cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9924347
title: Supporting Data RMBDs from Raw meat-based diets for companion animals: a potential source of transmission of pathogenic and antimicrobial-resistant Enterobacteriaceae

description: Strain and Sample IDs, Antibiograms and MLST data
DOI: 10.6084/m9.figshare.9924347.v1
title: Supporting Data RMBDs from Raw meat-based diets for companion animals: a potential source of transmission of pathogenic and antimicrobial-resistant Enterobacteriaceae

description: Strain and Sample IDs, Antibiograms and MLST data
DOI: 10.6084/m9.figshare.9924275
title: DATA SOURCE Pelon et al.

description: Data and R scripts used to generate the figures panels
DOI: 10.5281/zenodo.4002051
title: RVDB-prot, a reference viral protein database and its HMM profiles

description: We present RVDB-prot, a database corresponding to the protein equivalent of the nucleic acid reference virus database RVDB. Protein databases can be helpful to perform more sensitive protein sequence comparisons. Similarly to its homologous public repository, RVDB-prot aims to provide reliable and accurately annotated unique entries, while including also an Hidden Markov Model (HMM) protein profiles database for distant protein searching.
DOI: 10.5281/zenodo.4002050
title: RVDB-prot, a reference viral protein database and its HMM profiles

description: We present RVDB-prot, a database corresponding to the protein equivalent of the nucleic acid reference virus database RVDB. Protein databases can be helpful to perform more sensitive protein sequence comparisons. Similarly to its homologous public repository, RVDB-prot aims to provide reliable and accurately annotated unique entries, while including also an Hidden Markov Model (HMM) protein profiles database for distant protein searching.
DOI: 10.6084/m9.figshare.9923948
title: Supplementary Material for: Clinical Significance of Galactose-Deficient IgA1 by KM55 in Patients with IgA Nephropathy

description: <b><i>Background:</i></b> Aberrant galactose-deficient IgA1 molecules (Gd-IgA1) are important causal factors in IgA nephropathy (IgAN); however, the detection of Gd-IgA1 in IgAN is complicated and instable. A monoclonal antibody, KM55, which specifically recognizes Gd-IgA1 has been developed. In the present study, we further explored the clinical significance of Gd-IgA1 using KM55. <b><i>Methods:</i></b> In this study, we enrolled 75 patients with IgAN and 80 healthy controls and detected the plasma Gd-IgA1 levels using the KM55 ELISA method. We also stained ­mesangial Gd-IgA1 deposition using KM55. <b><i>Results:</i></b> We observed that the levels of plasma Gd-IgA1 in IgAN patients were elevated compared to the corresponding levels of healthy controls. Patients were divided into 2 groups based on the median of Gd-IgA1. Patients with high Gd-IgA1 levels had significantly higher levels of uric acid (UA) and IgA. The other clinical manifestations demonstrated that there were no differences in age, sex, blood pressure, initial proteinuria, hematuria, estimated glomerular filtration rate and Oxford pathological classification between the 2 groups of patients. In addition, positive correlations were observed between Gd-IgA1 and Bb, C3a, C4d and MAC. Mesangial Gd-IgA1 was positive in IgAN but negative in the normal renal tissue adjacent to neoplasm. We next analyzed the correlation between plasma Gd-IgA1 and mesangial Gd-IgA1 deposition. The results showed that a high level of plasma Gd-IgA1 was related to the deposition of mesangial Gd-IgA1, although the difference was not significant. <b><i>Conclusion:</i></b> We verified the elevated level of plasma and ­mesangial Gd-IgA1 in patients with IgAN by KM55, which provided an alternative, easy, and reliable tool for diagnosis and activity assessment of IgAN. The level of plasma Gd-IgA1 positively correlated with levels of UA, total IgA levels, and complement activation products.
DOI: 10.6084/m9.figshare.9923927
title: Supplementary Material for: Myeloid SOCS3 Deficiency Regulates Angiogenesis via Enhanced Apoptotic Endothelial Cell Engulfment

