in Jordan (n = 156). The data were analysed using path analysis to test hypotheses and build a theoretical model. We found evidence suggesting a process of shared social identity-based support among the refugees. We found that the general health of refugees to be predicted mainly by stress, but we also found that collective efficacy has a positive association with health, which suggests a buffering effect. These results shed light on the process of social support among refugees of war and suggest the role of shared identity, which can have a limited buffering effect on the health of the refugees, though not enough to fully mitigate the negative effect of secondary stressors. However, we suggest that such a process can be utilised as base for interventions that approach refugees of war as a group (i.e., at community rather than individual level).<br>
DOI: 10.25377/sussex.7117076.v1
title: Research data for paper: 'The Role of Emergent Shared Identity in Psychosocial Support among Refugees of Conflict in Developing Countries'. Turkey data set

description: Data-set from questionnaire survey of 234 Syrian refugees in Turkey, gathered 2015. Part of Alfadhli's PhD thesis and journal publication in International Review of Social Psychology, January 2019 (Expected date of publication)<br><br><b>Abstract</b>In spite of the harsh conditions that refugees of conflicts experience for many years in exile in developing countries, there is evidence showing that refugees of conflict help each other. This study aimed to explore one possible mechanism underlying such support and sought to answer three main research questions: Do refugees share an emergent identity that facilitates support among them (similar to people affected by disasters)? Does this identity-based support have an impact on their health? If so, does this positive impact help to mitigate the negative effect of exile stressors on refugees’ health? We carried out two questionnaire surveys among Syrian refugees, first in Turkey (n = 234) and then in Jordan (n = 156). The data were analysed using path analysis to test hypotheses and build a theoretical model. We found evidence suggesting a process of shared social identity-based support among the refugees. We found that the general health of refugees to be predicted mainly by stress, but we also found that collective efficacy has a positive association with health, which suggests a buffering effect. These results shed light on the process of social support among refugees of war and suggest the role of shared identity, which can have a limited buffering effect on the health of the refugees, though not enough to fully mitigate the negative effect of secondary stressors. However, we suggest that such a process can be utilised as base for interventions that approach refugees of war as a group (i.e., at community rather than individual level).<br>
DOI: 10.6084/m9.figshare.7117001
title: Supplementary Material for: Allergen Immunization Induces Major Changes in Microbiota Composition and Short-Chain Fatty Acid Production in Different Gut Segments in a Mouse Model of Lupine Food Allergy

description: <b><i>Background:</i></b> The incidence of food allergies in western countries has increased in recent decades. <b><i>Objectives:</i></b> To study the association between gut bacterial microbiota composition, short-chain fatty acids (SCFAs) and food allergy in a mouse model. <b><i>Methods:</i></b> After oral immunizations with the human food allergen lupine with the adjuvant cholera toxin (CT) (or buffer in controls), sensitization and anaphylactic responses were determined. Gastrointestinal content was collected from the distal ileum, cecum, colon, and fecal pellets, and the bacterial diversity and composition was determined by deep sequencing of the 16S rRNA gene. SCFAs in gastrointestinal content supernatants were determined by gas chromatography. <b><i>Results:</i></b> The microbiota signatures were profoundly affected by allergen immunization. Ten operational taxonomic units (OTUs) were significantly different between immunized and control animals for at least one of the intestinal segments; eight of these OTUs belonged to the Clostridia class. Although consistent across all four gut segments, the colon showed the highest number of OTUs significantly associated with allergic immunization. SCFA levels in the cecum were also altered by immunization. <b><i>Conclusions:</i></b> Allergen immunization with CT in the present food allergy model induced profound changes in the microbiome composition and SCFA production. The result suggests that the colon may be the most sensitive gut segment for investigating changes in the gut microbiome.