cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4558075
title: Supplementary Material for: Characterization of Two Temperate Lactobacillus paracasei Bacteriophages: Morphology, Kinetics and Adsorption

description: <b><i>Background/Aims:</i></b> Adsorption and kinetic parameters, latent period, burst size and burst time, are characteristics of phage/host systems and can be affected by several environmental factors. As only few studies have focused on temperate dairy phages, we characterized these parameters on temperate <i>Lactobacillus paracasei</i> phages Φ i<i>Lp</i>84 and Φ i<i>Lp</i>1308, infective for probiotic strains. <b><i>Methods:</i></b> Phages were characterized by transmission electron microscopy and genomic DNA restriction. Adsorption under different environmental conditions, phage kinetics and efficiency of plating (EOP) were determined using the double-layer titration method. <b><i>Results:</i></b> Phages Φ i<i>Lp</i>84 and Φ i<i>Lp</i>1308 belong to the <i>Siphoviridae</i> family and have genome sizes of 38 and 34 kbp, respectively. Adsorption was affected by calcium concentration, pH, temperature and host viability, and reached a limit at very high multiplicity of infection. Latency, burst time and burst size were of 85 min, 131 min and 46 for Φ i<i>Lp</i>84, and 51 min, 92 min and 28 for Φ i<i>Lp</i>1308, respectively, at 37°C. A clear influence of temperature on phage kinetics was observed. Regarding EOP, Φ i<i>Lp</i>84 produced plaques on only 1 out of 8 strains tested. <b><i>Conclusion:</i></b> Noticeable differences in adsorption, kinetics and EOP were found for two morphologically identical temperate <i>L. paracasei</i> phages of similar origin.
DOI: 10.6084/m9.figshare.4558087
title: Wheat Biomechanics in Milling data

description: Data set to support the publication entitled "Biomechanical properties of wheat grains:the implications on Milling" published in the Royal Society Interface 2017.<br>
DOI: 10.6084/m9.figshare.4558087.v1
title: Wheat Biomechanics in Milling data

description: Data set to support the publication entitled "Biomechanical properties of wheat grains:the implications on Milling" published in the Royal Society Interface 2017.<br>
DOI: 10.6084/m9.figshare.4558075.v1
title: Supplementary Material for: Characterization of Two Temperate Lactobacillus paracasei Bacteriophages: Morphology, Kinetics and Adsorption

description: <b><i>Background/Aims:</i></b> Adsorption and kinetic parameters, latent period, burst size and burst time, are characteristics of phage/host systems and can be affected by several environmental factors. As only few studies have focused on temperate dairy phages, we characterized these parameters on temperate <i>Lactobacillus paracasei</i> phages Φ i<i>Lp</i>84 and Φ i<i>Lp</i>1308, infective for probiotic strains. <b><i>Methods:</i></b> Phages were characterized by transmission electron microscopy and genomic DNA restriction. Adsorption under different environmental conditions, phage kinetics and efficiency of plating (EOP) were determined using the double-layer titration method. <b><i>Results:</i></b> Phages Φ i<i>Lp</i>84 and Φ i<i>Lp</i>1308 belong to the <i>Siphoviridae</i> family and have genome sizes of 38 and 34 kbp, respectively. Adsorption was affected by calcium concentration, pH, temperature and host viability, and reached a limit at very high multiplicity of infection. Latency, burst time and burst size were of 85 min, 131 min and 46 for Φ i<i>Lp</i>84, and 51 min, 92 min and 28 for Φ i<i>Lp</i>1308, respectively, at 37°C. A clear influence of temperature on phage kinetics was observed. Regarding EOP, Φ i<i>Lp</i>84 produced plaques on only 1 out of 8 strains tested. <b><i>Conclusion:</i></b> Noticeable differences in adsorption, kinetics and EOP were found for two morphologically identical temperate <i>L. paracasei</i> phages of similar origin.
DOI: 10.6084/m9.figshare.4558072
title: Publication, Power, and Patronage: On Inequality and Academic Publishing