description: Mononuclear phagocytes, such as macrophages and microglia, are key regulators of organ homeostasis including vascularization processes. Here, we investigated the role of the suppressor of cytokine signaling 3 (SOCS3) in myeloid cells as a regulator of mononuclear phagocyte function and their interaction with endothelial cells in the context of sprouting angiogenesis. As compared to SOCS3-sufficient counterparts, SOCS3-deficient microglia and macrophages displayed an increased phagocytic activity toward primary apoptotic endothelial cells, which was associated with an enhanced expression of the opsonin growth arrest-specific 6 (Gas6), a major prophagocytic molecule. Furthermore, we found that myeloid SOCS3 deficiency significantly reduced angiogenesis in an ex vivo mouse aortic ring assay, which could be reversed by the inhibition of the Gas6 receptor Mer. Together, SOCS3 in myeloid cells regulates the Gas6/Mer-dependent phagocytosis of endothelial cells, and thereby angiogenesis-related processes. Our findings provide novel insights into the complex crosstalk between mononuclear phagocytes and endothelial cells, and may therefore provide a new platform for the development of new antiangiogenic therapies.
DOI: 10.6084/m9.figshare.9923927.v1
title: Supplementary Material for: Myeloid SOCS3 Deficiency Regulates Angiogenesis via Enhanced Apoptotic Endothelial Cell Engulfment

description: Mononuclear phagocytes, such as macrophages and microglia, are key regulators of organ homeostasis including vascularization processes. Here, we investigated the role of the suppressor of cytokine signaling 3 (SOCS3) in myeloid cells as a regulator of mononuclear phagocyte function and their interaction with endothelial cells in the context of sprouting angiogenesis. As compared to SOCS3-sufficient counterparts, SOCS3-deficient microglia and macrophages displayed an increased phagocytic activity toward primary apoptotic endothelial cells, which was associated with an enhanced expression of the opsonin growth arrest-specific 6 (Gas6), a major prophagocytic molecule. Furthermore, we found that myeloid SOCS3 deficiency significantly reduced angiogenesis in an ex vivo mouse aortic ring assay, which could be reversed by the inhibition of the Gas6 receptor Mer. Together, SOCS3 in myeloid cells regulates the Gas6/Mer-dependent phagocytosis of endothelial cells, and thereby angiogenesis-related processes. Our findings provide novel insights into the complex crosstalk between mononuclear phagocytes and endothelial cells, and may therefore provide a new platform for the development of new antiangiogenic therapies.
DOI: 10.6084/m9.figshare.9923873
title: Genetic characteristics and diversity of Korean Jeju Black cattle by whole genome SNP markers

description: Jeju black, Hanwoo and Holstein cattle were genotyped by DNALink, Korea using Bovine 50 K v.3 Bead chip (Illumina, San Diego, CA, USA) from frozen semen straw and tail hair DNA hair. Brahman, Nellore, Angus and Hereford genotype data was provided from the two author (professor David Riley and professor Lauren Hulsman Hanna) in USA and Wagyu cattle breed data was provided by the professor Hideyuki Mannen of Kobe university, Japan. All cattle breed data except Jeju Black, Hanwoo and Korean Holstein was published for other study.
DOI: 10.6084/m9.figshare.9923873.v1
title: Genetic characteristics and diversity of Korean Jeju Black cattle by whole genome SNP markers

description: Jeju black, Hanwoo and Holstein cattle were genotyped by DNALink, Korea using Bovine 50 K v.3 Bead chip (Illumina, San Diego, CA, USA) from frozen semen straw and tail hair DNA hair. Brahman, Nellore, Angus and Hereford genotype data was provided from the two author (professor David Riley and professor Lauren Hulsman Hanna) in USA and Wagyu cattle breed data was provided by the professor Hideyuki Mannen of Kobe university, Japan. All cattle breed data except Jeju Black, Hanwoo and Korean Holstein was published for other study.
DOI: 10.6084/m9.figshare.9923768
title: Supplementary Material for: Does Oxygen Stable Isotope Composition in Primates Vary as a Function of Vertical Stratification or Folivorous Behaviour?

description: Stable isotopes of oxygen often vary within a community of primates. For example, folivorous monkeys that forage in the upper reaches of the forest canopy tend to evince high δ<sup>18</sup>O values, whereas those that prefer the understory tend to have lower δ<sup>18</sup>O values. Given that leaves also have high δ<sup>18</sup>O values, particularly higher in the canopy, there is uncertainty as to which behavioural variable – vertical stratification or folivory – is the primary determinant of variation in δ<sup>18</sup>O values. Here, we explore further δ<sup>18</sup>O values from the Taï Forest monkeys (<i>n</i> = 7 species; <i>n</i> = 33 individuals) by examining the interaction between diet and vertical stratification, thereby allowing us to differentiate the effects of each covariate. We found that δ<sup>18</sup>O values varied as a function of mean canopy height, but not folivory, resolving uncertainty about the primary cause of δ<sup>18</sup>O variation. This outcome revolves largely, but not entirely, on the behaviours of <i>Procolobus verus</i>, a highly folivorous but understory forager. Relatively elevated values in <i>Cercopithecus diana</i>, a frugivorous but middle-to-high canopy forager, raises the possibility that plant reproductive tissues (e.g., fruits, flowers) may be increasingly sensitive to evaporative fractionation at higher forest canopy levels. Overall, our results further affirm the value of using δ<sup>18</sup>O values to estimate the vertical behaviour of primate species in a fossil assemblage.
DOI: 10.6084/m9.figshare.9923777
title: Supplementary Material for: The Efficacy of Light Therapy in the Treatment of Seasonal Affective Disorder: A Meta-Analysis of Randomized Controlled Trials

