Miracle-dz/UniFAR-FTUs huggingface dataset:
Excess Risk of Lung Cancer Among Agriculture and Construction Workers in Indonesia

Background: In Indonesia, many occupations and industries involve a variety of hazardous and toxic materials. The ILO estimates that about 21.1% of the tracheal, bronchial, and lung cancer deaths among men were attributable to workplace hazardous substances. This study investigated the relationship between occupations or workplace exposure and the risk of lung cancer in the country. The results will help determine how Indonesia can best mitigate the risk for its workers. Objectives: This case-control study utilizes the Indonesian Standard of Industrial Classification (IndSIC) 2015 with the aim of exploring the risk of lung cancer among Indonesian workers. Methods: The study included patients aged 35 years old or older receiving thoracic CT at the radiology department of Persahabatan Hospital. The cases were histological-confirmed primary lung cancers, while the controls were negative thoracic CT scan for lung cancer. The subjects’ job titles and industries were classified according to IndSIC 2015 and blind to the patient’s grouping as a case or control. Logistic regression was used to determine the odds ratios for lung cancer among all sections and some divisions or groups of IndSIC 2015. Findings: The mean age was 58.1 (±10.23) years for lung cancer patients and 54.5 (±10.23) years for controls. The majority of subjects (19.6%) worked in Section G (Wholesale and retail trade; repair of motor vehicles and motorcycle). After adjusting for age, gender, level of education, and smoking habit, the risk of lung cancer was nearly three-times higher (OR = 2.8, 95% CI = 1.11–7.02) in workers of Division A01 (crop, animal production, and hunting) and two-times higher (OR = 1.9, 95% CI = 1.05–3.46) in workers of Section F (construction) compared to the workers in other sections or divisions. Conclusions: The excess risk of lung cancer among certain categories of workers confirms the need for improved policy, monitoring, and control of occupational exposure for primary cancer prevention and workers’ compensation purposes.
A Bibliographic Assessment Using the Degrees of Publication Method: Medicinal Plants from the Rural Greater Mpigi Region (Uganda)

In ethnopharmacological research, many field assessment tools exist. Yet, these miss that critical point of how to really determine which species merit the costly lab studies, e.g., evaluation of traditional use via pharmacological assays and isolation of bioactive secondary metabolites. This gap can be filled with the introduction of a new tool for literature assessment: the Degrees of Publication (DoPs). In this study, its application is illustrated through an extensive bibliographic assessment of 16 medicinal plant species that were recently identified in the Greater Mpigi region of Uganda as being frequently used by local traditional healers in the treatment of medical disorders (namely, Albizia coriaria, Cassine buchananii, Combretum molle, Erythrina abyssinica, Ficus saussureana, Harungana madagascariensis, Leucas calostachys, Microgramma lycopodioides, Morella kandtiana, Plectranthus hadiensis, Securidaca longipedunculata, Sesamum calycinum subsp. angustifolium, Solanum aculeastrum, Toddalia asiatica, Warburgia ugandensis, and Zanthoxylum chalybeum). These species are suspected to be understudied, and a thorough bibliographic assessment has not been previously performed. Thus, the objectives of our study were to undertake a comparative assessment of the degree to which each of these plant species has been studied in the past, including evaluation of the quality of the journals where results were published in. The determination of the DoPs enabled successful assessment of the degrees to which each individual plant species has been studied so far, while also taking into account the methodological “research chain of ethnopharmacology” from ethnobotanical studies (“traditional use”) to pharmacological assays (“bioactivity”) and finally to pharmacognostic research (“structure elucidation”). The significance of a research paper was assessed by determining whether its journal and publishing house were members of the Committee on Publication Ethics (COPE). In total, 634 peer-reviewed publications were reviewed covering the period of 1960–2019, 53.3% of which were published in journals and by publishing houses affiliated with COPE (338 publications). The literature assessment resulted in the identification of understudied plants among the selected species. The majority of plants reviewed have not been sufficiently studied; six species were classified as being highly understudied and three more as being understudied: C. buchananii, F. saussureana, L. calostachys, M. lycopodioides, M. kandtiana, and S. calycinum subsp. angustifolium and A. coriaria, P. hadiensis, and S. aculeastrum, respectively. The newly introduced DoPs are a useful tool for the selection of traditionally used species for future laboratory studies, especially for pharmacological bioassays, isolation procedures, and drug discovery strategies.
Identification and analysis of lncRNA, microRNA and mRNA expression profiles and construction of ceRNA network in Talaromyces marneffei-infected THP-1 macrophage

