Nevin Manimala

Protein Sci. 2021 Oct 15. doi: 10.1002/pro.4205. Online ahead of print.

ABSTRACT

The antibody repertoires of individuals and groups have been used to explore disease states, understand vaccine responses and drive therapeutic development. The arrival of B-cell receptor repertoire sequencing has enabled researchers to get a snapshot of these antibody repertoires and as more data is generated, increasingly in depth studies are possible. However, most publicly available data only exists as raw FASTQ files, making the data hard to access, process and compare. The Observed Antibody Space (OAS) database was created in 2018 to offer clean, annotated and translated repertoire data. In this paper we describe an update to OAS that has been driven by the increasing volume of data and the appearance of paired (VH/VL) sequence data. OAS is now accessible via a new web server, with standardised search parameters and a new sequence-based search option. The new database provides both nucleotides and amino acids for every sequence, with additional sequence annotations to make the data MiAIRR-compliant, and comments on potential problems with the sequence. OAS now contains 25 new studies, including SARS-CoV-2 data and paired sequencing data. The new database is accessible at http://opig.stats.ox.ac.uk/webapps/oas/ and all data is freely available for download. This article is protected by copyright. All rights reserved.

PMID:34655133 | DOI:10.1002/pro.4205

J Vet Intern Med. 2021 Oct 15. doi: 10.1111/jvim.16279. Online ahead of print.

ABSTRACT

BACKGROUND: The term big kidney-little kidney syndrome in cats has been used for many years, but the definitions are not consistent and relevant research is limited.

OBJECTIVE: To determine the factors that differ between normal and BKLK cats, as well as to develop models for predicting the 30-day survival of cats with ureteral obstruction (UO).

ANIMALS: Sixteen healthy cats and 64 cats with BKLK.

METHODS: Retrospective study. To define BKLK by reference to data from clinically healthy cats. The demographic and clinicopathological data among groups were statistically analyzed.

RESULTS: Big kidney-little kidney syndrome cats had higher blood urea nitrogen (BUN) (median [interquartile range] 69 [28-162] vs 21 [19-24] mg/dL, P < .001), creatinine (5.6 [1.9-13.3] vs 1.3 [1.05-1.40] mg/dL, P < .001), and white blood cells (10 800 [7700-17 500] vs 6500 [4875-9350] /μL, P < .001) and lower hematocrit (32.8 [27.1-38.4] vs 39.1 [38.1-40.4]%, P < .001), urine specific gravity (1.011 [1.009-1.016] vs 1.049 [1.044-1.057], P < .001) and pH (5.88 [5.49-6.44] vs 6.68 [6.00-7.18], P = .001) compared to the control cats. A lower body temperature (BT; 38.1 [37.9-38.2] vs 38.7 [38.3-39.2]°C, P = .009), higher BUN (189 [150-252] vs 91 [36-170] mg/dL, P = .04), and creatinine (15.4 [13.3-17.4] vs 9.0 [3.1-14.2] mg/dL, P = .03) were found among the UO cats that were not 30-day survivors. A combination of BUN, phosphorus, and BT can predict 30-day survival among UO cats with an area under receiver operating characteristic curve of 0.863. (P = .01).

CONCLUSION: An increase in the length difference between kidneys can indicate UO, but cannot predict outcome for BKLK cats.

PMID:34655128 | DOI:10.1111/jvim.16279

Int J Health Plann Manage. 2021 Oct 15. doi: 10.1002/hpm.3365. Online ahead of print.

ABSTRACT

BACKGROUND: Case-based payment has extensively been adopted to replace the fee-for-service payment in China. This paper aims to assess the impacts of case-based payment reform on the providers’ behaviour using cataract surgery as an example.

METHODS: A total of 400 cataract inpatients were sampled in a tertiary hospital. Data analysis consisted of descriptive statistics, Wilcoxon rank-sum test and Chi-square test.