description: <b><i>Background:</i></b> Bright light therapy (BLT) has been used as a treatment for seasonal affective disorder (SAD) for over 30 years. This meta-analysis was aimed to assess the efficacy of BLT in the treatment of SAD in adults. <b><i>Method:</i></b> We performed a systematic literature search including randomized, single- or double-blind clinical trials investigating BLT (≥1,000 lx, light box or light visor) against dim light (≤400 lx) or sham/low-density negative ion generators as placebo. Only first-period data were used from crossover trials. The primary outcome was the post-treatment depression score measured by validated scales, and the secondary outcome was the rate of response to treatment. <b><i>Results:</i></b> A total of 19 studies finally met our predefined inclusion criteria. BLT was superior over placebo with a standardized mean difference of –0.37 (95% CI: –0.63 to –0.12) for depression ratings (18 studies, 610 patients) and a risk ratio of 1.42 (95% CI: 1.08–1.85) for response to active treatment (16 studies, 559 patients). We found no evidence for a publication bias, but moderate heterogeneity of the studies and a moderate-to-high risk of bias. <b><i>Conclusions:</i></b> BLT can be regarded as an effective treatment for SAD, but the available evidence stems from methodologically heterogeneous studies with small-to-medium sample sizes, necessitating larger high-quality clinical trials.
DOI: 10.6084/m9.figshare.9923759
title: Supplementary Material for: Unit-Level Variations in Healthcare Professionals’ Availability for Preterm Neonates &lt;29 Weeks’ Gestation: An International Survey

description: <b><i>Introduction:</i></b> The availability of and variability in healthcare professionals in neonatal units in different countries has not been well characterized. Our objective was to identify variations in the healthcare professionals for preterm neonates in 10 national or regional neonatal networks participating in the International Network for Evaluating Outcomes (iNeo) of neonates. <b><i>Method:</i></b> Online, pre-piloted questionnaires about the availability of healthcare professionals were sent to the directors of 390 tertiary neonatal units in 10 international networks: Australia/New Zealand, Canada, Finland, Illinois, Israel, Japan, Spain, Sweden, Switzerland, and Tuscany. <b><i>Results:</i></b> Overall, 325 of 390 units (83%) responded. About half of the units (48%; 156/325) cared for 11–30 neonates/day and had team-based (43%; 138/325) care models. Neonatologists were present 24 h a day in 59% of the units (191/325), junior doctors in 60% (194/325), and nurse practitioners in 36% (116/325). A nurse-to-patient ratio of 1:1 for infants who are unstable and require complex care was used in 52% of the units (170/325), whereas a ratio of 1:1 or 1:2 for neonates requiring multisystem support was available in 59% (192/325) of the units. Availability of a respiratory therapist (15%, 49/325), pharmacist (40%, 130/325), dietitian (34%, 112/325), social worker (81%, 263/325), lactation consultant (45%, 146/325), parent buddy (6%, 19/325), or parents’ resource personnel (11%, 34/325) were widely variable between units. <b><i>Conclusions:</i></b> We identified variability in the availability and organization of the healthcare professionals between and within countries for the care of extremely preterm neonates. Further research is needed to associate healthcare workers’ availability and outcomes.
DOI: 10.6084/m9.figshare.9923747
title: Acaricide efficacy and honey bee toxicity of three new formic acid-based products to control <i>Varroa destructor</i>

