Miracle-dz/UniFAR-FTUs huggingface dataset:
Mycobacterium abscessus: insights from a bioinformatic perspective

Abstract Mycobacterium abscessus is a nontuberculous mycobacterium, associated with broncho-pulmonary infections in individuals suffering from cystic fibrosis, bronchiectasis, and pulmonary diseases. The risk factors for transmission include biofilms, contaminated water resources, fomites, and infected individuals. M. abscessus is extensively resistant to antibiotics. To date, there is no vaccine and combination antibiotic therapy is followed. However, drug toxicities, low cure rates, and high cost of treatment make it imperfect. Over the last 20 years, bioinformatic studies on M. abscessus have advanced our understanding of the pathogen. This review integrates knowledge from the analysis of genomes, microbiomes, genomic variations, phylogeny, proteome, transcriptome, secretome, antibiotic resistance, and vaccine design to further our understanding. The utility of genome-based studies in comprehending disease progression, surveillance, tracing transmission routes, and epidemiological outbreaks on a global scale has been highlighted. Furthermore, this review underlined the importance of using computational methodologies for pinpointing factors responsible for pathogen survival and resistance. We reiterate the significance of interdisciplinary research to fight M. abscessus. In a nutshell, the outcome of computational studies can go a long way in creating novel therapeutic avenues to control M. abscessus mediated pulmonary infections. Graphical Abstract
Feasibility of large-scale eOSCES: the simultaneous evaluation of 500 medical students during a mock examination

ABSTRACT The COVID-19 pandemic has led health schools to cancel many on-site training and exams. Teachers were looking for the best option to carry out online OSCEs, and Zoom was the obvious choice since many schools have used it to pursue education purposes. Methods: We conducted a feasibility study during the 2020–2021 college year divided into six pilot phases and the large-scale eOSCEs on Zoom on June 30th, 2021. We developed a specific application allowing us to mass create Zoom meetings and built an entire organization, including a technical support system (an SOS room and catching-up rooms) and teachers’ training sessions. We assessed satisfaction via an online survey. Results: On June 30th, 531/794 fifth-year medical students (67%) participated in a large-scale mock exam distributed in 135 Zoom meeting rooms with the mobilization of 298 teachers who either participated in the Zoom meetings as standardized patients (N =135, 45%) or examiners (N =135, 45%) or as supervisors in the catching-up rooms (N =16, 6%) or the SOS room (N =12, 4%). In addition, 32/270 teachers (12%) experienced difficulties connecting to their Zoom meetings and sought the help of an SOS room member. Furthermore, 40/531 students (7%) were either late to their station or had technical difficulties and declared those issues online and were welcomed in one of the catching-up rooms to perform their eOSCE stations. Additionally, 518/531 students (98%) completed the entire circuit of three stations, and 225/531 students (42%) answered the online survey. Among them, 194/225 (86%) found eOSCES helpful for training and expressed their satisfaction with this experience. Conclusion: Organizing large-scale eOSCEs on Zoom is feasible with the appropriate tools. In addition, eOCSEs should be considered complementary to on-site OSCEs and to train medical students in telemedicine.
A retrospective study of diabetes treatment in older adults: what should we AIM for?

ABSTRACT Objectives Management of diabetes in elderly individuals requires a complex approach, considering the negative consequences. Glycemic overtreatment and undertreatment are relatively common conditions among this population. This study aimed to determine the potential overtreatment and undertreatment frequencies in older adults and the factors associated with these conditions. Methods This retrospective study included 405 diabetic older adults aged >65 years. Sociodemographic characteristics, additional comorbidities, medications, HbA1c and fasting glucose levels of the patients have been recorded. Results The median age of the patients was 71 years. The frequency of potential overtreatment and undertreatment has been found to be 20.2% and 17.8%, respectively. Insulin and sulfonylureas were found to be associated with increased risk of potential overtreatment (p = 0.000, OR = 14.91 and p = 0.000, OR = 8.48, respectively) and reduced risk of potential undertreatment (p = 0.001, OR = 0.16 and p = 0.000, OR = 0.05, respectively), while DPP-4 inhibitors were found to be associated with reduced risk of potential undertreatment (p = 0.000, OR = 0.12). Conclusion Our study has shown that potential glycemic overtreatment and undertreatment are common problems in diabetic older adults. It was found that agents with a high risk of hypoglycemia, such as insulin and sulfonylureas, were more closely associated with potential overtreatment. In the management of diabetes in the elderly, it should be aimed to choose treatment agents that lead to less negative consequences and to follow up the patients more closely.
Validation of the Turkish version of the self-evaluation of negative symptoms scale (SNS)

