Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular evolution and SSRs analysis based on the chloroplast genome of Callitropsis funebris

Abstract Chloroplast genome sequences have been used to understand evolutionary events and to infer efficiently phylogenetic relationships. Callitropsis funebris (Cupressaceae) is an endemic species in China. Its phylogenetic position is controversial due to morphological characters similar to those of Cupressus, Callitropsis, and Chamaecyparis. This study used next‐generation sequencing technology to sequence the complete chloroplast genome of Ca. funebris and then constructed the phylogenetic relationship between Ca. funebris and its related species based on a variety of data sets and methods. Simple sequence repeats (SSRs) and adaptive evolution analysis were also conducted. Our results showed that the monophyletic branch consisting of Ca. funebris and Cupressus tonkinensis is a sister to Cupressus, while Callitropsis is not monophyletic; Ca. nootkatensis and Ca. vietnamensis are nested in turn at the base of the monophyletic group Hesperocyparis. The statistical results of SSRs supported the closest relationship between Ca. funebris and Cupressus. By performing adaptive evolution analysis under the phylogenetic background of Cupressales, the Branch model detected three genes and the Site model detected 10 genes under positive selection; and the Branch‐Site model uncovered that rpoA has experienced positive selection in the Ca. funebries branch. Molecular analysis from the chloroplast genome highly supported that Ca. funebris is at the base of Cupressus. Of note, SSR features were found to be able to shed some light on phylogenetic relationships. In short, this chloroplast genomic study has provided new insights into the phylogeny of Ca. funebris and revealed multiple chloroplast genes possibly undergoing adaptive evolution.
High Prevalence of Depressive Symptoms Among Ugandan Patients with Rheumatoid Arthritis

Background There is a scarcity of data on the burden of depression among Ugandans with rheumatoid arthritis (RA) patients. We aimed to screen for symptoms of depression, their severity and associated factors among patients with RA in Uganda. Patients and Methods A descriptive, cross-sectional study was conducted between September and December 2020 at Mulago National Referral Hospital (MNRH) and Nsambya Hospital. Patients with RA were enrolled consecutively. Data on demographics, disease course and comorbidities and depression symptomatology were collected through an interviewer administered questionnaire. Symptoms of depression were screened for using the depression/anxiety dimension of the EuroQoL questionnaire. Results Forty-eight patients with a median age of 52 (IQR: 43.5–60.5) years were recruited in the study. The majority of the patients were female (91.7%, n=44). Twenty-nine patients (60.4%) had comorbidities with a median Charlson comorbidity score of 3 (IQR: 2–4). Overall, 70.8% (n=34) had depressive symptoms. Patients attending MNRH were more likely to have depressive symptoms (p=0.025). Significantly, patients with depressive symptoms were younger (p=0.027), had lower health index value (p<0.001), and lower overall self-reported health status (p=0.013). At binary logistic regression, patients at MNRH (crude odds ratio (COR): 4.32, 95% confidence interval (CI): 1.16–16.15, P=0.030), patients aged <52 years (COR: 5.24, 95% CI: 1.23–22.28, P=0.025) and those with mild RA (COR: 5.71, 95% CI: 1.15–28.35, P=0.033) were significantly more likely to have depressive symptoms. Increase in age (COR: 0.94, 95% CI: 0.89–0.99, P=0.025), and high visual analogue score (COR: 0.94, 95% CI: 0.89–0.99, P=0.013) were protective. Conclusion Depressive symptoms were common among RA patients in Uganda. Routine screening, diagnosis and management of depression is recommended among young patients to improve quality of life and patient outcomes.
Prevalence of Obstructive Sleep Apnea Among Saudi Pilots

