Miracle-dz/UniFAR-FTUs huggingface dataset:
Pathogenic ecological characteristics of PCV2 in large-scale pig farms in China affected by African swine fever in the surroundings from 2018 to 2021

Porcine circovirus type 2 (PCV2) has been identified as the causal agent of postweaning multisystemic wasting syndrome (PMWS), an economically important multifactorial disease of the swine industry worldwide. This research designed a dual nested polymerase chain reaction (PCR) detection method to simultaneously monitor porcine circovirus type 2 (PCV2) and PCV3. The limit of detection (LoD) of sensitivity for PCV2 and PCV3 was ten copies/mL for both viruses. There was no cross-reaction with any other porcine pathogens tested and no non-specific amplification. The coincidence and repetition rates were both 100%. Through the systematic and clinical sampling, 15,130 samples collected from 30 large-scale pig farms in eight provinces in China (including Hubei, Hunan, Henan, Jiangxi, Shanxi, Guangdong, Hainan, and Heilongjiang) were subjected to early warning surveillance and/or clinical diagnosis. These results revealed that the overall positive rates of PCV3 and PCV2 were 0 and 28.29%, respectively, with the lowest level recorded in Jiangxi province. The highest carrying rate was observed in Hainan province. Pigs at different ages displayed varying carrying rates for PCV: fattening pigs and gilts had the highest and the lowest carrying rates for PCV, respectively. In addition, the excretion rates for PCV of colostrum, semen, and nasal, anal, and vulval swabs were tested. The colostrum, anal swabs, and semen had higher excretion rates for PCV; these were followed by the vulval and nasal swabs that had excretion rates for PCV. Furthermore, a high blood virus-carrying rate was detected in moribund pigs, especially in pigs with fever and red skin. As to the virus-carrying rate in the pig organs received from clinical necropsy, the highest rate was found in placental tissue, followed by the kidneys, and the virus also was detected in lymphoid organs, liver, stomach, and intestines. The PCV2-positive samples were sequenced to reveal the molecular epidemic dynamics of PCV2. The results indicated four major branches, namely, PCV2a, PCV2b, PCV2c, and PCV2d, concerning PCV2 molecular epidemiology in China, with PCV2a, PCV2b, and PCV2d dominating. In conclusion, the results obtained in this study elucidated the molecular epidemiology, transmission, and positive blood samples of PCV and provided new ideas for developing comprehensive PCV control technologies to begin eliminating the disease caused by PCV by cleaning pig farms.
Trace metal fate in soil after application of digestate originating from the anaerobic digestion of non-source-separated organic fraction of municipal solid waste

Introduction: Digestate originating from anaerobic digestion of non-source-separated organic fraction of municipal solid waste (OFMSW) is produced abundantly worldwide and generally discarded in landfills. However, it can be a valuable resource for many bioeconomy strategies as land restoration, only if a consolidated understanding of the contaminants’ presence and behaviour in digestate-amended soil is achieved. This study aimed to investigate the fate of trace metals, namely Zn, Cu, Pb, and Cr found in the digestate, along the soil profile after digestate application on soil, and the influence that other contaminants as pharmaceutical compounds can have on their behaviour in the soil system. Methods: For that, a 90-day soil column experiment was conducted using a fine loamy sand soil topped with a layer of digestate-amended soil. Digestate-amended soil had a soil to digestate proportion of 14 to 1 (dry weight). Two experimental conditions were tested: soil amended with digestate, and soil amended with digestate spiked with the antidiabetic drug metformin. Soil samples were taken at 4 depths on days 1, 7, 21, 35 and 90, and total trace metals concentrations and fractionation were determined via atomic absorption spectroscopy. Results: Results showed that Zn, Cu, Pb ad Cr initially present in the digestate were transferred from the digestate-amended soil layer to the underlying soil layer over time, although in low amounts. Nevertheless, no transfer was detected to the deeper soil layers. Trace metals in soil were predominantly in immobile and less bioavailable forms associated with clay and silicate mineral groups, whereas in the digestate-amended soil they were in more bioavailable forms, which could be related to metals’ migration in the soil layers below. Results also show that the presence of metformin had no influence on trace metal behaviour, giving insight also on possible interactions with other potentially present contaminants as microplastics. Conclusion: The current study showed that OFMSW digestate can be a promising organic nutrient-rich matrix for land restoration even if it may contain high metals’ concentrations because low metal mobility along the soil profile can be expected.
Laser interstitial thermal therapy for the treatment of insular lesions: A systematic review