Background Competitive endogenous RNA (ceRNA) reveals new mechanisms for interactions between RNAs, which have been considered to play a significant role in pathogen-host innate immune response. However, knowledge of ceRNA regulatory networks in Talaromyces marneffei (TM)-macrophages is still limited. Methods Next-generation sequencing technology (NGS) was used to obtain mRNA, miRNA and lncRNA expression profiles in TM-infected macrophages. The R package DESeq2 was used to identify differentially expressed lncRNA, miRNA and mRNA. The R package GOseq was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and the ceRNA network of lncRNA–miRNA–mRNA interaction was constructed in Cytoscape. Similarly, functional enrichment analysis on mRNA in the ceRNA network. Finally, two mRNAs and four lncRNAs in the ceRNA network were randomly selected to verify the expression using qRT-PCR. Results In total, 119 lncRNAs, 28 miRNAs and 208 mRNAs were identified as differentially expressed RNAs in TM-infected macrophages. The constructed ceRNA network contains 38 lncRNAs, 10 miRNAs and 45 mRNAs. GO and KEGG analysis of mRNA in the ceRNA network indicated that activated pathways in TM-infected macrophages were related to immunity, inflammation and metabolism. The quantitative validation of the expression of four randomly selected differentially expressed lncRNAs, AC006252.1, AC090197.1, IL6R-AS1, LINC02009 and two mRNAs, CSF1, NR4A3 showed that the expression levels were consistent with those in the RNA-sequencing. Conclusions The ceRNA network related to immunity, inflammation and metabolism plays an important role in TM-macrophage interaction. This study may provide effective and novel insights for further understanding the underlying mechanism of TM infection.
The Impact of Tai Chi on Motor Function, Balance, and Quality of Life in Parkinson's Disease: A Systematic Review and Meta-Analysis

Objective Parkinson's disease adversely affects function and quality of life, leading to increased mortality. The practice of Tai Chi has been associated with multifaceted improvements in health-related fitness. Considering the limited number of clinical studies included in previous reviews, inconsistent methodological quality, and inconclusive results, this meta-analysis aims to assess the effects of Tai Chi in patients with Parkinson's disease. Method Four English language databases and four Chinese databases were systematically searched for existing randomized controlled trials (RCTs) of Tai Chi in Parkinson's disease from database inception through August 1, 2020. Methodological quality was appraised with the Cochrane Risk of Bias tool. A meta-analysis of comparative effects was performed using the Review Manager v.5. 3 software. Results Seventeen published RCTs totaling 951 subjects were included. Results showed that Tai Chi has a statistically significant effect on the outcomes of gait velocity, unified Parkinson's disease rating scale (UPDRS) motor score, activities-specific balance confidence (ABC) score, and Berg Balance Scale (BBS). The effects on the Timed Up and Go Test (TUGT) and Parkinson's Disease Questionnaire-39 (PDQ-39) were not statistically significant. Conclusions This systematic review and meta-analysis of Parkinson's disease and Tai Chi suggests Tai Chi is a relatively safe activity that can result in gains in general motor function and improve bradykinesia and balance. It has no statistically significant advantage for quality of life and functional mobility. Further randomized trials with larger sample sizes and of higher methodological quality are needed to confirm these results and to assess the feasibility of Tai Chi intervention for potential different clinical applications.
Study of Flavonoid/Hydroxypropyl-β-Cyclodextrin Inclusion Complexes by UV-Vis, FT-IR, DSC, and X-Ray Diffraction Analysis

The objective of this study was to investigate characterization of inclusion complexes of flavonoids with hydroxypropyl-β-cyclodextrin (HP-β-CD). The inclusion complexes of flavonoids with HP-β-CD was prepared by the freeze-drying method and its characterization was investigated by different analytical techniques including ultraviolet-visible spectroscopy, Fourier transform infrared spectroscopy (FT-IR), differential scanning calorimetry, and X-ray diffractometry. The catechin/HP-β-CD complex exhibited the highest encapsulation efficiency (83.37%), followed by epicatechin/HP-β-CD (81.51%), morin hydrate/HP-β-CD (81.38%), and quercetin/HP-β-CD (81.16%). The inclusion complexes of HP-β-CD showed a decrease in the absorption of flavonoids with a small shift (≈2 nm) of the λmax, while similar to the characteristic absorption peak of flavonoids. However, the FT-IR spectra of the flavonoid/HP-β-CD inclusion complexes did not display any features that were like the pure flavonoids, although the spectra were very similar to that of HP-β-CD. The melting point of flavonoids disappeared, and the thermal properties of HP-β-CD were altered following formation of the inclusion complex between flavonoids and HP-β-CD, resulting in a shift in the melting peak.
Identification of Potential Gene and MicroRNA Biomarkers of Acute Kidney Injury

