Miracle-dz/UniFAR-FTUs huggingface dataset:
A Benchmarking Between Deep Learning, Support Vector Machine and Bayesian Threshold Best Linear Unbiased Prediction for Predicting Ordinal Traits in Plant Breeding

Genomic selection is revolutionizing plant breeding. However, still lacking are better statistical models for ordinal phenotypes to improve the accuracy of the selection of candidate genotypes. For this reason, in this paper we explore the genomic based prediction performance of two popular machine learning methods: the Multi Layer Perceptron (MLP) and support vector machine (SVM) methods vs. the Bayesian threshold genomic best linear unbiased prediction (TGBLUP) model. We used the percentage of cases correctly classified (PCCC) as a metric to measure the prediction performance, and seven real data sets to evaluate the prediction accuracy, and found that the best predictions (in four out of the seven data sets) in terms of PCCC occurred under the TGLBUP model, while the worst occurred under the SVM method. Also, in general we found no statistical differences between using 1, 2 and 3 layers under the MLP models, which means that many times the conventional neuronal network model with only one layer is enough. However, although even that the TGBLUP model was better, we found that the predictions of MLP and SVM were very competitive with the advantage that the SVM was the most efficient in terms of the computational time required.
Sero-molecular detection, multi-locus genotyping, and clinical manifestations of ocular toxoplasmosis in patients in northwest Iran

BACKGROUND Our goal was to use molecular techniques to verify and characterise clinical diagnoses of ocular toxoplasmosis. Clinical cases were evaluated against IgM and IgG Toxoplasma antibodies, and IgG avidity was tested. B1 gene was assessed for molecular detection, and multi-locus genotyping were conducted to type Toxoplasma infections. METHODS A cross-sectional study was conducted in 33 patients with suspected active ocular toxoplasmosis. Patients were examined by an ophthalmologist and clinical manifestations were recorded. Toxoplasma gondii IgG and IgM from serum samples were analysed by chemiluminescence immunoassay and ELISA. Acute vs chronic infection was evaluated by IgG avidity testing. Molecular diagnosis of T. gondii infection targeted the B1 gene, and the T. gondii genotype was determined by amplification of the GRA6, SAG2, SAG3, BTUB and APICO loci. The correlation of age, gender, occupation, education, contact with cats or soil, and the consumption of undercooked meat with the incidence of ocular toxoplasmosis was evaluated. RESULTS Twenty-eight patients (84.8%) were seropositive, two (6%) were both IgG and IgM positive, while one (3%) showed IgG avidity <40%. Molecular testing confirmed toxoplasmosis in 27 patients (81.8%). Chorioretinal scarring (p=0.014) and posterior uveitis (p=0.004) was significantly associated with ocular toxoplasmosis patients. Multi-locus genotyping showed genotype I. Ocular toxoplasmosis showed no significant correlation with gender, age, behaviours, occupation or education. CONCLUSION Clinical manifestations, serological and molecular detection of Toxoplasma were highly correlated in the diagnosis of ocular toxoplasmosis. Genotype I was predominant in ocular toxoplasmosis in northwest Iran. A larger comparative study should be conducted to provide a broader view of the molecular epidemiology of T. gondii genotypes and its role in toxoplasmosis.
The conserved aspartate ring of MCU mediates MICU1 binding and regulation in the mitochondrial calcium uniporter complex

The mitochondrial calcium uniporter is a Ca2+ channel that regulates intracellular Ca2+ signaling, oxidative phosphorylation, and apoptosis. It contains the pore-forming MCU protein, which possesses a DIME sequence thought to form a Ca2+ selectivity filter, and also regulatory EMRE, MICU1, and MICU2 subunits. To properly carry out physiological functions, the uniporter must stay closed in resting conditions, becoming open only when stimulated by intracellular Ca2+ signals. This Ca2+-dependent activation, known to be mediated by MICU subunits, is not well understood. Here, we demonstrate that the DIME-aspartate mediates a Ca2+-modulated electrostatic interaction with MICU1, forming an MICU1 contact interface with a nearby Ser residue at the cytoplasmic entrance of the MCU pore. A mutagenesis screen of MICU1 identifies two highly-conserved Arg residues that might contact the DIME-Asp. Perturbing MCU-MICU1 interactions elicits unregulated, constitutive Ca2+ flux into mitochondria. These results indicate that MICU1 confers Ca2+-dependent gating of the uniporter by blocking/unblocking MCU.
Roles of Efflux Pumps from Different Superfamilies in the Surface-Associated Motility and Virulence of Acinetobacter baumannii ATCC 17978