description: The replacement of synthetic acaricides with organic treatments is a big challenge in modern beekeeping. In summer 2015, we carried out in Central Italy a study to compare the varroacide efficacy and the toxicity on honey bees of the formic acid evaporator Nassenheider Professional<sup>®</sup> with two new formic acid-based gel formulations: MAQS<sup>®</sup> and Varterminator<sup>®</sup>. In the same apiary with 32 colonies, four homogeneous groups with eight hives each were prepared. The mean acaricide efficacy of Nassenheider Professional<sup>®</sup> was 73.2 ± 12.5%, while MAQS<sup>®</sup> and Varterminator<sup>®</sup> showed a mean efficacy of 49.3 ± 14.9 and 81.2 ± 16.0%, respectively. Colonies showed a statistically significant reduction of adult bees only after the MAQS<sup>®</sup> treatment with respect to the control group. All the treatments showed absent or quite moderate queen mortality (MAQS<sup>®</sup> and in Varterminator<sup>®</sup> groups 12.5%, Nassenheider professional<sup>®</sup>, and control groups 0%). Our study indicates that Nassenheider Professional<sup>®</sup> and Varterminator<sup>®</sup> may represent a sustainable and effective solution to control mite infestation during summer in temperate areas.
DOI: 10.6084/m9.figshare.9923750
title: From peaks to prairies: a time-of-travel synoptic survey of pesticides in watersheds of southern Alberta, Canada

description: A time-of-travel synoptic survey was conducted in August 2014 to assess pesticide occurrence in major river subbasins of southern Alberta, Canada. We collected 155 water samples from Alberta's South Saskatchewan River Basin (Bow, Oldman, Red Deer, and South Saskatchewan river subbasins) and analysed them for 106 pesticides. Samples were collected from mainstems (rivers) as well as tributaries and effluents (point sources) discharging into the rivers in an estimated time-of-travel to capture agricultural and urban contributions as the water flowed eastward from headwaters in the Rocky Mountains. The aim of the study was to assess point-source contributions of pesticides to Alberta's South Saskatchewan River Basin mainstems during low flow conditions. In addition to examining differences in pesticide contributions among source type and subbasins, the cumulative effect of inputs on the mainstem rivers, the influence of land use, and seasonality of pesticides in select effluents was analysed. We detected 17 pesticides and 1 metabolite, reflecting runoff from agricultural and urban land use. Pesticide detection frequency was significantly higher in effluents than in tributaries and mainstems, and pesticides were detected in effluents in summer and winter. Our evaluation of land-use relationships highlighted the influence of agriculture on pesticide occurrence in these aquatic agroecosystems. To our knowledge, this is the first watershed-wide time-of-travel survey of pesticides conducted in southern Alberta to measure contributions of pesticide loads from effluents and tributaries to the mainstems in all regions of Alberta's South Saskatchewan River Basin.
DOI: 10.6084/m9.figshare.9923756
title: tooth color (Influence of different types of whitening tooth pastes on the tooth color, enamel surface roughness and enamel morphology of human teeth).xlsx

description: Influence of different types of whitening tooth pastes on the tooth color, enamel surface roughness and enamel morphology of human teeth.<br><br>Tooth color parameters before and after bleaching using tooth pastes.<br>Surface roughness measurements before and after bleaching using tooth pastes.
DOI: 10.6084/m9.figshare.9923747.v1
title: Acaricide efficacy and honey bee toxicity of three new formic acid-based products to control <i>Varroa destructor</i>

description: The replacement of synthetic acaricides with organic treatments is a big challenge in modern beekeeping. In summer 2015, we carried out in Central Italy a study to compare the varroacide efficacy and the toxicity on honey bees of the formic acid evaporator Nassenheider Professional<sup>®</sup> with two new formic acid-based gel formulations: MAQS<sup>®</sup> and Varterminator<sup>®</sup>. In the same apiary with 32 colonies, four homogeneous groups with eight hives each were prepared. The mean acaricide efficacy of Nassenheider Professional<sup>®</sup> was 73.2 ± 12.5%, while MAQS<sup>®</sup> and Varterminator<sup>®</sup> showed a mean efficacy of 49.3 ± 14.9 and 81.2 ± 16.0%, respectively. Colonies showed a statistically significant reduction of adult bees only after the MAQS<sup>®</sup> treatment with respect to the control group. All the treatments showed absent or quite moderate queen mortality (MAQS<sup>®</sup> and in Varterminator<sup>®</sup> groups 12.5%, Nassenheider professional<sup>®</sup>, and control groups 0%). Our study indicates that Nassenheider Professional<sup>®</sup> and Varterminator<sup>®</sup> may represent a sustainable and effective solution to control mite infestation during summer in temperate areas.
DOI: 10.6084/m9.figshare.9923750.v2
title: From peaks to prairies: a time-of-travel synoptic survey of pesticides in watersheds of southern Alberta, Canada

