bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mortality and Morbidity in Kidney Transplant Recipients With a Failing Graft: A Matched Cohort Study
Authors: Lam Ngan N. , Boyne Devon J. , Quinn Robert R. , Austin Peter C. , Hemmelgarn Brenda R. , Campbell Patricia , Knoll Gregory A. , Tibbles Lee Anne , Yilmaz Serdar , Quan Hude , Ravani Pietro 
Published: April 2020

Background: Due to their history of renal disease and exposure to immunosuppression, kidney transplant recipients with a failing graft may be at higher risk of adverse outcomes compared to nontransplant controls. Understanding the burden of disease in transplant recipients may inform treatment decisions of people whose native kidneys are failing and may be eligible for a transplant. Objective: To compare mortality and morbidity in kidney transplant recipients with a failing graft to matched nontransplant controls. Design: Retrospective cohort study. Setting: Alberta, Canada. Patients: Kidney transplant recipients with a failing graft were identified as having at least 2 estimated glomerular filtration rate (eGFR) measurements between 15-30 mL/min/1.73 m2 (90-365 days apart). We also identified nontransplant controls with a similar degree of kidney dysfunction. Measurements: Mortality and hospitalization. Methods: We propensity-score matched 520 kidney transplant recipients with a failing graft to 520 nontransplant controls. Results: The median age of the matched cohort was 57 years and 40% were women. Compared to matched nontransplant controls, recipients with a failing graft had a higher hazard of death (hazard ratio, 1.54; 95% confidence interval [CI], 1.28-1.85; p < .001) and a higher rate of all-cause hospitalization (rate ratio, 1.67; 95% CI, 1.42-1.97; p < .001). Kidney transplant recipients also had a higher rate of several cause-specific hospitalizations including genitourinary, cardiovascular, and infectious causes. Limitations: Observational design with the risk of residual confounding. Conclusions: A failing kidney transplant is associated with an increased burden of mortality and morbidity beyond chronic kidney disease. This information may assist the discussion of prognosis in kidney transplant recipients with a failing graft and the design of strategies to minimize risks.
Infection and extrusion of a subcutaneous access port in a cat: a long-term postoperative complication of a subcutaneous ureteral bypass device
Authors: Fouhety Aurore , Boursier Jean-François 
Published: April 2020

Case summary A 5-year-old domestic shorthair neutered female cat was presented for a wound in the region of the subcutaneous ureteral bypass shunting port with externalisation of the device, 2 years after its initial positioning. The cat had had positive urine bacterial cultures over the previous year and a half without any clinical signs of urinary tract infection. Bacterial cultures of urine and the wound revealed the same bacteria, suggesting a complication caused by infected urine from the implanted system. The wound was successfully treated with surgery and at the time of writing, 3 months later, the cat is healthy with no evidence of recurrence. Relevance and novel information To our knowledge, this is the first report of a subcutaneous ureteral bypass shunting port extrusion as a long-term major complication of the bacterial infection of the device.
Progression of albuminuria in patients with sickle cell anemia: a multicenter, longitudinal study
Authors: Niss Omar , Lane Adam , Asnani Monika R. , Yee Marianne E. , Raj Ashok , Creary Susan , Fitzhugh Courtney , Bodas Prasad , Saraf Santosh L. , Sarnaik Sharada , Devarajan Prasad , Malik Punam 
Published: April 2020

AbstractSickle cell nephropathy results in chronic kidney disease (CKD), which is associated with significant morbidity and mortality in sickle cell anemia (SCA). Albuminuria is an early manifestation of sickle nephropathy; however, little is known about progression of albuminuria or its correlation with glomerular filtration rate (GFR) decline or CKD. We studied nephropathy progression in 303 SCA participants in a prospective, multicenter, longitudinal study. We collected steady-state urine and serum samples yearly and assessed albumin/creatinine ratio (ACR), estimated GFR (eGFR), and SCA and nephropathy biomarkers. Participants with albuminuria (ACR ≥30 mg/g) for ≥2 annual measurements were classified as having persistent albuminuria (PA). At baseline (mean age, 21 years; range, 2-64 years), 32% had albuminuria. In longitudinal multivariate analysis, ACR was associated with sex, anemia, older age, and higher bilirubin and kidney injury molecule-1 levels. Albuminuria increased with age by 3.5 mg/g per year (P &lt; .0001). Of 175 participants with ≥3 annual samples, 81% with baseline albuminuria ≥100 mg/g developed PA. Decreased eGFR and adult CKD were associated with PA (P = .002 and P = .02, respectively), but not with baseline albuminuria. Rate of eGFR decline was steeper among adults (but not children) with albuminuria, compared with those without (P = .02). Participants with PA were more likely to have rapid eGFR decline compared with those without (P = .03). In this longitudinal study, albuminuria progressed with age, and adults with albuminuria had worse eGFR decline than those without. Albuminuria ≥100 mg/g predicted PA, which was associated with rapid eGFR decline and CKD development in adults with SCA. This trial was registered at www.clinicaltrials.gov as #NCT02239016.
Nitric Oxide Enhances Rice Resistance to Rice Black-Streaked Dwarf Virus Infection
Authors: Lu Rongfei , Liu Zhiyang , Shao Yudong , Su Jiuchang , Li Xuejuan , Sun Feng , Zhang Yihua , Li Shuo , Zhang Yali , Cui Jin , Zhou Yijun , Shen Wenbiao , Zhou Tong 
Published: April 2020

