Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Classification Reveals Molecular Subgroups in Patients with Hepatitis B Virus

Hepatitis B virus (HBV) specifically infects hepatocytes, which can cause progressive liver fibrosis and a significantly increased risk of liver cancer. Multiple studies indicated host genetic, virological, and immunological factors could affect the HBV infection. However, the underlying mechanism involved in HBV infection remained unclear. Based on the analysis of gene expression data of 124 HBV patients (GEO accession: GSE84044), molecular subgroups of patients infected with hepatitis B virus were identified in this study, including C1, C2, and C3 groups. The age, fiber, degree of chemical and inflammation, and gene expression difference were also compared among the three sampling groups. Furthermore, the liver index was calculated using 93 liver-specific genes. The liver-specific gene expression in different molecular subgroups of HBV patients was thoroughly analyzed and then was compared with fibrosis and inflammation levels. Results showed that the C2 group was the youngest and the C3 group had the highest degree of fibrosis and inflammation. Enrichment analysis showed that metabolism-related pathways were mainly expressed in the C1 and C2 groups, and inflammation-related pathways and proteoglycans in cancer were highly expressed in the C1 and C3 groups. The liver index was higher in the C2 group than in the C1 and C3 groups, and it was the lowest in the C3 group. Macrophage M1/M2 and neutrophils were significantly different in the three groups. M1 was mainly abundant in the C3 group, and M2 and neutrophils were mainly abundant in the C2 group. This study provides novel information to understand the mechanisms of HBV infection in chronic hepatitis B (CHB) patients.
Sinus Node Dysfunction due to Occlusion of the Sinus Node Artery during Percutaneous Coronary Intervention

Background Sinus node artery occlusion (SNO) is a rare complication of percutaneous coronary intervention (PCI). We analyze both the short- and long-term consequences of SNO. Methods We retrospectively reviewed 1379 consecutive PCI's involving RCA and Cx arteries performed in our heart institute from 2016 to 2019. Median follow-up was 44 ± 5 months. Results Among the 4844 PCIs performed during the study period, 284 involved the RCA and the circumflex's proximal segment. Periprocedural SNO was estimated by angiography observed in 15 patients (5.3%), all originated from RCA. The majority of SNO occurred during urgent and primary PCIs following acute coronary syndrome (ACS). Sinus node dysfunction (SND) appeared in 12 (80%) of patients. Four (26.6%) patients had sinus bradycardia, which resolved spontaneously, and 8 (53.3%) patients had sinus arrest with an escaped nodal rhythm, which mostly responded to medical treatment during the first 24 hours. There was no association between PCI technique and outcome. Three patients (20%) required urgent temporary ventricular pacing. One patient had permanent pacemaker implantation. Pacemaker interrogation during follow-up revealed a recovery of the sinus node function after one month. Conclusion SNO is rare and seen mostly during angioplasty to the proximal segment of the RCA during ACS. The risk of developing sinus node dysfunction following SNO is high. SND usually appears during the first 24 h of PCI. The majority of SND patients responded to medical treatment, and only in rare cases were permanent pacemakers required.
Inertial-Based Human Motion Capture: A Technical Summary of Current Processing Methodologies for Spatiotemporal and Kinematic Measures

Inertial-based motion capture (IMC) has been suggested to overcome many of the limitations of traditional motion capture systems. The validity of IMC is, however, suggested to be dependent on the methodologies used to process the raw data collected by the inertial device. The aim of this technical summary is to provide researchers and developers with a starting point from which to further develop the current IMC data processing methodologies used to estimate human spatiotemporal and kinematic measures. The main workflow pertaining to the estimation of spatiotemporal and kinematic measures was presented, and a general overview of previous methodologies used for each stage of data processing was provided. For the estimation of spatiotemporal measures, which includes stride length, stride rate, and stance/swing duration, measurement thresholding and zero-velocity update approaches were discussed as the most common methodologies used to estimate such measures. The methodologies used for the estimation of joint kinematics were found to be broad, with the combination of Kalman filtering or complimentary filtering and various sensor to segment alignment techniques including anatomical alignment, static calibration, and functional calibration methods identified as being most common. The effect of soft tissue artefacts, device placement, biomechanical modelling methods, and ferromagnetic interference within the environment, on the accuracy and validity of IMC, was also discussed. Where a range of methods have previously been used to estimate human spatiotemporal and kinematic measures, further development is required to reduce estimation errors, improve the validity of spatiotemporal and kinematic estimations, and standardize data processing practices. It is anticipated that this technical summary will reduce the time researchers and developers require to establish the fundamental methodological components of IMC prior to commencing further development of IMC methodologies, thus increasing the rate of development and utilisation of IMC.
Infectious bronchitis associated with Escherichia coli infection in commercial broiler chickens: a case report

