Miracle-dz/UniFAR-FTUs huggingface dataset:
The Stair Climb Power Test as an Efficacy Outcome in Randomized Trials of Function Promoting Therapies in Older Men.

BACKGROUND Standardization of performance-based physical function measures that are reliable and responsive to intervention is necessary for efficacy trials of function promoting therapies (FPT). Herein, we describe a standardized method of measuring stair climbing power (SCP) and evaluate its ability to assess improvements in physical function in response to an FPT (testosterone) compared to gait speed. METHODS We used a 12-step SCP test with and without carrying a load (loaded, LSCP or unloaded, USCP) in two testosterone trials in older men. SCP was determined from mass, total step-rise, and time-of-ascent measured with an electronic timing system. Associations between SCP and leg press performance (strength and power), testosterone levels, and gait speed were assessed. Test-retest reliability was evaluated using interclass correlation and Bland-Altman analyses. RESULTS Baseline SCP was negatively associated with age and positively with leg strength and power and gait speed. Both tests of SCP were safe and showed excellent reliability (ICC 0.91 to 0.97 in both cohorts). Changes in testosterone concentrations were associated with changes in USCP and LSCP, but not gait speed in mobility-limited men. Changes in leg press performance were associated with SCP in both trials. CONCLUSIONS Both USCP and LSCP are safe and have high test-retest reliability. Compared to gait speed, SCP is associated more robustly with leg press performance and is sensitive to testosterone therapy. The LSCP might be a more responsive outcome than gait speed to evaluate the efficacy of FPT in randomized trials.
Systematic review of cochlear implantation in CHARGE syndrome

Objective: CHARGE syndrome presents with a collection of congenital anomalies affecting multiple organs. Ear and temporal bone anomalies, including hearing loss are highly prevalent. We present an aid to management of this challenging condition and report the strategies and outcomes of cochlear implantation. Methods: Systematic review of Medline, EMBASE, Web of Science, CENTRAL and clinicaltrials.gov was performed up to 21/10/2018 The review and meta-analysis of studies were performed according to the PRISMA statement. Patient demographics, comorbidity, anatomical factors, details of cochlear implantation and audiological outcome were extracted and summarized. Anatomical and surgical factors were evaluated by meta-analysis. Audiological outcomes reported were too heterogeneous for meta-analysis. All statistics were calculated with SPSS v23.0 (IBM, New York, USA). Results: Thirty-one studies reported 165 cochlear implants in 156 patients with CHARGE syndrome. Temporal bone and facial nerve anomalies were common. Discussion: The assessment and management of patients with CHARGE syndrome undergoing cochlear implantation is challenging. Outcomes may be affected by cochlear nerve deficiency, inner ear anomalies, and developmental delay. Surgery is almost invariably complicated by abnormal anatomy, and increased incidence of complications. Conclusion: A careful, case-by-case assessment of an individual's requirements within a multi-disciplinary setup is essential for achieving the best possible outcome.
Systematic analysis of Plasmodium myosins reveals differential expression, localisation, and function in invasive and proliferative parasite stages

The myosin superfamily comprises of actin-dependent eukaryotic molecular motors important in a variety of cellular functions. Although well studied in many systems, knowledge of their functions in Plasmodium, the causative agent of malaria, is restricted. Previously, six myosins were identified in this genus, including three Class XIV myosins found only in Apicomplexa and some Ciliates. The well characterised MyoA, is a class XIV myosin essential for gliding motility and invasion. Here, we characterize all other Plasmodium myosins throughout the parasite life cycle and show that they have very diverse patterns of expression and cellular location. MyoB and MyoE, the other two Class XIV myosins, are expressed in all invasive stages, with apical and basal locations, respectively. Gene deletion revealed that MyoE is involved in sporozoite motility, MyoF and MyoK are likely essential in the asexual blood stages, and MyoJ and MyoB are not essential. Both MyoB and its essential light chain (MCL-B) are localised at the apical end of ookinetes but expressed at completely different time points. This work provides a better understanding of the role of actomyosin motors in Apicomplexan parasites, particularly in the motile and invasive stages of Plasmodium during sexual and asexual development within the mosquito.
Strategy and factors for success: The Mexican handicraft sector

