Miracle-dz/UniFAR-FTUs huggingface dataset:
Motile Cilia on Kidney Proximal Tubular Epithelial Cells Are Associated With Tubular Injury and Interstitial Fibrosis

It is well established that mammalian kidney epithelial cells contain a single non-motile primary cilium (9 + 0 pattern). However, we noted the presence of multiple motile cilia with a central microtubular pair (9 + 2 pattern) in kidney biopsies of 11 patients with various kidney diseases, using transmission electron microscopy. Immunofluorescence staining revealed the expression of the motile cilia-specific markers Radial Spoke Head Protein 4 homolog A, Forkhead-box-protein J1 and Regulatory factor X3. Multiciliated cells were exclusively observed in proximal tubuli and a relative frequent observation in human kidney tissue: in 16.7% of biopsies with tubular injury and atrophy (3 of 18 tissues), in 17.6% of biopsies from patients with membranous nephropathy (3 of 17 tissues) and in 10% of the human kidney tissues derived from the unaffected pole after tumour nephrectomy (3 of 30 tissues). However, these particular tissues showed marked tubular injury and fibrosis. Further analysis showed a significant relation between the presence of multiciliated cells and an increased expression of alpha-smooth-muscle-actin (p-value < 0.01) and presence of Kidney-injury-molecule-1 (p-value < 0.01). Interestingly, multiciliated cells co-showed staining for the scattered tubular cell markers annexin A2, annexin A3, vimentin and phosphofructokinase platelet but not with cell senescence associated markers, like (p16) and degradation of lamin B. In conclusion, multiciliated proximal tubular cells with motile cilia were frequently observed in kidney biopsies and associated with tubular injury and interstitial fibrosis. These data suggest that proximal tubular cells are able to transdifferentiate into multiciliated cells. Graphical Abstract
Clinical and Laboratory Features of PCR-Confirmed and Clinically Suspected COVID-19 Pediatric Patients: A Single Hospital-Based Experience During the First COVID-19 Wave in the United Arab Emirates

Objective This study investigated clinical and laboratory differences between confirmed (RT-PCR-positive) and clinically suspected (RT-PCR-negative) COVID-19 pediatric patients, and explored factors associated with disease severity at presentation and duration of hospitalization. Methods Medical charts of COVID-19-confirmed and clinically suspected pediatric patients admitted to a tertiary hospital in Abu Dhabi were reviewed. Sociodemographic information and clinical and laboratory outcomes were retrieved and analyzed. Results Between 1 April to 30 June, 2020, 173 patients (mean age: 3.6 ± SD 3.2 years) presented with respiratory symptoms. Of them, 18.0% had confirmed contact with COVID-19 cases, 66.5% had symptoms for ≤3 days, and 86.7% were with moderate to severe disease. Twenty-eight (16.1%) patients tested positive while the rest (83.8%) tested negative in RT-PCR. COVID-19-confirmed and clinically suspected patients were statistically similar (p > 0.05) in all sociodemographic data, disease severity, and vital signs except residence status (89.3% vs. 58.6% were residents, respectively, p = 0.002) and contact with confirmed COVID-19 cases (82.1% vs. 5.5%, respectively, p < 0.001). Fever (100 and 91.0%) and cough (100 and 95.9%) were the most common symptoms in both confirmed and clinically suspected COVID-19 patients. All patients were statistically comparable in mean white blood cell and platelet counts and hemoglobin concentration, except in mean concentration of neutrophils (higher in clinically suspected, p = 0.019). C-reactive protein was two times higher in clinically suspected compared to confirmed patients (p = 0.043). Lymphocyte (OR: 1.31, p < 0.001), LDH (OR: 1.01, p = 0.001), D-dimer (OR: 1.92, p < 0.001), and ferritin levels after 24–36 h (OR: 9.25, p < 0.05), and SGPT (OR: 1.04, p < 0.05) were all associated with disease severity. Elevated ferritin (>300 μg/L) after 24–36 h was the only correlated factor with disease severity (aOR: 17.38, p < 0.05). Confirmed compared with clinically suspected patients (aOR: 4.00, 95% CI: 2.92–5.10) and children with moderate compared with mild disease (aOR: 5.87, 95% CI: 1.08–32.06) had longer hospitalization. Conclusion In pediatric patients with negative RT-PCR, COVID-19 is still suspected based on clinical symptoms and epidemiological data. A tentative diagnosis can be made based on a thorough examination, and proper medical management can be initiated promptly.
Relationships Among Arsenic-Related Traits, Including Rice Grain Arsenic Concentration and Straighthead Resistance, as Revealed by Genome-Wide Association

