Miracle-dz/UniFAR-FTUs huggingface dataset:
An evaluation study of DRP-4DVar approach with Lorenz-96 model

The current study evaluates the performance of the Dimension-Reduced Projection four dimensional variational data assimilation (DRP-4DVar) with the Lorenz-96 model. The idealized experiments over a period of 200 days have been conducted. The results show that the DRP-4DVar works well. It generates analysis equivalent to that of the Ensemble Kalman Filter (EnKF) before the two methods diverge if the synchronous observations are as-similated at the analysis time, while it produces more accurate analysis than the EnKF does when assimilating asynchronous observations at the correct time in an 18-hr assimilation window. The experiments also reveal that the impact of tangent linear assumption for the Lorenz-96 model in the DRP-4DVar over a 24-hr or shorter assimilation window is negligible. Furthermore, with a background error covariance matrix that has the nonsingular projection onto the ensemble space or is globally ﬂow-dependent, the DRP-4DVar performs even better.
Distinct phenotypic behaviours within a clonal population of Pseudomonas syringae pv. actinidiae

Bacterial canker of the kiwifruit caused by the etiological agent Pseudomonas syringae pv. actinidiae is the most severe disease in kiwifruit production. Since 2008 a hypervirulent Psa biovar 3 has spread rapidly worldwide. Different genomic and phenotypic approaches have been used to understand the origin of the dissemination and geographical evolution of populations associated with this pandemic. This study aimed to characterize the genetic and phenotypic diversity of 22 Psa isolates collected in different regions of Portugal between 2013 and 2017. Genotypic and phenotypic characterization was based on Multi-Locus Sequence Analysis (MLSA), motility, IAA production, Biolog GEN III, and copper sensitivity. No polymorphisms were detected for the concatenated sequence (1950 bp) of the housekeeping genes gltA, gapA, gyrB, and rpoD. Results support the analysed Portuguese Psa isolates (2013–2017) belonging to Psa3, and MLSA indicates high genetic clonality and stability of these populations. The phenotypic analysis through Biolog revealed a heterogeneous pattern in the Psa collection and its position in the Pseudomonas complex. This heterogeneity reflects a genomic diversity that may reflect distinct adaptive trends associated with the environmental conditions and widespread. The Portuguese Psa collection showed no resistance to copper. This information is relevant to kiwi producers that predominantly use Cu-treatments to control kiwifruit bacterial canker.
Human parainfluenza 3 and respiratory syncytial viruses detected in pangolins

ABSTRACT Pangolins have gained increasing global attention owing to their public health significance as potential zoonotic hosts since the identification of SARS-CoV-2-related viruses in them. Moreover, these animals could carry other respiratory viruses. In this study, we investigated the virome composition of 16 pangolins that died in 2018 with symptoms of pneumonia using metagenomic approaches. A total of eight whole virus sequences belonging to the Paramyxoviridae or Pneumoviridae families were identified, including one human parainfluenza virus 3, one human respiratory syncytial virus A, and six human respiratory syncytial virus B. All of these sequences showed more than 99% nucleotide identity with the virus isolated from humans at the whole-genome level and clustered with human viruses in the phylogenetic tree. Our findings provide evidence that pangolins are susceptible to HPIV3 and HRSV infection. Therefore, public awareness of the threat of pangolin-borne pathogens is essential to stop their human consumption and to prevent zoonotic viral transmission.
Research progress and application prospects of stable porcine pluripotent stem cells

Abstract Pluripotent stem cells (PSCs) harbor the capacity of unlimited self-renewal and multilineage differentiation potential, which are crucial for basic research and biomedical science. Establishment of PSCs with defined features was previously reported from mice and humans, while generation of stable large animal PSCs has experienced a relatively long trial stage and only recently has made breakthroughs. Pigs are regarded as ideal animal models for their similarities in physiology and anatomy to humans. Generation of porcine PSCs would provide cell resources for basic research, genetic engineering, animal breeding, and cultured meat. In this review, we summarize the progress on the derivation of porcine PSCs and reprogramed cells and elucidate the mechanisms of pluripotency changes during pig embryo development. This will be beneficial for understanding the divergence and conservation between different species involved in embryo development and the pluripotent-regulated signaling pathways. Finally, we also discuss the promising future applications of stable porcine PSCs. Even though challenges remain in the field of porcine stem cells, these progress and viewpoints would provide guidance in future research direction.
Magnetoresistance studies of two-dimensional Fe3GeTe2 nano-flake

