Miracle-dz/UniFAR-FTUs huggingface dataset:
Modified Bidirectional Encoder Representations From Transformers Extractive Summarization Model for Hospital Information Systems Based on Character-Level Tokens (AlphaBERT): Development and Performance Evaluation

Background Doctors must care for many patients simultaneously, and it is time-consuming to find and examine all patients’ medical histories. Discharge diagnoses provide hospital staff with sufficient information to enable handling multiple patients; however, the excessive amount of words in the diagnostic sentences poses problems. Deep learning may be an effective solution to overcome this problem, but the use of such a heavy model may also add another obstacle to systems with limited computing resources. Objective We aimed to build a diagnoses-extractive summarization model for hospital information systems and provide a service that can be operated even with limited computing resources. Methods We used a Bidirectional Encoder Representations from Transformers (BERT)-based structure with a two-stage training method based on 258,050 discharge diagnoses obtained from the National Taiwan University Hospital Integrated Medical Database, and the highlighted extractive summaries written by experienced doctors were labeled. The model size was reduced using a character-level token, the number of parameters was decreased from 108,523,714 to 963,496, and the model was pretrained using random mask characters in the discharge diagnoses and International Statistical Classification of Diseases and Related Health Problems sets. We then fine-tuned the model using summary labels and cleaned up the prediction results by averaging all probabilities for entire words to prevent character level–induced fragment words. Model performance was evaluated against existing models BERT, BioBERT, and Long Short-Term Memory (LSTM) using the Recall-Oriented Understudy for Gisting Evaluation (ROUGE) L score, and a questionnaire website was built to collect feedback from more doctors for each summary proposal. Results The area under the receiver operating characteristic curve values of the summary proposals were 0.928, 0.941, 0.899, and 0.947 for BERT, BioBERT, LSTM, and the proposed model (AlphaBERT), respectively. The ROUGE-L scores were 0.697, 0.711, 0.648, and 0.693 for BERT, BioBERT, LSTM, and AlphaBERT, respectively. The mean (SD) critique scores from doctors were 2.232 (0.832), 2.134 (0.877), 2.207 (0.844), 1.927 (0.910), and 2.126 (0.874) for reference-by-doctor labels, BERT, BioBERT, LSTM, and AlphaBERT, respectively. Based on the paired t test, there was a statistically significant difference in LSTM compared to the reference (P<.001), BERT (P=.001), BioBERT (P<.001), and AlphaBERT (P=.002), but not in the other models. Conclusions Use of character-level tokens in a BERT model can greatly decrease the model size without significantly reducing performance for diagnoses summarization. A well-developed deep-learning model will enhance doctors’ abilities to manage patients and promote medical studies by providing the capability to use extensive unstructured free-text notes.
Molecular detection of Coxiella burnetii in raw meat intended for pet consumption

The discovery of antibodies against Coxiella burnetii in cattery‐confined breeding cats indicating prior or current exposure (Shapiro et al., 2015) prompted an investigation into possible sources of infection. One hypothesis was that raw meat diets containing reservoir species may provide a source of C. burnetii transmission. The aim of this pilot study was to determine whether C. burnetii DNA was present in raw meat sold exclusively for companion animal consumption. The sample population consisted of raw meat packages (n = 58) of primarily kangaroo origin, with three to four aliquots (50–120 mg) randomly selected from each package. Genomic DNA was extracted from whole tissue in each of these aliquots using a modified protocol. Three quantitative PCR assays were used for the detection of C. burnetii targeting the IS1111 gene, the heat shock operon htpAB and the C. burnetii outer membrane protein‐coding gene, com1. Coxiella burnetii DNA was detected in 25/58 samples (43%) using the IS1111, htpAB and/or com1 PCR assays and confirmed by DNA sequencing. All samples amplifying a product in the com1 assay also amplified a product in the htpAB and IS1111 assays. A total of 17/58 (29%) packets were positive with all three genes, 4/58 (7%) were positive with two genes (IS1111 and htpAB) and 4/58 (7%) were positive with the IS1111 gene only. Coxiella burnetii DNA was five times more likely to be found in offal than skeletal muscle meat samples. All meat samples in which C. burnetii DNA was found were from kangaroo tissues, while samples labelled as non‐kangaroo meat (n = 4) were negative. Multi‐locus variable number of tandem repeat analysis (MLVA) identified three different genotypes of C. burnetii that have all been identified previously from Australian human clinical Q fever cases. Further investigations are required to determine the potential role of certain raw meats in the transmission of C. burnetii to cats and humans.
Naltrexone Use in Treating Hypersexuality Induced by Dopamine Replacement Therapy: Impact of OPRM1 A/G Polymorphism on Its Effectiveness

