[Clinical characteristics of hospitalized children with respiratory syncytial virus infection and risk prediction of severe illness during the post-COVID-19 era in Kunming]

Objective: To compare the epidemiological and clinical characteristics of hospitalized children with respiratory syncytial virus (RSV) infection in Kunming among the pre-and post-COVID-19 era, and to establish a prediction model for severe RSV infection in children during the post-COVID-19 period. Methods: This was a retrospective study. Clinical and laboratory data were collected from 959 children hospitalized with RSV infection in the Department of Pulmonary and Critical Care Medicine at Kunming Children's Hospital during January to December 2019 and January to December 2023. Patients admitted in 2019 were defined as the pre-COVID-19 group, while those admitted in 2023 were classified as the post-COVID-19 group. Epidemiological and clinical characteristics were compared between the two groups. Subsequently, comparison of the clinical severity among the two groups was performed based on propensity score matching (PSM). Furthermore, the subjects in the post-COVID-19 group were divided into severe and non-severe groups based on clinical severity. Chi-square test and Mann-Whitney U test were used for pairwise comparison between groups, and multivariate Logistic regression was applied for the identification of independent risk factors and construction of the prediction model. The receiver operating characteristic (ROC) curve and calibration curve were employed to evaluate the predictive performance of this model. Results: Among the 959 children hospitalized with RSV infection, there were 555 males and 404 females, with an onset age of 15.4 (7.3, 28.5) months. Of which, there were 331 cases in the pre-COVID-19 group and 628 cases in the post-COVID-19 group. The peak period of RSV hospitalization in the post-COVID-19 group were from May to October 2023, and the monthly number of inpatients for each of these months were as follows: 72 cases (11.5%), 98 cases (15.6%), 128 cases (20.4%), 101 cases (16.1%), 65 cases (10.4%), and 61 cases (9.7%), respectively. After PSM for general data, 267 cases were matched in each group. The proportion of wheezing in the post-COVID-19 group was lower than that in the pre-COVID-19 group (109 cases (40.8%) vs. 161 cases (60.3%), χ2=20.26, P<0.001), while the incidences of fever, tachypnea, seizures, severe case, neutrophil-to-lymphocyte ratio (NLR), C-reactive protein and interleukin-6 levels were all higher than those in the pre-COVID-19 group (146 cases (54.7%) vs. 119 cases (44.6%), 117 cases (43.8%) vs. 89 cases (33.3%), 37 cases (13.9%) vs. 14 cases (5.2%), 69 cases (25.8%) vs. 45 cases (16.9%), 3.6 (1.9, 6.4) vs. 2.3 (1.8, 4.6), 9.9 (7.1, 15.2) vs. 7.8 (4.5, 13.9) mg/L, 20.5 (15.7, 30.4) vs. 17.2 (11.0, 26.9) ng/L, χ2=5.46, 6.36, 11.47, 6.42, Z=4.13, 3.06, 2.96, all P<0.05). There were 252 cases and 107 cases with co-infection in the post-and pre-COVID-19 groups, respectively. The proportion of triple and quadruple infection in the post-COVID-19 group was higher than that in the pre-COVID-19 group (59 cases (23.4%) vs. 13 cases (12.1%), 30 cases (11.9%) vs. 5 cases (4.7%), χ2=5.94, 4.46, both P<0.05). Among the 252 cases with co-infection in post-COVID-19 group, the most prevalent pathogens involving in co-infections, in order, were Mycoplasma pneumoniae 56 cases (22.2%), Influenza A virus 53 cases (21.0%), Rhinovirus 48 cases (19.0%), Parainfluenza virus 35 cases (13.9%), and Adenovirus 28 cases (11.1%).The result of multivariate Logistic regression showed that age (OR=0.70, 95%CI 0.62-0.78, P<0.001), underlying diseases (OR=10.03, 95%CI 4.10-24.55, P<0.001), premature birth (OR=6.78, 95%CI 3.53-13.04, P<0.001), NLR (OR=1.85, 95%CI 1.09-3.15, P=0.023), and co-infection (OR=1.28, 95%CI 1.18-1.38, P<0.001) were independently associated with the development of severe RSV infection in the post-COVID-19 group. The ROC curve of the prediction model integrating the above five factors indicated an area under the curve of 0.85 (95%CI 0.80-0.89, P<0.001), with an optimal cutoff of 0.21, a sensitivity of 0.83 and a specificity of 0.80. The calibration curve showed that the predicted probability in this model did not differ significantly from the actual probability (P=0.319). Conclusions: In the post-COVID-19 era in Kunming, the peak in pediatric hospitalizations for RSV infection was from May to October, with declined incidence of wheezing and increased incidence of fever, tachypnea, seizures, severe cases, and rates of triple and quadruple co-infections. Age, underlying diseases, premature birth, NLR, and co-infection were identified as independent risk factors for severe RSV infection in the post-COVID-19 period. In this study, a risk prediction model for severe pediatric RSV infection was established, which had a good predictive performance.

[A single-center study on the oncological outcomes of active surveillance of thyroid nodules measuring≤1 cm with highly suspicious ultrasound features]

Objective: To investigate the oncological outcomes of active surveillance (AS) in patients showing thyroid nodules measuring≤1 cm with highly suspicious ultrasound features. Methods: A prospective single-center cohort study. A total of 534 patients with highly suspicious thyroid nodules (2015 American Thyroid Association Nodule Sonographic Patterns and Risk of Malignancy: High Suspicion) were enrolled in this study, the patients received AS at Peking Union Medical College Hospital between January 2017 and November 2022 to assess oncological outcomes (disease progression, recurrence/metastasis rate, etc). The patients were followed up every 6 months for physical examination and neck ultrasound examination. And the value of tumor volume changes in evaluating tumor enlargement was explored too. Results: There were 413 females and 121 males in this cohort, with a mean age of (42.6±11.8) years. During a median follow-up period of 45.6 months (ranged from 3.5 to 176.0 months), disease progression occurred in 26 patients (4.9%) with highly suspicious thyroid nodules, characterized by a minimum 3-mm increase in tumor diameter in 19 patients (3.6%) and lymph node metastases in 7 patients (1.3%). Forty-seven (8.8%) patients opted for delayed surgery, with 29 patients due to a change in preference. There was no significant differences in pathologic and follow-up outcomes between patients with disease progression and preference change. Patients aged≤40 years had a higher cumulative incidence of 5-year disease progression than those aged>40 years (4.9% vs 1.9%, P=0.060). No patients experienced distant metastases or deaths. Among the 595 high-risk thyroid nodules with continuous volume assessment results and an increase in nodule diameter of less than 3 mm (including all high-risk nodules in patients with single or multiple nodules), 184 (30.9%) and 79 (13.3%) nodules exhibited volume increases of more than 50% and 100%, respectively, in multiple measurements. Among the nodules with volume changes exceeding 50% and 100%, the proportion of nodules with a baseline tumor diameter of≤0.5 cm was significantly higher than those with a diameter of>0.5 cm, at 69.0% vs 31.0% (P<0.001) and 77.2% vs 22.8% (P<0.001), respectively. Conclusions: Active surveillance in patients with highly suspicious subcentimeter thyroid nodules has good short-term oncological outcomes and can be considered a safe alternative to surgery. Due to the large variability in the measurement results of tumor volume, it is not suitable as an indicator for evaluating tumor enlargement.

A multiline fitting method for measuring ethylene concentration based on WMS-2f/1f

Coal spontaneous combustion risk assessment is a global technical challenge for the sustainable development of deep mining technology, and C2H4 is a key indicator for early warning of coal spontaneous combustion. Tunable diode laser absorption spectroscopy (TDLAS) has the advantages of high selectivity, high sensitivity, high accuracy and real-time on-line measurement, and it can detect multiple gases simultaneously, so it has significant advantages in the accurate detection of coal spontaneous combustion indicator gases. To address the problem of cross-interference between the near-infrared absorption lines of CH4 and C2H4, which are the indicator gases of spontaneous combustion in coal, a multi-line fitting method was proposed in this study to calibrate the concentration of C2H4. The high-precision Environics2000 automatic standard gas dispenser from the United States, which has a built-in CPU computer control and data control and processing system, was used. Its gas concentration accuracy: ± 1.0%, gas flow accuracy: ± 1.0%, gas repeatability accuracy: ± 1.0%, flow linearity accuracy: ± 0.5%, and inlet operating pressure: minimum 10 psig (0.67 bar) ~ 75 psig (5.04 bar). The measured and simulated WMS-2f/1f signals were multilinearly fitted using a multilinear fitting algorithm and wavelength modulation spectroscopy (WMS), and the measurement of C2H4 concentration was achieved based on the extracted spectral line information. The results show that the maximum relative error of C2H4 concentration measurement is 2.40%, which is 54% lower than that of the conventional 2f peak measurement method, thus demonstrating the effectiveness of the multilinear fitting algorithm in the inversion of C2H4 concentration under the interference of absorption lines. In addition, this study has far-reaching implications for the application of TDLAS technology in the accurate detection of coal spontaneous combustion indicator gases.