RESULTS: The number of routine preoperative laboratory tests and drugs significantly declined after the case-based payment reform (p < 0.001). Healthcare providers significantly reduced the use frequency of systemic glucocorticoids (GCs) and antibiotics, adjuvant drugs, multiple antibiotic eye drops, generic drugs in cataract surgery after reform (p < 0.001), and they reduced non-ophthalmic medications after reform (p < 0.01). Notably, all patients were prescribed GC eye drops, antibiotic eye drops, and original drugs in both groups. Moreover, the preoperative, postoperative, and total length of stay (LOS) declined after the reform (p < 0.001). Nonetheless, no significant difference was noted in the care quality between the two group.

CONCLUSION: The case-based payment reform decreased the intensity of care by reducing unnecessary drugs and retaining necessary drugs on cataract surgery. Besides, the LOS was shortened. Further, an impaired care quality was not witnessed, however, cost-shifting warrants further attention.

PMID:34655114 | DOI:10.1002/hpm.3365

J Adv Nurs. 2021 Oct 15. doi: 10.1111/jan.15074. Online ahead of print.

ABSTRACT

AIM: To identify and differentiate the practice patterns of generalist, specialist and advanced practice nursing roles in specialist and central hospital contexts.

BACKGROUND: In Finland, as in other Nordic countries, advanced practice nursing roles emerged around 2000. There are over 60,000 registered nurses/midwives in Finland and the clinical career pathway from a registered nurse to advanced practice nurse has been described yet not fully implemented in healthcare organizations. However, the number and activities of nonadvanced and advanced practitioner roles are not well known.

DESIGN: A descriptive comparative study.

METHODS: An online self-report survey was conducted between August and October 2020 using an advanced practice role delineation tool. A census sample of registered nurses, registered midwives, specialist nurses and advanced practice nurses in five university hospitals and one central hospital was recruited. Descriptive statistics were used to summarize the characteristics of participants and group differences were compared using analysis of variance (ANOVA). The STROBE checklist was used as the reporting guideline.

RESULTS: A total of 1497 responses were obtained (response rate = 10%). Overall, nurses used comprehensive care and education activities most frequently. The least used activities were research and publication and professional leadership. Univariate analysis of variance test between role effects, when education and grouped age were taken into account, showed statistically significant difference in all of the observed five activities (p < .001).

CONCLUSION: Identifying activities in different levels of nursing is a crucial first step in delineating nursing roles thus improving the governance of the human resource management.

IMPACT: The study results add to the international literature, delineating nursing roles in the spectrum of generalist to advanced practice nursing. As these roles become more formalized, we may incorporate novel ways of promoting the career development and optimal use and assessment of nursing roles and practice in various career levels.

PMID:34655100 | DOI:10.1111/jan.15074

Stat Med. 2021 Oct 15. doi: 10.1002/sim.9226. Online ahead of print.

ABSTRACT

We consider five asymptotically unbiased estimators of intervention effects on event rates in non-matched and matched-pair cluster randomized trials, including ratio of mean counts r1 , ratio of mean cluster-level event rates r2 , ratio of event rates r3 , double ratio of counts r4 , and double ratio of event rates r5 . In the absence of an indirect effect, they all estimate the direct effect of the intervention. Otherwise, r1 , r2, and r3 estimate the total effect, which comprises the direct and indirect effects, whereas r4 and r5 estimate the direct effect only. We derive the conditions under which each estimator is more precise or powerful than its alternatives. To control bias in studies with a small number of clusters, we propose a set of approximately unbiased estimators. We evaluate their properties by simulation and apply the methods to a trial of seasonal malaria chemoprevention. The approximately unbiased estimators are practically unbiased and their confidence intervals usually have coverage probability close to the nominal level; the asymptotically unbiased estimators perform well when the number of clusters is approximately 32 or more per trial arm. Despite its simplicity, r1 performs comparably with r2 and r3 in trials with a large but realistic number of clusters. When the variability of baseline event rate is large and there is no indirect effect, r4 and r5 tend to offer higher power than r1 , r2, and r3 . We discuss the implications of these findings to the planning and analysis of cluster randomized trials.

PMID:34655097 | DOI:10.1002/sim.9226

Stat Med. 2021 Oct 15. doi: 10.1002/sim.9228. Online ahead of print.

