cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8168714.v1
title: Triceps surae muscle–subtendon interaction differs between young and older adults

description: <b><i>Background</i></b>: Mechanical power generated via triceps surae muscle-tendon interaction during walking is important for walking performance. This interaction is made complex by distinct “subtendons” arising from the lateral and medial gastrocnemius (GAS) and soleus (SOL) muscles. Comparative data and our own in vivo evidence allude to a reduced capacity for sliding between adjacent subtendons compromising the Achilles tendon in old age. However, its unclear if and how these changes affect muscle contractile behavior.<b><i>Objective</i></b>: We investigated aging effects on triceps surae muscle-subtendon interaction using dual-probe ultrasound imaging during isolated muscle contractions. We hypothesized that, compared to young adults, older adults would have more uniform subtendon tissue displacements that are accompanied by anatomically consistent differences in GAS versus SOL muscle length change behavior.<b><i>Materials and Methods</i></b>: 9 younger subjects (age: 25.1 ± 5.6 years) and 10 older adult subjects (age: 74.3 ± 3.4 years) completed a series of ramped maximum isometric voluntary contractions at ankle angles spanning 0° (neutral) to 30° plantarflexion. Two linear array ultrasound transducers simultaneously recorded GAS and SOL fascicle kinematics and tissue displacements in their associated tendinous structures.<b><i>Results</i></b>: We revealed that older adults have more uniform subtendon tissue displacements that extend to anatomically consistent and potentially unfavorable changes in muscle contractile behavior – evidenced by smaller differences between gastrocnemius and soleus peak shortening during isometric force generation.<b><i>Conclusions</i></b>: These findings provide an important biomechanical basis for previously reported correlations between more uniform Achilles subtendon behavior and reduced ankle moment generation during waking in older adults.
DOI: 10.6084/m9.figshare.8168822
title: HMGA1 negatively regulates NUMB expression at transcriptional and post transcriptional level in glioblastoma stem cells

description: Glioblastoma (GBM) is a lethal, fast-growing brain cancer, affecting 2–3 per 100,000 adults per year. It arises from multipotent neural stem cells which have reduced their ability to divide asymmetrically and hence divide symmetrically, generating increasing number of cancer stem cells, fostering tumor growth. We have previously demonstrated that the architectural transcription factor HMGA1 is highly expressed in brain tumor stem cells (BTSCs) and that its silencing increases stem cell quiescence, reduces self-renewal and sphere-forming efficiency in serial passages, suggesting a shift from symmetric to asymmetric division. Since NUMB expression is fundamental for the fulfillment of asymmetric division in stem cells, and is lost or reduced in many tumors, including GBM, we have investigated the ability of HMGA1 to regulate NUMB expression. Here, we show that HMGA1 negatively regulates NUMB expression at transcriptional level, by binding its promoter and counteracting c/EBP-β and at posttranscriptional level, by regulating the expression of MSI1 and of miR-146a. Finally, we report that HMGA1 knockdown-induced NUMB upregulation leads to the downregulation of the NOTCH1 pathway. Therefore, the data reported here indicate that HMGA1 negatively regulates NUMB expression in BTSCs, further supporting HMGA1 targeting as innovative and effective anti-cancer therapy.
DOI: 10.6084/m9.figshare.8168849
title: mRNA levels are buffered upon knockdown of RNA decay and translation factors via adjustment of transcription rates in human HepG2 cells

description: Evidence from yeast and mammals argues the existence of cross-talk between transcription and mRNA decay. Stabilization of transcripts upon depletion of mRNA decay factors generally leads to no changes in mRNA abundance, attributing this to decreased transcription rates. We show that knockdown of human XRN1, CNOT6 and ETF1 genes in HepG2 cells led to significant alteration in stability of specific mRNAs, alterations in half-life were inversely associated with transcription rates, mostly not resulting in changes in abundance. We demonstrate the existence of the gene expression buffering mechanism in human cells that responds to both transcript stabilization and destabilization to maintain mRNA abundance via altered transcription rates and may involve translation. We propose that this buffering may hold novel cancer therapeutic targets.
DOI: 10.6084/m9.figshare.8168882.v2
title: Habitat use of the white-winged snowfinch Montifringilla nivalis nivalis

description: Database of Snowfinch observations with coordinates and year.
DOI: 10.6084/m9.figshare.8168033.v1
title: Non-parametric analysis of the effects of αS1-casein genotype and parturition non-genetic factors on milk yield and composition in Murciano-Granadina goats