The magneto-transport properties of two-dimensional (2D) Fe3GeTe2 (FGT) nano-flakes are carefully investigated with the variation of the temperature and the direction of the applied magnetic field (B). Four magnetoresistance (MR) behavior are obtained at different temperatures with B paralleling the flake’s surface, because of the competition between the merging of different domains, spin fluctuation, and the spin momentum flipping. Different from the reported negative MR of bulk FGT, 2D FGT shows a positive MR behavior with the increase of B at a low temperature in a low B range, owning to the domination of the spin momentum flipping induced by the weakening of the coupling between different layers with the decrease of the thickness of the FGT flake. The angle-dependence of the FGT MR is also investigated and can be well explained by the competition mentioned above.
The association of 20 short tandem repeat loci of autosomal chromosome with male schizophrenia

Schizophrenia's heritability and familial transmission have been known for several decades. The male‐specific Y chromosome plays an important role in schizophrenia. Short tandem repeats (STRs)have been recognized as risk genes in the development of schizophrenia. Here, we investigated the association between male schizophrenia and Y‐chromosomal STRs loci.
Inhibition of histone H3-H4 chaperone pathways rescues C. elegans sterility by H2B loss

Oncohistone mutations are crucial drivers for tumorigenesis, but how a living organism governs the loss-of-function oncohistone remains unclear. We generated a histone H2B triple knockout (3KO) strain in Caenorhabditis elegans, which decreased the embryonic H2B, disrupted cell divisions, and caused animal sterility. By performing genetic suppressor screens, we uncovered that mutations defective in the histone H3-H4 chaperone UNC-85 restored H2B 3KO fertility by decreasing chromatin H3-H4 levels. RNA interference of other H3-H4 chaperones or H3 or H4 histones also rescued H2B 3KO sterility. We showed that blocking H3-H4 chaperones recovered cell division in C. elegans carrying the oncohistone H2BE74K mutation that distorts the H2B-H4 interface and induces nucleosome instability. Our results indicate that reducing chromatin H3-H4 rescues the dysfunctional H2B in vivo and suggest that inhibiting H3-H4 chaperones may provide an effective therapeutic strategy for treating cancers resulting from loss-of-function H2B oncohistone.
The metabolic syndrome is frequent in children and adolescents with type 1 diabetes compared to healthy controls

There is a rise in overweight and obesity among children and adolescents with type 1 diabetes (T1D) in parallel with the rise in the metabolic syndrome (MetS) among children and adolescents. The aim of the study was to describe the prevalence and characteristics of MetS in children and adolescents with T1D compared to their healthy counterparts.
Toward Improved Treatment and Empowerment of Individuals With Parkinson Disease: Design and Evaluation of an Internet of Things System

Background Parkinson disease (PD) is a chronic degenerative disorder that causes progressive neurological deterioration with profound effects on the affected individual’s quality of life. Therefore, there is an urgent need to improve patient empowerment and clinical decision support in PD care. Home-based disease monitoring is an emerging information technology with the potential to transform the care of patients with chronic illnesses. Its acceptance and role in PD care need to be elucidated both among patients and caregivers. Objective Our main objective was to develop a novel home-based monitoring system (named EMPARK) with patient and clinician interface to improve patient empowerment and clinical care in PD. Methods We used elements of design science research and user-centered design for requirement elicitation and subsequent information and communications technology (ICT) development. Functionalities of the interfaces were the subject of user-centric multistep evaluation complemented by semantic analysis of the recorded end-user reactions. The ICT structure of EMPARK was evaluated using the ICT for patient empowerment model. Results Software and hardware system architecture for the collection and calculation of relevant parameters of disease management via home monitoring were established. Here, we describe the patient interface and the functional characteristics and evaluation of a novel clinician interface. In accordance with our previous findings with regard to the patient interface, our current results indicate an overall high utility and user acceptance of the clinician interface. Special characteristics of EMPARK in key areas of interest emerged from end-user evaluations, with clear potential for future system development and deployment in daily clinical practice. Evaluation through the principles of ICT for patient empowerment model, along with prior findings from patient interface evaluation, suggests that EMPARK has the potential to empower patients with PD. Conclusions The EMPARK system is a novel home monitoring system for providing patients with PD and the care team with feedback on longitudinal disease activities. User-centric development and evaluation of the system indicated high user acceptance and usability. The EMPARK infrastructure would empower patients and could be used for future applications in daily care and research.
Does Nasal Screening for Methicillin-Resistant Staphylococcus aureus (MRSA) Prevent Deep Surgical Site Infections for Elective Cervical Spinal Fusion?

