Nevin Manimala

Hum Genet. 2022 Apr 16. doi: 10.1007/s00439-022-02455-8. Online ahead of print.

ABSTRACT

Reproducibility is not only essential for the integrity of scientific research but is also a prerequisite for model validation and refinement for the future application of predictive algorithms. However, reproducible research is becoming increasingly challenging, particularly in high-dimensional genomic data analyses with complex statistical or algorithmic techniques. Given that there are no mandatory requirements in most biomedical and statistical journals to provide the original data, analytical source code, or other relevant materials for publication, accessibility to these supplements naturally suggests a greater credibility of the published work. In this study, we performed a reproducibility assessment of the notable paper by Gerstung et al. (Nat Genet 49:332-340, 2017) by rerunning the analysis using their original code and data, which are publicly accessible. Despite an open science setting, it was challenging to reproduce the entire research project; reasons included: incomplete data and documentation, suboptimal code readability, coding errors, limited portability of intensive computing performed on a specific platform, and an R computing environment that could no longer be re-established. We learn that the availability of code and data does not guarantee transparency and reproducibility of a study; paradoxically, the source code is still liable to error and obsolescence, essentially due to methodological and computational complexity, a lack of reproducibility checking at submission, and updates for software and operating environment. The complex code may also hide problematic methodological aspects of the proposed research. Building on the experience gained, we discuss the best programming and software engineering practices that could have been employed to improve reproducibility, and propose practical criteria for the conduct and reporting of reproducibility studies for future researchers.

PMID:35429300 | DOI:10.1007/s00439-022-02455-8

Musculoskelet Surg. 2022 Apr 16. doi: 10.1007/s12306-022-00745-y. Online ahead of print.

ABSTRACT

PURPOSE: This study focused on a comparison of mid-term clinical, functional and radiographic outcomes of adults treated by open reduction and internal fixation (ORIF), radial head prosthesis (RHP) and resection (RHR).

METHODS: The retrospective evaluation concerned 47 surgically treated patients after a mean follow-up of 53 months. All patients were grouped according to the surgical procedure performed: 15 in the RHP group, 16 in the ORIF group and 16 in the RHR group. At the follow-up, outcome assessment was based on radiographs, range of motion (ROM) and functional rating scores.

RESULTS: Patients treated by RHR had significantly higher mean age and shorter operation time than other two groups. Compared to ROM, flexion, extension and pronation were significantly worse in patients treated by ORIF than those in the RHP group and the RHR group. Supination was significantly better in the RHP group. However, no statistical differences were observed in functional rating scores among the three groups. Regarding complications, instability was the only cause of revision surgery in the RHP group and the RHR group. On the other hand, the ORIF group revision rate was 50% and secondary displacement was the most frequent cause of failure.

CONCLUSION: The ORIF group did not show good results with greater elbow stiffness and higher revision rate than the other two techniques. RHR may be suitable for elderly patients with lower functional demands as it reported good clinical results and reduced operation time.

PMID:35429279 | DOI:10.1007/s12306-022-00745-y

Eur J Orthop Surg Traumatol. 2022 Apr 16. doi: 10.1007/s00590-022-03260-9. Online ahead of print.

ABSTRACT

PURPOSE: While the use of open reduction internal fixation (ORIF) has remained stable over the last decade, there has been a significant increase in the use of reverse total shoulder arthroplasty (RTSA) for proximal humerus fractures (PHFs). This study sought to compare the complication profiles of RTSA to ORIF in a large, validated, retrospective cohort.

METHODS: Patients who underwent surgical treatment for PHFs with RTSA or ORIF were identified in a national database (NSQIP) using CPT and ICD codes. Demographics and comorbidities were identified for each cohort of patients. Thirty-day complications were analyzed with univariate and multivariate analyses using Chi-square, Fischer’s exact and analysis of variance testing.

RESULTS: The total number of patients included in this study was 2157.522 (24.2%) underwent RTSA and 1635 (75.8%) underwent ORIF. Patients undergoing RTSA were older with an average age of 73.52 years compared with 63.84 years in those undergoing ORIF (p < 0.001). Patients with RTSA were more likely to experience any complications (p < 0.001), pulmonary complications (p = 0.029), extended length of stay > 3 days (p < 0.001), and perioperative transfusion requirement (p < 0.001) after univariate analysis. After controlling for demographic differences, the only statistically significant complication was perioperative transfusion requirement (OR 1.383).

