cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28578873.v1
title: Epigenetics in persons living with HIV: trauma, coping, and <i>FKBP5</i> and <i>SLC6A4</i> methylation

description: People living with HIV (PLWH) have an increased risk for lifetime trauma and mental health difficulties. However, no studies have evaluated stress-related genes in relation to early-life adversity, lifetime trauma, or post-traumatic stress disorder (PTSD) in PLWH. Using bisulfite pyrosequencing, we evaluated DNA methylation (DNAm) in intron 7 of FKBP5, a glucocorticoid feedback regulator, and in the promoter of SLC6A4, the serotonin transporter gene, in whole blood of a random sample of 70 PLWH recruited from an HIV program, and 51 individuals 2 years later (<i>n</i> = 48 at both time points). Exploratory regression analyses were conducted with DNAm in relation to trauma exposure, mental health symptoms, and coping strategies. Higher DNAm at one site of SLC6A4 was associated with lower levels of anxiety (B = −0.62 (SE = 0.23), <i>p</i> = 0.0109), depression (B = −0.06 (SE = 0.03), <i>p</i> = 0.0435), and PTSD symptoms at baseline (B = −0.03 (SE = 0.01), <i>p</i> = 0.0374). DNAm at FKBP5 was negatively associated with measures of anxiety (B = −0.30 (SE = 0.07), <i>p</i> = 0.0001) and depression symptoms (B = −0.2 (SE = 0.10), <i>p</i> = 0.0103). Various coping strategies were also associated with sites in both genes across time points, e.g. self-blame and substance use. Our findings generate intriguing hypotheses linking mental health symptoms and DNA methylation, to be replicated with larger samples. Many people living with HIV experience high levels of trauma and mental health difficulties in their lifetime. One way in which this trauma may affect mental health, is through a process called epigenetics, in which chemical changes are made to the DNA in response to different exposures. Small chemical groups called methyl groups are placed onto a cytosine (the C in our DNA), which can modify how available the DNA is to be expressed into a protein. These methylation patterns at stress-related genes can essentially tune up or down a body’s response to a stressor. In our study, we examined how these methylation differences at important regulatory locations in stress-related genes may be related to exposure to lifetime histories of trauma, as well as symptoms of depression, anxiety, and perceived stress, and various coping strategies people use to deal with trauma or stress, such as humor, denial, self-blame, or substance use. We found that higher DNA methylation levels at multiple positions in the two studied genes were related to lower levels of symptoms of anxiety, depression, and post-traumatic stress disorder (PTSD) in a population of adults living with HIV. Some of the coping strategies, such as self-blame and substance use, were also related to DNA methylation at both studied genes. These findings indicate that epigenetic differences may contribute to mental health symptoms in people with HIV.
DOI: 10.3535/ast-6fw-9yb
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/8avr-j6e9
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/k9h-m4p-hjy
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/rv5-s53-vm2
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/h5jc-qwzj
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.6084/m9.figshare.28426900
title: Identification of IL-34 and Slc7al as potential key regulators in MASLD progression through epigenomic profiling

description: Epigenetic alterations are critical regulators in the progression of metabolic dysfunction-associated steatotic liver disease (MASLD); however, the dynamic epigenomic landscapes are not well defined. Our previous study found that H3K27ac and H3K9me3 play important roles in regulating lipid metabolic pathways in the early stages of MASLD. However, the epigenomic status in the inflammation stages still needs to be determined. C57BL/6 male mice were fed with the methionine- and choline-deficient (MCD) or normal diet, and their serum and liver samples were collected after 6 weeks. Serum alanine aminotransferase (ALT), aspartate amino transferase (AST), total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) levels were measured. Chromatin immunoprecipitation sequencing (ChIP-Seq) for H3K27ac and H3K9me3 was performed together with RNA sequencing (RNA-seq) and key regulators were analyzed. The target genes of enhancers with increased H3K27ac and decreased H3K9me3 signals are enriched in lipid metabolism and immuno-inflammatory pathways. <i>Il-34</i> and <i>Slc7al</i> are identified as potential regulators in MASLD. Our study reveals that active enhancers and heterochromatin associated with metabolic and inflammatory genes are extensively reprogrammed in MCD-diet mice, and <i>Il-34</i> and <i>Slc7al</i> are potentially key genes regulating the progression of MASLD.
DOI: 10.6084/m9.figshare.28426900.v1
title: Identification of IL-34 and Slc7al as potential key regulators in MASLD progression through epigenomic profiling

