Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Morbillivirus as Putative Cause of Fetal Death and Encephalitis among Swine

Morbilliviruses are highly contagious pathogens. The Morbillivirus genus includes measles virus, canine distemper virus (CDV), phocine distemper virus (PDV), peste des petits ruminants virus, rinderpest virus, and feline morbillivirus. We detected a novel porcine morbillivirus (PoMV) as a putative cause of fetal death, encephalitis, and placentitis among swine by using histopathology, metagenomic sequencing, and in situ hybridization. Phylogenetic analyses showed PoMV is most closely related to CDV (62.9% nt identities) and PDV (62.8% nt identities). We observed intranuclear inclusions in neurons and glial cells of swine fetuses with encephalitis. Cellular tropism is similar to other morbilliviruses, and PoMV viral RNA was detected in neurons, respiratory epithelium, and lymphocytes. This study provides fundamental knowledge concerning the pathology, genome composition, transmission, and cellular tropism of a novel pathogen within the genus Morbillivirus and opens the door to a new, applicable disease model to drive research forward.
Properties of Plasmodium falciparum with a Deleted Apicoplast DNA Gyrase

Malaria parasites have three genomes: a nuclear genome, a mitochondrial genome, and an apicoplast genome. Since the apicoplast is a plastid organelle of prokaryotic origin and has no counterpart in the human host, it can be a source of novel targets for antimalarials. Plasmodium falciparum DNA gyrase (PfGyr) A and B subunits both have apicoplast-targeting signals. ABSTRACT Malaria parasites have three genomes: a nuclear genome, a mitochondrial genome, and an apicoplast genome. Since the apicoplast is a plastid organelle of prokaryotic origin and has no counterpart in the human host, it can be a source of novel targets for antimalarials. Plasmodium falciparum DNA gyrase (PfGyr) A and B subunits both have apicoplast-targeting signals. First, to test the predicted localization of this enzyme in the apicoplast and the breadth of its function at the subcellular level, nuclear-encoded PfGyrA was disrupted using CRISPR/Cas9 gene editing. Isopentenyl pyrophosphate (IPP) is known to rescue parasites from apicoplast inhibitors. Indeed, successful growth and characterization of PfΔGyrA was possible in the presence of IPP. PfGyrA disruption was accompanied by loss of plastid acyl-carrier protein (ACP) immunofluorescence and the plastid genome. Second, ciprofloxacin, an antibacterial gyrase inhibitor, has been used for malaria prophylaxis, but there is a need for a more detailed description of the mode of action of ciprofloxacin in malaria parasites. As predicted, PfΔGyrA clone supplemented with IPP was less sensitive to ciprofloxacin but not to the nuclear topoisomerase inhibitor etoposide. At high concentrations, however, ciprofloxacin continued to inhibit IPP-rescued PfΔGyrA, possibly suggesting that ciprofloxacin may have an additional nonapicoplast target in P. falciparum. Overall, we confirm that PfGyrA is an apicoplast enzyme in the malaria parasite, essential for blood-stage parasites, and a possible target of ciprofloxacin but perhaps not the only target.
Effects of folic acid and cobalt sulphate supplementation on growth performance, nutrient digestion, rumen fermentation and blood metabolites in Holstein calves