CONCLUSION: After controlling for demographic variables and comorbidities, RTSA placed patients at increased risk for perioperative blood transfusion. Patients undergoing RTSA should be counseled prior to surgery regarding the risk for transfusion and potentially optimized medically through multidisciplinary care if the surgeon elects to proceed with RTSA versus ORIF for the treatment of PHFs.

PMID:35429276 | DOI:10.1007/s00590-022-03260-9

Knee Surg Sports Traumatol Arthrosc. 2022 Apr 16. doi: 10.1007/s00167-022-06967-8. Online ahead of print.

ABSTRACT

PURPOSE: Lateral meniscus posterior root tears (LMPRTs) are commonly found in patients with anterior cruciate ligament (ACL) injuries. However, risk factors for LMPRTs are not well known. This study was designed to systematically review the available evidence regarding risk factors associated with LMPRTs.

METHODS: The PubMed, EMBASE, Cochrane Library, and Web of Science databases were searched for papers containing the key words “lateral meniscus posterior root tears”, “LMPRTs” and “risk factor”. Inclusion screening, data extraction, and quality assessment of the included articles were conducted independently by two authors. Statistical analysis was conducted to determine risk factors for LMPRTs.

RESULT: Seventeen studies with a total sample size of 6, 589 patients were identified. The pooled prevalence of LMPRTs was 9.6% (range, 5.1-33.8%) for ACL injury. Significant risk factors included a patient age of < 30 [OR = 1.4, 95% CI (1.07, 1.84), p = 0.01], male sex [OR = 1.50, 95% CI (1.24,1.81), p = 0.01], higher body mass index (BMI) [MD = 0.45, 95% CI (0.13, 0.76), p < 0.01], higher lateral posterior tibial slope (LPTS) [MD = 2.22, 95% CI (1.37, 3.07), p < 0.01], deep sulcus sign [OR = 5.76, 95% CI (1.35, 24.52), p < 0.01] and bone bruises on lateral femoral condyle [OR = 4.88, 95% CI (1.27, 18.77), p < 0.01], lateral meniscal extrusion > 1 mm [OR = 5.56, 95% CI (1.52, 20.29), p < 0.01] and > 3 mm [OR = 12.91 95% CI (1.28, 130.01), p < 0.01], medial meniscal tears [OR = 1.40, 95% CI (1.12, 1.75), p < 0.01], and medial ramp lesions [OR = 2.29, 95% CI (1.35, 3.89), p < 0.01].

CONCLUSION: Age below 30, male, higher BMI, higher LPTS, deep sulcus sign, bone bruises on lateral femoral condyle, lateral meniscal extrusion, medial meniscal tear, and medial ramp lesion are risk factors for LMPRTs.

LEVEL OF EVIDENCE: Level IV.

PMID:35429241 | DOI:10.1007/s00167-022-06967-8

Swiss Med Wkly. 2022 Apr 14;152:w30159. doi: 10.4414/smw.2022.w30159. eCollection 2022 Mar 28.

ABSTRACT

BACKGROUND: General Consent (GC) allows the further use of health-related data/samples for multiple, unspecified research projects and/or for the collection in databases and biobanks in Switzerland. The application of General Consent in the context of human research is regulated within the scope of the Human Research Act. At the University Hospital Zurich patients are informed about General Consent to which they can agree (GC = yes) or disagree (GC = no) to the use of their routinely collected data/samples in research. In this paper, we investigated the association of demographic and medical factors on a patient’s General Consent choice.

METHODS: In this cross-sectional study, we investigated the association of age, gender, number of visits and number of diagnoses on General Consent choice. The study population was stratified by General Consent status group (GC choice: Yes, No, Not issued) and examined by means of descriptive statistics, comparative statistics and a multinomial and logistic regression model. A p-value of 0.001 was determined as significant.

RESULTS: The female gender was found to associate with decreased odds in positive General Consent choice (<0.001) whereas age (<0.001) and number of diagnoses (<0.001) were associated with increased odds in positive General Consent choice (reference “GC = no” group). The number of visits (<0.001) as well as the number of diagnoses associated (<0.001) with increased General Consent collection (increase in positive as well as negative General Consent status).

CONCLUSION: General Consent is an innovative concept that simultaneously informs patients about human research in accordance with Swiss regulations and promotes research with routinely collected data and biological samples in an era with large information repositories. Our results show that medical and demographic factors may influence a patient’s choice. Therefore, approaching these populations and taking additional care to adequately inform and ensure ethical conformity and behaviour is essential. Flexible communication channels may help us reach this goal.

PMID:35429239 | DOI:10.4414/smw.2022.w30159

Diagn Cytopathol. 2022 Apr 16. doi: 10.1002/dc.24965. Online ahead of print.