Nonlinear interaction between double tearing mode and Kelvin-Helmholtz instability with different shear flows

The nonlinear interaction between the double tearing mode (DTM) and Kelvin-Helmholtz (KH) instabilities with different shear flow profiles has been numerically investigated via the use of a compressible magnetohydrodynamics (MHD) model. We focus on KH instabilities in weak and reversed magnetic shear plasmas with strong stabilizing effect of field line bending. Results show that KH instabilities coupled with DTMs occur in these plasmas and the KH mode dominates the instability dynamics, suggesting the crucial role of weak magnetic shear in the formation of high-mode harmonics. For symmetric flows, an asymmetric forced magnetic reconnection configuration is maintained during the growth phase, leading to interlocking of the modes. Additionally, this investigation of the DTM-KH instability interaction contributes to our understanding of the nonlinear reconnection mechanism in the regime of weak and reversed magnetic shear plasmas, which is relevant for astrophysical and fusion studies.

A Comprehensive Phylogenetic Analysis of SARS-CoV-2: Utilizing a Novel and Convenient In-House RT-PCR Method for Characterization without Virus Culture and BSL-3 Facilities

We developed a convenient method for amplifying the complete SARS-CoV-2 sequence using in-house RT-PCR without virus culture. Forty-one stored throat swabs and blood specimens were collected from eight SARS-CoV-2 infections at multiple time points. Total RNA was extracted using the QIAamp viral RNA mini kit and pooled for higher RNA levels. Only those positive specimens by commercial real-time RT-PCR (RT-qPCR) were selected and amplified by in-house RT-PCR for complete sequences, followed by sequencing. Phylogenetic trees and exploratory analyses were performed using MEGA 11 and Simplot 3.5.1 software. Swab samples had significantly higher total RNA concentrations than plasma (p < 0.01). Positive results were found mainly in swabs, but one was found in plasma. Successful gene amplification depended on Ct values (Ct < 38). A non-synonymous substitution was found in ORF1ab/Nsp3 (at NC045512.2 position 6312, C to A) and most spike protein mutations occurred in the S1 subunit (residues 14-685). The proposed method is time-saving and reliable for rapid genomic analysis. Increasing sample volume and pooling them for RNA extraction increases RNA concentration without culture. Combining nucleotide sequences from specific variable regions of the genome is more efficient than conventional methods.

[Clinical tolerability and pharmacokinetics of troxacitabine]

Objective: To investigate the safety and efficacy of troxatabine in advanced or relapsed malignant tumors resistant to standard therapy in China. Methods: This is a phase Ⅰ prospective study. During dose escalation, patients in Cancer Hospital, Chinese Academy of Medical Sciences received a single-dose intravenous infusion of troxacitabine. The planned dosing groups were 1.8, 3.6, 4.8, 6.4 and 8.0 mg/m(2) on days 1 and 8 every 3 weeks. The data of all patients were collected for safety analyses. Safety and tolerability were evaluated by monitoring adverse events. Results: Nineteen patients were enrolled from April 2018 to May 2019. The major adverse events were fatigue (89.5%, 17/19), leukopenia (84.2%, 16/19) and neutropenia (78.9%, 15/19). The dose limiting toxicity was neutropenia. The maximum tolerated dose was 6.4 mg/m(2). The best effect was stable disease (43.8%). The half-life of elimination phase from 15.91 hours to 76.63 hours in each dose group. Conclusions: The toxicity of troxacitabine is well tolerant. We recommend that the dose for Phase Ⅱ clinical trial should be 6.4 mg/m(2).

Chitosan derivatives as promising green corrosion inhibitors for carbon steel in acidic environment: Inhibition performance and interfacial adsorption mechanism

Among the biodegradable polysaccharide, chitosan is widely present in the cell membranes of bacteria and algae and in the cell walls of higher plants. As a promising biopolymer, chitosan has great potential as eco-friendly corrosion inhibitor. Herein, two synthetic chitosan derivatives (N-phenylthiourea chitosan (CS-PT), N-phenyl-O-benzylthiourea chitosan (CS-PT-Bn)) were investigated as high-efficient acidic corrosion inhibitors to deal with the corrosion issue of carbon steel. The anti-corrosion property of the chitosan derivatives was explored by electrochemical tests, surface characterization and theoretical calculations. The experimental results indicate that both CS-PT and CS-PT-Bn present high-efficient inhibition performance with the inhibition efficiency of 98.4% and 98.5% at the concentration of 100 mg/L, respectively. Their adsorption mechanism at steel/solution interface is revealed by quantum chemical calculations, molecular dynamics (MD) and GFN-xTB calculations. It is found that CS-PT and CS-PT-Bn adsorb at the steel/solution interface by forming Fe-N and Fe-S bonds. Compared to CS-PT molecule, the introduction of benzyl group endows CS-PT-Bn molecule with stronger electrostatic effect and hydrophobicity, which favors the interfacial adsorption of CS-PT-Bn molecule on carbon steel surface.

[Pulmonary granular cell tumors: a clinicopathological analysis of five cases]

Objective: To investigate the clinicopathological features of pulmonary granular cell tumors (pGCTs) and to improve the diagnostic accuracy of the tumor. Methods: A total of 5 pGCTs were diagnosed from February 2016 to January 2022 at Shanghai Pulmonary Hospital, Tongji University School of Medicine and Fudan University Shanghai Cancer Center, China. Immunohistochemical staining, and analysis of the clinicopathological characteristics were performed. Results: The average age of the pGCTs patients was 46 years (ranging from 24 to 54 years), with 3 females and 2 males. One case occurred in the bronchus with multiple nodules in the lung, 2 cases occurred in the bronchial opening, and 2 cases were solitary nodules in the lung. The maximum diameter of the tumors ranged from 12 to 15 mm (mean size 14 mm). Microscopically, the tumor showed infiltrative growth and consisted of round, oval or polygonal cells. Abundant eosinophilic cytoplasm was noted, and the nucleoli were prominent. None of the 5 cases showed any mitosis or necrosis. Immunohistochemical and histochemical study showed positive staining for S-100 (5/5), SOX10 (5/5), Vimentin (5/5), TFE3 (4/5), PAS (3/5), and amylase-digested-PAS (3/5), while 4 cases were negative for CD68. TFE3 FISH analyses on 2 cases showed that no signal abnormality was detected in these 2 cases. The average proliferation index of Ki-67 was 2.2% (range 0-5%). There was no recurrence in 4 cases of pGCTs with a follow-up time ranging from 2 months to 60 months. Conclusions: pGCTs are very rare tumors, most likely originating from Schwann cells. Immunohistochemical staining is the conventional diagnostic tool for pGCTs diagnosis. Recognition of this entity is essential for pathologists to avoid misdiagnosis and unnecessary treatments.

[Characteristics and risk factors of spinal epidural hematoma after unilateral biportal endoscopic lumbar interbody fusion]

Objective: To investigate the incidence, characteristics and risk factors of spinal epidural hematoma after unilateral biportal endoscopic (UBE) lumbar spine surgery. Methods: The clinical data of 105 patients who underwent lumbar spine surgery under UBE in Guangdong Provincial People's Hospital from February 2020 to March 2021 were retrospectively reviewed. Of the patients, 48(45.7%) were male and 57(54.3%) were female, the mean age was (60.1±11.4) years (ranged 26 to 85 years). The MRI images at the third day post-surgery were observed, and the occurrence of hematoma was counted. Patients were assigned to normal group and hematoma group based on the presence of hematoma or not. The related clinical indicators of each patients were collected and used for comparison between two different groups. Logistic stepwise regression model was used to analyze whether each index was a risk factor for hematoma after the UBE lumbar fusion. Results: The total hematoma incidence rate was 28.6%(30/105), the symptomatic hematoma rate was 6.7%(7/105), and the hematoma reoperation rate was 0.9%(1/105). Univariate logistic regression analysis showed that hypertension (OR=3.368, 95%CI: 1.389-8.171), diabetes (OR=3.589, 95%CI: 1.230-10.476), admission systolic blood pressure>140 mmHg (1 mmHg=0.133 kPa,OR=3.687, 95%CI: 1.493-9.017), platelets<200×10⁹/L (OR=0.300, 95%CI: 0.119-0.785), preoperative blood calcium<2.25 mmol/L (OR=0.340, 95%CI: 0.142-0.818), spinal stenosis grade D (OR=4.462, 95%CI: 1.810-10.996) were possible risk factors for spinal hematoma after UBE lumbar fusion. Multivariate logistic regression analysis showed that admission blood pressure systolic blood pressure>140 mmHg (OR=3.788, 95%CI:1.055-13.606), preoperative blood calcium<2.25 mmol/L (OR=78.544, 95%CI:3.895-1 584.058) and spinal stenosis grade D (OR=3.698, 95%CI:1.110-12.325) were risk factors for spinal hematoma after UBE lumbar fusion (all P<0.05). Conclusion: The types of spinal canal hematoma after UBE lumbar fusion include localized and extended type. The risk factors for hematoma include high systolic blood pressure on admission, low preoperative blood calcium and severe spinal stenosis.