Abstract
Background
Rice black-streaked dwarf virus (RBSDV) causes one of the most important rice virus diseases of plants in East Asia. However, molecular mechanism(s)controlling rice resistance to infection is largely unknown.

Results
In this paper, we showed that RBSDV infection in rice significantly induced nitric oxide (NO) production. This finding was further validated through a genetic approach using a RBSDV susceptible (Nipponbare) and a RBSDV resistant (15HPO187) cultivar. The production of endogenous NO was muchhigher in the 15HPO187 plants, leading to a much lower RBSDV disease incidence. Pharmacological studies showed that the applications of NO-releasingcompounds (i.e., sodium nitroprusside [SNP] and nitrosoglutathione [GSNO]) to rice plants reduced RBSDV disease incidence. After RBSDV infection, the levels of OsICS1, OsPR1b and OsWRKY 45 transcripts were significantly up-regulated by NO in Nipponbare. The increased salicylic acid contents were also observed. After the SNP treatment, protein S-nitrosylation in rice plants was also increased, suggesting that the NO-triggered resistance to RBSDV infection was partially mediated at the post-translational level. Although Osnia2 mutant rice produced less endogenous NO after RBSDV inoculation and showed a higher RBSDV disease incidence, its RBSDV susceptibility could be reduced by SNP treatment.

Conclusions
Collectively, our genetic and molecular evidence revealed that endogenous NO was a vital signal responsible for rice resistance to RBSDV infection.
Value of multiplex PCR for detection of antimicrobial resistance in samples retrieved from patients with orthopaedic infections
Authors: Sigmund Irene Katharina , Renz Nora , Feihl Susanne , Morgenstern Christian , Cabric Sabrina , Trampuz Andrej 
Published: April 2020

Abstract
Background
The performance of multiplex PCR (mPCR) for detection of antimicrobial resistance from clinical isolates is unknown. We assessed the ability of mPCR to analyse resistance genes directly from clinical samples.
Patients with orthopedic infections were prospectively included. Phenotypical and genotypical resistance was evaluated in clinical samples (synovial and sonication fluid) where identical pathogens were identified by culture and mPCR.

Result
A total of 94 samples were analysed, including 60 sonication fluid and 34 synovial fluid samples. For coagulase-negative staphylococcus strains, mPCR detected resistance to oxacillin in 10 of 23 isolates (44%) and to rifampin in none of 6 isolates. For S. aureus isolates, detection rate of oxacillin and rifampin-resistance was 100% (2/2 and 1/1, respectively). Fluoroquinolone-resistance was confirmed by mPCR in all 3 isolates of Enterobacteriaceae, in enterococci resistance to aminoglycoside-high level was detected in 1 of 3 isolates (33%) and in streptococci resistance to macrolides/lincosamides in none of 2 isolates. The overall sensitivity for different pathogens and antimicrobials was 46% and specificity 95%, the median concordance was 80% (range, 57–100%). Full agreement was observed for oxacillin in S. aureus, vancomycin in enterococci, carbapenems/cephalosporins in Enterobacteriaceae and rifampin in Cutibacterium species.

Conclusion
The overall sensitivity for detection of antimicrobial resistance by mPCR directly from clinical samples was low. False-negative mPCR results occurred mainly in coagulase-negative staphylococci, especially for oxacillin and rifampin. However, the specificity of mPCR was high and a positive result reliably predicted antimicrobial resistance. Including universal primers in the PCR test assay may improve the detection rate but requires additional sequencing step.