ABSTRACT

OBJECTIVE: This study has been designed in an effort to identify the clinico-radiological and cytological features that could effectively help in differentiating cellular fibroadenoma (CFA) and phyllodes tumors (PT), which have several overlapping characteristics.

METHOD: Histologically proven cases of CFA and PT were reviewed. Cytological features were assessed and categorized. Clinical and radiological details were also evaluated and he the two groups were compared statistically.

RESULTS: A total of 43 FA and 52 PT were specimens were reviewed. Mean age and tumor size for CFA and PT were 26.05 and 36.94 years, and 3.7 and 6.4 cm, respectively. Univariate analysis and regression models revealed that age >30 years, BIRADS grade of 4 or more, marked cellularity of stromal fragments, more than 30% spindle cells in background cell population and presence of traversing blood vessels in stromal fragments increased the odds of a tumor being phyllodes. The binary logistic regression model was able to predict PT accurately in 87.2% cases (p < .001).

CONCLUSION: PT and CFA could be differentiated if cytological findings are cautiously correlated clinically and radiologically. Age, BIRADS category along with assessment of stromal fragments and background population can effectively distinguish between CFA and PT.

PMID:35429232 | DOI:10.1002/dc.24965

Glob Chang Biol. 2022 Apr 16. doi: 10.1111/gcb.16201. Online ahead of print.

ABSTRACT

The dominance of vapor pressure deficit (VPD) and soil water content (SWC) for plant water stress is still under debate. These two variables are strongly coupled and influenced by climatic drivers. The impacts of climatic drivers on the relationships between gross primary production (GPP) and water stress from VPD/SWC and the interaction between VPD and SWC are not fully understood. Here, applying statistical methods and extreme gradient boosting models-Shapley additive explanations framework to eddy-covariance observations from the global FLUXNET2015 dataset, we found that the VPD-GPP relationship was strongly influenced by climatic interactions, and that VPD was more important for plant water stress than SWC across most plant functional types when we removed the effect of main climatic drivers, e.g. air temperature, incoming shortwave radiation and wind speed. However, we found no evidence for a significant influence of elevated CO₂ on stress alleviation, possibly because of the short duration of the records (approximately one decade). Additionally, the interactive effect between VPD and SWC differed from their individual effect. When SWC was high, the SHAP interaction value of SWC and VPD on GPP was decreased with increasing VPD, but when SWC was low, the trend was the opposite. Additionally, we revealed a threshold effect for VPD stress on GPP loss; above the threshold value, the stress on GPP was flattened off. Our results have important implications for independently identifying VPD and SWC limitations on plant productivity, which is meaningful for capturing the magnitude of ecosystem responses to water stress in dynamic global vegetation models.

PMID:35429206 | DOI:10.1111/gcb.16201

J Magn Reson Imaging. 2022 Apr 16. doi: 10.1002/jmri.28204. Online ahead of print.

ABSTRACT

BACKGROUND: There is an overlap comparing transition zone prostate cancer (TZ PCa) and benign prostatic hyperplasia (BPH) on T2-weighted imaging (T2WI) and diffusion-weighted imaging (DWI), creating additional challenges for assessment of TZ tumors on MRI.

PURPOSE: To evaluate whether amide proton transfer-weighted (APTw) imaging provides new diagnostic ideas for TZ PCa.

STUDY TYPE: Prospective.

POPULATION: A total of 51 TZ PCa patients (age, 49-89), 44 stromal BPH (age, 57-92), and 45 glandular BPH patients (age, 56-92).

FIELD STRENGTH/SEQUENCE: A 3 T; T2WI turbo spin echo (TSE), quantitative T2*-weighted imaging, DWI echo planar imaging, 3D APTw TSE.

ASSESSMENT: Differences in APTw, apparent diffusion coefficient (ADC), and T2* among three lesions were compared by one-way analysis of variance (ANOVA). Regions of interest were drawn by two radiologists (X.Q.Z. and X.Y.Q., with 21 and 15 years of experience, respectively).

STATISTICAL TESTS: Multivariable logistic regression analyses; ANOVA with post hoc testing; receiver operator characteristic curve analysis; Delong test. Significance level: P < 0.05.

