Miracle-dz/UniFAR-FTUs huggingface dataset:
Influenza A Hemagglutinin Passage Bias Sites and Host Specificity Mutations

Animal studies aimed at understanding influenza virus mutations that change host specificity to adapt to replication in mammalian hosts are necessarily limited in sample numbers due to high cost and safety requirements. As a safe, higher-throughput alternative, we explore the possibility of using readily available passage bias data obtained mostly from seasonal H1 and H3 influenza strains that were differentially grown in mammalian (MDCK) and avian cells (eggs). Using a statistical approach over 80,000 influenza hemagglutinin sequences with passage information, we found that passage bias sites are most commonly found in three regions: (i) the globular head domain around the receptor binding site, (ii) the region that undergoes pH-dependent structural changes and (iii) the unstructured N-terminal region harbouring the signal peptide. Passage bias sites were consistent among different passage cell types as well as between influenza A subtypes. We also find epistatic interactions of site pairs supporting the notion of host-specific dependency of mutations on virus genomic background. The sites identified from our large-scale sequence analysis substantially overlap with known host adaptation sites in the WHO H5N1 genetic changes inventory suggesting information from passage bias can provide candidate sites for host specificity changes to aid in risk assessment for emerging strains.
Effects of the Collaborative Assessment and Management of Suicidality (CAMS) Model: A Secondary Analysis of Moderation and Influencing Factors

In a randomized controlled trial, we found that suicidal patients who received Collaborative Assessment and Management of Suicidality (CAMS) reported greater improvements in suicidal ideation and mental health distress compared to participants who received treatment as usual (TAU). Here, we explored moderators and mediators of the effectiveness of CAMS. Compared to TAU, CAMS was more effective in reducing suicidal ideation when the working alliance, in particular its bond subcomponent, was low. In terms of reducing mental health distress, CAMS was superior to TAU only for participants who did not use illicit drugs and, more tentatively, only for patients without borderline personality traits. We suggest that CAMS may repair a difficult vantage point in terms of poor working alliance in patients with suicide ideation. To obtain superior benefits of CAMS upon more general mental health distress in patients with drug abuse or borderline traits, these problems may need to be more explicitly targeted in parallel.
Reassessment of the Species in the Euwallacea Fornicatus (Coleoptera: Curculionidae: Scolytinae) Complex after the Rediscovery of the “Lost” Type Specimen

Ambrosia beetles of the Euwallacea fornicatus (Eichhoff, 1868) species complex are emerging tree pests, responsible for significant damage to orchards and ecosystems around the world. The species complex comprises seven described species, all of which are nearly identical. Given that the morphology-defined species boundaries have been ambiguous, historically, there has been much disagreement on species validity, which was compounded by the presumed loss of the type series of E. fornicatus. The species complex was recently reviewed using morphometrics to associate the type specimens to the clades delineated with molecular data under the assumption of the lost type series. We rediscovered a syntype of Xyleborus fornicatus, and reevaluated the species in the complex using morphometrics. We propose the following taxonomic changes to the species complex: Euwallacea fornicatus (=E. tapatapaoensis (Schedl, 1951); = E. whitfordiodendrus (Schedl, 1942)) syn. res.); E. fornicatior (Eggers, 1923) (=E. schultzei (Schedl, 1951) syn. nov.); E. kuroshio (Gomez and Hulcr, 2018) and E. perbrevis (Schedl, 1951) stat. res. These taxonomic changes shift the species name associated with the widely used common names for two taxa, namely: Euwallacea fornicatus should be used for the “Polyphagous Shot Hole Borer”, and E. perbrevis for the “Tea Shot Hole Borer clade a”. A lectotype is designated for X. fornicatus in order to stabilize the use of the name.
Ab Initio Screening of Doped Mg(AlH4)2 Systems for Conversion-Type Lithium Storage