description: This data set accompanies our article, "Publication, Power, and Patronage: On Inequality and Academic Publishing," Critical Inquiry (July 2017): http://bit.ly/2vv5s2H<br>The data set contains metadata on institutional affiliation for over 5,000 academic articles published in four high-prestige journals within the humanities (PMLA, Critical Inquiry, New Literary History, Representations). Included in the metadata are the author's institutional affiliation at time of publication, the author's PhD institution, and the author's gender. 3,000+ authors are represented from over 300 PhD-granting institutions and 700 authorial institutions. We also include supplementary data on gender and publication on another 2,800 articles published since 2010 in 16 further journals. R code included to calculate all results, tables, and graphs.<br>
DOI: 10.6084/m9.figshare.4558069
title: Supplementary Material for: Stent Thrombosis with Biodegradable Polymer Drug-Eluting Stents versus Durable Polymer Sirolimus-Eluting Stents: An Update Meta-Analysis

description: <b><i>Objective:</i></b> Durable polymer sirolimus-eluting stents (DP-SES) are associated with a low risk of stent thrombosis; biodegradable polymer drug-eluting stents (BP-DES) were designed to reduce these risks. However, their benefits are still variable. <b><i>Method:</i></b> We undertook a meta-analysis of randomized trials identified by systematic searches of Medline, Embase, and the Cochrane Database. <b><i>Results:</i></b> Eleven studies (9,676 patients) with a mean follow-up of 22.6 months were included. Overall, compared with DP-SES, BP-DES significantly lowered the rate of definite or probable stent thrombosis (RR, 0.73; 95% CI, 0.55-0.97; p = 0.03; I<sup>2</sup> = 0.0%) due to a decreased risk of very late stent thrombosis (RR, 0.26; 95% CI, 0.11-0.63; p = 0.00; I<sup>2</sup> = 0.0%). However, BP-DES were associated with a comparable rate of early and late stent thrombosis. Meanwhile, BP-DES were associated with a broadly equivalent risk of target vessel revascularization (RR, 0.90; 95% CI, 0.78-1.03; p = 0.13; I<sup>2</sup> = 0.0%), cardiac death (RR, 0.89; 95% CI, 0.72-1.09; p = 0.24; I<sup>2</sup> = 0.0%), myocardial infarction (RR, 1.03; 95% CI, 0.84-1.26; p = 0.79; I<sup>2</sup> = 0.0%), and major adverse cardiac events (MACE; RR, 0.91; 95% CI, 0.83-1.0; p = 0.08; I<sup>2</sup> = 0.0%). Furthermore, angiographic data showed that in-stent and in-segment late luminal loss were similar between the two groups. <b><i>Conclusions:</i></b> Compared with DP-SES, BP-DES were associated with a lower rate of very late stent thrombosis and an equivalent risk of MACE. Larger randomized studies are needed to confirm this finding.
DOI: 10.6084/m9.figshare.4558015
title: Supplementary Material for: Systemic Infection Generates a Local-Like Immune Response of the Bacteriome Organ in Insect Symbiosis