[Effect of metformin combined with intermittent fasting on endoplasmic reticulum stress after cerebral ischemia-reperfusion in mice]

Objective: To explore the effect of metformin combined with intermittent fasting on endoplasmic reticulum stress after cerebral ischemia-reperfusion injury in mice. Methods: One hundred 10-Week-old healthy KM mice of SPF grade, weighing 25-28 g, were divided into 5 groups by the random number table method: sham group, focal cerebral ischemia group (I/R group), intermittent fasting group (IF group), metformin group (Met group), metformin+intermittent fasting group (Met+IF group). In IF group, food was provided ad libitum from 8∶00 to 16∶00 daily, but the mice were fasted for the rest of the time. In Met group, the mice underwent intraperitoneal injection of metformin (10 mg/kg). In Met+IF group, the mice received the same eating method as the IF group and the same method of metformin injection as Met Group. In Sham group, I/R group and IF group, the mice were intraperitoneally injected with equal volume of normal saline. Mice in all groups were not restricted to drinking water. Random plasma glucose and body weight changes in mice during preconditioning were monitored, and a focal cerebral ischemia-reperfusion model was established 14 days later. The cerebral infarction volume was measured after 1 hour of ischemia and 24 hours of reperfusion. The brain tissues of mice were subjected to Western blot to detect the contents of endoplasmic reticulum stress-related proteins, including glucose-regulated protein 78 (GRP78), C/EBP homologous protein (CHOP), and apoptosis proteins (Caspase-3 and Cleaved-caspase 3). Results: After different interventions, there was no significant difference in random plasma glucose changes among the four groups (all P<0.05). The blood glucose level of the mice in the Met+IF group was lower than the sham group, I/R group, IF group and Met group (all P<0.05). GRP78/β-actin in sham group, I/R group, IF group, Met group, IF+Met group were 0.48±0.05, 1.35±0.10, 0.94±0.05, 0.70±0.14, 0.41±0.37, respectively; CHOP/β-actin were 0.27±0.04, 1.03±0.03, 0.72±0.04, 0.63±0.04, 0.44±0.01, respectively; Caspase-3/β-actin were 0.51±0.04, 1.04±0.04, 0.83±0.03, 0.76±0.03, 0.63±0.05, respectively; Cleaved-Caspase-3/β-actin were 0.17±0.06, 1.01±0.20, 0.75±0.06, 0.51±0.12, 0.29±0.08, respectively, with statistically significant differences (all P<0.001). The counts of GRP78-positive cells in the hippocampus immunohistochemistry in the sham group, I/R group, IF group, Met group, and IF+Met group were 53±5, 192±11, 162±12, 140±10, 114±13, respectively, while the counts of CHOP-positive cells were 35±4, 177±12, 120±12, 100±7, 69±10, respectively, with statistically significant differences (all P<0.001). The relative volume of cerebral infarction in I/R group, IF group, Met group and IF+Met group were 0, 0.333±0.046, 0.258±0.023, 0.116±0.039, 0.111±0.039, respectively, and there were statistically significant differences (all P<0.001). Conclusion: Both Metformin and intermittent fasting can alleviate endoplasmic reticulum stress after cerebral ischemia and reperfusion in mice, and the combination of the two has a better effect.

Deciphering the evolution of composite-type GSKIP in mitochondria and Wnt signaling pathways

We previously revealed the origin of mammalian simple-type glycogen synthase kinase interaction protein (GSKIP), which served as a scavenger and a competitor in the Wnt signaling pathway during evolution. In this study, we investigated the conserved and nonconserved regions of the composite-type GSKIP by utilizing bioinformatics tools, site-directed mutagenesis, and yeast two-hybrid methods. The regions were denoted as the pre-GSK3β binding site, which is located at the front of GSK3β-binding sites. Our data demonstrated that clustered mitochondria protein 1 (CLU1), a type of composite-type GSKIP that exists in the mitochondria of all eukaryotic organisms, possesses the protein known as domain of unknown function 727 (DUF727), with a pre-GSK3β-binding site and a mutant GSK3β-binding flanking region. Another type of composite-type GSKIP, armadillo repeat containing 4 (ARMC4), which is known for cilium movement in vertebrates, contains an unintegrated DUF727 flanking region with a pre-GSK3β-binding site (115SPxF118) only. In addition, the sequence of the GSK3β-binding site in CLU1 revealed that Q126L and V130L were not conserved, differing from the ideal GSK3β-binding sequence of simple-type GSKIP. We further illustrated two exceptions, namely 70 kilodalton heat shock proteins (Hsp70/DnaK) and Mitofilin in nematodes, that presented an unexpected ideal GSK3β-binding region with a pre-GSK3β sequence; this composite-type GSKIP could only occur in vertebrate species. Furthermore, we revealed the importance of the pre-GSK3β-binding site (118F or 118Y) and various mutant GSK3β-binding sites of composite-type GSKIP. Collectively, our data suggest that the new composite-type GSKIP starts with a DUF727 domain followed by a pre-GSK3β-binding site, with the subsequent addition of the GSK3β-binding site, which plays vital roles for CLU1, Mitofilin, and ARMC4 in mitochondria and Wnt signaling pathways during evolution.

Genetic Diversity and Molecular Epidemiology of Circulating Respiratory Syncytial Virus in Central Taiwan, 2008-2017

In this study, we investigated the molecular evolution and phylodynamics of respiratory syncytial virus (RSV) over 10 consecutive seasons (2008–2017) and the genetic variability of the RSV genotypes ON1 and BA in central Taiwan. The ectodomain region of the G gene was sequenced for genotyping. The nucleotide and deduced amino acid sequences of the second hypervariable region of the G protein in RSV ON1 and BA were analyzed. A total of 132 RSV-A and 81 RSV-B isolates were obtained. Phylogenetic analysis revealed that the NA1, ON1, and BA9 genotypes were responsible for the RSV epidemics in central Taiwan in the study period. For RSV-A, the NA1 genotype predominated during the 2008–2011 seasons. The ON1 genotype was first detected in 2011 and replaced NA1 after 2012. For RSV-B, the BA9 and BA10 genotypes cocirculated from 2008 to 2010, but the BA9 genotype has predominated since 2012. Amino acid sequence alignments revealed the continuous evolution of the G gene in the ectodomain region. The predicted N-glycosylation sites were relatively conserved in the ON1 (site 237 and 318) and BA9 (site 296 and 310) genotype strains. Our results contribute to the understanding and prediction of the temporal evolution of RSV at the local level.

Phylodynamic analysis and spike protein mutations in porcine deltacoronavirus with a new variant introduction in Taiwan

Porcine deltacoronavirus (PDCoV) is a highly transmissible intestinal pathogen that causes mild to severe clinical symptoms, such as anorexia, vomiting, and watery diarrhea in pigs. By comparing the genetic sequences of the spike glycoprotein between historical and current Taiwanese PDCoV strains, we identified a novel PDCoV variant that displaced the PDCoV responsible for the 2015 epidemic. This PDCoV variant belongs to a young population within the US lineage, and infected pigs carry high concentrations of the virus. It also has several critical point mutations and an amino acid insertion at position 52 that may enhance the affinity between the B-cell epitopes located in the N-terminal domain with its complementarity regions, consequently facilitating binding or penetration between the fusion peptide and cellular membrane. Furthermore, viral protein structure prediction demonstrated that these amino acid changes may change the ability of the virus to bind to the receptor, which may consequently alter virus infectivity. Our results hence suggest the emergence of new PDCoV strains in Taiwan with the potential for greater transmission and pathogenesis.

[The 491st case: thrombocytosis, gastrointestinal hemorrhage, intestinal perforation]

Essential thrombocythemia (ET) is a chronic myeloproliferative neoplasm (MPN) featured by clonal proliferation of platelets, thrombosis and hemorrhage. Portal hypertension is a serious complication of ET associated with poor prognosis. We report a patient with ET complicated with acute upper gastrointestinal hemorrhage and intestinal perforation due to portal hypertension. She had an uneventful recovery after surgical and endoscopic treatment.

Detection and genetic characterization of the novel torque teno virus group 6 in Taiwanese general population

Torque teno virus (TTV) is one of the most common human viruses and can infect an individual with multiple genotypes chronically and persistently. TTV group 6 is a recently discovered phylogenetic group first isolated from eastern Taiwan indigenes, but whether the TTV group 6 was also prevalent in the general population still unknown. One hundred and three randomly collected blood samples from general population and 66 TTV positive DNA samples extracted from Taiwan indigenes were included. A group-6-specific PCR was developed for re-screen over TTV positive samples. Two TTV group 6 positive samples from general population were cloned and sequenced for identifying mix-infected TTVs and confirming their classification by maximum-likelihood and Bayesian inference phylogeny. TTV group 6 can be detected in 4.5% (4/89) and 7.6% (5/66) of TTV positive samples from Taiwanese general population and eastern Taiwan indigenes, respectively. Sample VC09 was mix-infected with TTV groups 3 and 6. Sample VC99 was mix-infected with TTV groups 3, 4 and 6. A highly diverse triple overlapping region was observed, which may represent a unique phenomenon of TTV. The group-6-specific PCR can successfully detect TTV group 6. TTV group 6 may be prevalent worldwide regardless of the geographic region and/or ethnic groups.