There is global concern that rice grains and foods can contain harmful amounts of arsenic (As), motivating breeders to produce cultivars that restrict As accumulation in grains to protect human health. Arsenic is also toxic to plants, with straighthead disorder (StHD), causing panicle sterility, being observed in rice. The genetic variation in StHD resistance suggests that plants have evolved mechanisms that reduce As toxicity, possibly via regulation of As uptake, transport, or detoxification/sequestration. Because these mechanisms could also underlie the wide (3- to 100-fold) differences in grain As concentration (grain-As) observed among diverse rice genotypes, it was hypothesized that some genes reduce both grain-As content and StHD susceptibility and may be detectable as co-located StDH and As quantitative trait loci (QTL). We used a machine-learning Bayesian network approach plus high-resolution genome-wide association study (GWAS) to identify QTL for grain-As and StHD resistance within the USDA Rice Minicore Collection (RMC). Arsenic enters roots through phosphorus (P) and silica (Si) transporters, As detoxification involves sulfur (S), and cell signaling to activate stress tolerance mechanisms is impacted by Si, calcium (Ca), and copper (Cu). Therefore, concentrations of Si, P, S, Ca, and Cu were included in this study to elucidate physiological mechanisms underlying grain-As and StHD QTL. Multiple QTL (from 9 to 33) were identified for each of the investigated As-associated traits. Although the QTL for StHD, Si, and grain-As did not overlap as heavily as our hypothesis predicted (4/33 StHD and 4/15 As QTL co-located), they do provide useful guidance to future research. Furthermore, these are the first StHD and Si QTL to be identified using high-density mapping, resulting in their being mapped to shorter, more precise genomic regions than previously reported QTL. The candidate genes identified provide guidance for future research, such as gene editing or mutation studies to further investigate the role of antioxidants and ROS scavenging to StHD resistance, as indicated by candidate genes around the commonly reported qStHD8-2 QTL. Other genes indicated for future study for improving grain-As and StHD include several multidrug and toxic compound extrusion (MATE) genes, F-box genes, and NIPs not documented to date to transport As.
SSH2.0: A Better Tool for Predicting the Hydrophobic Interaction Risk of Monoclonal Antibody

Therapeutic antibodies play a crucial role in the treatment of various diseases. However, the success rate of antibody drug development is low partially because of unfavourable biophysical properties of antibody drug candidates such as the high aggregation tendency, which is mainly driven by hydrophobic interactions of antibody molecules. Therefore, early screening of the risk of hydrophobic interaction of antibody drug candidates is crucial. Experimental screening is laborious, time-consuming, and costly, warranting the development of efficient and high-throughput computational tools for prediction of hydrophobic interactions of therapeutic antibodies. In the present study, 131 antibodies with hydrophobic interaction experiment data were used to train a new support vector machine-based ensemble model, termed SSH2.0, to predict the hydrophobic interactions of antibodies. Feature selection was performed against CKSAAGP by using the graph-based algorithm MRMD2.0. Based on the antibody sequence, SSH2.0 achieved the sensitivity and accuracy of 100.00 and 83.97%, respectively. This approach eliminates the need of three-dimensional structure of antibodies and enables rapid screening of therapeutic antibody candidates in the early developmental stage, thereby saving time and cost. In addition, a web server was constructed that is freely available at http://i.uestc. edu.cn/SSH2/.
Bioinformatics and Experimental Analysis of the Prognostic and Predictive Value of the CHPF Gene on Breast Cancer