Trial registration
www.clinicaltrials.gov No. NCT02530229, registered at 21 August 2015 (retrospectively registered).
Comparison of bacterial communities in soil samples with and without tomato bacterial wilt caused by Ralstonia solanacearum species complex
Authors: Zhang Ying , Hu Anna , Zhou Jianuan , Zhang Wenfei , Li Peng 
Published: April 2020

Abstract
Background
Ralstonia solanacearum is one of the most notorious soil-borne phytopathogens. It causes a severe wilt disease with deadly effects on many economically important crops. The microbita of disease-suppressive soils are thought that they can contribute to the disease resistance of crop plants, thus, evaluation of the microbial community and their interaction characteristics between suppressive soil (SS) and conducive soil (CS) will help to understand resistance mechanism. To do this, the bacterial community structure, correlation analysis with soil chemical properties, interaction network of SS (nearly no disease in three years), and CS (suffered heavy bacterial wilt disease) were analyzed.

Results
A higher bacterial community diversity index was found in SS, the relative abundance of Nocardioides, Gaiella and norank_f_Anaerolineaceae were significantly more than that of the CS. Moreover, the relative abundance of main genera Bacillus, norank_o_Gaiellales, Roseiflexus, and norank_o_Gemmatimonadaceae were significantly more than that of the CS. Redundancy analysis at the genus level indicated that the available phosphate played a key role in the bacterial community distribution, and its role was negatively correlated with soil pH, organic matter content, alkali-hydrolyzable nitrogen, and available potassium contents. Interaction network analysis further demonstrated that greater diversity at the genus level existed in the SS network and formed a stable network. Additionally, the species of Mycobacterium, Cyanobacteria, and Rhodobiaceae are the key components that sustain the network stability. Seven clusters of orthologous groups exhibited significant differences between SS and CS. Moreover, 55 bacterial strains with distinct antagonistic activities to R. solancearum were isolated and identified from the healthy tomato plant rhizosphere soil of the CS.

Conclusions
Our findings indicate that the bacterial diversity and interaction network differed between the CS and SS samples, providing a good foundation in the study of bacterial wilt.
Comparison of screening accuracy of the Patient Health Questionnaire-2 using two case-identification methods during pregnancy and postpartum
Authors: Slavin Valerie , Creedy Debra K. , Gamble Jenny 
Published: April 2020

Abstract
Background
Variation exists regarding perinatal depression screening. A two-step screening method has been recommended. According to a maternity-focused core outcome set developed by the International Consortium for Health Outcomes Measurement, women who score 3 or more on the PHQ-2 then complete the Edinburgh Postnatal Depression Scale (EPDS). Limited evidence exists regarding the screening accuracy of the PHQ-2 in childbearing women. An alternative case-identification method may be more sensitive for perinatal women. We aimed to [1] evaluate the screening accuracy of the PHQ-2 during the perinatal period using two case-identification methods, and [2] measure the variability of accuracy over four time-points during pregnancy and postpartum.

Methods
A prospective, longitudinal cohort study was conducted with 309 consecutive women who completed the PHQ-2 and EPDS during pregnancy (booking, 36-weeks) and postpartum (6-, 26-weeks). EPDS was the reference standard using cut-off scores for ‘at least probable minor depression’ during pregnancy (≥ 13) and postpartum (≥ 10) and for ‘probable major depression’ during pregnancy (≥ 15) and postpartum (≥ 13). PHQ-2 was analysed using two methods: [1] scored (cut-points ≥ 2 and ≥ 3), [2] dichotomous yes/no (positive response to either question) against EPDS cut-points for at least probable minor and probable major depression. Receiver operating characteristic analyses determined accuracy.

Results
Probable major depression: Over four timepoints PHQ-2 ≥ 3 revealed lowest sensitivity (36–79%) but highest specificity (94–98%). An alternative case-identification method revealed high sensitivity (93–100%), but lowest specificity (58–71%). Minor depression: PHQ-2 ≥ 3 revealed the lowest sensitivity (19–50%) but highest specificity (95–98%). An alternative case-identification method revealed the highest sensitivity (81–100%) and moderate specificity (60–74%).

