Miracle-dz/UniFAR-FTUs huggingface dataset:
Revealing Genomic Insights of the Unexplored Porcine Pathogen Actinobacillus pleuropneumoniae Using Whole Genome Sequencing

Pleuropneumonia is one of the most relevant respiratory infections in the swine industry. Despite Actinobacillus pleuropneumoniae (APP) being one of the most important pathogens in the pig production, this is the first comparative study including all available whole genome sequencing data from NCBI. ABSTRACT Actinobacillus pleuropneumoniae (APP) is the causative agent of pleuropneumonia in pigs, one of the most relevant bacterial respiratory diseases in the swine industry. To date, 19 serotypes have been described based on capsular polysaccharide typing with significant virulence dissimilarities. In this study, 16 APP isolates from Spanish origin were selected to perform antimicrobial susceptibility tests and comparative genomic analysis using whole genome sequencing (WGS). To obtain a more comprehensive worldwide molecular epidemiologic analyses, all APP whole genome assemblies available at the National Center for Biotechnology Information (NCBI) at the time of the study were also included. An in-house in silico PCR approach enabled the correct serotyping of unserotyped or incorrectly serotyped isolates and allowed for the discrimination between serotypes 9 and 11. A pangenome analysis identified the presence or absence of gene clusters to be serotype specific, as well as virulence profile analyses targeting the apx operons. Antimicrobial resistance genes were correlated to the presence of specific plasmids. Altogether, this study provides new insights into the genetic variability within APP serotypes, correlates phenotypic tests with bioinformatic analyses and manifests the benefits of populated databases for a better assessment of diversity and variability of relatively unknown pathogens. Overall, genomic comparative analysis enhances the understanding of transmission and epidemiological patterns of this species and suggests vertical transmission of the pathogen, including the resistance genes, within the Spanish integrated systems. IMPORTANCE Pleuropneumonia is one of the most relevant respiratory infections in the swine industry. Despite Actinobacillus pleuropneumoniae (APP) being one of the most important pathogens in the pig production, this is the first comparative study including all available whole genome sequencing data from NCBI. Moreover, this study also includes 16 APP isolates of Spanish origin with known epidemiological relationships through vertical integrated systems. Genomic comparisons provided a deeper understanding of molecular and epidemiological knowledge between different APP serotypes. Furthermore, determination of resistance and toxin profiles allowed correlation with the presence of mobile genetic elements and specific serotype, respectively.
Health care costs related to hepatitis B in Finland are mostly due to chronic infections: a register-based study

Abstract Background Finland is among the countries with low hepatitis B endemicity. We evaluate the hepatitis B-related disease and economic burden needed for evidence-based immunisation policy decision-making. Methods Hepatitis B-related cases in 2004–2012 were retrieved from population-based nationwide registers. We evaluated the incidence, health care resource use, health care costs, and life years lost due to hepatitis B-related outcomes. An episode of care was constructed from each individual’s hepatitis B-related events retrieved from individually linkable registers. Results The mean health care costs per an acute hepatitis B case were €450 (SD 240), €2030 (SD 350), and €5400 (SD 3370) in those aged 0–14, 15–64, and ≥65 years, respectively. For chronic infection, the mean cost per case among Finnish-born individuals was €990 and among foreign-born €1360. The costs per case of liver cirrhosis were €15,350 and liver cancer €19,080. In addition, the annual antiviral medication costs per case receiving antiviral medication were €4710 to €5530. Annually <10% of the chronic and approximately 20% of liver cirrhosis cases received antiviral medication. We identified annually 21 acute, 264 chronic, three liver cirrhosis, and four liver cancer cases and 63.7 life years lost due to hepatitis B per 5.3 million inhabitants. The total annual health care costs were €1.2 million of which 60% were antiviral medication costs and 86% accounted for chronic hepatitis B. Conclusions When planning prevention of hepatitis B infection, it is pivotal to notice that the overall disease and economic burden due to hepatitis B is mostly due to chronic infection.
Fixed-bed reactor packed with pumice-supported TiO2 for the treatment of polluted water by solar-driven photocatalytic oxidation

