Miracle-dz/UniFAR-FTUs huggingface dataset:
The First Complete Mitochondrial Genome of Lachninae Species and Comparative Genomics Provide New Insights into the Evolution of Gene Rearrangement and the Repeat Region

Simple Summary The Lachninae is a unique aphid lineage with some particular characteristics. The first complete mitochondrial genome from this subfamily is reported here, with Stomaphis sinisalicis as a representative. The gene arrangement of the new mitogenome differs greatly from the normal gene order of other aphids and insects. The existence of a tandem repeat region in the Lachninae mitogenome may suggest it is probably an ancient feature of aphid mitogenomes. Phylogenetic analysis indicates a basal position of Lachninae within Aphididae. Abstract Complete mitochondrial genomes are valuable resources for different research fields such as genomics, molecular evolution and phylogenetics. The subfamily Lachninae represents one of the most ancient evolutionary lineages of aphids. To date, however, no complete Lachninae mitogenome is available in public databases. Here we report the Stomaphis sinisalicis mitogenome, representing the first complete mitogenome of Lachninae. The S. sinisalicis mitogenome is consist of 13 protein-coding genes (PCGs), two rRNA genes (rRNAs), 22 tRNA genes (tRNAs), a control region and a large tandem repeat region. Strikingly, the mitogenome exhibits a novel, highly rearranged gene order between trnE and nad1 compared with that of other aphids. The presence of repeat region in the basal Lachninae may further indicate it is probably an ancestral feature of aphid mitogenomes. Collectively, this study provides new insights on mitogenome evolution and valuable data for future comparative studies across different insect lineages.
Engagement, Responsibility, Collaboration, and Abandonment: Nurses’ Experiences of Assessing Suicide Risk in Psychiatric Inpatient Care

Abstract Suicide risk assessment is a complex task for nurses working in psychiatric inpatient care. This study explored psychiatric inpatient nurses’ experiences of assessing suicide risk. A qualitative design was used, and 10 interviews were subjected to qualitative content analysis. Nurses described suicide risk assessments as requiring them to create caring alliances and to take responsibility. Collaborating with colleagues was another part of nurses’ experiences, as was feeling abandoned. To make the assessment safely, nurses need a combination of caring alliances, support from colleagues, clear guidelines, training and time for collegial reflection to create a supportive working climate.
Cutting Edge: Mouse SARS-CoV-2 Epitope Reveals Infection and Vaccine-Elicited CD8 T Cell Responses

Key Points N219-227 is a dominant B6 mouse epitope of SARS-CoV-2 nucleoprotein. SARS-CoV-2 infection in hACE2 mice and humans promotes CD8 T cells against N219-227. Vaccine route affects the location and number of SARS-CoV-2 N memory CD8 T cells. Visual Abstract The magnitude of SARS-CoV-2–specific T cell responses correlates inversely with human disease severity, suggesting T cell involvement in primary control. Whereas many COVID-19 vaccines focus on establishing humoral immunity to viral spike protein, vaccine-elicited T cell immunity may bolster durable protection or cross-reactivity with viral variants. To better enable mechanistic and vaccination studies in mice, we identified a dominant CD8 T cell SARS-CoV-2 nucleoprotein epitope. Infection of human ACE2 transgenic mice with SARS-CoV-2 elicited robust responses to H2-Db/N219-227, and 40% of HLA-A*02+ COVID-19 PBMC samples isolated from hospitalized patients responded to this peptide in culture. In mice, i.m. prime-boost nucleoprotein vaccination with heterologous vectors favored systemic CD8 T cell responses, whereas intranasal boosting favored respiratory immunity. In contrast, a single i.v. immunization with recombinant adenovirus established robust CD8 T cell memory both systemically and in the respiratory mucosa.
COVID‐19 in patients recovering from cardiac surgery: A surprising mild disease course

We describe the baseline, operative, and postoperative features of a group of 18 patients who contracted the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV2) infection in a rehabilitation facility after cardiac surgery, and present some potential explanations for the surprisingly benign course of the COVID‐19 in this cohort.
Hexavalent chromium removal from water using chitosan-Fe0 nanoparticles

Chitosan-Fe0 nanoparticles (chitosan-Fe0) were prepared using nontoxic and biodegradable chitosan as a stabilizer. Laboratory batch and column experiments were conducted to investigate the feasibility of using chitosan-Fe0 for in situ reductive removal of Cr(VI) from water. Batch kinetic tests indicated that the overall disappearance of Cr(VI) may include both physical adsorption of Cr(VI) onto the chitosan-Fe0 surface and subsequent reduction of Cr(VI) to Cr(III). The rate of reduction of Cr(VI) to Cr(III) can be expressed by a pseudo-first-order reaction kinetics and the rate constants increase with the increase in iron loading. Column experiments indicated that the chitosan-Fe0 were highly deliverable in the column. When the column was treated with Cr(VI) -contaminated deionized water, the removal capacity of chitosan-Fe0 was found to be about 32 mg Cr/g Fe(0). A 25% drop in the Cr(VI) removal capacity was found when treated with Cr(VI)-contaminated surface water.
Search for triorganotins along the Mar del Plata (Argentina) marine coast: finding of tributyltin in egg capsules of a snail Adelomelon brasiliana (Lamarck, 1822) population showing imposex effects