Background The surgical treatment of insular lesions has been historically associated with high morbidity. Laser interstitial thermal therapy (LITT) has been increasingly used in the treatment of insular lesions, commonly neoplastic or epileptogenic. Stereotaxis is used to guide laser probes to the insula where real-time magnetic resonance thermometry defines lesion creation. There is an absence of previously published reviews on insular LITT, despite a rapid uptake in use, making further study imperative. Methods Here we present a systematic review of the PubMed and Scopus databases, examining the reported clinical indications, outcomes, and adverse effects of insular LITT. Results A review of the literature revealed 10 retrospective studies reporting on 53 patients (43 pediatric and 10 adults) that were treated with insular LITT. 87% of cases were for the treatment of epilepsy, with 89% of patients achieving seizure outcomes of Engle I-III following treatment. The other 13% of cases reported on insular tumors and radiological improvement was seen in all cases following treatment. All but one study reported adverse events following LITT with a rate of 37%. The most common adverse events were transient hemiparesis (29%) and transient aphasia (6%). One patient experienced an intracerebral hemorrhage, which required a decompressive hemicraniectomy, with subsequent full recovery. Conclusion This systematic review highlights the suitability of LITT for the treatment of both insular seizure foci and insular tumors. Despite the growing use of this technique, prospective studies remain absent in the literature. Future work should directly evaluate the efficacy of LITT with randomized and controlled trials.
Impact of the malnutrition on mortality in Rheumatoid arthritis patients: A cohort study from NHANES 1999–2014

Background Patients with Rheumatoid arthritis (RA) are prone to malnutrition. However, it is rare studies assessing the relationship between malnutrition and all-cause mortality in patients with RA. Objective To investigate the relationship between malnutrition and all-cause mortality in patients with RA in a large national sample cohort. Methods We analyzed data on 1,976 adults ≥ 18 years of age during National Health and Nutrition Examination Survey (NHANES) 1999–2014. We chose the Controlled Nutritional Status Score (CONUT) and the Nutritional Risk Index (NRI) to assess the nutritional status of patients with RA. The Kaplan–Meier (KM) survival curves Cox proportional hazards regression models were used to analyze the associations between malnutrition and all-cause mortality. Results Of the 1,976 patients with RA (57.38 ± 0.40 years, female 59.9%, non-Hispanic white 69.9%), the prevalence of malnutrition was 18.8% by used the CONUT and 26.6% by used the NRI. The KM survival curves showed that malnutrition was associated with a higher incidence of all-cause mortality during the 10-year follow-up period (log-rank test, P < 0.001). In the fully corrected model, the adjusting hazard ratio (aHR) for all-cause mortality in patients with moderate to severe malnutrition with CONUT and NRI were 5.63 (95% CI, 2.55–12.45; P < 0.001) and 2.56 (95% CI, 1.81–3.62; P < 0.001), respectively, compared with patients without malnutrition. Conclusion Malnutrition is very prevalent in patients with RA, approximately 18.8% (CONUT) to 26.6% (NRI). Malnutrition is strongly associated with an increased risk of all-cause mortality. These findings underscore the importance of attention and intervention in the nutritional status of patients with RA. Further clinical trials are needed to prospectively assess the effect of nutritional interventions on the prognosis of patients with RA.
Clinical imaging of primary pulmonary nucleoprotein of the testis carcinoma