Study Design: Retrospective cohort study. Objective: The objective of this study was to determine the relationship between nasal methicillin-resistant Staphylococcus aureus (MRSA) testing and surgical site infection (SSI) rates in the setting of primary posterior cervical instrumented spine surgery. Summary of Background Data: Preoperative MRSA screening and decolonization has demonstrated success for some orthopedic subspecialties in prevention of SSIs. Spine surgery, however, has seen varied results, potentially secondary to the anatomic and surgical heterogeneity of the patients included in prior studies. Given that prior research has demonstrated greater propensity for gram positive SSIs in the cervical spine, we sought to investigate if MRSA screening would be more impactful in the cervical spine. Materials and Methods: Adult patients undergoing primary instrumented posterior cervical procedures from January 2015 to December 2019 were reviewed for MRSA testing <90 days before surgery, preoperative mupirocin, perioperative antibiotics, and SSI defined as operative incision and drainage (I&D) <90 days after surgery. Logistic regression modeling used SSI as the primary outcome, MRSA screening as primary predictor, and clinical and demographic factors as covariates. Results: This study included 668 patients, of whom MRSA testing was performed in 212 patients (31.7%) and 6 (2.8%) were colonized with MRSA. Twelve patients (1.8%) underwent an I&D. On adjusted analysis, preoperative MRSA testing was not associated with postoperative I&D risk. Perioperative vancomycin similarly had no association with postoperative I&D risk. Notably, 6 patients (50%) grew methicillin sensitive Staphylococcus aureus from intraoperative cultures, with no cases of MRSA. Conclusions: There was no association between preoperative nasal MRSA screening and SSIs in primary posterior cervical instrumented procedures, nor was there any association between vancomycin or infection rate. Furthermore, there was a preponderance of gram positive infections but none caused by MRSA. Given these findings, the considerable cost and effort associated with MRSA testing in the setting of primary posterior cervical instrumentation may not be justified. Further research should investigate if higher-risk scenarios demonstrate greater utility of preoperative testing.
Evaluation of the relationship between the disease severity and the level of physical activity in patients followed up with COVID-19 diagnosis

Objectives: To investigate the relationship between physical activity level and disease severity, anxiety level, sleep quality, and fatigue in patients followed up with COVID-19 diagnosis. Methods: This was a cross-sectional study of 111 volunteer patients who were receiving treatment with COVID-19 diagnosis at the Chest Diseases Polyclinic, Sanko University, Sani Konukoğlu Practice and Research Hospital, Gaziantep, Turkey between May 2021 and July 2021 were included in the study and classified clinically and radiologically. They were evaluated on the basis of demographic characteristics, International Physical Activity Questionnaire, Beck Anxiety Inventory, Pittsburgh Sleep Quality Index, and Fatigue Severity Scale. Results: Approximately 63% of the patients did not have a habit of exercise, while 52.3% of our patients were clinically mild cases, and 33.3% had normal lung tomography. While clinical disease severity was not associated with exercise habits, sleep quality was impaired in clinically severe patients. Conclusion: The results of our study suggested that physical inactivity is common. Anxiety is a frequent symptom in COVID-19 cases and also COVID-19 negatively affects sleep quality.
Epigenetic reactivation of transcriptional programs orchestrating fetal lung development in human pulmonary hypertension

Phenotypic alterations in resident vascular cells contribute to the vascular remodeling process in diseases such as pulmonary (arterial) hypertension [P(A)H]. How the molecular interplay between transcriptional coactivators, transcription factors (TFs), and chromatin state alterations facilitate the maintenance of persistently activated cellular phenotypes that consequently aggravate vascular remodeling processes in PAH remains poorly explored. RNA sequencing (RNA-seq) in pulmonary artery fibroblasts (FBs) from adult human PAH and control lungs revealed 2460 differentially transcribed genes. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed extensive differential distribution of transcriptionally accessible chromatin signatures, with 4152 active enhancers altered in PAH-FBs. Integrative analysis of RNA-seq and ChIP-seq data revealed that the transcriptional signatures for lung morphogenesis were epigenetically derepressed in PAH-FBs, including coexpression of T-box TF 4 (TBX4), TBX5, and SRY-box TF 9 (SOX9), which are involved in the early stages of lung development. These TFs were expressed in mouse fetuses and then repressed postnatally but were maintained in persistent PH of the newborn and reexpressed in adult PAH. Silencing of TBX4, TBX5, SOX9, or E1A-associated protein P300 (EP300) by RNA interference or small-molecule compounds regressed PAH phenotypes and mesenchymal signatures in arterial FBs and smooth muscle cells. Pharmacological inhibition of the P300/CREB-binding protein complex reduced the remodeling of distal pulmonary vessels, improved hemodynamics, and reversed established PAH in three rodent models in vivo, as well as reduced vascular remodeling in precision-cut tissue slices from human PAH lungs ex vivo. Epigenetic reactivation of TFs associated with lung development therefore underlies PAH pathogenesis, offering therapeutic opportunities. Description Aberrant epigenetic reactivation of developmental transcription factors underlies the pathogenesis of pulmonary hypertension. Deactivating developmental reactivation Pulmonary arterial hypertension (PAH) is a fatal disease, and current treatments do not restore vascular structure. Here, Chelladurai and colleagues integrated RNA sequencing and chromatin immunoprecipitation sequencing data from PAH pulmonary artery fibroblasts, revealing derepression of transcriptional signatures for lung morphogenesis. Silencing of TBX4, TBX5, and SOX9, as well as EP300, a regulator of developmental transcription factor expression, led to regression of mesenchymal signatures, and inhibition of the P300/CREB-binding protein complex using pharmacological compounds reduced vascular remodeling in precision-cut lung tissue slices. In three rat models of PAH, these compounds improved hemodynamics and reduced the muscularization of the distal pulmonary arteries, suggesting that controlling the epigenetic dysregulation of developmental transcription factors may be beneficial in this disease.
Comparison of CpG- and UpA-mediated restriction of RNA virus replication in mammalian and avian cells and investigation of potential ZAP-mediated shaping of host transcriptome compositions

