Notes

eggNOG-mapper v2: Practical Annotation, Orthology Assignments, and Site Idea at the Metagenomic Level.
We propose a vulnerability indicator framework that can become operational in a relatively short period of time, attempts to simplify data gathering efforts, and uses methods that aim to be more transparent and understandable to a broad group of stakeholders.Programmed death ligand 1 (PD-L1) immunohistochemistry (IHC) is accepted as a predictive biomarker for the selection of immune checkpoint inhibitors. We evaluated the staining quality and estimation of the tumor proportion score (TPS) in non-small-cell lung cancer during two external quality assessment (EQA) schemes by the European Society of Pathology. Participants received two tissue micro-arrays with three (2017) and four (2018) cases for PD-L1 IHC and a positive tonsil control, for staining by their routine protocol. After the participants returned stained slides to the EQA coordination center, three pathologists assessed each slide and awarded an expert staining score from 1 to 5 points based on the staining concordance. Expert scores significantly (p less then 0.01) improved between EQA schemes from 3.8 (n = 67) to 4.3 (n = 74) on 5 points. Participants used 32 different protocols the majority applied the 22C3 (56.7%) (Dako), SP263 (19.1%) (Ventana), and E1L3N (Cell Signaling) (7.1%) clones. Staining artifacts consisted mainly of very weak or weak antigen demonstration (63.0%) or excessive background staining (19.8%). Participants using CE-IVD kits reached a higher score compared with those using laboratory-developed tests (LDTs) (p less then 0.05), mainly attributed to a better concordance of SP263. The TPS was under- and over-estimated in 20/423 (4.7%) and 24/423 (5.7%) cases, respectively, correlating to a lower expert score. Additional research is needed on the concordance of less common protocols, and on reasons for lower LDT concordance. Laboratories should carefully validate all test methods and regularly verify their performance. EQA participation should focus on both staining concordance and interpretation of PD-L1 IHC.
Roentgen stereophotogrammetric analysis is a technique to make accurate assessments of the relative position and orientation of bone structures and implants in vivo. While the precision and accuracy of stereophotogrammetry for hip and knee arthroplasty is well documented, there is insufficient knowledge of the technique's precision and, especially accuracy when applied to rotational movements in the spinal region.

The motion of one cadaver lumbar spine segment (L3/L4) was analyzed in flexion-extension, lateral bending and internal rotation. The specific aim of this study was to examine the precision and accuracy of stereophotogrammetry in a controlled in vitro setting, taking the surrounding soft tissue into account. The second objective of this study was to investigate the effect of different focal spot values of X-ray tubes.

Overall, the precision of flexion-extension measurements was found to be better when using a 0.6mm focal spot value rather than 1.2mm (± 0.056° and ± 0.153°; respectively), and accuracy was also slightly better for the 0.6mm focal spot value compared to 1.2mm (-0.137° and -0.170°; respectively). The best values for precision and accuracy were obtained in lateral bending for both 0.6mm and 1.2mm focal spot values (precision ± 0.019° and ± 0.015°, respectively; accuracy -0.041° and -0.035°).

In summary, the results suggest stereophotogrammetry to be a highly precise method to analyze motion of the lumbar spine. Since precision and accuracy are better than 0.2° for both focal spot values, the choice between these is of minor clinical relevance.
In summary, the results suggest stereophotogrammetry to be a highly precise method to analyze motion of the lumbar spine. Since precision and accuracy are better than 0.2° for both focal spot values, the choice between these is of minor clinical relevance.The original article can be found online.Fatigue is considered a key symptom of major depressive disorder (MDD), yet the term lacks specificity. It can denote a state of increased sleepiness and lack of drive (i.e., downregulated arousal) as well as a state of high inner tension and inhibition of drive with long sleep onset latencies (i.e., upregulated arousal), the latter typically found in depression. It has been proposed to differentiate fatigue along the dimension of brain arousal. We investigated whether such stratification within a group of MDD patients would reveal a subgroup with distinct clinical features. Using an automatic classification of EEG vigilance stages, an arousal stability score was calculated for 15-min resting EEGs of 102 MDD patients with fatigue. selleck chemicals llc 23.5% of the patients showed signs of hypoarousal with EEG patterns indicating drowsiness or sleep; this hypoaroused subgroup was compared with remaining patients (non-hypoaroused subgroup) concerning self-rated measures of depressive symptoms, sleepiness, and sleep. The hypoaroused subgroup scored higher on the Beck Depression Inventory items "loss of energy" (Z = - 2.13, p = 0.033; ɳ2 = 0.044, 90% CI 0.003-0.128) and "concentration difficulty" (Z = - 2.40, p = 0.017; ɳ2 = 0.056, 90% CI 0.009-0.139), and reported higher trait and state sleepiness (p  less then  0.05) as compared to the non-hypoaroused group. The non-hypoaroused subgroup, in contrast, reported more frequently the presence of suicidal ideation (Chi2 = 3.81, p = 0.051; ɳ2 = 0.037, 90% CI 0.0008-0.126). In this study, we found some evidence that stratifying fatigued MDD patients by arousal may lead to subgroups that are pathophysiologically and clinically more homogeneous. Brain arousal may be a worth while target in clinical research for better understanding the mechanisms underlying suicidal tendencies and to improve treatment response.
To develop a predictive risk model (PRM) for patient-reported anxiety after treatment completion for early stage breast cancer suitable for use in practice and underpinned by advances in data science and risk prediction.

