cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11339078.v1
title: MOESM12 of Epigenetic analysis of high and low motile sperm populations reveals methylation variation in satellite regions within the pericentromeric position and in genes functionally related to sperm DNA organization and maintenance in Bos taurus

description: Additional file 12. Differentially Methylated Regions (DMRs) found at least in three samples in both high motile (HM) and low motile (LM) sperm populations overlapping BTSAT4 satellite. In each column are reported: Probe name, position (Chromosome, Start, End), False Discovery Rate (FDR), Feature, protein ID, Description, MRs percentage for each sample (1HM, 2HM, 3HM, 4HM, 1LM, 2LM, 3LM, 4LM, average HM, average LM and differences between averages Δ HM-LM).
DOI: 10.6084/m9.figshare.11339069
title: MOESM10 of Epigenetic analysis of high and low motile sperm populations reveals methylation variation in satellite regions within the pericentromeric position and in genes functionally related to sperm DNA organization and maintenance in Bos taurus

description: Additional file 10. Differentially Methylated Regions (DMRs) found at least in three samples in both high motile (HM) and low motile (LM) sperm populations downstream of genes (3’UTR). In each column are reported: Probe name, position (Chromosome, Start, End), False Discovery Rate (FDR), Feature, protein ID, Description, MRs percentage for each sample (1HM, 2HM, 3HM, 4HM, 1LM, 2LM, 3LM, 4LM).
DOI: 10.6084/m9.figshare.11339072
title: MOESM11 of Epigenetic analysis of high and low motile sperm populations reveals methylation variation in satellite regions within the pericentromeric position and in genes functionally related to sperm DNA organization and maintenance in Bos taurus

description: Additional file 11. Differentially Methylated Regions (DMRs) found at least in three samples in both high motile (HM) and low motile (LM) sperm populations overlapping CpG islands (CGIs). In each column are reported: Probe name, position (Chromosome, Start, End), False Discovery Rate (FDR), Feature, protein ID, Description, MRs percentage for each sample (1HM, 2HM, 3HM, 4HM, 1LM, 2LM, 3LM, 4LM).
DOI: 10.6084/m9.figshare.11339069.v1
title: MOESM10 of Epigenetic analysis of high and low motile sperm populations reveals methylation variation in satellite regions within the pericentromeric position and in genes functionally related to sperm DNA organization and maintenance in Bos taurus

description: Additional file 10. Differentially Methylated Regions (DMRs) found at least in three samples in both high motile (HM) and low motile (LM) sperm populations downstream of genes (3’UTR). In each column are reported: Probe name, position (Chromosome, Start, End), False Discovery Rate (FDR), Feature, protein ID, Description, MRs percentage for each sample (1HM, 2HM, 3HM, 4HM, 1LM, 2LM, 3LM, 4LM).
DOI: 10.6084/m9.figshare.11338988
title: Gene database of Listeria monocytogenes EGD-e

description: <i>Listeria monocytogenes</i> EGD-e is a flagellated Gram-positive bacterium capable of causing foodborne infections in humans. Able to adopt an intracellular lifestyle in human cells, <i>L. monocytogenes</i> EGD-e (NCBI Reference Sequence: NC_003210.1) is an important human pathogen. Various lines of enquiries have been extended to sought treatments for <i>L. monocytogenes</i> infections as well as understanding its pathogenesis mechanisms in lieu of discovering molecular targets for developing new therapeutics. By parsing the annotated genome sequence of <i>L. monocytogenes</i> EGD-e using an in-house MATLAB algorithm, this work sought to generate a gene database comprising gene names, gene function and gene sequence for aiding molecular research seeking to understand the provenance and mechanisms of <i>L. monocytogenes</i> infections.<br><br>
DOI: 10.6084/m9.figshare.11338970
title: RNA-seq Data for manuscript entitled "Dysregulation of Hypothalamic Gene Expression and the Oxytocinergic System by Soybean Oil Diets in Male Mice"

description: In this study we examined the effect of various high fat diets, high in either saturated fats (from coconut-oil) or unstaurated fats (from conventional soybean oil or a genetically modified, low linoleic acid soybean oil) on hypothalamic gene expression.<br>
DOI: 10.6084/m9.figshare.11338961
title: Reduced NGF Level Promotes Epithelial–Mesenchymal Transition in Human Lens Epithelial Cells Exposed to High Dexamethasone Concentrations

