Miracle-dz/UniFAR-FTUs huggingface dataset:
GIBBS ENERGY MINIMIZATION METHOD FOR ANALYSIS OF METHANE OXIDATION TO HIGHER HYDROCARBONS

Kaedah peminimuman jumlah tenaga Gibbs sangat berguna untuk menganalisis kemungkinan penukaran metana kepada hidrokarbon dan syngas pada suhu dan tekanan tertentu secara teoritikal. Keputusan numerik menunjukkan penukaran metana meningkat dengan peningkatan kepekatan oksigen dan suhu tindak balas. Bagaimanapun, kehadiran oksigen merencat pembentukan hidrokarbon tinggi yang kebanyakannya mengandungi aromatik, tetapi menggalakkan pembentukan hidrogen. Apabila tekanan sistem bertambah, hasil aromatik, olefin dan hidrogen berkurang, tetapi hasil parafin meningkat. Karbon monoksida menjadi produk mengandungi oksigen yang utama daripada pengoksidaan metana sementara hampir tiada H 2 O, CH 3 OH and HCOH yang dikesan walaupun sejumlah kecil karbon dioksida terbentuk pada suhu yang agak rendah dan tekanan tinggi. Kata kunci: Keseimbangan kimia termodinamik, peminimuman jumlah tenaga Gibbs, penukaran metana, hidrokarbon tinggi The total Gibbs energy minimization method is useful to theoretically analyze the feasibility of methane conversion to higher hydrocarbons and syngas at the selected temperature and pressure. Numerical results showed that the conversion of methane increased with oxygen concentration and reaction temperature, but decreased with pressure. Nevertheless, the presence of oxygen suppressed the formation of higher hydrocarbons that mostly consisted of aromatics, but enhanced the formation of hydrogen. As the system pressure increased, the aromatics, olefins and hydrogen yields diminished, but the paraffin yield improved. Carbon monoxide seemed to be the major oxygen-containing equilibrium product from methane oxidation whilst almost no H 2 O, CH 3 OH and HCOH were detected although traces amount of carbon dioxide were formed at relatively lower emperature and higher pressure. Key words: Thermodynamic chemical equilibrium, Gibbs energy minimization, methane conversion, higher hydrocarbons
A sugarcane cystatin (CaneCPI-5) alters microcosm biofilm formation and reduces dental caries

Abstract The antimicrobial and anticaries effects of CaneCPI-5 were evaluated. Ninety bovine enamel samples were treated for 60 s with either phosphate-buffered-saline (PBS), 0.12% chlorhexidine (CHX), 0.05 mg ml−1 CaneCPI-5, 0.1 mg ml−1 CaneCPI-5 or 0.5 mg ml−1 CaneCPI-5. They were incubated with inoculum (human saliva + McBain's saliva) for the first 8 h. From then until the end of the experiment, the enamel was exposed to McBain saliva with sucrose and, once a day, for 5 days, they were treated with the solutions. At the end of the experimental period, resazurin and viable plate count assays were performed. Enamel demineralization was also measured. All concentrations of CaneCPI-5 and CHX significantly reduced the activity of biofilms compared with PBS. For viable plate counts, all treatments similarly reduced the lactobacilli and total streptococci; for the mutans streptococci, 0.05 mg ml−1 CaneCPI-5 performed better than CHX. All CaneCPI-5 concentrations significantly reduced the integrated mineral loss. This study represents the first step regarding the use of CaneCPI-5 within the concept of acquired enamel pellicle and biofilm engineering to prevent dental caries.
Modifying Plant Photosynthesis and Growth via Simultaneous Chloroplast Transformation of Rubisco Large and Small Subunits.