description: A time-of-travel synoptic survey was conducted in August 2014 to assess pesticide occurrence in major river subbasins of southern Alberta, Canada. We collected 155 water samples from Alberta's South Saskatchewan River Basin (Bow, Oldman, Red Deer, and South Saskatchewan river subbasins) and analysed them for 106 pesticides. Samples were collected from mainstems (rivers) as well as tributaries and effluents (point sources) discharging into the rivers in an estimated time-of-travel to capture agricultural and urban contributions as the water flowed eastward from headwaters in the Rocky Mountains. The aim of the study was to assess point-source contributions of pesticides to Alberta's South Saskatchewan River Basin mainstems during low flow conditions. In addition to examining differences in pesticide contributions among source type and subbasins, the cumulative effect of inputs on the mainstem rivers, the influence of land use, and seasonality of pesticides in select effluents was analysed. We detected 17 pesticides and 1 metabolite, reflecting runoff from agricultural and urban land use. Pesticide detection frequency was significantly higher in effluents than in tributaries and mainstems, and pesticides were detected in effluents in summer and winter. Our evaluation of land-use relationships highlighted the influence of agriculture on pesticide occurrence in these aquatic agroecosystems. To our knowledge, this is the first watershed-wide time-of-travel survey of pesticides conducted in southern Alberta to measure contributions of pesticide loads from effluents and tributaries to the mainstems in all regions of Alberta's South Saskatchewan River Basin.
DOI: 10.6084/m9.figshare.9923672
title: Trace amine associated receptor 1 (TAAR1) expression and modulation of inflammatory cytokine production in mouse bone marrow-derived macrophages: a novel mechanism for inflammation in ulcerative colitis

description: <b>Context: </b>Tissue resident macrophages and peripherally infiltrating macrophages play a prominent role in maintaining homeostasis in the gastrointestinal tract (GIT), though aberrant activation is implicated in inflammatory conditions, including ulcerative colitis (UC). Recent metabolomic studies indicate that tyramine (TYR) is elevated in the stool of patients with UC. TYR activates the mammalian trace amine associated receptor 1 (TAAR1). Our previous work identified TAAR1 expression in mixed populations of immune cells, whereas a limited number of other studies have identified TAAR1-dependent effects in cytokine secretion and gene expression in T-cells and B-cells. <b>Objective: </b>To investigate whether TAAR1 may serve as a novel target for an anti-inflammatory therapeutic in UC, we explored TAAR1 expression in mouse bone marrow-derived macrophages (BMDMs), and its upregulation and activation in response to LPS and TYR. <b>Results:</b> Here, we demonstrate for the first time that TAAR1 is expressed in BMDM and undergoes agonist-induced upregulation. Additionally, TYR elicits significant increases in inflammatory cytokine gene expression in non-polarized and LPS-polarized BMDM, and the TAAR1 antagonist EPPTB inhibits the TYR-mediated upregulation of TAAR1 and inflammatory cytokine gene expression in BMDM. <b>Conclusions:</b> Our data suggest that TAAR1 is a mediator of macrophage inflammation and a potential therapeutic target to attenuate UC symptomology.
DOI: 10.6084/m9.figshare.9923666
title: Supplementary Material for: Factors Impacting on Decision-Making towards Prophylactic Surgeries in <b><i>BRCA</i></b> Mutation Carriers and Women with Familial Predisposition

description: <b><i>Background/Objectives:</i></b> <i>BRCA</i> mutation carriers and women at high risk of breast/ovarian cancer are faced with the intricate question to opt for prophylactic surgeries and/or a periodic screening. The aim of this study was therefore to identify objective and emotional factors that have an impact on the decision-making process. <b><i>Methods:</i></b> Ninety-five women with <i>BRCA</i> mutations or women at increased breast/ovarian cancer lifetime risk were counseled at our outpatient department and either opted for prophylactic surgery or periodic screening. To identify the psychological factors that could have influenced the decision-making, a standardized questionnaire was applied. Additionally, clinical data were collected and were reviewed by a personal talk. <b><i>Results:</i></b> Seventy-one of the patients opted for an increased surveillance only, 21 for prophylactic surgeries. Positive predictors for prophylactic surgeries were sociodemographic characteristics such as parity and objective variables such as verified mutation status. Hierarchical regression analysis revealed that the need for safety in health issues has been the only significant psychological predictor of surgery beyond the objective factors. Fear of surgical procedures, menopausal symptoms after surgery, loss of attractiveness, or fear of interferences with sexual life did not significantly affect decision-making. <b><i>Conclusion:</i></b> Decision-making towards prophylactic surgeries is influenced by objective but also emotional factors. Knowing that fear and anxiety also have an important impact on decision-making, distinct counselling about the procedures, the subsequent risk reduction as well as the psychological effects of prophylactic surgeries are essential.