cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11282159.v1
title: Emergence time dataset from Temporal isolation between sympatric host plants cascades across multiple trophic levels of host-associated insects

description: Phenological differences between host plants can promote temporal isolation among host-associated populations of insects with life cycles tightly coupled to plant phenology. Divergence in the timing of spring budbreak between two sympatric sister oak species has been shown to promote temporal isolation between host plants and their host-associated populations of a cynipid gall wasp. Here, we examined the generality of this mechanism by testing the hypothesis of cascading temporal isolation for five additional gall-formers and three natural enemy species associated with these same oak species. The timing of adult emergence from galls differed significantly between host-associated populations for all nine species and parallels the direction of the phenological differences between host plants. Differences in emergence timing can reduce gene flow between host-associated populations by diminishing mating opportunities and/or reducing the fitness of immigrants due to differences in the availability of ephemeral resources. Our study suggests that cascading temporal isolation could be a powerful ‘biodiversity generator’ across multiple trophic levels in tightly coupled plant–insect systems.
DOI: 10.6084/m9.figshare.11281103
title: Supplementary Material for: A Meta-Analysis of the Relationship between Tumor Necrosis Factor-α Polymorphisms and Psoriasis

description: <b><i>Background:</i></b> Some previous studies already explored associations between tumor necrosis factor-α (TNF-α) polymorphisms and psoriasis, with conflicting findings. Here, we aimed to better analyze the relationship between TNF-α polymorphisms and psoriasis in a larger pooled population by performing a meta-analysis. <b><i>Methods:</i></b> We searched Pubmed, Embase, Web of Science and CNKI for related articles. We calculated OR and 95% CI to estimate whether there are genetic associations between TNF-α polymorphisms and psoriasis. <b><i>Results:</i></b> Twenty-nine studies were included for this meta-analysis. TNF-α-238 G/A (dominant comparison: OR 0.44, 95% CI 0.34–0.59; recessive comparison: OR 1.63, 95% CI 1.03–2.57; overdominant comparison: OR 2.21, 95% CI 1.71–2.85; allele comparison: OR 0.48, 95% CI 0.36–0.62) and -857 C/T (dominant comparison: OR 0.58, 95% CI 0.41–0.80; overdominant comparison: OR 1.58, 95% CI 1.12–2.23; allele comparison: OR 0.62, 95% CI 0. 0.47–0.82) polymorphisms were found to be significantly associated with psoriasis in the general population. Subgroup analyses indicated that the –238 G/A polymorphism was significantly associated with psoriasis in Caucasians and East Asians, the –308 G/A polymorphism was significantly associated with psoriasis in East Asians, and the –857 C/T polymorphism was significantly associated with psoriasis in Caucasians. <b><i>Conclusions:</i></b> TNF-α –238 G/A, –308 G/A and –857 C/T polymorphisms could be used to identity individuals with elevated susceptibility to psoriasis in certain populations.
DOI: 10.6084/m9.figshare.11281595
title: Supplementary Material for: Antifungal in vitro Activity of Essential Oils against Clinical Isolates of <b><i>Malassezia pachydermatis</i></b> from Canine Ears: A Report from a Practice Laboratory

description: <b><i>Background:</i></b> The yeast <i>Malassezia pachydermatis</i> is a commensal but also the most isolated pathogenic yeast in canine otitis externa. Essential oils (EOs) exhibit antimicrobial activity and thus could be an alternative for treatment of otitis. <b><i>Objective:</i></b> The aim of this study was to analyse the in vitro efficacy of EOs against <i>M. pachydermatis</i> isolates from canine ears. <b><i>Materials and Methods:</i></b> Twenty-two EOs were tested for their in vitro activity against 15 <i>M. pachydermatis</i> isolates by agar disc diffusion. In addition, diluted EOs were tested and volatile antifungal activity was analysed by vapour assay. <b><i>Results:</i></b> Most EOs showed in vitro efficacy against <i>M. pachydermatis</i>. A different susceptibility pattern of tested isolates was found. Overall, the most potential EO was lemon grass. Also, cinnamon leaf, clove, manuka, Indian melissa, oregano, palmarosa, and winter savory oil exhibited a strong antifungal activity. Volatile activity was proven by the inhibiting effect in vapour assay. <b><i>Conclusion:</i></b> EOs show in vitro activity against <i>M. pachydermatis</i>. This study gives scientific background for the use of EOs in veterinary medicine. Diverse susceptibility patterns of different <i>M. pachydermatis</i> strains emphasise the helpfulness of an aromatogram as one lead for the best choice of an EO for therapy.
DOI: 10.6084/m9.figshare.11280578
title: Supplementary Table 1