[Retrospective study of thyroid invasion and central lymph node metastasis in 124 patients with hypopharyngeal carcinoma]

Objective: To investigate the characteristics of thyroid invasion and central lymph node metastasis of hypopharyngeal carcinoma, and the impact on survival rate and quality of life. Methods: A retrospective analysis of 124 cases (122 males and 2 females with age range from 36 to 78 years old) with laryngopharyngeal squamous cell carcinoma who were initially treated in the Department of Head and Neck Surgery, Beijing Tongren Hospital Affiliated to Capital Medical University from January 2014 to December 2017 was performed. The clinical data included tumor location, pathological T stage, pathological N stage, invasion of thyroid gland, central lymph node metastasis, surgical procedures and so on. Patients were grouped according to if presence of thyroid invasion and central lymph node metastasis. With follow-up, the survival was analyzed by Kaplan-Meier method, and tumor recurrence and metastasis were evaluated. Results: Of the patients, 12 patients had thyroid involvement and 5 patients had central lymph node metastasis. The incidence of thyroid involvement was 8.16% (8/98) in pyriform sinus, 1/18 in posterior pharyngeal wall and 3/8 in posterior cricoid wall, with statistically significant difference (χ²=15.076,P=0.008). The incidence of central lymph node metastasis was 1.02% (1/98) in pyriform sinus, 3/18 in posterior pharyngeal wall and 1/8 in posterior cricoid wall, also with statistically significant difference (χ²=11.205, P=0.008). There was no statistical correlation between thyroid invasion or central lymph node metastasis and gender, smoking or alcohol exposure history and tumor pathological differentiation (all P>0.05). The 3-year overall survival rate was 80.65% and the 3-year recurrence free rate was 85.48%. Totally 24 patients died in 3 years, including 4 cases in thyroid invasion group and 1 case in central lymph node metastasis group. Local recurrence occurred in 18 patients, including 4 cases in thyroid invasion group and 1 case in central lymph node metastasis group. There was no significant difference in survival between patients with and without thyroid invasion and central lymph node metastasis (all P>0.05). There were significantly difference in 3-year overall survival and relapse-free survival among the groups with different T stages, N stages, pathological stages and tumor pathological differentiation levels (all P<0.05). There were significantly differences in the levels of serum calcium and FT3 between the groups with or without thyroid invasion and central lymph node metastasis (all P<0.05). Conclusion: The incidences of thyroid invasion and central lymph node metastasis of hypopharyngeal carcinoma are rare, and the risk of occurrence is related to the primary site of tumor. Comprehensive evaluation, correct decision-making and accurate treatment could be helpful to cure radically the tumor, to prevent recurrence and to improve the quality of life of patients.

Effective corrosion inhibition of mild steel by eco-friendly thiourea functionalized glucosamine derivatives in acidic solution

In the view of environmental protection and sustainable development, the application of green effective inhibitors for metal corrosion in industry field is of great significance. In this work, two thiourea functionalized glucosamine derivatives, 5-hydroxy-1-phenyl-4-(1,2,3,4-tetrahydroxybutyl)imidazolidine-2-thione (GA-1) and 1-phenyl-3-(2,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl)thiourea (GA-2), were synthesized as eco-friendly corrosion inhibitors for mild steel (MS) in 1 M HCl solution, and their inhibition performance were evaluated by electrochemical tests and surface analyses. The electrochemical tests and surface analyses indicate that both GA-1 and GA-2 have high inhibition performance. Especially for GA-2, the inhibition efficiency reaches 97.7% with a concentration of 0.64 mM. Theoretical calculations were also conducted to elucidate the adsorption mechanism of GA-1 and GA-2 on MS surface.

[Study on syndromic deafness caused by novel pattern of compound heterozygous variants in the CDH23 gene]

Objective: To explore the pathogenic variants of a family with syndromic deafness by high-throughput sequencing. Methods: The family was from Puyang City, Henan Province, and had four members, including two with syndromic deafness. The proband and his sister had congenital deafness, and their parents had normal phenotypes. The clinical phenotype of the family was characterized using clinical examinations and pedigree analysis. The clinical examinations included imaging examination, audiometry (pure tone audiometry, acoustic immittance, brainstem auditory evoked potential, and otoacoustic emission), vestibular function test, and ophthalmic examination (visual acuity test, visual field test, fundus examination, visual evoked potential, and electroretinogram). Target exome sequencing of 129 known deafness genes and bioinformatics analysis were used to screen suspected pathogenic variants. Sanger sequencing and minigene assay were used to verify and functionally investigate the mutation detected, respectively. According to the standards and guidelines for interpreting genetic variants proposed by the American College of Medical Genetics and Genomics, the variants c.6049G>A and c.8699A>G were classified as pathogenic/likely pathogenic, and the variant c.9856C>G was classified as variants of uncertain significance. Results: The probands and his sister had severe sensorineural hearing loss with decreased binocular vision, night blindness, decreased peripheral visual field sensitivity and partial visual field defect, and normal vestibular function. Both of them had three CDH23 mutations, including CDH23 (NM_022124.5) c.6049G>A (p.Gly2017Ser),c.9856C>G (p.His3286Asp), and c.8699A>G (p. Asp2900Gly), The first two were inherited from the father, and the last one was from the mother. The missense variants c.9856C>G and c.8699A>G were not included in the gnomad database. The missense mutation c.6049G>A was located in the last position of exon 46 and was predicted to affect splicing by bioinformatics software. The minigene experiment showed that the mutation cause exon skipping of exon 46, resulting in an abnormal protein. Conclusions: Compound heterozygous variations of the CDH23 are the leading cause of USH1D in the family. This study confirms that the compound heterozygosity of splicing and missense variants of the CDH23 gene could lead to USH1D.

[Prognostic value of myocardial injury in patients with COVID-19]

Objective: To analyze the prognostic value of myocardial injury in patients with COVID-19. Method: Confirmed cases of COVID-19 patients admitted from January 31st to February 5th at isolation ward of Renmin Hospital of Wuhan University were divided into non-survival group and survival group according to the clinical outcomes 5 weeks after admission. Data including demographics, comorbidities, vital signs, laboratory results were obtained. Cardiac injury was defined as serum concentration of high sensitivity cardiac troponin I (hs-cTnI) above 0.04 μg/L. Univariate and multivariate Cox regression were used to analyze the prognostic value of myocardial injury in patients with COVID-19. Kaplan-Meier analysis was used to plotted survival curve and analyze the impact of myocardial injury on the survival outcome of COVID-19 patients. Results: A total of 202 patients were included, the age was 63 (51, 70) years old, 88 (43.6%) of them were male, 85 (42.1%) of them had comorbidities, 125 (61.9%) of them were severely to critically ill. Till March 11, 33 patients died, all of them were critically ill patients. The age, proportion of males, comorbidities, respire rate, serum levels of hs-cTnI and incidence of heart failure in the non-survival group were significantly higher than those in the survival group (all P<0.05). The hospitalization time of non-survival group was significantly shorter than that of survival group (6(4, 9) vs. 32(23, 36), P<0.001). Myocardial injury was an important prognostic factor of COVID-19 (HR=5.382, 95%CI 2.404-12.05, P<0.001). Kaplan-Meier survival analysis showed that the presence of myocardial injury was significantly associated with the reduced survival rate among COVID-19 patients (P<0.001). Conclusion: Myocardial injury is an important prognostic factor of COVID-19, COVID-19 patients with myocardial injury face a significantly higher risk of death.

[Chromosomal aberrations detection in chronic lymphocytic leukemia by conventional cytogenetics using DSP30 and IL-2]

Objective: To study the value of unmethylated cytosine guanine dinucleotide oligodeoxynucleotide (DSP30) and IL-2 in the conventional cytogenetic (CA) detection of the chromosomal aberrations in chronic lymphocytic leukemia (CLL) . Methods: Bone marrow or peripheral blood cells of CLL patients were cultured with DSP30 plus IL-2 for 72 h, following which R-banding analysis was conducted. Fluorescence in situ hybridization (FISH) was performed in 85 patients. CA results were compared with data obtained by FISH. Results: Among 89 CLL patients, the success rate of chromosome analysis was 94.38% (84/89) . Clonal aberrations were detected in 51 patients (51/84, 60.71%) . Of them, 27 (27/51, 52.94%) were complex karyotype. Among 85 CLL patients tested by FISH, chromosomal abnormalities were detected in 74 (74/85, 87.06%) patients, of which 2 (2/74) patients were complex karyotypes, accounting for 2.70%. Of the 85 CLL patients examined by FISH, 50 had abnormal karyotype analysis, 30 had normal karyotype, 5 failed to have chromosome analysis. Among them, 25 cases showed clonal aberrations by FISH assay but normal by CA, and 4 cases were normal by FISH but displayed aberrations in chromosome analysis, and totally 78 (91.76%) cases with abnormality detected by the combination of the two methods. The frequency of 13q- abnormality detected by FISH was significantly higher than that by CA analysis (69.41%vs 16.67%, P<0.001) , while the frequency of 11q-,+12 and 17p- detected by two methods showed no significant difference (P>0.05) . The detection rate of complex abnormalities in conventional karyotype analysis was higher than that in FISH (50.98%vs 2.70%) . In addition, 11 low-risk and 9 intermediate-risk patients according to FISH results showed complex karyotype by cytogenetics, and were classified into high-risk cytogenetic subgroup. Conclusion: DSP30 and IL-2 are effective in improving the detection rate of CA in CLL patients (60.71%) and CA is more effective to detect complex karyotype. However, FISH had a higher overall abnormality detection rate (87.06%) than CA, especially for 13q-. The combination of CA and FISH not only enhanced the detection rate of clonal aberrations to 91.76%, but also provided more precise prognosis stratification for CLL patients, thus to provide more information for clinical implication.