description: Limited sample sizes imply parametric assumptions could be violated, even if traits have been reported to fulfil parametric assumptions. Parametric studies have addressed a non-significant influence of CSN1S1 genes on Murciano-Granadina milk yield, fat, protein and dry extract. We used non-parametric categorical tests to find alternative statistical methods to analyse the power to explain the variability found in the population regarding milk yield and its components. We analysed 2090 records for milk yield, and its components from 710 Murciano-Granadina CSN1S1-genotyped goats. Categorical regression equations were issued to predict which and at what level these factors may determine milk yield (kg), fat (kg), protein (kg) and dry extract (kg). All environmental (farm and parturition year) and animal-inherent factors (genotype, birth type and age) resulted statistically significant (<i>p</i> Non-parametric tests are crucial if normality and heteroskedasticity analyses fail.Murciano-Granadina milk traits compared with highly selected international breeds’.E allele combinations and BB reported highest effects on milk components and yield. Non-parametric tests are crucial if normality and heteroskedasticity analyses fail. Murciano-Granadina milk traits compared with highly selected international breeds’. E allele combinations and BB reported highest effects on milk components and yield.
DOI: 10.6084/m9.figshare.8168822.v1
title: HMGA1 negatively regulates NUMB expression at transcriptional and post transcriptional level in glioblastoma stem cells

description: Glioblastoma (GBM) is a lethal, fast-growing brain cancer, affecting 2–3 per 100,000 adults per year. It arises from multipotent neural stem cells which have reduced their ability to divide asymmetrically and hence divide symmetrically, generating increasing number of cancer stem cells, fostering tumor growth. We have previously demonstrated that the architectural transcription factor HMGA1 is highly expressed in brain tumor stem cells (BTSCs) and that its silencing increases stem cell quiescence, reduces self-renewal and sphere-forming efficiency in serial passages, suggesting a shift from symmetric to asymmetric division. Since NUMB expression is fundamental for the fulfillment of asymmetric division in stem cells, and is lost or reduced in many tumors, including GBM, we have investigated the ability of HMGA1 to regulate NUMB expression. Here, we show that HMGA1 negatively regulates NUMB expression at transcriptional level, by binding its promoter and counteracting c/EBP-β and at posttranscriptional level, by regulating the expression of MSI1 and of miR-146a. Finally, we report that HMGA1 knockdown-induced NUMB upregulation leads to the downregulation of the NOTCH1 pathway. Therefore, the data reported here indicate that HMGA1 negatively regulates NUMB expression in BTSCs, further supporting HMGA1 targeting as innovative and effective anti-cancer therapy.
DOI: 10.6084/m9.figshare.8168849.v1
title: mRNA levels are buffered upon knockdown of RNA decay and translation factors via adjustment of transcription rates in human HepG2 cells

description: Evidence from yeast and mammals argues the existence of cross-talk between transcription and mRNA decay. Stabilization of transcripts upon depletion of mRNA decay factors generally leads to no changes in mRNA abundance, attributing this to decreased transcription rates. We show that knockdown of human XRN1, CNOT6 and ETF1 genes in HepG2 cells led to significant alteration in stability of specific mRNAs, alterations in half-life were inversely associated with transcription rates, mostly not resulting in changes in abundance. We demonstrate the existence of the gene expression buffering mechanism in human cells that responds to both transcript stabilization and destabilization to maintain mRNA abundance via altered transcription rates and may involve translation. We propose that this buffering may hold novel cancer therapeutic targets.
DOI: 10.6084/m9.figshare.8168882
title: Habitat use of the white-winged snowfinch Montifringilla nivalis nivalis

description: Database of Snowfinch observations with coordinates and year.
DOI: 10.6084/m9.figshare.8168882.v1
title: Habitat use of the white-winged snowfinch Montifringilla nivalis nivalis

description: Database of Snowfinch observations with coordinates and year.
DOI: 10.6084/m9.figshare.8174561
title: Basic principles of the virulence of <i>Cryptococcus</i>