Hypersexuality is a well-known adverse side effect of dopamine replacement therapy (DRT), and anti-craving drugs could be an effective therapeutic option. Our aim was to update the knowledge on this issue, particularly on the influence of an Opioid Receptor Mu 1 (OPRM1) genetic polymorphism. A systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. We also analyzed a case of iatrogenic hypersexuality that occurred in a patient treated with DRT. An analysis of the OPRM1 gene was performed on said patient. Our search identified 597 publications, of which only 7 were included in the final data synthesis. All seven publications involved naltrexone use. Five of them were case reports. None of the publications mentioned DRT side effects, nor did they report genetic data. Regarding our case report, the introduction of naltrexone corresponded with the resolution of the patient’s hypersexuality. Moreover, the patient carried the A/G genotype, which has been reported to be associated with a stronger response to naltrexone for patients with an alcohol use disorder. Although studies are inconclusive so far, naltrexone could be an interesting therapeutic option for resistant hypersexuality due to DRT. Carrying the A/G genotype could help explain a good response to treatment.
COVID-19: An Early Review of Its Global Impact and Considerations for Parkinson’s Disease Patient Care

While many infectious disorders are unknown to most neurologists, COVID-19 is very different. It has impacted neurologists and other health care workers, not only in our professional lives but also through the fear and panic within our own families, colleagues, patients and their families, and even in the wider public. COVID-19 affects all sorts of individuals, but the elderly with underlying chronic conditions are particularly at risk of severe disease, or even death. Parkinson’s disease (PD) shares a common profile as an age-dependent degenerative disorder, frequently associated with comorbidities, particularly cardiovascular diseases, so PD patients will almost certainly fall into the high-risk group. Therefore, the aim of this review is to explore the risk of COVID-19 in PD based on the susceptibility to severe disease, its impact on PD disease severity, potential long-term sequelae, and difficulties of PD management during this outbreak, where neurologists face various challenges on how we can maintain effective care for PD patients without exposing them, or ourselves, to the risk of infection. It is less than six months since the identification of the original COVID-19 case on New Year’s Eve 2019, so it is still too early to fully understand the natural history of COVID-19 and the evidence on COVID-19-related PD is scant. Though the possibilities presented are speculative, they are theory-based, and supported by prior evidence from other neurotrophic viruses closely related to SARS-CoV-2. Neurologists should be on high alert and vigilant for potential acute and chronic complications when encountering PD patients who are suspected of having COVID-19.
The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control

A pneumonia outbreak with unknown etiology was reported in Wuhan, Hubei province, China, in December 2019, associated with the Huanan Seafood Wholesale Market. The causative agent of the outbreak was identified by the WHO as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), producing the disease named coronavirus disease-2019 (COVID-19). The virus is closely related (96.3%) to bat coronavirus RaTG13, based on phylogenetic analysis. Human-to-human transmission has been confirmed even from asymptomatic carriers. The virus has spread to at least 200 countries, and more than 1,700,000 confirmed cases and 111,600 deaths have been recorded, with massive global increases in the number of cases daily. Therefore, the WHO has declared COVID-19 a pandemic. The disease is characterized by fever, dry cough, and chest pain with pneumonia in severe cases. In the beginning, the world public health authorities tried to eradicate the disease in China through quarantine but are now transitioning to prevention strategies worldwide to delay its spread. To date, there are no available vaccines or specific therapeutic drugs to treat the virus. There are many knowledge gaps about the newly emerged SARS-CoV-2, leading to misinformation. Therefore, in this review, we provide recent information about the COVID-19 pandemic. This review also provides insights for the control of pathogenic infections in humans such as SARS-CoV-2 infection and future spillovers.
Gram-negative endophthalmitis: A prospective study examining the microbiology, clinical associations and visual outcomes following infection.