ABSTRACT

Control risk regression is a diffuse approach for meta-analysis about the effectiveness of a treatment, relating the measure of risk with which the outcome occurs in the treated group to that in the control group. The severity of illness is a source of between-study heterogeneity that can be difficult to measure. It can be approximated by the rate of events in the control group. Since the estimate is a surrogate for the underlying risk, it is prone to measurement error. Correction methods are necessary to provide reliable inference. This article illustrates the extent of measurement error effects under different scenarios, including departures from the classical normality assumption for the control risk distribution. The performance of different measurement error corrections is examined. Attention will be paid to likelihood-based structural methods assuming a distribution for the control risk measure and to functional methods avoiding the assumption, namely, a simulation-based method and two score function methods. Advantages and limits of the approaches are evaluated through simulation. In case of large heterogeneity, structural approaches are preferable to score methods, while score methods perform better for small heterogeneity and small sample size. The simulation-based approach has a satisfactory behavior whichever the examined scenario, with no convergence issues. The methods are applied to a meta-analysis about the association between diabetes and risk of Parkinson disease. The study intends to make researchers aware of the measurement error problem occurring in control risk regression and lead them to the use of appropriate correction techniques to prevent fallacious conclusions.

PMID:34655089 | DOI:10.1002/sim.9228

Sociol Health Illn. 2021 Oct 15. doi: 10.1111/1467-9566.13386. Online ahead of print.

ABSTRACT

Despite numerous studies on social relationships and health, the empirical focus has often been on middle-aged or older adults, even though young adulthood is a period of considerable change in social networks. We investigated whether the associations between social relationships and allostatic load, a multisystem physiological dysregulation index that reflects chronic stress responses, vary by type of relationship and stages of the lifecourse. Relationships with spouse/partner, immediate family and friends were assessed in terms of emotional support and social strain. Poisson regression models on multiple imputed data sets from waves 2-3 (2010-2012) of the UK Household Longitudinal Study (N = 10,380) were estimated. Social strain, particularly from partners and immediate family, appeared to elicit greater stress related dysregulation during early adulthood (age 21-34 years), corresponding to a predicted difference in the allostatic load index (range 0-12) between high and low strained relationships of 1.1 (95% CI: 0.5-1.6) among young women and 0.6 (95% CI: -0.04 to 1.2) among young men. There was little evidence of an association between allostatic load and any of the social relationships among older men and women. Models of social relationships over the lifecourse need to take account of how stressful social relationships become biologically embedded in early adulthood.

PMID:34655081 | DOI:10.1111/1467-9566.13386

Urol J. 2021 Oct 16. doi: 10.22037/uj.v18i.6626. Online ahead of print.

ABSTRACT

PURPOSE: Prostate canceris the most commonly diagnosed type of cancer and one of the leading causes of cancer-related death in men.Numerous efforts have been made to improve existing diagnostic methods and develop a new biomarker to identify patients with prostate cancer. In line with current literature, we preferred new serum-based biochemical markers as Pentraxin-3, Fetuin-A and Sirtuin-7 in the present study.

MATERIALS AND METHODS: A total of 174 patients aged 42-76 years were included in the study. Patients with prostate cancer (n=38) were enrolled as Group 1 and patients with benign prostatic hyperplasia (n=136) as Group 2. The serum levels of Pentraxin-3, Fetuin-A and Sirtuin-7 levels were compared between the groups.

RESULTS: The mean age of the patients was 61.9±7.6 years (p= .001). The mean serum Prostate Specific Antigen levels 32.0±59.6 (2.6-336) ng/mL and 10.0±11.3 (2.5-77.4) ng/mL in Group 1 and 2, respectively (p= .029). The mean serum levels of Pentraxin-3 and Fetuin-Ain Group 1 were statistically significantlydifferent from Group 2(3.3±4.4 ng/mL vs 1.8±2.4 ng/mL, p= .002 and 466.8±11.0 µg/mL vs 513.3±11.0 µg/mL,p= .041,respectively). There was no significant difference between Group 1 and 2 according to serum levels of Sirtuin-7 (12.7±8.2 ng/mL vs 12.7±12.4 ng/mL respectively, p= .145).