description: Supplementary Table 1 Two hundred and six new miRs identified in the bladder
DOI: 10.6084/m9.figshare.11281088
title: Immediate Changes in Peripapillary Retinal Vasculature after Intraocular Pressure Elevation -an Optical Coherence Tomography Angiography Study

description: <b>Purpose</b>: To investigate changes in peripapillary retinal vessel density after acute intraocular pressure (IOP) elevation caused by laser peripheral iridotomy (LPI) in primary angle-closure suspects (PACS) by optical coherence tomography angiography (OCTA). <b>Materials and Methods</b>: Ninety-seven participants with PACS were included in this cross-sectional observational study. OCTA and IOP measurement were performed at baseline and 1 h after LPI. PACS eyes were further divided into three groups according to IOP increase 1 h after LPI (group 1 = IOP elevation &lt;5 mmHg, 42eyes; group 2 = IOP elevation ≥5 mmHg and &lt;10 mmHg, 34 eyes; group 3 = IOP elevation ≥10 mmHg, 21eyes). The changes of vessel density in radial peripapillary capillary (RPC) and entire retina were compared among groups. <b>Results</b>: When all eyes were included, the vessel density of RPC and entire retina 1 h after LPI were significantly decreased compared to the baseline (RPC: 64.5 ± 7.9 vs.67.8 ± 6.8, <i>P</i> &lt; .001; retina: 86.3 ± 4.6 vs.88.3 ± 3.8, <i>P</i> &lt; .001). There were significant differences among the three groups in the RPC and retinal vessel density at 1 h after LPI (RPC: 67.4 ± 7.3 vs. 63.2 ± 7.6 vs. 60.9 ± 7.5, <i>P</i> = .003; retinal: 87.7 ± 4.0 vs. 85.8 ± 4.5 vs. 84.3 ± 5.2, <i>P</i> = .015). In group 2 with an increased IOP from 5 mmHg to 10 mmHg, the reduction of vessel density in the RPC was more significant than that of the entire retina (RPC vs. retina: 7.1 ± 10.0% vs. 3.0 ± 4.4%, <i>P</i> = .006). <b>Conclusions</b>: LPI-induced IOP spikes resulted in a decrease in retina vessel density with PACS eyes by OCTA. The reduction of RPC vessel density was more significant than that of the entire retina in the subgroup of IOP increase from 5 to 10 mmHg. This suggests that vessel density in RPC was more sensitive to IOP increase than that of the entire retina in the peripapillary area.
DOI: 10.6084/m9.figshare.11281595.v1
title: Supplementary Material for: Antifungal in vitro Activity of Essential Oils against Clinical Isolates of <b><i>Malassezia pachydermatis</i></b> from Canine Ears: A Report from a Practice Laboratory