In this work, we have explored the potential applications of pure and various doped Mg(AlH4)2 as Li-ion battery conversion electrode materials using density functional theory (DFT) calculations. Through the comparisons of the electrochemical specific capacity, the volume change, the average voltage, and the electronic bandgap, the Li-doped material is found to have a smaller bandgap and lower average voltage than the pure system. The theoretical specific capacity of the Li-doped material is 2547.64 mAhg−1 with a volume change of 3.76% involving the electrode conversion reaction. The underlying reason for property improvement has been analyzed by calculating the electronic structures. The strong hybridization between Lis-state with H s-state influences the performance of the doped material. This theoretical research is proposed to help the design and modification of better light-metal hydride materials for Li-ion battery conversion electrode applications.
RNA Secondary Structure Prediction with Pseudoknots Using Chemical Reaction Optimization Algorithm

RNA molecules play a significant role in cell function especially including pseudoknots. In past decades, several methods have been developed to predict RNA secondary structure with pseudoknots and the most popular one uses minimum free energy. It is a nondeterministic polynomial-time hard (NP-hard) problem. We have proposed an approach based on a metaheuristic algorithm named Chemical Reaction Optimization (CRO) to solve the RNA pseudoknotted structure prediction problem. The reaction operators of CRO algorithm have been redesigned and used on the generated population to find the structure with the minimum free energy. Besides, we have developed an additional operator called Repair operator which has a great influence on our algorithm in increasing accuracy. It helps to increase the true positive base pairs while decreasing the false positive and false negative base pairs. Four energy models have been applied to calculate the energy. To evaluate the performance, we have used four datasets containing RNA pseudoknotted sequences taken from the RNA STRAND and Pseudobase++ database. We have compared the proposed approach with some existing algorithms and shown that our CRO based model is a better prediction method in terms of accuracy and speed.
Association between Anemia and Cognitive Impairment among Elderly Patients with Heart Failure

Cognitive impairment is more prevalent in heart failure (HF) patients. Anemia can influence cognitive ability and is likely more prevalent in elderly patients with HF. However, there are limited data on the association of anemia with cognitive impairment in elderly HF patients. This study aimed to identify the association between anemia and cognitive impairment in elderly HF patients. This secondary data analysis included 181 patients aged 60 years or older with HF. Patients were categorized into an anemic or non-anemic group based on World Health Organization (WHO) criteria. We assessed the cognitive function using the Modified Mini-Mental State (3MS) at the time of enrollment. The prevalence of anemia and cognitive impairment in older patients with HF was the same at 35.4%. The main finding of the multiple logistic regression indicated that compared to a non-anemic status, anemia increased the risk of cognitive impairment (odds ratio (OR) = 4.268, 95% confidence interval (CI) = 1.898–9.593, p < 0.001). Healthcare providers should recognize the value of the significance of early assessment of anemic status and cognitive function following HF. A prospective cohort study should identify the pathway of the association between anemia and incidence of cognitive impairment.
Structural Insights on Retroviral DNA Integration: Learning from Foamy Viruses

Foamy viruses (FV) are retroviruses belonging to the Spumaretrovirinae subfamily. They are non-pathogenic viruses endemic in several mammalian hosts like non-human primates, felines, bovines, and equines. Retroviral DNA integration is a mandatory step and constitutes a prime target for antiretroviral therapy. This activity, conserved among retroviruses and long terminal repeat (LTR) retrotransposons, involves a viral nucleoprotein complex called intasome. In the last decade, a plethora of structural insights on retroviral DNA integration arose from the study of FV. Here, we review the biochemistry and the structural features of the FV integration apparatus and will also discuss the mechanism of action of strand transfer inhibitors.
Increased prevalence of psychopathy and childhood trauma in homicide offenders with schizophrenia compared to nonviolent individuals with schizophrenia