Objective: In this case report, we have investigated the infectious bronchitis (IB) virus (IBV) outbreak with the co-infection of Escherichia coli in 28–33-day-old broiler chickens in Malaysia. Materials and Methods: A farmer complained that Cobb 500 chickens, raised in the open house, were having bloody diarrhea, open mouth breathing, non-uniform growth, and ruffled feathers. The mortality was about 100 birds (from about 7000 birds) per day. The sick birds were isolated and subjected to physical examination, postmortem, and histopathological analyses. Gross lesions were observed and recorded. The lung samples have proceeded with histopathological evaluations. The lungs, kidneys, trachea, air sac, and heart samples were collected to isolate bacteria and fungi through a series of conventional cultural methods, followed by molecular confirmation of the IBV. Results: Postmortem examination revealed air sacculitis, hemorrhagic tracheitis, pulmonary congestion, fibrin deposition in the liver and air sac, hemorrhagic enteritis, and renomegaly. The bacterial culture and biochemical tests revealed E. coli in the lungs, trachea, liver, intestine, and kidney samples. However, no fungus could be isolated from those samples. Histological evaluation of lung samples demonstrated infiltration of inflammatory cells in the pulmonary tissues. Apart from this, reverse transcription-polymerase chain reaction confirmed the presence of avian coronavirus responsible for infectious bronchitis (IB). Conclusion: The chickens were diagnosed with IB concurrent with E.coli. The chickens exhibited typical nephropathogenic strain of IBV infection, causing high mortality.
The Inhibitory Effects of Ficin on Streptococcus mutans Biofilm Formation

To investigate the effects of ficin on biofilm formation of conditionally cariogenic Streptococcus mutans (S. mutans). Biomass and metabolic activity of biofilm were assessed using crystal violet assay, colony-forming unit (CFU) counting, and MTT assay. Extracellular polysaccharide (EPS) synthesis was displayed by SEM imaging, bacteria/EPS staining, and anthrone method while acid production was revealed by lactic acid assay. Growth curve and live/dead bacterial staining were conducted to monitor bacterial growth state in both planktonic and biofilm form. Total protein and extracellular proteins of S. mutans biofilm were analyzed by protein/bacterial staining and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), severally. qRT-PCR was conducted to detect acid production, acid tolerance, and biofilm formation associated genes. Crystal violet assay, CFU counting, and MTT assay showed that the suppression effect of ficin on S. mutans biofilm formation was concentration dependent. 4 mg/mL ficin had significant inhibitory effect on S. mutans biofilm formation including biomass, metabolic activity, EPS synthesis, and lactic acid production (p < 0.05). The growth curves from 0 mg/mL to 4 mg/mL ficin were aligned with each other. There was no significant difference among different ficin groups in terms of live/dead bacterial staining result (p > 0.05). Protein/bacterial staining outcome indicated that ficin inhibit both total protein and biofilm formation during the biofilm development. There were more relatively small molecular weight protein bands in extracellular proteins of 4 mg/mL ficin group when compared with the control. Generally, ficin could inhibit biofilm formation and reduce cariogenic virulence of S. mutans effectively in vitro; thus, it could be a potential anticaries agent.
Reproduction of Meloidogyne arenaria race 2 on Flue-cured tobacco possessing resistance genes Rk1 and/or Rk2

