Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the AUDIT factor structure in adolescents between 18 and 19 years

ABSTRACT OBJECTIVE: To determine the factor structure of the instrument Alcohol Use Disorders Identification Test (AUDIT) in a representative sample of adolescents aged 18 to 19 years. METHODS: Cross-sectional study performed with adolescents born in São Luís (MA). The internal consistency of the instrument was determined by the Cronbach's alpha coefficient, and the validity of the construct was assessed by Confirmatory Factor Analysis (CFA). The Kaiser-Meyer-Olkin (KMO) was estimated to analyze the adequacy of the sample. The fit quality of the factor model was analyzed according to the indexes of the Chi-square adjustment test, comparative fit index (CFI), Tucker-Lewis index (TLI) and root mean square error of approximation (RMSEA). RESULTS: The sample of the study was composed of 1,002 adolescents aged from 18 to 19 years, being 56.8% girls, 68.5% with 18 years, 63.3% brown, 48.6% belonging to class C, 15.4% did not work or did not study, and 52.1% had divorced parents. The sample was suitable for confirmatory factor analysis (KMO = 0.79); Cronbach's alpha coefficient was 0.70, demonstrating satisfactory internal consistency with factor loads above 0.5, except for item 9, “was injured or someone else was injured due to drinking. ” Confirmatory factor analysis revealed the validity of the three-factor model for the studied sample based on the indices of psychometric adjustments. CONCLUSION: The three-factor AUDIT factor structure was confirmed for the population of adolescents between 18 and 19 years old living in São Luís, ratifying the original conceptual domains proposed by the World Health Organization. AUDIT proved to be a reliable instrument to identify the consumption of alcohol.
ImageJ and CellProfiler: Complements in Open‐Source Bioimage Analysis

ImageJ and CellProfiler have long been leading open‐source platforms in the field of bioimage analysis. ImageJ's traditional strength is in single‐image processing and investigation, while CellProfiler is designed for building large‐scale, modular analysis pipelines. Although many image analysis problems can be well solved with one or the other, using these two platforms together in a single workflow can be powerful. Here, we share two pipelines demonstrating mechanisms for productively and conveniently integrating ImageJ and CellProfiler for (1) studying cell morphology and migration via tracking, and (2) advanced stitching techniques for handling large, tiled image sets to improve segmentation. No single platform can provide all the key and most efficient functionality needed for all studies. While both programs can be and are often used separately, these pipelines demonstrate the benefits of using them together for image analysis workflows. ImageJ and CellProfiler are both committed to interoperability between their platforms, with ongoing development to improve how both are leveraged from the other. © 2021 Wiley Periodicals LLC.
Protective and therapeutic experience of perioperative safety in extremely elderly patients with biliary diseases

Abstract To explore the protective and therapeutic measures of improving perioperative safety in extremely elderly patients with biliary diseases, so as to improve the therapeutic efficacy of surgery. A retrospective case–control study of 412 elderly patients with biliary diseases was carried out from July 2013 to July 2019. Seventy eight cases were divided into the high age (HA) group (≥80 years) and 334 into the middle–low age (MLA) group (60–79 years). In the HA compared with MLA group,1. Preoperative coexisting diseases: the occurrence of coexisting coronary heart disease (CHD), hypertension, chronic bronchitis with emphysema, hypoproteinemia, and anemia were significantly increased;2. Laboratory examinations: function of liver, kidneys, heart, lungs, and blood coagulation significantly declined;3. Surgical procedures: open cholecystectomy with transcystic common bile duct (CBD) exploration significantly higher, while laparoscopic cholecystectomy significantly lower;4. Operative effects: intraoperative blood loss, operation time, postoperative hospital stay, and length of hospitalization significantly increased or prolonged;5. Postoperative complications: postoperative respiratory failure, pulmonary infection, anemia and electrolyte disorder significantly increased;6. Therapeutic outcomes: no significant difference in the therapeutic effects. Although the surgical risk was significantly increased, there was no significant difference in the therapeutic efficacy in the HA compared with MLA group, suggesting that surgical treatment in extremely elderly patients with biliary diseases is safe and feasible. The key is to actively treat preoperative coexisting diseases, strictly adhere to surgical indications, reasonably select surgical procedures, precisely perform the operation, closely monitor and control intraoperative emergencies, timely prevent and treat postoperative complications, so as to improve the perioperative safety of extremely elderly patients with biliary diseases.
A Multicenter, Randomized, Controlled Trial for Assessing the Usefulness of Suppressing Thyroid Stimulating Hormone Target Levels after Thyroid Lobectomy in Low to Intermediate Risk Thyroid Cancer Patients (MASTER): A Study Protocol