This study analyzed the success factors in the Mexican handicraft sector on the basis of marketing strategies. As a result of this work, 23 factors for success that artisans use as marketing strategies were determined. The most important, because it was related to all of the other elements of success, was a pricing strategy oriented to profits. The second most important strategy was to use personal recommendations to promote the products. Product diversification and the information artisans gave to customers were, respectively, the third and fourth strategies.
HIV-1 Transmission Patterns in Men Who Have Sex with Men: Insights from Genetic Source Attribution Analysis

Abstract Near 60% of new HIV infections in the United Kingdom are estimated to occur in men who have sex with men (MSM). Age-disassortative partnerships in MSM have been suggested to spread the HIV epidemics in many Western developed countries and to contribute to ethnic disparities in infection rates. Understanding these mixing patterns in transmission can help to determine which groups are at a greater risk and guide public health interventions. We analyzed combined epidemiological data and viral sequences from MSM diagnosed with HIV at the national level. We applied a phylodynamic source attribution model to infer patterns of transmission between groups of patients. From pair probabilities of transmission between 14,603 MSM patients, we found that potential transmitters of HIV subtype B were on average 8 months older than recipients. We also found a moderate overall assortativity of transmission by ethnic group and a stronger assortativity by region. Our findings suggest that there is only a modest net flow of transmissions from older to young MSM in subtype B epidemics and that young MSM, both for Black or White groups, are more likely to be infected by one another than expected in a sexual network with random mixing.
Growth prediction of two bacterial populations in co-culture with lactic acid bacteria

The co-culture growth of Staphylococcus aureus, Escherichia coli and lactic acid bacteria starter culture in milk was quantitatively evaluated and modelled with a set of coupled differential equations originally proposed by Baranyi and Roberts and by Gimenez and Dalgaard (BR–GD model). The lactic acid bacteria starter culture showed the ability to induce an early stationary phase of both E. coli and S. aureus populations at different combination of temperature (ranging from 12 to 37 ℃) and lactic acid bacteria inocula (from approx. 103 to 106 CFU/ml). First, the prediction ability was performed only with parameters estimated from individual growth curves of E. coli, S. aureus and the lactic acid bacteria in milk (Dataset 1, 21 experiments). Subsequently, the model was extended with the average competition coefficients (E-BR–GD model) that represented quantitative relations among the populations. The prediction ability of this model was validated with the second dataset consisting of seven experiments. Results and also their statistical indices (accuracy and bias factors) showed that the E-BR–GD model improved growth prediction of all involved populations. Thus, the total root mean square error decreased from 0.457, 0.840 and 0.322 log CFU/ml (BR–GD model) to 0.290, 0.245 and 0.333 log CFU/ml (E-BR–GD) for S. aureus, E. coli and lactic acid bacteria, respectively. This approach in growth prediction of multiple competing microbial populations can be used in assessment of S. aureus and E. coli exposure from raw milk cheeses consumption and contribute to decision making in prevention of staphylococcal enterotoxin production.
Using crying to cope: Physiological responses to stress following tears of sadness.

This research tested the hypothesis that emotional crying facilitates coping and recovery, specifically through physiological changes that occur during crying. Female undergraduate students (N = 197) were randomly assigned to either a sad or neutral condition using short videos. Sad videos were selected for their extreme emotion elicitation. We predicted that compared to those who did not cry to the stimuli and those who were exposed to neutral videos, people who cried would (a) be able to withstand a stressful task for longer; (b) show lower levels of cortisol following crying and exposure to the stressor; and (c) have faster recovery (i.e., return to baseline levels of affect). The final groups consisted of the neutral group (n = 65), sad criers (n = 71), and sad noncriers (n = 61). After a 5-min baseline period, participants watched either the sad or neutral videos for 17 min and then completed a physical stressor (cold pressor test). Heart rate and respiration were continuously recorded, whereas salivary samples for cortisol were taken at 4 separate time points during testing. Analyses revealed no differences between the 3 groups in time withstanding the stressor or cortisol changes. Respiration rate, however, increased in the neutral group and noncriers while watching the videos, with criers' respiration remaining stable. Furthermore, heart rate was found to decelerate just before crying, with a return to baseline during the first crying period. These results suggest that crying may assist in generally maintaining biological homeostasis, perhaps consciously through self-soothing via purposeful breathing and unconsciously through regulation of heart rate. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Retirement and decline in episodic memory: analysis from a prospective study of adults in England.

