Miracle-dz/UniFAR-FTUs huggingface dataset:
Stable Attenuation of Human Respiratory Syncytial Virus for Live Vaccines by Deletion and Insertion of Amino Acids in the Hinge Region between the mRNA Capping and Methyltransferase Domains of the Large Polymerase Protein

Despite tremendous efforts, there are no FDA-approved vaccines for human respiratory syncytial virus (RSV). A live attenuated RSV vaccine is one of the most promising vaccine strategies for RSV. However, it has been a challenge to identify an RSV vaccine strain that has an optimal balance between attenuation and immunogenicity. In this study, we generated a panel of recombinant RSVs carrying a single and double deletion or a single alanine insertion in the large (L) polymerase protein that are genetically stable, sufficiently attenuated, and grow to high titer in cultured cells, while retaining high immunogenicity. Thus, these recombinant viruses may be promising vaccine candidates for RSV. ABSTRACT Human respiratory syncytial virus (RSV) is the leading viral cause of lower respiratory tract disease in infants and children worldwide. Currently, there are no FDA-approved vaccines to combat this virus. The large (L) polymerase protein of RSV replicates the viral genome and transcribes viral mRNAs. The L protein is organized as a core ring-like domain containing the RNA-dependent RNA polymerase and an appendage of globular domains containing an mRNA capping region and a cap methyltransferase region, which are linked by a flexible hinge region. Here, we found that the flexible hinge region of RSV L protein is tolerant to amino acid deletion or insertion. Recombinant RSVs carrying a single or double deletion or a single alanine insertion were genetically stable, highly attenuated in immortalized cells, had defects in replication and spread, and had a delay in innate immune cytokine responses in primary, well-differentiated, human bronchial epithelial (HBE) cultures. The replication of these recombinant viruses was highly attenuated in the upper and lower respiratory tracts of cotton rats. Importantly, these recombinant viruses elicited high levels of neutralizing antibody and provided complete protection against RSV replication. Taken together, amino acid deletions or insertions in the hinge region of the L protein can serve as a novel approach to rationally design genetically stable, highly attenuated, and immunogenic live virus vaccine candidates for RSV. IMPORTANCE Despite tremendous efforts, there are no FDA-approved vaccines for human respiratory syncytial virus (RSV). A live attenuated RSV vaccine is one of the most promising vaccine strategies for RSV. However, it has been a challenge to identify an RSV vaccine strain that has an optimal balance between attenuation and immunogenicity. In this study, we generated a panel of recombinant RSVs carrying a single and double deletion or a single alanine insertion in the large (L) polymerase protein that are genetically stable, sufficiently attenuated, and grow to high titer in cultured cells, while retaining high immunogenicity. Thus, these recombinant viruses may be promising vaccine candidates for RSV.
Comparison of non-contrast enhanced dental magnetic resonance imaging and cone-beam computed tomography in assessing the horizontal and vertical components of furcation defects in maxillary molars: An in vivo feasibility study.

AIM To compare non-contrast-enhanced dental magnetic resonance imaging (NCE-dMRI) and cone-beam computed tomography (CBCT) in assessing horizontal and vertical furcation defects in maxillary molars in vivo. MATERIAL AND METHODS NCE-dMRI and CBCT were performed in 23 patients with severe periodontitis. 65 first/second maxillary molars (195 furcation entrances) were analyzed by two independent observers on both modalities to assess the horizontal and vertical components of furcation defects. Reliability of defect classification was evaluated using weighted kappa (κ) statistics. Agreement between NCE-dMRI and CBCT was determined by Bland-Altman analysis. Sensitivity and specificity of NCE-dMRI were calculated using CBCT as the reference. RESULTS Interradicular bone loss was observed in 94 furcation entrances. Intra- and inter-rater κ-values were ≥ 0.9 for both NCE-dMRI and CBCT. Bland-Altman analysis showed mean differences (95% limits of agreement) of 0.12 mm (-0.67-0.90) for horizontal, and 0.12 mm (1.27-1.50) for vertical measurements. For detection of furcation defects, sensitivity/specificity of NCE-dMRI was 98%/100% for horizontal, and 99%/99% for vertical components. For defect classification, sensitivity values of NCE-dMRI were 88%/89%/100% (horizontal degree I/II/III) and 95%/91%/80% (vertical subclass A/B/C), respectively. CONCLUSIONS NCE-dMRI demonstrated high reliability and high agreement with CBCT for the assessment of furcation defects in maxillary molars.
PDGFRA in vascular adventitial MSCs promotes neointima formation in arteriovenous fistula in chronic kidney disease

