cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7992313.v1
title: Effects of compressive ratio and sintering temperature on mechanical properties of biocompatible collagen/hydroxyapatite composite scaffolds fabricated for bone tissue engineering

description: A sponge template method was used to synthesize scaffolds from hydroxyapatite (HAp) using varying sintering temperatures and compressive ratios. The HAp scaffolds were fabricated with collagen (COL) or collagen/HAp particles under room temperature coating conditions. The microstructure and mechanical properties of the fabricated biomaterials were analyzed by FE-SEM and EZ Test, respectively. The FE-SEM micrographs showed microporous structure of the fabricated composite scaffolds. Incorporation of COL or COL/HAp into pure HAp scaffolds under coating conditions significantly reduced the porosity and enhanced the mechanical properties. The results demonstrated that the porosity of fabricated scaffolds was reduced by lowering the compressive pressure and increasing the sintering temperature. The maximum estimated compressive moduli at 1000, 1100 and 1200 °C for HAp-COL and HAp-COL/HAp composite scaffolds were 4.36, 2.93, 5.09 MPa and 4.57, 8.19, 5.02 MPa, respectively, at a 50% compressive ratio. It was assumed that porosity was effectively reduced to the maximum level at a 50% compressive ratio. An in vitro stem cell study showed significant cell adhesion and proliferation over the fabricated HAp-COL and HAp-COL/HAp composite scaffolds. These results confirmed that fabrication of pure HAp with COL and COL/HAp materials had advanced effects on the mechanical properties of fabricated porous composite scaffolds.
DOI: 10.6084/m9.figshare.7992457.v1
title: Age-dependent accumulation of oligomeric SNCA/α-synuclein from impaired degradation in mutant LRRK2 knockin mouse model of Parkinson disease: role for therapeutic activation of chaperone-mediated autophagy (CMA)

description: Parkinson disease (PD) is an age-related neurodegenerative disorder associated with misfolded SNCA/α-synuclein accumulation in brain. Impaired catabolism of SNCA potentiates formation of its toxic oligomers. <i>LRRK2</i> (leucine-rich repeat kinase-2) mutations predispose to familial and sporadic PD. Mutant LRRK2 perturbs chaperone-mediated-autophagy (CMA) to degrade SNCA. We showed greater age-dependent accumulation of oligomeric SNCA in striatum and cortex of aged LRRK2<sup>R1441G</sup> knockin (KI) mice, compared to age-matched wildtype (WT) by 53% and 31%, respectively. Lysosomal clustering and accumulation of CMA-specific LAMP2A and HSPA8/HSC70 proteins were observed in aged mutant striatum along with increased GAPDH (CMA substrate) by immunohistochemistry of dorsal striatum and flow cytometry of ventral midbrain cells. Using our new reporter protein clearance assay, mutant mouse embryonic fibroblasts (MEFs) expressing either SNCA or CMA recognition ‘KFERQ’-like motif conjugated with photoactivated-PAmCherry showed slower cellular clearance compared to WT by 28% and 34%, respectively. However, such difference was not observed after the ‘KFERQ’-motif was mutated. LRRK2 mutant MEFs exhibited lower lysosomal degradation than WT indicating lysosomal dysfunction. LAMP2A-knockdown reduced total lysosomal activity and clearance of ‘KFERQ’-substrate in WT but not in mutant MEFs, indicating impaired CMA in the latter. A CMA-specific activator, AR7, induced neuronal LAMP2A transcription and lysosomal activity in MEFs. AR7 also attenuated the progressive accumulation of both intracellular and extracellular SNCA oligomers in prolonged cultures of mutant cortical neurons (DIV21), indicating that oligomer accumulation can be suppressed by CMA activation. Activation of autophagic pathways to reduce aged-related accumulation of pathogenic SNCA oligomers is a viable disease-modifying therapeutic strategy for PD. <b>Abbreviations:</b> 3-MA: 3-methyladenine; AR7: 7-chloro-3-(4-methylphenyl)-2H-1,4-benzoxazine; CMA: chaperone-mediated autophagy; CQ: chloroquine; CSF: cerebrospinal fluid; DDM: n-dodecyl β-D-maltoside; DIV: days in vitro; ELISA: enzyme-linked immunosorbent assay; FACS: fluorescence-activated cell sorting; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GWAS: genome-wide association studies; HSPA8/HSC70: heat shock protein 8; KFERQ: CMA recognition pentapeptide; KI: knockin; LAMP1: lysosomal-associated membrane protein 1; LAMP2A: lysosomal-associated membrane protein 2A; LDH: lactate dehydrogenase; LRRK2: leucine-rich repeat kinase 2; MEF: mouse embryonic fibroblast; NDUFS4: NADH:ubiquinone oxidoreductase core subunit S4; NE: novel epitope; PD: Parkinson disease; RARA/RARα: retinoic acid receptor, alpha; SNCA: synuclein, alpha; TUBB3/TUJ1: tubulin, beta 3 class III; WT: wild-type
DOI: 10.6084/m9.figshare.7992233
title: Dataset 2.1: Human proteome data