Abstract Resistance to Meloidogyne incognita races 1 and 3 and race 1 of M. arenaria is imparted to flue-cured tobacco by the gene Rk1. Meloidogyne arenaria race 2 is not controlled by Rk1 and has become prevalent in Virginia. A second form of resistance effective against M. javanica, Rk2, is also increasingly available commercially. Greenhouse and field trials including a root-knot susceptible cultivar, cultivars homozygous for Rk1 or Rk2, and cultivars possessing both genes were conducted in 2018 and 2019 to investigate the effect of Rk1 and/or Rk2 on parasitism and reproduction of M. arenaria race 2. Plants were inoculated with 5,000 M. arenaria race 2 eggs in the greenhouse or infested by a native nematode population in the field. Data were collected after 28 days (greenhouse) or every 3 weeks following transplant until 18 weeks in the field and included root galling index, nematodes present in roots, egg mass numbers, and egg counts; reproductive indices were also calculated. We found that the combination of Rk1 and Rk2 provides greater resistance to M. arenaria race 2 than either gene alone. While the effect of either gene alone was inconsistent, we did observe some significant reductions in galling and reproduction associated with each gene relative to the susceptible control.
The role of the isolation of the marginal seas during the Pleistocene in the genetic structure of black sea bream Acanthopagrus schlegelii (Bleeker, 1854) in the coastal waters of Japan

The black sea bream Acanthopagrus schlegelii (Bleeker, 1854) is a commercially important species in Japanese waters. Assessing its population structure is essential to ensure its sustainability. In the Northwestern Pacific, historical glacial and interglacial periods during the Pleistocene have shaped the population structure of many coastal marine fishes. However, whether these events affected the population of black sea bream remains unknown. To test this hypothesis and to assess the population structure of black sea bream, we used 1,046 sequences of the mitochondrial control region from individuals collected throughout almost the entire Japanese coastal waters and combined them with 118 sequences from populations distributed in other marginal seas of the Northwestern Pacific Ocean. As in other coastal marine fish with similar distribution, we also found evidence that the glacial refugia on the marginal seas prompted the formation of three lineages in black sea bream. These lineages present signatures of population growth that coincided with the interglacial periods of the Pleistocene. While the origin of Lineages B and C remains unclear, the higher relative frequency of Lineage A in the southernmost location suggests its origin in the South China Sea. The non-significant pairwise ΦST and AMOVA of Japanese populations and the presence of these three lineages mixed in Japanese waters; strongly suggest that these lineages are homogenized in both the Sea of Japan and the Pacific Ocean. Our results indicate that the black sea bream should be managed as a single stock in Japan until the strength of connectivity in contemporary populations is further addressed using non-coding nuclear markers.
Molecular optimization, docking, and dynamic simulation profiling of selective aromatic phytochemical ligands in blocking the SARS-CoV-2 S protein attachment to ACE2 receptor: an in silico approach of targeted drug designing

Objectives: The comprehensive in silico study aims to figure out the most effective aromatic phytochemical ligands among a number from a library, considering their pharmacokinetic efficacies in blocking “angiotensin-converting enzyme 2 (ACE2) receptor–severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S protein” complex formation as part of a target-specific drug designing. Materials and Methods: A library of 57 aromatic pharmacophore phytochemical ligands was prepared from where the top five ligands depending on Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) and quantitative structure-activity relationship (QSAR)-based pharmacokinetic properties were considered. The selected ligands were optimized for commencing molecular docking and dynamic simulation as a complex with the ACE2 receptor to compare their blocking efficacy with the control drug. The ligand–receptor complexes’ accuracy in preventing the Spike (S) protein of SARS-CoV-2 penetration inside the host cells has been analyzed through hydrogen–hydrophobic bond interactions, principal component analysis (PCA), root mean square deviation (RMSD), root mean square fluctuation (RMSF), and B-Factor. Advanced in silico programming language and bioanalytical software were used for high throughput and authentic results. Results: ADMET and QSAR revealed Rhamnetin, Lactupicrin, Rhinacanthin D, Flemiflavanone D, and Exiguaflavanone A as the ligands of our interest to be compared with the control Cassiarin D. According to the molecular docking binding affinity to block ACE2 receptor, the efficiency mountings were Rhinacanthin D > Flemiflavanone D > Lactupicrin > Exiguaflavanone A > Rhamnetin. The binding affinity of the Cassiarin D–ACE2 complex was (−10.2 KJ/mol) found inferior to the Rhinacanthin D–ACE2 complex (−10.8 KJ/mol), referring to Rhinacanthin D as a more stable candidate to use as drugs. The RMSD values of protein–ligand complexes evaluated according to their structural conformation and stable binding pose ranged between 0.1~2.1 Å. The B-factor showed that very few loops were present in the protein structure. The RMSF peak fluctuation regions ranged 5–250, predicting efficient ligand–receptor interactions. Conclusion: The experiment sequentially measures all the parameters required in referring to any pharmacophore as a drug, considering which all aromatic components analyzed in the study can strongly be predicted as target-specific medication against the novel coronavirus 2019 infection.
Dietary Riboflavin Intake and Riboflavin Status in Young Adult Women Living in Metro Vancouver, Canada