Objective Primary pulmonary nucleoprotein of the testis (NUT) carcinoma is very rare in the clinic. In this study, the clinicopathological manifestations and imaging features of the primary pulmonary NUT carcinoma were investigated to improve the diagnosis of this disease. Methods Six patients with pathologically diagnosed pulmonary NUT carcinoma were analyzed, including three males and three females, aged 19–64 (49.00 ± 16.40) years, with clinical manifestations of cough in two cases, hoarseness in one case, blood in sputum in one case, chest pain in one case, and physical examination findings in one case, with a disease duration of 5 days to 4 months. The clinical and imaging data including CT and PET/CT were retrospectively analyzed. Further literature reviews were analyzed in both pulmonary and extrapulmonary NUT carcinoma cases who performed 18F-FDG PET/CT. Results Most of the patients with pulmonary NUT carcinomas presented as heterogeneous lobulated masses (83.33%), four cases (66.67%) were located in the upper lobe of the left lung, one case (16.67%) in the middle lobe of the right lung, and one case (16.67%) in the lower lobe of the right lung, with the maximum diameter ranging from 1.30 to 8.90 cm and the median of 3.55 cm, most of them were irregularly shaped, with more lobulated margins and more heterogeneous density (83.33%), and the enhancement was mild. PET/CT showed increased 18F-FDG uptake in the lesion and metastatic areas. Both the pulmonary NUT patients in this study and literature reviews showed the SUVmax of the tumor ranged from 5 to 40 with an average value of 12.8, whereas that of extrapulmonary lesions had a range of SUVmax at 4.5–64.1 and a mean of 13.8. Conclusion In patients with central lung masses, rapid disease progression, and poor response to initial treatment, the possibility of NUT cancer should be considered and anti-NUT monoclonal antibody immunohistochemical staining, combined with genetic detection, if necessary, should be performed as soon as possible. CT and PET/CT imaging are essential for the staging, management, treatment response assessment, and monitoring of pulmonary NUT cancer.
Mixed-Resolution Ensemble Data Assimilation

AbstractEnsemble Kalman filters perform data assimilation by forming a background covariance matrix from an ensemble forecast. Most of the literature on ensemble Kalman filters assumes that all ensemble members come from the same model. This article presents and tests a modified local ensemble transform Kalman filter (LETKF) that takes its background covariance from a combination of a high-resolution ensemble and a low-resolution ensemble. The computational time and the accuracy of this mixed-resolution LETKF are explored and compared to the standard LETKF on a high-resolution ensemble, using simulated observation experiments with the Lorenz models II and III (more complex versions of the Lorenz-96 model). In a variety of scenarios, mixed-resolution analysis can obtain higher accuracy with similar computation time (or similar accuracy with a reduced computation time) compared to single-resolution analysis.
Sex-related differences in incidence, phenotype and risk of sudden cardiac death in inherited arrhythmia syndromes

Inherited Arrhythmia Syndromes (IAS) including long QT and Brugada Syndrome, are characterized by life-threatening arrhythmias in the absence of apparent structural heart disease and are caused by pathogenic variants in genes encoding cardiac ion channels or associated proteins. Studies of large pedigrees of families affected by IAS have demonstrated incomplete penetrance and variable expressivity. Biological sex is one of several factors that have been recognized to modulate disease severity in IAS. There is a growing body of evidence linking sex hormones to the susceptibility to arrhythmias, yet, many sex-specific disease aspects remain underrecognized as female sex and women with IAS are underinvestigated and findings from male-predominant cohorts are often generalized to both sexes with minimal to no consideration of relevant sex-associated differences in prevalence, disease manifestations and outcome. In this review, we highlight current knowledge of sex-related biological differences in normal cardiac electrophysiology and sex-associated factors that influence IAS phenotypes.
Joys or Sorrows of Parenting During the COVID-19 Lockdown: A Scoping Review