Abstract To investigate the influences of cobalt (Co) and folic acid (FA) on growth performance and rumen fermentation, Holstein male calves (n 40) were randomly assigned to four groups according to their body weights. Cobalt sulphate at 0 or 0·11 mg Co/kg DM and FA at 0 or 7·2 mg/kg DM were used in a 2 × 2 factorial design. Average daily gain was elevated with FA or Co supplementation, but the elevation was greater for supplementing Co in diets without FA than with FA. Supplementing FA or Co increased DM intake and total-tract nutrient digestibility. Rumen pH was unaltered with FA but reduced with Co supplementation. Concentration of rumen total volatile fatty acids was elevated with FA or Co inclusion. Acetate percentage and acetate to propionate ratio were elevated with FA inclusion. Supplementing Co decreased acetate percentage and increased propionate percentage. Activities of xylanase and α-amylase and populations of total bacteria, fungi, protozoa, Ruminococcus albus, Fibrobacter succinogenes and Prevotella ruminicola increased with FA or Co inclusion. Activities of carboxymethyl-cellulase and pectinase increased with FA inclusion and population of methanogens decreased with Co addition. Blood folates increased and homocysteine decreased with FA inclusion. Blood glucose and vitamin B12 increased with Co addition. The data suggested that supplementing 0·11 mg Co/kg DM in diets containing 0·09 mg Co/kg DM increased growth performance and nutrient digestibility but had no improvement on the effects of FA addition in calves.
Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families on Schistocerca grasshopper genomes

Multigene families are essential components of eukaryotic genomes and play key roles either structurally and functionally. Their modes of evolution remain elusive even in the era of genomics, because multiple multigene family sequences coexist in genomes, particularly in large repetitive genomes. Here, we investigate how the multigene families 18S rDNA, U2 snDNA, and H3 histone evolved in 10 species of Schistocerca grasshoppers with very large and repeat‐enriched genomes. Using sequenced genomes and fluorescence in situ hybridization mapping, we find substantial differences between species, including the number of chromosomal clusters, changes in sequence abundance and nucleotide composition, pseudogenization, and association with transposable elements (TEs). The intragenomic analysis of Schistocerca gregaria using long‐read sequencing and genome assembly unveils conservation for H3 histone and recurrent pseudogenization for 18S rDNA and U2 snDNA, likely promoted by association with TEs and sequence truncation. Remarkably, TEs were frequently associated with truncated copies, were also among the most abundant in the genome, and revealed signatures of recent activity. Our findings suggest a combined effect of concerted and birth‐and‐death models driving the evolution of multigene families in Schistocerca over the last 8 million years, and the occurrence of intra‐ and interchromosomal rearrangements shaping their chromosomal distribution. Despite the conserved karyotype in Schistocerca, our analysis highlights the extensive reorganization of repetitive DNAs in Schistocerca, contributing to the advance of comparative genomics for this important grasshopper genus.
Role of dephasing on the conductance signatures of Majorana zero modes

Conductance signatures that signal the presence of Majorana zero modes in a three terminal nanowire-topological superconductor hybrid system are analyzed in detail, in both the clean nanowire limit and in the presence of non-coherent dephasing interactions. In the coherent transport regime for a clean wire, we point out contributions of the local Andreev reflection and the non-local transmissions toward the total conductance lineshapes while clarifying the role of contact broadening on the Majorana conductance lineshapes at the magnetic field parity crossings. Interestingly, at larger B-field parity crossings, the contribution of the Andreev reflection process decreases which is compensated by the non-local processes in order to maintain the conductance quantum regardless of contact coupling strength. In the non-coherent transport regime, we include dephasing that is introduced by momentum randomization processes, that allows one to smoothly transition to the diffusive limit. Here, as expected, we note that while the Majorana character of the zero modes is unchanged, there is a reduction in the conductance peak magnitude that scales with the strength of the impurity scattering potentials. Dephasing due to fluctuating impurities is shown to affect the conductance lineshapes in ways that are distinguishable from the effects of contact-induced tunnel broadening. Most importantly our results reveal that the addition of dephasing in the set up does not lead to any notable length dependence to the conductance of the zero modes, contrary to what one would expect in a gradual transition to the diffusive limit. We believe this work paves a way for a systematic introduction of scattering processes into the realistic modeling of Majorana nanowire hybrid devices and assessing topological signatures in such systems in the presence of non-coherent scattering processes.
Transfer, Amplification, Storage and Complete Self-Recovery of Supramolecular Chirality in Achiral Polymer System.

