Miracle-dz/UniFAR-FTUs huggingface dataset:
Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture

Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents, Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3’UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3’UTR architecture among different CHIKV lineages.
Reduction of traffic-related particulate matter by roadside plants: effect of traffic pressure and sampling height

Abstract Atmospheric particulate matters (PM) caused by urban traffic system put residents’ health at serious risk. As a method of phytoremediation to mitigate this risk, roadside plants show significant potential to remove PM from the air. However, the relationship between traffic pressure, height, and leaves’ capturing capacity is rarely reported. In this study, two common effective roadside plants (Hedera helix, Taxus baccata) with typical leaf shapes (broad and needle-leaved) were selected to explore the foliage capacity under high, middle and low traffic burden. A green wall covered by H. helix was tested to find out the relationship between heights and the amount of accumulated PM. Although the PM capturing capacity varied between different traffic pressures, needle-leaved species generally accumulated more PM than broad-leaved species. For PM10 capturing, needle-leaved species showed higher capacity under all traffic pressures except under the low traffic pressure. For PM2.5 capturing, needle-leaved species accumulated more PM only under the high traffic pressure. Needle-leaved plants were more sensitive to the change of traffic pressures, its PM capturing capacity changed notably between different traffic pressures because its leaf wax is more susceptible to be corroded. Leaf surface contact angle was slightly affected by the change of traffic pressure for broad-leaved species, but for needle-leaved species, it changed greatly. Leaf surface was the main zone for large PM capturing because the large PM was more likely to be stuck in grooves on the leaf surface, while leaf wax was mainly for fine PM absorption because PM with small sizes could adhere to the surface of the wax crystal. By comparing the amount of captured PM by leaf surface of urban roadside plants under different traffic pressures and height ranges, this study optimizes the benefits of roadside plants as traffic-related PM filter under different traffic conditions.
A Novel Bacterium-Like Particle Vaccine Displaying the MERS-CoV Receptor-Binding Domain Induces Specific Mucosal and Systemic Immune Responses in Mice

Middle East respiratory syndrome coronavirus (MERS-CoV), a new coronavirus that has been causing severe and fatal acute respiratory illnesses in humans since its outbreak in 2012, has raised public fear worldwide. The development of prophylactics and therapeutics is urgently needed to prevent and control MERS-CoV infections. In this study, a bacterium (Lactococcus lactis)-like particle (BLP) vaccine displaying the MERS-CoV receptor-binding domain (RBD) was developed, and gram-positive enhancer matrix (GEM) particles were used as substrates to externally bind to the MERS-CoV RBD through a protein anchor (PA). The designs included different numbers of lysin motif (LysM) repeats in the PAs linked by linkers (RBD-linker-PA2 (RLP2), RBD-linker-PA3 (RLP3) and RBD-PA3 (RP3)), and three LysM repeats and a linker in the fusion proteins increased the binding activity to the RBD. The specific immune responses were tested by intranasally immunizing mice with RLP3-GEM with or without the adjuvant GEL01. The results showed that GEL01-adjuvanted RLP3-GEM increased the systemic humoral, cellular and local mucosal immune responses in the mouse model, especially in the intestinal tract. The above results indicate that the MERS-CoV BLP product has the potential to be developed into a promising mucosal candidate vaccine to protect against MERS-CoV infections.
LONG-RUN EFFECT OF A DISASTER : DECOMPOSING REGION SPECIFIC STRUCTURAL CHANGE

Okuyama (2010) found that the long-run effects of the Kobe Earthquake, occurred in 1995, appear to be significant, lasting for several years in an increasing manner, based on the time-series analysis of regional economic data, such as GRP. It also suggested that a large part of the economic effects be resulted from structural changes of the Kobe economy caused by the damages of and reconstruction activities after the earthquake. In order to investigate the long-run effects further, this paper aims to analyze the extent and structure of the disaster effects, based on the input-output framework. The structural changes are measured based on time-series of Kobe regional input-output tables. Since 1995 Kobe regional input-output table was not compiled due to the earthquake occurrence, the 1995 table is estimated using the available regional data. Based on these tables, the region specific structural change of the Kobe economy is decomposed using structural decomposition technique and shift-share analysis.
Aggregation States of Aβ1–40, Aβ1–42 and Aβp3–42 Amyloid Beta Peptides: A SANS Study

Aggregation states of amyloid beta peptides for amyloid beta Aβ1–40 to Aβ1–42 and Aβp3–42 are investigated through small angle neutron scattering (SANS). The knowledge of these small peptides and their aggregation state are of key importance for the comprehension of neurodegenerative diseases (e.g., Alzheimer’s disease). The SANS technique allows to study the size and fractal nature of the monomers, oligomers and fibrils of the three different peptides. Results show that all the investigated peptides have monomers with a radius of gyration of the order of 10 Å, while the oligomers and fibrils display differences in size and aggregation ability, with Aβp3–42 showing larger oligomers. These properties are strictly related to the toxicity of the corresponding amyloid peptide and indeed to the development of the associated disease.
Evolution, Microbes, and Changing Ocean Conditions.