Cases of imposex were clearly identified in Adelomelon brasiliana living in the Mar del Plata (Argentina) coastal area; percentages as high as 50.0% were determined among the samples studied. These were the first reported cases of ocurrence of imposex in this type of gastropod. Since this is one of the known tributyltin (TBTs) effects, and no previous reports of determination of TBTs in gastropods eggs were found, methods were developed for the speciation and quantitative determination of organotins in A. brasiliana egg capsules. Determination of organotins in samples collected in the Mar del Plata area showed contents of tributyltin chloride (TBT) as high as 400 ng l−1 in water and 6.50 µg g−1 in sediments of areas of intensive boat traffic. The results showed the presence of TBT in the egg capsules of A. brasiliana at three different instars (range 0.264–1.86 µg per egg). As far as we know, this is the first report of the finding of TBT in gastropod egg capsules. Copyright © 2004 John Wiley & Sons, Ltd.
Mitochondrial DNA profiling reveals two lineages of sun bears in East and West Malaysia.

Sun bear populations are fragmented and at risk from habitat loss and exploitation for body parts. These threats are made worse by significant gaps in knowledge of sun bear population genetic diversity, population connectivity, and taxonomically significant management units. Using a complete sun bear mitochondrial genome, we developed a set of mitochondrial markers to assess haplotype variation and the evolutionary history of sun bears from Peninsular (West) Malaysia, and Sabah (East Malaysia). Genetic samples from 28 sun bears from Peninsular Malaysia, 36 from Sabah, and 18 from Thailand were amplified with primers targeting a 1,800 bp region of the mitochondrial genome including the complete mitochondrial control region and adjacent genes. Sequences were analyzed using phylogenetic methods. We identified 51 mitochondrial haplotypes among 82 sun bears. Phylogenetic and network analyses provided strong support for a deep split between Malaysian sun bears and sun bears in East Thailand and Yunnan province in China. The Malaysian lineage was further subdivided into two clades: Peninsular Malaysian and Malaysian Borneo (Sabah). Sun bears from Thailand occurred in both Sabah and Peninsular Malaysian clades. Our study supports recent findings that sun bears from Sundaland form a distinct clade from those in China and Indochina with Thailand possessing lineages from the three clades. Importantly we demonstrate a more recent and clear genetic delineation between sun bears from the Malay Peninsula and Sabah indicating historical barriers to gene flow within the Sundaic region.
Characteristics and etiologies of hepatocellular carcinoma in patients without cirrhosis: When East meets West

Background/Aims A recent study from the United States reported that nearly 12% of hepatocellular carcinomas (HCCs) occurred in patients without cirrhosis. Non-alcoholic fatty liver disease (NAFLD) was the most common liver disease in these patients. We aim to evaluate the characteristics, etiologies, and outcomes of cases of non‐cirrhotic HCC in East Asia, where there is a higher prevalence of hepatitis B virus (HBV)-associated non-cirrhotic HCC. Methods This retrospective study consecutively enrolled de novo HCC patients managed at our institution from 2011 to 2017. The presence of cirrhosis was assessed by histology; if histology was not available, it was assessed by image study. Results 2055 patients with HCC were enrolled in this study. Among them, 529 (25.7%) were non-cirrhotic. The non-cirrhotic patients were younger (60.9 vs. 62.5 years, p = 0.006), included a greater proportion of males (78.1% vs. 71.3%, p = 0.002), and had a lower body mass index (24.3 vs. 25.3 kg/m2, p<0.001) than the cirrhotic patients. Among the non‐cirrhotic patients, HBV was the most common liver disease (49.0%). The patients with non‐cirrhotic HCC had larger tumors (5.9 vs. 4.7 cm, p<0.001), underwent liver resection at a higher rate (66.0% vs. 17.4%, p<0.001), and had better overall survival than the cirrhotic HCC patients (median 5.67 vs. 2.83 years, p<0.001). Conclusions Nearly 26% of the HCCs occurred in patients without cirrhosis. HBV was the most common liver disease in these patients, and the survival was better in the non‐cirrhotic patients than the cirrhotic patients.
Photografting of vinyl polymers onto ultrafine inorganic particles: Photopolymerization of vinyl monomers initiated by AZO groups introduced onto these surfaces

