cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7067897.v1
title: M. oryzae homologues to S. cerevisiae nucleolar proteins

description: Nucleolar proteins in the MoCKa pulldown and annotation of <i>M. oryzae</i> with the help of <i>S. cereviseae</i> annotation.
DOI: 10.6084/m9.figshare.7067690
title: Phylogeny and genetic structure of the goitered gazelle (Artiodactyla, Bovidae) in north-western China indicated by the hypervariable mitochondrial control region

description: The goitered gazelle, <i>Gazella subgutturosa</i>, is a medium-sized ungulate inhabiting arid and semi-arid regions in the Middle East and central Asia. The intraspecific classification of the species remains unclear. We analysed the genetic diversity in mitochondrial DNA control region (CR) sequences (976 bp) from 104 wild samples from the Xinjiang Uyghur Autonomous Region (XUAR) in north-west China, and reconstructed phylogeny with additional sequences from across the species’ range. We detected 58 haplotypes in XUAR populations, all but three of which were specific to single sampling sites. The phylogenetic analysis displayed two obvious clades of mtDNA haplotypes and the other haplotypes differed from the two clades. A median-joining network showed three groups of haplotypes were to a high extent concordant with the phylogenetic tree. The haplotype clustering was consistent with their geographic distribution. Nei’s net sequence divergences amongst the three groups ranged from 0.010 to 0.018 and indicated three subspecies, two of which inhabit XUAR. We detected strong differentiation between northern (NX) and southern (SX) XUAR populations overall (<i>F</i><sub>ST</sub> = 0.4448, <i>P</i>
DOI: 10.6084/m9.figshare.7067690.v1
title: Phylogeny and genetic structure of the goitered gazelle (Artiodactyla, Bovidae) in north-western China indicated by the hypervariable mitochondrial control region

description: The goitered gazelle, <i>Gazella subgutturosa</i>, is a medium-sized ungulate inhabiting arid and semi-arid regions in the Middle East and central Asia. The intraspecific classification of the species remains unclear. We analysed the genetic diversity in mitochondrial DNA control region (CR) sequences (976 bp) from 104 wild samples from the Xinjiang Uyghur Autonomous Region (XUAR) in north-west China, and reconstructed phylogeny with additional sequences from across the species’ range. We detected 58 haplotypes in XUAR populations, all but three of which were specific to single sampling sites. The phylogenetic analysis displayed two obvious clades of mtDNA haplotypes and the other haplotypes differed from the two clades. A median-joining network showed three groups of haplotypes were to a high extent concordant with the phylogenetic tree. The haplotype clustering was consistent with their geographic distribution. Nei’s net sequence divergences amongst the three groups ranged from 0.010 to 0.018 and indicated three subspecies, two of which inhabit XUAR. We detected strong differentiation between northern (NX) and southern (SX) XUAR populations overall (<i>F</i><sub>ST</sub> = 0.4448, <i>P</i>
DOI: 10.6084/m9.figshare.7067675
title: Should we remediate small molecule structures? If so, who should do it?

description: Problems can arise in crystallographic databases with errors and omissions in the representation of data that impede searches, and with errors in the actual data. While the Cambridge Crystallographic Data Centre with its Improvement Projects has solved many of the first category of problems, errors in atomic coordinates and other crystallographic data are surprisingly common. Although modern software warns of many types of error, such errors appear even in recently deposited Crystallographic Information Files. Richard Marsh found many examples of missed symmetry in assignment of the space group; such errors are now waning. Hydrogen atoms are commonly placed in calculated positions. Particularly for OH and NH groups involved in hydrogen bonds, occupancy factors may need to be reduced to 0.5 or the hydrogen atom positions may require amendment. Examples of acids and imidazole derivatives are provided, showing that sometimes only consideration of bond distances and angles at the heteroatom can distinguish between OH or NH and unprotonated O or N. Significant work by other researchers correcting mis-positioned hydrogen atoms in dihydrogen phosphates and water aggregates as well as mis-identified elements is also summarized. This review concludes with some suggestions for more comprehensive detection and correction of errors in deposited data.
DOI: 10.6084/m9.figshare.7067675.v1
title: Should we remediate small molecule structures? If so, who should do it?