Purpose To evaluate the presence of obstructive sleep apnea (OSA), using home sleep testing in pilots and first officers in Saudi-based airlines. This will allow for proper diagnosis and management of OSA in that group which can help in minimizing any possible aviation accidents related to sleep disturbances secondary to OSA. Materials and Methods This is a cross-sectional study conducted through Saudi-based aviation among pilots and first officers who were in service, active, and flying short- to medium-haul flights. Forty-one participants met the inclusion criteria. However, 39 out of 41 completed the study questionnaires (Berlin questionnaire, Epworth sleepiness scale, Pittsburgh sleep quality index (PSQI), Fatigue severity scale (FSS), Visual analog fatigue scale (VAFS), and Patient health questionnaire (PHQ9), along with home sleep testing. Results Sixty-nine percent of the study population had OSA by home sleep testing. Majority of which had mild OSA (64%) and 5% had moderate and severe OSA (2.5% each). Results of different questionnaires showed one-third of the participants had insomnia, 33.3% of the participants had severe fatigue, excessive daytime sleepiness was found in 23.1% of the participants, and 10.3% had moderate depression, while 25.6% were classified as having mild depression symptoms. Conclusion Sleep apnea is prevalent among the studied Saudi-based airline pilots and first officers. Screening for workers of this high-risk occupation needs to be considered. Fatigue, depression, and insomnia can be secondary consequences of sleep apnea and should be assessed and treated early.
Clinical Significance of Isolated Third Cranial Nerve Palsy in Traumatic Brain Injury: A Detailed Description of Four Different Mechanisms of Injury through the Analysis of Our Case Series and Review of the Literature

Third cranial nerve palsy (3cnP) following traumatic brain injury (TBI) is a worrying neurological sign and is often associated with an expanding mass lesion, such as extradural or acute subdural haematomas. Isolated 3cnP can be found in the absence of posttraumatic space-occupying mass lesion, yet it is often considered as a devastating prognostic factor in the context of diffuse axonal injury (DAI). Through the analysis of five exemplificative cases and a thorough review of the literature, we identified four possible mechanisms leading to 3cnP: (1) a partial rootlet avulsion at the site of exit from the midbrain, representing a direct shearing injury to the nerve; (2) a direct traction injury due to the nerve stretching against the posterior petroclinoid ligament at the base of the oculomotor triangle secondary to the downward displacement of the brainstem at the time of impact; (3) a direct vascular compression as a result of internal carotid artery (ICA) dissection or pseudoaneurysm; (4) an indirect injury caused by impaired blood supply to the third nerve in addition to the detrimental biochemical effects of the underlying brain injury itself. Understanding the exact mechanism underlying the onset of 3cnP is key to provide an informed clinical decision-making to the patients and ensure their best chances of recovery. Our experience corroborates data from the literature showing that, even in Grade III DAI, prompt recognition of isolated 3cnP can guide adequate treatment. Nonetheless, even when an overall good neurological outcome is achieved, recovery of isolated 3cnP is dismal, and only rarely the visual deficit completely resolves.
Electrophysiological Evaluation in Identifying Unique Sleep Features Among Anti-LGI1 Encephalitis Patients During Active and Recovery Phase

Objective The purpose of this study was to illustrate the electrophysiological features of sleep disturbances in patients with anti-leucine-rich glioma-inactivated protein 1 (anti-LGI1) encephalitis in both active and recovery stages. Methods Retrospectively filed video electroencephalogram (VEEG) and polysomnography (PSG) data in 24 patients with anti-LGI1 encephalitis were analyzed in comparison with that in 20 individuals without sleep disorders as control group. Results Sleep efficiency (SE) and total sleep time involving REM and NREM sleep were significantly decreased in patients with anti-LGI1 encephalitis during the active stage compared to that during the recovery stage and in the control group. Imbalanced sleep structure was found, demonstrated by elevated N1, decreased N3 and REM components, as well as abnormal N2 structure characterized with significantly lower spindle duration and density during the active stage. These findings were independent of the presence of nocturnal episodic events or sleep hyperkinetic movements (HMs). HMs were present in 11/23 patients throughout NREM and REM sleep (nonspecific in sleep stages) during the active stage. During the recovery stage, SE and sleep structures were dramatically improved, including the percentage of N3 and REM sleep, spindle duration and density. Ten of 11 patients with HMs were followed up. HMs were totally remitted in 3 patients and still persistent in 1, while evolved into REM sleep behavior disorder (RBD) in 4 with comorbid periodic limb movement syndrome (PLMS) in 3/4, and only PLMS in 2. Conclusion Sleep disturbances were remarkable and intrinsic features in active anti-LGI1 encephalitis, marked by overall disruptions of both NREM and REM sleep, as well as the presence of HMs, which tend to evolve into RBD or PLMS during the recovery stage. Long-term follow-up with PSG is needed, especially for those patients with severe sleep disturbances during the active phase.
Inhibitory control in children with tic disorder: aberrant fronto-parietal network activity and connectivity