description: <b>Purpose</b>: To investigate the protective effects of nerve growth factor (NGF) against steroid-induced cataract formation in dexamethasone (Dex)-treated human lens epithelial B-3 (HLE-B3) cells and the possible molecular mechanisms underlying this protection. <b>Materials and Methods</b>: HLE-B3 cells were treated with Dex, and cell viability was assessed using the Cell Counting Kit-8 (CCK-8) assay. The levels of expression of NGF, fibronectin, α-smooth muscle actin (α-SMA), and E-cadherin mRNAs were measured by real-time quantitative polymerase chain reaction (qPCR), and the levels of NGF, fibronectin, α-SMA, E-cadherin, tropomyosin receptor kinase A (TrkA), and Akt proteins were measured by Western blot analysis. Gene expression profiles of growth factors in Dex-treated HLE-B3 cells were determined by PCR arrays. In addition, anterior capsule tissue was obtained during cataract surgery, and the specimens were also examined expressions of NGF. <b>Results</b>: NGF was expressed in HLE-B3 cells and also in lens epithelial cells of anterior lens capsules. Dex treatment of HLE-B3 cells increased their expression of epithelial–mesenchymal transition (EMT) markers and migration activity, while markedly downregulating the expression of NGF. NGF treatment significantly reduced the expression of α-SMA and fibronectin, as well as cell proliferation. The decreased phosphorylation of p38 MAPK and Akt induced by Dex treatment was significantly reversed by treatment with NGF. <b>Conclusion</b>: NGF/TrkA may repress EMT by targeting the p38 MAPK and pAkt pathways in Dex-treated HLE-B3 cells. NGF may be a novel therapeutic target for patients with steroid-induced cataract.
DOI: 10.6084/m9.figshare.11338961.v1
title: Reduced NGF Level Promotes Epithelial–Mesenchymal Transition in Human Lens Epithelial Cells Exposed to High Dexamethasone Concentrations

description: <b>Purpose</b>: To investigate the protective effects of nerve growth factor (NGF) against steroid-induced cataract formation in dexamethasone (Dex)-treated human lens epithelial B-3 (HLE-B3) cells and the possible molecular mechanisms underlying this protection. <b>Materials and Methods</b>: HLE-B3 cells were treated with Dex, and cell viability was assessed using the Cell Counting Kit-8 (CCK-8) assay. The levels of expression of NGF, fibronectin, α-smooth muscle actin (α-SMA), and E-cadherin mRNAs were measured by real-time quantitative polymerase chain reaction (qPCR), and the levels of NGF, fibronectin, α-SMA, E-cadherin, tropomyosin receptor kinase A (TrkA), and Akt proteins were measured by Western blot analysis. Gene expression profiles of growth factors in Dex-treated HLE-B3 cells were determined by PCR arrays. In addition, anterior capsule tissue was obtained during cataract surgery, and the specimens were also examined expressions of NGF. <b>Results</b>: NGF was expressed in HLE-B3 cells and also in lens epithelial cells of anterior lens capsules. Dex treatment of HLE-B3 cells increased their expression of epithelial–mesenchymal transition (EMT) markers and migration activity, while markedly downregulating the expression of NGF. NGF treatment significantly reduced the expression of α-SMA and fibronectin, as well as cell proliferation. The decreased phosphorylation of p38 MAPK and Akt induced by Dex treatment was significantly reversed by treatment with NGF. <b>Conclusion</b>: NGF/TrkA may repress EMT by targeting the p38 MAPK and pAkt pathways in Dex-treated HLE-B3 cells. NGF may be a novel therapeutic target for patients with steroid-induced cataract.
DOI: 10.6084/m9.figshare.11338922
title: <i>In vivo</i> biodistribution of venlafaxine-PLGA nanoparticles for brain delivery: plain vs. functionalized nanoparticles