IMPORTANCE This is the largest Gram-negative endophthalmitis specific series and provides important evidence to guide management. BACKGROUND Endophthalmitis is a sight-threatening emergency. Gram-negative infections are associated with poorer visual outcomes; however, there is limited literature pertaining to this uncommon condition. DESIGN Prospective case series. PARTICIPANTS All patients presenting with endophthalmitis to a tertiary institution over a twenty-year period. METHODS Data were collected prospectively and entered into a registry. Patients with microbiological evidence of Gram-negative infection were included the analysis. MAIN OUTCOMES MEASURES Final visual acuity, precipitating events, causative organisms, antibiotic sensitivity profiles, and risk factors for poor visual outcomes were reported. RESULTS One hundred Gram-negative organisms were isolated in 97 eyes. Final visual acuity was worse than 6/60 in 65 (67.0%) eyes at follow-up and 29 (29.9%) eyes were eviscerated or enucleated. Microbial keratitis (26.8%, n = 26) and Pseudomonas aeruginosa (34.0%, n = 34) were the most common precipitating event and causative organism, respectively. Eight (8.0%) isolates were third-generation cephalosporin resistant; of which, 7 (88.0%) were sensitive to ciprofloxacin. Preceding microbial keratitis (OR = 13.16, P = 0.015) or Pseudomonas aeruginosa infection (OR = 3.40, P = 0.045) were strongly associated with poorer visual outcomes (worse than 6/60). CONCLUSIONS AND RELEVANCE Visual outcomes following Gram-negative endophthalmitis are extremely poor, with almost 30% of patients being eviscerated or enucleated. A majority of ceftazidime resistant organisms are sensitive to ciprofloxacin, providing evidence to support the empirical use of quinolones. Clinicians should be mindful that infections secondary to Pseudomonas aeruginosa or microbial keratitis carry a particularly poor prognosis. This article is protected by copyright. All rights reserved.
Redefining Pathways into Acute Rehabilitation during the COVID‐19 Crisis

The coronavirus disease 2019 (COVID‐19) pandemic has necessitated drastic changes across the spectrum of health care, all of which have occurred with unprecedented rapidity. The need to accommodate change on such a large scale has required ingenuity and decisive thinking. The field of physical medicine and rehabilitation has been faced with many of these challenges. Healthcare practitioners in New York City, the epicenter of the pandemic in the United States, were among the first to encounter many of these challenges. One of the largest lessons included learning how to streamline admissions and transfer process into an acute rehabilitation hospital as part of a concerted effort to make acute care hospital beds available as quickly as possible.
Perceived challenges in delivering comprehensive care for patients following stroke: a qualitative study of stroke care providers in Guangdong Province, China

Abstract Purpose To understand the challenges in delivering comprehensive care for patients recovering from stroke in Guangdong Province, China. Methods A cross-sectional qualitative study was conducted in two tertiary hospitals with different socio-economic characteristics in Guangdong Province, Southern China. Interviews were conducted with 16 stroke care providers including doctors, nurses, rehabilitation therapists and care workers. The interviews were audiotaped, transcribed and translated from Mandarin to English. Thematic analysis was used to draw out descriptive and analytical themes relating to care providers’ experiences of existing routine stroke care services and the perceptions of challenges in delivering comprehensive stroke care. Results The interviews with stroke care providers highlighted three key factors that hinder the capacity of the two hospitals to deliver comprehensive stroke care. First, expertise and knowledge regarding stroke and stroke care are lacking among both providers and patients; second, stroke care systems are not fully integrated, with inadequate coordination of the stroke team and inconsistency in care following discharge of stroke patients; third, stroke patients have insufficient social support. Conclusions While comprehensive stroke care has become a priority in China, our study highlights some important gaps in the current provision of stroke care. IMPLICATIONS FOR REHABILITATION Comprehensive integrated stroke care is essential to maximize the effectiveness of stroke services and in China it needs to be further improved. Multidisciplinary stroke care systems should strengthen collaborations across all relevant disciplines and should include a clear role for registered nurses. Follow-up care after discharge needs more engagement with family caregivers.
It’s Not All Sunshine: Non-sun-related Melanoma Risk-factors