Background Recent studies in the United States have shown that breast cancer accounts for 30% of all new cancer diagnoses in women and has become the leading cause of cancer deaths in women worldwide. Chondroitin Polymerizing Factor (CHPF), is an enzyme involved in chondroitin sulfate (CS) elongation and a novel key molecule in the poor prognosis of many cancers. However, its role in the development and progression of breast cancer remains unclear. Methods The transcript expression of CHPF in the Cancer Genome Atlas-Breast Cancer (TCGA-BRCA), Gene Expression Omnibus (GEO) database was analyzed separately using the limma package of R software, and the relationship between CHPF transcriptional expression and CHPF DNA methylation was investigated in TCGA-BRCA. Kaplan-Meier curves were plotted using the Survival package to further assess the prognostic impact of CHPF DNA methylation/expression. The association between CHPF transcript expression/DNA methylation and cancer immune infiltration and immune markers was investigated using the TIMER and TISIDB databases. We also performed gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis with the clusterProfiler package. Western blotting and RT-PCR were used to verify the protein level and mRNA level of CHPF in breast tissue and cell lines, respectively. Small interfering plasmids and lentiviral plasmids were constructed for transient and stable transfection of breast cancer cell lines MCF-7 and SUM1315, respectively, followed by proliferation-related functional assays, such as CCK8, EDU, clone formation assays; migration and invasion-related functional assays, such as wound healing assay and transwell assays. We also conducted a preliminary study of the mechanism. Results We observed that CHPF was significantly upregulated in breast cancer tissues and correlated with poor prognosis. CHPF gene transcriptional expression and methylation are associated with immune infiltration immune markers. CHPF promotes proliferation, migration, invasion of the breast cancer cell lines MCF-7 and SUM1315, and is significantly enriched in pathways associated with the ECM-receptor interaction and PI3K-AKT pathway. Conclusion CHPF transcriptional expression and DNA methylation correlate with immune infiltration and immune markers. Upregulation of CHPF in breast cancer promotes malignant behavior of cancer cells and is associated with poorer survival in breast cancer, possibly through ECM-receptor interactions and the PI3K-AKT pathway.
Investigation of Allergic Sensitizations in Children With Allergic Rhinitis and/or Asthma

Objective Allergic rhinitis (AR) and asthma are becoming one of the most prevalent diseases in children. Identifying sensitization to aeroallergens is seemed to be valuable for diagnosing allergic disease and guiding its treatment. This study aimed to analyze the profiles of sensitization to aeroallergen in children with AR and/or asthma by skin prick test (SPT) and explore the differences of sensitization between different kinds of allergic diseases, different sexes, and different ages. Methods A total of 230 children with AR and/or asthma who were hospitalized in our hospital from June 2017 to September 2019 were eligible in this retrospective study. All patients completed standardized questionnaires and SPT. Based on the sex, age, or classification of allergic disease, the sensitizations to 13 aeroallergens were compared. Results Of the 230 patients, 67.4% of enrolled were positive for SPT; the top 5 allergens were Dermatophagoides pteronyssinus (Der.p) (59.3%), Dermatophagoides farina (Der.f ) (58.7%), Blomia tropicalis (Blot.) (40.3%), dog hair (36.1%), and Blattella germanica (20.4%). More than 90% of patients were sensitized to two or more allergens. As to the effect of age on aeroallergens, we found that the sensitizations of Blot. , dog fur, and multiple sensitizations (≥5 allergens) were more common in adolescence (P < 0.01, P < 0.05). Regarding sex, we found that the positive rate of SPT and the percentages of double-allergen sensitizations in boys were much higher than girls (P < 0.01, P < 0.01), and the positive rate to Der.p, Der.f , and ragweed were also significantly higher in boys (P < 0.01, P < 0.05, and P < 0.05, respectively). Furthermore, we found that asthma–rhinitis multimorbidity increased the incidences of sensitizations; patients with AR and asthma had significantly higher positive rates to Der.p and Der.f when compared with the AR or asthma group (P < 0.05, P < 0.05). Conclusion Allergic sensitizations were common in children with AR and/or asthma; sex, age, and asthma–rhinitis multimorbidity might affect the prevalence of sensitizations to aeroallergens.
Drug-Eluting Bead Bronchial Arterial Chemoembolization With and Without Microwave Ablation for the Treatment of Advanced and Standard Treatment-Refractory/Ineligible Non-Small Cell Lung Cancer: A Comparative Study

