Miracle-dz/UniFAR-FTUs huggingface dataset:
BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria

Abstract Recent technological advances have led to an exponential expansion of biological sequence data and extraction of meaningful information through Machine Learning (ML) algorithms. This knowledge has improved the understanding of mechanisms related to several fatal diseases, e.g. Cancer and coronavirus disease 2019, helping to develop innovative solutions, such as CRISPR-based gene editing, coronavirus vaccine and precision medicine. These advances benefit our society and economy, directly impacting people’s lives in various areas, such as health care, drug discovery, forensic analysis and food processing. Nevertheless, ML-based approaches to biological data require representative, quantitative and informative features. Many ML algorithms can handle only numerical data, and therefore sequences need to be translated into a numerical feature vector. This process, known as feature extraction, is a fundamental step for developing high-quality ML-based models in bioinformatics, by allowing the feature engineering stage, with design and selection of suitable features. Feature engineering, ML algorithm selection and hyperparameter tuning are often manual and time-consuming processes, requiring extensive domain knowledge. To deal with this problem, we present a new package: BioAutoML. BioAutoML automatically runs an end-to-end ML pipeline, extracting numerical and informative features from biological sequence databases, using the MathFeature package, and automating the feature selection, ML algorithm(s) recommendation and tuning of the selected algorithm(s) hyperparameters, using Automated ML (AutoML). BioAutoML has two components, divided into four modules: (1) automated feature engineering (feature extraction and selection modules) and (2) Metalearning (algorithm recommendation and hyper-parameter tuning modules). We experimentally evaluate BioAutoML in two different scenarios: (i) prediction of the three main classes of noncoding RNAs (ncRNAs) and (ii) prediction of the eight categories of ncRNAs in bacteria, including housekeeping and regulatory types. To assess BioAutoML predictive performance, it is experimentally compared with two other AutoML tools (RECIPE and TPOT). According to the experimental results, BioAutoML can accelerate new studies, reducing the cost of feature engineering processing and either keeping or improving predictive performance. BioAutoML is freely available at https://github.com/Bonidia/BioAutoML.
Does Temporal Stability Moderate Reasoned Action Approach Relations With Covid-19 Preventive Behaviors?

Abstract Background Preventive behaviors continue to play an important role in reducing the spread of the SARS-CoV-2 virus. Purpose This study aimed to apply the reasoned action approach (RAA) to predict Covid-19 preventive intentions and behavior and to test whether temporal stability moderates relations between RAA constructs and behavior. Methods A representative sample of UK adults (N = 603) completed measures of RAA variables (i.e., experiential attitudes, instrumental attitudes, injunctive norms, descriptive norms, capacity, autonomy and intention) in relation to six Covid-19 preventive behaviors (i.e., wearing face coverings, social distancing, hand sanitizing, avoiding the three Cs [closed spaces, crowded places, and close contacts], cleaning surfaces, and coughing/sneezing etiquette) at baseline (December 2020) and after 1 month. Self-reported behavior was assessed at baseline and after 1 and 2 months. Results The RAA was predictive of Covid-19 preventive intentions at time 1 and time 2; instrumental attitudes, descriptive norms, and capability were the strongest predictors at each time point. The RAA also predicted subsequent behavior across time points with intention, descriptive norms, and capability the strongest/most consistent predictors. Temporal stability moderated a number of RAA–behavior relationships including those for intention, descriptive norms, and capability. In each case, the relationships became stronger as temporal stability increased. Conclusions Health cognitions as outlined in the RAA provide appropriate targets for interventions to promote Covid-19 preventive intentions and behavior. Moreover, given that continued performance of Covid-19 preventive behaviors is crucial for reducing transmission of the SARS-CoV-2 virus, the results highlight the need for consistent messaging from governments and public health organizations to promote positive intentions and maintain preventive behavior.
Albumin-corrected Zn and available free Zn-binding capacity as indicators of Zn status – potential for clinical implementation