There is increasing evidence that the behaviour of naevi and melanoma is under significant genetic and/ or epigenetic control. Melanoma tumours behaves similarly all over the world. Many genes have now been implicated in melanoma risk and naevi number. Embryogenesis has also been important in the discovery of links between several neurological diseases and melanoma susceptibility. Telomere biology, which regulates cell senescence, is increasingly relevant in melanoma. Melanoma is often found in the context of family cancer syndromes and the identification of these families is important as screening for cancer will save lives. Melanoma is also one of the most immunogenic cancer as the behaviour of naevi and melanoma differ in patients with vitiligo or eczema. The search for non-sun-related melanoma risk factors should continue as it is likely to lead to important discoveries which will, in turn, have an impact on therapeutic targets for this tumour.
Prevalence of Periodontal Disease among Obese Young Adult Population in Saudi Arabia—A Cross-Sectional Study

Background and objectives: We aimed to assess the prevalence of periodontal disease among obese young adults in Saudi Arabia and to analyze the association between different body mass indexes and the severity of periodontal disease. Materials and methods: This descriptive cross-sectional study consisted of 307 obese patients aged 18–39 years, with body mass index (BMI) ≥30. Demographic variables for periodontal disease, anthropometric parameters such as BMI along with clinical parameters such as oral hygiene index-simplified, community periodontal index (CPI) score and loss of attachment (LOA), were assessed. Multivariate binary logistic regression analysis was used to identify the predictors for chronic periodontitis in obese young adults between 18–40 years of age. Results: The majority of the participants (71.3%) had periodontal disease. Obese and extremely obese patients together showed a statistically significant difference in the age group of 21-30 years in terms of CPI score for inflammation (p < 0.05) and LOA (p < 0.001). Logistic regression analysis showed age (OR: 3.180; 95%CL: 1.337–7.561; p <.001), occasional dental visit (OR: 5.965; 95%CL: 3.130–11.368; p < 0.001), smoking >10 cigarettes (OR: 11.868; 95%CL: 3.588–39.254; p < 0.001) and poor oral hygiene status (OR: 17.250; 95%CL: 6.958–42.764; p < 0.001) were associated with a significantly higher risk of having periodontal disease. Conclusions: This study showed a high prevalence of periodontal disease in obese patients among the Saudi Arabian population.
Diversidade de Euglossini (Hymenoptera: Apidae) em áreas de Cerrado do Triângulo Mineiro, MG.

Os Euglossini sao abelhas tipicas de matas tropicais umidas, mas poucos estudos tem sido feitos estimando parâmetros ecologicos desse grupo em outras fitofisionomias. O objetivo deste trabalho foi estudar a diversidade de Euglossini em areas de cerrado sentido restrito, proximas ao municipio de Uberlândia-MG. Foram realizadas coletas na Reserva Ecologica do Clube Caca e Pesca Itororo (CCPIU) e na Estacao Ecologica do Panga (EEP), entre Outubro de 2003 e setembro de 2004. No total foram coletadas 213 abelhas pertencentes a nove especies. Eulaema (Apeulaema) nigrita, Euglossa (Euglossa) melanotricha e Euglossa (Glossura) imperialis foram as especies mais abundantes. Verificou-se uma baixa similaridade de especies entre as duas areas (PS=0,409).
Cardiovascular Outcomes Among Patients with Type 2 Diabetes Newly Initiated on Sodium-Glucose Cotransporter-2 Inhibitors, Glucagon-Like Peptide-1 Receptor Agonists, and Other Antidiabetic Medications