Acute kidney injury (AKI) is a disease that seriously endangers human health. At present, AKI lacks effective treatment methods, so it is particularly important to find effective treatment measures and targets. Bioinformatics analysis has become an important method to identify significant processes of disease occurrence and development. In this study, we analyzed the public expression profile with bioinformatics analysis to identify differentially expressed genes (DEGs) in two types of common AKI models (ischemia-reperfusion injury and cisplatin). DEGs were predicted in four commonly used microRNA databases, and it was found that miR-466 and miR-709 may play important roles in AKI. Then, we found key nodes through protein-protein interaction (PPI) network analysis and subnetwork analysis. Finally, by detecting the expression levels in the renal tissues of the two established AKI models, we found that Myc, Mcm5, E2f1, Oip5, Mdm2, E2f8, miR-466, and miR-709 may be important genes and miRNAs in the process of AKI damage repair. The findings of our study reveal some candidate genes, miRNAs, and pathways potentially involved in the molecular mechanisms of AKI. These data improve the current understanding of AKI and provide new insight for AKI research and treatment.
Methicillin-Resistant Coagulase-Negative Staphylococci Carriage is a Protective Factor of Methicillin-Resistant Staphylococcus Aureus Nasal Colonization in HIV-Infected Patients: A Cross-Sectional Study

Background Methicillin-resistant coagulase-negative Staphylococci (MRCoNS) is regarded as the repository of mecA gene for methicillin-resistant Staphylococcus aureus (MRSA) and may develop methicillin-susceptible Staphylococcus aureus (MSSA) to MRSA. Therefore, we aimed to explore whether MRCoNS carriage is a risk factor of MRSA colonization. Phenotypic characteristics were performed to further assess the associations between MRSA and MRCoNS. Methods This cross-sectional study was conducted in Guangzhou, China. Participants completed a questionnaire and provided a nasal swab for further analysis. The risk factors of MRSA colonization were analyzed using nonconditional logistic regression models. The phenotypic characteristics between MRSA and MRCoNS were compared by Chi-square test. Results Among the 1001 HIV-infected patients, a total of 119 (11.89%) participants were positive for MRSA, and 34.45% (41/119) of all MRSA carriers were positive for MRCoNS. We found MRCoNS carriage was a protective factor of MRSA colonization (adjusted odds ratio = 0.59, 95% confidence interval: 0.38–0.91). A significant difference in the proportions of antibiotic resistance between MRSA and MRCoNS isolates was found except for penicillin, clindamycin, tetracycline, and teicoplanin. The main STs and CC types of MRSA isolates in this population were ST188 (15.1%) and CC59 (17.6%), respectively. Conclusions HIV-infected patients remain a highly vulnerable population for MRSA colonization. Though who carried MRCoNS is less likely to have MRSA colonization, similarity of some antibiotic resistance between MRSA and MRCoNS was found in this study. Regular surveillance on the colonization and antibiotic patterns of MRSA and MRCoNS is still necessary.
Ordered and twinned structure in hexagonal-based potassium tungsten bronze nanosheets

Non-stoichiometric hexagonal-based potassium tungsten bronze (KxWO3) nanosheets were synthesized by oxidizing tungsten foil in potassium hydroxide. The tungsten bronze nanosheets exhibited an ordered monoclinic superstructure as revealed by X-ray diffraction patterns. Further detailed structural investigation by employing electron microscopy techniques showed the coexistence of 120° rotation twinning variants in the superstructure phase, which may result from the rotation symmetry reduction induced by the ordered arrangements of K vacancies during crystal growth.
A new caimanine alligatorid from the Middle Eocene of Southwest Texas and implications for spatial and temporal shifts in Paleogene crocodyliform diversity