Background Postoperative thyroid stimulating hormone (TSH) suppression therapy is recommended for patients with intermediate- and high-risk differentiated thyroid cancer to prevent the recurrence of thyroid cancer. With the recent increase in small thyroid cancer cases, the extent of resection during surgery has generally decreased. Therefore, questions have been raised about the efficacy and long-term side effects of TSH suppression therapy in patients who have undergone a lobectomy. Methods This is a multicenter, prospective, randomized, controlled clinical trial in which 2,986 patients with papillary thyroid cancer are randomized into a high-TSH group (intervention) and a low-TSH group (control) after having undergone a lobectomy. The principle of treatment includes a TSH-lowering regimen aimed at TSH levels between 0.3 and 1.99 μIU/mL in the low-TSH group. The high-TSH group targets TSH levels between 2.0 and 7.99 μIU/mL. The dose of levothyroxine will be adjusted at each visit to maintain the target TSH level. The primary outcome is recurrence-free survival, as assessed by neck ultrasound every 6 to 12 months. Secondary endpoints include disease-free survival, overall survival, success rate in reaching the TSH target range, the proportion of patients with major cardiovascular diseases or bone metabolic disease, the quality of life, and medical costs. The follow-up period is 5 years. Conclusion The results of this trial will contribute to establishing the optimal indication for TSH suppression therapy in low-risk papillary thyroid cancer patients by evaluating the benefit and harm of lowering TSH levels in terms of recurrence, metabolic complications, costs, and quality of life.
RALDH Activity Induced by Bacterial/Fungal Pathogens in CD16+ Monocyte-Derived Dendritic Cells Boosts HIV Infection and Outgrowth in CD4+ T Cells

Key Points CD16+ MDDCs exhibit high RALDH activity upon exposure to bacterial/fungal pathogens. CD16+ MDDCs promote HIV trans infection in S. aureus–reactive CD4+ T cells. MDDCs loaded in bacterial/fungal pathogens promote HIV outgrowth in CD4+ T cells. HIV reservoirs persist in gut-homing CD4+ T cells of people living with HIV and receiving antiretroviral therapy, but the antigenic specificity of such reservoirs remains poorly documented. The imprinting for gut homing is mediated by retinoic acid (RA), a vitamin A–derived metabolite produced by dendritic cells (DCs) exhibiting RA-synthesizing (RALDH) activity. RALDH activity in DCs can be induced by TLR2 ligands, such as bacterial peptidoglycans and fungal zymosan. Thus, we hypothesized that bacterial/fungal pathogens triggering RALDH activity in DCs fuel HIV reservoir establishment/outgrowth in pathogen-reactive CD4+ T cells. Our results demonstrate that DCs derived from intermediate/nonclassical CD16+ compared with classical CD16− monocytes exhibited superior RALDH activity and higher capacity to transmit HIV infection to autologous Staphylococcus aureus–reactive T cells. Exposure of total monocyte-derived DCs (MDDCs) to S. aureus lysates as well as TLR2 (zymosan and heat-killed preparation of Listeria monocytogenes) and TLR4 (LPS) agonists but not CMV lysates resulted in a robust upregulation of RALDH activity. MDDCs loaded with S. aureus or zymosan induced the proliferation of T cells with a CCR5+integrin β7+CCR6+ phenotype and efficiently transmitted HIV infection to these T cells via RALDH/RA–dependent mechanisms. Finally, S. aureus– and zymosan-reactive CD4+ T cells of antiretroviral therapy-treated people living with HIV carried replication-competent integrated HIV-DNA, as demonstrated by an MDDC-based viral outgrowth assay. Together, these results support a model in which bacterial/fungal pathogens in the gut promote RALDH activity in MDDCs, especially in CD16+ MDDCs, and subsequently imprint CD4+ T cells with gut-homing potential and HIV permissiveness. Thus, nonviral pathogens play key roles in fueling HIV reservoir establishment/outgrowth via RALDH/RA–dependent mechanisms that may be therapeutically targeted.
Relationship between mental health diagnoses and COVID-19 test positivity, hospitalization, and mortality in Southeast Wisconsin