Chronic kidney disease (CKD) induces the failure of arteriovenous fistulas (AVFs) and promotes the differentiation of vascular adventitial GLI1-positive mesenchymal stem cells (GMCs). However, the roles of GMCs in forming neointima in AVFs remain unknown. GMCs isolated from CKD mice showed increased potential capacity of differentiation into myofibroblast-like cells. Increased activation of expression of PDGFRA and hedgehog (HH) signaling were detected in adventitial cells of AVFs from patients with end-stage kidney disease and CKD mice. PDGFRA was translocated and accumulated in early endosome when sonic hedgehog was overexpressed. In endosome, PDGFRA-mediated activation of TGFB1/SMAD signaling promoted the differentiation of GMCs into myofibroblasts, extracellular matrix deposition, and vascular fibrosis. These responses resulted in neointima formation and AVF failure. KO of Pdgfra or inhibition of HH signaling in GMCs suppressed the differentiation of GMCs into myofibroblasts. In vivo, specific KO of Pdgfra inhibited GMC activation and vascular fibrosis, resulting in suppression of neointima formation and improvement of AVF patency despite CKD. Our findings could yield strategies for maintaining AVF functions.
A GWAS approach to find SNPs associated with salt removal in rice leaf sheath.

BACKGROUND AND AIMS The ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice. Thus, understanding the genetic control of the salt removal capacity in leaf sheaths will help improve the molecular breeding of salt-tolerant rice varieties and speed up future varietal development to increase productivity in salt-affected areas. We report a genome-wide association study (GWAS) conducted to find single nucleotide polymorphisms (SNPs) associated with salt removal in leaf sheaths of rice. METHODS In this study, 296 accessions of a rice (Oryza sativa) diversity panel were used to identify salt removal-related traits and conduct GWAS using 36 901 SNPs. The sheath:blade ratio of Na+ and Cl- concentrations was used to determine the salt removal ability in leaf sheaths. Candidate genes were further narrowed via Gene Ontology and RNA-seq analysis to those whose putative function was likely to be associated with salt transport and were up-regulated in response to salt stress. KEY RESULTS For the association signals of the Na+ sheath:blade ratio, significant SNPs were found only in the indica sub-population on chromosome 5. Within candidate genes found in the GWAS study, five genes were upregulated and eight genes were downregulated in the internal leaf sheath tissues in the presence of salt stress. CONCLUSIONS These GWAS data imply that rice accessions in the indica variety group are the main source of genes and alleles associated with Na+ removal in leaf sheaths of rice under salt stress.
Statistical Design of Sustained-Release Tablet Garcinia cambogia Extract and Bioconverted Mulberry Leaf Extract for Anti-Obesity

Obesity is a major health concern worldwide, and it is leading to worsening disease morbidity and mortality. Herbal supplements and diet-based therapies have attracted interest in the treatment of obesity. It is known that Garcinia cambogia (GA) and mulberry leaf, which contain polyphenols, have anti-obesity activity. Herein, we developed a combined tablet consisting of GA extract and bioconverted mulberry leaf extract (BMUL) using a statistical design approach. The ratio and amount of sustained polymers were set as factors. In the cell study, the combination of GA and BMUL showed synergistic anti-obesity activity. In a statistical model, the optimized amounts of hydroxypropyl methylcellulose 2208 (HPMC 2208) and polyethylene oxide 303 (POLYOX 303) were 41.02% and 58.98%, respectively. Additionally, the selected ratio of microcrystalline cellulose (MCC) was 0.33. When the release, hardness, and friability of the GABMUL tablet were evaluated, the error percentages of the response were lower than 10%. This indicates that the GABMUL tablet was successfully prepared.
Building better polymerases: Engineering the replication of expanded genetic alphabets