description: Dataset of protein features for <i>Homo sapiens</i> (human) uniprot reference proteome
DOI: 10.6084/m9.figshare.7992230
title: Dataset 1.1: Yeast proteome data

description: Dataset of protein features for <i>Saccharomyces cerevisiae</i> uniprot reference proteome
DOI: 10.6084/m9.figshare.7992233.v1
title: Dataset 2.1: Human proteome data

description: Dataset of protein features for <i>Homo sapiens</i> (human) uniprot reference proteome
DOI: 10.6084/m9.figshare.7992224
title: Molecular discrimination of <i>Ancistrus</i> lineages (Siluriformes: Loricariidae) using barcode DNA tool

description: Although several species of <i>Ancistrus</i> have been described from the Amazon and Paraguay river basins in the states of Amazonas and Mato Grosso, Brazil, the taxonomic status of most specimens from these regions remains doubtful. In the present work, cytogenetic and molecular data were used to discriminate and isolate unexpected <i>Ancistrus</i> lineages from the Amazon and Paraguay basins. For that, it was used DNA barcoding based on mitochondrial Cytochrome Oxidase Subunit I (COI) gene and cytogenic data to perform such molecular discrimination. The analyzed sequences had 669 bp, of which 171 bp were conserved and 491 bp were variable. The Neighbor-joining and Bayesian analysis revealed 21 distinct groups in topology. The genetic distances within each group was 0.4%, 21 times smaller than the mean distance observed among groups, which was 8.4%. These values showed seven distinct lineages of <i>Ancistrus</i> from the studied points of the Amazon basin and eight lineages from the Paraguay basin points. Our results illustrate the efficiency of this technique for the discrimination of the <i>Ancistrus</i> lineages once it indicates the occurrence of cryptic species in these regions, which cannot yet be identified either with just chromosomal or morphological analyzes.
DOI: 10.6084/m9.figshare.7992218
title: Hydrothermal synthesis and crystal structure of three-dimensional supramolecular zinc, manganese coordination polymers

description: Two new complexes [Zn<sub>2</sub>(pzdc)(L)<sub>2</sub>(H<sub>2</sub>O)]<sub>2n</sub>·2nH<sub>2</sub>O <b>(1)</b> and [Mn(<i>µ</i><sub>2</sub>-O)(H<sub>2</sub>O)<sub>2</sub>-(HL)]<sub>2n</sub>·2nNIPH <b>(2)</b> (H<sub>2</sub>pzdc = pyrazine-2,3-dicarboxylic acid, HL = 3-(2-Pyridyl) pyrazole, H<sub>2</sub>NIPH = 5-nitroisophthalic acid) have been hydrothermally synthesized and structurally characterized by elemental analysis, IR spectrum, UV spectrum, TG, fluorescence spectrum and single-crystal X-ray diffraction. Complex <b>1</b> shows two-dimensional (2D) network, which was stabilized by O–H···O, C–H···O hydrogen bonding and <i>π</i>-<i>π</i> interactions and extended into 3 D supramolecular architecture. Complex <b>2</b> is zero-dimensional structure, which was further extended into 3 D supramolecular framework through N–H···O, O–H···O, C–H···O hydrogen bonds and <i>π</i>-<i>π</i> interactions.
DOI: 10.6084/m9.figshare.7992206
title: Association between ultraviolet radiation exposure dose and cataract in Han people living in China and Taiwan: a cross-sectional study