description: Endosymbiosis is common in insects thriving in nutritionally unbalanced habitats. The cereal weevil, <i>Sitophilus oryzae</i>, houses <i>Sodalis pierantonius</i>, a Gram-negative intracellular symbiotic bacterium (endosymbiont), within a dedicated organ called a bacteriome. Recent data have shown that the bacteriome expresses certain immune genes that result in local symbiont tolerance and control. Here, we address the question of whether and how the bacteriome responds to insect infections involving exogenous bacteria. We have established an infection model by challenging weevil larvae with the Gram-negative bacterium <i>Dickeya dadantii</i>. We showed that <i>D. dadantii</i> infects host tissues and triggers a systemic immune response. Gene transcript analysis indicated that the bacteriome is also immune responsive, but it expresses immune effector genes to a lesser extent than the systemic and intestinal responses. Most genes putatively involved in immune pathways remain weakly expressed in the bacteriome following <i>D. dadantii</i> infection. Moreover, quantitative PCR experiments showed that the endosymbiont load is not affected by insect infection or the resulting bacteriome immune activation. Thus, the contained immune effector gene expression in the bacteriome may prevent potentially harmful effects of the immune response on endosymbionts, whilst efficiently protecting them from bacterial intruders.
DOI: 10.6084/m9.figshare.4558018
title: Supplementary Material for: Low-Dose RATG with or without Basiliximab in Renal Transplantation: A Matched-Cohort Observational Study

description: <b><i>Background/Aims:</i></b> In renal transplantation, peri-operative low-dose rabbit-antithymocyte-globulin (RATG) plus basiliximab induction prevented acute allograft rejection more effectively than post-operative RATG plus basiliximab induction. We investigated the specific antirejection contribution of basiliximab in this context. <b><i>Methods:</i></b> This single-center, observational, matched-cohort study evaluated allograft rejections (primary outcome), steroid exposure and side effects, GFR (iohexol plasma clearance) and treatment costs in 16 deceased-donor renal transplant recipients induced with RATG (0.5 mg/kg/day) and 32 age-, gender- and treatment-matched reference-patients given RATG plus basiliximab (20 mg on days 0 and 4). <b><i>Results:</i></b> Induction was well tolerated. At 18 months, 8 patients (50%) vs. 3 reference-patients (9.4%) rejected the graft [HR (95% CI): 6.53 (1.73-24.70), p = 0.006]. Difference was significant (p &lt; 0.01) even after adjusting for recipient/donor age and gender, cold ischemia time and HLA mismatches. There were 1 antibody-mediated rejection and 2 moderate cellular rejections in patients vs. none in reference-patients (p = 0.032). The median (interquartile range) prednisone cumulative dose was remarkably higher in patients than reference-patients [4.78 (1.12-6.10) vs. 0.19 (0.18-3.81) grams, p = 0.002]. Three patients vs. 24 reference-patients were off-steroid at study end (p &lt; 0.001). Three patients vs. no reference-patient developed new-onset diabetes (p = 0.003). Both inductions similarly depleted B-cells. Outcomes of AZA- vs. MMF-treated participants were similar. GFR was similar in all groups. Compared to MMF, AZA therapy saved ≈ EUR 2,500/year and by month 14.3 post-transplant compensated basiliximab costs. <b><i>Conclusion:</i></b> In renal transplantation, basiliximab plus peri-operative low-dose RATG more efficiently prevented allograft rejection than RATG monotherapy, and minimized steroid exposure and toxicity. AZA- vs MMF-based maintenance immunosuppression largely compensated the extra costs of basiliximab.
DOI: 10.6084/m9.figshare.4558018.v1
title: Supplementary Material for: Low-Dose RATG with or without Basiliximab in Renal Transplantation: A Matched-Cohort Observational Study