description: Epigenetic alterations are critical regulators in the progression of metabolic dysfunction-associated steatotic liver disease (MASLD); however, the dynamic epigenomic landscapes are not well defined. Our previous study found that H3K27ac and H3K9me3 play important roles in regulating lipid metabolic pathways in the early stages of MASLD. However, the epigenomic status in the inflammation stages still needs to be determined. C57BL/6 male mice were fed with the methionine- and choline-deficient (MCD) or normal diet, and their serum and liver samples were collected after 6 weeks. Serum alanine aminotransferase (ALT), aspartate amino transferase (AST), total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) levels were measured. Chromatin immunoprecipitation sequencing (ChIP-Seq) for H3K27ac and H3K9me3 was performed together with RNA sequencing (RNA-seq) and key regulators were analyzed. The target genes of enhancers with increased H3K27ac and decreased H3K9me3 signals are enriched in lipid metabolism and immuno-inflammatory pathways. <i>Il-34</i> and <i>Slc7al</i> are identified as potential regulators in MASLD. Our study reveals that active enhancers and heterochromatin associated with metabolic and inflammatory genes are extensively reprogrammed in MCD-diet mice, and <i>Il-34</i> and <i>Slc7al</i> are potentially key genes regulating the progression of MASLD.
DOI: 10.3535/49n-d41-ty5
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/kve-g09-hhj
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/j7ry-6yn4
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/agt-ekl-y05
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/tan-k87-fma
title: Stelliferidium furcatum (Deunff, 1961) Deunff, Gorka and Rauscher, 1974

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/5kzv-78kj
title: Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.48597/pter-tn8b
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.48597/t5c6-x8v5
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/1fq-8qb-l8y
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/55w-w0e-wnn
title: Oxyloma elegans (Risso, 1826)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/tprz-b5da
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/1sg-vbj-lmg
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/tmd-4n6-286
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/waca-mjgc
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/0lf-br5-xmq
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/sjmu-njxd
title: Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.48597/xqcr-cam4
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/50d-pec-m9h
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/p5g-tsp-egv
title: Euconulus fulvus (O. F. Müller, 1774)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/2ph6-2dzv
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/dtv-cyt-xt4
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/q4c-cdz-jcz
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/63ev-y96w
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.48597/97tp-3qew
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/654-xhw-egt
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zwm-pkn-grq
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/9c6m-vfhp
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/nh1-zx9-ger
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xch-70r-mze
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/cpuf-6x38
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/53f-gy8-wd5
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/q6k-c86-dr5
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/s7yf-93b3
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/faq-ehn-467
title: Vallonia pulchella (O. F. Müller, 1774)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ltc-cj2-xcb
title: Cymatiogalea messaoudensis Jardiné, Combaz, Magloire, Peniguel and Vachey 1974, 1974

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/yku6-2w7k
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/3ml-mgf-nk6
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5wg-x34-tat
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/ywsn-jsvr
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/je1-m2d-9c7
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/rgs-vpn-kwe
title: Perpolita petronella (L. Pfeiffer, 1853)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.48597/zaxd-8gfq
title: Measurement of Inorganics in precipitation at Donon

description: Measurement of Inorganics in precipitation at Donon
DOI: 10.3535/090-p26-wj8
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/hz0-4gl-nm5
title: Tremataspis mammillata Patten, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wqt-gtq-s06
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/x98-f28-x61
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.14199179.v1
title: Datasets.zip