[Clinical analysis of 7 cases with anti-Caspr2 antibody-associated autoimmune encephalitis]

Objective: To investigate the clinical features, laboratory tests, imaging features, electroencephalogram (EEG) manifestations, treatment and prognosis of anti-CASPR2 antibody-associated autoimmune encephalitis with the purpose to improve the understanding of the disease. Methods: Seven patients diagnosed with CASPR2 antibody-associated encephalitis in the Fifth and first Affiliated Hospital of Zhengzhou University from January 2017 to January 2019 were selected. The clinical manifestations, course of disease, imaging, treatment plan and prognosis of the patients were retrospectively analyzed. Results: Of the 7 patients, 4 were male and 3 were female. The median age of onset was 34 years old (range, 11-66 years). Seizures (6/7), memory decline(5/7), and neuropsychiatric disorders (4/7) were common clinical manifestations. CASPR2 antibody was detected in the CSF of 3 patients (3/7) and the serum of all patients (7/7). Notable imaging changes were observed in 5 patients (5/7). All patients received immunotherapy and were followed up for 1 month to 2 years. One patient was diagnosed with rectal cancer with a poor prognosis; all the others got a good prognosis. Conclusions: CASPR2 antibody-related encephalitis is a rare autoimmune disease. It is considered to present with seizures, memory loss, psychiatric symptoms, dizziness and sleep disorders as the main clinical manifestations. Early identification and treatment of the disease can help the patients achieve a good prognosis.

Source identification of HIV-1 transmission in three lawsuits Using Ultra-Deep pyrosequencing and phylogenetic analysis

BACKGROUND/PURPOSE

Intentional transmission of HIV-1 is a crime. Identifying the source of transmission between HIV-1 infected cases using phylogenetic analysis has limitations, including delayed examinations after the initiation of infection and ambiguity of phyletic relationships. This study was the first to introduce phylogenetic tree Results as forensic evidence in a trial in Taiwan.

METHODS

Three lawsuit cases from different district courts in Taiwan were chosen for this study. We identified the source of transmission between individuals in each lawsuit based on the maximum likelihood and Bayesian phylogenetic tree analyses using the HIV-1 sequences from molecular cloning and ultra-deep pyrosequencing (UDPS). Two gene regions of the HIV genome, env and gag, were involved.

RESULTS

The results of phylogenetic analysis using sequences from molecular cloning were clear and evidential enough in lawsuits 1 and 3. Due to the delayed sampling time, the result of sequences from molecular cloning in lawsuit 2 was ambiguous. Combined with the analyzed result of sequences from UDPS and epidemiological information, the source of transmission in lawsuit 2 was further identified.

CONCLUSION

Hence phylogenetic analyses cannot exclude the possibility of unsampled intermediaries, the data interpretation should be more careful and conservative, and it should not be considered as the only evidence for the source identification in a trial without epidemiological or serological information. The evaluation of the introduced UDPS method in the identification of transmission source has shown that the validity and evidential effects were still limited and need further optimization.

[Effect of vascular changes on prognosis after induced chemotherapy for advanced hypopharyngeal carcinoma]

Objective: To analyze the clinical characteristics of two groups(vascular classification declines or not in narrow band imaging (NBI) of patients with advanced hypopharyngeal carcinoma after induced chemotherapy, to follow-up and compare the survival differences between the two groups, and to explore the effect of vascular changes on clinical prognosis after induced chemotherapy in patients with advanced hypopharyngeal carcinoma. Methods: Clinical data of 56 patients with advanced hypopharyngeal carcinoma from August 2014 to September 2016 in Beijing Tongren Hospital, Capital Medical University were collected. The patients were divided into two groups according to NBI vascular classification declines or not after induced chemotherapy. The survival of patients and the impact of different factors on the prognosis were retrospectively analyzed. SPSS 24.0 statistical software was used for analysis. Frequency data were compared between the two groups using χ(2) test. Kaplan-Meier method and Cox regression analysis were employed for survival analysis and Log-Rank test was used for inter-group comparison, P<0.05 was statistically significant. Results: There was significant difference in overall survival rate(OS) between two groups of patients with advanced hypopharyngeal carcinoma after induced chemotherapy (P<0.05). Multivariate analysis showed that NBI vascular classification changes after induced chemotherapy was the impact factor for prognosis of advanced hypopharyngeal carcinoma after induced chemotherapy. Conclusion: In addition to recurrence and metastasis, NBI vascular classification changes is the important impact factor for prognosis of advanced hypopharyngeal carcinoma after induced chemotherapy. Patients with NBI vascular classification declines have significant survival benefit. The patients with advanced hypopharyngeal carcinoma should be checked with NBI examination before and after induced chemotherapy. NBI should be included in the routine screening indicators for prognosis of advanced hypopharyngeal carcinoma.

Effects of different degrees of depression on inflammatory response and immune function in patients with ovarian cancer

The aim of this study was to explore the effect of depression of different degrees on inflammatory response and immune function in patients with ovarian cancer. One hundred and eight cases of ovarian cancer according to the Federation Internationale of Gynecologie and Obstetrigue (FIGO) stage II~III who visited the Gynecology Department of Affiliated HongQi Hospital of MuDanJiang Medical University between September 2015 and May 2017 were enrolled in the study. After being hospitalized, they were divided into two groups according to their Beck Depression Inventory (BDI) scores. The total score of BDI is 63, with 0~4 for the normal group (25 cases), 5~13 for the mild depression group (24 cases), 14~20 for the moderate depression group (28 cases), and 21~63 for the severe depression group (31 cases). The immune function, inflammatory reaction, tumor markers [CA125, human epididymis protein-4 (HE4), insulin-like growth factor-I (IGF-I)], platelet technology and D-dimer index were compared between the four groups. The results showed that there were different levels of depression in patients with ovarian cancer in II~III stage, and the degree of depression could stimulate the level of serum-6, and TNF -α in serum increased. The proportion of CD3+, CD4+ and NK cells in patients with severe depression decreased, and their immunity also decreased. Depression increased the levels of CA125, HE4 and IGF-I in serum and ascites of ovarian cancer patients, and increased the risk of tumor progression and recurrence. Hypercoagulability existed in patients with ovarian cancer, and tumor associated depression could increase platelet count in plasma and increase D-dimer level. To sum up, depression can affect the level of micro inflammation in patients with ovarian cancer. In particular, depression can reduce cellular immune responses, affect the progression free survival of ovarian cancer patients, and reduce their overall survival rate.

Magnetic correlations in the intermetallic antiferromagnet Nd3Co4Sn13

Specific heat, magnetic susceptibility, and neutron scattering have been used to investigate the nature of the spin system in the antiferromagnet Nd₃Co₄Sn₁₃. At room temperature Nd₃Co₄Sn₁₃ has a cubic, Pm-3n structure similar to Yb₃Rh₄Sn₁₃. Antiferromagnetic interactions between, Nd³⁺ ions dominate the magnetic character of this sample and at 2.4 K the Nd spins enter a long range order state with a magnetic propagation vector q  =  (0 0 0) with an ordered moment of 1.78(2) µ_B at 1.5 K. The magnetic Bragg intensity grows very slowly below 1 K, reaching ~2.4 µ_B at 350 mK. The average magnetic Nd³⁺ configuration corresponds to the 3D irreducible representation Γ₇. This magnetic structure can be viewed as three sublattices of antiferromagnetic spin chains coupled with each other in the 120°-configuration. A well-defined magnetic excitation was measured around the 1 1 1 zone centre and the resulting dispersion curve is appropriate for an antiferromagnet with a gap of 0.20(1) meV.