description: <b>Background</b>: Actually, no drugs provide therapeutic benefit to approximately one-third of depressed patients. Depression is predicted to become the first global disease by 2030. So, new therapeutic interventions are imperative. <b>Research design and methods</b>: Venlafaxine-loaded poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) were surface functionalized with two ligands against transferrin receptor to enhance access to brain. An <i>in vitro</i> blood–brain barrier model using hCMEC/D3 cell line was developed to evaluate permeability. <i>In vivo</i> biodistribution studies were performed using C57/bl6 mice. Particles were administered intranasal and main organs were analyzed. <b>Results</b>: Particles were obtained as a lyophilized powder easily to re-suspend. Internalization and permeability studies showed the following cell association sequence: TfRp-NPs&gt;Tf-NPs&gt;plain NPs. Permeability studies also showed that encapsulated VLF was not affected by P-gP pump efflux increasing its concentration in the basolateral side after 24 h. <i>In vivo</i> studies showed that 25% of plain NPs reach the brain after 30 min of one intranasal administration while less than 5% of functionalized NPs get the target. <b>Conclusions</b>: Plain NPs showed the highest ability to reach the brain vs. functionalized NPs after 30 min by intranasal administration. We suggest plain NPs probably travel via direct nose-to-brian route whereas functionalized NPs reach the brain by receptor-mediated endocytosis.
DOI: 10.6084/m9.figshare.11338922.v1
title: <i>In vivo</i> biodistribution of venlafaxine-PLGA nanoparticles for brain delivery: plain vs. functionalized nanoparticles

description: <b>Background</b>: Actually, no drugs provide therapeutic benefit to approximately one-third of depressed patients. Depression is predicted to become the first global disease by 2030. So, new therapeutic interventions are imperative. <b>Research design and methods</b>: Venlafaxine-loaded poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) were surface functionalized with two ligands against transferrin receptor to enhance access to brain. An <i>in vitro</i> blood–brain barrier model using hCMEC/D3 cell line was developed to evaluate permeability. <i>In vivo</i> biodistribution studies were performed using C57/bl6 mice. Particles were administered intranasal and main organs were analyzed. <b>Results</b>: Particles were obtained as a lyophilized powder easily to re-suspend. Internalization and permeability studies showed the following cell association sequence: TfRp-NPs&gt;Tf-NPs&gt;plain NPs. Permeability studies also showed that encapsulated VLF was not affected by P-gP pump efflux increasing its concentration in the basolateral side after 24 h. <i>In vivo</i> studies showed that 25% of plain NPs reach the brain after 30 min of one intranasal administration while less than 5% of functionalized NPs get the target. <b>Conclusions</b>: Plain NPs showed the highest ability to reach the brain vs. functionalized NPs after 30 min by intranasal administration. We suggest plain NPs probably travel via direct nose-to-brian route whereas functionalized NPs reach the brain by receptor-mediated endocytosis.
DOI: 10.6084/m9.figshare.11338910
title: mRNA expressions of androgen receptor and its variants in matched hormone-sensitive and castration-resistant prostate cancer

description: <b>Objectives:</b> Androgen receptor splice variants (AR-Vs), especially androgen receptor splice variant 7 (AR-V7), are considered as important factors in developing castration-resistance of prostate cancer and also as candidate predictive factors. Our aim was to evaluate changes in the mRNA expression of full-length AR (AR-FL) and AR-Vs in the primary prostate cancers from the same patients before and after ADT. <b>Methods:</b> We compared morphologic differences and evaluated AR-FL, AR-V7, AR-V4, ARv567es, AR-V3 and AR8 mRNA expression in matched samples of primary hormone-sensitive and castration-resistant prostate cancer (CRPC) from 19 patients. <b>Results:</b> mRNA expression of AR-FL, AR-V7, ARv567es and AR-V3 was present in hormone sensitive prostate cancer (HSPC) and was significantly increased in CRPC in 81.2% (13/16). There were strong positive correlations between AR-FL and AR-V7 (<i>r</i> = 0.93, <i>p</i> r = 0.72, <i>p</i> r = 0.81, <i>p</i> 30%) increased after ADT in 25% (4/16) of the patients, who showed significantly (<i>p</i> <b>Conclusion:</b> We demonstrated that the expression of AR-V7 is present at low levels in HSPC and is increased in CRPC and the increase is an active process possibly related to aggressive clinical course.
DOI: 10.6084/m9.figshare.11338910.v1
title: mRNA expressions of androgen receptor and its variants in matched hormone-sensitive and castration-resistant prostate cancer

description: <b>Objectives:</b> Androgen receptor splice variants (AR-Vs), especially androgen receptor splice variant 7 (AR-V7), are considered as important factors in developing castration-resistance of prostate cancer and also as candidate predictive factors. Our aim was to evaluate changes in the mRNA expression of full-length AR (AR-FL) and AR-Vs in the primary prostate cancers from the same patients before and after ADT. <b>Methods:</b> We compared morphologic differences and evaluated AR-FL, AR-V7, AR-V4, ARv567es, AR-V3 and AR8 mRNA expression in matched samples of primary hormone-sensitive and castration-resistant prostate cancer (CRPC) from 19 patients. <b>Results:</b> mRNA expression of AR-FL, AR-V7, ARv567es and AR-V3 was present in hormone sensitive prostate cancer (HSPC) and was significantly increased in CRPC in 81.2% (13/16). There were strong positive correlations between AR-FL and AR-V7 (<i>r</i> = 0.93, <i>p</i> r = 0.72, <i>p</i> r = 0.81, <i>p</i> 30%) increased after ADT in 25% (4/16) of the patients, who showed significantly (<i>p</i> <b>Conclusion:</b> We demonstrated that the expression of AR-V7 is present at low levels in HSPC and is increased in CRPC and the increase is an active process possibly related to aggressive clinical course.
DOI: 10.6084/m9.figshare.11338874
title: DFT simulation of Watson–Crick-like guanine–thymine mismatch in quaternary systems involving DNA bases

description: The aim of this work is to theoretically investigate the guanine–thymine mismatch in the presence of adenine–thymine and guanine–cytosine base pairs. At M06-2X/6-311++G(d,p) level, the absolute values of formation energy of quaternary systems increase by going from systems having enol form of guanine (G*) to those containing enol tautomer of thymine (T*). Moreover, the stacking between T* and purine bases, in comparison with pyrimidine bases, increases the stability of quaternary systems having T*. On the other hand, the stacking between G* and pyrimidine bases more stabilises systems involving G*. From a thermodynamic point of view, the quaternary systems containing G−T* can transform their geometries into systems having G*−T. To gain a better understanding of the influence of hydrogen bonds on the stability of systems, the atoms in molecules and natural bond orbital analyses are used to evaluate the strength of hydrogen bonds in the investigated systems.
DOI: 10.6084/m9.figshare.11338874.v1
title: DFT simulation of Watson–Crick-like guanine–thymine mismatch in quaternary systems involving DNA bases

description: The aim of this work is to theoretically investigate the guanine–thymine mismatch in the presence of adenine–thymine and guanine–cytosine base pairs. At M06-2X/6-311++G(d,p) level, the absolute values of formation energy of quaternary systems increase by going from systems having enol form of guanine (G*) to those containing enol tautomer of thymine (T*). Moreover, the stacking between T* and purine bases, in comparison with pyrimidine bases, increases the stability of quaternary systems having T*. On the other hand, the stacking between G* and pyrimidine bases more stabilises systems involving G*. From a thermodynamic point of view, the quaternary systems containing G−T* can transform their geometries into systems having G*−T. To gain a better understanding of the influence of hydrogen bonds on the stability of systems, the atoms in molecules and natural bond orbital analyses are used to evaluate the strength of hydrogen bonds in the investigated systems.
DOI: 10.6084/m9.figshare.11338829
title: ‘I saw it on Facebook’: an experimental analysis of political learning through social media

description: The maldistribution of political knowledge in society has important consequences for individual-level political behavior and the representativeness of governmental policies. Increased media selectivity threatens to widen the gap between the politically well-informed and the less-informed by decreasing chance encounters with incidental political information. This study asks: Does exposure to incidental political information through social media promote political learning among users? We conduct two longitudinal, controlled experiments administered through the Facebook platform, and find no statistical difference in the levels of factual political knowledge among participants exposed to political information compared to those who were not. However, those in the treatment group with low political interest may be more likely to venture an incorrect guess than those in the control group, suggesting that exposure to incidental political information through social media may lead to an increase in self-perceived knowledge among some.
DOI: 10.6084/m9.figshare.11338829.v1
title: ‘I saw it on Facebook’: an experimental analysis of political learning through social media

description: The maldistribution of political knowledge in society has important consequences for individual-level political behavior and the representativeness of governmental policies. Increased media selectivity threatens to widen the gap between the politically well-informed and the less-informed by decreasing chance encounters with incidental political information. This study asks: Does exposure to incidental political information through social media promote political learning among users? We conduct two longitudinal, controlled experiments administered through the Facebook platform, and find no statistical difference in the levels of factual political knowledge among participants exposed to political information compared to those who were not. However, those in the treatment group with low political interest may be more likely to venture an incorrect guess than those in the control group, suggesting that exposure to incidental political information through social media may lead to an increase in self-perceived knowledge among some.
DOI: 10.6084/m9.figshare.11338673
title: Evidence that dissociation of Spt16 from transcribed genes is partially dependent on RNA Polymerase II termination