DNA polymerases are today used throughout scientific research, biotechnology, and medicine, in part for their ability to interact with unnatural forms of DNA created by synthetic biologists. Here especially, natural DNA polymerases often do not have the “performance specifications” needed for transformative technologies. This creates a need for science-guided rational (or semi-rational) engineering to identify variants that replicate unnatural base pairs (UBPs), unnatural backbones, tags, or other evolutionarily novel features of unnatural DNA. In this review, we provide a brief overview of the chemistry and properties of replicative DNA polymerases and their evolved variants, focusing on the Klenow fragment of Taq DNA polymerase (Klentaq). We describe comparative structural, enzymatic, and molecular dynamics studies of WT and Klentaq variants, complexed with natural or noncanonical substrates. Combining these methods provides insight into how specific amino acid substitutions distant from the active site in a Klentaq DNA polymerase variant (ZP Klentaq) contribute to its ability to replicate UBPs with improved efficiency compared with Klentaq. This approach can therefore serve to guide any future rational engineering of replicative DNA polymerases.
CSF Biomarkers in Patients With COVID-19 and Neurologic Symptoms

Objective To explore whether hospitalized patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and neurologic symptoms have evidence of CNS infection, inflammation, and injury using CSF biomarker measurements. Methods We assessed CSF SARS-CoV-2 RNA along with CSF biomarkers of intrathecal inflammation (CSF white blood cell count, neopterin, β2-microglobulin, and immunoglobulin G index), blood-brain barrier integrity (albumin ratio), and axonal injury (CSF neurofilament light chain protein [NfL]) in 6 patients with moderate to severe coronavirus disease 2019 (COVID-19) and neurologic symptoms who had undergone a diagnostic lumbar puncture. Neurologic symptoms and signs included features of encephalopathies (4 of 6), suspected meningitis (1 of 6), and dysgeusia (1 of 6). SARS-CoV-2 infection was confirmed by real-time PCR analysis of nasopharyngeal swabs. Results SARS-CoV-2 RNA was detected in the plasma of 2 patients (cycle threshold [Ct] value 35.0–37.0) and in CSF at low levels (Ct 37.2, 38.0, 39.0) in 3 patients in 1 but not in a second real-time PCR assay. CSF neopterin (median 43.0 nmol/L) and β2-microglobulin (median 3.1 mg/L) were increased in all. Median immunoglobulin G index (0.39), albumin ratio (5.35), and CSF white blood cell count (<3 cells/µL) were normal in all, while CSF NfL was elevated in 2 patients. Conclusion Our results in patients with COVID-19 and neurologic symptoms suggest an unusual pattern of marked CSF inflammation in which soluble markers were increased but white cell response and other immunologic features typical of CNS viral infections were absent. While our initial hypothesis centered on CNS SARS-CoV-2 invasion, we could not convincingly detect SARS-CoV-2 as the underlying driver of CNS inflammation. These features distinguish COVID-19 CSF from other viral CNS infections and raise fundamental questions about the CNS pathobiology of SARS-CoV-2 infection.
The importance of artificial coastal structures (tetrapods) as refuge and settlement area for fish and crustacea

This thesis focused on the effects of coastal defence structures on the fish and crustacean community in a subtidal area in the southern North Sea. The findings represent significant effects of natural and artificial substrate characteristics on the species. Through SCUBA, fixed quadrats along line-transects were used to assess firstly the demersal fish and decapod crustacean abundances in relation to natural substratum types (rock, cobbles and large pebbles). The results indicated that significant micro-scale species-habitat associations, especially for native fish, occur. In the same study area experimental fields were established, consisting of four-footed breakwaters (tetrapods) to investigate ecological impacts on the biota. Over a two-year period the fish and decapod community was assessed again, but now in combination with the experimental fields and in distance to the artificial structures. The results demonstrate a significant decrease of fish abundances in the surrounding area caused by migration effects towards the artificial structures. Furthermore, more young-of-the-year fish were observed directly at the structures within the second year after the establishment. I suggest that the availability of adequate refuge in combination with additionally food opportunities were the main factors, which attracted native fish species in greater numbers. Concerning the macro crustaceans it was not possible to give clear statements about the impact on the assemblage in general. The species reacted differently to the alteration of their surrounding. I suggest that for some crustacean species the composition of the tetrapods are attractive as shelter. For smaller species, however, this habitat form may not be optimal because of the lack of microhabitats. I concluded that the preference for a habitat type depends mainly on ecological requirements such as substratum colouration, adequate shelter size and specific species features.
Efficacy and Safety of Baricitinib Combined With Topical Corticosteroids for Treatment of Moderate to Severe Atopic Dermatitis