Abstract Purpose: Schizophrenia is associated with an increased homicide risk. Personality pathology, particularly antisocial personality disorder and psychopathic traits, has been associated with increased violence risk in schizophrenia. Childhood trauma, more specifically physical abuse, has been associated with violence risk in healthy populations and in individuals with mental illness. It is, however, unclear how childhood trauma relates to homicide in schizophrenia. This is, to our knowledge, the first study to concurrently examine personality pathology and childhood trauma in a group consisting solely of homicide offenders with schizophrenia (HOS). HOS is compared to nonviolent participants with the same diagnosis (non-HOS). Additionally, currently assessed demographical and clinical characteristics of a Norwegian sample of HOS are reported. Materials and methods: Two groups of participants with schizophrenia were recruited in collaboration with in and outpatient clinics across Norway, HOS (n= 26) and non-HOS (n= 28). Assessments of personality pathology and childhood trauma were conducted, and information about clinical and demographical characteristics was registered. Results: HOS participants had significantly higher psychopathy scores, and more frequently reported moderate to severe childhood physical abuse than non-HOS participants. When simultaneously added to a logistic regression model, only psychopathy uniquely contributed to explaining group membership. Conclusions: Psychopathy and physical abuse was more prevalent among HOS participants compared to non-HOS, but only psychopathy independently predicted homicidal status. These results confirm the importance of including an evaluation of psychopathic traits in violence risk assessments of individuals with schizophrenia.
Emergency Department Pediatric Readiness and Mortality in Critically Ill Children

This study evaluates the impact of ED pediatric readiness on the mortality of critically ill children who initially present to an ED. BrightcoveDefaultPlayer10.1542/6138649550001PEDS-VA_2019-0568 Video Abstract BACKGROUND: Emergency departments (EDs) vary in their level of readiness to care for pediatric emergencies. We evaluated the effect of ED pediatric readiness on the mortality of critically ill children. METHODS: We conducted a retrospective cohort study in Florida, Iowa, Massachusetts, Nebraska, and New York, focusing on patients aged 0 to 18 years with critical illness, defined as requiring intensive care admission or experiencing death during the encounter. We used ED and inpatient administrative data from the Agency for Healthcare Research and Quality’s Healthcare Cost and Utilization Project linked to hospital-specific data from the 2013 National Pediatric Readiness Project. The relationship between hospital-specific pediatric readiness and encounter mortality in the entire cohort and in condition-specific subgroups was evaluated by using multivariable logistic regression and fractional polynomials. RESULTS: We studied 20 483 critically ill children presenting to 426 hospitals. The median weighted pediatric readiness score was 74.8 (interquartile range: 59.3–88.0; range: 29.6–100). Unadjusted in-hospital mortality decreased with increasing readiness score (mortality by lowest to highest readiness quartile: 11.1%, 5.4%, 4.9%, and 3.4%; P < .001 for trend). Adjusting for age, chronic complex conditions, and severity of illness, presentation to a hospital in the highest readiness quartile was associated with decreased odds of in-hospital mortality (adjusted odds ratio compared with the lowest quartile: 0.25; 95% confidence interval: 0.18–0.37; P < .001). Similar results were seen in specific subgroups. CONCLUSIONS: Presentation to hospitals with a high pediatric readiness score is associated with decreased mortality. Efforts to increase ED readiness for pediatric emergencies may improve patient outcomes.
The Perfect Bacteriophage for Therapeutic Applications—A Quick Guide