Supramolecular chirality and its complete self-recovery ability are highly mystical in nature and biological systems, which remains a major challenge today. Herein, we firstly demonstrate that the partially cross-linked azobenzene (Azo) units can be employed as the potential chiral trigger to fully heal the destroyed helical superstructure in achiral nematic polymer system. Combining the self-assembly of Azo units and terminal hydroxyl in polymer side chains allows vapor-induced chiral nematic phase and covalent fixation of the superstructure via acetal reaction. The induced helical structure of Azo units can be stored by the inter-chain cross-linking, even after the removal of chiral source. Most interestingly, the stored chiral information can trigger the perfect chiral self-recovery (CSR) behaviours after being destroyed by UV light, heat and solvent. The results pave a new way for producing novel chiroptical materials with reversible chirality from achiral sources.
Feasibility and clinical impact of a portable bi-level ventilation device in patients with severe chronic obstructive pulmonary disease and exertional dyspnea: preliminary results from a clinical series

ABSTRACT We explore home use of a portable bi-level ventilation device among patients with severe chronic obstructive pulmonary disease (COPD), and describe changes in the patients’ physical activity levels, perceived dyspnea, anxiety and depression, as well as their satisfaction with the device, after one month of use. Methods. Forty patients with severe COPD and exertional dyspnea were instructed to use VitaBreath® device (Philips, Respironics) during efforts or activities of daily living for 4 weeks, and agreed to answer questionnaires on anxiety, depression, dyspnea and physical activity. Results. Twenty-six (65%) patients used the VitaBreath® device for four weeks, while 14 patients (35%) stopped early for various reasons. Among patients who completed the 4-week course, no differences in dyspnea and physical activity were observed between baseline and follow-up (p-values 0.41 and 0.19, respectively). Thirteen (50%) and 15 (57%) patients experienced reduced anxiety and depression, respectively. Patients with greater functional impairment and less autonomy in activities of daily living tended to view the device more positively. Conclusion. Home use of portable bi-level positive-pressure ventilation devices by patients with COPD may alleviate disease-related anxiety and depression, particularly in more severe cases of COPD. Future portable device design should feature adjustable inspiratory/expiratory pressures.
Amino‐Functionalized Conjugated Polymer as an Efficient Electron Transport Layer for High‐Performance Planar‐Heterojunction Perovskite Solar Cells

An amino‐functionalized copolymer with a conjugated backbone composed of fluorene, naphthalene diimide, and thiophene spacers (PFN‐2TNDI) is introduced as an alternative electron transport layer (ETL) to replace the commonly used [6,6]‐Phenyl‐C61‐butyric acid methyl ester (PCBM) in the p–i–n planar‐heterojunction organometal trihalide perovskite solar cells. A combination of characterizations including photoluminescence (PL), time‐resolved PL decay, Kelvin probe measurement, and impedance spectroscopy is used to study the interfacial effects induced by the new ETL. It is found that the amines on the polymer side chains not only can passivate the surface traps of perovskite to improve the electron extraction properties, they also can reduce the work function of the metal cathode by forming desired interfacial dipoles. With these dual functionalities, the resulted solar cells outperform those based on PCBM with power conversion efficiency (PCE) increased from 12.9% to 16.7% based on PFN‐2TNDI. In addition to the performance enhancement, it is also found that a wide range of thicknesses of the new ETL can be applied to produce high PCE devices owing to the good electron transport property of the polymer, which offers a better processing window for potential fabrication of perovskite solar cells using large‐area coating method.
Microexon alternative splicing of small GTPase regulators: Implication in central nervous system diseases

