cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4581022.v1
title: Table S4. Spectral count data for differentially expressed proteins identified between Adult and Nymph CLas(-) ACP. Average spectral count calculated from three biological replicates analyzed from each sample category. Statistical analysis using Fisher's exact test (p-value&lt;0.05 with Hochberg-Benjamini multiple testing correction) was used to determine significance of spectral count differences between categories

description: The Asian citrus psyllid (<i>Diaphorina citri)</i> is the insect vector responsible for the worldwide spread of ‘<i>Candidatus</i> Liberibacter asiaticus’ (CLas), the bacterial pathogen associated with citrus greening disease. Developmental changes in the insect vector impact pathogen transmission, such that <i>D. citri</i> transmission of CLas is more efficient when bacteria are acquired by nymphs when compared with adults. We hypothesize that expression changes in the <i>D. citri</i> immune system and commensal microbiota occur during development and regulate vector competency. In support of this hypothesis, more proteins, with greater fold changes, were differentially expressed in response to CLas in adults when compared with nymphs, including insect proteins involved in bacterial adhesion and immunity. Compared with nymphs, adult insects had a higher titre of CLas and the bacterial endosymbionts Wolbachia, Profftella and Carsonella. All Wolbachia and Profftella proteins differentially expressed between nymphs and adults are upregulated in adults, while most differentially expressed Carsonella proteins are upregulated in nymphs. Discovery of protein interaction networks has broad applicability to the study of host–microbe relationships. Using protein interaction reporter technology, a <i>D. citri</i> haemocyanin protein highly upregulated in response to CLas was found to physically interact with the CLas coenzyme A (CoA) biosynthesis enzyme phosphopantothenoylcysteine synthetase/decarboxylase. CLas pantothenate kinase, which catalyses the rate-limiting step of CoA biosynthesis, was found to interact with a <i>D. citri</i> myosin protein. Two Carsonella enzymes involved in histidine and tryptophan biosynthesis were found to physically interact with <i>D. citri</i> proteins. These co-evolved protein interaction networks at the host–microbe interface are highly specific targets for controlling the insect vector responsible for the spread of citrus greening.
DOI: 10.6084/m9.figshare.4581016.v1
title: Table S3. Spectral count data for differentially expressed proteins identified between Adult and Nymph CLas(+) ACP. Average spectral count calculated from three biological replicates analyzed from each sample category. Statistical analysis using Fisher's exact test (p-value&lt;0.05 with Hochberg-Benjamini multiple testing correction) was used to determine significance of spectral count differences between categories

description: The Asian citrus psyllid (<i>Diaphorina citri)</i> is the insect vector responsible for the worldwide spread of ‘<i>Candidatus</i> Liberibacter asiaticus’ (CLas), the bacterial pathogen associated with citrus greening disease. Developmental changes in the insect vector impact pathogen transmission, such that <i>D. citri</i> transmission of CLas is more efficient when bacteria are acquired by nymphs when compared with adults. We hypothesize that expression changes in the <i>D. citri</i> immune system and commensal microbiota occur during development and regulate vector competency. In support of this hypothesis, more proteins, with greater fold changes, were differentially expressed in response to CLas in adults when compared with nymphs, including insect proteins involved in bacterial adhesion and immunity. Compared with nymphs, adult insects had a higher titre of CLas and the bacterial endosymbionts Wolbachia, Profftella and Carsonella. All Wolbachia and Profftella proteins differentially expressed between nymphs and adults are upregulated in adults, while most differentially expressed Carsonella proteins are upregulated in nymphs. Discovery of protein interaction networks has broad applicability to the study of host–microbe relationships. Using protein interaction reporter technology, a <i>D. citri</i> haemocyanin protein highly upregulated in response to CLas was found to physically interact with the CLas coenzyme A (CoA) biosynthesis enzyme phosphopantothenoylcysteine synthetase/decarboxylase. CLas pantothenate kinase, which catalyses the rate-limiting step of CoA biosynthesis, was found to interact with a <i>D. citri</i> myosin protein. Two Carsonella enzymes involved in histidine and tryptophan biosynthesis were found to physically interact with <i>D. citri</i> proteins. These co-evolved protein interaction networks at the host–microbe interface are highly specific targets for controlling the insect vector responsible for the spread of citrus greening.
DOI: 10.6084/m9.figshare.4581019.v1
title: Table S1. Spectral count data for differentially expressed proteins identified between CLas(+)/(-) adult ACP. Average spectral count calculated from three biological replicates analyzed from each sample category. Statistical analysis using Fisher's exact test (p-value&lt;0.05 with Hochberg-Benjamini multiple testing correction) was used to determine significance of spectral count differences between categories