Objectives: The aim of this scoping review was to map out the existing evidence of the impact of the COVID-19 lockdown on parents of children and adolescents. We sought to: 1) identify parenting domains that were particularly affected by lockdown measures, 2) describe the challenges and opportunities of lockdown measures in these domains, and 3) define protective and exacerbating factors modulating the effect of lockdown measures on parents. Methods: We identified five main domains investigated in the context of parenting during the early COVID-19 lockdown derived from 84 studies: health and wellbeing, parental role, couple functioning, family and social relationships, and paid and unpaid work. For each domain, we listed challenges and opportunities, as well as discriminant factors. Results: The lockdown impacted all five different but interconnected domains, introduced new roles in parents’ lives, and particularly affected women and vulnerable populations. Conclusion: This scoping review highlights the importance of approaching public health policymaking from a social justice perspective. Such an approach argues for social and public health policies to promote health accounting for its social, economic, political, and commercial determinants.
Functional changes in cytotoxic CD8+ T-cell cross-reactivity against the SARS-CoV-2 Omicron variant after mRNA vaccination

Understanding the T-cell responses involved in inhibiting COVID-19 severity is crucial for developing new therapeutic and vaccine strategies. Here, we characterized SARS-CoV-2 spike-specific CD8+ T cells in vaccinees longitudinally. The BNT162b2 mRNA vaccine can induce spike-specific CD8+ T cells cross-reacting to BA.1, whereas the T-cell receptor (TCR) repertoire usages decreased with time. Furthermore the mRNA vaccine induced spike-specific CD8+ T cells subpopulation expressing Granzyme A (GZMA), Granzyme B (GZMB) and Perforin simultaneously in healthy donors at 4 weeks after the second vaccination. The induced subpopulation was not maintained at 12 weeks after the second vaccination. Incorporating factors that efficiently induce CD8+ T cells with highly cytotoxic activity could improve future vaccine efficacy against such variants.
Selection of minimizers for one‐dimensional Ginzburg‐Landau functional with 3‐well potential by singular lower‐order term

We consider a variant of the Ginzburg‐Landau type functional in one dimension with 3‐well potential, penalized by lower‐order term which has singularity in one of the zeros of the potential function. Based on the approach developed in the paper G. Alberti, S. Muller: A new approach to variational problems with multiple scales, Comm. Pure Appl. Math. 54, 761‐825 (2001), we obtain Gamma‐convergence and provide description of the minimizers as small parameter epsilon tends to zero. We show that introduction of singular lower‐order term results in appropriate selection of the minimizers. (© 2011 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Genetic heritability as a tool to evaluate the precision of 24-hour recall dietary questionnaire variables in UK Biobank

A variety of statistical approaches in nutritional epidemiology have been developed to enhance the precision of dietary variables derived from longitudinal questionnaires. Correlation with biomarkers is often used to assess the relative validity of these different approaches, however, validated biomarkers do not always exist and are costly and laborious to collect. We present a novel high-throughput approach which utilizes the modest but importantly non-zero influence of genetic variation on variation in dietary intake to compare different statistical transformations of dietary variables. Specifically, we compare the heritability of crude averages with Empirical Bayes weighted averages for 302 correlated dietary variables from multiple 24-hour recall questionnaires in 177 K individuals in UK Biobank. Overall, the crude averages for frequency of consumption are more heritable than their Empirical Bayes counterparts only when the reliability of that item across questionnaires is high (measured by intra-class correlation), otherwise, the Empirical Bayes approach (for both unreliably measured frequencies and for average quantities independent of reliability) leads to higher heritability estimates. We also find that the more heritable versions of each dietary variable lead to stronger underlying statistical associations with specific genetic loci, many of which have well-known mechanisms, further supporting heritability as an alternative metric for relative validity in nutritional epidemiology and beyond.
Recent advances in immunoassay technologies for the detection of human coronavirus infections

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the seventh coronavirus (CoV) that has spread in humans and has become a global pandemic since late 2019. Efficient and accurate laboratory diagnostic methods are one of the crucial means to control the development of the current pandemic and to prevent potential future outbreaks. Although real-time reverse transcription-polymerase chain reaction (rRT-PCR) is the preferred laboratory method recommended by the World Health Organization (WHO) for diagnosing and screening SARS-CoV-2 infection, the versatile immunoassays still play an important role for pandemic control. They can be used not only as supplemental tools to identify cases missed by rRT-PCR, but also for first-line screening tests in areas with limited medical resources. Moreover, they are also indispensable tools for retrospective epidemiological surveys and the evaluation of the effectiveness of vaccination. In this review, we summarize the mainstream immunoassay methods for human coronaviruses (HCoVs) and address their benefits, limitations, and applications. Then, technical strategies based on bioinformatics and advanced biosensors were proposed to improve the performance of these methods. Finally, future suggestions and possibilities that can lead to higher sensitivity and specificity are provided for further research.
Conjugation of plasmid harboring blaNDM-1 in a clinical Providencia rettgeri strain through the formation of a fusion plasmid

