Miracle-dz/UniFAR-FTUs huggingface dataset:
ECGT2T: Towards Synthesizing Twelve-Lead Electrocardiograms from Two Asynchronous Leads

Electrocardiograms (ECGs) are a non-invasive measurement used to observe the condition of the heart. Modern wearable devices can record ECGs, but typically provide fewer leads–signal outputs from electrodes–than the 12 in standard electrocardiograms. Consequently, data generated from these devices may be insufficient for accurately diagnosing more complex cardiac conditions. To bridge this gap, we propose ECGT2T, a deep generative model that synthesizes ten leads from an asynchronous Lead I and Lead II input to simulate a 12-lead ECG. Compared to the R-peaks of the original wave-forms, the generated signals had timing and amplitude errors under 15 milliseconds and 10%, respectively. Experiments on two widely used ECG datasets show classifiers trained on synthesized 12-lead electrocardiograms generated with ECGT2T outperforms models trained on one- or two-lead ECGs in detecting myocardial infarction and arrhythmia.
Social Sustainability of the ILVA Taranto Steelmaking plant

The social impact of the steel industry has been at the centre of the discussion on sustainable development since the Brundtland Commission’s definition (1987):“Development that meets the needs of the present without compromising the ability of future generations to meet their own needs”. The European steel industry is committed to sustainable development, according to the conviction that economic growth is closely related to social progress and the environmental quality. The purpose of the present papers is to provide, according to the research perspectives in this field, the industrial strategies of ILVA-RIVAGROUP, the leader steelmaker in Italy and one of the most important steel producer in the world. Within the panorama of worldwide steel industry, the ILVA-RIVA GROUP is committed to sustainable development, through the conviction that: • the profit cannot be released by the environmental, social and economic problem solving; • the industrial activities must have positive impacts on social development. The ILVA plant in Taranto is one of the main steel plant in Europe, which produces more than 10 million tonnes of steel per year. The present paper shows the results of a recent research, which indicates that the social and economic impact of the Taranto ILVA plant in its local environment is positive. Moreover, the company policy is committed towards the awareness that responsibility to people are becoming essential for successful business. On this subject the trust of the workers towards the firm has increased for the improvement in the performance in all the three aspects of an actual sustainable development, i.e. economic, environmental and social aspect. In fact, together with remarkable investments in environmental issues, new steelmaking technologies, new steels and processes development, the ILVA-RIVAGROUP is committed to improvement: employment and training of young people; health and safety of workers; competence and training of employees; motivation of employees and the workers rights protection.
Bioinformatic analyses of plasmid resistome changes in pOXA-48

Infections caused by carbapenem resistant Enterobacteriales (CPE) represent a significant threat in clinical settings. blaOXA-48 is one of the most frequent carbapenemase genes among Enterobacteriales. The blaOXA-48 is typically encoded on the prototypical IncL conjugative pOXA-48 plasmid. The pOXA-48 plasmid encodes only the blaOXA-48 resistance gene. However, aminoglycoside and extended spectrum β-lactamase (ESBL) resistance genes have also been detected on the same pOXA-48 plasmid backbone. These pOXA-48 plasmids encoding additional antimicrobial resistance (AMR) genes have been associated with both poor patient outcome and increased minimal inhibitory concentrations (MICs) to antibiotics including broad-spectrum cephalosporins. The blaOXA-48 gene was sourced from the pOXA-48 reference plasmid and set as a query using the BLASTn tool. Non-duplicate blaOXA-48 containing plasmids were downloaded, incompatibility typed and annotated for resistance genes using ResFinder 4.0. Bioinformatic analyses identified three distinct variants of the pOXA-48 plasmid encoding 4, 5, and 6 antimicrobial resistance genes. All plasmids encoded the ESBL blaCTX-M-14b, blaOXA-48 and either 2, 3 or 4 aminoglycoside resistance genes, in addition to conjugative transfer machinery. Plasmid variants 1 and 3 encoded aminoglycoside genes bracketed between IS26 and ISEc63 insertion elements, forming a potential transposon. The potential transposon structure had resemblance to the Tn5393 transposon (accession: M96392), including both aph(3’’)-Ib, aph(6)-Id genes, and a Tn3 resolvase. The IS element ISEcp1 lies upstream of blaCTX-M-14b. All three plasmid variants appear related. Notably, all pOXA-48 plasmid variants were identified in multiple countries. In particular, variant 1 including 6 AMR genes was detected in 7 unique countries. Plasmids encoding additional AMR genes were associated with clinical/surveillance samples suggesting antibiotic pressure in clinical settings may promote changes in the resistome of pOXA-48. Acquisition of pOXA-48 resistant plasmids carrying additional AMR genes beyond blaOXA-48 can change the resistome of susceptible isolates in a single-step, rendering previously susceptible strains refractory to almost all available treatment options.
Retinal neuroblast migration and laminar organization requires the cytoskeletal-interacting protein Mllt11