description: Phytoplankton are not only the main bearer of the nitrogen biological cycle, but also a key link driving the nitrogen cycle. However, most phytoplankton cannot directly utilize N<sub>2</sub>, they must uptake nitrogenous nutrients (ammonium, nitrate, and urea) to meet their photosynthesis needs. We examined the uptake and assimilation of several nitrogenous substrates using stable isotope technique and identified the potential nitrogen transformations. Our results revealed that urea can meet the spring partial nitrogen requirement of phytoplankton, according to the random forest models, the greater uptake rate depending on the urease, Chl a, and nitrate concentrations, redundancy analysis demonstrated that the phytoplankton community composed of <i>Fragilaria</i>, <i>Ulothrix</i>, and <i>Synedra</i>. The uptake rates of nitrate and urea were comparable and lower than those of ammonium in summer, the major contributors were ammonium, urease, and dissolved oxygen (DO), and the assemblages were dominated by <i>Microcystis</i>, <i>Actinastrum</i>, and <i>Melosira</i>. The effects observed indicated that ammonium was taken up preferentially in autumn and phytoplankton (<i>Cyclotella</i>, <i>Chlorella</i>, and <i>Pseudanabaena</i>) appeared to be able to respond to changes in nitrogen forms by adjusting their community composition.
DOI: 10.6084/m9.figshare.28407835
title: Nanoencapsulation enhanced the performance of β-carotene for ameliorating inflammation in patient-derived organoids

description: This study aims to develop a nanocarrier system for the oral delivery of β-Carotene (BC) (as a model therapeutic agent) and to test its efficacy in ameliorating inflammation in an ulcerative colitis (UC) patient-derived organoid. BC was encapsulated in a zein protein nano-cage surface-functionalized with pectin and polyethyleneglycol (PEG). The nanoencapsulated BC (nBC) was characterized for physicochemical properties (size, charge, surface chemistry) and functional properties (radical scavenging, mucoadhesion and penetration, release in simulated digestive fluids). Further, we evaluated the performance of nBC in ameliorating inflammation in Caco-2 and UC patient-derived organoid models. nBC achieved 75% encapsulation efficiency with improved stability and functional properties when compared to free BC. The nanocarrier was non-cytotoxic and improved mucoadhesion, mucopenetration, and the anti-inflammatory potential of BC. In UC organoids, nBC suppressed dextran sulfate sodium (DSS)-induced TNF-α and IL-8 production by approximately 70% and 31%, respectively, which was significantly higher than free BC at comparable concentrations. The protein-polymer nanoencapsulation strategy showed promise in protecting BC and overcoming intestinal mucus barriers for an improved anti-inflammatory effect in the organoid model. Further studies using animal models are warranted for establishing pharmacokinetics, tissue distribution, and therapeutic index of orally delivered nBC.
DOI: 10.6084/m9.figshare.28407835.v1
title: Nanoencapsulation enhanced the performance of β-carotene for ameliorating inflammation in patient-derived organoids

description: This study aims to develop a nanocarrier system for the oral delivery of β-Carotene (BC) (as a model therapeutic agent) and to test its efficacy in ameliorating inflammation in an ulcerative colitis (UC) patient-derived organoid. BC was encapsulated in a zein protein nano-cage surface-functionalized with pectin and polyethyleneglycol (PEG). The nanoencapsulated BC (nBC) was characterized for physicochemical properties (size, charge, surface chemistry) and functional properties (radical scavenging, mucoadhesion and penetration, release in simulated digestive fluids). Further, we evaluated the performance of nBC in ameliorating inflammation in Caco-2 and UC patient-derived organoid models. nBC achieved 75% encapsulation efficiency with improved stability and functional properties when compared to free BC. The nanocarrier was non-cytotoxic and improved mucoadhesion, mucopenetration, and the anti-inflammatory potential of BC. In UC organoids, nBC suppressed dextran sulfate sodium (DSS)-induced TNF-α and IL-8 production by approximately 70% and 31%, respectively, which was significantly higher than free BC at comparable concentrations. The protein-polymer nanoencapsulation strategy showed promise in protecting BC and overcoming intestinal mucus barriers for an improved anti-inflammatory effect in the organoid model. Further studies using animal models are warranted for establishing pharmacokinetics, tissue distribution, and therapeutic index of orally delivered nBC.
DOI: 10.3535/alk-c37-h8g
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.28435614
title: Polyol-modified deformable liposomes fortified contact lenses for improved ocular permeability