description: <b><i>Background/Aims:</i></b> In renal transplantation, peri-operative low-dose rabbit-antithymocyte-globulin (RATG) plus basiliximab induction prevented acute allograft rejection more effectively than post-operative RATG plus basiliximab induction. We investigated the specific antirejection contribution of basiliximab in this context. <b><i>Methods:</i></b> This single-center, observational, matched-cohort study evaluated allograft rejections (primary outcome), steroid exposure and side effects, GFR (iohexol plasma clearance) and treatment costs in 16 deceased-donor renal transplant recipients induced with RATG (0.5 mg/kg/day) and 32 age-, gender- and treatment-matched reference-patients given RATG plus basiliximab (20 mg on days 0 and 4). <b><i>Results:</i></b> Induction was well tolerated. At 18 months, 8 patients (50%) vs. 3 reference-patients (9.4%) rejected the graft [HR (95% CI): 6.53 (1.73-24.70), p = 0.006]. Difference was significant (p &lt; 0.01) even after adjusting for recipient/donor age and gender, cold ischemia time and HLA mismatches. There were 1 antibody-mediated rejection and 2 moderate cellular rejections in patients vs. none in reference-patients (p = 0.032). The median (interquartile range) prednisone cumulative dose was remarkably higher in patients than reference-patients [4.78 (1.12-6.10) vs. 0.19 (0.18-3.81) grams, p = 0.002]. Three patients vs. 24 reference-patients were off-steroid at study end (p &lt; 0.001). Three patients vs. no reference-patient developed new-onset diabetes (p = 0.003). Both inductions similarly depleted B-cells. Outcomes of AZA- vs. MMF-treated participants were similar. GFR was similar in all groups. Compared to MMF, AZA therapy saved ≈ EUR 2,500/year and by month 14.3 post-transplant compensated basiliximab costs. <b><i>Conclusion:</i></b> In renal transplantation, basiliximab plus peri-operative low-dose RATG more efficiently prevented allograft rejection than RATG monotherapy, and minimized steroid exposure and toxicity. AZA- vs MMF-based maintenance immunosuppression largely compensated the extra costs of basiliximab.
DOI: 10.6084/m9.figshare.4558072.v2
title: Publication, Power, and Patronage: On Inequality and Academic Publishing

description: This data set accompanies our article, "Publication, Power, and Patronage: On Inequality and Academic Publishing," Critical Inquiry (forthcoming).<br>The data set contains metadata on institutional affiliation for 5,593 academic articles published in four prestige journals within the humanities (PMLA, Critical Inquiry, New Literary History, Representations). Included in the metadata are the author's institutional affiliation at time of publication, the author's PhD institution, and the author's gender. 3,510 authors are represented from 341 PhD-granting institutions and 741 authorial institutions. We also include supplementary data on gender and publication on another 2,828 articles published since 2010 in 16 further journals. R code included to calculate all results, tables, and graphs.
DOI: 10.6084/m9.figshare.4558000
title: Supplementary Material for: Stress-Induced Glucocorticoid Release Upregulates Uncoupling Protein-2 Expression and Enhances Resistance to Endotoxin-Induced Lethality

description: <b><i>Objective:</i></b> Although psychological and/or physiological stress has been well documented to influence immune responses, the precise mechanism for immunomodulation remains to be elucidated. The present work describes the role of the hypothalamic-pituitary-adrenal (HPA) axis in the mechanism of stress-mediated enhanced-resistance to lethality after lipopolysaccharide (LPS) injection. <b><i>Methods/Results:</i></b> Preconditioning with restraint stress (RS) resulted in enhanced activation of the HPA axis in response to LPS injection and suppressed LPS-induced release of proinflammatory cytokines and nitric oxide metabolites. Melanocortin 2 receptor-deficient mice (MC2R<sup>-/-</sup>) failed to increase plasma levels of glucocorticoids in response to LPS injection, and exhibited high sensitivity to LPS-induced lethality with enhanced release of proinflammatory cytokines as compared with MC2R<sup>+/-</sup> mice. Real-time PCR analysis revealed that RS induced upregulation of uncoupling protein-2 (UCP2) in macrophages in the lung and the liver of MC2R<sup>+/-</sup>, but not of MC2R<sup>-/-</sup>, mice. In addition, RS increased UCP2-dependent uncoupling activity of isolated mitochondria from the liver of MC2R<sup>+/-</sup>, but not of MC2R<sup>-/-</sup>, mice. In vitro study revealed that corticosterone and dexamethasone directly increased UCP2 expression in mouse RAW 264.7 macrophages and suppressed the generation of LPS-induced mitochondrial reactive oxygen species (ROS) and TNF-α production. Knockdown of UCP2 by small interfering RNA blunted the dexamethasone action for suppressing LPS-induced mitochondrial ROS and TNF-α production. <b><i>Conclusion:</i></b> The present work suggests that RS enhances activation of the HPA axis to release glucocorticoids and upregulation of UCP2 in macrophages, thereby increasing the resistance to endotoxin-induced systemic inflammation and death.
DOI: 10.6084/m9.figshare.4558012
title: FIT_dataset.dta