description: <b><i>Background:</i></b> The yeast <i>Malassezia pachydermatis</i> is a commensal but also the most isolated pathogenic yeast in canine otitis externa. Essential oils (EOs) exhibit antimicrobial activity and thus could be an alternative for treatment of otitis. <b><i>Objective:</i></b> The aim of this study was to analyse the in vitro efficacy of EOs against <i>M. pachydermatis</i> isolates from canine ears. <b><i>Materials and Methods:</i></b> Twenty-two EOs were tested for their in vitro activity against 15 <i>M. pachydermatis</i> isolates by agar disc diffusion. In addition, diluted EOs were tested and volatile antifungal activity was analysed by vapour assay. <b><i>Results:</i></b> Most EOs showed in vitro efficacy against <i>M. pachydermatis</i>. A different susceptibility pattern of tested isolates was found. Overall, the most potential EO was lemon grass. Also, cinnamon leaf, clove, manuka, Indian melissa, oregano, palmarosa, and winter savory oil exhibited a strong antifungal activity. Volatile activity was proven by the inhibiting effect in vapour assay. <b><i>Conclusion:</i></b> EOs show in vitro activity against <i>M. pachydermatis</i>. This study gives scientific background for the use of EOs in veterinary medicine. Diverse susceptibility patterns of different <i>M. pachydermatis</i> strains emphasise the helpfulness of an aromatogram as one lead for the best choice of an EO for therapy.
DOI: 10.6084/m9.figshare.11281088.v1
title: Immediate Changes in Peripapillary Retinal Vasculature after Intraocular Pressure Elevation -an Optical Coherence Tomography Angiography Study

description: <b>Purpose</b>: To investigate changes in peripapillary retinal vessel density after acute intraocular pressure (IOP) elevation caused by laser peripheral iridotomy (LPI) in primary angle-closure suspects (PACS) by optical coherence tomography angiography (OCTA). <b>Materials and Methods</b>: Ninety-seven participants with PACS were included in this cross-sectional observational study. OCTA and IOP measurement were performed at baseline and 1 h after LPI. PACS eyes were further divided into three groups according to IOP increase 1 h after LPI (group 1 = IOP elevation &lt;5 mmHg, 42eyes; group 2 = IOP elevation ≥5 mmHg and &lt;10 mmHg, 34 eyes; group 3 = IOP elevation ≥10 mmHg, 21eyes). The changes of vessel density in radial peripapillary capillary (RPC) and entire retina were compared among groups. <b>Results</b>: When all eyes were included, the vessel density of RPC and entire retina 1 h after LPI were significantly decreased compared to the baseline (RPC: 64.5 ± 7.9 vs.67.8 ± 6.8, <i>P</i> &lt; .001; retina: 86.3 ± 4.6 vs.88.3 ± 3.8, <i>P</i> &lt; .001). There were significant differences among the three groups in the RPC and retinal vessel density at 1 h after LPI (RPC: 67.4 ± 7.3 vs. 63.2 ± 7.6 vs. 60.9 ± 7.5, <i>P</i> = .003; retinal: 87.7 ± 4.0 vs. 85.8 ± 4.5 vs. 84.3 ± 5.2, <i>P</i> = .015). In group 2 with an increased IOP from 5 mmHg to 10 mmHg, the reduction of vessel density in the RPC was more significant than that of the entire retina (RPC vs. retina: 7.1 ± 10.0% vs. 3.0 ± 4.4%, <i>P</i> = .006). <b>Conclusions</b>: LPI-induced IOP spikes resulted in a decrease in retina vessel density with PACS eyes by OCTA. The reduction of RPC vessel density was more significant than that of the entire retina in the subgroup of IOP increase from 5 to 10 mmHg. This suggests that vessel density in RPC was more sensitive to IOP increase than that of the entire retina in the peripapillary area.
DOI: 10.6084/m9.figshare.11280443
title: Supplementary Material for: Data Mining Approach for the Characterization of Functional Bowel Disorders According to Symptom Intensity Provides a Small Numberof Homogenous Groups