Conclusions
Recommended method of case-identification (PHQ-2 ≥ 3) missed an unacceptable number of women at-risk of depression. As a clinical decision-making tool, an alternative, dichotomous method maximized case-identification and is recommended. Further, the literature identified inconsistent reporting of the PHQ-2 and the alternative case-identification method hindering the ability to synthesise data. The future use and reporting of consistent question wording and response format will improve outcome reporting and synthesis. Further research in larger and diverse maternity populations is recommended.
Cause and predictors of neonatal mortality among neonates admitted to neonatal intensive care units of public hospitals in eastern Ethiopia: a facility-based prospective follow-up study
Authors: Desalew Assefa , Sintayehu Yitagesu , Teferi Nardos , Amare Firehiwot , Geda Bifitu , Worku Teshager , Abera Kebebush , Asefaw Abiyot 
Published: April 2020

Abstract
Background
The first month is the most crucial period for child survival. Neonatal mortality continues to remain high with little improvement over the years in Sub-Saharan Africa, including Ethiopia. This region shows the least progress in reducing neonatal mortality and continues to be a significant public health issue. In this study setting, the causes and predictors of neonatal death in the neonatal intensive care units are not well documented. Hence, this study aimed to determine the causes and predictors of neonatal mortality among infants admitted to neonatal intensive care units in eastern Ethiopia.

Methods
A facility-based in prospective follow-up study was conducted among neonates admitted to neonatal intensive care units of public hospitals of eastern Ethiopia from November 1 to December 30, 2018. Data were collected using a pre-tested structured questionnaire and a follow-up checklist. The main outcomes and causes of death were set by pediatricians and medical residents. EpiData 3.1 and Statistical Package for Social Sciences Version 25 software were used for data entry and analysis, respectively. Multivariable logistic regression was used to identify the predictors of facility-based neonatal mortality.

Results
The proportion of facility-based neonatal mortality was 20% (95% CI:16.7–23.8%). The causes of death were complications of preterm birth (28.58%), birth asphyxia (22.45%), neonatal infection (18.36%), meconium aspiration syndrome (9.18%), respiratory distress syndrome (7.14%), and congenital malformation (4.08%). Low birth weight, preterm births, length of stay of the neonatal intensive care unit, low 5 min APGAR score, hyperthermia, and initiation of feeding were predictors of neonatal death among infants admitted to the neonatal intensive care units of public hospitals in eastern Ethiopia.

Conclusions
The proportion of facility-based neonatal deaths was unacceptably high. The main causes of death were preventable and treatable. Hence, improving the timing and quality of antenatal care is essential for early detection, anticipating high-risk newborns, and timely interventions. Furthermore, early initiation of feeding and better referral linkage to tertiary health facilities could lead to a reduction in neonatal death in this setting.
Evaluation of dialysis centres: values and criteria of the stakeholders
Authors: Parra Eduardo , Arenas María Dolores , Fernandez-Reyes Luis María José , Blasco Forcén Angel , Alvarez-Ude Fernando , Aguarón Joven Juan , Altuzarra Casas Alfredo , Moreno-Jiménez José María 
Published: April 2020

Abstract
Background
Evaluation of renal replacement therapy with haemodialysis is essential for its improvement. Remarkably, outcomes vary across centres. In addition, the methods used have important epistemological limitations, such as ignoring significant features (e.g., quality of life) or no relevance given to the patient’s perspective in the indicator’s selection. The present study aimed to determine the opinions and preferences of stakeholders (patients, clinicians, and managers) and establish their relative importance, considering the complexity of their interactions, to facilitate a comprehensive evaluation of haemodialysis centres.

Methods
Successive working groups (WGs) were established using a multicriteria methodology. WG1 created a draft of criteria and sub-criteria, WG2 agreed, using a qualitative structured analysis with pre-established criteria, and WG3 was composed of three face-to-face subgroups (WG3-A, WG3-B, and WG3-C) that weighted them using two methodologies: weighted sum (WS) and analytic hierarchy process (AHP). Subsequently, they determined a preference for the WS or AHP results. Finally, via the Internet, WG4 weighted the criteria and sub-criteria by the method preferred by WG3, and WG5 analysed the results.

Results
WG1 and WG2 identified and agreed on the following evaluation criteria: evidence-based variables (EBVs), annual morbidity, annual mortality, patient-reported outcome measures (PROMs), and patient-reported experience measures (PREMs). The EBVs consisted of five sub-criteria: type of vascular access, dialysis dose, haemoglobin concentration, ratio of catheter bacteraemia, and bone mineral disease. The patients rated the PROMs with greater weight than the other stakeholders in both face-to-face WG3 (WS and AHP) and WG4 via the Internet. The type of vascular access was the most valued sub-criterion. A performance matrix of each criterion and sub-criterion is presented as a reference for assessing the results based on the preferences of the stakeholders.