description: Dataset of costeffectiveness analysis along a cluster randomized trial of nurse-led care to prevent disability in general practice. Appoved by Medical Ethics Committee of Academic Medical Centre, University of Amsterdam
DOI: 10.6084/m9.figshare.4558000.v1
title: Supplementary Material for: Stress-Induced Glucocorticoid Release Upregulates Uncoupling Protein-2 Expression and Enhances Resistance to Endotoxin-Induced Lethality

description: <b><i>Objective:</i></b> Although psychological and/or physiological stress has been well documented to influence immune responses, the precise mechanism for immunomodulation remains to be elucidated. The present work describes the role of the hypothalamic-pituitary-adrenal (HPA) axis in the mechanism of stress-mediated enhanced-resistance to lethality after lipopolysaccharide (LPS) injection. <b><i>Methods/Results:</i></b> Preconditioning with restraint stress (RS) resulted in enhanced activation of the HPA axis in response to LPS injection and suppressed LPS-induced release of proinflammatory cytokines and nitric oxide metabolites. Melanocortin 2 receptor-deficient mice (MC2R<sup>-/-</sup>) failed to increase plasma levels of glucocorticoids in response to LPS injection, and exhibited high sensitivity to LPS-induced lethality with enhanced release of proinflammatory cytokines as compared with MC2R<sup>+/-</sup> mice. Real-time PCR analysis revealed that RS induced upregulation of uncoupling protein-2 (UCP2) in macrophages in the lung and the liver of MC2R<sup>+/-</sup>, but not of MC2R<sup>-/-</sup>, mice. In addition, RS increased UCP2-dependent uncoupling activity of isolated mitochondria from the liver of MC2R<sup>+/-</sup>, but not of MC2R<sup>-/-</sup>, mice. In vitro study revealed that corticosterone and dexamethasone directly increased UCP2 expression in mouse RAW 264.7 macrophages and suppressed the generation of LPS-induced mitochondrial reactive oxygen species (ROS) and TNF-α production. Knockdown of UCP2 by small interfering RNA blunted the dexamethasone action for suppressing LPS-induced mitochondrial ROS and TNF-α production. <b><i>Conclusion:</i></b> The present work suggests that RS enhances activation of the HPA axis to release glucocorticoids and upregulation of UCP2 in macrophages, thereby increasing the resistance to endotoxin-induced systemic inflammation and death.
DOI: 10.6084/m9.figshare.4557973
title: Supplementary Material for: Exacerbating Factors Induce Different Gene Expression Profiles in Peripheral Blood Mononuclear Cells from Asthmatics, Patients with Chronic Obstructive Pulmonary Disease and Healthy Subjects