description: Among fungal pathogens, <i>Cryptococcus neoformans</i> has gained great importance among the scientific community of several reasons. This fungus is the causative agent of cryptococcosis, a disease mainly associated to HIV immunosuppression and characterized by the appearance of meningoencephalitis. Cryptococcal meningitis is responsible for hundreds of thousands of deaths every year. Research of the pathogenesis and virulence mechanisms of this pathogen has focused on three main different areas: Adaptation to the host environment (nutrients, pH, and free radicals), mechanism of immune evasion (which include phenotypic variations and the ability to behave as a facultative intracellular pathogen), and production of virulence factors. <i>Cryptococcus neoformans</i> has two phenotypic characteristics, the capsule and synthesis of melanin that have a profound effect in the virulence of the yeast because they both have protective effects and induce host damage as virulence factors. Finally, the mechanisms that result in dissemination and brain invasion are also of key importance to understand cryptococcal disease. In this review, I will provide a brief overview of the main mechanisms that makes <i>C. neoformans</i> a pathogen in susceptible patients. <b>Abbreviations</b>: RNS: reactive nitrogen species; BBB: brain blood barrier; GXM: glucuronoxylomannan; GXMGal: glucuronoxylomannogalactan
DOI: 10.22023/mdx.8168135.v2
title: Zoe Burt - Ceres - MoDA arts residency

description: The aim of the residency was to use objects from MoDA's collection as a starting point for exploration of natural prints and dyes with the aim of raising the awareness of sustainability in design research.<br><br>These documents highlight the inspiration and design process together with outcomes.<br>
DOI: 10.6084/m9.figshare.8174558
title: A simple and versatile authenticity assay of coffee products by single-nucleotide polymorphism genotyping

description: Interspecific single-nucleotide polymorphisms (SNPs) in the <i>rbcL</i> DNA barcode have been strictly validated and adopted as a designed SNP genotyping maker to discriminate between two major coffee species, <i>Coffea arabica</i> and <i>C. canephora</i>, and to estimate the mixing ratio of DNA from <i>C. arabica</i>/<i>C. canephora</i> in this study. The SNP genotyping is applicable to not only green (unroasted) coffee beans, but also processed coffee products (roasted coffee beans and instant coffee powder), in which genomic DNA is degraded, because the genotyping developed in this study requires only 10 copies of 63-bp-long DNA fragments of <i>rbcL</i> gene. The authenticity assay established in this study has several advantages: a high versatility to DNA sample conditions; simple and rapid procedures (only two steps; DNA extraction and SNP genotyping); the feasibility in coffee business for practical use to prevent false advertising and provide quality control. <b>Abbreviations:</b> SNP: single-nucleotide polymorphism; SBS: single base substitution; ISR: intergenic spacer region; INDEL: insertion-deletion. SNP Genotyping: Required only 10 copies of 63-bp-long DNA fragment of rbcL gene.
DOI: 10.6084/m9.figshare.8174711.v1
title: Mutation pressure and natural selection on codon usage in chloroplast genes of two species in <i>Pisum</i> L. (Fabaceae: Faboideae)

description: This study was attempted to focus on the pattern of codon usage bias (CUB) of chloroplast genes in two species of <i>Pisum viz</i>. <i>P. fulvum</i> and <i>P. sativum</i> and to identify the factors which influence CUB. Bioinformatic tools were used to understand codon usage pattern in the protein-coding sequences of <i>Pisum</i> chloroplast genomes. It was found that GC content was lower than AT content in the genes. Low synonymous codon usage order (SCUO) values of genes indicated low CUB in chloroplast genes of <i>Pisum</i> species. Heatmaps showed positive correlations of GC3 with all the GC and AT ending codons. Neutrality plot analysis revealed that natural selection might have played a prominent role over mutation pressure in sculpturing the CUB of chloroplast genes in these two taxa. Positive correlation between SCUO and mRNA free energy (mFE) suggested that higher energy release by entire mRNA was related to high degree of CUB. Further, highly significant (<i>p</i>
DOI: 10.22023/mdx.8168351.v1
title: Zoe Burt - Ceres - MoDA arts residency

description: The aim of the residency was to use objects from MoDA's collection as a starting point for exploration of natural prints and dyes with the aim of raising the profile of MoDA's collection for textile research in practise and to bring greater awareness of sustainability in design research.
DOI: 10.6084/m9.figshare.8174297
title: Preliminary report on the genetic structure of <i>Glyphoglossus molossus</i> (Anura: Microhylidae) from the Khorat Plateau, north-eastern Thailand