Abstract Objectives The Self-Evaluation of Negative Symptoms Scale (SNS) is a self-report scale that evaluates a patient’s subjective experience on all five domains of the negative symptoms. This study aimed to present the adaptation and validation study of the Turkish version of SNS(SNS-TR). Methods Seventy-five patients and 50 controls were recruited for this study. After the approval of the translation, participants were asked to fill out SNS-TR by themselves. They were interviewed with the Brief Negative Symptoms Scale (BNSS), Positive and Negative Syndrome Scale (PANSS), and Calgary Depression Scale for Schizophrenia (CDSS). Results SNS-TR showed good internal consistency in the reliability analysis with Cronbach’s alpha= 0.873. Subscale-total score correlation coefficients were significant (p < 0.01). In the validity analyses, the total and subscale scores of SNS-TR showed positive correlations with the total and subscales of BNSS, with only one exception of BNSS lack of distress subscales. The total score of SNS-TR demonstrated a significant correlation with PANSS-total, PANSS-negative subscale, PANSS-general subscale, and CDSS scores. Confirmatory factor analysis showed acceptable values for the five-factor structure, similar to the original version. Conclusion To conclude, our study indicates that SNS-TR is an easily applicable self-evaluation tool with good psychometric properties for assessing negative symptoms. KEY POINTS SNS is a novel and easily applicable self-report scale for examining negative symptoms in schizophrenia patients, allowing them to evaluate their subjective experience on all five domains of the negative symptoms. It shows good internal consistency (α= 0.873) which is similar to the original version (α = 0.867). Confirmatory factor analysis scores were found in acceptable ranges and SNS-TR confirm the five-factor structure. Using this scale in clinical practice would empower both the physician’s examinations and patient participation through treatment and follow-up course.
Suicide risk among undergraduate students in Brazil in the periods before and during the COVID-19 pandemic: results of the SABES-Grad national survey

Abstract Background Undergraduate students present high rates of psychological distress, including suicide risk. Due to the coronavirus disease 2019 (COVID-19) pandemic, this scenario may have been aggravated. Thus, the objective of the current study was to evaluate changes in the suicide risk rate from the period before to during the COVID-19 pandemic, as well as the factors associated with this outcome among Brazilian undergraduate students. Methods This was a nationwide survey carried out in Brazil with a cross-sectional design, including two data collection periods: a single-center in-person collection in 2019 and another multicenter online collection in 2020/2021. Data were collected using self-administered instruments. The outcome was a high risk of suicide, measured through the Mini International Neuropsychiatric Interview. Analyses were carried out on data from two periods, i.e. before and during the pandemic (bivariate analysis and interaction tests), and a model of associated factors (multivariate analysis using Poisson regression) was developed including all participating universities distributed in the five regions of Brazil. Results In total, 6716 Brazilian undergraduate students participated (996 in 2019 and 5720 in 2020/2021). The prevalence of a high suicide risk rose from 11.3% to 17.0%, especially among women and poorer individuals. The prevalence of a high risk of suicide among Brazilian undergraduates was 19.6% and was associated with several socioeconomic, academic, pandemic, and mental health factors. Conclusions The prevalence of a high suicide risk increased from prepandemic to during the pandemic, appearing to be largely influenced by social determinants, in conjunction with the implications of the COVID-19 pandemic.
Evaluation of Diagnostic Strategies for Identifying SARS-CoV-2 Infection in Clinical Practice: a Systematic Review and Compliance with the Standards for Reporting Diagnostic Accuracy Studies Guideline (STARD)