BACKGROUND Work has been associated with cognitive health. We examined whether retirement from work is associated with a decrease in episodic memory and whether this effect differs when considering workers' occupational class. METHODS In this prospective study using the English Longitudinal Study of Ageing (ELSA), we examined 1629 persons aged 50-75 years who were in paid work at baseline. A two-slope random effects linear regression centred at retirement was used to study the effect of retirement on episodic memory. The potential effect modification by occupational class was examined. RESULTS While memory trajectories show slightly decreasing memory scores before and afterretirement, the decreasing rates for both periods were similar [episodic memory β2b-β2a= -0.03, 95% confidence interval (CI) -0.08, 0.02]. When stratifying by occupational class, there was also no substantial difference in episodic memory trajectories before and after retirement. However, the lower occupational class showed a clear decline in episodic memory with time (pre-retirement β2a = -0.11, 95% CI -0.19, -0.03; post-retirement β2b = -0.13, 95% CI -0.19, -0.07) which was not evident for the higher occupational classes. CONCLUSIONS Our results show no observable difference in trajectories of change in episodic memory before and after retirement. However, the steeper memory decline in workers belonging to the lower occupational class may limit their prospect of prolonging their working lives. Hence enrichment programmes for the prevention of memory decline for these workers should be considered.
A pressure difference sensor inspired by fish canal lateral line

It is of interest to exploit the insight from the lateral line system of fish for flow sensing applications. In this paper, a novel fish canal lateral line-inspired pressure difference sensor is proposed by embedding an ionic polymer-metal composite (IPMC) sensor within a canal filled with viscous fluid. Such a sensor could be used by underwater robots and vehicles for object detection, angle of attack measurement, and source localization. Unlike the biological counterpart that has open ends on the surface of the body, the proposed sensor has two pores covered with a latex membrane, which prevents the canal fluid from mixing with the ambient fluid. The design and fabrication of the sensor are presented, where the sensor is integrated with a fish-like body. The sensor output is experimentally characterized as the fish-like body is rotated with respect to a dipole source, which confirms that the sensor is capable of capturing the pressure difference between the two pores. Finite element modeling and simulation that capture fluid-structure interactions and IPMC physics are conducted to shed light on the sensor behavior. Finally, the utility of the sensor in underwater robotics is illustrated via orienting the fish-like body towards the dipole source using feedback from the proposed sensor.
Assessment and detection of depression in patients with coronary artery disease: validation of the Persian version of the PHQ-9

Background: Depression is a common comorbidity in patients with coronary artery disease (CAD), which often remains undetected and untreated. Objective: This study aimed to examine the psychometric properties of the Depression Module of the Patient Health Questionnaire (PHQ-9) on a sample of cardiac patients in Iran. Method: The Persian version of the PHQ-9 was developed and administered to 150 patients with CAD, admitted to a tertiary hospital in Tehran, Iran. The major depression module of the International Neuropsychiatric Interview (MINI) was used as the gold standard for the diagnosis of depression. Results: The Persian PHQ-9 demonstrated acceptable internal consistency, with Cronbach’s alpha coefficient of 0.80. The optimal cut-off score of ≥7 showed a sensitivity of 76, specificity of 78, and the area under curve of 0.82. Conclusion: The Persian PHQ-9 has acceptable psychometric properties to screen for and detect a current depressive episode in patients with CAD, with recommended cut-off score of ≥7.
Cap-Assisted Technique versus Conventional Methods for Esophageal Food Bolus Extraction: A Comparative Study