Engineering improved Rubisco for the enhancement of photosynthesis is challenged by the alternate locations of the chloroplast rbcL gene and nuclear RbcS genes. Here we develop an RNAi-RbcS tobacco (Nicotiana tabacum) master-line, tobRrΔS, for producing homogenous plant Rubisco by rbcL-rbcS operon chloroplast transformation. Four genotypes encoding alternative rbcS genes and adjoining 5'-intergenic sequences revealed that Rubisco production was highest (50% of the wild type) in the lines incorporating a rbcS gene whose codon use and 5' untranslated-region matched rbcL. Additional tobacco genotypes produced here incorporated differing potato (Solanum tuberosum) rbcL-rbcS operons that either encoded one of three mesophyll small subunits (pS1, pS2, and pS3) or the potato trichome pST-subunit. The pS3-subunit caused impairment of potato Rubisco production by ∼15% relative to the lines producing pS1, pS2, or pST. However, the βA-βB loop Asn-55-His and Lys-57-Ser substitutions in the pS3-subunit improved carboxylation rates by 13% and carboxylation efficiency (CE) by 17%, relative to potato Rubisco incorporating pS1 or pS2-subunits. Tobacco photosynthesis and growth were most impaired in lines producing potato Rubisco incorporating the pST-subunit, which reduced CE and CO2/O2 specificity 40% and 15%, respectively. Returning the rbcS gene to the plant plastome provides an effective bioengineering chassis for introduction and evaluation of novel homogeneous Rubisco complexes in a whole plant context.
A nuclear export sequence promotes CRM1-dependent targeting of the nucleoporin Nup214 to the nuclear pore complex

ABSTRACT Nup214 is a major nucleoporin on the cytoplasmic side of the nuclear pore complex with roles in late steps of nuclear protein and mRNA export. It interacts with the nuclear export receptor CRM1 (also known as XPO1) via characteristic phenylalanine-glycine (FG) repeats in its C-terminal region. Here, we identify a classic nuclear export sequence (NES) in Nup214 that mediates Ran-dependent binding to CRM1. Nup214 versions with mutations in the NES, as well as wild-type Nup214 in the presence of the selective CRM1 inhibitor leptomycin B, accumulate in the nucleus of Nup214-overexpressing cells. Furthermore, physiological binding partners of Nup214, such as Nup62 and Nup88, are recruited to the nucleus together with Nup214. Nuclear export of mutant Nup214 can be rescued by artificial nuclear export sequences at the C-terminal end of Nup214, leading also to a correct localization of Nup88. Our results suggest a function of the Nup214 NES in the biogenesis of the nuclear pore complex and/or in terminal steps of CRM1-dependent protein export. Summary: A nuclear export sequence in Nup214 may help to localize the protein to the cytoplasmic side of the nuclear pore complex.
Expression of virulence factors under different environmental conditions in Aggregatibacter actinomycetemcomitans

Aggregatibacter actinomycetemcomitans is a facultative anaerobic Gram‐negative bacterium associated with periodontal diseases, especially aggressive periodontitis. The virulence factors of this pathogen, including adhesins, exotoxins, and endotoxin, have been extensively studied. However, little is known about their gene expression mode in the host. Herein, we investigated whether culture conditions reflecting in vivo environments, including serum and saliva, alter expression levels of virulence genes in the strain HK1651, a JP2 clone. Under aerobic conditions, addition of calf serum (CS) into a general medium induced high expression of two outer membrane proteins (omp100 and omp64). The high expression of omp100 and omp64 was also induced by an iron‐limited medium. RNA‐seq analysis showed that the gene expressions of several factors involved in iron acquisition were increased in the CS‐containing medium. When HK1651 was grown on agar plates, genes encoding many virulence factors, including the Omps, cytolethal distending toxin, and leukotoxin, were differentially expressed. Then, we investigated their expression in five other A. actinomycetemcomitans strains grown in general and CS‐containing media. The expression pattern of virulence factors varied among strains. Compared with the other five strains, HK1561 showed high expression of omp29 regardless of the CS addition, while the gene expression of leukotoxin in HK1651 was higher only in the medium without CS. HK1651 showed reduced biofilm in both CS‐ and saliva‐containing media. Coaggregation with Fusobacterium nucleatum was remarkably enhanced using HK1651 grown in the CS‐containing medium. Our results indicate that the expression of virulence factors is altered by adaptation to different conditions during infection.
Geoestatística na avaliação dos atributos físicos em latossolo sob floresta nativa e pastagem na Região de Manicoré, Amazonas