description: <b><i>Background:</i></b> Despite several common phenotypic features, chronic obstructive pulmonary disease (COPD) and severe asthma differ with regard to their causative factors and pathophysiology. Both diseases may be exacerbated by environmental factors, however, the molecular profiles of disease episodes have not been comprehensively studied. We identified differences in gene and protein expression profiles expressed by peripheral blood mononuclear cells (PBMC) of COPD patients, patients with atopic asthma and healthy subjects when challenged with exacerbating factors in vitro: lipopolysaccharide (LPS), house dust mite (HDM) and cat allergen. <b><i>Methods:</i></b> PBMC isolated from patients with severe atopic asthma and COPD, as well as healthy subjects were stimulated with rDer p 1 DG, rFel d 1 DG and LPS. The changes in the expression of 47 genes belonging to five groups (phospholipase A<sub>2</sub>, eicosanoids, transcription factors, cytokines and airway remodeling) were studied using TaqMan low density array cards. Immunoblotting was used to study relative protein expression. <b><i>Results:</i></b> rDer p 1 significantly up-regulated the expression of <i>PLA2G4A, PLA2G6, PLA2G15, CYSLTR1, LB4R2, PTGS1, PTGS2</i>, <i>FOXP1</i>, <i>GATA3</i>, <i>HDAC2</i>, <i>IREB2</i>, <i>PPARG</i>, <i>STAT4</i>, <i>TSLP </i>and<i> CHI3L1</i> genes in asthmatics in comparison to healthy subjects. LPS induced significant expression of <i>ANXA1</i> and<i> LTA4H </i>in asthmatics when compared to COPD patients and healthy subjects. <i>SOX6,</i><i>STAT4 </i>and <i>IL1RL1 </i>were induced in COPD after LPS stimulation. Analysis of protein expression revealed a pattern similar to mRNA expression. <b><i>Conclusions:</i></b> LPS-induced exacerbation of asthma and COPD is characterized by differential expression of selected genes in PBMC. HDM allergen changed the expression profile of inflammatory genes between patients with asthma of atopic origin and healthy controls.
DOI: 10.6084/m9.figshare.4557994
title: Supplementary Material for: Endoscopic Evaluation and Dissection of the Anterior Vitreous Base

description: The specific concept of pathological anterior vitreous base (AVB) and of its endoscopy-assisted dissection was elaborated during our 20 years' experience with endoscopy for observing the ‘in vivo' anatomy and pathoanatomy of the AVB, and for dissecting the anterior vitreous cortex in over 2,000 consecutive eyes. Endoscopy provides a 360° view of the entire vitreous cavity akin to the surgeon's eye being inside the operated eye. Evaluation of the capsulozonular complex, ciliary body, and AVB is not only independent of anterior media transparency, but unimpeded by scleral depression and magnified. High magnification dissection of the AVB gel can be conducted in an individualized and unmatched fashion.
DOI: 10.6084/m9.figshare.4557967
title: Supplementary Material for: Bilateral Pedunculopontine Nucleus Stimulation for Progressive Supranuclear Palsy

description: The pedunculopontine nucleus (PPN) is a potential target for gait disorders. We report 4 cases of bilateral PPN stimulation in progressive supranuclear palsy (PSP) patients with short-term (6 months) and long-term (18 months) follow-ups. Patients with PSP who had gait disturbances, but were able to walk with or without assistance, were selected. The patients' median age was 64 years and the disease duration 3 years. Bilateral PPN deep brain stimulation (DBS) was performed. The pacemaker was programmed using a bipolar mode and lower frequencies (20-45 Hz). The PSP rating scores (PSPRS) and their gait subscores (No. 25, 26, 27 and 28) along with PSP staging scores were used as primary end points. The total Unified Parkinson's Disease Rating Scale (UPDRS), UPDRS III and the 39-item Parkinson's Disease Questionnaire were considered as secondary end points. Video recordings of the gaits were performed before surgery and at the 6- and 18-month follow-ups. These were retrospectively reviewed by a blinded neurologist for the primary end points. At the 6- and 18-month follow-ups, the median change in PSPRS was from 33 (baseline) to 37.5 and 47, respectively. Similarly, the PSP staging changed from 3 to 2.5 and 3.5, item 25 from 1.5 to 2 and 3.5, item 26 from 2.5 to 2 and 3.5, item 27 from 3.5 to 3 and 3.5 and item 28 from 1.5 to 1.5 and 3. Two patients in the study with the PSP-parkinsonism phenotype experienced improvement in their gait until the last follow-up. Bilateral PPN DBS can be safely performed in PSP patients despite mid-brain atrophy.