description: Problems can arise in crystallographic databases with errors and omissions in the representation of data that impede searches, and with errors in the actual data. While the Cambridge Crystallographic Data Centre with its Improvement Projects has solved many of the first category of problems, errors in atomic coordinates and other crystallographic data are surprisingly common. Although modern software warns of many types of error, such errors appear even in recently deposited Crystallographic Information Files. Richard Marsh found many examples of missed symmetry in assignment of the space group; such errors are now waning. Hydrogen atoms are commonly placed in calculated positions. Particularly for OH and NH groups involved in hydrogen bonds, occupancy factors may need to be reduced to 0.5 or the hydrogen atom positions may require amendment. Examples of acids and imidazole derivatives are provided, showing that sometimes only consideration of bond distances and angles at the heteroatom can distinguish between OH or NH and unprotonated O or N. Significant work by other researchers correcting mis-positioned hydrogen atoms in dihydrogen phosphates and water aggregates as well as mis-identified elements is also summarized. This review concludes with some suggestions for more comprehensive detection and correction of errors in deposited data.
DOI: 10.6084/m9.figshare.7067546
title: Manuscript RSBL-2018-0432.R1 FIRST SET

description: This is raw data for manuscript Environmental heterogeneity promotes spatial resilience of phototrophic biofilms in streambeds published in Biology Letters.<br>
DOI: 10.6084/m9.figshare.7067546.v1
title: Manuscript RSBL-2018-0432.R1 FIRST SET

description: This is raw data for manuscript Environmental heterogeneity promotes spatial resilience of phototrophic biofilms in streambeds published in Biology Letters.<br>
DOI: 10.6084/m9.figshare.7067513
title: Supplementary Material for: Artemisinin-Daumone Hybrid Inhibits Cancer Cell-Mediated Osteolysis by Targeting Cancer Cells and Osteoclasts

description: <b><i>Background/Aims:</i></b> Bone metastasis of cancer cells decreases patient survival and quality of life. Hybridization via the covalent coupling of two bioactive natural products is a useful strategy for developing more potent anticancer agents by enhancing their bioavailability and avoiding drug resistance<b><i>.</i></b> <b><i>Methods:</i></b> The <i>in vivo</i> activities of artemisinin-daumone hybrid 15 (ARTD) were estimated in cancer cell-inoculated mice and ovariectomized mice. The viability, migration, and invasion of cancer cells were measured via MTT, wound-healing, and transwell invasion assays. ARTD-regulated transcription factors were detected with an RT<sup>2</sup> profiler PCR array kit and Western blotting. Osteoclastogenesis and osteoclast activity were detected with tartrate-resistant acid phosphatase staining, a pit formation assay, gelatin zymography, and a cathepsin K ELISA assay. <b><i>Results:</i></b> ARTD blocked cancer-associated osteolysis more potently than artemisinin in mice with intratibially inoculated breast cancer or lung cancer cells. ARTD inhibited the viability, migration, and invasion of breast and lung cancer cells in the absence or presence of transforming growth factor-β1. ARTD treatment induced the expression of tumor suppressive activating transcription factor 3 and inhibited oncogenic E2F transcription factor 1 expression at the mRNA and protein levels. ARTD inhibited receptor activator of nuclear factor kappa-B ligand-induced osteoclast formation and bone resorbing activity by reducing the secreted levels of matrix metalloproteinase-9 and cathepsin K. Furthermore, ARTD prevented estrogen deficiency-induced bone loss in ovariectomized mice. <b><i>Conclusion:</i></b> ARTD may be a promising candidate for inhibiting cancer-induced bone destruction. The application of ARTD may be extended to patients with chemotherapy-induced ovarian failure or postmenopausal osteoporosis.
DOI: 10.6084/m9.figshare.7067501
title: Mapping mammalian replication domains using the ion torrent semiconductor sequencing platform

description: Here, we show that semiconductor-based sequencing technology can be used to map mammalian replication domains, chromosomal units with similar DNA replication timing. Replicating DNA purified from mammalian cells was successfully sequenced by the Ion Torrent platform. The resultant replication domain map of mouse embryonic stem cells is comparable to those obtained by the conventional microarray-based method.
DOI: 10.6084/m9.figshare.7067501.v1
title: Mapping mammalian replication domains using the ion torrent semiconductor sequencing platform