description: <b>Purpose:</b> We investigated associations between ocular ultraviolet (UV) radiation exposure dose and cataract opacities among Han people living in China and Taiwan, to assess the effects of UV exposure intensity.<b></b> <b>Methods: </b>This cross-sectional study included Han people aged ≥40 years (1,801 individuals, 450 in Sanya, 636 in Taiyuan, and 715 in Taichung) as subjects who completed a questionnaire including items about diabetes, smoking, steroid use, work history, and time spent outdoors, and underwent an ophthalmic examination. Right eye axial length was measured using A-mode ultrasonography or IOLMaster. Slit-lamp imaging under maximum mydriasis was used to classify cataracts into three major types [cortical (COR), nuclear (NUC), and posterior subcapsular cataracts (PSC)] and two subtypes [retrodots (RD) and waterclefts (WC)] by one ophthalmologist. COR was divided into opacity presence (CEN+) or absence (CEN-) in the central 3-mm diameter area of the pupil. COR was also subdivided into three groups according to opacity shape: axle-shaped opacity concomitant with WC, wedge-shaped opacity around the pupil to the eye center, and ring-shaped opacity in the lens equator along the pupillary margin. The cumulative ocular UV exposure (COUV) was calculated. A logistic regression analysis was used for multivariate analysis. <b>Results: </b>Cataract odds ratios in high COUV eyes were 5.35 for NUC, 1.87 for PSC, and 1.35 for RD. In eyes with WC, risk of COR ring-shaped opacity significantly increased but that of wedge-shaped opacity (CEN+) significantly decreased. In eyes without WC, risk of COR axle-shaped opacity (CEN–) and ring-shaped opacity significantly increased but that of wedge-shaped opacity (CEN+) significantly decreased. <b>Conclusions:</b> Increased COUV level among Han people may be a risk factor for the development of nuclear cataracts, PSC, retrodots and ring-shaped cortical cataract. Risk of ocular UV exposure for cortical cataract may differ by opacity shape.
DOI: 10.6084/m9.figshare.7992224.v1
title: Molecular discrimination of <i>Ancistrus</i> lineages (Siluriformes: Loricariidae) using barcode DNA tool

description: Although several species of <i>Ancistrus</i> have been described from the Amazon and Paraguay river basins in the states of Amazonas and Mato Grosso, Brazil, the taxonomic status of most specimens from these regions remains doubtful. In the present work, cytogenetic and molecular data were used to discriminate and isolate unexpected <i>Ancistrus</i> lineages from the Amazon and Paraguay basins. For that, it was used DNA barcoding based on mitochondrial Cytochrome Oxidase Subunit I (COI) gene and cytogenic data to perform such molecular discrimination. The analyzed sequences had 669 bp, of which 171 bp were conserved and 491 bp were variable. The Neighbor-joining and Bayesian analysis revealed 21 distinct groups in topology. The genetic distances within each group was 0.4%, 21 times smaller than the mean distance observed among groups, which was 8.4%. These values showed seven distinct lineages of <i>Ancistrus</i> from the studied points of the Amazon basin and eight lineages from the Paraguay basin points. Our results illustrate the efficiency of this technique for the discrimination of the <i>Ancistrus</i> lineages once it indicates the occurrence of cryptic species in these regions, which cannot yet be identified either with just chromosomal or morphological analyzes.
DOI: 10.6084/m9.figshare.7992230.v2
title: Dataset 1.1: Yeast proteome data