Background The vertebrate retina is an organized laminar structure comprised of distinct cell types populating three nuclear layers. During development, each retinal cell type follows a stereotypical temporal order of genesis, differentiation, and migration, giving rise to its stratified organization. Once born, the precise positioning of cells along the apico-basal (radial) axis of the retina is critical for subsequent connections to form, relying on orchestrated migratory processes. While these processes are critical for visual function to arise, the regulators of cellular migration and retinal lamination remain largely unexplored. Results We report a role for a microtubule-interacting protein, Mllt11 (Myeloid/lymphoid or mixed-lineage leukemia; translocated to chromosome 11/All1 Fused Gene From Chromosome 1q) in mammalian retinal cell migration during retinogenesis. We show that Mllt11 loss-of-function in mouse retinal neuroblasts affected the migration of ganglion and amacrine cells into the ganglion cell layer, and led to their ectopic accumulation in the inner plexiform layer. Conclusions We demonstrate that Mllt11 plays a critical role in the migration and lamination of neurons in the retina, and its loss impacted formation of the basal-most retinal layers.
Hull content and chemical composition of whole seeds, hulls and germs in cultivars of rapeseed (Brassica napus)

Objective : To study of the compositional breakdown of seed components between the integument and the germ and its variability according to genetic and environmental factors. Methods: The study used 19 rapeseed lots grown in two areas of contrasted agronomical potential harvested in 2011. Pure fractions of hulls and germs were mechanically separated by centrifuge impacts after freezing the seeds. Chemical composition of the whole seeds and the pure kernel and hull fractions was determined. The results were used to calculate the seed hull content. Results: Hull accounted for 18.2% of total seed content. Real oil content of the hulls (8.4% dry basis) was lower than in the literature. Hulls contained 2.9% of the oil, 11.2% of the proteins, 73% of the NDF; 80% of the ADF, 95% of the lignin and 6.0% of the glucosinolates of the whole seed. The percentage of hulls in total seed content shows low variability, although the oil and the protein content of the fractions were significantly affected by cultivar and to a lesser extent by geographic location of the crops. Conclusion: Completely dehulled seeds could result in a meal with 48.3% protein (dry basis) and low fiber content (10.8% NDF, 6.6% ADF, 0.5% ADL) but higher glucosinolate content (130% compared to defatted seeds).
Machine learning-aided multidimensional phenotyping of Parkinson’s disease patient stem cell-derived midbrain dopaminergic neurons

Combining multiple Parkinson’s disease (PD) relevant cellular phenotypes might increase the accuracy of midbrain dopaminergic (mDA) in vitro models. We differentiated patient-derived induced pluripotent stem cells (iPSCs) with a LRRK2 G2019S mutation, isogenic control and genetically unrelated iPSCs into mDA neurons. Using automated fluorescence microscopy in 384-well plate format, we identified elevated levels of α-synuclein and Serine 129 phosphorylation (pS129), reduced dendritic complexity, and mitochondrial dysfunction. Next, we measured additional image-based phenotypes and used machine learning (ML) to accurately classify mDA neurons according to their genotype. Additionally, we show that chemical compound treatments, targeting LRRK2 kinase activity or α-synuclein levels, are detectable when using ML classification based on multiple image-based phenotypes. We validated our approach using a second isogenic patient derived SNCA gene triplication mDA neuronal model. This phenotyping and classification strategy improves the exploitability of mDA neurons for disease modelling and the identification of novel PD drug targets.
Inferring cell-specific gene regulatory networks from single cell gene expression data