A utilizacao das tecnicas geoestatisticas permite detectar a existencia da dependencia e distribuicao espacial dos atributos do solo, constituindo importante ferramenta na analise e descricao detalhada do comportamento dos atributos fisicos do solo. Este trabalho teve como objetivo o uso da geoestatistica na avaliacao dos atributos fisicos em Latossolo sob floresta nativa e pastagem na regiao de Manicore no Amazonas. Nas areas de floresta nativa e pastagem, foram estabelecidas malhas com dimensao 70 × 70 m e demarcados pontos nessas malhas espacados a cada 10 m, totalizando 64 pontos. Esses pontos foram georreferenciados e, em seguida, foram feitas as coletadas de solo em cada ponto da malha nas camadas de 0,00-0,20 e 0,40-0,60 m para determinacao dos atributos fisicos, totalizando 128 amostras de solo em cada malha. Essas malhas encontram-se paralelas com uma distância uma da outra de 100 m e o solo nessas areas e classificado como Latossolo. Determinaram-se textura, densidade do solo e de particulas, macroporosidade, microporosidade, porosidade total e estabilidade dos agregados em agua. Apos a tabulacao dos dados, foram realizadas analises estatisticas descritivas e geoestatistica. A pastagem apresentou leve variacao nos seus atributos fisicos em relacao a floresta nativa, com coeficiente de variacao alto e dependencia espacial fraca. Os semivariogramas escalonados conseguiram reproduzir de forma satisfatoria o comportamento espacial dos atributos no mesmo padrao dos semivariogramas individuais, e o uso do parâmetro alcance do semivariograma mostrou-se eficiente para determinar a densidade amostral ideal para os ambientes em estudo. Os resultados geoestatisticos indicaram que a retirada da floresta nativa para a implantacao da pastagem alterou a variabilidade natural dos atributos fisicos.
Exercise Plus Presleep Protein Ingestion Increases Overnight Muscle Connective Tissue Protein Synthesis Rates in Healthy Older Men.

Protein ingestion and exercise stimulate myofibrillar protein synthesis rates. When combined, exercise further increases the postprandial rise in myofibrillar protein synthesis rates. It remains unclear whether protein ingestion with or without exercise also stimulates muscle connective tissue protein synthesis rates. The authors assessed the impact of presleep protein ingestion on overnight muscle connective tissue protein synthesis rates at rest and during recovery from resistance-type exercise in older men. Thirty-six healthy, older men were randomly assigned to ingest 40 g intrinsically L-[1-13C]-phenylalanine and L-[1-13C]-leucine-labeled casein protein (PRO, n = 12) or a nonprotein placebo (PLA, n = 12) before going to sleep. A third group performed a single bout of resistance-type exercise in the evening before ingesting 40 g intrinsically-labeled casein protein prior to sleep (EX+PRO, n = 12). Continuous intravenous infusions of L-[ring-2H5]-phenylalanine and L-[1-13C]-leucine were applied with blood and muscle tissue samples collected throughout overnight sleep. Presleep protein ingestion did not increase muscle connective tissue protein synthesis rates (0.049 ± 0.013 vs. 0.060 ± 0.024%/hr in PLA and PRO, respectively; p = .73). Exercise plus protein ingestion resulted in greater overnight muscle connective tissue protein synthesis rates (0.095 ± 0.022%/hr) when compared with PLA and PRO (p < .01). Exercise increased the incorporation of dietary protein-derived amino acids into muscle connective tissue protein (0.036 ± 0.013 vs. 0.054 ± 0.009 mole percent excess in PRO vs. EX+PRO, respectively; p < .01). In conclusion, resistance-type exercise plus presleep protein ingestion increases overnight muscle connective tissue protein synthesis rates in older men. Exercise enhances the utilization of dietary protein-derived amino acids as precursors for de novo muscle connective tissue protein synthesis during overnight sleep.
Intratumoral CXCL13+CD8+T cell infiltration determines poor clinical outcomes and immunoevasive contexture in patients with clear cell renal cell carcinoma