According to this review, the inclusion of more than one diagnostic test in the diagnostic process for COVID-19 infection shows high diagnostic accuracy values. Imaging characteristics, patients’ symptoms, demographic characteristics, and lymphocyte count were the variables most frequently included in the diagnostic models. ABSTRACT We aimed to review strategies for identifying SARS-CoV-2 infection before the availability of molecular test results, and to assess the reporting quality of the studies identified through the application of the STARD guideline. We screened 3,821 articles published until 30 April 2021, of which 23 met the inclusion criteria: including at least two diagnostic variables, being designed for use in clinical practice or in a public health context and providing diagnostic accuracy rates. Data extraction and application of STARD criteria were performed independently by two researchers and discrepancies were discussed with a third author. Most of the studies (16, 69.6%) included symptomatic patients with suspected infection, six studies (26.1%) included patients already diagnosed and one study (4.3%) included individuals with close contact to a COVID-positive patient. The main variables considered in the studies, which included symptomatic patients, were imaging and demographic characteristics, symptoms, and lymphocyte count. The values for area under the receiver operating characteristic curve (AUC)ranged from 53-97.4. Seven studies (30.4%) validated the diagnostic model in an independent sample. The average number of STARD criteria fulfilled was 17.6 (maximum, 27 and minimum, 5). High diagnostic accuracy values are shown when more than one diagnostic variable is considered, mainly imaging and demographic characteristics, symptoms, and lymphocyte count. This could offer the potential to identify individuals with SARS-CoV-2 infection with high accuracy when molecular testing is not available. However, external validation for developed models and evaluations in populations as similar as possible to those in which they will be applied is urgently needed. IMPORTANCE According to this review, the inclusion of more than one diagnostic test in the diagnostic process for COVID-19 infection shows high diagnostic accuracy values. Imaging characteristics, patients’ symptoms, demographic characteristics, and lymphocyte count were the variables most frequently included in the diagnostic models. However, developed models should be externally validated before reaching conclusions on their utility in practice. In addition, it is important to bear in mind that the test should be evaluated in populations as similar as possible to those in which it will be applied in practice.
“Do not resuscitate” order and end‐of‐life treatment in a cohort of deceased in a Norwegian University Hospital

A “Do not resuscitate” (DNR) order implies that cardiopulmonary resuscitation will not be started. Absent or delayed DNR orders in advanced chronic disease may indicate suboptimal communication about disease stage, prognosis, and treatment goals. The study objective was to determine clinical practice and patient involvement regarding DNR and the prevalence of life‐prolonging treatment in the last week of life.
Liver resection after Transjugular Portosystemic Stent Shunt (TIPSS)

Abstract Hepatocellular carcinoma (HCC) often arises in cirrhotic livers. Generally, decompensated liver cirrhosis is a contraindication to surgery. Even in compensated liver cirrhosis, liver resection for HCC carries a high risk of post-hepatectomy liver failure and decompensation of cirrhosis. Thus, in current staging systems such as the Barcelona Classification of Liver Cancer (BCLC) or the Hong Kong Classification of Liver Cancer (HKLC), liver resection is limited to smaller tumors in compensated cirrhosis. While transjugular portosystemic stent shunts (TIPSS) are widely used for the treatment of complications of portal hypertension such as recurrent esophageal bleeding or refractory ascites, the presence of a TIPSS is generally considered a contraindication for liver resection. Herein, we describe – to our knowledge for the first time – liver resection of an intermediate HCC with a diameter of 11 cm in a patient who had previously received a TIPSS for decompensated cirrhosis. With open surgery, radical resection (R0) was able to be achieved, and the patient left the hospital after 6 days following an uncomplicated postoperative course. Thus, in highly selected cases, liver resection following TIPSS may be considered.
Cerebrospinal fluid proteomic profiling of individuals with mild cognitive impairment and suspected non‐Alzheimer's disease pathophysiology

Suspected non‐Alzheimer's disease pathophysiology (SNAP) is a biomarker concept that encompasses individuals with neuronal injury but without amyloidosis. We aim to investigate the pathophysiology of SNAP, defined as abnormal tau without amyloidosis, in individuals with mild cognitive impairment (MCI) by cerebrospinal fluid (CSF) proteomics.
Disparities in Treatment Satisfaction and Supportive Care Receipt for Young Adult Oncology Patients on the Basis of Residential Location