description: Here, we show that semiconductor-based sequencing technology can be used to map mammalian replication domains, chromosomal units with similar DNA replication timing. Replicating DNA purified from mammalian cells was successfully sequenced by the Ion Torrent platform. The resultant replication domain map of mouse embryonic stem cells is comparable to those obtained by the conventional microarray-based method.
DOI: 10.6084/m9.figshare.7067456
title: Supplementary Material for: Cutaneous Arteriolosclerosis Is Not Specific to Ischemic Hypertensive Leg Ulcers

description: <b><i>Background:</i></b> The histological characteristic of hypertensive leg ulcers (HLU) is the presence of “arteriolosclerosis.” The pertinence of performing a skin biopsy to diagnose HLU is questionable, as cutaneous arteriolosclerosis may be related to patient comorbidities. The objective here was to evaluate the frequency of arteriolosclerosis in skin leg biopsies performed in patients without ulcer and in control patients with HLU. <b><i>Methods:</i></b> We performed a retrospective study between January 2013 and July 2014. Patients were included if they had undergone a deep skin biopsy on the lower limbs, in the absence of any leg ulcer. Controls were patients with typical HLU. <b><i>Results:</i></b> Fifty-eight patients and 6 controls were included. Hypertension was present in 25 patients (43%). Arteriolosclerosis, defined as fibrous endarteritis, was present in 35 out of 58 patients (60%) and in all of the controls. No hyalinosis or hyperplastic proliferative arteriolosclerosis was observed in the patients or controls. Only age was an independent factor associated with the presence of cutaneous arteriolosclerosis (<i>p</i> &lt; 0.0001). <b><i>Conclusion:</i></b> Cutaneous arteriolosclerosis is significantly and independently associated with age. Thus, skin biopsy seems not to be necessary for the diagnosis of HLU but only for a differential diagnosis.
DOI: 10.6084/m9.figshare.7067456.v1
title: Supplementary Material for: Cutaneous Arteriolosclerosis Is Not Specific to Ischemic Hypertensive Leg Ulcers

description: <b><i>Background:</i></b> The histological characteristic of hypertensive leg ulcers (HLU) is the presence of “arteriolosclerosis.” The pertinence of performing a skin biopsy to diagnose HLU is questionable, as cutaneous arteriolosclerosis may be related to patient comorbidities. The objective here was to evaluate the frequency of arteriolosclerosis in skin leg biopsies performed in patients without ulcer and in control patients with HLU. <b><i>Methods:</i></b> We performed a retrospective study between January 2013 and July 2014. Patients were included if they had undergone a deep skin biopsy on the lower limbs, in the absence of any leg ulcer. Controls were patients with typical HLU. <b><i>Results:</i></b> Fifty-eight patients and 6 controls were included. Hypertension was present in 25 patients (43%). Arteriolosclerosis, defined as fibrous endarteritis, was present in 35 out of 58 patients (60%) and in all of the controls. No hyalinosis or hyperplastic proliferative arteriolosclerosis was observed in the patients or controls. Only age was an independent factor associated with the presence of cutaneous arteriolosclerosis (<i>p</i> &lt; 0.0001). <b><i>Conclusion:</i></b> Cutaneous arteriolosclerosis is significantly and independently associated with age. Thus, skin biopsy seems not to be necessary for the diagnosis of HLU but only for a differential diagnosis.
DOI: 10.6084/m9.figshare.7067441
title: POSTER_Rodrigo Liscovsky Barrera.pdf

description: Inspired by recent discussions on the responsible use of scientometrics in research evaluation, I seek to develop a multi-level and mixed-method approach to study the interaction of traditional and emerging patterns of internationalisation in contemporary South American biomedical research. This poster presents a proposal to achieve this based on methodological reflections and preliminary findings from a recent exploratory fieldwork conducted in Argentina, Chile and Uruguay.
DOI: 10.6084/m9.figshare.7067441.v1
title: POSTER_Rodrigo Liscovsky Barrera.pdf