Background/Aims Food bolus impaction is the most common form of esophageal foreign body impaction observed in adults. Clinical guidelines recommend using the push technique or retrieval methods in such cases. The push technique can cause injuries in certain clinical situations. Notably, conventional retrieval methods are time and effort consuming. Cap-assisted endoscopic extraction of an impacted food bolus is an easy and effective technique; however, more data are needed for its validation. This study compared the capassisted extraction technique with conventional methods. Methods This prospective observational multicenter study compared the success and en bloc removal rates, total procedure time, and adverse events in both techniques. Results The study included 303 patients who underwent food bolus extraction. The push technique was used in 87 patients (28.7%) and a retrieval procedure in 216 patients (71.3%). Cap-assisted extraction was performed in 106 patients and retrieval using conventional methods in 110 patients. The cap-assisted technique was associated with a higher rate of en bloc removal (80.2% vs. 15%, p<0.01), shorter procedure time (6.9±3.5 min vs. 15.7±4.1 min, p<0.001), and fewer adverse events (0/106 vs. 9/110, p<0.001). Conclusions Cap-assisted extraction showed no adverse events, higher efficacy, and a shorter procedure time compared with conventional retrieval procedures.
Effectiveness of a Bundled Intervention Including Adjunctive Corticosteroids on Outcomes of Hospitalized Patients With Community-Acquired Pneumonia: A Stepped-Wedge Randomized Clinical Trial.

Importance Community-acquired pneumonia remains a leading cause of hospitalization, mortality, and health care costs worldwide. Randomized clinical trials support the use of adjunctive corticosteroids, early progressive mobilization, antibiotic switching rules, and dietary interventions in improving outcomes. However, it is uncertain whether implementing these interventions will translate into effectiveness under routine health care conditions. Objective To evaluate the effectiveness of a bundle of evidence-supported treatments under conditions of routine care in a representative population hospitalized for community-acquired pneumonia. Design, Setting, and Participants A double-blind, stepped-wedge, cluster-randomized clinical trial with 90-day follow-up was conducted between August 1, 2016, and October 29, 2017, in the general internal medicine service at 2 tertiary hospitals in Melbourne, Australia, among a consecutive sample of patients with community-acquired pneumonia. The primary analysis and preparation of results took place between May 14 and November 25, 2018. Interventions Treating clinical teams were advised to prescribe prednisolone acetate, 50 mg/d, for 7 days (in the absence of any contraindication) and de-escalate from parenteral to oral antibiotics according to standardized criteria. Algorithm-guided early mobilization and malnutrition screening and treatment were also implemented. Main Outcomes and Measures Hospital length of stay, mortality, readmission, and intervention-associated adverse events (eg, gastrointestinal bleeding and hyperglycemia). Results A total of 917 patients were screened, and 816 (351 women and 465 men; mean [SD] age, 76 [13] years) were included in the intention-to-treat analysis, with 401 patients receiving the intervention and 415 patients in the control group. An unadjusted geometric mean ratio of 0.95 (95% CI, 0.78-1.16) was observed for the difference in length of stay (days) between the intervention and control groups. Similarly, no significant differences were observed for the secondary outcomes of mortality and readmission, and the results remained unchanged after further adjustment for sex and age. The study reported higher proportions of gastrointestinal bleeding in the intervention group (9 [2.2%]) compared with the controls (3 [0.7%]), with an unadjusted estimated difference in mean proportions of 0.008 (95% CI, 0.005-0.010). Conclusions and Relevance This bundled intervention including adjunctive corticosteroids demonstrated no evidence of effectiveness and resulted in a higher incidence of gastrointestinal bleeding. Efficacy of individual interventions demonstrated in clinical trials may not necessarily translate into effectiveness when implemented in combination and may even result in net harm. Trial Registration ClinicalTrials.gov identifier: NCT02835040.
Monitoring of immunoglobulin N- and O-glycosylation in health and disease