Conclusions
The use of a multicriteria methodology allows the relative importance of the indicators to be determined, reflecting the values of the different stakeholders. In a performance matrix, the inclusion of values and intangible aspects in the evaluation could help in making clinical and organizational decisions.
Recombinant lipidated Zika virus envelope protein domain III elicits durable neutralizing antibody responses against Zika virus in mice
Authors: Chen Mei-Yu , Chai Kit Man , Chiang Chen-Yi , Wu Chiao-Chieh , Yu Guann-Yi , Liu Shih-Jen , Chen Hsin-Wei 
Published: April 2020

Abstract
Background
The emergence of Zika virus (ZV) in tropical and subtropical areas of the world has created an urgent need for vaccines against ZV. However, approved vaccines that prevent ZV infection are not available. To develop an effective vaccine against ZV infection, a lipidated form of ZV envelope protein domain III that possesses an intrinsic adjuvant property was rationally designed. Our goal was to examine the immunogenicity of recombinant lipidated ZV envelope protein domain III (rLZE3) and evaluate its potential as a vaccine candidate against ZV.

Methods
Recombinant ZV envelope protein domain III (rZE3) and rLZE3 were prepared with an Escherichia coli-based system. Dendritic cell surface marker expression and cytokine production upon stimulation were analyzed to evaluate the function of rLZE3. Neutralizing antibody capacities were evaluated using focus reduction neutralization tests after immunization. To investigate the protective immunity in immunized mice, serum samples collected from immunized mice were adoptively transferred into AG129 mice, and then viremia levels and survival times were examined after ZV challenge.

Results
rLZE3 alone but not rZE3 alone efficiently activated dendritic cells in vitro and was taken up by dendritic cells in vivo. Immunization of C57BL/6 mice with rLZE3 alone (without exogenous adjuvant) could induce ZV-specific neutralizing antibody responses. Furthermore, serum samples obtained from rLZE3-immunized mice provided protection as indicated by a reduction in viremia levels and prolongation of survival times after ZV challenge.

Conclusion
These results indicate that rLZE3 is an excellent vaccine candidate and has great potential that should be evaluated in further preclinical studies.
The abnormal lipid profile in obesity and coronary heart disease (CHD) in Pakistani subjects
Authors: Shabana  , Shahid Saleem Ullah , Sarwar Sumbal 
Published: April 2020

Abstract
Background
Obesity has become global epidemic in the last three decades, whereas Coronary Heart Disease (CHD) still remains the most important cause of mortality in the world. The study was aimed at determining the pattern of lipid profile for the obese and CHD population in Pakistan. As obesity is a strong predisposing risk factor for CHD, we aimed to analyze the lipid parameters in both conditions and compare them with the healthy controls of the same ethnicity.

Methods
Blood samples were collected from one thousand individuals (500 with CHD, 250 with obesity, 250 healthy controls). The lipid profile (total Cholesterol, triglycerides, HDL-C, LDL-C and VLDL) was measured using commercially available kits. The pattern of dyslipidemia was then studied by comparing the results in both groups with controls as well as population cutoffs. The quantitative variables were checked for normality and log transformation was done for variables where appropriate. Analysis of variance and logistic regression were done to check the association of lipid parameters with obesity and CHD.

Results
The obese and CHD groups showed a dyslipidemic profile than the healthy controls. CHD group had a higher proportion of CHD in any of the first degree blood relatives (36.0% vs. 1.8%), a similar trend was observed in the obese group, where 63.9% cases had positive family history. Among cases, 50.7% had combined lipid abnormalities, i.e., the values of TC, LDL-C, TG and HDL-C, all were deranged. Whereas 49.52% had TC more than normal cut off (> 200 mg/dl), 51.6% had LDL-C > 100 mg/dl. Similarly, 80.4% of patients had TG levels more than upper normal range (> 150 mg/dl) and 64% had HDL values in moderate CHD risk group (< 50 mg/dl). The results show that Pakistani cases are hyperlipidemic for lipid traits except for HDL which is lowered. Patients with comorbidities also had lipid profiles deviated from the normal range.

Conclusion
The study provides information regarding the aberration of lipid profile in the metabolic disorders that can increase the predisposition to complications.