description: <i>Glyphoglossus molossus</i>, is one of the most economically important amphibians in the Khorat Plateau, north-eastern Thailand. It is categorised as a near-threatened species by IUCN due to over-exploitation. Here, we examined the genetic structure of <i>G. molossus</i> using partial mitochondrial cytochrome-b gene sequences from specimens collected at 11 localities. The sequence analysis revealed the presence of 15 haplotypes, 5 of which are shared by 2 or more populations, and 10 haplotypes that are confined to a single population. The relatively low haplotype (<i>h</i>) and nucleotide (<i>π</i>) diversities suggest that the Phu Phan Mountain Range is not high enough to act as an effective dispersal barrier between the Sakon Nakhon and Khorat Basins. However, AMOVA and phylogenetic analyses based on Maximum likelihood (ML) and Bayesian inference (BI) strongly supported the presence of two genetically divergent clades, Sakon Nakhon Basin and the northern part of the Khorat Basin (clade A) and the southern part of the Khorat Basin (clade B). These two lineages are separated by substantial geographical distance, which has putatively resulted in a reduction of gene flow. Further studies, with more extensive genetic sampling, especially from throughout the species range will aid in better interpreting our results.
DOI: 10.6084/m9.figshare.8174591.v1
title: Nectar robbing does not affect female reproductive success of an endangered <i>Antirrhinum</i> species, Plantaginaceae

description: <b>Background:</b> Nectar robbers in many plant species affect female reproductive success, usually decreasing the amount of seed produced by plants, which can affect populations persistence. <b>Aims:</b> To evaluate the impact of nectar robbers on the viability of the populations, we investigated the effects of nectar robbing on the female reproductive success of a threatened snapdragon species in four populations over 2 years. <b>Methods:</b> We observed insect visitors and their behaviour and quantified the percentage of robbed and non-robbed flowers and the production of fruits and seeds. <b>Results:</b> The results showed the degree of variation in nectar robbing among the populations and between years within the populations. Nectar robbers were detected in only two populations, and all were <i>Bombus terrestris</i>. Differences in flower size among populations were not related to the nectar robbing behaviour of <i>B. terrestris</i>. A comparison of the percentage of fructification and seed production between flowers that were and were not robbed showed no evidence of a negative effect of nectar robbing. <b>Conclusions:</b> Our study reports for the first time on nectar robbing in <i>Antirrhinum</i> species and concludes that this does not affect the female reproductive success of individuals or the viability of <i>A. valentinum</i> populations.
DOI: 10.6084/m9.figshare.8174711
title: Mutation pressure and natural selection on codon usage in chloroplast genes of two species in <i>Pisum</i> L. (Fabaceae: Faboideae)

description: This study was attempted to focus on the pattern of codon usage bias (CUB) of chloroplast genes in two species of <i>Pisum viz</i>. <i>P. fulvum</i> and <i>P. sativum</i> and to identify the factors which influence CUB. Bioinformatic tools were used to understand codon usage pattern in the protein-coding sequences of <i>Pisum</i> chloroplast genomes. It was found that GC content was lower than AT content in the genes. Low synonymous codon usage order (SCUO) values of genes indicated low CUB in chloroplast genes of <i>Pisum</i> species. Heatmaps showed positive correlations of GC3 with all the GC and AT ending codons. Neutrality plot analysis revealed that natural selection might have played a prominent role over mutation pressure in sculpturing the CUB of chloroplast genes in these two taxa. Positive correlation between SCUO and mRNA free energy (mFE) suggested that higher energy release by entire mRNA was related to high degree of CUB. Further, highly significant (<i>p</i>
DOI: 10.6084/m9.figshare.8174879
title: Analysis of pig transcriptomes suggests a global regulation mechanism enabling temporary bursts of circular RNAs