description: The Asian citrus psyllid (<i>Diaphorina citri)</i> is the insect vector responsible for the worldwide spread of ‘<i>Candidatus</i> Liberibacter asiaticus’ (CLas), the bacterial pathogen associated with citrus greening disease. Developmental changes in the insect vector impact pathogen transmission, such that <i>D. citri</i> transmission of CLas is more efficient when bacteria are acquired by nymphs when compared with adults. We hypothesize that expression changes in the <i>D. citri</i> immune system and commensal microbiota occur during development and regulate vector competency. In support of this hypothesis, more proteins, with greater fold changes, were differentially expressed in response to CLas in adults when compared with nymphs, including insect proteins involved in bacterial adhesion and immunity. Compared with nymphs, adult insects had a higher titre of CLas and the bacterial endosymbionts Wolbachia, Profftella and Carsonella. All Wolbachia and Profftella proteins differentially expressed between nymphs and adults are upregulated in adults, while most differentially expressed Carsonella proteins are upregulated in nymphs. Discovery of protein interaction networks has broad applicability to the study of host–microbe relationships. Using protein interaction reporter technology, a <i>D. citri</i> haemocyanin protein highly upregulated in response to CLas was found to physically interact with the CLas coenzyme A (CoA) biosynthesis enzyme phosphopantothenoylcysteine synthetase/decarboxylase. CLas pantothenate kinase, which catalyses the rate-limiting step of CoA biosynthesis, was found to interact with a <i>D. citri</i> myosin protein. Two Carsonella enzymes involved in histidine and tryptophan biosynthesis were found to physically interact with <i>D. citri</i> proteins. These co-evolved protein interaction networks at the host–microbe interface are highly specific targets for controlling the insect vector responsible for the spread of citrus greening.
DOI: 10.6084/m9.figshare.4580998
title: Supplementary Data Table S3 from Structural, mechanistic and functional insight into gliotoxin <i>bis</i>-thiomethylation in <i>Aspergillus fumigatus</i>

description: Supplementary Data Table S3 (Quantitaitve proteomic data)
DOI: 10.6084/m9.figshare.4580995
title: Table S2. Spectral count data for differentially expressed proteins identified between CLas(+)/(-) nymph ACP. Average spectral count calculated from three biological replicates analyzed from each sample category. Statistical analysis using Fisher's exact test (p-value&lt;0.05 with Hochberg-Benjamini multiple testing correction) was used to determine significance of spectral count differences between categories

description: The Asian citrus psyllid (<i>Diaphorina citri)</i> is the insect vector responsible for the worldwide spread of ‘<i>Candidatus</i> Liberibacter asiaticus’ (CLas), the bacterial pathogen associated with citrus greening disease. Developmental changes in the insect vector impact pathogen transmission, such that <i>D. citri</i> transmission of CLas is more efficient when bacteria are acquired by nymphs when compared with adults. We hypothesize that expression changes in the <i>D. citri</i> immune system and commensal microbiota occur during development and regulate vector competency. In support of this hypothesis, more proteins, with greater fold changes, were differentially expressed in response to CLas in adults when compared with nymphs, including insect proteins involved in bacterial adhesion and immunity. Compared with nymphs, adult insects had a higher titre of CLas and the bacterial endosymbionts Wolbachia, Profftella and Carsonella. All Wolbachia and Profftella proteins differentially expressed between nymphs and adults are upregulated in adults, while most differentially expressed Carsonella proteins are upregulated in nymphs. Discovery of protein interaction networks has broad applicability to the study of host–microbe relationships. Using protein interaction reporter technology, a <i>D. citri</i> haemocyanin protein highly upregulated in response to CLas was found to physically interact with the CLas coenzyme A (CoA) biosynthesis enzyme phosphopantothenoylcysteine synthetase/decarboxylase. CLas pantothenate kinase, which catalyses the rate-limiting step of CoA biosynthesis, was found to interact with a <i>D. citri</i> myosin protein. Two Carsonella enzymes involved in histidine and tryptophan biosynthesis were found to physically interact with <i>D. citri</i> proteins. These co-evolved protein interaction networks at the host–microbe interface are highly specific targets for controlling the insect vector responsible for the spread of citrus greening.
DOI: 10.6084/m9.figshare.4580998.v1
title: Supplementary Data Table S3 from Structural, mechanistic and functional insight into gliotoxin <i>bis</i>-thiomethylation in <i>Aspergillus fumigatus</i>