PURPOSE: Adolescent and young adult oncology programs are critical but exist primarily in academic centers, prompting potential disparities in care on the basis of patient residence. We studied the impact of residential location on supportive care receipt and treatment satisfaction in young adults (YAs) with cancer age 19-39 years treated at the University of Wisconsin Carbone Cancer Center (UWCCC). METHODS: YA patients with cancer age 19-39 years seen at UWCCC from March 30, 2019, to March 29, 2020, were sent a survey assessing supportive care receipt and satisfaction. Survey results were compared with retrospective chart review of YAs seen at UWCCC between April 1, 2011, and April 1, 2021. Data were categorized on the basis of residential location using distance from UWCCC and 2013 Rural-Urban Continuum Code (RUCC). RESULTS: Survey results were obtained for 145 YAs, including 29 from nonmetro RUCC (20.0%) and 81 living > 20 miles from UWCCC (55.9%). YAs from nonmetro locations had lower satisfaction with available treatments (79.3% v 91.4%, P = .005), and distant YAs living > 20 miles from UWCCC more frequently identified location as a barrier to supportive care receipt (35.6% v 15.8%, P = .02). Metro YAs more frequently listed fertility consultations as unavailable (38.0% v 16.0%, P = .04) in the survey despite chart review data showing higher rates of sexual health assessments (48.2% v 20.4%, P = .002) and fertility visits (29.6% v 18.5%, P = .18). CONCLUSION: We identified differences in both supportive care receipt and treatment satisfaction on the basis of residential location. These findings support the need for measures to successfully meet treatment and supportive care needs regardless of residential location.
Prevalence and determinants of scabies among school-age children in Central Armachiho district, Northwest, Ethiopia

Background Scabies is a major global public health issue that might affect people from all socioeconomic levels. Globally, scabies affects more than 200 million people at any time. It remains one of the commonest skin diseases seen in developing countries including Ethiopia. Therefore, this study aimed to assess the prevalence and determinants of scabies among school-age children in Central Armachiho district, Northwest Ethiopia. Methods A community-based cross-sectional study was conducted from August to September 2020. A multi-stage sampling technique was used to select 850 study populations. Data was checked for its completeness, coded, and entered by using EPI-INFO version 7 and exported to the SPSS version 20 for analysis. A Binary logistic regression model was fitted to identify the determinants of scabies. Crude odds ratio (COR) and adjusted odds ratio (AOR) with 95% CI were used as measurements for the associations. P-values <0.005 were considered significant. Result Prevalence of scabies among the 850 participants studied was 10.82% (95% CI: 8.7–12.9). Contact history with confirmed scabies patient (AOR = 5.28,95% CI: 2.96–9.44), child not attending school (AOR = 3.08, 95% CI;1.45–6.54), rarely changing clothes (AOR = 2.43,95% CI: 1.27–4.62), sleeping on the floor (AOR = 4.11, 95% CI:1.95–8.67), bed sharing; (AOR = 3.38, 95% CI:2.86–6.15), rarely washing cloth: (AOR = 5.08,95% CI:2.75–9.36), living with internally displaced people; (AOR,95% CI: 3.47 (1.30–9.24) and using only water to wash hands; (AOR = 3.18,95% CI:1.74–5.80) had a statistically significant association with scabies infestation among school-age children. Conclusion The current study found nearly one out of ten school-age children had scabies. Not attended school, contact history with confirmed scabies patient, not washing cloth, infrequent changing clothes, bedding sharing, sleeping on the floor, living with internally displaced people, and only using water for handwashing practice were the independent predictors for the occurrence of scabies. Health education better to given to the parents or caregivers about the washing of clothing, changing clothes at least once per week, and avoid physical contact with known scabies cases.
High blood pressure screening in pharmacies during May Measurement Month campaigns in Switzerland