[Analysis of high-risk HPV infection and cervical cytologic screening in HIV positive women]

Objective: To analysis of high-risk HPV infection and cervical cytologic screening in HIV positive women, and to study the relationship between HIV infection and high-risk HPV infection. Methods: From June 2011 to May 2016, 58 cases of HIV positive women in Beijing Ditan Hospital for cervical screening were selected as the experimental group, and 59 cases of HIV negative women were selected as control group, thin-prep cytologic test(TCT)and HPV detection were used in two groups of subjects. The abnormal rate of TCT and the incidence rate of HPV were observed in the two groups, the relationship between HIV infection and HPV infection was analyzed. Results: TCT abnormal rate(91.4%, 53/58)of the experimental group was obviously higher than that of the control group(45.8%, 27/59), with statistically significant(χ²=12.365, P=0.036). High-risk HPV infection incidence(34.5%, 20/58)of the experimental group was significantly higher than that of the control group(16.9%, 10/59), with traditional significance(χ²=10.359, P=0.041). CD₄⁺ T lymphocytes and CD₄⁺/CD₈⁺ ratio of high-risk HPV positive patients had significant difference with high-risk HPV negative patients(χ²=10.378, P=0.042; χ²=9.245, P=0.045). The proportion of different AIDS clinical stages of high-risk HPV positive patients had obvious difference with high-risk HPV negative patients(P<0.05). Conclusion: HIV positive women maybe have a large proportion of abnormal TCT and the infection with high-risk HPV, and infection of high-risk HPV in HIV positive women has relationship with CD₄⁺ T lymphocytes, CD₄⁺/CD₈⁺ ratio and AIDS clinical stage.

Evaluation on the germplasm of maize (Zea mays L.) landraces from southwest China

Because of their local adaptation and economic factors that limit the adoption of commercial hybrids, farmer-saved maize landraces are still grown over a considerable area concentrated in southwest China. To evaluate the potential of using maize landraces, the germplasm characteristics of 96 landraces from southwest China were evaluated at phenotypic, cellular, and molecular levels. The existence of high phenotypic variation and elite germplasm tolerant to low-N, low-P, as well as drought stress was observed. Of the total landraces, 81.25, 7.29, 5.21, and 2.08% were found with 0, 1, 2, 3, and 4 B chromosomes. Using 42 microsatellite (simple sequence repeat) loci, 246 alleles were detected among the landraces. The number of alleles per SSR locus varied from 2 to 10, averaging 5.67 allele per locus, which revealed a high level of genetic diversity of maize landraces in southwest China. Cluster analysis showed that 96 landraces could distinctly be clustered into four groups, which tended to associate with their geographic origins. We propose that the genetic diversity center of maize landraces in southwest China might be in Sichuan. A sharp genetic deviation from Hardy-Weinberg equilibrium was observed from heterozygosity deficiency and a considerable genetic variation was revealed within, rather than among, the landraces. Based on their germplasm characteristics, the innovation and utilization of maize landraces in southwestern China for theoretical and applied research could be achieved by constructing heterosis groups, developing inbred lines with high combining ability, and maintaining the landraces with elite germplasm and B chromosomes using bulked pollen.

Role of XRCC1 gene polymorphisms in non-small cell lung cancer cisplatin-based chemotherapy, and their effect on clinical and pathological characteristics

Non-small cell lung cancer (NSCLC) is the most common cancer globally. The XRCC1 protein interacts with ligase and poly(ADP-ribose) polymerase to repair cisplatin-induced DNA damage. The authors of previous studies have reported XRCC1 Arg399Gln, Arg280His, and Arg194Trp polymorphisms and advanced NSCLC prognosis, but the results are inconclusive. We investigated the association between clinical outcome and XRCC1 Arg399Gln, Arg280His, and Arg194Trp polymorphisms in advanced NSCLC patients treated with cisplatin. We recruited 252 patients with advanced NSCLC (TNM stages: IIIB and IV) and used polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) to genotype the polymorphisms. Patients with the TT genotype of XRCC1 Arg194Trp showed a significantly better response to chemotherapy than those with the CC genotype. The GA+AA genotype of Arg194Trp was correlated with better response to chemotherapy than the wild-type form. The TT genotype of Arg194Trp was associated with longer survival time than the CC genotype. The TT genotype of Arg194Trp was correlated with lower risk of death from all causes than the CC genotype. The Arg194Trp polymorphisms interacted with squamous cell carcinoma and affected overall survival of advanced NSCLC. However, there was no association between Arg399Gln and Arg280His polymorphisms and response to cisplatin-based chemotherapy and overall survival in advanced NSCLC. The results suggest that the TT genotype of Arg194Trp is significantly associated with better response to chemotherapy and longer overall survival of advanced NSCLC patients than the wild-type form. Our investigation offers insight into the influence of XRCC1 gene polymorphisms on the treatment outcome of advanced NSCLC.

Evolution of mustard (Brassica juncea Coss) subspecies in China: evidence from the chalcone synthase gene

To explore the phylogenetic relationship, genome donor, and evolutionary history of the polyploid mustard (Brassica juncea) from China, eighty-one sequences of the chalcone synthase gene (Chs) were analyzed in 43 individuals, including 34 B. juncea, 2 B. rapa, 1 B. nigra, 2 B. oleracea, 1 B. napus, 1 B. carinata, and 2 Raphanus sativus. A maximum likelihood analysis showed that sequences from B. juncea were separated into two well-supported groups in accordance with the A and B genomes, whereas the traditional phenotypic classification of B. juncea was not wholly supported by the molecular results. The SplitsTree analysis recognized four distinct groups of Brassicaceae, and the median-joining network analysis recognized four distinct haplotypes of Chs. The estimates of Tajima's D, Fu and Li's D, and Fu and Li's F statistic for the Chs gene in the B genome were negative, while those in the A genome were significant. The results indicated that 1) the Chs sequences revealed a high level of sequence variation in Chinese mustard, 2) both tree and reticulate evolutions existed, and artificial selection played an important role in the evolution of Chinese mustard, 3) the original parental species of Chinese mustard are B. rapa var. sinapis arvensis and B. nigra (derived from China), 4) nucleotide variation in the B genome was higher than that in the A genome, and 5) cultivated mustard evolved from wild mustard, and China is one of the primary origins of B. juncea.

Spatial Temporal Dynamics and Molecular Evolution of Re-Emerging Rabies Virus in Taiwan

Taiwan has been recognized by the World Organization for Animal Health as rabies-free since 1961. Surprisingly, rabies virus (RABV) was identified in a dead Formosan ferret badger in July 2013. Later, more infected ferret badgers were reported from different geographic regions of Taiwan. In order to know its evolutionary history and spatial temporal dynamics of this virus, phylogeny was reconstructed by maximum likelihood and Bayesian methods based on the full-length of glycoprotein (G), matrix protein (M), and nucleoprotein (N) genes. The evolutionary rates and phylogeographic were determined using Beast and SPREAD software. Phylogenetic trees showed a monophyletic group containing all of RABV isolates from Taiwan and it further separated into three sub-groups. The estimated nucleotide substitution rates of G, M, and N genes were between 2.49 × 10⁻⁴–4.75 × 10⁻⁴ substitutions/site/year, and the mean ratio of dN/dS was significantly low. The time of the most recent common ancestor was estimated around 75, 89, and 170 years, respectively. Phylogeographic analysis suggested the origin of the epidemic could be in Eastern Taiwan, then the Formosan ferret badger moved across the Central Range of Taiwan to western regions and separated into two branches. In this study, we illustrated the evolution history and phylogeographic of RABV in Formosan ferret badgers.

New Phylogenetic Groups of Torque Teno Virus Identified in Eastern Taiwan Indigenes

Torque teno virus (TTV) is a single-stranded DNA virus highly prevalent in the world. It has been detected in eastern Taiwan indigenes with a low prevalence of 11% by using N22 region of which known to underestimate TTV prevalence excessively. In order to clarify their realistic epidemiology, we re-analyzed TTV prevalence with UTR region. One hundred and forty serum samples from eastern Taiwanese indigenous population were collected and TTV DNA was detected in 133 (95%) samples. Direct sequencing revealed an extensive mix-infection of different TTV strains within the infected individual. Entire TTV open reading frame 1 was amplified and cloned from a TTV positive individual to distinguish mix-infected strains. Phylogenetic analysis showed eleven isolates were clustered into a monophyletic group that is distinct from all known groups. In addition, another our isolate was clustered with recently described Hebei-1 strain and formed an independent clade. Based on the distribution pattern of pairwise distances, both new clusters were placed at phylogenetic group level, designed as the 6th and 7th phylogenetic group. In present study, we showed a very high prevalence of TTV infection in eastern Taiwan indigenes and indentified new phylogenetic groups from the infected individual. Both intra- and inter-phylogenetic group mix-infections can be found from one healthy person. Our study has further broadened the field of human TTVs and proposed a robust criterion for classification of the major TTV phylogenetic groups.

Emergence of a sylvatic enzootic formosan ferret badger-associated rabies in Taiwan and the geographical separation of two phylogenetic groups of rabies viruses

Taiwan had been declared rabies-free in humans and domestic animals for five decades until July 2013, when surprisingly, three Formosan ferret badgers (FB) were diagnosed with rabies. Since then, a variety of wild carnivores and other wildlife species have been found dead, neurologically ill, or exhibiting aggressive behaviors around the island. To determine the affected animal species, geographic areas, and environments, animal bodies were examined for rabies by direct fluorescent antibody test (FAT). The viral genomes from the brains of selected rabid animals were sequenced for the phylogeny of rabies viruses (RABV). Out of a total of 1016 wild carnivores, 276/831 (33.2%) Formosan FBs were FAT positive, with occasional biting incidents in 1 dog and suspected spillover in 1 house shrew. All other animals tested, including dogs, cats, bats, mice, house shrews, and squirrels, were rabies-negative. The rabies was badger-associated and confined to nine counties/cities in sylvatic environments. Phylogeny of nucleoprotein and glycoprotein genes from 59 Formosan FB-associated RABV revealed them to be clustered in two distinct groups, TWI and TWII, consistent with the geographic segregation into western and eastern Taiwan provided by the Central Mountain Range and into northern rabies-free and central-southern rabies-affected regions by a river bisecting western Taiwan. The unique features of geographic and genetic segregation, sylvatic enzooticity, and FB-association of RABV suggest a logical strategy for the control of rabies in this nation.