Abstract Chronic tic disorders, including Tourette syndrome, are typically thought to have deficits in cognitive inhibition and top down cognitive control due to the frequent and repetitive occurrence of tics, yet studies reporting task performance results have been equivocal. Despite similar behavioural performance, individuals with chronic tic disorder have exhibited aberrant patterns of neural activation in multiple frontal and parietal regions relative to healthy controls during inhibitory control paradigms. In addition to these top down attentional control regions, widespread alterations in brain activity across multiple neural networks have been reported. There is a dearth, however, of studies examining event-related connectivity during cognitive inhibitory paradigms among affected individuals. The goal of this study was to characterize neural oscillatory activity and effective connectivity, using a case–control design, among children with and without chronic tic disorder during performance of a cognitive inhibition task. Electroencephalogram data were recorded in a cohort of children aged 8–12 years old (60 with chronic tic disorder, 35 typically developing controls) while they performed a flanker task. While task accuracy did not differ by diagnosis, children with chronic tic disorder displayed significant cortical source-level, event-related spectral power differences during incongruent flanker trials, which required inhibitory control. Specifically, attenuated broad band oscillatory power modulation within the anterior cingulate cortex was observed relative to controls. Whole brain effective connectivity analyses indicated that children with chronic tic disorder exhibit greater information flow between the anterior cingulate and other fronto-parietal network hubs (midcingulate cortex and precuneus) relative to controls, who instead showed stronger connectivity between central and posterior nodes. Spectral power within the anterior cingulate was not significantly correlated with any connectivity edges, suggesting lower power and higher connectivity are independent (versus resultant) neural mechanisms. Significant correlations between clinical features, task performance and anterior cingulate spectral power and connectivity suggest this region is associated with tic impairment (r = −0.31, P = 0.03) and flanker task incongruent trial accuracy (r’s = −0.27 to −0.42, P’s = 0.0008–0.04). Attenuated activation of the anterior cingulate along with dysregulated information flow between and among nodes within the fronto-parietal attention network may be neural adaptations that result from frequent engagement of neural pathways needed for inhibitory control in chronic tic disorder.
Prevalence and Risk Factors of Type 2 Diabetes and Prediabetes Among 53,288 Middle-Aged and Elderly Adults in China: A Cross-Sectional Study

Background Diabetes is a metabolic disorder that causes a heavy burden on healthcare systems worldwide. The aim of this study was to determine the prevalence of type 2 diabetes and prediabetes and its associated factors among eight communities in Nanchong, China. Methods This was an observational cross-sectional study conducted throughout eight communities in Nanchong, China. The participants were 53,288 individuals aged 45 years or older. The participants’ characteristics, comorbidities, health behaviors, family history, and dietary intake were assessed. Multinomial logistic regression models were fitted to identify factors associated with type 2 diabetes and prediabetes. Results The prevalence of diabetes and prediabetes was 13.9% (95% confidence interval [CI], 13.6–14.2) and 3.1% (95% CI, 2.9–3.2) of the population, respectively. After adjusting for other risk factors, advanced age, overweight, obesity, abdominal obesity, comorbidities, smoking, a family history of diabetes, and Chinese cooking vegetable intake were associated with an increased risk of type 2 diabetes and prediabetes. Conclusion The prevalence of type 2 diabetes in the Chinese population is rising compared with data from the past. The risk factors of type 2 diabetes and prediabetes identified in this study will aid the identification of individuals at a high-risk of diabetes and the implementation of effective health promotion programs and campaigns. Clinical Trial Registry Number ChiCTR-HOC-17013200.
Statistical Emulation of Winter Ambient Fine Particulate Matter Concentrations From Emission Changes in China