RESULTS: APTw among TZ PCa, stromal BPH, and glandular BPH (3.48% ± 0.83% vs. 2.76% ± 0.49% vs. 2.72% ± 0.45%, respectively) were significantly different except between stromal BPH and glandular BPH (P > 0.99). Significant differences were found in ADC (TZ PCa 0.76 ± 0.16 × 10^-3 mm² /sec vs. stromal BPH 0.91 ± 0.14 × 10^-3 mm² /sec vs. glandular BPH 1.08 ± 0.18 × 10^-3 mm² /sec) among three lesions. APTw (OR = 12.18, 11.80, respectively) and 1/ADC (OR = 703.87, 181.11, respectively) were independent predictors of TZ PCa from BPH and stromal BPH. The combination of APTw and ADC had better diagnostic performance in the identification of TZ PCa from BPH and stromal BPH.

DATA CONCLUSION: APTw imaging has the potential to be of added value to ADC in differentiating TZ PCa from BPH and stromal BPH.

EVIDENCE LEVEL: 2 TECHNICAL EFFICACY: Stage 2.

PMID:35429190 | DOI:10.1002/jmri.28204

Integr Environ Assess Manag. 2022 Apr 16. doi: 10.1002/ieam.4620. Online ahead of print.

ABSTRACT

According to the latest projections of the IPCC, at the end of the century, coastal zones and low-lying ecosystems will be increasingly threatened by rising global mean sea levels. In order to support integrated coastal zone management and advance the basic “source-pathway-receptor-consequence” approach focused on traditional receptors (e.g. population, infrastructure, economy), a novel risk framework is proposed able to evaluate potential risks of loss or degradation of ecosystem services (ESs) due to projected extreme sea level scenarios in the Italian coast. Three risk scenarios for the reference period (1969-2010) and future time frame up to 2050 under RCP4.5 and RCP8.5 are developed by integrating extreme water-level projections related to changing climate conditions, with vulnerability information about the topography, distance from coastlines, and presence of artificial protections. A risk assessment is then performed considering the potential effects of the spatial-temporal variability of inundations and land use on the supply level and spatial distribution of ESs. The results of the analysis are summarized into a spatially-explicit risk index, useful to rank coastal areas more prone to ESs losses or degradation due to coastal inundation at the national scale. Overall, the Northern Adriatic coast is scored at high risk of ESs loss or degradation in the future scenario. Other small coastal strips with medium risk scores are the Eastern Puglia coast, Western Sardinia, and Tuscany’s coast. The ESs coastal risk index provides an easy-to-understand screening assessment that could support the prioritization of areas for coastal adaptation at the national scale. Moreover, this index allows the direct evaluation of the public value of ecosystems and supports more effective territorial planning and environmental management decisions. In particular, it could support the mainstreaming of ecosystem-based approaches (e.g. ecological engineering, green infrastructures) to mitigate the risks of climate change and extreme events while protecting ecosystems and biodiversity. This article is protected by copyright. All rights reserved.© 2022 Society of Environmental Toxicology & Chemistry (SETAC).

PMID:35429140 | DOI:10.1002/ieam.4620

J Appl Clin Med Phys. 2022 Apr 15:e13602. doi: 10.1002/acm2.13602. Online ahead of print.

ABSTRACT

PURPOSE: The EPID PSM is a useful EPID calibration method for QA applications. The dependence of the EPID PSM on the photon beam used to acquire it has been investigated in this study for the four available PSM methods. The aim is to inform upon the viability of applying a single PSM for all available photon beams to simplify PSM implementation and maintenance.

METHODS: Four methods of PSM determination were each measured once in a single session on a single TrueBeam ® STx linac using 6 MV, 10 MV, 6 MV Flattening-Filter-Free (FFF), and 10 MV FFF photon beams. The resultant PSM was assessed for both intra- and inter-method beam dependence via comparison between PSM of the same method compared to the 6 MV PSM and via comparison between PSM of the same beam with the corresponding Monte Carlo PSM. Comparisons were performed via 2D percentage deviation plots with associated histograms, 1D crossplane profiles, and via mean, median, and standard deviation percentage deviation statistics. Generated beam-response was compared qualitatively via 1D crossplane profile comparison and quantitatively via symmetry assessment with comparison to the IC profiler device.

RESULTS: The Varian method provided the most consistent PSM with varying photon beam, with median percent deviation from the 6 MV PSM within 0.14% for all other beams. Qualitatively, each method provided similar beam-response profiles. The measured beam-response symmetry agreed to within 0.2% between the Calvary Mater Newcastle (CMN) method and IC profiler, but agreement reduced to within 0.9% and 2.2% for the Varian and WashU methods. PSM percent deviation with Monte Carlo PSM was within 0.75% for all methods and beams.

CONCLUSION: Results suggest that the PSM may be independent of photon beam to clinically relevant levels. The Varian method of PSM determination introduces the least beam dependence into the measured PSM.

PMID:35429117 | DOI:10.1002/acm2.13602