ABSTRACT Background Nutrition surveys suggest that <10% of Canadian adults have inadequate riboflavin intakes. However, biochemical riboflavin deficiency [erythrocyte glutathione reductase activity coefficient (EGRac) ≥1.40] has been reported in 41% of young adult women living in Metro Vancouver. Canadian Chinese ethnicity comprise >25% of Vancouver's population and are postulated to have poorer riboflavin status than those of European ethnicity because they could be less likely to consume dairy products and fortified wheat. Objectives The objectives of this study were to determine dietary riboflavin intake and food sources, and to assess the association between riboflavin intake and status in young women of European (n = 107) and Chinese (n = 91) ethnicities living in Metro Vancouver, Canada. Methods This was a cross-sectional study conducted in women (aged 19–45 y). Women were healthy, not pregnant or breastfeeding, of European or Chinese ethnicities, and not taking riboflavin-containing supplements for the past 4 mo. Dietary riboflavin intake was assessed using the past-year Diet History Questionnaire II, and riboflavin status (EGRac) was measured in fasting venous blood samples. Results Only 7% of participants had dietary riboflavin intakes below the Estimated Average Requirement (0.9 mg/d), but 40% of women had biochemical riboflavin deficiency (EGRac ≥1.40). Although more Canadian women of European ethnicity than Chinese ethnicity had biochemical riboflavin deficiency (46% and 34%; P < 0.001), median dietary riboflavin intake did not differ (1.73 and 1.82 mg/d; P = 0.587). Dairy products and vegetables contributed the most to riboflavin intake. Energy-adjusted dietary riboflavin intake was inversely associated with EGRac (B = −0.04, 95% CI: −0.07, −0.01). However, after further adjustment the relation was not significant. Conclusions Overall, women of reproductive age living in Metro Vancouver, Canada, had a low prevalence of inadequate dietary riboflavin intake despite the high prevalence of apparent biochemical riboflavin deficiency.
Reliability of Spike Gene Target Failure for ascertaining SARS-CoV-2 lineage B.1.1.7 prevalence in a hospital setting

The appearance of the SARS-CoV-2 lineage B.1. 1.7 in the UK in late 2020, associated with faster transmission, sparked the need to find effective ways to monitor its spread. The set of mutations that characterise this lineage include a deletion in position 69 and 70 of the spike protein, which is known to be associated with Spike Gene Target Failure (SGTF) in a commonly used three gene diagnostic qPCR assay. The lower cost and faster turnaround times compared to whole genome sequencing make the use of qPCR for monitoring of the variant spread an attractive proposition. However, there are several potential issues with this approach. Here we use 826 SARS-CoV-2 samples collected in a hospital setting as part of the Hospital Onset COVID Infection (HOCI) study where qPCR was used for viral detection, followed by whole genome sequencing (WGS), to identify the factors to consider when using SGTF to infer lineage B.1. 1.7 prevalence in a hospital setting, with potential implications for locations where this variant has recently been introduced.
GWAS and ExWAS of blood mitochondrial DNA copy number identifies 71 loci and highlights a potential causal role in dementia