The ability of zinc finger antiviral protein (ZAP) to recognize and respond to RNA virus sequences with elevated frequencies of CpG dinucleotides has been proposed as a functional part of the vertebrate innate immune antiviral response. It has been further proposed that ZAP activity shapes compositions of cytoplasmic mRNA sequences to avoid self-recognition, particularly mRNAs for interferons (IFNs) and IFN-stimulated genes (ISGs) expressed during the antiviral state. We investigated whether restriction of the replication of mutants of influenza A virus (IAV) and the echovirus 7 (E7) replicon with high CpG and UpA frequencies varied in different species of mammals and birds. Cell lines from different bird orders showed substantial variability in restriction of CpG-high mutants of IAV and E7 replicons, whereas none restricted UpA-high mutants, in marked contrast to universal restriction of both mutants in mammalian cells. Dinucleotide representation in ISGs and IFN genes was compared with those of cellular transcriptomes to determine whether potential differences in inferred ZAP activity between species shaped dinucleotide compositions of highly expressed genes during the antiviral state. While mammalian type 1 IFN genes typically showed often profound suppression of CpG and UpA frequencies, there was no oversuppression of either in ISGs in any species, irrespective of their ability to restrict CpG- or UpA-high mutants. Similarly, genome sequences of mammalian and avian RNA viruses were compositionally equivalent, as were IAV strains recovered from ducks, chickens and humans. Overall, we found no evidence for host variability in inferred ZAP function shaping host or viral transcriptome compositions.
The livestock farming digital transformation: implementation of new and emerging technologies using artificial intelligence

Abstract Livestock welfare assessment helps monitor animal health status to maintain productivity, identify injuries and stress, and avoid deterioration. It has also become an important marketing strategy since it increases consumer pressure for a more humane transformation in animal treatment. Common visual welfare practices by professionals and veterinarians may be subjective and cost-prohibitive, requiring trained personnel. Recent advances in remote sensing, computer vision, and artificial intelligence (AI) have helped developing new and emerging technologies for livestock biometrics to extract key physiological parameters associated with animal welfare. This review discusses the livestock farming digital transformation by describing (i) biometric techniques for health and welfare assessment, (ii) livestock identification for traceability and (iii) machine and deep learning application in livestock to address complex problems. This review also includes a critical assessment of these topics and research done so far, proposing future steps for the deployment of AI models in commercial farms. Most studies focused on model development without applications or deployment for the industry. Furthermore, reported biometric methods, accuracy, and machine learning approaches presented some inconsistencies that hinder validation. Therefore, it is required to develop more efficient, non-contact and reliable methods based on AI to assess livestock health, welfare, and productivity.
Assessment of key characteristics, methodology, and effect size measures used in meta‐analysis of human‐health‐related animal studies

Since the early 1990s the number of systematic reviews (SR) of animal studies has steadily increased. There is, however, little guidance on when and how to conduct a meta‐analysis of human‐health‐related animal studies. To gain insight about the methods that are currently used we created an overview of the key characteristics of published meta‐analyses of animal studies, with a focus on the choice of effect size measures. An additional goal was to learn about the rationale behind the meta‐analysis methods used by the review authors. We show that important details of the meta‐analyses are not fully described, only a fraction of all human‐health‐related meta‐analyses provided rationales for their decision to use specific effect size measures. In addition, our data may suggest that authors make post‐hoc decisions to switch to another effect size measure during the course of their meta‐analysis, and possibly search for significant effects. Based on analyses in this paper we recommend that review teams: 1) publish a review protocol before starting the conduct of a SR, prespecifying all methodological details (providing special attention to the planned meta‐analysis including the effect size measure and the rational behind choosing a specific effect size, prespecifying subgroups and restricting the number of subgroup analyses), 2) always use the Preferred Reporting Items for Systematic Review and Meta‐Analyses (PRISMA) checklist to report your SR of animal studies, and 3) use the random effects model (REM) in human‐health‐related meta‐analysis of animal studies, unless the assumptions for using the fixed effect model (FEM) are all met.