description: <b><i>Background/Aims:</i></b> The aim of the present study is to evaluate if the intensity of the cardinal symptoms of functional bowel disorders could be used to identify homogenous groups of patients defined by the Rome criteria. <b><i>Method:</i></b> In this observational study, 1,729 consecutive outpatients (73% females) filled out the Rome III questionnaire and 10-point Likert scales for constipation, diarrhea, bloating (BL)/distension, abdominal pain (AP) during the week before the medical consultation. A Gaussian mixture model was used for clustering the patients according to the intensity of symptoms without a priori information, and a classification tree was constructed from this clustering. Data were analyzed using analysis of variance and logistic regression analysis. <b><i>Results:</i></b> According to the intensity of symptoms, the patients are divided into 8 groups named according to their main symptomatology: “painful constipation” (PFC), “mild pain constipation” (MPC), “painful diarrhea” (PFD), “mild pain diarrhea” (MPD), “mixed transit” (MT), “BL,” “AP,” and “nonspecific” (NS). The study of the relationship between the Rome III classification and this new grouping shows that irritable bowel syndrome (IBS)-constipation is associated with PFC, IBS-diarrhea with PFD and MPD, SII-mixed with MT, SII-unspecified with BL, functional constipation with PFC and MPC, functional diarrhea with MPD and NS, BL with “BL” and NS, nonspecific functional bowel disorders (FBD) with NS, and functional AP with “BL” and AP (<i>p</i> &lt; 0.01 for all associations). <b><i>Conclusion:</i></b> A symptom intensity-based classification of FBD patients could simplify clinical phenotype, give homogeneous groups of patients, and could eventually be used by nongastroenterologists and in clinical research.
DOI: 10.6084/m9.figshare.11280578.v1
title: Supplementary Table 1

description: Supplementary Table 1 Two hundred and six new miRs identified in the bladder
DOI: 10.6084/m9.figshare.11280356
title: 4. Boundary file for endorheic and five limnetic regions in mainland of China

description: This is the boundary file for endorheic and five limnetic regions
DOI: 10.6084/m9.figshare.11280392
title: ND-NU Analysis.xlsx

description: These data show the firing rate of RVLM neurons in animals positioned 20 deg nose-down (ND) vs. 20 deg. nose-up (NU). Each tab shows data for trials for different cells. This dataset is linked to Fig. 9 in https://doi.org/10.1101/693408, "Responses of Neurons in the Rostral Ventrolateral Medulla (RVLM) of Conscious Felines to Anticipated and Passive Movements."
DOI: 10.6084/m9.figshare.11280392.v1
title: ND-NU Analysis.xlsx

description: These data show the firing rate of RVLM neurons in animals positioned 20 deg nose-down (ND) vs. 20 deg. nose-up (NU). Each tab shows data for trials for different cells. This dataset is linked to Fig. 9 in https://doi.org/10.1101/693408, "Responses of Neurons in the Rostral Ventrolateral Medulla (RVLM) of Conscious Felines to Anticipated and Passive Movements."
DOI: 10.6084/m9.figshare.11280356.v1
title: 4. Boundary file for endorheic and five limnetic regions in mainland of China

description: This is the boundary file for endorheic and five limnetic regions
DOI: 10.6084/m9.figshare.11279000
title: NCBI Pathogen hosts considered as animals

description: Text file providing a list of host names to classify NCBI isolates into the "animal" environmental class, as described in the original publication
DOI: 10.6084/m9.figshare.11279000.v1
title: NCBI Pathogen hosts considered as animals

description: Text file providing a list of host names to classify NCBI isolates into the "animal" environmental class, as described in the original publication
DOI: 10.6084/m9.figshare.11278157
title: <i>Pmr-1</i> gene affects susceptibility of <i>Caenorhabditis elegans</i> to <i>Staphylococcus aureus</i> infection through glycosylation and stress response pathways' alterations