Abstract Protein N- and O-glycosylation are well known co- and post-translational modifications of immunoglobulins. Antibody glycosylation on the Fab and Fc portion is known to influence antigen binding and effector functions, respectively. To study associations between antibody glycosylation profiles and (patho) physiological states as well as antibody functionality, advanced technologies and methods are required. In-depth structural characterization of antibody glycosylation usually relies on the separation and tandem mass spectrometric (MS) analysis of released glycans. Protein- and site-specific information, on the other hand, may be obtained by the MS analysis of glycopeptides. With the development of high-resolution mass spectrometers, antibody glycosylation analysis at the intact or middle-up level has gained more interest, providing an integrated view of different post-translational modifications (including glycosylation). Alongside the in-depth methods, there is also great interest in robust, high-throughput techniques for routine glycosylation profiling in biopharma and clinical laboratories. With an emphasis on IgG Fc glycosylation, several highly robust separation-based techniques are employed for this purpose. In this review, we describe recent advances in MS methods, separation techniques and orthogonal approaches for the characterization of immunoglobulin glycosylation in different settings. We put emphasis on the current status and expected developments of antibody glycosylation analysis in biomedical, biopharmaceutical and clinical research.
High-Throughput Segmentation of Tiled Biological Structures using Random-Walk Distance Transforms

Abstract Various 3D imaging techniques are routinely used to examine biological materials, the results of which are usually a stack of grayscale images. In order to quantify structural aspects of the biological materials, however, they must first be extracted from the dataset in a process called segmentation. If the individual structures to be extracted are in contact or very close to each other, distance-based segmentation methods utilizing the Euclidean distance transform are commonly employed. Major disadvantages of the Euclidean distance transform, however, are its susceptibility to noise (very common in biological data), which often leads to incorrect segmentations (i.e., poor separation of objects of interest), and its limitation of being only effective for roundish objects. In the present work, we propose an alternative distance transform method, the random-walk distance transform, and demonstrate its effectiveness in high-throughput segmentation of three microCT datasets of biological tilings (i.e., structures composed of a large number of similar repeating units). In contrast to the Euclidean distance transform, the random-walk approach represents the global, rather than the local, geometric character of the objects to be segmented and, thus, is less susceptible to noise. In addition, it is directly applicable to structures with anisotropic shape characteristics. Using three case studies—tessellated cartilage from a stingray, the dermal endoskeleton of a starfish, and the prismatic layer of a bivalve mollusc shell—we provide a typical workflow for the segmentation of tiled structures, describe core image processing concepts that are underused in biological research, and show that for each study system, large amounts of biologically-relevant data can be rapidly segmented, visualized, and analyzed.
Risk assessment for hepatitis E virus infection from domestic pigs introduced into an experimental animal facility in a medical school

Hepatitis E virus (HEV) is known to cause zoonotic infections from pigs, wild boars and deer. Domestic pigs have been used as an experimental animal model in medical research and training; however, the risks of HEV infection from pigs during animal experiments are largely unknown. Here, we retrospectively investigated the seroprevalence and detection rates of viral RNA in 73 domestic pigs (average 34.5 kg) introduced into an animal experimental facility in a medical school during 2012–2016. We detected anti-HEV immunoglobulin G antibodies in 24 of 73 plasma samples (32.9%), though none of the samples were positive for viral RNA. Plasma samples of 18 pigs were sequentially monitored and were classified into four patterns: sustained positive (5 pigs), sustained negative (5 pigs), conversion to positive (6 pigs) and conversion to negative (2 pigs). HEV genomes were detected in 2 of 4 liver samples from pigs that were transported from the same farm during 2016–2017. Two viral sequences of the overlapping open reading frame (ORF) 2/3 region (97 bp) were identical and phylogenetically fell into genotype 3. A 459-bp length of the ORF2 region of an amplified fragment from a pig transported in 2017 was clustered with the wbJYG1 isolate (subgenotype 3b) with 91.5% (420/459 bp) nucleotide identity. Based on our results, we suggest that domestic pigs introduced into animal facilities carry a potential risk of HEV infection to researchers, trainees and facility staff. Continuous surveillance and precautions are important to prevent HEV infection in animal facilities.