Although the relationship between Acinetobacter baumannii efflux pumps and antimicrobial resistance is well documented, less is known about the involvement of these proteins in the pathogenicity of this nosocomial pathogen. In previous work, we identified the AbaQ major facilitator superfamily (MFS) efflux pump and demonstrated its participation in the motility and virulence of A. baumannii. ABSTRACT Although the relationship between Acinetobacter baumannii efflux pumps and antimicrobial resistance is well documented, less is known about the involvement of these proteins in the pathogenicity of this nosocomial pathogen. In previous work, we identified the AbaQ major facilitator superfamily (MFS) efflux pump and demonstrated its participation in the motility and virulence of A. baumannii. In the present study, we examined the role in these processes of A. baumannii transporters belonging to different superfamilies of efflux pumps. Genes encoding known or putative permeases belonging to efflux pump superfamilies other than the MFS were selected, and the corresponding knockouts were constructed. The antimicrobial susceptibilities of these mutants were consistent with previously reported data. In mutants of A. baumannii strain ATCC 17978 carrying inactivated genes encoding the efflux pumps A1S_2736 (resistance nodulation division [RND]), A1S_3371 (multidrug and toxic compound extrusion [MATE]), and A1S_0710 (small multidrug resistance [SMR]), as well as the newly described ATP-binding cassette (ABC) permeases A1S_1242 and A1S_2622, both surface-associated motility and virulence were reduced compared to the parental strain. However, inactivation of the genes encoding the known ABC permeases A1S_0536 and A1S_1535, the newly identified putative ABC permeases A1S_0027 and A1S_1057, or the proteobacterial antimicrobial compound efflux (PACE) transporters A1S_1503 and A1S_2063 had no effects on bacterial motility or virulence. Our results demonstrate the involvement of antimicrobial transporters belonging at least to five of the six known efflux pump superfamilies in both surface-associated motility and virulence in A. baumannii ATCC 17978.
Educating good decisions

Abstract Can we educate decision-makers to make better decisions? In the present paper, I argue that we can in at least two broad ways: (1) teaching concrete knowledge about a specific decision or decision type; and (2) teaching more abstract decision-making competencies that are thought to lead to better decisions. Teaching knowledge can be done using decision aids and similar techniques that provide important information about a specific choice (e.g. a medical treatment option). In these cases, information presented using evidence-based techniques to improve comprehension and use of information will have greater effects on judgements and choices. Teaching more abstract decision competencies, on the other hand, involves formal schooling (with the bulk of formal education falling during childhood) or training in a specific competency that is important to decision processes and outcomes; I use numeracy interventions as an exemplar.
Overcoming Intrinsic and Acquired Cetuximab Resistance in RAS Wild-Type Colorectal Cancer: An In Vitro Study on the Expression of HER Receptors and the Potential of Afatinib