Microexons are small sized (≤51 bp) exons which undergo extensive alternative splicing in neurons, microglia, embryonic stem cells, and cancer cells, giving rise to cell type specific protein isoforms. Due to their small sizes, microexons provide a unique challenge for the splicing machinery. They frequently lack exon splicer enhancers/repressors and require specialized neighboring trans‐regulatory and cis‐regulatory elements bound by RNA binding proteins (RBPs) for their inclusion. The functional consequences of including microexons within mRNAs have been extensively documented in the central nervous system (CNS) and aberrations in their inclusion have been observed to lead to abnormal processes. Despite the increasing evidence for microexons impacting cellular physiology within CNS, mechanistic details illustrating their functional importance in diseases of the CNS is still limited. In this review, we discuss the unique characteristics of microexons, and how RBPs participate in regulating their inclusion and exclusion during splicing. We consider recent findings of microexon alternative splicing and their implication for regulating the function of small GTPases in the context of the microglia, and we extrapolate these findings to what is known in neurons. We further discuss the emerging evidence for dysregulation of the Rho GTPase pathway in CNS diseases and the consequences contributed by the mis‐splicing of microexons.
Sowing forests: a synthesis of seed dispersal and predation by agoutis and their influence on plant communities

Granivorous rodents have been traditionally regarded as antagonistic seed predators. Agoutis (Dasyprocta spp.), however, have also been recognized as mutualistic dispersers of plants because of their role as scatter‐hoarders of seeds, especially for large‐seeded species. A closer look shows that such definitions are too simplistic for these Neotropical animals because agoutis can influence plant communities not only through seed dispersal of large seeds but also through predation of small seeds and seedlings, evidencing their dual role. Herein, we summarize the literature on plant–agouti interactions, decompose agouti seed dispersal into its quantitative and qualitative components, and discuss how environmental factors and plant traits determine whether these interactions result in mutualisms or antagonisms. We also look at the role of agoutis in a community context, assessing their effectiveness as substitutes for extinct megafaunal frugivores and comparing their ecological functions to those of other extant dispersers of large seeds. We also discuss how our conclusions can be extended to the single other genus in the Dasyproctidae family (Myoprocta). Finally, we examine agoutis’ contribution to carbon stocks and summarize current conservation threats and efforts. We recorded 164 interactions between agoutis and plants, which were widespread across the plant phylogeny, confirming that agoutis are generalist frugivores. Seed mass was a main factor determining seed hoarding probability of plant species and agoutis were found to disperse larger seeds than other large‐bodied frugivores. Agoutis positively contributed to carbon storage by preying upon seeds of plants with lower carbon biomass and by dispersing species with higher biomass. This synthesis of plant–agouti interactions shows that ecological services provided by agoutis to plant populations and communities go beyond seed dispersal and predation, and we identify still unanswered questions. We hope to emphasise the importance of agoutis in Neotropical forests.
UPDATES TO THE CARBON BOND MECHANISM FOR VERSION 6 (CB6)

The Carbon Bond (CB) mechanism (Gery et al., 1989) describes tropospheric oxidant chemistry in a concise manner suitable for use in complex 3-dimensional atmospheric models. Existing versions (CB4 and CB05) are used in photochemical grid models for ozone and particulate matter (PM) such as CMAQ, CAMx and WRF-Chem. This paper describes the development and evaluation of version 6 of the Carbon Bond mechanism (CB6). The development of CB6 was performed for the Texas Commission on Environmental Quality (TCEQ) which is responsible for developing the Texas State Implementation Plan (SIP) for ozone. Ozone SIP development in Texas relies upon modeling using the Comprehensive Air Quality Model with Extensions (CAMx) photochemical model (ENVIRON, 2010) and the CB05 chemical mechanism (Yarwood et al., 2005). The chemical mechanism is a critical component in ozone SIP development because it forms the linkage between emissions of ozone precursors, namely Nitrogen Oxides (NOx) and Volatile Organic Compounds (VOC), and ozone concentrations in the photochemical model. Research in atmospheric chemistry continually provides new information that should be evaluated and potentially incorporated into chemical mechanisms to maintain their accuracy and thereby provide the best possible strategies for improving ozone air quality.
Rheumatoid arthritis serotype and synthetic disease-modifying anti-rheumatic drugs in patients with periodontitis: A case-control study