description: Supplementary Data Table S3 (Quantitaitve proteomic data)
DOI: 10.6084/m9.figshare.4580995.v1
title: Table S2. Spectral count data for differentially expressed proteins identified between CLas(+)/(-) nymph ACP. Average spectral count calculated from three biological replicates analyzed from each sample category. Statistical analysis using Fisher's exact test (p-value&lt;0.05 with Hochberg-Benjamini multiple testing correction) was used to determine significance of spectral count differences between categories

description: The Asian citrus psyllid (<i>Diaphorina citri)</i> is the insect vector responsible for the worldwide spread of ‘<i>Candidatus</i> Liberibacter asiaticus’ (CLas), the bacterial pathogen associated with citrus greening disease. Developmental changes in the insect vector impact pathogen transmission, such that <i>D. citri</i> transmission of CLas is more efficient when bacteria are acquired by nymphs when compared with adults. We hypothesize that expression changes in the <i>D. citri</i> immune system and commensal microbiota occur during development and regulate vector competency. In support of this hypothesis, more proteins, with greater fold changes, were differentially expressed in response to CLas in adults when compared with nymphs, including insect proteins involved in bacterial adhesion and immunity. Compared with nymphs, adult insects had a higher titre of CLas and the bacterial endosymbionts Wolbachia, Profftella and Carsonella. All Wolbachia and Profftella proteins differentially expressed between nymphs and adults are upregulated in adults, while most differentially expressed Carsonella proteins are upregulated in nymphs. Discovery of protein interaction networks has broad applicability to the study of host–microbe relationships. Using protein interaction reporter technology, a <i>D. citri</i> haemocyanin protein highly upregulated in response to CLas was found to physically interact with the CLas coenzyme A (CoA) biosynthesis enzyme phosphopantothenoylcysteine synthetase/decarboxylase. CLas pantothenate kinase, which catalyses the rate-limiting step of CoA biosynthesis, was found to interact with a <i>D. citri</i> myosin protein. Two Carsonella enzymes involved in histidine and tryptophan biosynthesis were found to physically interact with <i>D. citri</i> proteins. These co-evolved protein interaction networks at the host–microbe interface are highly specific targets for controlling the insect vector responsible for the spread of citrus greening.
DOI: 10.6084/m9.figshare.4580899
title: PowerPoint Slides for: Mortality after Renal Allograft Failure and Return to Dialysis

description: <b><i>Introduction:</i></b> The outcomes of patients who fail their kidney transplant and return to dialysis (RTD) has not been investigated in a nationally representative sample. We hypothesized that variations in management of transplant chronic kidney disease stage 5 leading to kidney allograft failure (KAF) and RTD, such as access, nutrition, timing of dialysis, and anemia management predict long-term survival. <b><i>Methods:</i></b> We used an incident cohort of patients from the United States Renal Data System who initiated hemodialysis between January 1, 2003 and December 31, 2008, after KAF. We used Cox regression analysis for statistical associations, with mortality as the primary outcome. <b><i>Results:</i></b> We identified 5,077 RTD patients and followed them for a mean of 30.9 ± 22.6 months. Adjusting for all possible confounders at the time of RTD, the adjusted hazards ratio (AHR) for death was increased with lack of arteriovenous fistula at initiation of dialysis (AHR 1.22, 95% CI 1.02-1.46, <i>p</i> = 0.03), albumin &lt;3.5 g/dL (AHR 1.33, 95% CI 1.18-1.49, <i>p</i> = 0.0001), and being underweight (AHR 1.30, 95% CI 1.07-1.58, <i>p</i> = 0.006). Hemoglobin &lt;10 g/dL (AHR 0.96, 95% CI 0.86-1.06, <i>p</i> = 0.46), type of insurance, and zip code-based median household income were not associated with higher mortality. Glomerular filtration rate &lt;10 mL/min/1.73 m<sup>2</sup> at time of dialysis initiation (AHR 0.83, 95% CI 0.75-0.93, <i>p</i> = 0.001) was associated with reduction in mortality. <b><i>Conclusions:</i></b> Excess mortality risk observed in patients starting dialysis after KAF is multifactorial, including nutritional issues and vascular access. Adequate preparation of patients with failing kidney transplants prior to resuming dialysis may improve outcomes.
DOI: 10.6084/m9.figshare.4580887
title: Supplementary Material for: Methotrexate Induces Apoptosis of Postpartum Placental Cytotrophoblasts