Abstract A bench-scale tubular photo-reactor was built to evaluate the solar-driven TiO2–based photocatalytic degradation of synthetic polluted water samples. The reactor was designed as a compound-parabolic-collector and operated in batch mode using TiO2 P25 immobilized on a bed of pumice. The immobilization of TiO2 on pumice was carried out using a facile dip impregnation method followed by heat treatment. The obtained material was characterized by SEM, EDS, XRD, and nitrogen adsorption. It was possible to impregnate up to 68.5 mg of TiO2 per gram of pumice stones of 8–14 mm. Conversions of up to 35–40 and 62–69%, after 4 h of treatment and UV doses of 20.8 ± 3.5 kJ L−1, were achieved when the catalyst was used immobilized on pumice stone and in the form of a suspension, respectively. The stability and reusability of the catalyst–coated support was tested through a series of consecutive photocatalytic experiments. After four consecutive runs, the immobilized catalyst showed a decrease in its photoactivity leading to removal levels of 23%.
How Rice Fights Pandemics: Nature–Crop–Human Interactions Shaped COVID-19 Outcomes

Wealthy nations led health preparedness rankings in 2019, yet many poor nations controlled COVID-19 better. We argue that a history of rice farming explains why some societies did better. We outline how traditional rice farming led to tight social norms and low-mobility social networks. These social structures helped coordinate societies against COVID-19. Study 1 compares rice- and wheat-farming prefectures within China. Comparing within China allows for controlled comparisons of regions with the same national government, language family, and other potential confounds. Study 2 tests whether the findings generalize to cultures globally. The data show rice-farming nations have tighter social norms and less-mobile relationships, which predict better COVID outcomes. Rice-farming nations suffered just 3% of the COVID deaths of nonrice nations. These findings suggest that long-run cultural differences influence how rice societies—with over 50% of the world’s population—controlled COVID-19. The culture was critical, yet the preparedness rankings mostly ignored it.
Attention Deficit Hyperactivity Disorder Symptoms, Smoking Initiation, and Social Integration among Adolescents

This observational, longitudinal study’s purpose was to investigate whether social network integration has a moderating effect on smoking initiation among those with attention deficit hyperactivity disorder (ADHD). Data were drawn from the National Longitudinal Study of Adolescent to Adult Health, a nationally representative longitudinal dataset. Social network and smoking data were collected in schools, with a 6-year follow-up that included ADHD symptoms and reported smoking. Social integration was measured as peer friendship nominations (degree) and the influence of an individual on the entire social network (centrality). Multilevel logistic regression found a main effect for ADHD symptoms and low numbers of friendship nominations on smoking initiation, but social network measures were not significant moderators of the relationship between ADHD symptoms and smoking initiation among adolescents. Further investigation of the drivers of smoking initiation among those with ADHD is warranted.
Persistence of Anxiety/Depression Symptoms in Early Adolescence: A Prospective Study of Daily Life Stress, Rumination, and Daytime Sleepiness in a Genetically Informative Cohort

Abstract In this prospective study of mental health, we examine the influence of three interrelated traits — perceived stress, rumination, and daytime sleepiness — and their association with symptoms of anxiety and depression in early adolescence. Given the known associations between these traits, an important objective is to determine the extent to which they may independently predict anxiety/depression symptoms. Twin pairs from the Queensland Twin Adolescent Brain (QTAB) project were assessed on two occasions (N = 211 pairs aged 9−14 years at baseline and 152 pairs aged 10−16 years at follow-up). Linear regression models and quantitative genetic modeling were used to analyze the data. Prospectively, perceived stress, rumination, and daytime sleepiness accounted for 8−11% of the variation in later anxiety/depression; familial influences contributed strongly to these associations. However, only perceived stress significantly predicted change in anxiety/depression, accounting for 3% of variance at follow-up after adjusting for anxiety/depression at baseline, although it did not do so independently of rumination and daytime sleepiness. Bidirectional effects were found between all traits over time. These findings suggest an underlying architecture that is shared, to some degree, by all traits, while the literature points to hypothalamic–pituitary–adrenal (HPA) axis and/or circadian systems as potential sources of overlapping influence and possible avenues for intervention.
COVID-19 vaccination and mask wearing behaviors in the United States, August 2020 - June 2021