The photografting of polymers onto ultrafine inorganic particles, such as silica and titanium oxide, initiated by azo groups introduced onto these surfaces was investigated. The introduction of azo groups onto the particles was achieved by the reaction of 4,4′-azobis(4-cyanopentanoic acid) with surface isocyanate groups, which were introduced by the treatment with tolylene 2,4-diisocyanate. It was found that the photopolymerization of vinyl monomers, such as methyl methacrylate (MMA), styrene, and N-vinylcarbazole, is initiated by ultrafine particles having azo groups. The corresponding polymers were effectively grafted onto these surfaces through the propagation of the polymer from the surface radicals formed by the photodecomposition of the azo groups: e.g., the percentage of grafting of PMMA and polystyrene onto silica was reached to 112 and 176%, respectively. The percentage of grafting onto silica in the graft polymerization initiated by photodecomposition of surface azo groups was much larger than that initiated by thermal decomposition. Polymer-grafted ultrafine particles thus obtained gave a stable colloidal dispersion in good solvents for the grafted chain. © 1994 John Wiley & Sons, Inc.
Association Analysis in Young and Middle-Aged Mothers—Relation between Expression of Cardiovascular Disease Associated MicroRNAs and Abnormal Clinical Findings

The principal goal of the study was to map common postpartal alterations in gene expression of microRNAs associated with diabetes/cardiovascular/cerebrovascular diseases induced by most frequently occurring pregnancy-related complications (gestational hypertension, preeclampsia, fetal growth restriction, gestational diabetes mellitus, preterm prelabor rupture of membranes, or spontaneous preterm birth). In addition, the association analyses between individual abnormal clinical findings (overweight/obesity, central obesity, hypertension, on blood pressure treatment, history of infertility treatment, actual hormonal contraceptive use, the presence of trombophilic gene mutations, actual smoking status, increased serum levels of total cholesterol, HDL (high density lipoprotein) cholesterol, LDL (low density lipoprotein) cholesterol, triglycerides, lipoprotein A, CRP (C-reactive protein), and uric acid, and increased plasma levels of homocysteine) and microRNA expression levels were performed in mothers with respect/regardless to previous course of gestation. The prior exposure to gestational hypertension, preeclampsia, fetal growth restriction, gestational diabetes mellitus, preterm prelabor rupture of membranes, or spontaneous preterm birth caused that a significant proportion of mothers (52.42% at 90.0% specificity) had substantially altered microRNA expression profile, which might originate lifelong cardiovascular risk. 26 out of 29 tested microRNAs were up-regulated in mothers with a history of such complicated pregnancies. MicroRNA expression profiles were also able to differentiate between mothers with normal and abnormal clinical findings (BMI (body mass index), waist circumference, systolic blood pressure, on blood pressure treatment, history of infertility treatment, and the presence of trombophilic gene mutations) irrespective of previous course of gestation. The treatment of hypertension even intensified upregulation of some microRNAs (miR-24-3p, and miR-342-3p) already present in women after complicated pregnancies. Newly, the presence of overweight/obesity (miR-155-5p), systolic hypertension (miR-92a-3p, and miR-210-3p), treatment for infertility (miR-155-5p), and treatment for hypertension (miR-210-3p) induced upregulation of several microRNAs. In general, mothers after complicated pregnancies are at increased risk of development of cardiovascular complications. Especially those mothers indicated to have postpartally altered microRNA expression profiles might be considered as a highly risky group that would benefit from dispensarization and implementation of primary prevention strategies.
School-based obesity interventions in the metropolitan area of Rio De Janeiro, Brazil: pooled analysis from five randomised studies

Abstract School-based studies, despite the large number of studies conducted, have reported inconclusive results on obesity prevention. The sample size is a major constraint in such studies by requiring large samples. This pooled analysis overcomes this problem by analysing 5926 students (mean age 11·5 years) from five randomised school-based interventions. These studies focused on encouraging students to change their drinking and eating habits, and physical activities over the one school year, with monthly 1-h sessions in the classroom; culinary class aimed at developing cooking skills to increase healthy eating and attempts to family engagement. Pooled intention-to-treat analysis using linear mixed models accounted for school clusters. Control and intervention groups were balanced at baseline. The overall result was a non-significant change in BMI after one school year of positive changes in behaviours associated with obesity. Estimated mean BMI changed from 19·02 to 19·22 kg/m2 in the control group and from 19·08 to 19·32 kg/m2 in the intervention group (P value of change over time = 0·09). Subgroup analyses among those overweight or with obesity at baseline also did not show differences between intervention and control groups. The percentage of fat measured by bioimpedance indicated a small reduction in the control compared with intervention (P = 0·05). This large pooled analysis showed no effect on obesity measures, although promising results were observed about modifying behaviours associated with obesity.
Single and Combined Effect of Acute Sleep Restriction and Mental Fatigue on Basketball Free-Throw Performance.