Patients with rheumatoid arthritis (RA) experience a higher prevalence of periodontitis. This study aimed to examine the variation of periodontitis experienced with different serotypes suffered by RA patients and to examine the relationship between the different medications taken for RA that may influence this relationship. Two hundred and sixty RA and control participants underwent standardized periodontal examinations. Medical, serological and radiological (Sharp/van der Heijde) records were assessed. Functional status was assessed using the administered Health Assessment Questionnaire. Moreover, disease parameters, including disease activity (DAS28-ESR) and anti-citrullinated protein antibodies (ACPA) and rheumatoid factor (RF) seropositivity were evaluated. Periodontitis was higher in RA (71.54%) compared with controls (54.62%). The stage of periodontitis experienced by ACPA-positive participants were higher than APCA-negative participants. The probing pocket depth and recession experienced by RF-positive participants were higher than those who were RF-negative. RA participants on methotrexate had lower clinical attachment loss and lower periodontal probing depth compared with participants on a combination methotrexate and other disease-modifying antirheumatic drugs. Participants taking corticosteroids had lower gingival index scores. The association between seropositivity and the type of medications taken with periodontal health parameters in this group of patients suggests that both seropositivity and medications taken are important modifiers in the relationship between periodontitis and RA.
The blood–brain and gut–vascular barriers: from the perspective of claudins

ABSTRACT In some organs, such as the brain, endothelial cells form a robust and highly selective blood-to-tissue barrier. However, in other organs, such as the intestine, endothelial cells provide less stringent permeability, to allow rapid exchange of solutes and nutrients where needed. To maintain the structural and functional integrity of the highly dynamic blood–brain and gut–vascular barriers, endothelial cells form highly specialized cell-cell junctions, known as adherens junctions and tight junctions. Claudins are a family of four-membrane-spanning proteins at tight junctions and they have both barrier-forming and pore-forming properties. Tissue-specific expression of claudins has been linked to different diseases that are characterized by barrier impairment. In this review, we summarize the more recent progress in the field of the claudins, with particular attention to their expression and function in the blood–brain barrier and the recently described gut–vascular barrier, under physiological and pathological conditions. Abbreviations: 22q11DS 22q11 deletion syndrome; ACKR1 atypical chemokine receptor 1; AD Alzheimer disease; AQP aquaporin; ATP adenosine triphosphate; Aβ amyloid β; BAC bacterial artificial chromosome; BBB blood-brain barrier; C/EBP-α CCAAT/enhancer-binding protein α; cAMP cyclic adenosine monophosphate (or 3ʹ,5ʹ-cyclic adenosine monophosphate); CD cluster of differentiation; CNS central nervous system; DSRED discosoma red; EAE experimental autoimmune encephalomyelitis; ECV304 immortalized endothelial cell line established from the vein of an apparently normal human umbilical cord; EGFP enhanced green fluorescent protein; ESAM endothelial cell-selective adhesion molecule; GLUT-1 glucose transporter 1; GVB gut-vascular barrier; H2B histone H2B; HAPP human amyloid precursor protein; HEK human embryonic kidney; JACOP junction-associated coiled coil protein; JAM junctional adhesion molecules; LYVE1 lymphatic vessel endothelial hyaluronan receptor 1; MADCAM1 mucosal vascular addressin cell adhesion molecule 1; MAPK mitogen-activated protein kinase; MCAO middle cerebral artery occlusion; MMP metalloprotease; MS multiple sclerosis; MUPP multi-PDZ domain protein; PATJ PALS-1-associated tight junction protein; PDGFR-α platelet-derived growth factor receptor α polypeptide; PDGFR-β platelet-derived growth factor receptor β polypeptide; RHO rho-associated protein kinase; ROCK rho-associated, coiled-coil-containing protein kinase; RT-qPCR real time quantitative polymerase chain reactions; PDGFR-β soluble platelet-derived growth factor receptor, β polypeptide; T24 human urinary bladder carcinoma cells; TG2576 transgenic mice expressing the human amyloid precursor protein; TNF-α tumor necrosis factor α; WTwild-type; ZO zonula occludens.