Background Chemokine (C-X-C motif) ligand 13 (CXCL13) was known as a selective chemotaxis for B cells, a product of follicular helper CD4+T cells (TFH) and a contributor to tertiary lymphoid structures (TLS). Although secretion and function of CXCL13 produced by TFH have been deeply explored, the immune function and prognostic significance of CXCL13 secreted by CD8+T cells still remain unrevealed. This study aims to investigate the clinical merit of CXCL13+CD8+T cells in clear cell renal cell carcinoma (ccRCC). Methods We analyzed prognostic value and immune contexture that associated with CXCL13+CD8+T cells infiltration level in a total of 755 patients from Zhongshan Hospital cohort (n=223) and The Cancer Genome Atlas cohort (n=532). In vitro analyses were conducted on 42 samples of resected tumor tissue from Zhongshan Hospital in order to detect the immune status of CXCL13+CD8+T cells and total CD8+T cells. Immunohistochemistry (IHC) and flow cytometry were applied to characterize immune cells and portray the tumor microenvironment (TME) in ccRCC. Results Intratumoral CXCL13+CD8+T cells abundance was associated with inferior overall survival and disease-free survival. CXCL13+CD8+T cells possessed higher level of immune checkpoints like programmed cell-death protein 1 (PD-1), T-cell immunoglobulin mucin 3 (Tim-3), T cell immunoreceptor with Ig and ITIM domains (TIGIT) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), higher Ki-67 expression and lower tumor necrosis factor α (TNF-α), interferon γ (IFN-γ) expression. Total CD8+T cells in high-level CXCL13+CD8+T cells infiltration subgroup exhibited elevated exhausted markers (PD-1, Tim-3, TIGIT) and descended activated markers (TNF-α, IFN-γ) without quantity variance. Furthermore, the abundance of intratumoral CXCL13+CD8+T cell was correlated with immunoevasive TME accompanied by increased T helper 2 cells, tumor-associated macrophages, Foxp3+ regulatory T cells, TLS and decreased natural killer cells, GZMB+ cells. Conclusions Intratumoral CXCL13+CD8+T cells infiltration indicated inferior clinical outcome in patients with ccRCC. CXCL13+CD8+T cells possessed increased exhausted markers, decreased effector molecules and better proliferation ability. CXCL13+CD8+T cells abundance impaired total CD8+T cells’ immune function. Intratumoral CXCL13+CD8+T cells abundance was associated with immunoevasive contexture. The abundance of CXCL13+CD8+T cells was an independent prognosticator and a potential immunotherapeutic target marker for ccRCC treatment.
Phase 4 Safety and Efficacy Study of Antihemophilic Factor (Recombinant) in Previously Treated Chinese Patients With Severe/Moderately Severe Hemophilia A

Antihemophilic factor (recombinant) (rAHF; ADVATE®; Baxalta US Inc., a Takeda company, Lexington, MA, USA) is indicated for the treatment and prevention of bleeding in patients with hemophilia A. We aimed to assess the safety and efficacy of standard prophylaxis versus on-demand treatment with rAHF in previously treated Chinese patients with severe/moderately severe hemophilia A. This open-label, sequential, interventional, postapproval study (NCT02170402) conducted in China included patients of any age with hemophilia A with factor VIII (FVIII) level ≤2%. Patients received 6 months’ on-demand rAHF then 6 months’ rAHF prophylaxis (20-40 IU/kg every 48 ± 6 hours). The primary objective was percentage reduction in annualized bleeding rate (ABR) in the per-protocol analysis set (PPAS); secondary objectives included ABR by bleeding subtype, hemostatic efficacy, immunogenicity, and safety. Of 72 patients who received ≥1 rAHF dose, 61 were included in the PPAS. Total ABR was lower during prophylaxis (mean 2.5, 95% CI 1.5-3.7; median 0) versus on-demand treatment (mean 58.3, 95% CI 52.5-64.7; median 53.9), representing a 95.9% risk reduction. Similar findings in favor of prophylaxis were observed for all types of bleeding event by cause and location. rAHF hemostatic efficacy was rated as “excellent”/“good” in 96.1% of treated bleeding events. Transient FVIII inhibitors (0.6-1.7 BU) in 4 patients resolved before study end; no unexpected safety issues were observed. rAHF prophylaxis in this study of previously treated Chinese patients with severe/moderately severe hemophilia A resulted in a clear reduction in bleeding events versus rAHF on-demand treatment, with no change in safety profile.
Clonal similarities and sequence-type diversity of invasive and carriage Streptococcus pneumoniae in India among children under 5 Years

Background: Pneumococcal pneumonia is one of the major causes of mortality in children less than 5 years in Asia, especially in India. Available PCVs have less serotype coverage in India compared to western countries. Moreover, the baseline pneumococcal serotype and sequence type data is limited and available data doesn't represent the entire India. With this background we aimed to characterize invasive and carriage isolates of S. pneumoniae from a tertiary care hospital in South India. Materials and Methods: A total of 221 S. pneumoniae isolates, invasive (n=138) and carriage (n=83) between the time period of 2012-2018 were included. Isolates was identified and confirmed using standard laboratory protocols. Serotyping was performed by Customized sequential multiplex PCR and MLST as described in www.pubmlst. org. Results: The major serotypes were 19F, 6B, 14, 6A and 19A and the sequence types (ST) were ST63, 236 and 230. Predominant STs in invasive was ST 63 whereas in carriage were ST4894 and 1701. High level ST diversity in carriage was observed. Majority of the STs were SLVs or DLVs of previously reported STs or PMEN clones. Phylogenetic analyses of the STs revealed gradual expansion of three PMEN CCs CC320, 63 and 230. Conclusion: The vaccine serotypes were the predominant ones found to be associated with IPD, PMEN clones, new STs and antimicrobial resistance. Accordingly, PCV13 is expected to provide invasive serotype coverage of 75% in Indian children less than 5 years. This study provides baseline serotype and sequence type data prior to the introduction of PCV in South India.
Prevalence of NAFLD, MAFLD and associated advanced fibrosis in the contemporary United States population