description: Calcium signaling can elicit different pathways involved in an extreme variety of biological processes. Calcium levels must be tightly regulated in a spatial and temporal manner in order to be efficiently and properly utilized in the host physiology. The Ca<sup>2+</sup>-ATPase, encoded by <i>pmr-1</i> gene, was first identified in yeast and localized to the Golgi and it appears to be involved in calcium homeostasis. PMR-1 function is evolutionary conserved from yeast to human, where mutations in the orthologous gene ATP2C1 cause Hailey-Hailey disease. In this work, we used the <i>Caenorhabditis elegans</i> model system to gain insight into the downstream response elicited by the loss of <i>pmr-1</i> gene. We found that <i>pmr-1</i> knocked down animals not only showed defects in the oligosaccharide structure of glycoproteins at the cell surface but also were characterized by reduced susceptibility to bacterial infection. Although increased resistance to the infection might be related to lack of regular recognition of <i>C. elegans</i> surface glycoproteins by microbial agents, we provide genetic evidence that <i>pmr-1</i> interfered nematodes mounted a stronger innate immune response to Gram-positive bacterial infection. Thus, our observations indicate <i>pmr-1</i> as a candidate gene implicated in mediating the worm’s innate immune response.
DOI: 10.6084/m9.figshare.11278007
title: Surgical management of spine injuries in severe polytrauma patients: a retrospective study

description: <b>Background:</b> Optimal surgical management of spinal injuries as part of life-threatening multiple traumas remains challenging. We provide insights into the surgical management of spinal injuries in polytrauma patients. <b>Methods:</b> All patients from our polytrauma care network who both met at least one positive Vittel criteria and an injury severity score (ISS) &gt;15 at admission and who underwent surgery for a spinal injury were included retrospectively. Demographic data, clinical data demonstrating the severity of the trauma and imaging defining the spinal and extraspinal number and types of injuries were collected. <b>Results:</b> Between January 2012 and December 2016, 302 (22.2%) patients suffered from spinal injury (143 total injuries) and 83 (6.1%) met the inclusion criteria. Mean ISS was 36.2 (16–75). Only 48 (33.6%) injuries led to neurological impairment involving the thoracic (<i>n</i> = 23, 16.1%) and lower cervical (<i>n</i> = 15, 10.5%) spine. The most frequent association of injuries involved the thoracic spine (<i>n</i> = 42). 106 spinal surgeries were performed. The 3-month mortality rate was 2.4%. <b>Conclusions:</b> We present data collected on admission and in the early postoperative period referring to injury severity, the priority of injuries, and development of multi-organ failure. We revealed trends to guide the surgical support of spinal lesions in polytrauma patients.
DOI: 10.6084/m9.figshare.11278157.v1
title: <i>Pmr-1</i> gene affects susceptibility of <i>Caenorhabditis elegans</i> to <i>Staphylococcus aureus</i> infection through glycosylation and stress response pathways' alterations

description: Calcium signaling can elicit different pathways involved in an extreme variety of biological processes. Calcium levels must be tightly regulated in a spatial and temporal manner in order to be efficiently and properly utilized in the host physiology. The Ca<sup>2+</sup>-ATPase, encoded by <i>pmr-1</i> gene, was first identified in yeast and localized to the Golgi and it appears to be involved in calcium homeostasis. PMR-1 function is evolutionary conserved from yeast to human, where mutations in the orthologous gene ATP2C1 cause Hailey-Hailey disease. In this work, we used the <i>Caenorhabditis elegans</i> model system to gain insight into the downstream response elicited by the loss of <i>pmr-1</i> gene. We found that <i>pmr-1</i> knocked down animals not only showed defects in the oligosaccharide structure of glycoproteins at the cell surface but also were characterized by reduced susceptibility to bacterial infection. Although increased resistance to the infection might be related to lack of regular recognition of <i>C. elegans</i> surface glycoproteins by microbial agents, we provide genetic evidence that <i>pmr-1</i> interfered nematodes mounted a stronger innate immune response to Gram-positive bacterial infection. Thus, our observations indicate <i>pmr-1</i> as a candidate gene implicated in mediating the worm’s innate immune response.
DOI: 10.6084/m9.figshare.11277950
title: Pearl Millet Fungus

description: Raw reads of ITS1 region rDNA sequencing of root of wild and cultivated pearl millet in three areas agro-ecological in Senegal (Darou-Mousty, Dya and Nioro)
DOI: 10.6084/m9.figshare.11278007.v1
title: Surgical management of spine injuries in severe polytrauma patients: a retrospective study