Abstract We have established and describe two measurement procedures to diagnose possible zinc (Zn) deficiency; albumin-corrected Zn concentration and available free Zn-binding capacity. Reference intervals for both biomarkers were established in healthy adults from the Danish population. The clinical usefulness of the measurement procedures was investigated in patients with cirrhosis and in patients given parenteral nutrition due to short bowel syndrome. The results of both methods indicate that there is a risk of overdiagnosing Zn deficiency based on low plasma Zn concentrations. Needless Zn supplementation may thus be avoided by using the albumin-corrected Zn concentration or available free Zn-binding capacity.
Diagnostic criteria and evolving molecular characterisation of pulmonary neuroendocrine carcinomas

Neuroendocrine carcinomas of the lung are currently classified into two categories: small‐cell lung carcinoma and large‐cell neuroendocrine carcinoma. Diagnostic criteria for small‐cell and large‐cell neuroendocrine carcinoma are based solely on tumour morphology; however, overlap in histologic and immunophenotypic features between the two types of carcinomas can potentially make their classification challenging. Accurate diagnosis of pulmonary neuroendocrine carcinomas is paramount for patient management, as clinical course and treatment differ between small‐cell and large‐cell neuroendocrine carcinoma. Molecular‐genetic, transcriptomic, and proteomic data published over the past decade suggest that small‐cell and large‐cell neuroendocrine carcinomas are not homogeneous categories but rather comprise multiple groups of distinctive malignancies. Nuances in the susceptibility of small‐cell lung carcinoma subtypes to different chemotherapeutic regimens and the discovery of targetable mutations in large‐cell neuroendocrine carcinoma suggest that classification and treatment of neuroendocrine carcinomas may be informed by ancillary molecular and protein expression testing going forward. This review summarizes the current diagnostic criteria, prognostic and predictive correlates of classification, and evidence of previously unrecognised subtypes of small‐cell and large‐cell neuroendocrine carcinoma.
Paradoxes, nurses’ roles and Medical Assistance in Dying: A grounded theory

Background In June 2016, the Parliament of Canada passed federal legislation allowing eligible adults to request Medical Assistance in Dying (MAID). Since its implementation, there likely exists a degree of hesitancy among some healthcare providers due to the law being inconsistent with personal beliefs and values. It is imperative to explore how nurses in Quebec experience the shift from accompanying palliative clients through “a natural death” to participating in “a premeditated death. ” Research question/aim/objectives This study aims to explore how Quebec nurses personally and professionally face the new practice of MAID and their role evolution. Research design A grounded theory design was used. Participants and research context We recruited 37 nurses who participated in or coordinated at least one MAID. Semi-structured interviews and focus groups were conducted and audiotaped. Data collection and analysis followed Strauss and Corbin steps. Ethical considerations Ethics approval was received from the investigator’s affiliated University. Participants were informed regarding the research goal, signed a written consent, and were assigned pseudonyms. Findings/results Results show that nurses experienced the wide range of paradoxe during MAID centering around the following eight elements: 1) confrontation abouth death, 2) choice, 3) time of death, 4) emotional load, 5) new Bill, 6) relationship with the person, 7) communication skills, and 8) healthcare setting. The shifting of views and values in this new role is presented by the contradiction of opposites. Conclusions A better understanding of the paradox experienced by nurses involved with MAID paves the way for the development of interventions.
Congenital Cytomegalovirus Knowledge, Practices, and Beliefs Among Primary Care Physicians and Newborn Hospitalists