Experimental evolution and the associated theory are underutilized in marine microbial studies; the two fields have developed largely in isolation. Here, we review evolutionary tools for addressing four key areas of ocean global change biology: linking plastic and evolutionary trait changes, the contribution of environmental variability to determining trait values, the role of multiple environmental drivers in trait change, and the fate of populations near their tolerance limits. Wherever possible, we highlight which data from marine studies could use evolutionary approaches and where marine model systems can advance our understanding of evolution. Finally, we discuss the emerging field of marine microbial experimental evolution. We propose a framework linking changes in environmental quality (defined as the cumulative effect on population growth rate) with population traits affecting evolutionary potential, in order to understand which evolutionary processes are likely to be most important across a range of locations for different types of marine microbes. Expected final online publication date for the Annual Review of Marine Science, Volume 12 is January 3, 2020. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
Implementing a multidisciplinary psychotropic medication review among nursing home residents with dementia: a process evaluation

ABSTRACT Objectives: Before drawing conclusions on the contribution of an effective intervention to daily practice and initiating dissemination, its quality and implementation in daily practice should be optimal. The aim of this process evaluation was to study these aspects alongside a randomized controlled trial investigating the effects of a multidisciplinary biannual medication review in long-term care organizations (NTR3569). Design: Process evaluation with multiple measurements. Setting: Thirteen units for people with dementia in six long-term care organizations in the Netherlands. Participants: Physicians, pharmacists, and nursing staff of participating units. Intervention: The PROPER intervention is a structured and biannually repeated multidisciplinary medication review supported by organizational preparation and education, evaluation, and guidance. Measurements: Web-based questionnaires, interviews, attendance lists of education sessions, medication reviews and evaluation meetings, minutes, evaluation, and registration forms. Results: Participation rates in education sessions (95%), medication reviews (95%), and evaluation meetings (82%) were high. The intervention’s relevance and feasibility and applied implementation strategies were highly rated. However, the education sessions and conversations during medication reviews were too pharmacologically oriented for several nursing staff members. Identified barriers to implementation were required time, investment, planning issues, and high staff turnover; facilitators were the positive attitude of professionals toward the intervention, the support of higher management, and the appointment of a local implementation coordinator. Conclusion: Implementation was successful. The commitment of both higher management and professionals was an important factor. This may partly have been due to the subject being topical; Dutch long-term-care organizations are pressed to lower inappropriate psychotropic drug use.
The T-Cell Response to Type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV)

Porcine reproductive and respiratory syndrome virus (PRRSV) continues to cause severe reproductive and respiratory pathologies resulting in immense monetary and welfare costs for the swine industry. The vaccines against PRRSV are available; but they struggle with providing protection against the plethora of heterologous PRRSV strains. To improve PRRSV vaccine development, the aim of this study was to provide an in-depth analysis of the crucial heterologous T-cell response to type-2 PRRSV. Following PRRSV modified live virus (MLV) vaccination or infection using one high- or one low-pathogenic PRRSV-strain, this nine-week study evaluated the T-cell response to different PRRSV strains. Our results demonstrate an important role for T cells in this homo- and heterologous response. Specifically, the T-helper cells were the main responders during viremia. Their peak response at 28 dpi correlated with a reduction in viremia, and their homing receptor expression indicated the additional importance for the anti-PRRSV response in the lymphatic and lung tissue. The cytotoxic T lymphocyte (CTL) response was the strongest at the site of infection—the lung and bronchoalveolar lavage. The TCR-γδ T cells were the main responders post viremia and PRRSV induced their expression of the lymph node homing the chemokine receptor, CCR7: This indicates a crucial role for TCR-γδ T cells in the anti-PRRSV response in the lymphatic system.
Effects of Sleep Deprivation on the Acute Skeletal Muscle Recovery after Exercise.