description: Dataset of protein features for <i>Saccharomyces cerevisiae</i> uniprot reference proteome
DOI: 10.6084/m9.figshare.7992218.v1
title: Hydrothermal synthesis and crystal structure of three-dimensional supramolecular zinc, manganese coordination polymers

description: Two new complexes [Zn<sub>2</sub>(pzdc)(L)<sub>2</sub>(H<sub>2</sub>O)]<sub>2n</sub>·2nH<sub>2</sub>O <b>(1)</b> and [Mn(<i>µ</i><sub>2</sub>-O)(H<sub>2</sub>O)<sub>2</sub>-(HL)]<sub>2n</sub>·2nNIPH <b>(2)</b> (H<sub>2</sub>pzdc = pyrazine-2,3-dicarboxylic acid, HL = 3-(2-Pyridyl) pyrazole, H<sub>2</sub>NIPH = 5-nitroisophthalic acid) have been hydrothermally synthesized and structurally characterized by elemental analysis, IR spectrum, UV spectrum, TG, fluorescence spectrum and single-crystal X-ray diffraction. Complex <b>1</b> shows two-dimensional (2D) network, which was stabilized by O–H···O, C–H···O hydrogen bonding and <i>π</i>-<i>π</i> interactions and extended into 3 D supramolecular architecture. Complex <b>2</b> is zero-dimensional structure, which was further extended into 3 D supramolecular framework through N–H···O, O–H···O, C–H···O hydrogen bonds and <i>π</i>-<i>π</i> interactions.
DOI: 10.6084/m9.figshare.7992230.v1
title: Dataset 1.1 : Yeast proteome data

description: Dataset of protein features for <i>Saccharomyces cerevisiae</i> uniprot reference proteome
DOI: 10.6084/m9.figshare.7992185
title: Supplementary materials for: Sidorov, 2019

description: <b>Supplementary materials for: Sidorov D.A. 2019. </b><b>Groundwater dependent fauna of coastal rivers and springs of the South Kuril Islands: first evidence on subterranean amphipods (Crustacea: Amphipoda). </b><b>Proceedings of the section of natural sciences of the Montenegrin Academy of Sciences and Arts - a tribute to academician Gordan S. Karaman 23: 209-221.</b><b><br></b> SUPPLEMENTARY FILE 1. Table 1. Source data and samples. SUPPLEMENTARY FILE 2. GMT map of the area.
DOI: 10.6084/m9.figshare.7992206.v1
title: Association between ultraviolet radiation exposure dose and cataract in Han people living in China and Taiwan: a cross-sectional study

description: <b>Purpose:</b> We investigated associations between ocular ultraviolet (UV) radiation exposure dose and cataract opacities among Han people living in China and Taiwan, to assess the effects of UV exposure intensity.<b></b> <b>Methods: </b>This cross-sectional study included Han people aged ≥40 years (1,801 individuals, 450 in Sanya, 636 in Taiyuan, and 715 in Taichung) as subjects who completed a questionnaire including items about diabetes, smoking, steroid use, work history, and time spent outdoors, and underwent an ophthalmic examination. Right eye axial length was measured using A-mode ultrasonography or IOLMaster. Slit-lamp imaging under maximum mydriasis was used to classify cataracts into three major types [cortical (COR), nuclear (NUC), and posterior subcapsular cataracts (PSC)] and two subtypes [retrodots (RD) and waterclefts (WC)] by one ophthalmologist. COR was divided into opacity presence (CEN+) or absence (CEN-) in the central 3-mm diameter area of the pupil. COR was also subdivided into three groups according to opacity shape: axle-shaped opacity concomitant with WC, wedge-shaped opacity around the pupil to the eye center, and ring-shaped opacity in the lens equator along the pupillary margin. The cumulative ocular UV exposure (COUV) was calculated. A logistic regression analysis was used for multivariate analysis. <b>Results: </b>Cataract odds ratios in high COUV eyes were 5.35 for NUC, 1.87 for PSC, and 1.35 for RD. In eyes with WC, risk of COR ring-shaped opacity significantly increased but that of wedge-shaped opacity (CEN+) significantly decreased. In eyes without WC, risk of COR axle-shaped opacity (CEN–) and ring-shaped opacity significantly increased but that of wedge-shaped opacity (CEN+) significantly decreased. <b>Conclusions:</b> Increased COUV level among Han people may be a risk factor for the development of nuclear cataracts, PSC, retrodots and ring-shaped cortical cataract. Risk of ocular UV exposure for cortical cataract may differ by opacity shape.
DOI: 10.6084/m9.figshare.7992101
title: III Simpósio Norte e Nordeste de Bioinformática