ABSTRACT Background During the rollout of COVID-19 vaccination, many states relaxed mask wearing guidance for those vaccinated. The aim of this study was to examine the association between vaccination status and mask wearing behaviors. Methods Seven waves of surveys (n = 6721) were conducted between August 2020 and June 2021. Participants were asked about initiation of COVID-19 vaccination and mask wearing behavior at work/school or a grocery store. Odds ratios (ORs) and 95% confidence intervals (CIs) from logistic regression were used to estimate associations between vaccination status and mask wearing at work/school and at the grocery store. Results Between April and June 2021, mask wearing at work or school declined among both those vaccinated (74% to 49%) and unvaccinated (46% to 35%). There was a similar decline for mask wearing at grocery stores. The odds of wearing a mask were 2.35 times higher at work/school (95% CI: 1.82, 3.04) and 1.65 times at a grocery store (95% CI: 1.29, 2.11) among the vaccinated compared to unvaccinated. Conclusion Mask wearing decreased after mask guidelines were relaxed, with consistently lower mask wearing among the unvaccinated, indicating a reluctance among the unvaccinated to adopt COVID-19 risk reduction behaviors.
Does substrate matter in the deep sea? A comparison of bone, wood, and carbonate rock colonizers

Continental margins host methane seeps, animal falls and wood falls, with chemosynthetic communities that may share or exchange species. The goal of this study was to examine the existence and nature of linkages among chemosynthesis-based ecosystems by deploying organic fall mimics (bone and wood) alongside defaunated carbonate rocks within high and lesser levels of seepage activity for 7.4 years. We compared community composition, density, and trophic structure of invertebrates on these hard substrates at active methane seepage and transition (less seepage) sites at Mound 12 at ~1,000 m depth, a methane seep off the Pacific coast of Costa Rica. At transition sites, the community composition on wood and bone was characteristic of natural wood- and whale-fall community composition, which rely on decay of the organic substrates. However, at active sites, seepage activity modified the relationship between fauna and substrate, seepage activity had a stronger effect in defining and homogenizing these communities and they depend less on organic decay. In contrast to community structure, macrofaunal trophic niche overlap between substrates, based on standard ellipse areas, was greater at transition sites than at active sites, except between rock and wood. Our observations suggest that whale- and wood-fall substrates can function as stepping stones for seep fauna even at later successional stages, providing hard substrate for attachment and chemosynthetic food.
Understanding the multidimensional cognitive deficits of logopenic variant primary progressive aphasia

Abstract The logopenic variant of primary progressive aphasia is characterized by early deficits in language production and phonological short-term memory, attributed to left-lateralized temporoparietal, inferior parietal and posterior temporal neurodegeneration. Despite patients primarily complaining of language difficulties, emerging evidence points to performance deficits in non-linguistic domains. Temporoparietal cortex, and functional brain networks anchored to this region, are implicated as putative neural substrates of non-linguistic cognitive deficits in logopenic variant primary progressive aphasia, suggesting that degeneration of a shared set of brain regions may result in co-occurring linguistic and non-linguistic dysfunction early in the disease course. Here, we provide a Review aimed at broadening the understanding of logopenic variant primary progressive aphasia beyond the lens of an exclusive language disorder. By considering behavioural and neuroimaging research on non-linguistic dysfunction in logopenic variant primary progressive aphasia, we propose that a significant portion of multidimensional cognitive features can be explained by degeneration of temporal/inferior parietal cortices and connected regions. Drawing on insights from normative cognitive neuroscience, we propose that these regions underpin a combination of domain-general and domain-selective cognitive processes, whose disruption results in multifaceted cognitive deficits including aphasia. This account explains the common emergence of linguistic and non-linguistic cognitive difficulties in logopenic variant primary progressive aphasia, and predicts phenotypic diversification associated with progression of pathology in posterior neocortex.
Deletion of the P/Q-Type Calcium Channel from Serotonergic Neurons Drives Male Aggression in Mice