BACKGROUND: Cardiovascular disease (CVD) remains the most prevalent cause of morbidity and mortality in patients with type 2 diabetes (T2D) and is a primary driver for health care costs associated with diabetes management. Sodium-glucose cotransporter-2 inhibitors (SGLT-2is) and glucagon-like peptide-1 receptor agonists (GLP-1 RAs) have demonstrated significant reductions in cardiovascular endpoints in clinical trials compared with placebo. However, it is uncertain whether these findings can be applied to the broader T2D population because these trials specifically included high-risk patients with established CVD. OBJECTIVE: To evaluate and compare cardiovascular outcomes among adults with T2D newly initiated on SGLT-2is, GLP-1 RAs, and other antidiabetic medications (oADMs) in a real-world setting. METHODS: This retrospective new-user cohort study used administrative claims and electronic health record data from an integrated delivery network in Texas. Patients aged ≥18 years with T2D and ≥1 prescription claim for an SGLT-2i, a GLP-1 RA, or an oADM filled between April 2013 and December 2018 were included. Patients were divided into three 1:1 propensity-matched groups according to index medication identified. Primary outcomes were heart failure hospitalization and a composite end-point of myocardial infarction, stroke, unstable angina, or coronary revascularization. Cox proportional hazards regression was used to compare cumulative incidence of all outcome variables. RESULTS: Among 9,477 patients, 1,134 were initiated on SGLT-2is, 1,072 on GLP-1 RAs, and 7,271 on oADMs. Patients initiating SGLT-2is versus oADMs had significantly lower risk of the composite endpoint (HR = 0.64, 95% CI = 0.46-0.90), heart failure hospitalization (HR = 0.56, 95% CI = 0.39-0.81), and unstable angina requiring hospitalization (HR = 0.56, 95% CI = 0.39-0.81). Patients initiating GLP-1 RAs compared with oADMs had significantly lower risk of the composite endpoint (HR = 0.71, 95% CI = 0.52-0.98) and unstable angina requiring hospitalization (HR = 0.60, 95% CI = 0.41-0.86). No differences in cardiovascular outcomes were found between SGLT-2is and GLP-1 RAs. CONCLUSIONS: Both SGLT-2is and GLP-1 RAs showed significant reductions in the composite outcome and unstable angina requiring hospitalization versus oADMs. However, only SGLT-2is were associated with a lower risk for heart failure hospitalizations. Nevertheless, cardiovascular outcomes were similar between SGLT-2is and GLP-1 RAs.
Comparative Application of BioID and TurboID for Protein-Proximity Biotinylation

BioID is a well-established method for identifying protein–protein interactions and has been utilized within live cells and several animal models. However, the conventional labeling period requires 15–18 h for robust biotinylation which may not be ideal for some applications. Recently, two new ligases termed TurboID and miniTurbo were developed using directed evolution of the BioID ligase and were able to produce robust biotinylation following a 10 min incubation with excess biotin. However, there is reported concern about inducibility of biotinylation, cellular toxicity, and ligase stability. To further investigate the practical applications of TurboID and ascertain strengths and weaknesses compared to BioID, we developed several stable cell lines expressing BioID and TurboID fusion proteins and analyzed them via immunoblot, immunofluorescence, and biotin-affinity purification-based proteomics. For TurboID we observed signs of protein instability, persistent biotinylation in the absence of exogenous biotin, and an increase in the practical labeling radius. However, TurboID enabled robust biotinylation in the endoplasmic reticulum lumen compared to BioID. Induction of biotinylation could be achieved by combining doxycycline-inducible expression with growth in biotin depleted culture media. These studies should help inform investigators utilizing BioID-based methods as to the appropriate ligase and experimental protocol for their particular needs.
Aucklandia lappa Causes Cell Wall Damage in Candida albicans by Reducing Chitin and (1,3)-β-D-Glucan

The fungal cell wall is a major target of antifungals. In this study, we report the antifungal activity of an ethanol extract from Aucklandia lapp against Candida albicans. We found that the extract caused cell wall injury by decreasing chitin synthesis or assembly and (1,3)-β-D-glucan synthesis. A sorbitol protection assay demonstrated that the minimum inhibitory concentration (MIC) of the A. lappa extract against C. albicans cells increased eight-fold from 0.78 to 6.24 mg/ml in 72 h. Cell aggregates, which indicate damage to the cell wall or membrane, were commonly observed in the A. lappa- treated C. albicans cells through microscopic analysis. In addition, the relative fluorescence intensities of the C. albicans cells incubated with the A. lappa extract for 3, 5, and 6 h were 92.1, 84.6, and 79.8%, respectively, compared to the controls, estimated by Calcofluor White binding assay. This result indicates that chitin content was reduced by the A. lappa treatment. Furthermore, synthesis of (1,3)-β-D-glucan polymers was inhibited to 84.3, 79.7, and 70.2% of that of the control treatment following incubation of C. albicans microsomes with the A. lappa extract at a final concentration equal to its MIC, 2× MIC, and 4× MIC, respectively. These findings suggest that the A. lappa ethanol extract may aid the development of a new antifungal to successfully control Candida- associated disease.