description: III Simpósio Norte e Nordeste de Bioinformática - PDF do Anal
DOI: 10.6084/m9.figshare.7992104
title: Modelling land cover changes in the tropical dry forest surrounding the Chamela-Cuixmala biosphere reserve, Mexico

description: Land-use change is one of the main threats to biodiversity conservation in tropical landscapes and natural protected areas are particularly threatened because of the transformation occurring at their neighbouring environments. We analysed the ‘land-cover’ change (LCC) occurring in the areas surrounding the Chamela-Cuixmala Biosphere Reserve (CCBR) in the Pacific coast of Jalisco, Mexico, during the last 40 years (split in two periods, 1970–1993/94 and 1993/94–2011/12). Supervised classifications were generated by applying a multi-temporal approach on Landsat Thematic Mapper (1993/94) and Satellite Pour l’Observation de la Terre SPOT (2011/12) imagery. The base line (t<sub>0</sub>) consisted of an historical 1:50,000 scale map of land-use/land-cover (LULC) made in 1970. In addition to LCC predictions for the next four decades, this study generated a variety of indicators identifying the location and intensity of LCC occurring in the CCBR’s surrounding landscapes. The main vegetation formations, tropical dry forest (TDF), and semi-deciduous tropical forest (SDTF), decreased in area 25% and 50%, respectively, during the 1970–1993/94 period. However, annual rates of change (ARC) showed a deacceleration in the reduction of main vegetation formations, for the period 1993/94–2011/12. This study generated indicators identifying the location and intensity of ‘land-cover’ changes occurring in the CCBR’s surrounding landscapes. Potential transition models made evident the CCBR’s key role as a reservoir of the region’s biodiversity associated to main vegetation types such as the tropical deciduous forest and the semi-deciduous forest.
DOI: 10.6084/m9.figshare.7992182.v1
title: Between Khyber And Bolan FULL

description: We have consistently held that there were two waves of dispersals of ‘Indo-Europeans’ into Indian sub-continent, the first around 8,000 BCE and the second around 2,000 BCE, of kṣatrīya and brāmhaṇ respectively. [Gadgil et al ,1998 : Peopling Of India, in Balasubramanian& Rao, The Indian Human Heritage, 115; The Two Waves, 08 Apr 18] Now the time has come to look for hard evidence on this distinction. We also need to bring accuracy into the loose expression ‘Central Asia / Near East’; because, though the two are contiguous, they are distinct. Such a distinction becomes all the more imperative if we are to distinguish between the kāṭhīyāvāḍī caḍḍī and the brāmhaṇ in Kōṁkaṇ. And it calls into question the very term ‘Indo-Europeans’ or ‘Aryans’ that has been used for so long.
DOI: 10.6084/m9.figshare.7992185.v1
title: Supplementary materials for: Sidorov2019

description: <b>Supplementary materials for: Sidorov2019, </b><b>Groundwater dependent fauna of coastal rivers and springs of the South Kuril Islands: first evidence on subterranean amphipods (Crustacea: Amphipoda)</b> SUPPLEMENTARY FILE 1. Table 1. Source data and samples. SUPPLEMENTARY FILE 2. GMT map of the area.
DOI: 10.6084/m9.figshare.7992104.v1
title: Modelling land cover changes in the tropical dry forest surrounding the Chamela-Cuixmala biosphere reserve, Mexico