Single cell gene expression datasets have been used to uncover differences between single cells, leading to discoveries of new cell types and cell identities, which are usually defined by the transcriptome profiles of cells. Biological networks, in particular, gene regulatory networks (GRNs), can be viewed as another feature of the cells, that contributes to the uniqueness of each single cell. However, methods that reconstruct cell-specific GRNs are still missing. We propose CeSpGRN ( Ce ll Sp ecific GRN ), which infers cell-specific GRNs from single cell gene expression data. CeSpGRN uses a Gaussian weighted kernel which allows the GRN of a given cell to be learned from the gene expression profile of this cell and cells that are upstream and downstream of this cell in the developmental process. CeSpGRN can be applied to infer cell-specific GRNs in cell popula-tions of any trajectory or cluster structure, and it does not require time information of cells as additional input. We compared the performance of CeSpGRN and baseline methods on simulated datasets obtained under various settings. CeSpGRN showed superior performance in reconstructing the GRN for each cell, as well as in detecting the regulatory interactions that differ between cells. We also applied CeSpGRN to real datasets including THP-1 human myeloid monocytic leukemia cells and mouse embryonic stem cells, where CeSpGRN suggested a set of interactions between genes that rewire during the differentiation process in these cells. CeSpGRN is available at https://github.com/PeterZZQ/CeSpGRN .
Highly efficient generation of blastocyst-like structures from mouse totipotent blastomere-like cells

Mammalian embryogenesis begins with a totipotent zygote. Early embryogenesis can be recapitulated by aggregated extended pluripotent stem cells (EPSCs) in a 3D culture system. However, the efficiency of generating blastoids is low and whether other reported totipotent stem cells retained a similar capacity remains unknown. Here we show that spliceosomal repressed totipotent blastomere-like cells (TBLCs) form blastocyst-like structures when aggregated in 3D microwells with around 80% efficiency. TBLC-blastoids resemble blastocyst in morphology and cell-lineage allocation, show similar transcriptional profile with natural blastocyst and contain more TE cells and fewer undefined intermediate cells compared to blastoids from EPSCs. Moreover, TBLC-blastoids can develop beyond the implantation stage in vitro and induce decidualization after transferred into uterus. In summary, we supply an alternative cell type to generate ameliorated blastoids highly efficiently for studying early mouse embryogenesis.
Past and Future Explanations for Depersonalization and Derealization Disorder: A Role for Predictive Coding

Depersonalization (DP) and derealization (DR) refer to states of dissociation in which one feels a sense of alienation in relation to one’s self and environment, respectively. Whilst transient episodes often diminish without treatment, chronic experiences of DP and DR may last for years, with common treatments lacking a strong evidence base for their efficacy. We propose a theoretical explanation of DP and DR based on interoceptive predictive coding, and discuss how transient experiences of DP and DR may be induced in the non-clinical population using virtual reality. Further, we review the use of heartbeat evoked potentials in detecting the neural correlates of DP and DR allowing for an objective measure of these experiences in the non-clinical population. Finally, we discuss how the induction and detection of transient experiences of DP and DR in the non-clinical population could shed light on how the brain constructs one’s sense of self and reality.
An Update on African Trypanocide Pharmaceutics and Resistance