The epidermal growth factor receptor (EGFR) is an important therapeutic target in colorectal cancer (CRC). After the initial promising results of EGFR-targeted therapies such as cetuximab, therapeutic resistance poses a challenging problem and limits the success of effective anti-EGFR cancer therapies in the clinic. In order to overcome resistance to these EGFR-targeted therapies, new treatment options are necessary. The objective of this study was to investigate the expression of human epidermal growth factor (HER) receptors and the efficacy of afatinib, a second-generation irreversible EGFR-tyrosine kinase inhibitor, in RAS wild-type CRC cell lines with different cetuximab sensitivities. CRC cell lines with different sensitivities to cetuximab showed rather low EGFR expression but high HER2 and HER3 expression. These results were in line with the The Cancer Genome Atlas (TCGA) data from CRC patients, where higher mRNA levels of HER2 and HER3 were also detected compared to EGFR. Therefore, the targets of afatinib were indeed expressed on the CRC cell lines used in this study and in CRC patients. Furthermore, cetuximab resistance had no significant influence on the expression levels of HER receptors in CRC cell lines (p ≥ 0.652). This study also demonstrated that afatinib was able to induce a concentration-dependent cytotoxic effect in RAS wild-type CRC cell lines with different cetuximab sensitivities. Neither cetuximab resistance (p = 0.233) nor hypoxia (p = 0.157) significantly influenced afatinib’s cytotoxic effect. In conclusion, our preclinical data support the hypothesis that treatment with afatinib might be a promising novel therapeutic strategy for CRC patients experiencing intrinsic and acquired cetuximab resistance.
Nasal swab bacteriology by PCR during the first 24‐months of life: A prospective birth cohort study

Most respiratory bacterial carriage studies in children are based on cross‐sectional samples or longitudinal studies with infrequent sampling points. The prospective Observational Research in Childhood Infectious Diseases birth cohort study intensively evaluated the community‐based epidemiology of respiratory viruses and bacteria during the first 2‐years of life. Here we report the bacteriologic findings.
Efficacy of anastrozole after tamoxifen in early breast cancer patients with chemotherapy‐induced ovarian function failure

The DATA study (NCT00301457) compared 6 and 3 years of anastrozole in postmenopausal women with hormone receptor‐positive early breast cancer after 2–3 years of tamoxifen. Patients with chemotherapy‐induced ovarian function failure (CIOFF) were also eligible, but could be at risk of ovarian function recovery (OFR). The current analysis compared the survival of women with CIOFF with definitely postmenopausal women and examined the influence of OFR on survival. Therefore, we selected patients from the DATA study aged 45–57 years at randomization who had received (neo)adjuvant chemotherapy. They were classified by reversibility of postmenopausal status: possibly reversible in case of CIOFF (n = 395) versus definitely postmenopausal (n = 261). The former were monitored by E2 measurements for OFR. The occurrence of OFR was incorporated as a time‐dependent covariate in a Cox‐regression model for calculating the hazard ratio (HR). We used the landmark method to calculate residual 5‐year survival rates. When comparing CIOFF women with definitely postmenopausal women, the survival was not different. Among CIOFF women with available E2 follow‐up values (n = 329), experiencing OFR (n = 39) had an unfavorable impact on distant recurrence‐free survival (HR 2.27 [95% confidence interval [CI] 0.98–5.25; p = 0.05] and overall survival (HR 2.61 [95% CI 1.11–6.13; p = 0.03]). After adjusting for tumor features, the HRs became 2.11 (95% CI 0.89–5.02; p = 0.09) and 2.24 (95% CI 0.92–5.45; p = 0.07), respectively. The residual 5‐year rate for distant recurrence‐free survival was 76.9% for women with OFR and 92.1% for women without OFR, and for 5‐year overall survival 80.8% and 94.4%, respectively. Women with CIOFF receiving anastrozole may be at increased risk of disease recurrence if experiencing OFR.
Progress towards a Nordic standard for the investigation of hematuria: 2019

Abstract Objective: To describe the management of patients with hematuria in the Nordic countries in relation to bladder cancer epidemiology, especially in the context of introducing fast track pathways with the aim of proposing a common guideline. Materials and methods: Epidemiological data on bladder cancer from each country, and the combined cancer registry, Nordcan, were analyzed. The evolution of the different national recommendations and the introduction of fast track pathways were assessed. Patients' demographics, type of hematuria and cancer detection rates were analysed if available. Results: The crude incidence of bladder cancer has increased substantially since the 1960s, while the age standardized incidence has been stable during recent decades. The relative survival has increased in all countries, while the mortality has been stable. For those with microscopic hematuria there has been a clear trend towards less rigorous investigations. In the fast track pathways, introduced in three of five countries, about one in five patients with macroscopic hematuria had a cancer diagnosis. Data show that time to diagnosis has been reduced. Conclusions: The number of patients with bladder cancer is increasing in the Nordic region. The introduction of fast track pathways has been important in improving the management of patients with suspicion of the disease. Our recommendation is to focus on macroscopic hematuria in the fast track pathways. Microhematuria without any symptoms should not be an indication for cystoscopy. However, urinary tract symptoms accompanied by microhematuria can still be investigated according to respective guidelines but not necessarily within fast track pathways.
Advances in cellular and humoral immunotherapy – implications for the treatment of poor risk childhood, adolescent, and young adult B‐cell non‐Hodgkin lymphoma