Abstract Purpose May Measurement Month (MMM) is an international screening campaign for arterial hypertension (HT) organised by the International Society of Hypertension and the World Hypertension League. It aims at raising the awareness of elevated blood pressure (BP) in the population. The goal of this analysis was to assess the results obtained in Swiss pharmacies during a 3-year campaign. Material and methods Swiss data from the MMM17 to MMM19 campaigns were extracted from the global MMM database. The analysis was conducted specifically on measures taken in pharmacies. BP and a questionnaire including demographical and clinical information were recorded for each participant. To assess BP control, ESH 2018 thresholds of <140/90 mmHg and ESH 2021 pharmacy-thresholds of <135/85 mmHg were used. Results From an initial sample of 3634 Swiss participants included during this 3-year campaign, 2567 participants (73.2%women and 26.8% men, p<.001) had their BP measured in triplicates in pharmacies. The first BP measurement was associated with 2.0 ± 4.9 mmHg effect on systolic blood pressure (SBP) (p<.001) and 0.7 ± 3.7 mmHg on diastolic blood pressure (DBP) (p<.001) compared to the mean of the second and third measurements. Based on the ESH 2018 and the ESH 2021 pharmacy thresholds, prevalence of HT (mean of second and third measurements) increased from 29.5% to 38.3%, respectively. In treated participants, 58.3% (279) had an average BP < 140/90 mmHg and 40.3% (193) had an average BP < 135/85 mmHg. Conclusions HT screening campaigns in pharmacies recruits mainly women. It helps the detection of untreated hypertensive participants and uncontrolled treated participants. Our data suggest that the average BP should be calculated on the second and third measurements due to a significant first measure effect in pharmacies measurement. Summary High blood pressure (BP) is a major global public health issue as the leading risk factor of global death. World-wide initiatives like May Measurement Month (MMM) aim to screen thousands of people each year to raise awareness of hypertension (HT). Switzerland participated in MMM 2017–2019 and screened more than 2500 participants in pharmacies. When adopting the recent proposed thresholds of HT diagnosis in pharmacies (ESH 2021 > 135/85 mmHg), HT prevalence in Switzerland is high (38.3%) with only 2/3 of treated hypertensive achieving the BP goals. Women are more likely to participate in such campaigns taking place in pharmacies. A first measurement effect (FME) was also present in pharmacies, highlighting that taking three BP measurements in pharmacies and discarding the first should be also considered in the pharmacy setting. Involving a routine pharmacy-based health care of patients would help to identify more hypertensive patients and uncontrolled treated patients, who may not have had access to BP measurement.
Pseudomonas aeruginosa susceptibility, antibiogram and clinical interpretation, and antimicrobial prescribing behaviors for dogs with otitis in the Midwestern United States.

Pseudomonas aeruginosa (P. aeruginosa) can cause otitis in dogs that is nonresponsive to empirical therapy. This study evaluated P. aeruginosa isolates (N = 216) from canine ear swabs submitted to the Kansas State Veterinary Diagnostic Laboratory from 2018-2020 to create an antibiogram and minimum inhibitory concentration distributions using Clinical Laboratory Standards Institutes breakpoints. Multidrug resistance was defined as non-susceptibility to ≥1 drug from ≥3 antimicrobial classes. Submitting veterinarians (N = 83) were invited to complete a survey about antimicrobial use and otitis management. Susceptibility was higher for aminoglycosides [gentamicin (82%, 177/216) and amikacin (81%, 175/216)] than fluoroquinolones [marbofloxacin (67%, 145/216), enrofloxacin (32%, 70/216), and orbifloxacin (18%, 39/216)]. Most responding veterinarians (54%, 15/28) prescribe topical aminoglycosides as first-line therapy for canine otitis, but 71% (15/21) prescribe fluoroquinolones if rods are seen cytologically. Ceftazidime, imipenem, and piperacillin-tazobactam showed high susceptibility and are used rarely. Multidrug resistance was present in 13% (28/216) of isolates. Based on in vitro susceptibility, topical aminoglycosides might be more effective than fluoroquinolones for P. aeruginosa otitis, but efficacy studies are required. Susceptibility testing is encouraged for cases not responding to empirical therapy but has limitations because topical preparations have high concentrations and otic breakpoints are not available.