Air pollution exposure remains a leading public health problem in China. The use of chemical transport models to quantify the impacts of various emission changes on air quality is limited by their large computational demands. Machine learning models can emulate chemical transport models to provide computationally efficient predictions of outputs based on statistical associations with inputs. We developed novel emulators relating emission changes in five key anthropogenic sectors (residential, industry, land transport, agriculture, and power generation) to winter ambient fine particulate matter (PM2.5) concentrations across China. The emulators were optimized based on Gaussian process regressors with Matern kernels. The emulators predicted 99.9% of the variance in PM2.5 concentrations for a given input configuration of emission changes. PM2.5 concentrations are primarily sensitive to residential (51%–94% of first‐order sensitivity index), industrial (7%–31%), and agricultural emissions (0%–24%). Sensitivities of PM2.5 concentrations to land transport and power generation emissions are all under 5%, except in South West China where land transport emissions contributed 13%. The largest reduction in winter PM2.5 exposure for changes in the five emission sectors is by 68%–81%, down to 15.3–25.9 μg m−3, remaining above the World Health Organization annual guideline of 10 μg m−3. The greatest reductions in PM2.5 exposure are driven by reducing residential and industrial emissions, emphasizing the importance of emission reductions in these key sectors. We show that the annual National Air Quality Target of 35 μg m−3 is unlikely to be achieved during winter without strong emission reductions from the residential and industrial sectors.
Epidemiology of antimicrobial resistance (AMR) on California dairies: descriptive and cluster analyses of AMR phenotype of fecal commensal bacteria isolated from adult cows

Background This study describes the occurrence of antimicrobial resistance (AMR) in commensal Escherichia coli and Enterococcus/Streptococcus spp. (ES) isolated from fecal samples of dairy cows and assesses the variation of AMR profiles across regions and seasons following the implementation of the Food and Agricultural Code (FAC) Sections 14400–14408 (formerly known as Senate Bill, SB 27) in California (CA). Methods The study was conducted on ten dairies distributed across CA’s three milk sheds: Northern California (NCA), Northern San Joaquin Valley (NSJV), and the Greater Southern California (GSCA). On each study dairy, individual fecal samples were collected from two cohorts of lactating dairy cows during the fall/winter 2018 and spring/summer 2019 seasons. Each cohort comprised of 12 cows per dairy. The fecal samples were collected at enrollment before calving (close-up stage) and then monthly thereafter for four consecutive time points up to 120 days in milk. A total of 2,171 E. coli and 2,158 ES isolates were tested for antimicrobial susceptibility using the broth microdilution method against a select panel of antimicrobials. Results The E. coli isolates showed high resistance to florfenicol (83.31% ± 0.80) and sulphadimethoxine (32.45%), while resistance to ampicillin (1.10% ± 0.21), ceftiofur (1.93% ± 0.29), danofloxacin (4.01% ± 0.42), enrofloxacin (3.31% ± 0.38), gentamicin (0.32% ± 0.12) and neomycin (1.61% ± 0.27) had low resistance proportions. The ES isolates were highly resistant to tildipirosin (50.18% ± 1.10), tilmicosin (48% ± 1.10), tiamulin (42%) and florfenicol (46% ± 1.10), but were minimally resistant to ampicillin (0.23%) and penicillin (0.20%). Multidrug resistance (MDR) (resistance to at least 1 drug in ≥3 antimicrobial classes) was observed in 14.14% of E. coli isolates and 39% of ES isolates. Escherichia coli isolates recovered during winter showed higher MDR prevalence compared to summer isolates (20.33% vs. 8.04%). A higher prevalence of MDR was observed in NSJV (17.29%) and GSCA (15.34%) compared with NCA (10.10%). Conclusions Our findings showed high rates of AMR to several drugs that are not labeled for use in lactating dairy cattle 20 months of age or older. Conversely, very low resistance was observed for drugs labeled for use in adult dairy cows, such as cephalosporins and penicillin. Overall, our findings identified important differences in AMR by antimicrobial class, region and season.
Mathematical Modeling of Brain Activity under Specific Auditory Stimulation