PURPOSE Sleep is considered essential for muscle recovery, mainly due to its effect on hormone secretion. Total sleep deprivation or restriction is known to alter not only blood hormones but also cytokines that might be related to skeletal muscle recovery. This study aimed to evaluate whether total sleep deprivation after eccentric exercise-induced muscle damage (EEIMD) modifies the profiles of blood hormones and cytokines. METHODS In two separate conditions, with a crossover and randomized model, ten men (aged = 24.5 ± 2.9 y; body mass index = 22.7 ± 2.3 kg / m) performed a unilateral EEIMD protocol that comprised 240 eccentric contractions of the knee extensor muscles using an isokinetic dynamometer. In one condition, a 'muscle damage' protocol was followed by 48 h of total sleep deprivation and 12 h of normal sleep (DEPRIVATION). In the other condition, the same muscle damage protocol was conducted, followed by three nights of regular sleep (SLEEP). Isometric muscle voluntary contraction (MVC) tests and blood samples were collected serially throughout the protocol and analyzed for creatine kinase (CK), free and total testosterone, IGF-1, cortisol, tumor necrosis factor-alpha, interleukin (IL)-1beta, IL-6, receptor antagonist of IL-1 and IL-10. RESULTS MVC and serum CK increased equally over the study period in both conditions. From the cytokines evaluated, only IL-6 increased in DEPRIVATION. No differences were detected in testosterone levels between conditions, but IGF-1, cortisol and cortisol to total testosterone ratio were higher in DEPRIVATION. CONCLUSIONS Total sleep deprivation after EEIMD does not delay muscle strength recovery but modifies inflammatory and hormonal responses.
The critique of the common theory of narrative fiction in narratology: Pursuing difference

Abstract This article aims to characterize a commonly misunderstood and neglected critique of narratology and insists that the critique could advance the narratological discussions if taken more seriously. I describe the notions of three individual critics and one group of critics and their suggested alternatives to what they hold to be the dominating description of narrative fiction in narratology. In turn, I take up Sylvie Patron’s linguistic approach, Lars-Åke Skalin’s aesthetic approach, and Richard Walsh’s pragmatic approach, as well as unnatural narratology (which is less radical), and suggest that they have a Difference approach to narrative fiction. The critique is contrasted with what I refer to as a Sameness approach, guiding the dominating description of narrative fiction in narratology. The Sameness approach relates novels and short stories to a notion of a default mode of “narrative” which is based on situated speech about something that has happened. This is, according to the critics, a mistake. The main thrust of the critics, although with some exceptions, is instead that narrative fiction needs to be approached as sui generis in order to be described effectively. Yet how this should be done is still open for debate.
The Effect of Thermocycling on Surface Layer Properties of Light Cured Polymer Matrix Ceramic Composites (PMCCs) Used in Sliding Friction Pair

This paper discusses the problem of thermocycling effect of light-curing polymer–ceramic composites. Cyclic thermal shocks were simulated in laboratory conditions. As a rule, these loads were supposed to reproduce the actual conditions of biomaterials exploitation. Periodically variable stresses occurring in dental restorations are associated with the wear of cold and hot foods and beverages. They lead to changes in the properties of composites, including the properties of the surface layer. The aim of the work was to assess the impact of cyclic hydrothermal interactions on the properties of the surface layer of composites relevant to the operational quality. Two commercial materials manufactured by the world’s leading producer (3M ESPE)—Filtek Z550, Filtek Flow and two experimental, micro-hybrid and flow type composites marked Ex-mhyb(P) and Ex-flow(P), respectively. All tests were carried out before and after hydro-thermal cycles (flowing water thermocycling). Micro-hardness test using the Vickers method, indentation hardness, and resistance to tribological wear in a ball–disc system in sliding friction conditions were performed. In addition, observations of the surface layer of composites on the SEM (scanning electron microscope) were carried out. It was noticed that semi-liquid composites, containing a smaller amount of filler, retain higher stability of mechanical and tribological properties of the surface layer under cyclic hydro-thermal loads. Coefficient of friction of samples after hydro-thermal cycles increased for micro-hybrid materials and Filtek Flow (FFlow) composite. In the case of Ex-flow(P) material, the coefficient of friction decreased. The microhardness of composites also changed, the variability of this size depended on the type of material. Composites with a higher content of filler particles were characterized by greater variability of microhardness under the influence of thermocycles. The resistance to tribological wear also changed in a similar way. Composites containing higher volume fraction of inorganic filler showed higher tribological wear after thermocycling. The wear resistance of flow composites changed to a lesser extent, after thermocycling increased. The paper also showed that, in real kinematic nodes, the surface layer of light-curing ceramic–polymer composites is exposed to significant non-tribological (erosive, thermal, and chemical) defects that synergize with tribological ones. In slip pairs loaded dynamically, under mixed friction conditions, tribological wear of PMCCs (polymer matrix ceramic composites) is manifested by spalling (spalling of the material flakes, in particular the polymer phase) and pitting (crushing wear caused by wear products, in particular large filler particles or clusters, previously adhesively extracted).
Molecular Characterisation of Aflatoxigenic and Non-Aflatoxigenic Strains of Aspergillus Section Flavi Isolated from Imported Peanuts along the Supply Chain in Malaysia