Mitochondrial DNA copy number (mtDNA-CN) is an accessible blood-based measurement believed to capture underlying mitochondrial function. The specific biological processes underpinning its regulation, and whether those processes are causative for disease, is an area of active investigation. We developed a novel method for array-based mtDNA-CN estimation suitable for biobank-scale studies, called AutoMitoC. We applied AutoMitoC to 395,781 UKBiobank study participants and performed genome and exome-wide association studies, identifying novel common and rare genetic determinants. Overall, genetic analyses identified 73 loci for mtDNA-CN and implicated genes involved in rare mtDNA depletion disorders, dNTP metabolism, and the mitochondrial central dogma. Rare variant analysis identified SAMHD1 mutation carriers as having higher mtDNA-CN (beta=0.23 SDs; 95% CI, 0.18-0.29; P=2.6x10-19), thus potentially representing a therapeutic target for patients with mtDNA depletion disorders but at the detriment of increased breast cancer risk (OR=1.91; 95% CI, 1.52-2.40; P=2.7x10-8). Finally, Mendelian randomization analyses support a potentially causal effect of low mtDNA-CN on dementia risk (OR=1.94 per 1 SD decrease in mtDNA-CN; 95% CI, 1.55-2.32; P=7.5x10-4). Altogether, our genetic findings indicate that mtDNA-CN is a complex biomarker reflecting specific mitochondrial processes related to mtDNA regulation and that these processes are causally related to human disease pathogenesis.
Soft Drink and Juice Consumption and Renal Cell Carcinoma Incidence and Mortality in the European Prospective Investigation into Cancer and Nutrition

Background: Renal cell carcinoma (RCC) accounts for more than 80% of kidney cancers in adults, and obesity is a known risk factor. Regular consumption of sweetened beverages has been linked to obesity and several chronic diseases, including some types of cancer. It is uncertain whether soft drink and juice consumption is associated with risk of RCC. We investigated the associations of soft drink and juice consumption with RCC incidence and mortality in the European Prospective Investigation into Cancer and Nutrition (EPIC). Methods: A total of 389,220 EPIC participants with median age of 52 years at recruitment (1991–2000) were included. Cox regression yielded adjusted HRs and 95% confidence intervals (CI) for RCC incidence and mortality in relation to intakes of juices and total, sugar-sweetened, and artificially sweetened soft drinks. Results: A total of 888 incident RCCs and 356 RCC deaths were identified. In models including adjustment for body mass index and energy intake, there was no higher risk of incident RCC associated with consumption of juices (HR per 100 g/day increment = 1.03; 95% CI, 0.97–1.09), total soft drinks (HR = 1.01; 95% CI, 0.98–1.05), sugar-sweetened soft drinks (HR = 0.99; 95% CI, 0.94–1.05), or artificially sweetened soft drinks (HR = 1.02; 95% CI, 0.96–1.08). In these fully adjusted models, none of the beverages was associated with RCC mortality (HR, 95% CI per 100 g/day increment 1.06, 0.97–1.16; 1.03, 0.98–1.09; 0.97, 0.89–1.07; and 1.06, 0.99–1.14, respectively). Conclusions: Consumption of juices or soft drinks was not associated with RCC incidence or mortality after adjusting for obesity. Impact: Soft drink and juice intakes are unlikely to play an independent role in RCC development or mortality.
Association of Adult Socioeconomic Status with Body Mass Index: A Within- and Between-Twin Study

Abstract Adult socioeconomic status (SES) has been consistently associated with body mass index (BMI), but it is unclear whether it is linked to BMI independently of childhood SES or other potentially confounding factors. Twin studies can address this issue by implicitly controlling for childhood SES and unmeasured confounders. This co-twin control study used cross-sectional data from Twins Research Australia’s Health and Lifestyle Questionnaire (N = 1918 twin pairs). We investigated whether adult SES, as measured by both the Index of Relative Socioeconomic Disadvantage (IRSD) and the Australian Socioeconomic Index 2006 (AUSEI06), was associated with BMI after controlling for factors shared by twins within a pair. The primary analysis was a linear mixed-effects model that estimated effects both within and between pairs. Between pairs, a 10-unit increase in AUSEI06 was associated with a 0.29 kg/m2 decrease in BMI (95% CI [−.42, −.17], p < .001), and a 1-decile increase in IRSD was associated with a 0.26 kg/m2 decrease in BMI (95% CI [−.35, −.17], p < .001). No association was observed within pairs. In conclusion, higher adult SES was associated with lower BMI between pairs, but no association was observed within pairs. Thus, the link between adult SES and BMI may be due to confounding factors common to twins within a pair.