Dramatic early Cenozoic climatic shifts resulted in faunal reorganization on a global scale. Among vertebrates, multiple groups of mammals (e.g., adapiform and omomyiform primates, mesonychids, taeniodonts, dichobunid artiodactyls) are well known from the Western Interior of North America in the warm, greenhouse conditions of the early Eocene, but a dramatic drop in the diversity of these groups, along with the introduction of more dry-tolerant taxa, occurred near the Eocene–Oligocene boundary. Crocodyliforms underwent a striking loss of diversity at this time as well. Pre-Uintan crocodyliform assemblages in the central Western Interior are characterized by multiple taxa, whereas Chadronian assemblages are depauperate with only Alligator prenasalis previously known. Crocodyliform diversity through the intervening Uintan and Duchesnean is not well understood. The middle Eocene Devil’s Graveyard Formation (DGF) of southwest Texas provides new data from southern latitudes during that crucial period. A new specimen from the middle member of the DGF (late Uintan–Duchesnean) is the most complete cranial material of an alligatorid known from Paleogene deposits outside the Western Interior. We identify this specimen as a caimanine based on notched descending laminae of the pterygoids posterior to the choanae and long descending processes of the exoccipitals that are in contact with the basioccipital tubera. Unlike Eocaiman cavernensis, the anterior palatine process is rounded rather than quadrangular. The relationships and age of this new taxon support the hypothesis that the modern distribution of caimanines represents a contraction of a more expansive early Cenozoic distribution. We hypothesize that the range of caimanines tracked shifting warm, humid climatic conditions that contracted latitudinally toward the hothouse-icehouse transition later in the Eocene.
Identification of a novel association for the WWOX/HIF1A axis with gestational diabetes mellitus (GDM)

Background Although the WW-domain-containing oxidoreductase (WWOX)/Hypoxia-inducible factor 1 (HIF1) pathway is a well-known regulator of cellular glucose and energy metabolism in pathophysiological processes, its role in gestational diabetes mellitus (GDM), remains elusive. We undertook this study to determine the effect of WWOX/HIF1A signaling on the expression of glucose metabolism genes in GDM patients. Methods Leukocytes were obtained from 135 pregnant women with (n = 98) or without (n = 37) GDM and, in turn, 3 months (n = 8) and 1 year (n = 12) postpartum. Quantitative RT-PCR was performed to determine gene expression profiles of the WWOX/HIF1A-related genes, including those involved in glucose transport (SLC2A1, SLC2A4), glycolytic pathway (HK2, PKM2, PFK, LDHA), Wnt pathway (DVL2, CTNNB1), and inflammatory response (NFKB1). Results GDM patients displayed a significant downregulation of WWOX with simultaneous upregulation of HIF1A which resulted in approximately six times reduction in WWOX/HIF1A ratio. As a consequence, HIF1A induced genes (SLC2A1, HK2, PFK, PKM) were found to be overexpressed in GDM compared to normal pregnancy and negative correlate with WWOX/HIF1A ratio. The postpartum WWOX expression was higher than during GDM, but its level was comparable to that observed in normal pregnancy. Conclusions The obtained results suggest a significant contribution of the WWOX gene to glucose metabolism in patients with gestational diabetes. Decreased WWOX expression in GDM compared to normal pregnancy, and in particular reduction of WWOX/HIF1A ratio, indicate that WWOX modulates HIF1α activity in normal tissues as described in the tumor. The effect of HIF1α excessive activation is to increase the expression of genes encoding proteins directly involved in the glycolysis which may lead to pathological changes in glucose metabolism observed in gestational diabetes.
Astaxanthin Alleviates Ochratoxin A-Induced Cecum Injury and Inflammation in Mice by Regulating the Diversity of Cecal Microbiota and TLR4/MyD88/NF-κB Signaling Pathway