Purpose To compare the outcomes of drug-eluting bead bronchial arterial chemoembolization (DEB-BACE) with and without microwave ablation (MWA) for the treatment of advanced and standard treatment-refractory/ineligible non-small cell lung cancer (ASTRI-NSCLC). Materials and Methods A total of 77 ASTRI-NSCLC patients who received DEB-BACE combined with MWA (group A; n = 28) or DEB-BACE alone (group B; n = 49) were included. Clinical outcomes were compared between groups A and B. Kaplan–Meier methods were used to compare the median progression-free survival (PFS) or overall survival (OS) between the two groups. Univariate and multivariate Cox proportional hazards analyses were used to investigate the predictors of OS for ASTRI-NSCLC treated with DEB-BACE. Results No severe adverse event was found in both groups. Pneumothorax was the predominant MWA-related complication in group A, with an incidence rate of 32.1% (9/28). Meanwhile, no significant difference was found in DEB-BACE-related complications between groups A and B. The overall disease control rate (DCR) was 61.0% (47/77), with a significantly higher DCR in group A (85.7% vs. 46.9%, P = 0.002). The median PFS in groups A and B was 7.0 and 4.0 months, respectively, with a significant difference (P = 0.037). The median OS in groups A and B was both 8.0 months, with no significant difference (P = 0.318). The 6-month PFS and OS rates in groups A and B were 75.0% and 78.6%, 22.4% and 59.2%, respectively, while the 12-month PFS and OS rates in groups A and B were 17.9% and 28.6%, 14.3% and 22.4%, respectively. Of these, a significantly higher 6-month PFS rate was found in group A (75.0% vs. 22.4%; P < 0.001). The cycles of DEB-BACE/bronchial artery infusion chemotherapy [hazard ratio (HR): 0.363; 95% confidence interval (CI): 0.202–0.655; P = 0.001] and postoperative immunotherapy (HR: 0.219; 95% CI: 0.085–0.561; P = 0.002) were identified as the predictors of OS in ASTRI-NSCLC treated with DEB-BACE. Conclusion MWA sequentially combined with DEB-BACE was superior to DEB-BACE alone in the local control of ASTRI-NSCLC. Although the combination therapy reveals a trend of prolonging the OS, long-term prognosis warrants an investigation with a longer follow-up.
Can the Ratio SUVmax of the Lesion/SUVmax of Mediastinal Tissues Guide the Choice of Surgical Access for the Resection of Thymic Epithelial Tumors?

Background There are studies showing the utility of the 18-fluorodeoxyglucose positron emission tomography (18FDG PET) scan in the management of patients with thymic epithelial tumors. It seems to be a correlation between the standard uptake value (SUVmax) of thymic epithelial tumors and the histological type and the stage. This study aims to use the ratio of the SUVmax of the lesion to the SUVmax of the adjacent mediastinal tissues in order to guide the choice of the surgical access. Methods All patients who presented an anterior mediastinal lesion with a high suspicion of being of thymic origin were included in a prospective database. A ratio inferior to 1 could predict a benign nature and less aggressive behavior, and a minimally invasive approach was performed. A ratio superior to 1 suggested a malignant and aggressive behavior, and a median sternotomy (or a thoracotomy) was performed. Results There were 15 male (mean age 44.6 ± 16.26 years, range 25–73) and 15 female patients (mean age 50.1 ± 16.94 years, range 25–76). When the ratio is inferior to 1, it predicts benign disease in 80% of cases. When it is superior to 1, it predicts in half of cases advanced histological types (high risk thymomas and thymic carcinomas). On the contrary, it can quite accurately predict advanced Masaoka–Koga stages. Conclusions The protocol of this study is in accordance with the current literature showing the utility of 18FDG PET scan in the treatment of thymic epithelial tumors. This study goes one step further since the choice of surgical access is based on the SUVmax values. The ratio SUVmax of the lesion/SUVmax of the mediastinal tissues could be a new marker, more pertinent than absolute SUVmax values.
First Report of a Methicillin-Resistant, High-Level Mupirocin-Resistant Staphylococcus argenteus