Background: Congenital cytomegalovirus (cCMV) affects 1 in every 200 United States infants, at present there are 9 states which mandate newborn cCMV screening. With more infants being diagnosed, more children will need continuing care from providers who are knowledgeable about cCMV. Objectives: To examine pediatric provider knowledge, practices, and beliefs around cCMV. Methods: Primary care and newborn hospitalist pediatricians (N = 103) from Michigan, who “regularly care for infants” were invited to participate in a survey about their cCMV-related knowledge, clinical practices, and beliefs. Results: Respondents had low knowledge of typical cCMV presentation and sequelae, with mixed knowledge of screening and testing standards. Most (68%) reported rarely/never screening for cCMV, though 71% strongly agreed/agreed that primary care providers should test for cCMV. Most (90%) strongly agreed/agreed that infants who fail/refer on their newborn hearing screen should be tested for cCMV, yet 81% expressed not being comfortable diagnosing and managing cCMV. Most (72%) felt that cCMV was not sufficiently covered in their medical training; almost all respondents endorsed interest in learning more. Conclusions: Primary care and newborn hospitalists in this study expressed mixed knowledge about, infrequent practice of and low comfort with screening and caring for children with cCMV. This may present a prime opportunity for education and clinician support by professional organizations.
On the polar decomposition of the aluthge transformation and related results

Let T = U|T| be the polar decomposition of a bounded linear operator T on a Hilbert space. The transformation e T = |T| 1 2U|T| 1 2 is called the Aluthge transformation and e Tn means the n-th Aluthge transformation. In this paper, firstly, we show that e
Comparative Effectiveness of Postdischarge Smoking Cessation Interventions for Hospital Patients

Key Points Question How can health systems most effectively provide smoking cessation treatment to patients after hospital discharge to promote long-term tobacco abstinence? Findings This randomized clinical trial of 1409 hospitalized smokers compared 2 models for delivering tobacco cessation treatment after discharge: health system–based care or referral to a community-based quitline. Health system–based care produced better treatment use and more tobacco abstinence throughout the 3 months of treatment but not 6 months after discharge. Meaning These findings suggest that continuing treatment beyond 3 months might have sustained end-of-treatment superiority of the health system–based model.
Active edible films with plant extracts: a updated review of their types, preparations, reinforcing properties, and applications in muscle foods packaging and preservation

Abstract Currently, edible films have been increasingly explored to solve muscle food spoilage during storage, especially through the incorporation of plant extracts to develop edible packaging materials. Natural polymers matrices with plant extracts are befitting for fabricating edible films by casting methods. In the films system, the structure and physicochemical properties were strengthened via chemical interactions between active molecules in plant extracts and the reactive groups in the polymer chain. The antibacterial and antioxidant properties were dramatically reinforced through both physical and chemical actions of the plant extracts. Additionally, edible films imbedded with color-rich plant extracts could be considered as potential sensitive indicators to monitor the spoilage degree of muscle foods in response to change in gas or temperature. Furthermore, these films could increase sensory acceptability, improve quality and prolong the shelf life of muscle foods. In this article, the types, preparation methods and reinforcing properties of the edible films with plant extracts were discussed. Also, the applications of these films were summarized on quality maintenance and shelf-life extension and intelligent monitoring in muscle foods. Finally, a novel technology for film preparation achieving high-stability and sustained release of active compounds will become an underlying trend for application in muscle food packaging.
An online survey of perimenopausal women to determine their attitudes and knowledge of the menopause

Introduction: Women are not usually taught about the menopause formally, and many general practitioners have relatively little training. The aim of this study was to explore perimenopausal women’s attitudes and knowledge of the menopause. Method: An online survey was designed to evaluate attitudes and knowledge of the menopause in women older than 40 years. The survey was generated with Qualtrics XM® and promoted via social media. In all, 3150 women started the survey. In this study, data from 947 perimenopausal women were analysed. Results: Regarding women’s attitudes to the menopause, 38.8% were accepting of it but more than 30% were dreading it. The women had experienced a number of menopause symptoms including mood swings (68.9%), brain fog (68.3%), and fatigue (66.8%). More than 90% of women had never been taught about the menopause at school, and more than 60% did not feel informed at all about the menopause. School was thought to be the best place for menopause education to start (83.6%). In all, 68.2% of women had only looked for information about the menopause as their symptoms started and they had talked to friends and used a variety of websites to look for information. When asked for their free-text views on the menopause, thematic analysis produced four themes: the overarching knowledge gap, the onset and impact of symptoms, perimenopause: the hidden phenomenon, and managing symptoms: differing schools of thought. Conclusion: Lack of education for women and their general practitioners is causing perimenopausal women to go through this important stage in their lives with a lack of knowledge and appropriate medical care. It is essential that women are taught about the menopause, from school onwards and that we offer health professionals appropriate training starting from the medical school curriculum.
Epigenetic rewiring of pathways related to odour perception in immune cells exposed to SARS-CoV-2 in vivo and in vitro