CONCLUSION: Pentraxin-3, Fetuin-A and Sirtuin-7 may be effective in the diagnosis of prostate cancerin light of the current literature.In this study, it was found that Pentraxin-3 and Fetuin-A were significantly different in the diagnosis of prostate cancer.Larger-scale prospective studies are needed to determine the importance of Pentraxin-3 and Fetuin-A in the diagnosis of prostate cancer.

PMID:34655076 | DOI:10.22037/uj.v18i.6626

Urol J. 2021 Oct 13. doi: 10.22037/uj.v18i.6503. Online ahead of print.

ABSTRACT

PURPOSE: The prevalence of erectile dysfunction in men is increasing. As well, the prevalence of diabetes, as one of the causes of sexual dysfunction, is rising in many countries. Due to the failure of common therapies in some patients with sexual dysfunction, it is necessary to develop an effective alternative treatment, such as stem cell therapy, for this problem.

MATERIALS AND METHODS: In this randomized single-blinded clinical trial, 20 diabetic patients with erectile dysfunction, who were resistant to common treatments, were selected and divided into two groups of intervention and control (n=10 per group). Autologous mesenchymal stem cells (MSCs) were extracted from oral mucosa and then infused via intracavernosal injection (50-60 106 cells) to the participants of the intervention group. Normal saline was injected in the control group. The patients were followed up with the International Index of Erectile Function (IIEF5) questionnaire, as well as color Doppler duplex ultrasound. Peak systolic velocity (PSV), end diastolic velocity (EDV), and resistance index (RI) were determined at three and six months after the interventions.

RESULTS: The mean IIEF5 scores in the intervention group were 7.2 ± 2.1, 9.2 ± 3.4, and 10.6 ± 4.7 before, three months, and six months after the injection, respectively, showing a significant ascending trend (p value = 0.01). Comparing the intervention and control groups, there was a significant difference in the IIEF5 score change during six months after the injection (p value = 0.02). Regarding the PSV and RI of penis vessels, there were no statistically significant differences between the two groups. However, these parameters showed upward and improving trends in the intervention group.

CONCLUSION: Intracavernosal injection of stem cells improved sexual function and PSV and RI indices of penile arteries in diabetic patients.

PMID:34655071 | DOI:10.22037/uj.v18i.6503

Thorac Cardiovasc Surg. 2021 Oct 15. doi: 10.1055/s-0041-1735496. Online ahead of print.

ABSTRACT

BACKGROUND: Unilateral diaphragmatic paralysis or paresis (UDP) in adults is an often overlooked disease which relevantly impairs the patient’s lung function and quality of life. Particularly in idiopathic UDP, there is no evidence for conservative therapy and only little evidence for surgical therapy.

METHODS: The method involves retrospective single-center analysis of patients with UDP persistent for at least 1 year who were operated by diaphragmatic resection, plication, and augmentation with a polypropylene mesh. The patients were tested for lung and diaphragmatic function, six-minute walk test (6MWT), and blood gas analysis before, 3 and 12 months after surgery.

RESULTS: In total, 85 patients received surgery for UDP. The most frequent reasons for UDP were idiopathic (67%), iatrogenic (mainly cardiac and cervical spine surgery; 24%), and trauma (9%). The mean operation time was 84 ± 24 minutes, the length of hospital stay 8.4 ± 3.9 days, chest tubes were removed after 11.7 ± 4.1 days. Overall morbidity was 42%, mortality 0%. Forced expiratory volume in one second (FEV₁) in supine position improved by 12.4% absolute, vital capacity by 11.8% absolute, and sniff nasal inspiratory pressure by 1.4 kPa 12 months after surgery (p <0.001 each). Total lung capacity increased by 6.8% absolute at 12 months (p = 0.001) The 6MWT distance improved by 45.9 m at 3 months and 50.9 m at 12 months (p = 0.001, each).

CONCLUSION: Surgical therapy for UDP is highly effective in the long term. The superiority over conservative treatments needs to be evaluated prospectively with standardized physiotherapeutic protocols. FEV₁ in supine position and 6MWT are easy to perform tests and represent statistically and patient-relevant outcomes.

PMID:34655069 | DOI:10.1055/s-0041-1735496