description: <b>Background:</b> Optimal surgical management of spinal injuries as part of life-threatening multiple traumas remains challenging. We provide insights into the surgical management of spinal injuries in polytrauma patients. <b>Methods:</b> All patients from our polytrauma care network who both met at least one positive Vittel criteria and an injury severity score (ISS) &gt;15 at admission and who underwent surgery for a spinal injury were included retrospectively. Demographic data, clinical data demonstrating the severity of the trauma and imaging defining the spinal and extraspinal number and types of injuries were collected. <b>Results:</b> Between January 2012 and December 2016, 302 (22.2%) patients suffered from spinal injury (143 total injuries) and 83 (6.1%) met the inclusion criteria. Mean ISS was 36.2 (16–75). Only 48 (33.6%) injuries led to neurological impairment involving the thoracic (<i>n</i> = 23, 16.1%) and lower cervical (<i>n</i> = 15, 10.5%) spine. The most frequent association of injuries involved the thoracic spine (<i>n</i> = 42). 106 spinal surgeries were performed. The 3-month mortality rate was 2.4%. <b>Conclusions:</b> We present data collected on admission and in the early postoperative period referring to injury severity, the priority of injuries, and development of multi-organ failure. We revealed trends to guide the surgical support of spinal lesions in polytrauma patients.
DOI: 10.6084/m9.figshare.11277746
title: RNA Sequencing Identifies Inflammatory Network as a Potential Key Orchestrator of Benign Prostate Hyperplasia

description: Differentially expressed genes of RNA-seq of healthy vs hyperplastic prostates. <br>
DOI: 10.6084/m9.figshare.11276936
title: Table S2 from Otolith chemistry indicates recent worsened Baltic cod condition is linked to hypoxia exposure

description: Lifetime average data used in the study.
DOI: 10.6084/m9.figshare.11276366
title: Syntheses, characterization, crystal structures, and antimicrobial activity of oxidovanadium(V) complexes with hydrazone and pyrone ligands

description: A pair of new oxidovanadium(V) complexes, [VOLL<sup>1</sup>] (1) and [VOLL<sup>2</sup>] (2), where L is the dianionic form of the hydrazone ligand <i>N′</i>-(2-hydroxy-3-methoxybenzylidene)-3-methylbenzohydrazide (H<sub>2</sub>L), L<sup>1</sup> and L<sup>2</sup> are the deprotonated form of 3-hydroxy-2-methyl-4<i>H</i>-pyran-4-one (HL<sup>1</sup>) and 3-hydroxy-2-ethyl-4<i>H</i>-pyran-4-one (HL<sup>2</sup>), respectively, have been prepared and characterized by elemental analyses, IR, UV-Vis, <sup>1</sup>H NMR and single crystal X-ray determination. The V atoms in the complexes are in octahedral coordination, with the hydrazone ligand coordinates to the metal atoms through the phenolate O, imino N, and enolate O atoms, and with the pyrone ligands through the carbonyl and hydroxyl O atoms. The effect of the compounds on the antimicrobial activity against <i>Staphylococcus aureus</i>, <i>Escherichia coli</i>, and <i>Candida albicans</i> was studied.
DOI: 10.6084/m9.figshare.11276933
title: Table S1 from Otolith chemistry indicates recent worsened Baltic cod condition is linked to hypoxia exposure

description: Annulus data used in the study.
DOI: 10.6084/m9.figshare.11276936.v1
title: Table S2 from Otolith chemistry indicates recent worsened Baltic cod condition is linked to hypoxia exposure

description: Lifetime average data used in the study.
DOI: 10.6084/m9.figshare.11277746.v1
title: RNA Sequencing Identifies Inflammatory Network as a Potential Key Orchestrator of Benign Prostate Hyperplasia

description: Differentially expressed genes of RNA-seq of healthy vs hyperplastic prostates. <br>
DOI: 10.6084/m9.figshare.11276933.v1
title: Table S1 from Otolith chemistry indicates recent worsened Baltic cod condition is linked to hypoxia exposure

description: Annulus data used in the study.