Abstract Background There is a paucity of literature on the relationship between pre-existing mental health conditions and coronavirus disease-2019 (COVID-19) outcomes. The aim was to examine the association between pre-existing mental health diagnosis and COVID-19 outcomes (positive screen, hospitalization, mortality). Methods Electronic medical record data for 30 976 adults tested for COVID-19 between March 2020 and 10th July 2020 was analyzed. COVID-19 outcomes included positive screen, hospitalization among screened positive, and mortality among screened positive and hospitalized. Primary independent variable, mental health disorders, was based on ICD-10 codes categorized as bipolar, internalizing, externalizing, and psychoses. Descriptive statistics were calculated, unadjusted and adjusted logistic regression and Cox proportional hazard models were used to investigate the relationship between each mental health disorder and COVID-19 outcomes. Results Adults with externalizing (odds ratio (OR) 0.67, 95%CI 0.57–0.79) and internalizing disorders (OR 0.78, 95% CI 0.70–0.88) had lower odds of having a positive COVID-19 test in fully adjusted models. Adults with bipolar disorder had significantly higher odds of hospitalization in fully adjusted models (OR 4.27, 95% CI 2.06–8.86), and odds of hospitalization were significantly higher among those with externalizing disorders after adjusting for demographics (OR 1.71, 95% CI 1.23–2.38). Mortality was significantly higher in the fully adjusted model for patients with bipolar disorder (hazard ratio 2.67, 95% CI 1.07–6.67). Conclusions Adults with mental health disorders, while less likely to test positive for COVID-19, were more likely to be hospitalized and to die in the hospital. Study results suggest the importance of developing interventions that incorporate elements designed to address smoking cessation, nutrition and physical activity counseling and other needs specific to this population to improve COVID-19 outcomes.
Localization of kisspeptin, NKB, and NK3R in the hypothalamus of gilts treated with the progestin altrenogest

Abstract Mechanisms in the brain controlling secretion of gonadotropin hormones in pigs, particularly luteinizing hormone (LH), are poorly understood. Kisspeptin is a potent LH stimulant that is essential for fertility in many species, including pigs. Neurokinin B (NKB) acting through neurokinin 3 receptor (NK3R) is involved in kisspeptin-stimulated LH release, but organization of NKB and NK3R within the porcine hypothalamus is unknown. Hypothalamic tissue from ovariectomized (OVX) gilts was used to determine the distribution of immunoreactive kisspeptin, NKB, and NK3R cells in the arcuate nucleus (ARC). Almost all kisspeptin neurons coexpressed NKB in the porcine ARC. Immunostaining for NK3R was distributed throughout the preoptic area (POA) and in several hypothalamic areas including the periventricular and retrochiasmatic areas but was not detected within the ARC. There was no colocalization of NK3R with gonadotropin-releasing hormone (GnRH), but NK3R-positive fibers in the POA were in close apposition to GnRH neurons. Treating OVX gilts with the progestin altrenogest decreased LH pulse frequency and reduced mean circulating concentrations of LH compared with OVX control gilts (P < 0.01), but the number of kisspeptin and NKB cells in the ARC did not differ between treatments. The neuroanatomical arrangement of kisspeptin, NKB, and NK3R within the porcine hypothalamus confirms they are positioned to stimulate GnRH and LH secretion in gilts, though differences with other species exist. Altrenogest suppression of LH secretion in the OVX gilt does not appear to involve decreased peptide expression of kisspeptin or NKB. Summary sentence Components of the KNDy system in the pig are characterized for the first time and pig-specific features such as a lack of immunopositive NK3R expression in the ARC and resistance to inhibition of kisspeptin protein expression by a progestin are identified.
2020 Korean Guidelines for Cardiopulmonary Resuscitation. Part 8. Neonatal resuscitation