Patients with relapsed, refractory or advanced stage B non‐Hodgkin lymphoma (NHL) continue to have a dismal prognosis. This review summarises current and novel cellular and immunotherapy for these high‐risk populations, including haematopoietic stem cell transplant, bispecific antibodies, viral‐derived cytotoxic T cells, chimeric antigen receptor (CAR) T cells, and natural killer (NK) cell therapy, as discussed at the 6th International Symposium on Childhood, Adolescent and Young Adult Non‐Hodgkin Lymphoma on September 26th–29th 2018 in Rotterdam, the Netherlands, and explores the future of NK/CAR NK therapies.
Discussing factors associated with quality of life in cancer follow-up appointments: a preliminary test of a pragmatic model for clinical practice

Objective: The aim of this study is to perform a preliminary test of a practical, evidence-based model to enable discussions around quality of life–related concerns during cancer follow-up appointments. Design: Cross-sectional study measuring quality of life, illness perceptions, emotional distress, fatigue, and subjective cognitive complaints. Setting: Cancer outpatient follow-up clinics in four National Health Services in the United Kingdom. Participants: Working-age post-treatment cancer patients, treated with curative intent. Interventions: Not applicable. Main measures: European Organisation for the Research and Treatment of Cancer – Quality of Life Questionnaire – Core 30, Illness Perceptions Questionnaire – Revised, Hospital Anxiety and Depression Scale, Chalder Fatigue Scale, and Cognitive Failures Questionnaire. Results: Fifty-seven cancer patients, with a mean age of 36 years and on average 2.75 years post treatment, returned the completed questionnaires. Anxiety partially mediated the association between subjective cognitive complaints and illness identity (60%) and timeline (25%). Cognitive complaints mediated the relationships between quality of life and anxiety (45%), depression (30%), and fatigue (62%). Depression mediated the relationships between quality of life and illness identity (48%) and timeline (40%). Conclusion: Our study provides a preliminary test of an evidence-based model to help elicit quality of life–related concerns during cancer follow-up appointments. Illness perceptions are associated with quality of life through the mediation of other cancer-relevant factors. Discussing the type, origin, and expected duration of symptoms may elicit other concerns, such as emotional distress, fatigue, or cognitive complaints, which explained a significant amount of the relationship between illness perceptions and quality of life.
Improving learner outcomes in EFL: Does early instruction lead to greater achievement?

Language education curricula and programs worldwide have begun emphasizing foreign language instruction for learners as young as 5-6 years, particularly in English. Yet, while studies have argued for the benefits of early language instruction, the results of this trend in terms of actual achievement are not clear. For this reason, the researchers designed this study to illustrate the connection between age of onset of English as a foreign language (EFL) instruction and learner achievement, examining international language curricula from countries where English is taught as a foreign language beginning at the pre-primary and primary level alongside the corresponding scores on the Test of English as a Foreign Language (TOEFL). The findings indicate that, although early onset of EFL instruction may be beneficial in many respects, it is not, in itself, a guarantee of success, and other elements, such as class size, number of hours dedicated to English instruction, and teacher qualifications, must also be considered.
Anaerobic co-digestion of poultry litter and wheat straw affected by solids composition, free ammonia and carbon/nitrogen ratio