The alarming spread of multiresistant infections has kick-started the quest for alternative antimicrobials. In a way, given the steady increase in untreatable infectious diseases, success in this endeavor has become a matter of life and death. Perhaps we should stop searching for an antibacterial panacea and explore a multifaceted strategy in which a wide range of compounds are available on demand depending on the specific situation. In the context of this novel tailor-made approach to combating bacterial pathogens, the once forgotten phage therapy is undergoing a revival. Indeed, the compassionate use of bacteriophages against seemingly incurable infections has been attracting a lot of media attention lately. However, in order to take full advantage of this strategy, bacteria’s natural predators must be taken from their environment and then carefully selected to suit our needs. In this review, we have explored the vast literature regarding phage isolation and characterization for therapeutic purposes, paying special attention to the most recent studies, in search of findings that hint at the most efficient strategies to identify suitable candidates. From this information, we will list and discuss the traits that, at the moment, are considered particularly valuable in phages destined for antimicrobial therapy applications. Due to the growing importance given to biofilms in the context of bacterial infections, we will dedicate a specific section to those characteristics that indicate the suitability of a bacteriophage as an antibiofilm agent. Overall, the objective is not just to have a large collection of phages, but to have the best possible candidates to guarantee elimination of the target pathogens.
Skipping Breakfast and the Risk of Cardiovascular Disease and Death: A Systematic Review of Prospective Cohort Studies in Primary Prevention Settings

Several studies have associated skipping (not having) breakfast with cardiometabolic risk factors such as obesity, high blood pressure, unfavorable lipid profiles, diabetes, and metabolic syndrome. We examined the available evidence regarding the effect of skipping breakfast on cardiovascular morbidity and mortality, as well as all-cause mortality. Medline, Embase, and Web of Science were searched from inception until May 2019 to identify prospective cohort studies that examined the association between skipping breakfast and the risk of cardiovascular morbidity and mortality and all-cause death. Electronic searches were supplemented by manual screening of the references of retrieved studies. Out of 456 citations identified, four studies (from Japan and the US) were included. The included studies involved a total of 199,634 adults (aged ≥40 years; 48.5% female) without known cardiovascular disease (CVD) at baseline followed over a median duration of 17.4 years. The pooled data suggested that people who regularly skipped breakfast were about 21% more likely (hazard ratio (HR) 1.21, 95% confidence interval (CI) 1.08–1.35; I2 = 17.3%, p = 0.304) to experience incident CVD or die from it than people who regularly consumed breakfast. Also, the risk of all-cause death was 32% higher (HR 1.32, 95% CI 1.17–1.48; I2 = 7.6%, p = 0.339) in people who regularly skipped breakfast than in people who regularly consumed breakfast. However, the definition of skipping breakfast was heterogenous and adjustment for confounders varied significantly. Therefore, residual confounding could not be ruled out and caution is required in the interpretation of the findings. Hence, large prospective studies with a consistent definition of skipping breakfast, and conducted across different populations, are needed to provide more robust evidence of the health effects of skipping breakfast.
Prognostic value of preoperative hematological markers combined with molecular pathology in patients with diffuse gliomas

The prediction of clinical outcome for patients with infiltrative gliomas is challenging. Although preoperative hematological markers have been proposed as predictors of survival in glioma and other cancers, systematic investigations that combine these data with other relevant clinical variables are needed to improve prognostic accuracy and patient outcomes. We investigated the prognostic value of preoperative hematological markers, alone and in combination with molecular pathology, for the survival of 592 patients with Grade II-IV diffuse gliomas. On univariate analysis, increased neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and monocyte-to-lymphocyte ratio (MLR), and decreased albumin-to-globulin ratio (AGR), all predicted poor prognosis in Grade II/III gliomas. Multivariate analysis incorporating tumor status based on the presence of IDH mutations, TERT promoter mutations, and 1p/19q codeletion showed that in lower-grade gliomas, high NLR predicted poorer survival for the triple-negative, IDH mutation only, TERT mutation only, and IDH and TERT mutation groups. NLR was an independent prognostic factor in Grade IV glioma. We therefore propose a prognostic model for diffuse gliomas based on the presence of IDH and TERT promoter mutations, 1p/19q codeletion, and NLR. This model classifies lower-grade gliomas into nine subgroups that can be combined into four main risk groups based on survival projections.
CMOS-Compatible, Flexible, Intracortical Neural Probes