Molecular Epidemiology and Phylogenetic Analysis of Human Adenovirus Caused an Outbreak in Taiwan during 2011

An outbreak of adenovirus has been surveyed in Taiwan in 2011. To better understand the evolution and epidemiology of adenovirus in Taiwan, full-length sequence of hexon and fiber coapsid protein was analyzed using series of phylogenetic and dynamic evolution tools. Six different serotypes were identified in this outbreak and the species B was predominant (HAdV-3, 71.50%; HAdV-7, 15.46%). The most frequent diagnosis was acute tonsillitis (54.59%) and bronchitis (47.83%). Phylogenetic analysis revealed that hexon protein gene sequences were highly conserved for HAdV-3 and HAdV-7 circulation in Taiwan. However, comparison of restriction fragment length polymorphism (RFLP) analysis and phylogenetic trees of fiber gene in HAdV-7 clearly indicated that the predominant genotype in Taiwan has shifted from 7b to 7d. Several positive selection sites were observed in hexon protein. The estimated nucleotide substitution rates of hexon protein of HAdV-3 and HAdV-7 were 0.234×10^-3 substitutions/site/year (95% HPD: 0.387~0.095×10^-3) and 1.107×10^-3 (95% HPD: 0. 541~1.604) respectively; those of the fiber protein of HAdV-3 and HAdV-7 were 1.085×10^-3 (95% HPD: 1.767~0.486) and 0.132×10^-3 (95% HPD: 0.283~0.014) respectively. Phylodynamic analysis by Bayesian skyline plot (BSP) suggested that using individual gene to evaluate the effective population size might possibly cause miscalculation. In summary, the virus evolution is ongoing, and continuous surveillance of this virus evolution will contribute to the control of the epidemic.

Synthesis and phase evolutions in layered structure of Ga2S3 semiconductor thin films on epiready GaAs (111) substrates

We report on synthesis and properties of p-type Ga2S3 semiconductor thin films that were prepared by sulfurizing epiready n-type GaAs (111) surface at elevated temperatures. Comparisons of structural and optical properties among the thin films, peeling-off resulted microtubes, and the remains after peeling-off give a clear clue to the crystal growth and phase evolutions of Ga2S3. Three layers of Ga2S3 are clearly identified in the thin films. They are layer i, cubic Ga2S3 epitaxially grown on the GaAs (111) substrate; layer ii, polycrystalline cubic Ga2S3 on top of layer-i; and layer iii, monoclinic and/or hexagonal Ga2S3 on top of layer ii. The onset of peeling-off occurred in layer i and/or at the interface between layer i and ii. Both the phase evolutions and the location of peeling-off are associated with a Ga out diffusion growth mechanism. Absorption spectroscopy revealed a direct bandgap of 3.0 eV, whereas photoluminescence spectra showed defects (excited Ga vacancies) related red (1.62 eV) and green (2.24 eV) emissions of the Ga2S3 films; both are qualitatively consistent with those reported values obtained at lower sample temperatures from Ga2S3 single crystals. These results, together with a large on/off current ratio (i.e., ∼14 at a bias of 4.0 V) of the resultant hetero p-Ga2S3/n-GaAs junction under a blue laser (405 nm, 3.0 mW) illumination, shed light on consequent integrations of Ga2S3- and GaAs-based optoelectronic devices, e.g., high-power laser radiation sensors.

Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom

Adaptation of enzymes in a metabolic pathway can occur not only through changes in amino acid sequences but also through variations in transcriptional activation, mRNA splicing and mRNA translation. The heme biosynthesis pathway, a linear pathway comprised of eight consecutive enzymes in animals, provides researchers with ample information for multiple types of evolutionary analyses performed with respect to the position of each enzyme in the pathway. Through bioinformatics analysis, we found that the protein-coding sequences of all enzymes in this pathway are under strong purifying selection, from cnidarians to mammals. However, loose evolutionary constraints are observed for enzymes in which self-catalysis occurs. Through comparative genomics, we found that in animals, the first intron of the enzyme-encoding genes has been co-opted for transcriptional activation of the genes in this pathway. Organisms sense the cellular content of iron, and through iron-responsive elements in the 5′ untranslated regions of mRNAs and the intron-exon boundary regions of pathway genes, translational inhibition and exon choice in enzymes may be enabled, respectively. Pathway product (heme)-mediated negative feedback control can affect the transport of pathway enzymes into the mitochondria as well as the ubiquitin-mediated stability of enzymes. Remarkably, the positions of these controls on pathway activity are not ubiquitous but are biased towards the enzymes in the upstream portion of the pathway. We revealed that multiple-level controls on the activity of the heme biosynthesis pathway depend on the linear depth of the enzymes in the pathway, indicating a new strategy for discovering the molecular constraints that shape the evolution of a metabolic pathway.

Molecular epidemiology of enterovirus 71 infection in the central region of Taiwan from 2002 to 2012

Enterovirus 71 (EV71), a causative agent of hand, foot, and mouth disease can be classified into three genotypes and many subtypes. The objectives of this study were to conduct a molecular epidemiological study of EV71 in the central region of Taiwan from 2002–2012 and to test the hypothesis that whether the alternative appearance of different EV71 subtypes in Taiwan is due to transmission from neighboring countries or from re-emergence of pre-existing local strains. We selected 174 EV71 isolates and used reverse transcription-polymerase chain reaction to amplify their VP1 region for DNA sequencing. Phylogenetic analyses were conducted using Neighbor-Joining, Maximum Likelihood and Bayesian methods. We found that the major subtypes of EV71 in Taiwan were B4 for 2002 epidemic, C4 for 2004–2005 epidemic, B5 for 2008–2009 epidemic, C4 for 2010 epidemic and B5 for 2011–2012 epidemic. Phylogenetic analysis demonstrated that the 2002 and 2008 epidemics were associated with EV71 from Malaysia and Singapore; while both 2010 and 2011–2012 epidemics originated from different regions of mainland China including Shanghai, Henan, Xiamen and Gong-Dong. Furthermore, minor strains have been identified in each epidemic and some of them were correlated with the subsequent outbreaks. Therefore, the EV71 infection in Taiwan may originate from pre-existing minor strains or from other regions in Asia including mainland China. In addition, 101 EV71 isolates were selected for the detection of new recombinant strains using the nucleotide sequences spanning the VP1-2A-2B region. No new recombinant strain was found. Analysis of clinical manifestations showed that patients infected with C4 had significantly higher rates of pharyngeal vesicles or ulcers than patients infected with B5. This is the first study demonstrating that different EV 71 genotypes may have different clinical manifestations and the association of EV71 infections between Taiwan and mainland China.

Exploring the molecular epidemiology and evolutionary dynamics of influenza A virus in Taiwan

The evolution and population dynamics of human influenza in Taiwan is a microcosm of the viruses circulating worldwide, which has not yet been studied in detail. We collected 343 representative full genome sequences of human influenza A viruses isolated in Taiwan between 1979 and 2009. Phylogenetic and antigenic data analysis revealed that H1N1 and H3N2 viruses consistently co-circulated in Taiwan, although they were characterized by different temporal dynamics and degrees of genetic diversity. Moreover, influenza A viruses of both subtypes underwent internal gene reassortment involving all eight segments of the viral genome, some of which also occurred during non-epidemic periods. The patterns of gene reassortment were different in the two subtypes. The internal genes of H1N1 viruses moved as a unit, separately from the co-evolving HA and NA genes. On the other hand, the HA and NA genes of H3N2 viruses tended to segregate consistently with different sets of internal gene segments. In particular, as reassortment occurred, H3HA always segregated as a group with the PB1, PA and M genes, while N2NA consistently segregated with PB2 and NP. Finally, the analysis showed that new phylogenetic lineages and antigenic variants emerging in summer were likely to be the progenitors of the epidemic strains in the following season. The synchronized seasonal patterns and high genetic diversity of influenza A viruses observed in Taiwan make possible to capture the evolutionary dynamic and epidemiological rules governing antigenic drift and reassortment and may serve as a "warning" system that recapitulates the global epidemic.

Wire network behavior in superconducting Nb films with diluted triangular arrays of holes

We present results of transport measurements on superconducting Nb films with diluted triangular arrays (honeycomb and kagomé) of holes. The patterned films have large disk-shaped interstitial regions even when the edge-to-edge separations between nearest neighboring holes are comparable to the coherence length. Changes in the field interval of two consecutive minima in the field dependent resistance R(H) curves are observed. In the low field region, fine structures in the R(H) and T(c)(H) curves are identified in both arrays. Comparison of experimental data with calculation results reveals that these structures observed in honeycomb and kagomé hole arrays resemble those in wire networks with triangular and T(3) symmetries, respectively. The findings suggest that even in these specified periodic hole arrays with very large interstitial regions, the low field fine structures are determined by the connectivity of the nanostructures.