African trypanosomiasis is associated with Trypanosoma evansi, T. vivax, T. congolense, and T. brucei pathogens in African animal trypanosomiasis (AAT) while T. b gambiense and T. b rhodesiense are responsible for chronic and acute human African trypanosomiasis (HAT), respectively. Suramin sodium suppresses ATP generation during the glycolytic pathway and is ineffective against T. vivax and T. congolense infections. Resistance to suramin is associated with pathogen altered transport proteins. Melarsoprol binds irreversibly with pyruvate kinase protein sulfhydryl groups and neutralizes enzymes which interrupts the trypanosome ATP generation. Melarsoprol resistance is associated with the adenine-adenosine transporter, P2, due to point mutations within this transporter. Eflornithine is used in combination with nifurtimox. Resistance to eflornithine is caused by the deletion or mutation of TbAAT6 gene which encodes the transmembrane amino acid transporter that delivers eflornithine into the cell, thus loss of transporter protein results in eflornithine resistance. Nifurtimox alone is regarded as a poor trypanocide, however, it is effective in melarsoprol-resistant gHAT patients. Resistance is associated with loss of a single copy of the genes encoding for nitroreductase enzymes. Fexinidazole is recommended for first-stage and non-severe second-stage illnesses in gHAT and resistance is associated with trypanosome bacterial nitroreductases which reduce fexinidazole. In AAT, quinapyramine sulfate interferes with DNA synthesis and suppression of cytoplasmic ribosomal activity in the mitochondria. Quinapyramine sulfate resistance is due to variations in the potential of the parasite's mitochondrial membrane. Pentamidines create cross-links between two adenines at 4–5 pairs apart in adenine-thymine-rich portions of Trypanosoma DNA. It also suppresses type II topoisomerase in the mitochondria of Trypanosoma parasites. Pentamidine resistance is due to loss of mitochondria transport proteins P2 and HAPT1. Diamidines are most effective against Trypanosome brucei group and act via the P2/TbAT1 transporters. Diminazene aceturate resistance is due to mutations that alter the activity of P2, TeDR40 (T. b. evansi). Isometamidium chloride is primarily employed in the early stages of trypanosomiasis and resistance is associated with diminazene resistance. Phenanthridine (homidium bromide, also known as ethidium bromide) acts by a breakdown of the kinetoplast network and homidium resistance is comparable to isometamidium. In humans, the development of resistance and adverse side effects against monotherapies has led to the adoption of nifurtimox-eflornithine combination therapy. Current efforts to develop new prodrug combinations of nifurtimox and eflornithine and nitroimidazole fexinidazole as well as benzoxaborole SCYX-7158 (AN5568) for HAT are in progress while little comparable progress has been done for the development of novel therapies to address trypanocide resistance in AAT.
Insights From the Lactobacillus johnsonii Genome Suggest the Production of Metabolites With Antibiofilm Activity Against the Pathobiont Candida albicans

Lactobacillus johnsonii is a probiotic bacterial species with broad antimicrobial properties; however, its antimicrobial activities against the pathobiont Candida albicans are underexplored. The aim of this study was to study the interactions of L. johnsonii with C. albicans and explore mechanisms of bacterial anti-fungal activities based on bacterial genomic characterization coupled with experimental data. We isolated an L. johnsonii strain (MT4) from the oral cavity of mice and characterized its effect on C. albicans growth in the planktonic and biofilm states. We also identified key genetic and phenotypic traits that may be associated with a growth inhibitory activity exhibited against C. albicans. We found that L. johnsonii MT4 displays pH-dependent and pH-independent antagonistic interactions against C. albicans, resulting in inhibition of C. albicans planktonic growth and biofilm formation. This antagonism is influenced by nutrient availability and the production of soluble metabolites with anticandidal activity.
Kam Sweet Rice (Oryza sativa L.) Is a Special Ecotypic Rice in Southeast Guizhou, China as Revealed by Genetic Diversity Analysis