We describe the identification of a methicillin-resistant, high-level mupirocin-resistant Staphylococcus argenteus. The isolate (1801221) was characterized as t6675-ST2250-SCCmecIVc, and whole-genome sequencing revealed that the isolate possessed two plasmids. One plasmid (34,870 bp), designated p1_1801221 with rep23, harboured the mupirocin resistance (mupA) gene. The second plasmid (20,644 bp), assigned as p2_1801221 with rep5a and rep16, carried the resistance determinants for penicillin (blaZ) and cadmium (cadD). Phylogenetic analysis revealed that the isolate clustered with the European ST2250 lineage. The overall high similarity of both plasmids in S. argenteus with published DNA sequences of Staphylococcus aureus plasmids strongly suggests an interspecies transfer. The pathogenic potential, community and nosocomial spread, and acquisition of antibiotic resistance gene determinants, including the mupA gene by S. argenteus, highlight its clinical significance and the need for its correct identification.
Grating coupler design based on silicon-on-insulator

Silicon-on-insulator has become a promising platform for high-density integrated photonics circuits. The large refractive index contrast between the functional silicon layer and its cladding raises a coupling issue between an optical fibre and on-chip devices. Grating coupler provides a compact and efficient way to tackle the coupling issue between the optical fibre and silicon waveguide. In this thesis, a universal design methodology, which accommodates various etch depths, silicon thicknesses, and cladding materials has been demonstrated and verified by both FDTD simulation and measurement results. A fully etched grating coupler with a sub-wavelength grating structure has been proposed to reduce the large back reflection of existing fully etched grating couplers. Back reflection of the proposed fully etched grating coupler has been reduced from more than 20% to about 5%. The insertion loss and bandwidth of the proposed structure have also been improved. In addition, a bidirectional grating coupler for vertical coupling has been proposed to improve the insertion loss and bandwidth of the traditional grating coupler. A simulated insertion loss of -1.5dB with a 3dB bandwidth of more 100nm has been achieved with the proposed structure.
Reconfigurable narrow-frame antenna for LTE/WWAN metal-rimmed smartphone applications

A reconfigurable narrow-frame coupled-loop antenna capable of providing hepta-band long term evolution/wireless wide area network (LTE/WWAN) for metal-rimmed smartphone applications is proposed. The ground clearance of this proposed antenna is only 7 × 70 mm 2 which is promising for narrow-frame smartphone applications. Moreover, this proposed antenna can realise the miniaturisation by employing a positive intrinsic negative diode (PIN diode), which can provide two working states. When the PIN diode is OFF, it can provide coverage for GSM850/DCS/PCS/UMTS2100/LTE2300/2500 operations. When the PIN diode is ON, the obtained bands are GSM900/DCS/PCS/UMTS2100/LTE2300/2500. Hence, by combining these two working states, GSM850/900/DCS/PCS/UMTS2100/LTE2300/2500 operations are achieved. In addition, the feasibility of realising decoupled multi-antennas is demonstrated and its performances are well-suited for future smartphone applications. Detailed design considerations of the proposed antenna are described. Both experimental and simulated results are also presented and discussed.
Effect of Ethnochemistry Instructional Approach on Secondary School Students’ Interest in Chemistry in Bayelsa State

The study determined the effects of ethnochemistry instructional approach (EIA) on interest of students in chemistry. Two research questions and three hypotheses guided the stdudy. The quasi-experimental design was adopted, specifically the pretest-posttest non-randomized control group was used. The population of the study was 4, 955 senior secondary year two (SS2) students offering chemistry in Yenagoa Education Zone out of which 153 students were selected for the study using purposive and random sampling techniques. The instrument for data collection was Chemistry Interest Scale (CIS) validated experts in Departments of Science Education and Educational Foundation, from NnamdiAzikiwe University, Awka and one experienced secondary school chemistry teacher. The reliability of CIS was established using Cronbach Alpha to be 0.78. Analysis of data for the study was done using mean and standard deviation and analysis of covariance. The result of the study showed that students taught using EIA has higher gains in mean interestscores than those in the conventional instructional approach. The findings of the study revealed that there was a significant difference between mean interest scores of students taught chemistry using EIA and conventional instructional approach in favour of EIA. It was concluded that EIA is an effective instructional approach for improving students’ interest. It was recommended that chemistry teachers should adopt EIA in teaching chemistry concepts so as to enable students marry their learning with the common realities in their immediate environment, thereby making them interested in learning chemistry.