description: Inspired by recent discussions on the responsible use of scientometrics in research evaluation, I seek to develop a multi-level and mixed-method approach to study the interaction of traditional and emerging patterns of internationalisation in contemporary South American biomedical research. This poster presents a proposal to achieve this based on methodological reflections and preliminary findings from a recent exploratory fieldwork conducted in Argentina, Chile and Uruguay.
DOI: 10.6084/m9.figshare.7067435
title: Supplementary Material for: Recall and Retention of Consent Procedure Contents and Decisions: Results of a Randomized Controlled Trial

description: <b><i>Background:</i></b> Residual tissue samples, i.e., samples excised for diagnosis or during treatment, are commonly used for medical research. In the Netherlands, they can be used provided the patient did not opt out of this use. Previous research has shown that recall of the informed consent procedure for tissue use is poor. Here, we investigate recall of three consent procedures: informed consent, opt-out, and opt-out plus (an opt-out procedure with an information procedure similar to that of informed consent). <b><i>Methods:</i></b> Patients (<i>n</i> = 1,319) with a variety of diseases were randomized into three trial arms: informed consent, opt-out plus, and opt-out. Questionnaires were administered 6 weeks and 6 months after randomization. <b><i>Results:</i></b> Six hundred and seventy-three and 553 patients returned the 6-week and 6-month questionnaire, respectively. In the informed consent arm, recall of having received a brochure (55.3%) or oral information (69.4%) was similar to that in the opt-out plus arm (48.5 and 71.6%, respectively), at the 6-week assessment. Significantly more respondents in the informed consent and the opt-out plus arms versus the opt-out arm recalled that they had been informed about being able to control tissue use and which consent procedure they had experienced (6-week questionnaire range 53.2–75.8 vs. 13.9–16.1%; 6-month questionnaire range 43.5–84.2 vs. 3.2–35.4%). There were no significant differences between the informed consent and opt-out plus arms in this regard. <b><i>Conclusions:</i></b> Recall of the consent procedure was similar in opt-out plus and informed consent procedures. Overall, recall was moderate, indicating that there is room for improvement in the quality of information provision.
DOI: 10.6084/m9.figshare.7067411
title: AAA STL file from Accounting for residence-time in blood rheology models: do we really need non-Newtonian blood flow modelling in large arteries?

description: AAA computer model
DOI: 10.6084/m9.figshare.7067411.v1
title: AAA STL file from Accounting for residence-time in blood rheology models: do we really need non-Newtonian blood flow modelling in large arteries?

description: AAA computer model
DOI: 10.6084/m9.figshare.7067402
title: Supplementary Material for: Panax Quinquefolium Saponins Attenuate Myocardial Dysfunction Induced by Chronic Ischemia

description: <b><i>Background/Aims:</i></b> Previous studies in rat models of myocardial ischemia showed that Panax quinquefolium saponins (PQS) could attenuate ischemic/reperfusion injury, increase vessel density and improve cardiac function. In the current study, we examined whether PQS could attenuate myocardial dysfunction in a swine model of chronic myocardial ischemia (CMI). <b><i>Methods:</i></b> CMI was established in Bama mini-pigs by placing amroid constrictor on the left anterior descending artery (LAD). Starting from 2 months after the surgery, pigs randomly received PQS (30 mg/kg/day), atorvastatin (1.5 mg/kg/day), or no drug for one month (n=6). A group of pigs receiving sham surgery was included as an additional control. Glucose utilization was assessed with positron emission tomography-computer tomography (PET-CT). Cardiac function was assessed with echocardiography. Myocyte size, nuclear density, and arteriolar density were examined in tissue section obtained from the ischemia area. Potential molecular targets of PQS were identified using proteomic analysis with isobaric tags for relative and absolute quantitation (iTARQ) and network pharmacology. <b><i>Results:</i></b> In comparison to the sham controls, pigs implanted with ameroid constrictor had decreased ventricular wall motion, left ventricular ejection fraction (LVEF), and glucose utilization. PQS significantly increased cardiac function and glucose utilization. Arteriole density and myocyte nuclear density were increased. Myocyte diameter was decreased. PQS also attenuated the CMI-induced change of protein expression profile. The effects of atorvastatin were generally similar to that of PQS. However, PQS attenuated the reduction of left ventricular systolic WT induced by CMI more robustly than atorvastatin. <b><i>Conclusion:</i></b> The results from the current study supports the use of PQS in patients with coronary artery disease.
DOI: 10.6084/m9.figshare.7067357
title: Supplementary Material for: Local Anaesthetic (Medical) Thoracoscopy Services in the UK