Secondary analysis of a prospective survey of > 800 women at the end of treatment and again 6 months later using patient reported outcome (PRO) the hospital anxiety and depression scale-anxiety (HADS-A) and > 20 candidate predictors. Multiple imputation using chained equations (for missing data) and least absolute shrinkage and selection operator (LASSO) were used to select predictors. Final multivariable linear model performance was assessed (R
) and bootstrapped for internal validation.

Five predictors of anxiety selected by LASSO were HADS-A (Beta 0.73; 95% CI 0.681, 0.785); HAD-depression (Beta 0.095; 95% CI 0.020, 0.182) and having caring responsibilities (Beta 0.488; 95% CI 0.084, 0.866) increased risk, whereas being older (Beta - 0.010; 95% CI -0.028, 0.004) and owning a home (Beta 0.432; 95% CI -0.954, 0.078) reduced the risk. The final model explained 60% of variance and bias was low (- 0.006 to 0.002).

Different modelling approaches are needed to predict rather than explain patient reported outcomes. link2 We developed a parsimonious and pragmatic PRM. External validation is required prior to translation to digital tool and evaluation of clinical implementation. The routine use of PROs and data driven PRM in practice provides a new opportunity to target supportive care and specialist interventions for cancer patients.
Different modelling approaches are needed to predict rather than explain patient reported outcomes. We developed a parsimonious and pragmatic PRM. External validation is required prior to translation to digital tool and evaluation of clinical implementation. The routine use of PROs and data driven PRM in practice provides a new opportunity to target supportive care and specialist interventions for cancer patients.
Echocardiography is a common tool for cardiac and hemodynamic assessments in critical care research. However, interpretation (and applications) of results and between-study comparisons are often difficult due to the lack of certain important details in the studies. PRICES (Preferred Reporting Items for Critical care Echocardiography Studies) is a project endorsed by the European Society of Intensive Care Medicine and conducted by the Echocardiography Working Group, aiming at producing recommendations for standardized reporting of critical care echocardiography (CCE) research studies.

The PRICE panel identified lists of clinical and echocardiographic parameters (the "items") deemed important in four main areas of CCE research left ventricular systolic and diastolic functions, right ventricular function and fluid management. Each item was graded using a critical index (CI) that combined the relative importance of each item and the fraction of studies that did not report it, also taking experts' opinion into account.

A list of items in each area that deemed essential for the proper interpretation and application of research results is recommended. Additional items which aid interpretation were also proposed.

The PRICES recommendations reported in this document, as a checklist, represent an international consensus of experts as to which parameters and information should be included in the design of echocardiography research studies. PRICES recommendations provide guidance to scientists in the field of CCE with the objective of providing a recommended framework for reporting of CCE methodology and results.
The PRICES recommendations reported in this document, as a checklist, represent an international consensus of experts as to which parameters and information should be included in the design of echocardiography research studies. PRICES recommendations provide guidance to scientists in the field of CCE with the objective of providing a recommended framework for reporting of CCE methodology and results.
To assess changes in quality of life (QoL) and sexual function outcomes at 1year after tension-free vaginal tape (TVT) versus polyacrylamide hydrogel injection (PAHG).

In a randomized trial comparing TVT (n= 111) and PAHG (n= 113) treatments of stress urinary incontinence (SUI), we compared urinary incontinence and health-related QoL using the Urogenital Distress Inventory (UDI-6), Incontinence Impact Questionnaire, Short Form (IIQ-7), Pelvic Organ Prolapse/Urinary Incontinence Sexual Questionnaire (PISQ-12) and RAND-36 Item Health Survey (RAND-36) at baseline and 1year.

UDI-6 and IIQ-7 showed improved incontinence-related QoL (p= 0.001) from baseline in both groups except for difficulty emptying the bladder and pain/discomfort. At 1year, TVT patients experienced less urinary symptom-related distress compared to PAHG (p< 0.001). Sexual function improved in both groups (p< 0.001 for TVT and p= 0.01 for PAHG) with higher scores for the physical section subscale (p < 0.001) for TVT. Health-related QoL (RAND-36) improved from baseline in both groups in physical and social functioning (p < 0.001) with better outcome in the TVT group for physical functioning (p < 0.001). Increase in pain from baseline (p= 0.02) was detected for TVT, but not for PAHG. However, there was no difference between the groups (p= 0.78).

In primary SUI, TVT and PAHG treatments both improved QoL and sexual function at 1year. However, incontinence and health-related QoL scores were better in the TVT group. More pain compared to the baseline was reported after TVT, although there was no difference between groups. Clinical significance needs to be evaluated in long-term follow-up.
In primary SUI, TVT and PAHG treatments both improved QoL and sexual function at 1 year. However, incontinence and health-related QoL scores were better in the TVT group. link3 More pain compared to the baseline was reported after TVT, although there was no difference between groups. Clinical significance needs to be evaluated in long-term follow-up.
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