description: Land-use change is one of the main threats to biodiversity conservation in tropical landscapes and natural protected areas are particularly threatened because of the transformation occurring at their neighbouring environments. We analysed the ‘land-cover’ change (LCC) occurring in the areas surrounding the Chamela-Cuixmala Biosphere Reserve (CCBR) in the Pacific coast of Jalisco, Mexico, during the last 40 years (split in two periods, 1970–1993/94 and 1993/94–2011/12). Supervised classifications were generated by applying a multi-temporal approach on Landsat Thematic Mapper (1993/94) and Satellite Pour l’Observation de la Terre SPOT (2011/12) imagery. The base line (t<sub>0</sub>) consisted of an historical 1:50,000 scale map of land-use/land-cover (LULC) made in 1970. In addition to LCC predictions for the next four decades, this study generated a variety of indicators identifying the location and intensity of LCC occurring in the CCBR’s surrounding landscapes. The main vegetation formations, tropical dry forest (TDF), and semi-deciduous tropical forest (SDTF), decreased in area 25% and 50%, respectively, during the 1970–1993/94 period. However, annual rates of change (ARC) showed a deacceleration in the reduction of main vegetation formations, for the period 1993/94–2011/12. This study generated indicators identifying the location and intensity of ‘land-cover’ changes occurring in the CCBR’s surrounding landscapes. Potential transition models made evident the CCBR’s key role as a reservoir of the region’s biodiversity associated to main vegetation types such as the tropical deciduous forest and the semi-deciduous forest.
DOI: 10.6084/m9.figshare.7992185.v2
title: Supplementary materials for: Sidorov2019

description: <b>Supplementary materials for: Sidorov2019, </b><b>Groundwater dependent fauna of coastal rivers and springs of the South Kuril Islands: first evidence on subterranean amphipods (Crustacea: Amphipoda)</b> SUPPLEMENTARY FILE 1. Table 1. Source data and samples. SUPPLEMENTARY FILE 2. GMT map of the area.
DOI: 10.6084/m9.figshare.12870002.v1
title: R0191_20170925a_videos

description: Rat 0191, skilled reaching data collected on 9/25/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12873044.v5
title: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna
DOI: 10.6084/m9.figshare.12873044.v7
title: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna
DOI: 10.6084/m9.figshare.7991999.v1
title: Genome annotation for Argopecten irradians irradians and Argopecten irradians concentricus

description: Genome annotation for Argopecten irradians irradians and Argopecten irradians concentricus
DOI: 10.6084/m9.figshare.12873017.v1
title: Additional file 1 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 1:Description Daphnia magna cDNA libraries from NCBI GenBank. EST sequences and cDNA library types of D. magna sequences retrieved from GenBank at the time of the analysis. (XLS 27 KB)
DOI: 10.6084/m9.figshare.12873044.v8
title: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna
DOI: 10.6084/m9.figshare.12873017
title: Additional file 1 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 1:Description Daphnia magna cDNA libraries from NCBI GenBank. EST sequences and cDNA library types of D. magna sequences retrieved from GenBank at the time of the analysis. (XLS 27 KB)
DOI: 10.6084/m9.figshare.12873020.v1
title: Additional file 2 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 2:Natural populations of Daphnia magna used for SNP validation and their environmental characteristics. List of populations from Belgium used for SNP validation and their environmental characteristics. N = population size; Fish = presence (1)/absence (0) of fish; Land use = high (1)/low (0) land use intensity; Parasite = presence (1)/absence (0) of the parasite Pasteuria ramosa. Sampling date and environmental variables as measured at the sampling sites are also listed. Transparency was measured by means of Secchi disk. (XLS 20 KB)
DOI: 10.6084/m9.figshare.12873044.v6
title: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna