Miracle-dz/UniFAR-FTUs huggingface dataset:
TB or not TB? Definitive determination of species within the M ycobacterium tuberculosis complex in unprocessed sputum from adults with presumed multidrug‐resistant tuberculosis

Differences among Mycobacterium tuberculosis complex (MTC) species may predict drug resistance or treatment success. Thus, we optimised and deployed the genotype MTBC assay (gMTBC) to identify MTC to the species level, and then performed comparative genotypic drug‐susceptibility testing to anti‐tuberculosis drugs from direct sputum of patients with presumed multidrug‐resistant tuberculosis (MDR‐TB) by the MTBDRplus/sl reference method.
Communicating Uncertainties About the Effects of Medical Interventions Using Different Display Formats

Communicating uncertainties in scientific evidence is important to accurately reflect scientific knowledge , increase public understanding of uncertainty, and to signal transparency and honesty in reporting. While techniques have been developed to facilitate the communication of uncertainty, many have not been empirically tested, compared for communicating different types of uncertainty, or their effects on different cognitive, trust, and behavioral outcomes have not been evaluated. The present study examined how a point estimate, imprecise estimate, conflicting estimates, or a statement about the lack of evidence about treatment effects, influenced participant's responses to communications about medical evidence. For each type of uncertainty, we adapted three display formats to communicate the information: tables, bar graphs, and icon arrays. We compared participant's best estimates of treatment effects, as well as effects on recall, subjective evaluations (understandability and usefuleness), certainty perceptions, perceptions of trustworthiness of the information, and behavioral intentions. We did not find any detrimental effects from communicating imprecision or conflicting estimates relative to a point estimate across any outcome. Furthermore, there were more favorable responses to communicating imprecision or conflicting estimates relative to lack of evidence, where participants estimated the treatment would improve outcomes by 30–50% relative to a placebo. There were no differences across display formats, suggesting that, if well‐designed, it may not matter which format is used. Future research on specific display formats or uncertainty types and with larger sample sizes would be needed to detect small effects. Implications for the communication of uncertainty are discussed.
Modulation of polyamine metabolism in Arabidopsis thaliana by salicylic acid

Polyamines (PAs) play important roles in plant defense against pathogens, but the regulation of PA metabolism by hormone-mediated defense signaling pathways has not been studied in depth. In this study, the modulation of PA metabolism in Arabidopsis by salicylic acid (SA) was analyzed, by combining the exogenous application of this hormone with the use of PA biosynthesis and SA synthesis/signaling mutants. SA induced notable modifications of polyamine metabolism, mainly consisting in putrescine accumulation both in whole-plant extracts and apoplastic fluids. Put was accumulated at the expense of increased biosynthesis by arginine decarboxylase 2 and decreased oxidation by copper amine oxidase. Enhancement of Put levels by SA was independent of the regulatory protein Non-Expressor of Pathogenesis Related 1 (NPR1) and the signaling kinases MKK4 and MPK3, but depended on MPK6. On its part, plant infection by Pseudomonas syringae pv. tomato DC3000 elicited Put accumulation in a SA-dependent way. The present study demonstrates a clear connection between SA signaling and plant PA metabolism in Arabidopsis and contributes to understand the mechanisms by which SA modulates PA levels during plant-pathogen interactions. Highlight Salicylic acid modulates polyamine biosynthesis and catabolism in Arabidopsis. Regulatory effects of salicylic acid are independent of the master regulator NPR1 and are mediated by the MPK6 kinase.
Social network analysis and whole-genome sequencing to evaluate disease transmission in a large, dynamic population: A study of avian mycobacteriosis in zoo birds

This study combined a social network analysis and whole-genome sequencing (WGS) to test for general patterns of contagious spread of a mycobacterial infection for which pathways of disease acquisition are not well understood. Our population included 275 cases diagnosed with avian mycobacteriosis that were nested in a source population of 16,430 birds at San Diego Zoo Wildlife Alliance facilities from 1992 through mid-2014. Mycobacteria species were determined using conventional methods and whole genome sequencing (WGS). Mycobacterium avium avium (MAA) and Mycobacterium genavense were the most common species of mycobacteria identified and were present in different proportions across bird taxa. A social network for the birds was constructed from the source population to identify directly and indirectly connected cases during time periods relevant to disease transmission. Associations between network connectivity and genetic similarity of mycobacteria (as determined by clusters of genotypes separated by few single nucleotide polymorphisms, or SNPs) were then evaluated in observed and randomly generated network permutations. Findings showed that some genotypes clustered along pathways of bird connectivity, while others were dispersed throughout the network. The proportion of directly connected birds having a similar mycobacterial genotype was 0.36 and significant (p<0.05). This proportion was higher (0.58) and significant for MAA but not for M. genavense. Evaluations of SNP distributions also showed genotypes of MAA were more related in connected birds than expected by chance; however, no significant patterns of genetic relatedness were identified for M. genavense, although data were sparse. Integrating the WGS analysis of mycobacteria with a social network analysis of their host birds revealed significant genetic clustering along pathways of connectivity, namely for MAA. These findings are consistent with a contagious process occurring in some, but not all, case clusters.
Effectiveness of multipoint cardiac resynchronizing therapy in heart failure: a systematic review and meta-analysis of randomized controlled trials

ABSTRACT Background Cardiac resynchronization therapy is an important validated technique for patients with dyssynchrony and heart failure. However, the response rate to conventional resynchronization is approximately 50%; therefore, new techniques and schedules have emerged. This study aimed to evaluate the different clinical and echocardiographic variables of conventional versus multipoint cardiac resynchronization therapy. Research design and method A systematic review was conducted of randomized clinical trials in the PubMed, Cochrane, and Embase databases on cardiac resynchronization intervention with multipoint stimulation clinical and echocardiographic outcomes evaluated before and 3 months after the intervention. Results Three studies (N = 139) were ultimately selected, and 100% of patients had a New York Heart Association functional class of II–IV, QRS > 120 ms, and a left ventricular ejection fraction < 35%. Significantly greater improvement was observed in the functional class of patients who underwent multipoint versus conventional therapy. The final systolic volume and ejection fraction improved in the multipoint group, but the difference was not statistically significant. Conclusions The literature lacks sufficient randomized controlled studies to enable conclusions regarding cardiac resynchronization therapy responses using different strategies. Moreover, the improvement in functional class in the multipoint pacing group involved few patients and had slight statistical relevance.
NHBS-Net: A Feature Fusion Attention Network for Ultrasound Neonatal Hip Bone Segmentation

Ultrasound is a widely used technology for diagnosing developmental dysplasia of the hip (DDH) because it does not use radiation. Due to its low cost and convenience, 2-D ultrasound is still the most common examination in DDH diagnosis. In clinical usage, the complexity of both ultrasound image standardization and measurement leads to a high error rate for sonographers. The automatic segmentation results of key structures in the hip joint can be used to develop a standard plane detection method that helps sonographers decrease the error rate. However, current automatic segmentation methods still face challenges in robustness and accuracy. Thus, we propose a neonatal hip bone segmentation network (NHBS-Net) for the first time for the segmentation of seven key structures. We design three improvements, an enhanced dual attention module, a two-class feature fusion module, and a coordinate convolution output head, to help segment different structures. Compared with current state-of-the-art networks, NHBS-Net gains outstanding performance accuracy and generalizability, as shown in the experiments. Additionally, image standardization is a common need in ultrasonography. The ability of segmentation-based standard plane detection is tested on a 50-image standard dataset. The experiments show that our method can help healthcare workers decrease their error rate from 6%-10% to 2%. In addition, the segmentation performance in another ultrasound dataset (fetal heart) demonstrates the ability of our network.
Structural anatomy and morphometric analyses of sacra in greyhounds

This study was conducted to provide structural and morphological data on the sacra of greyhounds. Descriptive quantitative investigation was carried out on 171 sacra of greyhound`s cadavers and then classified into standard and fused sacra based on the number of fused sacral vertebrae. The weight, length and width of sacrum of sacra were measured. Both standard (59%) and fused sacra (41%) were identified. The average length and width of the standard sacrum were found to be 46.14 ± 2.53 mm and 57.89 ± 3.54 mm, respectively. The sacral length was 1.61‐mm longer in males (p < .01), and the sacral width was 0.46‐mm shorter in males but not significant (p = .51). The average weight of a standard sacrum was 26.54 ± 4.55 g and was 1.18 g heavier in males but not statistically significant (p = .24). Results showed that one‐kilogram increase in the body mass was associated with a 0.3 mm (p < .001) increase in sacral length, and a 0.54 mm (p < .001) increase in sacral width, respectively. The morphological data of the standard and fused sacra provided in this study might help the veterinary community to improve treatment and rehabilitation and help the trainer to design the right training protocol for racing greyhounds. In addition, the results of this study are a step to understand the sacrum’s functions and how the greyhound's body functions and future studies are required to investigate the biological importance of these findings.
Self-Management in Older Pakistanis Living With Multimorbidity in East London

In this article, we explore how older British Pakistani people experience multimorbidity (defined as the coexistence of two or more medical conditions) and engage with self-management within the context of their life histories and relationships. We conducted biographical narrative interviews in Urdu and/or English with 15 first-generation Pakistani migrants living with multimorbidity, at their homes in East London. Our analysis showed that the triadic construct of family, faith, and health was central to how participants made sense of their lives, constituting notions of “managing” in the context of multimorbidity. For Pakistani patients, the lived experience of health was inseparable from a situated context of family and faith. Our findings have implications for existing public health strategies of self-management, underpinned by neoliberal discourses that focus on individual responsibility and agency. Health care provision needs to better integrate the importance of relationships between family, faith, and health when developing services for these patients.
The exploration-exploitation dilemma in pain: an experimental investigation.

ABSTRACT Daily life consists of a chain of decisions. Typically, individuals may choose to pursue what they already know (exploitation), or to search for other options (exploration). This exploration-exploitation dilemma is a topic of interest across multiple scientific fields. Here we propose that investigating how individuals solve this dilemma may improve our understanding of how individuals make behavioral decisions (e.g., avoidance) when facing pain. To this end, we present the data of three experiments in which healthy individuals were given the opportunity to choose between four different movements, with each movement being associated with different probabilities of receiving a painful outcome only (Experiment 1), or pain and/or a reward (Experiment 2). We also investigated whether participants stuck to their decisions when the contingencies between each movement and the painful/rewarding outcome changed during the task (Experiment 3). The key findings across all experiments are the following: First, after initial exploration, participants most often exploited the safest option. Second, participants weighted rewards more heavily than receiving pain. Lastly, after receiving a painful outcome, participants were more inclined to explore than to exploit a rewarding movement. We argue that by focusing more on how individuals in pain solve the exploration-exploitation dilemma is helpful in understanding behavioral decision-making in pain.
The Role of Thrombo-Inflammatory Biomarkers in the Prognosis of Cerebral Venous Sinus Thrombosis.

BACKGROUND The role of inflammation in the prognosis of cerebral venous sinus thrombosis (CVST) has been demonstrated in a small number of studies. The platelet-to-lymphocyte ratio (PLR), neutrophil-to-lymphocyte ratio (NLR), and the systemic immune-inflammatory index (SII) have been studied as prognostic inflammatory biomarkers in numerous thrombo-embolic diseases. However, the number of studies evaluating the relationship between these parameters and CVST is very low. OBJECTIVES The purpose of this retrospective study was to investigate the relationship between PLR, NLR, and SII values on admission and long-term prognosis in patients with CVST in the acute-subacute period. METHODS Fifty-one patients diagnosed with CVST and 51 healthy controls were included in the study. The patient and control groups were compared in terms of NLR, PLR, and SII values. Patients were classified into good and poor prognosis groups, based on sixth-month modified Rankin scale scores (mRS) (0 - 2: good prognosis, 3 - 6: poor prognosis). Clinical and radiological features and PLR, NLR, and SII values were compared between the good and poor prognosis groups. Multivariate logistic regression analysis was used to identify independent prognostic factors for poor prognosis. The Receiver Operating Curve (ROC) was used to demonstrate the predictive power of PLR, NLR, and SII. RESULTS Higher NLR and SII emerged as independent factors for poor prognosis in patients with CVST. NLR was the strongest parameter in predicting poor prognosis in CVST (AUC: 0.817, 95% CI: 0.63 - 1.00, sensitivity: 70%, specificity: 92.7%, p: 0.002). CONCLUSION Higher NLR and SII on admission may be a predictor of poor long-term prognosis in patients with acute-subacute CVST.
Characteristics, Risk Factors and Predictors for Candidemia in the Pediatric Intensive Care Unit at the University Hospital Centre Zagreb in Croatia

Background: Candidemia is one of the leading causes of bloodstream infections in the pediatric intensive care unit (PICU). The aim of this study was to define characteristics and risk factors for candidemia in the PICU setting and propose a predictive model to identify the patients at risk. Methods: This was a retrospective matched case-control study in the PICU during a 9-year period. Patients with candidemia were studied and matched with control patients without candidemia. Univariate analysis was performed for potential risk factors and multivariate analysis was conducted to determine the prediction score for candidemia. Results: Forty-two cases of candidemia were matched with 84 control patients. Candida parapsilosis was the most common (71.4%) species. Risk factors independently associated with candidemia were: the use of >2 antibiotics in a maximum period of 4 weeks before the candidemia (odds ratio [OR]: 10.59; 95% confidence interval [CI]: 2.05–54.83), a previous bacterial infection in a maximum period of 4 weeks before the candidemia (OR: 5.56; 95% CI: 1.44–21.5) and the duration of PICU stay of >10 days (OR: 4.22; 95% CI: 1.02–17.41). The proposed predictive scoring system has a sensitivity of 95.24%, specificity of 76.12%, OR 64.0, 95% CI 14.2–288.6, the positive predictive value of 66.67% and the negative predictive value of 96.97%. Conclusions: Previously reported risk factors for candidemia have been confirmed and some new have been detected. The presented scoring system can help identify patients who would benefit from prophylactic antifungal therapy.
Knowledge, attitudes and practices of patients with chronic illnesses during the COVID-19 pandemic: A cross-sectional survey from Pakistan

Objectives We studied the impact of the Covid-19 pandemic on the physical and mental health of patients with chronic illnesses and their behavioural responses. Methods We conducted a cross-sectional knowledge, attitudes and practices (KAP) survey among outpatients with chronic illnesses in Lahore, Pakistan. Results Four hundred and one participants were surveyed (84% above 50 years of age). One or two chronic illnesses were present in 130 (32%), three or four in 211 (53%) and more than four in 60 (15%). The majority correctly identified the sources of Covid-19 infection and higher risk patients. Of the respondents, 127 (32%) described feeling more vulnerable. Respondents reported a lack of trust in the community response (199; 49.6%) and hospital measures (167; 41.6%) to slow the spread of Covid-19 and 369 (92%) practiced some degree of social distancing. Respondents described negative impacts of lockdown measures on their physical and mental health (235; 58.6% and 262; 65.3%, respectively). Many reported difficulty in getting medical help during the pandemic (302; 75.2%). Half of the respondents (200; 49.8%) felt that delays in receiving care had adversely affected their health. Conclusions Respondents with chronic illnesses frequently reported negative behavioural and health impacts during the Covid-19 pandemic.
Reference Values for Skeletal Muscle Mass at the Third Lumbar Vertebral Level Measured by Computed Tomography in a Healthy Korean Population

Background Sarcopenia is defined as the loss of skeletal muscle mass and is associated with negative clinical outcomes. This study aimed to establish sex-specific cutoff values for the skeletal muscle area (SMA) and skeletal muscle index (SMI) at the third lumbar vertebral (L3) level using computed tomography (CT) imaging to identify sarcopenia in healthy Korean liver donors. Methods This retrospective study included 659 healthy liver donors (408 men and 251 women) aged 20 to 60 years who had undergone abdominal CT examinations between January 2017 and December 2018. Assessment of body composition was performed with an automated segmentation technique using a deep-learning system. Sex-specific SMA and SMI distributions were assessed, and cutoff values for determining sarcopenia were defined as values at either two standard deviations (SDs) below the mean reference value or below the fifth percentile. Results Using the SD definition, cutoff values for SMA and SMI were 117.04 cm2 and 39.33 cm2/m2, respectively, in men and 71.39 cm2 and 27.77 cm2/m2, respectively, in women. Using the fifth percentile definition, cutoff values for SMA and SMI were 126.88 cm2 and 40.96 cm2/m2, respectively, in men and 78.85 cm2 and 30.60 cm2/m2, respectively, in women. Conclusion Our data provide sex-specific cutoff values for the SMA and SMI at the L3 level measured by CT imaging in a healthy Korean population, which may be applicable for identifying sarcopenia in this population.
Beyond faith: Biomolecular evidence for changing urban economies in multi-faith medieval Portugal.

OBJECTIVES During the Middle Ages, Portugal witnessed unprecedented socioeconomic and religious changes under transitioning religious political rule. The implications of changing ruling powers for urban food systems and individual diets in medieval Portugal is poorly understood. This study aimed to elucidate the dietary impact of the Islamic and Christian conquests. MATERIALS AND METHODS Radiocarbon dating, peptide mass fingerprinting (ZooMS) and stable isotope analysis (δ13 C, δ15 N) of animal (n = 59) and human skeletal remains (n = 205) from Muslim and Christian burials were used to characterize the diet of a large historical sample from Portugal. A Bayesian stable isotope mixing model (BSIMM) was used to estimate the contribution of marine protein to human diet. RESULTS Early medieval (8-12th century), preconquest urban Muslim populations had mean (±1SD) values of -18.8 ± 0.4 ‰ for δ13 C 10.4 ± 1 ‰ for δ15 N, indicating a predominantly terrestrial diet, while late medieval (12-14th century) postconquest Muslim and Christian populations showed a greater reliance on marine resources with mean (±1SD) values of -17.9 ± 1.3‰ for δ13 C and 11.1 ± 1.1‰ for δ15 N. BSIMM estimation supported a significant increase in the contribution of marine resources to human diet. DISCUSSION The results provide the first biomolecular evidence for a dietary revolution that is not evidenced in contemporaneous historical accounts. We find that society transitioned from a largely agro-pastoral economy under Islamic rule to one characterized by a new focus on marine resources under later Christian rule. This economic change led to the naissance of the marine economy that went on to characterize the early-modern period in Portugal and its global expansion.
The efficacy of cognitive behavioural therapy on stress, anxiety and depression of infertile couples: a systematic review and meta-analysis

Abstract Infertility is considered globally to be a stressful and hard experience that affects the couples psychologically, socially and individually. The aim of this study was to systematically review the effectiveness of cognitive behavioural therapy (CBT) on depression, stress and anxiety in infertile couples. In this systematic review and meta-analysis, databases were searched up to August 2019. Twelve articles were included in the meta-analysis and analysed with Comprehensive Meta-Analysis (CMA) v2. The results of pooled studies showed that the mean scores for depression and anxiety decreased in patients receiving CBT as compared to the control group. The results of three pooled studies showed no significant difference on stress in patients receiving CBT as compared to the control group. The findings of this study provides valuable suggestions for improving mental health status through applying CBT to manage anxiety and depression in infertile couples.