description: <b><i>Background:</i></b> Though methotrexate (MTX) is known to inhibit proliferation of trophoblasts derived from ectopic and intrauterine pregnancies, its action on trophoblasts derived from postpartum placenta remains questionable. This study was designed to ascertain the efficacy of MTX in inducing cell death of postpartum placental cytotrophoblasts (PPTC). <b><i>Methodology:</i></b> Primary human cytotrophoblasts were isolated from placentae of 1st and 2nd trimester intrauterine pregnancies and from postpartum placentae. The isolated trophoblasts were identified based on the expression of cytokeratin 7. MTX-induced inhibition of proliferation of cytotrophoblasts was detected by flow cytometry combined with the WST-1 assay. Secretion of HCG-β and invasiveness were evaluated to assess the effect of MTX on blocking the differentiated cellular function of cytotrophoblasts in relation to the gestational age. The efficacy of MTX in inducing apoptosis of cytotrophoblasts was estimated by terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling. <b><i>Results:</i></b> MTX significantly inhibited the proliferation and differentiation of cytotrophoblasts. MTX-induced cell apoptosis of PPTC was confirmed by increased expression of Fas, FasL, Bax, cleaved caspases 3, 7, 8, and 9, and decreased expression of Bcl-2. <b><i>Conclusion:</i></b> MTX inhibits replication and differentiation of cytotrophoblasts and appears to be an efficient inducer of PPTC apoptosis.
DOI: 10.6084/m9.figshare.4580845
title: Single-stage versus two-stage models to estimate creatinine corrected urinary analyte concentrations

description: The ability to detect 'known' differences in urinary analyte concentrations due to gender, age, and race/ethnicity when adjusted for similar differences in urinary creatinine concentrations were evaluated by a single-stage and a two-stage model by ten simulation studies. Log10 transformed values of observed urinary analyte concentration were used as the dependent variable and age, gender, and race/ethnicity were used as the categorical independent variables. In addition, while single-stage model used log10 transformed values of urinary creatinine as a covariate, two-stage model used a correction factor (CF) determined during the first stage of the model by fitting a secondary model for urinary creatinine. Single-stage model was almost always able to statistically significantly detect 'known' differences due to age, gender, and race/ethnicity. On the other hand, two-stage model was able to statistically significantly detect 'known' differences due to age, gender, and race/ethnicity a maximum of 87.2% of the times and as low as 10.6% of the times primarily because of the presence of multicollinearity between CF and urinary creatinine concentrations. Consequently, as long as the sole objective is to estimate the urinary analyte concentrations adjusted for the effect of all factors including urinary creatinine, single-stage models are the models of choice.
DOI: 10.6084/m9.figshare.4580890
title: Supplementary Material for: Association of Albuminuria and Estimated Glomerular Filtration Rate with Functional Performance Measures in Older Adults with Chronic Kidney Disease