Interface characterization of epitaxial Fe/MgO/Fe magnetic tunnel junctions

Following predictions by first-principles theory of a huge tunnel magnetoresistance (TMR) effect in epitaxial Fe/MgO/Fe magnetic tunnel junctions (MTJs), measured magnetoresistance (MR) ratios of about 200% at room temperature (RT) have been reported in MgO-based epitaxial MTJs. Recently, a MR ratio of about 600% has been reported at RT in MgO-based MTJs prepared by magnetron sputtering, using amorphous CoFeB as the ferromagnetic electrode. These MTJs show great potential for application in spintronic devices. Fully epitaxial MTJs are excellent model systems that enhance our understanding of the spin-dependent tunneling process as the interface is well defined and can be fully characterized. Both theoretical calculations and experimental results clearly indicate that the interfacial structure plays a crucial role in the coherent tunneling across a single crystal MgO barrier, especially in epitaxial MgO-based MTJs grown by molecular beam epitaxy (MBE). Surface X-ray diffraction, Auger electron spectroscopy, X-ray absorption spectra, and X-ray magnetic circular dichroism techniques have been reported previously for interface characterization. However, no consistent viewpoint has been reached on the interfacial structures (such as FeO layer formation at the bottom Fe/MgO interface), and it is still an open issue. In this article, our recent studies on the interface characterization of MgO-based epitaxial MTJs by X-ray photoelectron spectroscopy, high resolution transmission electron microscopy, and spin-dependent tunneling spectroscopy, will be presented.

Risk factors for HIV-1 seroconversion among Taiwanese men visiting gay saunas who have sex with men

Background

Men having sex with men (MSM) accounts for 33.6% of all reported cases of HIV-1 infection in Taiwan. The aim of this study was to investigate the epidemiology of HIV-1 infection among MSM in gay saunas in Taiwan.

Methods

Patrons of 5 gay saunas were recruited for a weekly volunteer counseling and testing program from 2001 to 2005. Questionnaires were collected for a risk factor analysis. HIV-1 subtypes were determined using DNA sequencing and phylogenetic analyses.

Results

HIV-1 prevalence rates among MSM in gay saunas in 2001 through 2005 were 3.4%, 5.1%, 8.9%, 8.5%, and 8.3%, respectively. In total, 81 of 1, 093 (7.4%) MSM had HIV-1 infection. Fifty-two HIV-1 strains were genotyped, and all of them were subtype B. HIV-seropositive men were significantly younger than the seronegatives. Only 37.1% used condoms every time during sexual intercourse. A multivariate logistic regression analysis showed that the risk factors for HIV-1 were being uncircumcised (odds ratio (OR) = 2.19; 95% confidence interval (CI), 1.08~4.45); having sexual intercourse with at least 2 partners during each sauna visit (≥ 2 vs. ≤ 1, OR = 1.71; 95% CI, 1.02~2.89); and the role played during anal intercourse (versatile vs. an exclusively insertive role, OR = 2.76; 95% CI, 1.42~5.36).

Conclusions

Overall, 7.4% Taiwanese MSM participating in this study had HIV-1 subtype B infection. Uncircumcised, being versatile role during anal intercourse, and having sex with more than one person during each sauna visit were main risk factors for HIV-1 infection.

Molecular epidemiology of HCV genotypes among injection drug users in Taiwan: Full-length sequences of two new subtype 6w strains and a recombinant form_2b6w

Human immunodeficiency virus type 1 (HIV-1) circulating recombinant form (CRF) 07_BC strain has caused serious outbreaks among injection drug users in Taiwan since 2004. The objective of this study was to conduct a molecular epidemiological study of HCV genotypes in intravenous drug users in Taiwan. Blood samples and questionnaires from 591 intravenous drug users infected with HIV-1 were collected nationwide. In total, 180 samples were selected for HCV genotyping using multiplex PCR and phylogenetic analysis of the core, E1 and NS5B regions. The Inno-Lipa assay was used to confirm multiple infections with different genotypes. Eighty percent had a single infection with subtype 1b being the most common subtype (24%), 12% had double infections and two had triple infections. In addition, three recombinant forms (RFs)-2a1a, 3a1b, and 2b6w were identified. Phylogenetic analyses showed that the 3a, 6a, and 6n strains were clustered with strains present in Thailand and mainland China. Full-length sequence analysis showed that two 6w strains shared 89.4-90.2% sequence homology with the 6(r) strain from the Guangdong Province, China. Bootscan analysis revealed that the recombination breakpoint of RF_2b6w was located at the NS2-NS3 junction. In summary, the distribution of HCV genotypes among Taiwanese intravenous drug users was complex and more than 12% of the drug users were infected with more than one genotype of HCV.

Influenza A virus in Taiwan, 1980-2006: Phylogenetic and antigenic characteristics of the hemagglutinin gene

Limited amount of information is available in Taiwan on the genetic or antigenic characteristics of influenza A virus prior to the establishment of a Taiwan surveillance network in 2000. Isolates of H1N1 and H3N2 viruses in Taiwan between 1980 and 2006 were studied, and part of the hemagglutinin gene was analyzed due to its importance in terms of viral infection and antibody neutralization. Results from a phylogenetic analysis indicate continuous evolutionary topology in H3N2 isolates, and two distinct H1N1 lineages. Many genetic relationships between vaccine strains and epidemic isolates appearing in Taiwan before other global locations were also observed and recorded in addition to a gradual increase in the number of N‐linked glycosylation sites on partial HA1 proteins since 1980. The results from pairwise comparisons of HA1 nucleotide and deduced amino acid sequences indicate shared identities within groups organized according to their bootstrap and P‐values of approximately 95.5–100% and 95.7–100% in H1N1 and 94.5–100% and 93.2–100% in H3N2 viruses, respectively. Comparisons of amino acid substitutions in the five antigenic regions reveal highly non‐synonymous changes occurring in the Sb region of H1N1 and in the B region of H3N2. The results of an antigenic analysis using a hemagglutinin inhibition (HI) test indicate the presence of some epidemic strains 1–2 years earlier in Taiwan than in other parts of the world, as well as higher vaccine mismatch rates. This information supports the need for continuous surveillance of emerging influenza viruses in Taiwan, which will be useful for making global vaccine decisions. J. Med. Virol. 81:1457–1470, 2009. © 2009 Wiley‐Liss, Inc.

Molecular analysis of HLA-DRB1 allelic associations with systemic lupus erythematous and lupus nephritis in Taiwan

To evaluate the association of human leukocyte antigen (HLA)–DRB1 alleles with systemic lupus erythematosus (SLE) and lupus nephritis (LN) in the Taiwanese population, and to investigate the possible association of HLA-DRB1 alleles with disease severity in LN. HLA-DRB1 alleles were studied in 105 SLE patients (82 patients with LN, 23 patients without LN) and 855 healthy controls by polymerase chain reaction and sequence-based typing assays. The frequency of the HLA class II alleles DRB1*0301 (Odds ratio [OR] = 2.01, 95% confidence interval [CI] = 1.31–3.10, Pc = 0.02) and DRB1*1501 (OR = 2.06, 95% CI = 1.36–3.13, Pc = 0.01) were both increased in SLE patients, compared to healthy controls. The frequency of DRB1*1202 was significantly lower in LN patients than in SLE patients without nephritis (OR = 0.23, 95% CI = 0.09–0.57, Pc = 0.01). No specific allele was significantly associated with an increased or decreased risk for severity of LN in this sample. In Taiwanese people, the DRB1*0301 and DRB1*1501 alleles are significant risk factors for SLE, while the DRB1*1202 allele is protective for LN.

Clinical and genetic analysis of Human Bocavirus in children with lower respiratory tract infection in Taiwan

BACKGROUND

Human Bocavirus (HBoV) is a likely etiologic agent of acute respiratory disease in children. The prevalence of this virus has been studied in several sites worldwide. We conducted the first clinical and molecular study of HBoV in Taiwan at the Centers for Diseases Control, Taiwan.

OBJECTIVES

To investigate the genomic and epidemiologic profiles of HBoV infection in Taiwan.

STUDY DESIGN

Throat swabs or nasopharyngeal aspirates were obtained from hospitalized pediatric patients with acute lower respiratory tract infections. Specimens negative for other respiratory viruses by molecular screening were examined for HBoV.

RESULTS

HBoV was the only virus detected in 30 (5.6%) of 531 samples. Of these positive cases, 56.7% were from children less than 2 years old. Two groups of HBoV co-circulated in Taiwan during the study. Results of evolutionary networks evaluation suggest that HBoV might have had an opportunity for interbreeding of viruses and genetic recombinations among the different genes.

CONCLUSION

HBoV may have circulated in Taiwan for some time and it appears to be one of the etiological agents responsible for lower respiratory tract infection in children.