ABSTRACT A majority of SARS-CoV-2 recoverees develop only mild-to-moderate symptoms, while some remain completely asymptomatic. Although viruses, including SARS-CoV-2, may evade host immune responses by epigenetic mechanisms including DNA methylation, little is known about whether these modifications are important in defence against and healthy recovery from COVID-19 in the host. To this end, epigenome-wide DNA methylation patterns from COVID-19 convalescents were compared to uninfected controls from before and after the pandemic. Peripheral blood mononuclear cell (PBMC) DNA was extracted from uninfected controls, COVID-19 convalescents, and symptom-free individuals with SARS-CoV-2-specific T cell-responses, as well as from PBMCs stimulated in vitro with SARS-CoV-2. Subsequently, the Illumina MethylationEPIC 850K array was performed, and statistical/bioinformatic analyses comprised differential DNA methylation, pathway over-representation, and module identification analyses. Differential DNA methylation patterns distinguished COVID-19 convalescents from uninfected controls, with similar results in an experimental SARS-CoV-2 infection model. A SARS-CoV-2-induced module was identified in vivo, comprising 66 genes of which six (TP53, INS, HSPA4, SP1, ESR1, and FAS) were present in corresponding in vitro analyses. Over-representation analyses revealed involvement in Wnt, muscarinic acetylcholine receptor signalling, and gonadotropin-releasing hormone receptor pathways. Furthermore, numerous differentially methylated and network genes from both settings interacted with the SARS-CoV-2 interactome. Altered DNA methylation patterns of COVID-19 convalescents suggest recovery from mild-to-moderate SARS-CoV-2 infection leaves longstanding epigenetic traces. Both in vitro and in vivo exposure caused epigenetic modulation of pathways thataffect odour perception. Future studies should determine whether this reflects host-induced protective antiviral defense or targeted viral hijacking to evade host defence.
Volatile versus Propofol General Anesthesia and Long-term Survival after Breast Cancer Surgery: A National Registry Retrospective Cohort Study

Background: Several retrospective studies using administrative or single-center data have failed to show any difference between general anesthesia using propofol versus inhaled volatiles on long-term survival after breast cancer surgery. Although randomized controlled trials are ongoing, validated data from national clinical registries may advance the reliability of existing knowledge. Methods: Data on breast cancer surgery performed under general anesthesia between 2013 and 2019 from the Swedish PeriOperative Registry and the National Quality Registry for Breast Cancer were record-linked. Overall survival was compared between patients receiving propofol and patients receiving inhaled volatile for anesthesia maintenance. Results: Of 18,674 subjects, 13,873 patients (74.3%) received propofol and 4,801 (25.7%) received an inhaled volatile for general anesthesia maintenance. The two cohorts differed in most respects. Patients receiving inhaled volatile were older (67 yr vs. 65 yr), sicker (888 [19.0%] American Society of Anesthesiologists status 3 to 5 vs. 1,742 [12.8%]), and the breast cancer to be more advanced. Median follow-up was 33 months (interquartile range, 19 to 48). In the full, unmatched cohort, there was a statistically significantly higher overall survival among patients receiving propofol (13,489 of 13,873 [97.2%]) versus inhaled volatile (4,039 of 4,801 [84.1%]; hazard ratio, 0.80; 95% CI, 0.70 to 0.90; P < 0.001). After 1:1 propensity score matching (4,658 matched pairs), there was no statistically significant difference in overall survival (propofol 4,284 of 4,658 [92.0%]) versus inhaled volatile (4,288 of 4,658 [92.1%]; hazard ratio, 0.98; 95% CI, 0.85 to 1.13; P = 0.756). Conclusions: Among patients undergoing breast cancer surgery under general anesthesia, no association was observed between the choice of propofol or an inhaled volatile maintenance and overall survival. Using data combining two national Swedish clinical registries from 2013 to 2019 for 18,674 breast cancer surgery patients, the authors observed that 13,873 (74.3%) received propofol general anesthesia and 4,801 (25.7%) received inhaled volatile general anesthesia. In a propensity score–matched cohort of 9,316 patients, there was no difference in overall survival between patients receiving propofol general anesthesia (4,284 of 4,658; 92.0%) versus inhaled volatile general anesthesia (4,288 of 4,658; 92.1%).
Clinical and genetic features of congenital bile acid synthesis defect with a novel mutation in AKR1D1 gene sequencing