Aggressive behavior is one of the most conserved social interactions in nature and serves as a crucial evolutionary trait. Serotonin (5-HT) plays a key role in the regulation of our emotions, such as anxiety and aggression, but which molecules and mechanisms in the serotonergic system are involved in violent behavior are still unknown. In this study, we show that deletion of the P/Q-type calcium channel selectively from serotonergic neurons in the dorsal raphe nuclei (DRN) augments aggressive behavior in male mice, while anxiety is not affected. These mice demonstrated increased induction of the immediate early gene c-fos and in vivo serotonergic firing activity in the DRN. The ventrolateral part of the ventromedial hypothalamus is also a prominent region of the brain mediating aggression. We confirmed a monosynaptic projection from the DRN to the ventrolateral part of the ventromedial hypothalamus, and silencing these projections with an inhibitory designer receptor exclusively activated by a designer drug effectively reduced aggressive behavior. Overall, our findings show that deletion of the P/Q-type calcium channel from DRN neurons is sufficient to induce male aggression in mice and regulating its activity may serve as a therapeutic approach to treat violent behavior. SIGNIFICANCE STATEMENT In this study, we show that P/Q-type calcium channel is mediating aggression in serotonergic neurons from the dorsal raphe nucleus via monosynaptic projections to the ventrolateral part of the ventromedial hypothalamus. More importantly, silencing these projections reduced aggressive behavior in mice and may serve as a therapeutic approach for treating aggression in humans.
Measuring extremist archetypes: Scale development and validation

Previous work has often disregarded the psychological heterogeneity of violent extremists. This research aimed to contribute to a more nuanced understanding of the psychological diversity of violent extremists. Based on qualitative work, we developed and validated the Extremist Archetypes Scale, identifying five distinct archetype dimensions: “adventurer,” “fellow traveler,” “leader,” “drifter” and “misfit. ” Study 1 identified five dimensions among White majority members (N = 307), four of which were related to extremist violent intentions and which dissociated in terms of sociopolitical ideologies and intergroup attitudes. Preregistered Study 2 (N = 308) confirmed the scale’s five-factor solution in another sample of White majority members, replicated relationships with violent intentions, and demonstrated the dimensions’ distinct personality correlates. As in Study 1, the archetype dimensions had positive associations with extremist violent intentions and tapped onto different psychological profiles in terms of major personality traits. Study 3 (N = 317) replicated these results in a sample of Muslim minority members. Measurement equivalence was established across gender, age, political orientation, and ethnicity (majority and minority).
Hsa_circ_0097922 promotes tamoxifen resistance and cell malignant behaviour of breast cancer cells by regulating ACTN4 expression via miR‐876‐3p