Peanuts are widely consumed in many local dishes in southeast Asian countries, especially in Malaysia which is one of the major peanut-importing countries in this region. Therefore, Aspergillus spp. and aflatoxin contamination in peanuts during storage are becoming major concerns due to the tropical weather in this region that favours the growth of aflatoxigenic fungi. The present study thus aimed to molecularly identify and characterise the Aspergillus section Flavi isolated from imported peanuts in Malaysia. The internal transcribed spacer (ITS) and β-tubulin sequences were used to confirm the species and determine the phylogenetic relationship among the isolates, while aflatoxin biosynthesis genes (aflR, aflP (omtA), aflD (nor-1), aflM (ver-1), and pksA) were targeted in a multiplex PCR to determine the toxigenic potential. A total of 76 and one isolates were confirmed as A. flavus and A. tamarii, respectively. The Maximum Likelihood (ML) phylogenetic tree resolved the species into two different clades in which all A. flavus (both aflatoxigenic and non-aflatoxigenic) were grouped in the same clade and A. tamarii was grouped in a different clade. The aflatoxin biosynthesis genes were detected in all aflatoxigenic A. flavus while the non-aflatoxigenic A. flavus failed to amplify at least one of the genes. The results indicated that both aflatoxigenic and non-aflatoxigenic A. flavus could survive in imported peanuts and, thus, appropriate storage conditions preferably with low temperature should be considered to avoid the re-emergence of aflatoxigenic A. flavus and the subsequent aflatoxin production in peanuts during storage.
Abnormal neural functions associated with motor inhibition deficits in schizophrenia and bipolar disorder

Deficits in response inhibition have been observed in schizophrenia and bipolar disorder; however, the neural origins of the abnormalities and their relevance to genetic liability for psychosis are unknown. We used a stop‐signal task to examine motor inhibition and associated neural processes in schizophrenia patients (n = 57), bipolar disorder patients (n = 21), first‐degree biological relatives of patients with schizophrenia (n = 34), and healthy controls (n = 56). Schizophrenia patients demonstrated motor control deficits reflected in longer stop‐signal reaction times and elongated reaction times. With the possibility of needing to inhibit a button press, both schizophrenia and bipolar disorder patients showed diminished reductions of the P300 brain response and only the healthy controls demonstrated adjustments in response execution time, as measured by response‐locked lateralized readiness potentials. Schizotypal traits in the biological relatives were associated with less P300 modulation consistent with the motor‐related anomalies being associated with subtle schizophrenia‐spectrum symptomatology in family members. The two patient groups had elongated response selection processes as manifest in the delayed onset of the stimulus‐locked lateralized readiness potential. The bipolar disorder group was unique in showing significantly diminished neural responses to the stop‐signal to inhibit a response. Antipsychotic medication dosage was related to worse motor inhibition, thus motor inhibition deficits in schizophrenia may be partially explained by the effect of pharmacological agents. Failed modulation of brain processes in relation to response inhibition probability and the lengthening of motor response selection appear to be transdiagnostic abnormalities spanning schizophrenia and bipolar disorder.
Converging Fate of the Oxidation and Reduction of 8-Thioguanosine

Thione-containing nucleobases have attracted the attention of the scientific community for their application in oncology, virology, and transplantology. The detailed understanding of the reactivity of the purine derivative 8-thioguanosine (8-TG) with reactive oxygen species (ROS) and free radicals is crucial for its biological relevance. An extensive investigation on the fate of 8-TG under both reductive and oxidative conditions is here reported, and it was tested by employing steady-state photooxidation, laser flash photolysis, as well as γ-radiolysis in aqueous solutions. The characterization of the 8-TG T1 excited state by laser flash photolysis and the photooxidation experiments confirmed that singlet oxygen is a crucial intermediate in the formation of the unexpected reduced product guanosine, without the formation of the usual oxygenated sulfinic or sulfonic acids. Furthermore, a thorough screening of different radiolytic conditions upon γ-radiation afforded the reduced product. These results were rationalized by performing control experiments in the predominant presence of each reactive species formed by radiolysis of water, and the mechanistic pathway scenario was postulated on these bases.