Abstract In this study, the effects of three total solids levels (2%, 5% and 10% TS) of the mixtures of poultry litter and wheat straw at different percent volatile solids from wheat straw (0%, 25% and 50% VSWS), free ammonia nitrogen (FAN) and C/N ratio on co-digesting poultry litter with wheat straw were studied in batch experiments operated at 37 °C. The results showed that adjusting the substrate C/N ratio alone could not always result in high methane yields and biogas volumes. The maximum CH4 yield of 201 mL g–1 initial VS was observed in the 5% TS category with VSWS being 50%. The highest specific biogas volume produced (318 mL g–1 initial VS) was also obtained in the same solid category. A polynomial regression between FAN and the methanogenic activity was obtained with the correlation coefficient being 0.9472. A FAN inhibitory threshold concentration of 253.9 mg L–1 was found, and a total loss of methane production occurred when the FAN concentration reached 1000 mg L–1. An optimal TS content for anaerobic digestion of poultry litter with wheat straw was around 4.15% to achieve the best biogas yield. Similarly, for digesting poultry litter without addition of wheat straw, the TS content should be kept at around 6.8%.
Re-Examining Genetic Screening and Oral Contraceptives: A Patient-Centered Review

The World Health Organization classifies combined hormonal contraception as an unacceptable health risk in the presence of a known thrombogenic mutation but advises against routine thrombophilia screening before initiating combined oral contraceptives (COCs) on the grounds of high screening costs and low prevalence. From the perspective of patient-centered care, we examine cost, prevalence, and other published arguments for and against thrombophilia screening before initiating COCs. Our patient-centered review draws on relevant empirical evidence concerning the advantages and disadvantages of thrombophilia screening, while placing the discussion in the broader context of evolving attitudes toward genetic testing and a shifting policy landscape that provides many women direct access to COCs and/or thrombophilia screening. Given variation in prior probabilities of thrombophilia, expected exposure to other risk factors for venous thromboembolism, attitudes towards risk, expected reactions to a positive test result, ability to pay, and concerns about genetic discrimination, we conclude that the current one-size-fits-most approach is not consistent with patient-centered care. Instead, we advocate for greater patient and provider education concerning the implications of thrombophilia screening. Moreover, we recommend offering patients optional thrombophilia screening before initiating COCs.
Social anxiety disorder and avoidant personality disorder from an interpersonal perspective.

OBJECTIVES The general objective of this article is to study the unclear and overlapping relationship between social anxiety disorder (SAD) and avoidant personality disorder (AvPD) from an interpersonal perspective. The first specific objective is to compare the disorders with regard to interpersonal problems and general symptom distress. The second specific objective is to examine interpersonal subgroups and pathoplasticity. DESIGN In a cross-sectional design, patients from an outpatient psychotherapy clinic diagnosed with social anxiety disorder (SAD, n = 299), avoidant personality disorder (AvPD, n = 180), or the comorbid condition of both disorders (AvPD + SAD, n = 29) were assessed before treatment. METHODS Patients filled out the Inventory of Interpersonal Problems (IIP-64) and the Symptom Checklist-Revised (SCL-R-90) before treatment. RESULTS AND CONCLUSIONS From an interpersonal perspective, the relationship between the diagnostic groups is well described by the severity continuum hypothesis, with similar interpersonal problems related to Nonassertiveness and lower levels of general interpersonal stress in the SAD group compared to the two AvPD groups. However, other differences in severity do not fit the severity continuum hypothesis, as there are no differences in severity on the global severity index, and, moreover, the SAD group has the most severe problems on the SCL-90 phobic anxiety scale. Interpersonal pathoplasticity is not found in the diagnostic groups or in the full sample. However, three interpersonal subgroups are identified in the full sample, designated as Nonassertive, Friendly-submissive, and Cold-submissive. Implications for treatment are discussed. PRACTITIONER POINTS SAD is characterized by a lower level of interpersonal distress compared to AvPD, but the two disorders are similar in having Nonassertiveness as their general interpersonal problem. Contrary to expectation, SAD and AvPD did not differ in general level of symptom severity, and patients with SAD reported more problems with phobic anxiety than AvPD patients did. When understanding SAD and AvPD as different conceptualizations of the same disorder and analysing all patients together, three distinct interpersonal subgroups emerge, which can be identified as Nonassertive, Friendly-submissive, and Cold-submissive.