An increasing number of findings have verified the critical roles of circular RNAs (circRNAs) in human cancers, and chemotherapy resistance is a poor prognostic factor for breast cancer (BC). This study is designed to explore the function of hsa_circ_0097922 in the tamoxifen resistance of breast cancer. Hsa_circ_0097922, microRNA‐876‐3p (miR‐876‐3p), and alpha‐actinin 4 (ACTN4) level were detected by real‐time quantitative polymerase chain reaction (RT‐qPCR). Cell survival, proliferation, apoptosis, migration and invasion were detected by Cell Counting Kit‐8 (CCK‐8), 5‐ethynyl‐2′‐deoxyuridine (EdU), and flow cytometry, wound healing and Transwell assays. Protein levels of proliferating cell nuclear antigen (PCNA), B‐cell lymphoma‐2 (Bcl‐2), cleaved caspase 3, matrix metalloproteinase 9 (MMP9), and ACTN4 were determined using western blot assay. Using bioinformatics software, the binding between miR‐876‐3p and hsa_circ_0097922 or ACTN4 was predicted, followed by confirmation by RNA immunoprecipitation (RIP) and RNA pull‐down assays. A xenograft tumour model in vivo analysed the biological role of hsa_circ_0097922 on BC tumour growth and drug resistance. Hsa_circ_0097922 and ACTN4 were increased, and miR‐876‐3p was decreased in tamoxifen resistance BC cells. Moreover, hsa_circ_0097922 knockdown can block BC cell malignant behaviour and tamoxifen resistance in vitro. Mechanically, hsa_circ_0097922 acted as a sponge of miR‐876‐3p to regulate ACTN4 expression. Hsa_circ_0097922 silencing increased the drug sensitivity of BC in vivo. Hsa_circ_0097922 might regulate BC cell malignant behaviour and tamoxifen resistance partly by regulating the miR‐876‐3p/ACTN4 axis, hinting at a promising therapeutic target for the BC treatment.
Magnetic Resonance Imaging Characteristics Associated with Treatment Success from Basivertebral Nerve Ablation: An Aggregated Cohort Study of Multicenter Prospective Clinical Trials Data

Abstract Objective Investigate associations between endplate and motion segment magnetic resonance imaging (MRI) characteristics and treatment outcomes following basivertebral nerve radiofrequency ablation (BVN RFA) in patients with clinically suspected vertebral endplate pain (VEP). Design Aggregated cohort study of 296 participants treated with BVN RFA from three prospective clinical trials. Methods Baseline MRI characteristics were analyzed using stepwise logistic regression to identify factors associated with treatment success. Predictive models used three definitions of treatment success: (1) ≥50% low back pain (LBP) visual analog scale (VAS), (2) ≥15-point Oswestry Disability Index (ODI), and (3) ≥50% VAS or ≥15-point ODI improvements at 3-months post-BVN RFA. Results The presence of lumbar facet joint fluid (odds ratio [OR] 0.586) reduced the odds of BVN RFA treatment success in individuals with clinically suspected VEP. In patients with a less advanced degenerative disc disease (DDD) profile, a > 50% area of the endplate with bone marrow intensity changes (BMIC) was predictive of treatment success (OR 4.689). Both regressions areas under the curve (AUCs) were under 70%, indicating low predictive value. All other vertebral endplate, intervertebral disc, nerve roots facet joint, spinal segmental alignment, neuroforamina, lateral recesses, and central canal MRI characteristics were not associated with BVN RFA success. Conclusions In patients with vertebrogenic low back pain with Modic changes, the presence of degenerative findings of the anterior and posterior column was not associated with a clinically important impact on BVN RFA treatment success. None of the models demonstrated strong predictive value, indicating that the use of objective imaging biomarkers (Type 1 and/or 2 Modic changes) and a correlating presentation of pain remain the most useful patient selection factors for BVN RFA.
Epigenetic mechanisms and potential therapeutic targets in stroke

Accumulating evidence indicates a central role for epigenetic modifications in the progression of stroke pathology. These epigenetic mechanisms are involved in complex and dynamic processes that modulate post-stroke gene expression, cellular injury response, motor function, and cognitive ability. Despite decades of research, stroke continues to be classified as a leading cause of death and disability worldwide with limited clinical interventions. Thus, technological advances in the field of epigenetics may provide innovative targets to develop new stroke therapies. This review presents the evidence on the impact of epigenomic readers, writers, and erasers in both ischemic and hemorrhagic stroke pathophysiology. We specifically explore the role of DNA methylation, DNA hydroxymethylation, histone modifications, and epigenomic regulation by long non-coding RNAs in modulating gene expression and functional outcome after stroke. Furthermore, we highlight promising pharmacological approaches and biomarkers in relation to epigenetics for translational therapeutic applications.