Key Points Question What is the efficacy and safety of 4 mg and 2 mg of baricitinib in combination with background topical corticosteroid (TCS) therapy in adults with moderate to severe atopic dermatitis (AD)? Findings In this randomized clinical trial of 329 adults with moderate to severe AD, at week 16, a validated Investigator Global Assessment for Atopic Dermatitis score of 0 (clear) or 1 (almost clear) was achieved by 31% of patients receiving 4 mg of baricitinib with TCS therapy and 24% of patients receiving 2 mg of baricitinib with TCS therapy compared with 15% receiving placebo with TCS therapy. Meaning This study found a clinical benefit of Janus kinase inhibition in combination with TCS therapy, the mainstay treatment for AD.
Co-Occurrence and Levels of Mycotoxins in Fish Feeds in Kenya

This study determined the presence, levels and co-occurrence of mycotoxins in fish feeds in Kenya. Seventy-eight fish feeds and ingredients were sampled from fish farms and fish feed manufacturing plants and analysed for 40 mycotoxins using high-performance liquid chromatography-high resolution mass spectrometry. Twenty-nine (73%) mycotoxins were identified with 76 (97%) samples testing positive for mycotoxins presence. Mycotoxins with the highest prevalences were enniatin B (91%), deoxynivalenol (76%) and fumonisin B1 (54%) while those with the highest maximum levels were sterigmatocystin (<30.5–3517.1 µg/kg); moniliformin (<218.9–2583.4 µg/kg) and ergotamine (<29.3–1895.6 µg/kg). Mycotoxin co-occurrence was observed in 68 (87%) samples. Correlations were observed between the fumonisins; enniatins B and zearalenone and its metabolites. Fish dietary exposure estimates ranged between <0.16 and 43.38 µg/kg body weight per day. This study shows evidence of mycotoxin presence and co-occurrence in fish feeds and feed ingredients in Kenya. Fish exposure to these levels of mycotoxins over a long period of time may lead to adverse health effects due to their possible additive, synergistic or antagonist toxic effects. Measures to reduce fish feed mycotoxin contamination should be taken to avoid mycotoxicosis in fish and subsequently in humans and animals through residues.
The Efficacy of Medium- to Long-term Anti-TNF-α Antibody-based Maintenance Therapy in Behçet's Disease Patients with Intestinal Lesions

Objective Anti-tumor necrosis factor (TNF)-α antibody-based regimens are effective in Behçet's disease (BD) with intestinal lesions. We therefore evaluated the efficacy of medium- to long-term anti-TNF-α antibody-based maintenance therapy of BD intestinal and non-intestinal lesions. Methods In this retrospective study, the response to the treatment was assessed endoscopically and clinically. Treatment responders were transferred to maintenance therapy. We evaluated the sustain rate of maintenance therapy, reductions in the dose of prednisolone (PSL), and the presence of non-intestinal BD involvement before and after the start of anti-TNF-α antibody-based the maintenance therapy. Patients We assessed 20 BD patients with intestinal lesions who underwent anti-TNF-α antibody-based therapy. Results Treatment was discontinued in 3 patients (18%). Loss of response was noted in 1 (5.9%) patient. Maintenance therapy was continued in 13 (76%) patients. The cumulative sustain rates to maintenance therapy after 2, 4, and 6 years were 94%, 87%, and 72%, respectively. In the 13 patients with remission of intestinal lesions, the mean PSL dose decreased from 13.4±2.16 mg/day before treatment to 0.92±0.47 after treatment (p<0.0001). PSL was discontinued in 9 (69%) patients. Five of the 13 (38%) patients developed clinical features of non-intestinal BD during the remission-maintenance treatment. Conclusion Our results demonstrated the efficacy of medium- to long-term anti-TNF-α antibody-based maintenance treatment against BD intestinal lesions. Nevertheless, some cases with well-controlled intestinal lesions developed active non-intestinal BD symptoms. The results highlight the importance of a carefully planned treatment strategy for BD patients with intestinal involvement.
Non-Adherence to Statin Treatment in Older Patients with Peripheral Arterial Disease Depending on Persistence Status