Ochratoxin A (OTA) is a common environmental pollutant found in a variety of foods and grains, and excessive OTA consumption causes serious global health effects on animals and humans. Astaxanthin (AST) is a natural carotenoid that has anti-inflammatory, antiapoptotic, immunomodulatory, antitumor, antidiabetes, and other biological activities. The present study is aimed at investigating the effects of AST on OTA-induced cecum injury and its mechanism of action. Eighty C57 mice were randomly divided into four groups, including the control group, OTA group (5 mg/kg body weight), AST group (100 mg/kg body weight), and AST intervention group (100 mg/kg body weight AST+5 mg/kg body weight OTA). It was found that AST decreased the endotoxin content, effectively prevented the shortening of mouse cecum villi, and increased the expression levels of tight junction (TJ) proteins, consisting of occludin, claudin-1, and zonula occludens-1 (ZO-1). AST increased the number of goblet cells, the contents of mucin-2 (MUC2), and defensins (Defa5 and β-pD2) significantly, while the expression of mucin-1 (MUC1) decreased significantly. The 16S rRNA sequencing showed that AST affected the richness and diversity of cecum flora, decreased the proportion of lactobacillus, and also decreased the contents of short-chain fatty acids (SCFAs) (acetate and butyrate). In addition, AST significantly decreased the expression of TLR4, MyD88, and p-p65, while increasing the expression of p65. Meanwhile, the expression of inflammatory factors including TNF-α and INF-γ decreased, while the expression of IL-10 increased. In conclusion, AST reduced OTA-induced cecum injury by regulating the cecum barrier function and TLR4/MyD88/NF-κB signaling pathway.
Freezing of Gait in Parkinson's Disease: Risk Factors, Their Interactions, and Associated Nonmotor Symptoms

Background Freezing of gait (FOG) is a debilitating and incompletely understood symptom in Parkinson's disease (PD). Objective To determine the principal clinical factors predisposing to FOG in PD, their interactions, and associated nonmotor symptoms. Methods 164 PD subjects were assessed in a cross-sectional retrospective study, using the MDS-UPDRS scale, MMSE, and Clinical Dementia Rating Scale. Clinical factors associated with FOG were determined using univariate analysis and nominal logistic regression. Receiver operating characteristic curves were computed, to obtain measures of sensitivity and specificity of predictors of FOG. Subgroups of patients with FOG were compared with those without FOG, based on defining aspects of their clinical phenotype. Results Relative to non-FOG patients, those with FOG had a longer disease duration, higher PIGD and balance-gait score, higher LED, and more motor complications (p < 0.0001) and were more likely to exhibit urinary dysfunction (p < 0.0003), cognitive impairment, hallucinations, and psychosis (p=0.003). The balance-gait score and motor complications, at their optimum cutoff values, together predicted FOG with 86% accuracy. Interactions were noted between cognitive dysfunction and both the Bal-Gait score and motor complication status, cognitive impairment or dementia increasing the likelihood of FOG in subjects without motor complications (p=0.0009), but not in those with motor complications. Conclusions Both disease and treatment-related factors, notably LED, influence the risk of FOG in PD, with a selective influence of cognitive dysfunction in patients with balance-gait disorder but not in those with motor fluctuations. These findings may help to inform clinical management and highlight distinct subgroups of patients with PD-FOG, which are likely to differ in their network pathophysiology.
Birth Defects and Long-Term Neurodevelopmental Abnormalities in Infants Born During the Zika Virus Epidemic in the Dominican Republic

Background: When acquired during pregnancy, Zika virus (ZIKV) infection can cause substantial fetal morbidity, however, little is known about the long-term neurodevelopmental abnormalities of infants with congenital ZIKV exposure without microcephaly at birth. Methods: We conducted a cross sectional study to characterize infants born with microcephaly, and a retrospective cohort study of infants who appeared well at birth, but had possible congenital ZIKV exposure. We analyzed data from the Dominican Ministry of Health’s (MoH) National System of Epidemiological Surveillance. Neurodevelopmental abnormalities were assessed by pediatric neurologists over an 18-month period using Denver Developmental Screening Test II. Results: Of 800 known live births from 1,364 women with suspected or confirmed ZIKV infection during pregnancy, 87 (11%) infants had confirmed microcephaly. Mean head circumference (HC) at birth was 28.1 cm (SD ± 2.1 cm) and 41% had a HC on the zero percentile for gestational age. Of 42 infants with possible congenital ZIKV exposure followed longitudinally, 52% had neurodevelopmental abnormalities, including two cases of postnatal onset microcephaly, during follow-up. Most abnormalities resolved, though two infants (4%) had neurodevelopmental abnormalities that were likely associated with ZIKV infection and persisted through 15–18 months. Conclusions: In the DR epidemic, 11% of infants born to women reported to the MoH with suspected or confirmed ZIKV during pregnancy had microcephaly. Some 4% of ZKV-exposed infants developed postnatal neurocognitive abnormalities. Monitoring of the cohort through late childhood and adolescence is needed.