Kam Sweet Rice (KSR) is a special kind of rice landrace that has been domesticated for thousands of years by the local Dong people in southeast Guizhou province, China. KSR has many distinguishing characteristics including strong fragrance; high resistance to diseases, pests, and adverse abiotic conditions; difficulty of threshing; and glutinous texture. There is a lack of systematic research on its genetic diversity. In this study, we analyzed the levels and patterns of genetic diversity and nucleotide variation in 1,481 rice germplasm using simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) haplotype analysis of six unlinked nuclear loci. The accessions included 315 KSR resources from southeast Guizhou, 578 rice landraces from six rice-growing ecological zones in Guizhou, 546 rice landraces from nine provinces around Guizhou, and 42 wild rice sources. Genetic diversity and heterozygosity of KSR were both low, and thus KSR might be close to a pure rice line. Population structure analysis showed that KSR was isolated into a single type of rice, which had a large genetic distance and a unique genetic background compared to the local varieties in Guizhou province, indicating that KSR is a special rice ecotype. Haplotype analysis of the target genes showed that the population of KSR was rich in haplotypes for resistance to bacterial blight (Xa23) and rice blast (Pid3), and identified unique haplotypes that were different from those of the six rice ecotypes in Guizhou. This study shows that KSR is an excellent rice germplasm resource, provides important information for the improvement and utilization of rice landraces, and serves as a reference for formulating effective rice conservation measures.
Value of CRP, PCT, and NLR in Prediction of Severity and Prognosis of Patients With Bloodstream Infections and Sepsis

Objective To investigate the value of C-reactive protein (CRP), procalcitonin (PCT), and neutrophil to lymphocyte ratio (NLR) in assessing the severity of disease in patients with bloodstream infection and sepsis, and to analyze the relationship between the levels of three inflammatory factors and the prognosis of patients. Methods The clinical data of 146 patients with bloodstream infection and sepsis admitted to our intensive care unit (ICU) from October 2016 to May 2020 were retrospectively analyzed. The differences in the levels of inflammatory indicators such as CRP, PCT, and NLR within 24 h in patients with bloodstream infection sepsis with different conditions (critical group, non-critical group) and the correlation between these factors and the condition (acute physiology and chronic health evaluation II, APACHE II score) were analyzed. In addition, the prognosis of all patients within 28 days was counted, and the patients were divided into death and survival groups according to their mortality, and the risk factors affecting their death were analyzed by logistic regression, and the receiver operating characteristic (ROC) curve was used to analyze the value of the relevant indicators in assessing the prognosis of patients. Results The levels of NLR, CRP, PCT, total bilirubin (TBIL), glutamic oxaloacetic transaminase (AST), and serum creatinine (Scr) were significantly higher in the critically ill group than in the non-critically ill group, where correlation analysis revealed a positive correlation between CRP, PCT, and NLR and APACHE II scores (P < 0.05). Univariate logistic regression analysis revealed that CRP, PCT, NLR, and APACHE II scores were associated with patient prognosis (P < 0.05). Multi-factor logistic regression analysis found that PCT, NLR, and APACHE II scores were independent risk factors for patient mortality within 28 days (P < 0.05). ROC curve analysis found that PCT and NLR both had an AUC area > 0.7 in predicting patient death within 28 days (P < 0.05). Conclusion Inflammatory factors such as NLR, CRP, and PCT have important clinical applications in the assessment of the extent of disease and prognosis of patients with bloodstream infection and sepsis.
Roles of Arbuscular Mycorrhizal Fungi on Soil Fertility: Contribution in the Improvement of Physical, Chemical, and Biological Properties of the Soil

Many of the world's soils are experiencing degradation at an alarming rate. Climate change and some agricultural management practices, such as tillage and excessive use of chemicals, have all contributed to the degradation of soil fertility. Arbuscular Mycorrhizal Fungi (AMFs) contribute to the improvement of soil fertility. Here, a short review focusing on the role of AMF in improving soil fertility is presented. The aim of this review was to explore the role of AMF in improving the chemical, physical, and biological properties of the soil. We highlight some beneficial effects of AMF on soil carbon sequestration, nutrient contents, microbial activities, and soil structure. AMF has a positive impact on the soil by producing organic acids and glomalin, which protect from soil erosion, chelate heavy metals, improve carbon sequestration, and stabilize soil macro-aggregation. AMF also recruits bacteria that produce alkaline phosphatase, a mineralization soil enzyme associated with organic phosphorus availability. Moreover, AMFs influence the composition, diversity, and activity of microbial communities in the soil through mechanisms of antagonism or cooperation. All of these AMF activities contribute to improve soil fertility. Knowledge gaps are identified and discussed in the context of future research in this review. This will help us better understand AMF, stimulate further research, and help in sustaining the soil fertility.