PURPOSE This study aimed to investigate the single and combined effects of sleep restriction (SR) and mental fatigue (MF) on free-throw (FT) performance among adult male basketball players. METHODS A total of 19 amateur male basketball players performed, in a randomized, counterbalanced, and crossover order, 2 identical experimental sessions separated by an interval of 1 week. The difference between the 2 sessions was in the quantity of sleep the night before the sessions, as follows: in one case, the participants followed their habitual sleep-wake routines; in the other session, they were forced to sleep not more than 5 hours. During the experimental sessions, the participants performed 60 basketball FTs on 2 occasions, separated by watching a basketball tactical video for 30 minutes designed to induce MF. As such, the FT test was completed in 4 different conditions: control, MF, SR, and SR and MF combined. RESULTS The participants registered a significantly lower total sleep time in acute SR (P < .001). The subjective rating of MF was lower in the control than in MF, SR, and SR and MF combined (P < .001). There were no differences between conditions for the subjective ratings of motivation. FT accuracy was higher in the control than in MF, SR, and SR and MF combined (P = .010), while no differences were observed between the 3 experimental conditions (all P > .05). CONCLUSION The results indicate that a combined effect of MF and SR induces a small reduction in basketball FT performance, similar to MF or SR alone.
The Effectiveness of Alcohol Impact Areas in Reducing Crime in Washington Neighborhoods.

BACKGROUND We evaluated the effectiveness of Alcohol Impact Areas (AIA) in reducing crime around off-premise alcohol outlets in 3 AIAs in Spokane and Tacoma, Washington, using an interrupted time series design with comparison groups. AIAs only exist in Washington and include designated areas in a city where specific brands of malt liquor are restricted. We hypothesized that mandatory restrictions on malt liquor sales in AIAs would be significantly associated with decreases in crime, especially less-serious crime. METHODS In Spokane and Tacoma, targets were 3 AIAs and 3 comparison areas with demographically similar neighborhoods without malt liquor restrictions in the same respective city. Nine different crime outcomes were evaluated: Part I selected crimes, Part II selected crimes (further split into nuisance crimes and other Part II crimes), assaults, vandalism, narcotics, disorderly conduct, and all selected crimes combined. Crime was typically compared 3 years prior to and 3 years following policy adoption using time series and negative-binomial modeling. Separate models were run for each area and each crime. RESULTS Study hypotheses were partially supported. Malt liquor restrictions in AIAs were associated with significant decreases in crime, particularly certain Part II crimes and assaults (simple and aggravated) in 12 of the 23 models. The strength of the observed associations varied by AIA. Average monthly crime counts across all crime categories decreased more in the Tacoma AIA than in Spokane AIAs, and average monthly crime decreased more in Spokane AIA 2 (East Central) than in AIA 1 (Downtown Core). Malt liquor restrictions were significantly associated with increases in disorderly conduct in the Tacoma AIA; the increase, however, was small. CONCLUSIONS Findings suggest that malt liquor policies such as AIAs may be one of a number of tools local officials can use to reduce alcohol-related crime in cities, especially less-serious crime.
Sialadenoma Papilliferum of the Bronchus: An Unrecognized Bronchial Counterpart of the Salivary Gland Tumor With Frequent BRAF V600E Mutations.

Sialadenoma papilliferum (SP) is a rare benign tumor of the salivary glands, and only 3 unequivocal cases of SP arising in the bronchus have been reported. We herein describe the histomorphologic and molecular features of 4 bronchial SP cases and discuss the differential diagnosis of this entity and the relationship with its clinicopathologic mimics, in particular, glandular papilloma and mixed squamous cell and glandular papilloma (GP/MP). We encountered 2 male and 2 female patients with bronchial SP (mean: 66.8 y old). All 4 tumors arose in the central bronchus and were characterized by a combination of surface exophytic endobronchial papillary proliferation and a submucosal multicystic component with complex architecture. The neoplastic epithelium consisted predominantly of nonciliated stratified columnar cells with ciliated, squamous, and mucinous cells present focally. While 2 tumors (50%) harbored a BRAF V600E mutation by molecular and immunohistochemical analysis, similar to GP/MP, no KRAS, HRAS, AKT1, or PIK3CA mutations were detected in any of the cases. Two patients were treated with limited resection, while 2 patients underwent lobectomy based on the diagnosis of adenocarcinoma or possible squamous cell carcinoma in situ in the preoperative biopsy. All survived without recurrence or metastasis for 23 to 122 months after treatment. SP can develop in the central bronchus as the bronchial counterpart of the salivary gland tumor and should be considered in the differential diagnosis of endobronchial tumors. In addition, some histologic resemblance and frequent BRAF V600E mutation raise the possibility of SP and GP/MP being on the same disease spectrum.
Extracellular Metabolism Sets the Table for Microbial Cross-Feeding

The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. SUMMARY The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.