The effectiveness of statins in secondary prevention of peripheral arterial disease (PAD) largely depends on patients’ adherence to treatment. The aims of our study were: (a) to analyze non-adherence during the whole follow-up in persistent patients, and only during persistence for non-persistent patients; (b) to identify factors associated with non-adherence separately among persistent and non-persistent patients. A cohort of 8330 statin users aged ≥65 years, in whom PAD was newly diagnosed between January 2012–December 2012, included 5353 patients persistent with statin treatment, and 2977 subjects who became non-persistent during the 5-year follow-up. Non-adherence was defined using the proportion of days covered <80%. Patient- and statin-related characteristics associated with non-adherence were identified with binary logistic regression. A significantly higher proportion of non-adherent patients was found among non-persistent patients compared to persistent subjects (43.6% vs. 29.6%; p < 0.001). Associated with non-adherence in both persistent and non-persistent patients was high intensity statin treatment, while in non-persistent patients, it was employment and increasing number of medications. In patients with a poor adherence during their persistent period, an increased risk for discontinuation may be expected. However, there is also non-adherence among persistent patients. There are differences in factors associated with non-adherence depending on patients’ persistence.
Language-Related Disparities in Pain Management in the Post-Anesthesia Care Unit for Children Undergoing Laparoscopic Appendectomy

Race and ethnicity are associated with disparities in pain management in children. While low English language proficiency is correlated with minority race/ethnicity in the United States, it is less frequently explored in the study of health disparities. We therefore investigated whether English language proficiency influenced pain management in the post-anesthesia care unit (PACU) in a cohort of children who underwent laparoscopic appendectomy at our pediatric hospital in San Francisco. Our primary exposure was English language proficiency, and our primary outcome was administration of any opioid medication in the PACU. Secondary outcomes included the amount of opioid administered in the PACU and whether any pain score was recorded during the patient’s recovery period. Statistical analysis included adjusting for demographic covariates including race in estimating the effect of language proficiency on these outcomes. In our cohort of 257 pediatric patients, 57 (22.2%) had low English proficiency (LEP). While LEP and English proficient (EP) patients received the same amount of opioid medication intraoperatively, in multivariable analysis, LEP patients had more than double the odds of receiving any opioid in the PACU (OR 2.45, 95% CI 1.22–4.92). LEP patients received more oral morphine equivalents (OME) than EP patients (1.64 OME/kg, CI 0.67–3.84), and they also had almost double the odds of having no pain score recorded during their PACU recovery period (OR 1.93, CI 0.79–4.73), although the precision of these estimates was limited by small sample size. Subgroup analysis showed that children over the age of 5 years, who were presumably more verbal and would therefore undergo verbal pain assessments, had over triple the odds of having no recorded pain score (OR 3.23, CI 1.48–7.06). In summary, English language proficiency may affect the management of children’s pain in the perioperative setting. The etiology of this language-related disparity is likely multifactorial and should be investigated further.
The involvement of nucleotide excision repair proteins in the removal of oxidative DNA damage

Abstract The six major mammalian DNA repair pathways were discovered as independent processes, each dedicated to remove specific types of lesions, but the past two decades have brought into focus the significant interplay between these pathways. In particular, several studies have demonstrated that certain proteins of the nucleotide excision repair (NER) and base excision repair (BER) pathways work in a cooperative manner in the removal of oxidative lesions. This review focuses on recent data showing how the NER proteins, XPA, XPC, XPG, CSA, CSB and UV-DDB, work to stimulate known glycosylases involved in the removal of certain forms of base damage resulting from oxidative processes, and also discusses how some oxidative lesions are probably directly repaired through NER. Finally, since many glycosylases are inhibited from working on damage in the context of chromatin, we detail how we believe UV-DDB may be the first responder in altering the structure of damage containing-nucleosomes, allowing access to BER enzymes.
Calcium signalling and tumorigenesis

*Correspondence: Dr. Juan A. Rosado, Faculty of Veterinary Medicine, Department of Physiology, University of Extremadura. Av. Universidad s/n, 10071 C ceres. Spain; Phone: +34 927257154; Fax: +34 927257154; e-mail: jarosado@unex.es