description: <b><i>Background:</i></b> Chronic kidney disease (CKD) is increasingly common and disproportionately affects older adults. The contribution of kidney disease to the functional impairment noted in the elderly CKD population is unclear. <b><i>Methods:</i></b> This is a cross-sectional analysis of a hypertensive cohort of people aged ≥75 years from the Systolic Blood Pressure Intervention Trial. We evaluated estimated glomerular filtration rate (eGFR) and urine albumin-to-creatinine ratio (UACR) as predictors of 3 measures of functional status: EuroQol-5 Dimensional (EQ-5D) score, Falls Efficacy Scale (FES) score, and gait speed. Linear regression models were used to evaluate the associations between our independent variables and outcome measures. <b><i>Results:</i></b> Our analysis included 2,620 participants, mean age of 79.9 (4.0) years. Unadjusted models showed that lower eGFR level and higher UACR level were associated with lower EQ-5D (<i>p</i> &lt; 0.001 for both) and slower gait speed (<i>p</i> &lt; 0.001 for both) and worse scores on FES (<i>p</i> = 0.032 and <i>p</i> = 0.039). In the fully adjusted models, higher levels of UACR remained significantly associated with lower EQ-5D scores and slower gait speed (<i>p</i> = 0.011 and <i>p</i> = 0.002, respectively). In contrast, level of eGFR was not associated with any functional outcome measures when accounting for covariates. <b><i>Conclusions:</i></b> In individuals aged ≥75 years, albuminuria and eGFR were associated with impairments in physical performance and self-reported functional status; however, only the association with albuminuria remained after adjusting for relevant demographics and comorbidities. Evaluation of albuminuria may provide an additional tool for identifying older individuals at risk for functional impairment.
DOI: 10.6084/m9.figshare.4580899.v1
title: PowerPoint Slides for: Mortality after Renal Allograft Failure and Return to Dialysis

description: <b><i>Introduction:</i></b> The outcomes of patients who fail their kidney transplant and return to dialysis (RTD) has not been investigated in a nationally representative sample. We hypothesized that variations in management of transplant chronic kidney disease stage 5 leading to kidney allograft failure (KAF) and RTD, such as access, nutrition, timing of dialysis, and anemia management predict long-term survival. <b><i>Methods:</i></b> We used an incident cohort of patients from the United States Renal Data System who initiated hemodialysis between January 1, 2003 and December 31, 2008, after KAF. We used Cox regression analysis for statistical associations, with mortality as the primary outcome. <b><i>Results:</i></b> We identified 5,077 RTD patients and followed them for a mean of 30.9 ± 22.6 months. Adjusting for all possible confounders at the time of RTD, the adjusted hazards ratio (AHR) for death was increased with lack of arteriovenous fistula at initiation of dialysis (AHR 1.22, 95% CI 1.02-1.46, <i>p</i> = 0.03), albumin &lt;3.5 g/dL (AHR 1.33, 95% CI 1.18-1.49, <i>p</i> = 0.0001), and being underweight (AHR 1.30, 95% CI 1.07-1.58, <i>p</i> = 0.006). Hemoglobin &lt;10 g/dL (AHR 0.96, 95% CI 0.86-1.06, <i>p</i> = 0.46), type of insurance, and zip code-based median household income were not associated with higher mortality. Glomerular filtration rate &lt;10 mL/min/1.73 m<sup>2</sup> at time of dialysis initiation (AHR 0.83, 95% CI 0.75-0.93, <i>p</i> = 0.001) was associated with reduction in mortality. <b><i>Conclusions:</i></b> Excess mortality risk observed in patients starting dialysis after KAF is multifactorial, including nutritional issues and vascular access. Adequate preparation of patients with failing kidney transplants prior to resuming dialysis may improve outcomes.
DOI: 10.6084/m9.figshare.4580812
title: ODMeasurements of MIC.xlsx

description: The MIC values were determined using a 96-well Microtiter plate assay. Antibiotics were prepared after sugested concentrations of J.M. Andrews (2001). The plate layout used for the MIC tests were all the same. Bacteriocins in row A-D and antibiotics in row E-H, The test solutions were undiluted in column 1 and two-fold dilutions were made from column 2-10. Column 11 and 12 were controls, a growth control with inoculated Müller-Hinton broth (MHB) and a sterility control with MHB. The pathogens were taken from glycerol stocks and were incubated in MHB overnight, except S. pneumoniae which were incubated for 6h. After incubation OD450 were measured and the cultures were diluted in an appropriate volume of MHB to a OD450 = 0, 01. Each well in column 1-11 were inoculated with the same pathogen and covered with film. Each plate setup was done in triplets and incubated at 37oC for 16h. After incubation OD450 were measured for further analysis.