Ju Sun Heo*, Su Yeong Kim*, Hye Won Park*, Yong-Sung Choi, Chan-Wook Park, Geum Joon Cho, Ah Young Oh, Eun Kyung Jang, Han-Suk Kim, Ai-Rhan Ellen Kim, Sung Oh Hwang; on behalf of the Steering Committee of 2020 Korean Guidelines for Cardiopulmonary Resuscitation and Emergency Cardiovascular Care Department of Pediatrics, Korea University College of Medicine, Seoul, Korea Department of Pediatrics, Chung-Ang University College of Medicine, Seoul, Korea Department of Pediatrics, Konkuk University School of Medicine, Seoul, Korea Department of Pediatrics, Kyung Hee University School of Medicine, Seoul, Korea Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea Department of Obstetrics and Gynecology, Korea University College of Medicine, Seoul, Korea 7 Department of Anesthesiology and Pain Medicine, Seoul National University College of Medicine, Seoul, Korea Office of Patient Safety, Yonsei University Severance Hospital, Seoul, Korea Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea Department of Pediatrics, Ulsan University College of Medicine, Seoul, Korea Department of Emergency Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea Clin Exp Emerg Med 2021;8(S):S96-S115 https://doi.org/10.15441/ceem.21. 028
An improved method for assessing the technical accuracy of optical tracking systems for orthopaedic surgical navigation

Optical tracking systems (OTSs) are essential components of many modern computer assisted orthopaedic surgery (CAOS) systems but patient movement is often neglected in the evaluation of the accuracy. The aim of this study was to develop a representative test to assess the accuracy of OTSs including patient movement and demonstrate the effect of pointer design and OTS choice.
Assessment of the Potential for Veverimer Drug-Drug Interactions

Veverimer is a polymer being developed as a potential treatment of metabolic acidosis in patients with chronic kidney disease. Veverimer selectively binds and removes hydrochloric acid from the gastrointestinal tract, resulting in an increase in serum bicarbonate. Veverimer is not systemically absorbed, so potential drug-drug interactions (DDIs) are limited to effects on the absorption of other oral drugs through binding to veverimer in the gastrointestinal tract or increases in gastric pH caused by veverimer binding to hydrochloric acid. In in vitro binding experiments using a panel of 16 test drugs, no positively charged, neutral, or zwitterionic drugs bound to veverimer. Three negatively charged drugs (furosemide, aspirin, ethacrynic acid) bound to veverimer; however, this binding was reduced or eliminated in the presence of normal physiologic concentrations (100–170 mM) of chloride. Veverimer increased gastric pH in vivo by 1.5–3 pH units. This pH elevation peaked within 1 hour and had returned to baseline after 1.5–3 hours. Omeprazole did not alter the effect of veverimer on gastric pH. The clinical relevance of in vitro binding and the transient increase in gastric pH was evaluated in human DDI studies using two drugs with the most binding to veverimer (furosemide, aspirin) and two additional drugs with pH-dependent solubility effecting absorption (dabigatran, warfarin). None of the four drugs showed clinically meaningful DDI with veverimer in human studies. Based on the physicochemical characteristics of veverimer and results from in vitro and human studies, veverimer is unlikely to have significant DDIs. SIGNIFICANCE STATEMENT Patients with chronic kidney disease, who are usually on many drugs, are vulnerable to drug-drug interactions (DDIs). The potential for DDIs with veverimer was evaluated based on the known site of action and physicochemical structure of the polymer, which restricts the compound to the gastrointestinal tract. Based on the findings from in vitro and human studies, we conclude that veverimer is unlikely to have clinically significant DDIs.
On the origin and correction for inner filter effects in fluorescence. Part II: secondary inner filter effect -the proper use of front-face configuration for highly absorbing and scattering samples