Data are limited on the epidemiological implications of the recent change in terminology from nonalcoholic fatty liver disease (NAFLD) to metabolic dysfunction‐associated fatty liver disease (MAFLD). We therefore performed a cross‐sectional study of adults recruited in the 2017‐2018 National Health and Nutrition Examination Survey, a representative sample of the general US population. The prevalence of NAFLD and MAFLD based on controlled attenuation parameter (CAP) and liver stiffness measurement (LSM) obtained through vibration‐controlled transient elastography (VCTE) were 37.1% (95% CI 34.0‐40.4) and 39.1% (95% CI 36.3‐42.1), respectively, with higher rates among Hispanic individuals. Agreement between the two definitions was high (Cohen's κ 0.92). Patients with NAFLD and MAFLD also showed similar risk of advanced liver fibrosis (7.5% and 7.4% respectively). Our results suggest that the recent change in diagnostic criteria did not affect the prevalence of the condition in the general United States population.
Several geranylgeranyl diphosphate synthase isoforms supply metabolic substrates for carotenoid biosynthesis in tomato

Geranylgeranyl diphosphate (GGPP) produced by GGPP synthase (GGPPS) serves as a precursor for many plastidial isoprenoids, including carotenoids. Here we show that five different GGPPS isoforms exist in tomato (Solanum lycopersicum). From these, SlGGPPS1, 2 and 3 (or SlG1-3 in short) produce GGPP in plastids and exhibit similar kinetic parameters. Phytoene synthase (PSY) converts GGPP into phytoene, the first committed intermediate of the carotenoid pathway. Gene expression and co-expression network analyses showed a preferential association of individual GGPPS and PSY isoforms in processes linked to carotenoid biosynthesis such as root mycorrhization, seedling deetiolation and fruit ripening. Co-immunoprecipitation experiments showed that SlG2, but not SlG3, physically interacts with PSY proteins. By contrast, CRISPR-Cas9 mutants defective in SlG3 showed a stronger impact on carotenoid levels and derived metabolic, physiological and developmental phenotypes that those impaired in SlG2. Double mutants with a simultaneous knockout of both genes could not be found. Our work demonstrates that the bulk of GGPP production in tomato chloroplasts and chromoplasts relies on two cooperating GGPPS paralogs, unlike other plant species such as Arabidopsis thaliana, rice or pepper, which produce their essential plastidial isoprenoids using a single GGPPS isoform.
A causal relationship between rheumatoid arthritis and bronchiectasis? A systematic review and meta-analysis

Rheumatoid arthritis (RA) is a chronic autoimmune disease primarily affecting joints but often also associated with lung involvement such as bronchiectasis (BE). The aim of the present systematic review and meta-analysis is to provide an update on the current evidence regarding the prevalence and association between RA and BE. This systematic review and meta-analysis was performed in accordance with the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines with literature search using the terms ‘Bronchiectasis AND Rheumatoid Arthritis’ without a date limitation on PubMed during May 2020. A total of 28 studies fulfilled the predefined criteria and were included in the present review, with 19 being cross-sectional studies. Twenty-three studies were included in the meta-analysis. The pooled prevalence estimate was 2.69% (95% CI 1.63–4.42) in clinically defined BE, and 24.9% (95% CI 19.21–31.67) in radiologic disease. Many inconsistencies exist regarding potential risk factors for BE in RA patients such as gender, RA duration and severity, as both negative and positive associations have been reported. Although very little is known about possible causative mechanisms between RA and BE, potential pathways might be antigenic stimulation from pulmonary mucus and/or systemic inflammation from joint disease affecting the lungs. At present, the available evidence of bronchiectasis in patients with RA is insufficient to identify RA-associated risk factors for the development of BE, possibly apart from duration of RA, and, consequently, also to fully explore a possible causal relationship between the two disease. However, the increased prevalence of BE in RA patients warrants further studies to explore the association between RA and BE.