Understanding the connection between different stimuli and the brain response represents a complex research area. However, the use of mathematical models for this purpose is relatively unexplored. The present study investigates the effects of three different auditory stimuli on cerebral biopotentials by means of mathematical functions. The effects of acoustic stimuli (S1, S2, and S3) on cerebral activity were evaluated by electroencephalographic (EEG) recording on 21 subjects for 20 minutes of stimulation, with a 5-minute period of silence before and after stimulation. For the construction of the mathematical models used for the study of the EEG rhythms, we used the Box-Jenkins methodology. Characteristic mathematical models were obtained for the main frequency bands and were expressed by 2 constant functions, 8 first-degree functions, a second-degree function, a fourth-degree function, 6 recursive functions, and 4 periodic functions. The values obtained for the variance estimator are low, demonstrating that the obtained models are correct. The resulting mathematical models allow us to objectively compare the EEG response to the three stimuli, both between the stimuli itself and between each stimulus and the period before stimulation.
The Yunnan national medicine Maytenus compound inhibits the proliferation of hepatocellular carcinoma (HCC) by suppressing the activation of the EGFR-PI3K-AKT signaling pathway

Objective: To investigate the effects of Maytenus compound on the proliferation of hepatocellular carcinoma (HCC) cells in vitro and in vivo and to explore the underlying mechanism. Methods: The half maximal inhibitory concentration (IC50) values of Maytenus compound in HepG2 and BEL-7402 cells were determined by the MTS assay. HepG2 and BEL-7402 cells were treated with different concentrations of Maytenus compound. MTS assay, colony formation assay and cell cycle analysis were performed to clarify the inhibitory effect of Maytenus compound on the proliferation of HepG2 and BEL-7402 cells in vitro. After subcutaneous injection of HepG2 cells, nude mice were randomly divided into a vehicle control group and a drug intervention group, which were intragastrically administered ddH2O or Maytenus compound, respectively. The inhibitory effect of Maytenus compound on the proliferation of HepG2 cells in vivo was analyzed using subcutaneous tumor growth curves, tumor weight, the tumor growth inhibition rate and the immunohistochemical detection of BrdU-labeled cells in S phase. The organ toxicity of Maytenus compound was initially evaluated by comparing the weight difference and organ index of the two groups of nude mice. The main proteins in the EGFR-PI3K-AKT signaling pathway were detected by Western blot after Maytenus compound intervention in vivo and in vitro. Results: Maytenus compound showed favorable antiproliferation activity against HepG2 and BEL-7402 cells with IC50 values of 79.42±11.71 µg/mL and 78.48±8.87 µg/mL, respectively. MTS assay, colony formation assay and cell cycle analysis showed that Maytenus compound at different concentration gradients within the IC50 concentration range significantly suppressed the proliferation of HepG2 and BEL-7402 cells in vitro and inhibited cell cycle progression from G1 to S phase. Additionally, Maytenus compound, at an oral dose of 2.45 g/kg, dramatically inhibited, without obvious organ toxicity, the proliferation of subcutaneous tumors formed by HepG2 cells in nude mice. In addition, the tumor growth inhibition rate for Maytenus compound was 66.94%. Furthermore, Maytenus compound inhibited the proliferation of liver orthotopic transplantation tumors in nude mice. Western blot analysis showed that Maytenus compound significantly downregulated the expression of p-EGFR, p-PI3K, and p-AKT and upregulated the expression of p-FOXO3a, p27, and p21 in vivo and in vitro. Conclusion: Maytenus compound significantly inhibited the proliferation of HCC cells in vitro and in vivo. The downregulation of the EGFR-PI3K-AKT signaling pathway and subsequent inhibition of cell cycle progression from G1 to S phase is one of the possible mechanisms. Maytenus compound has a high tumor growth inhibition rate and has no obvious organ toxicity, which may make it a potential anti-HCC drug, but the results from this study need to be confirmed by further clinical trials in HCC patients.