Fluorescence is an established technology for studying molecular processes and molecular interactions. More recently fluorescence became a leading method for detection, sensing, medical diagnostics, biotechnology, imaging, DNA analysis, and gene expression. Consequently, precise and accurate measurements in various conditions have become more critical for proper result interpretations. Previously, in Part 1, we discussed inner filter effect type I, which is a consequence of the instrumental geometrical sensitivity factor and absorption of the excitation. In this part, we analyze inner filter effect type II and discuss the practical consequences for fluorescence measurements in samples of high optical density (absorbance/scattering). We consider both the standard square and front-face experimental configurations, discuss experimental approaches to limit/mitigate the effect and discuss methods for correcting and interpreting experimental results.
Prognostic impact according to the proportion of the lepidic subtype in stage IA acinar‐predominant lung adenocarcinoma

Adenocarcinoma is the most common type of lung cancer and most adenocarcinomas have heterogeneous subtypes. Acinar‐predominant adenocarcinoma is the most common. This study aimed to identify the prognostic impact of other mixed histological subtypes in acinar‐predominant lung adenocarcinoma.
SAR by MS for Functional Genomics (Structure-Activity Relation by Mass Spectrometry)

Large-scale functional genomics will require fast, high-throughput experimental techniques, coupled with sophisticated computer algorithms for data analysis and experiment planning. In this paper, we introduce a combined experimental-computational protocol called Structure-Activity Relation by Mass Spectrometry (SAR by MS), which can be used to elucidate the function of protein-DNA or protein-protein complexes. We present algorithms for SAR by MS and analyze their complexity. Carefully-designed Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI TOF) and Electrospray Ionization (ESI) assays require only femtomolar samples, take only microseconds per spectrum to record, enjoy a resolution of up to one dalton in $10^6$, and (in the case of MALDI) can operate on protein complexes up to a megadalton in mass. Hence, the technique is attractive for high-throughput functional genomics. In SAR by MS, selected residues or nucleosides are 2H-, 13C-, and/or 15N-labeled. Second, the complex is crosslinked. Third, the complex is cleaved with proteases and/or endonucleases. Depending on the binding mode, some cleavage sites will be shielded by the crosslinking. Finally, a mass spectrum of the resulting fragments is obtained and analyzed. The last step is the Data Analysis phase, in which the mass signatures are interpreted to obtain constraints on the functional binding mode. Experiment Planning entails deciding what labeling strategy and cleaving agents to employ, so as to minimize mass degeneracy and spectral overlap, in order that the constraints derived in data analysis yield a small number of binding hypotheses. A number of combinatorial and algorithmic questions arise in deriving algorithms for both Experiment Planning and Data Analysis. We explore the complexity of these problems, obtaining upper and lower bounds. Experimental results are reported from an implementation of our algorithms.
Learning Invariant Patterns Based on a Convolutional Neural Network and Big Electroencephalography Data for Subject-Independent P300 Brain-Computer Interfaces

A brain-computer interface (BCI) measures and analyzes brain activity and converts this activity into computer commands to control external devices. In contrast to traditional BCIs that require a subject-specific calibration process before being operated, a subject-independent BCI learns a subject-independent model and eliminates subject-specific calibration for new users. However, building subject-independent BCIs remains difficult because electroencephalography (EEG) is highly noisy and varies by subject. In this study, we propose an invariant pattern learning method based on a convolutional neural network (CNN) and big EEG data for subject-independent P300 BCIs. The CNN was trained using EEG data from a large number of subjects, allowing it to extract subject-independent features and make predictions for new users. We collected EEG data from 200 subjects in a P300-based spelling task using two different types of amplifiers. The offline analysis showed that almost all subjects obtained significant cross-subject and cross-amplifier effects, with an average accuracy of more than 80%. Furthermore, more than half of the subjects achieved accuracies above 85%. These results indicated that our method was effective for building a subject-independent P300 BCI, with which more than 50% of users could achieve high accuracies without subject-specific calibration.