Providencia rettgeri has recently gained increased importance owing to the New Delhi metallo-β-lactamase (NDM) and other β-lactamases produced by its clinical isolates. These enzymes reduce the efficiency of antimicrobial therapy. Herein, we reported the findings of whole-genome sequence analysis and a comprehensive pan-genome analysis performed on a multidrug-resistant P. rettgeri 18004577 clinical strain recovered from the urine of a hospitalized patient in Shandong, China, in 2018. Providencia rettgeri 18004577 was found to have a genome assembly size of 4.6 Mb with a G + C content of 41%; a circular plasmid p18004577_NDM of 273.3 Kb, harboring an accessory multidrug-resistant region; and a circular, stable IncT plasmid p18004577_Rts of 146.2 Kb. Additionally, various resistance genes were identified in its genome, including blaNDM-1, blaOXA-10, blaPER-4, aph(3′)-VI, ant(2′′)-Ia, ant(3′)-Ia, sul1, catB8, catA1, mph(E), and tet. Conjugation experiments and whole-genome sequencing revealed that the blaNDM-1 gene could be transferred to the transconjugant via the formation of pJ18004577_NDM, a novel hybrid plasmid. Based on the genetic comparison, the main possible formation process for pJ18004577_NDM was the insertion of the [ΔISKox2-IS26-ΔISKox2]-aph(3′)-VI-blaNDM-1 translocatable unit module from p18004577_NDM into plasmid p18004577_Rts in the Russian doll insertion structure (ΔISKox2-IS26-ΔISKox2), which played a role similar to that of IS26 using the “copy-in” route in the mobilization of [aph(3′)-VI]-blaNDM-1. The array, multiplicity, and diversity of the resistance and virulence genes in this strain necessitate stringent infection control, antibiotic stewardship, and periodic resistance surveillance/monitoring policies to preempt further horizontal and vertical spread of the resistance genes. Roary analysis based on 30 P. rettgeri strains pan genome identified 415 core, 756 soft core, 5,744 shell, and 12,967 cloud genes, highlighting the “close” nature of P. rettgeri pan-genome. After a comprehensive pan-genome analysis, representative biological information was revealed that included phylogenetic distances, presence or absence of genes across the P. rettgeri bacteria clade, and functional distribution of proteins. Moreover, pan-genome analysis has been shown to be an effective approach to better understand P. rettgeri bacteria because it helps develop various tailored therapeutic strategies based on their biological similarities and differences.
Precipitation variations of western equatorial pacific during glacial–interglacial cycles since MIS8: Evidence from multi–proxies of abyssal sediment

As an important global water vapor source, the Western Pacific warm pool (WPWP) influences precipitation changes in middle and low latitudes. The low-latitude water cycle is a key climate parameter at different time scales, as it contributes to various feedback processes. However, at present, indicators of precipitation variability in the equatorial western Pacific are limited. In this work, we used the sedimentary record of the southern margin of the WPWP to study the precipitation variability over the western equatorial Pacific since MIS8. The age framework based on plankton-foraminifera δ18O was used to analyze changes in geochemical elements, clay minerals, and magnetic parameters of a marine sediment core H10. As new precipitation records, our precipitation records (TiO2, χ, and SIRM concentration without carbonate base) are closely related to monsoon and Intertropical Convergence Zone and generally in inverse phase with the oxygen isotope records of stalagmites from caves in China. A spectral analysis showed an obvious precession period. The southern margin of the WPWP water cycle is closely related to the East Asian monsoon in the last four climate cycles, and is influenced by both high and low latitudes.