Flexible intracortical neural probes elicit a lower foreign body response when compared to rigid implants. However, by incorporating complementary metal-oxide-semiconductor (CMOS) circuitry, silicon-based neural probes can offer an improved scalability and more functionalities than any other currently available technology. Objective: Our goal is the development of a novel neural probe that combines flexibility with the functionalities of active CMOS-based probes. Methods: We interface CMOS-based probe tips of only a few millimeters in length with flexible polyimide cables, which enable the complete implantation of the tips into brain tissue. The multilayer platinum metallization of the cables is patterned using a novel combination of ion beam and plasma etching. Implantation of the flexible probes is verified in brain models using stiff insertion shuttles. Result: We assembled neural probes from passive and active tips as short as 1.5 mm and less than 180 μm in width. Active probes feature electrode arrays with 72 recording sites and multiplexing to 16 parallel output lines. We reliably patterned cables with signal lines of 2 μm in width and 3 μm in spacing. Ion beam etching deteriorated the composition of the polyimide substrate and its resistance to around 1 kΩ. An additional plasma treatment re-established high insulation resistances and recovered the chemical composition. Probes were successfully implanted to a depth of 7 mm using insertion shuttles and withstood forces of 63 mN. Conclusions: This study presents the methods required for the fabrication and application of a new generation of neural probes. Significance: The synergetic approach surpasses the limitation of each individual probe technology and should be considered in future developments.
The modernisation of HIV and AIDS’ nomenclatures in Nigeria’s majorlanguages

Although the level of awareness of HIV has significantly improved over the past decade following the coordinated activities of the National Agency for the Control of AIDS (NACA), Nigeria still remains one of the most burdened countries in the world with about 3 million people living with HIV. Increasing enlightenment campaigns on HIV and AIDS have not been able to achieve remarkable behaviour change as a result of the non-use of appropriate nomenclatures. Given the low literacy rate of Nigerians in English (about 61% based on UNESCO Institute for Statistics), communication strategies can only be effective when indigenous Nigerian languages have standardised and appropriate nomenclatures for HIV and AIDS. This study argues that the use of appropriate terms in the local languages in referring to HIV and AIDS is capable of reducing the stigmatisation and discrimination of people living with HIV and AIDS, and consequently reduce the spread of HIV through behaviour change. Accordingly, the study embarks on the lexical modernisation of HIV and AIDS nomenclatures in Nigeria’s three major languages (i.e. Hausa, Igbo and Yoruba) in line with current developments around the world in the management of the two health conditions.
The Prognosis Value of PIWIL1 and PIWIL2 Expression in Pancreatic Cancer

Pancreatic cancer is a highly aggressive manifestation of cancer, and currently presents poor clinical outcome due to its late diagnosis with metastasic disease. Surgery is the only approach with a curative intend; however, the survival rates seen in this type of patient are still low. After surgery, there is a lack of predictive prognosis biomarkers to predict treatment response and survival to establish a personalized medicine. Human P-element-induced wimpy testis 1 (PIWIL1) and P-element-induced wimpy testis 2 (PIWIL2) proteins act as protectors of germline, and their aberrant expression has been described in several types of tumors. In this study, we aimed to assess an association between PIWIL1 and PIWIL2 expression and the prognosis of biliopancreatic cancer patients. For this, we analyzed protein expression in complete resected tumor samples, and found a significant association between PIWIL2 expression and both progression-free and overall survival (p = 0.036 and p = 0.012, respectively). However, PIWIL2 expression was significantly associated with progression-free survival (p = 0.029), and overall survival (p = 0.025) of such tumors originated in the pancreas, but not in the bile duct or ampulla of Vater. Further analysis revealed that PIWIL1 and PIWIL2, at both mRNA and protein expression levels, correlated positively with factors associated to the progenitor molecular subtype of pancreatic cancer. Based on these findings, PIWIL1 and PIWIL2 expression may be considered a potential prognostic biomarker for resectable pancreatic cancer and may serve to guide subsequent adjuvant treatment decisions.