description: To investigate the dynamics of circRNA expression in pig testes, we designed specific strategies to individually study circRNA production from intron lariats and circRNAs originating from back-splicing of two exons. By applying these methods on seven Total-RNA-seq datasets sampled during the testicular puberty, we detected 126 introns in 114 genes able to produce circRNAs and 5,236 exonic circRNAs produced by 2,516 genes. Comparing our RNA-seq datasets to datasets from the literature (embryonic cortex and postnatal muscle stages) revealed highly abundant intronic and exonic circRNAs in one sample each in pubertal testis and embryonic cortex, respectively. This abundance was due to higher production of circRNA by the same genes in comparison to other testis samples, rather than to the recruitment of new genes. No global relationship between circRNA and mRNA production was found. We propose ExoCirc-9244 (<i>SMARCA5</i>) as a marker of a particular stage in testis, which is characterized by a very low plasma estradiol level and a high abundance of circRNA in testis. We hypothesize that the abundance of testicular circRNA is associated with an abrupt switch of the cellular process to overcome a particular challenge that may have arisen in the early stages of steroid production. We also hypothesize that, in certain circumstances, isoforms and circular transcripts from different genes share functions and that a global regulation of circRNA production is established. Our data indicate that this massive production of circRNAs is much more related to the structure of the genes generating circRNAs than to their function. <b>Abbreviations:</b> PE: Paired Ends; CR: chimeric Read; SR: Split Read; circRNA: circular RNA; NC: non conventional; ExoCirc-RNA: exonic circular RNA; IntroLCirc-: name of a porcine intronic lariat circRNA; ExoCirc-: name of a porcine exonic circRNA; IntronCircle-: name of a porcine intron circle; sisRNA: stable intronic sequence RNA; P: porcine breed Pietrain; LW: porcine breed Large White; RT: reverse transcription/reverse transcriptase; Total-RNA-seq: RNA-seq obtained from total RNA after ribosomal depletion; mRNA-seq: RNA-seq of poly(A) transcripts; TPM: transcripts per million; CR-PM: chimeric reads per million; RBP: RNA binding protein; miRNA: micro RNA; E2: estradiol; DHT: dihydrotestesterone
DOI: 10.6084/m9.figshare.8174561.v1
title: Basic principles of the virulence of <i>Cryptococcus</i>

description: Among fungal pathogens, <i>Cryptococcus neoformans</i> has gained great importance among the scientific community of several reasons. This fungus is the causative agent of cryptococcosis, a disease mainly associated to HIV immunosuppression and characterized by the appearance of meningoencephalitis. Cryptococcal meningitis is responsible for hundreds of thousands of deaths every year. Research of the pathogenesis and virulence mechanisms of this pathogen has focused on three main different areas: Adaptation to the host environment (nutrients, pH, and free radicals), mechanism of immune evasion (which include phenotypic variations and the ability to behave as a facultative intracellular pathogen), and production of virulence factors. <i>Cryptococcus neoformans</i> has two phenotypic characteristics, the capsule and synthesis of melanin that have a profound effect in the virulence of the yeast because they both have protective effects and induce host damage as virulence factors. Finally, the mechanisms that result in dissemination and brain invasion are also of key importance to understand cryptococcal disease. In this review, I will provide a brief overview of the main mechanisms that makes <i>C. neoformans</i> a pathogen in susceptible patients. <b>Abbreviations</b>: RNS: reactive nitrogen species; BBB: brain blood barrier; GXM: glucuronoxylomannan; GXMGal: glucuronoxylomannogalactan
DOI: 10.6084/m9.figshare.8174687.v1
title: Transthyretin stabilization activity of the catechol-<i>O</i>-methyltransferase inhibitor tolcapone (SOM0226) in hereditary ATTR amyloidosis patients and asymptomatic carriers: proof-of-concept study<sup>#</sup>

description: <b>Objective:</b> To assess the transthyretin (TTR) stabilization activity of tolcapone (SOM0226) in patients with hereditary ATTR amyloidosis, asymptomatic carriers and healthy volunteers. <b>Methods:</b> A phase IIa proof-of-concept trial included two phases separated by a 6-week washout period. Phase A: single 200 mg dose of tolcapone; phase B: three 100 mg doses taken at 4 h intervals. The primary efficacy variable was TTR stabilization. <b>Results:</b> Seventeen subjects were included (wild type, <i>n</i> = 6; mutation TTR Val30Met, <i>n</i> = 11). TTR stabilization was observed in all participants. Two hours after dosing, 82% of participants in phase A and 93% of those in phase B reached a TTR stabilization value of at least 20%. In phase A, there was an increase of 52% in TTR stabilization vs baseline values 2 h after dosing, which decreased to 22.9% at 8 h. In phase B, there was a significant increase of 38.8% in TTR stabilization 2 h after the first 100 mg dose. This difference was maintained after 10 h and decreased after 24 h. No serious adverse events were observed. <b>Conclusions:</b> The ability of tolcapone for stabilizing TTR supports further development and repositioning of the drug for the treatment of ATTR amyloidosis. <b>Trial registration:</b> EudraCT identifier: 2014-001586-27 <b>Trial registration:</b>ClinicalTrials.gov identifier: NCT02191826.