description: To develop a glycerol modified liposomes to effectively deliver active agents into posterior segment of the eye for the management of posterior uveitis. The modified liposome enhanced with glycerol as an edge activator was fabricated using a 3<sup>2</sup> experimental design with independent variables being soya lecithin (mg) (X<sub>1</sub>) and glycerol (%) (X<sub>2</sub>) and vesicle size (nm) (Y<sub>1</sub>), deformability index (%) (Y<sub>2</sub>), and entrapment efficiency (%) (Y<sub>3</sub>) as dependent variable with improve permeability and entrapment efficacy. These modified liposomes were then integrated into pHEMA-based contact lenses via free radical polymerization using different monomer mixture, co-polymer, crosslinker, and photo-initiator to extend drug release. Nano-vesicles resulted in size and deformability index of 200.5 ± 15 nm and 11.58, respectively, with entrapment efficiency of 80.98% of the drug. Moreover, the optimized lenses demonstrated 71%) of swelling and transmittance of 87%). In addition, <i>in vitro</i> release of active component from the therapeutic contact lens demonstrated sustained drug release over 24 h. Whereas <i>ex vivo</i> studies displayed a 5-fold increase in drug permeation, compared to tested conventional eye drops. The results suggested that glycerosomes-loaded contact lens can be a promising alternative for regulated delivery of dexamethasone sodium phosphate in the management of posterior uveitis.
DOI: 10.6084/m9.figshare.28435614.v1
title: Polyol-modified deformable liposomes fortified contact lenses for improved ocular permeability

description: To develop a glycerol modified liposomes to effectively deliver active agents into posterior segment of the eye for the management of posterior uveitis. The modified liposome enhanced with glycerol as an edge activator was fabricated using a 3<sup>2</sup> experimental design with independent variables being soya lecithin (mg) (X<sub>1</sub>) and glycerol (%) (X<sub>2</sub>) and vesicle size (nm) (Y<sub>1</sub>), deformability index (%) (Y<sub>2</sub>), and entrapment efficiency (%) (Y<sub>3</sub>) as dependent variable with improve permeability and entrapment efficacy. These modified liposomes were then integrated into pHEMA-based contact lenses via free radical polymerization using different monomer mixture, co-polymer, crosslinker, and photo-initiator to extend drug release. Nano-vesicles resulted in size and deformability index of 200.5 ± 15 nm and 11.58, respectively, with entrapment efficiency of 80.98% of the drug. Moreover, the optimized lenses demonstrated 71%) of swelling and transmittance of 87%). In addition, <i>in vitro</i> release of active component from the therapeutic contact lens demonstrated sustained drug release over 24 h. Whereas <i>ex vivo</i> studies displayed a 5-fold increase in drug permeation, compared to tested conventional eye drops. The results suggested that glycerosomes-loaded contact lens can be a promising alternative for regulated delivery of dexamethasone sodium phosphate in the management of posterior uveitis.
DOI: 10.6084/m9.figshare.28588835
title: Femtosecond laser-ablative aqueous synthesis of multi-drug antiviral nanoparticles

description: Nanomedicine offers a number of innovative strategies to address major public health burdens, including complex respiratory illnesses. In this work, we introduce a multi-drug nanoparticle fabricated using femtosecond laser ablation for the treatment of influenza, SARS-CoV-2, and their co-infections. The SARS-CoV-2 antiviral, remdesivir; the influenza antiviral, baloxavir marboxil; and the anti-inflammatory, dexamethasone, were co-crystalized and then ablated in aqueous media using a femtosecond pulsed laser and subsequently surface modified with the cationic polymer, chitosan, or poly-d-lysine. Physical and chemical properties were then characterized using multiple complimentary techniques. Finally, a clinically relevant <i>in vitro</i> primary mouse trachea epithelial cell-air-liquid interface culture model was used to analyze the antiviral effect of our nanoparticles against Influenza Virus A. Our final nanoparticle exhibited a positive zeta potential with a diameter of ~73 nm. Remdesivir, baloxavir marboxil, and dexamethasone were all present in the nanoparticle suspension at a 1:1:1 ratio. Notably, these particles exhibited a potent anti-influenza effect, decreasing the viral titer by ≈ 4 logs in comparison to vehicle controls. Overall, these findings demonstrate great promise both for the use of laser ablation to generate multi-drug nanoparticles and for the anti-viral effects of our nanoformulation against respiratory illness.