description: FACT (FAcilitates Chromatin Transactions) is a highly conserved histone chaperone complex in eukaryotic cells that can interact and manipulate nucleosomes in order to promote a variety of DNA-based processes and to maintain the integrity of chromatin throughout the genome. Whereas key features of the physical interactions that occur between FACT and nucleosomes <i>in vitro</i> have been elucidated in recent years, less is known regarding FACT functional dynamics <i>in vivo</i>. Using the <i>Saccharomyces cerevisiae</i> system, we now provide evidence that at least at some genes dissociation of the FACT subunit Spt16 from their 3′ ends is partially dependent on RNA Polymerase II (Pol II) termination. Combined with other studies, our results are consistent with a two-phase mechanism for FACT dissociation from genes, one that occurs upstream from Pol II dissociation and is Pol II termination-independent and the other that occurs further downstream and is dependent on Pol II termination.
DOI: 10.6084/m9.figshare.11338670
title: Temperate mesophotic ecosystems: gaps and perspectives of an emerging conservation challenge for the Mediterranean Sea

description: Mesophotic habitats, hosting benthic assemblages totally unknown and unexpected in the early 2000s, are attracting an increasing interest from scientists. Realizing that many long living and habitat forming species are playing a unique pocket of biodiversity in the frame of climate crisis, it is important to recognize the potential of the mesophotic zone in conservation strategies. The mesophotic zone is characterized by environmental factors generally more stable than the shallow counterpart; therefore, it represents a refuge habitat to preserve species that, in shallow waters, may be involved in bleaching events, massive mortalities or other pathologies generally triggered by thermal anomalies. The definition of the mesophotic zone in the temperate seas is confused, creating possible misunderstandings and problems not only from a scientific point of view but also in communication and outreach strategies. Here, we review the scientific literature to build the best definition possible based on the maximum consensus coming from papers analysis. Moreover, the key roles of mesophotic habitats, including ecosystem engineers as animal forests, have been schematized to enhance the perception of the potential risks we are running in case of damage or loss of these habitats.
DOI: 10.6084/m9.figshare.11338673.v1
title: Evidence that dissociation of Spt16 from transcribed genes is partially dependent on RNA Polymerase II termination

description: FACT (FAcilitates Chromatin Transactions) is a highly conserved histone chaperone complex in eukaryotic cells that can interact and manipulate nucleosomes in order to promote a variety of DNA-based processes and to maintain the integrity of chromatin throughout the genome. Whereas key features of the physical interactions that occur between FACT and nucleosomes <i>in vitro</i> have been elucidated in recent years, less is known regarding FACT functional dynamics <i>in vivo</i>. Using the <i>Saccharomyces cerevisiae</i> system, we now provide evidence that at least at some genes dissociation of the FACT subunit Spt16 from their 3′ ends is partially dependent on RNA Polymerase II (Pol II) termination. Combined with other studies, our results are consistent with a two-phase mechanism for FACT dissociation from genes, one that occurs upstream from Pol II dissociation and is Pol II termination-independent and the other that occurs further downstream and is dependent on Pol II termination.
DOI: 10.6084/m9.figshare.11338670.v1
title: Temperate mesophotic ecosystems: gaps and perspectives of an emerging conservation challenge for the Mediterranean Sea

description: Mesophotic habitats, hosting benthic assemblages totally unknown and unexpected in the early 2000s, are attracting an increasing interest from scientists. Realizing that many long living and habitat forming species are playing a unique pocket of biodiversity in the frame of climate crisis, it is important to recognize the potential of the mesophotic zone in conservation strategies. The mesophotic zone is characterized by environmental factors generally more stable than the shallow counterpart; therefore, it represents a refuge habitat to preserve species that, in shallow waters, may be involved in bleaching events, massive mortalities or other pathologies generally triggered by thermal anomalies. The definition of the mesophotic zone in the temperate seas is confused, creating possible misunderstandings and problems not only from a scientific point of view but also in communication and outreach strategies. Here, we review the scientific literature to build the best definition possible based on the maximum consensus coming from papers analysis. Moreover, the key roles of mesophotic habitats, including ecosystem engineers as animal forests, have been schematized to enhance the perception of the potential risks we are running in case of damage or loss of these habitats.