description: <b><i>Background:</i></b> Local anaesthetic thoracoscopy (LAT) is an important procedure in the management pathway of patients with pleural effusions, particularly those with suspected malignancy. The last survey evaluating the use and development of LAT services in the UK was conducted over a decade ago. <b><i>Objectives:</i></b> We performed a survey of LAT practices in the UK to explore procedural preferences and variations in practice. <b><i>Methods:</i></b> The online survey was cascaded via regional pleural specialists to sites performing LAT. One response per site was accepted. <b><i>Results:</i></b> Thirty-seven responses were received from England, Scotland and Wales. Most centres have regular access to a dedicated list and a designated area to perform LAT. 97% of the centres have at least 2 trained thoracoscopists. Some variation in practice is seen with patient preparation pre-procedure and medication use. Other procedures, such as insertion of indwelling pleural catheters and adhesiolysis, are not uncommon to be undertaken at the time of LAT. <b><i>Conclusions:</i></b> Overall, the results are comparable, excepting some minor variations in patient preparation pre-procedure. We hope that this survey functions as an information resource for centres developing a LAT service or for those considering expansion.
DOI: 10.6084/m9.figshare.7067357.v1
title: Supplementary Material for: Local Anaesthetic (Medical) Thoracoscopy Services in the UK

description: <b><i>Background:</i></b> Local anaesthetic thoracoscopy (LAT) is an important procedure in the management pathway of patients with pleural effusions, particularly those with suspected malignancy. The last survey evaluating the use and development of LAT services in the UK was conducted over a decade ago. <b><i>Objectives:</i></b> We performed a survey of LAT practices in the UK to explore procedural preferences and variations in practice. <b><i>Methods:</i></b> The online survey was cascaded via regional pleural specialists to sites performing LAT. One response per site was accepted. <b><i>Results:</i></b> Thirty-seven responses were received from England, Scotland and Wales. Most centres have regular access to a dedicated list and a designated area to perform LAT. 97% of the centres have at least 2 trained thoracoscopists. Some variation in practice is seen with patient preparation pre-procedure and medication use. Other procedures, such as insertion of indwelling pleural catheters and adhesiolysis, are not uncommon to be undertaken at the time of LAT. <b><i>Conclusions:</i></b> Overall, the results are comparable, excepting some minor variations in patient preparation pre-procedure. We hope that this survey functions as an information resource for centres developing a LAT service or for those considering expansion.
DOI: 10.6084/m9.figshare.7067369.v1
title: Collection of morphological matrices (some including extinct taxa) and related phylogenetic inferences

description: This file set contains (version 1) information, and analysis files, related to morphological data matrices collected from literature (including some we published) to sum up some principal features of these matrices, mainly how tree(un)like they are.<br>Version 1 includes<b>XLXS-File <i>OverviewTables</i> </b>summarising general signal information (behaviour under parsimony and NJ tree-building in relation to matrix and individual Delta Values, a measure for treelikeness.<b> </b><br><b>7z-Archive <i>Cycadales </i></b>including the matrices of Stevenson (<i>Mem. NY Bot. Garden, </i><b>57</b>: 8–55, 1990) and my extension of it (Grimm GW. 1999. Diploma thesis. Eberhard Karls Universität) including extinct (potential) cycads as well as some inference based on them. Matrices are provided in NEXUS format (*.nex), trees in NEWICK (*.tre – single tree; *.trees – tree collections) and networks in Splits-NEXUS format (*.nxs; *.dist; use SplitsTree): MPT = most-parsimonious tree samples, BioNJ = neighbour-joining tree fulfilling the least-squares optimality criterion), MD = neighbour-net splits graphs.<br>