Abstract Rationale: Congenital bile acid synthesis defect (BASD) is a rare disease caused by mutations in the aldo-keto reductase 1D1 gene, which encodes the primary Δ4-3-oxosteroid 5β-reductase enzyme. Early disease diagnosis is critical for early treatment with bile acid replacement therapy, with an excellent chance for recovery. In contrast, protracted diagnosis and treatment may lead to poor outcomes, including decompensated hepatic cirrhosis, liver transplant, and even death. Patient concerns: Three clinical congenital bile acid synthesis defect cases in the Vietnamese population are herein reported. These pediatric patients presented with symptoms of prolonged postpartum jaundice and abnormal loose stool (mucus, lipids, and white). The clinical examinations showed hepatosplenomegaly. Urinalysis showed a very low fraction of primary bile acids and atypical 3-oxo-Δ4- bile acids in all three patients. Diagnoses: The patients were diagnosed with primary Δ4-3-oxosteroid 5β-reductase deficiency. Next-generation gene sequencing revealed two homozygous mutations in the aldo-keto reductase family 1 member D1 gene. The first is a documented variant, c.797G>A (p.Arg266Gln), and the second is a novel mutation at c.155T>C (p.Ile52Thr). Interventions: Immediately after diagnosis, patients were treated with oral chenodeoxycholate 5 mg/kg/d. Outcomes: The patients’ symptoms, signs, and primary bile acids levels improved significantly. Lessons: Clinicians should consider genetic disorders related to cholestasis for effective and life-saving treatment. A prompt genetic analysis by next-generation gene sequencing enables patients to access bile acid replacement therapy earlier, significantly improving short- and long-term outcomes.
Care coordination, consistency and continuity: the case of the key worker role in children’s cancer care

ABSTRACT Purpose The overall aim was to evaluate the key worker role across principal treatment centres for children with cancer in England, Wales and Scotland. Methods Mixed-methods case study gathering data from multiple perspectives using questionnaires, interviews, focus groups and reports/performance documents over a two-year period. Framework approach was adopted to analyse transcripts and documentary data. Results Participants included: 22 nurse specialist key workers, 103 parents, 85 professionals and 10 children/young people. Qualitative and quantitative data were woven together, to best illuminate key worker services. Four main models of care were described as well as the context of care and process of care. Key working effectiveness centred around three pillars: care coordination; expert knowledge, experience and expertise; relationship. These were essential to improved family experience, emotional wellbeing, and delivery of individualized care closer to home. Conclusions The role is complex and diverse, responding to local needs. Certain conditions, (e.g., high caseload) placed limits on enacting the three pillars, diminishing the positive experience of families. When they worked well, key workers reduced the fragmented nature of services and families placed great value on keeping the same key worker from diagnosis into long-term care. Retaining these roles, where already in place, or including, if not, we would recommend, factoring into budgets to sustain and expand such roles.