Miracle-dz/UniFAR-FTUs huggingface dataset:
A special satellite-like RNA of a novel hypovirus from Pestalotiopsis fici broadens the definition of fungal satellite

Satellites associated with plant or animal viruses have been largely detected and characterized, while those from mycoviruses together with their roles remain far less determined. Three dsRNA segments (dsRNA 1 to 3 termed according to their decreasing sizes) were identified in a strain of phytopathogenic fungus Pestalotiopsis fici AH1-1 isolated from a tea leaf. The complete sequences of dsRNAs 1 to 3, with the sizes of 10316, 5511, and 631 bp, were determined by random cloning together with a RACE protocol. Sequence analyses support that dsRNA1 is a genome of a novel hypovirus belonging to genus Alphahypovirus of the family Hypoviridae, tentatively named Pestalotiopsis fici hypovirus 1 (PfHV1); dsRNA2 is a defective RNA (D-RNA) generating from dsRNA1 with septal deletions; and dsRNA3 is the satellite component of PfHV1 since it could be co-precipitated with other dsRNA components in the same sucrose fraction by ultra-centrifuge, suggesting that it is encapsulated together with PfHV1 genomic dsRNAs. Moreover, dsRNA3 shares an identical stretch (170 bp) with dsRNAs 1 and 2 at their 5′ termini and the remaining are heterogenous, which is distinct from a typical satellite that generally has very little or no sequence similarity with helper viruses. More importantly, dsRNA3 lacks a substantial open reading frame (ORF) and a poly (A) tail, which is unlike the known satellite RNAs of hypoviruses, as well as unlike those in association with Totiviridae and Partitiviridae since the latters are encapsidated in coat proteins. As up-regulated expression of RNA3, dsRNA1 was significantly down-regulated, suggesting that dsRNA3 negatively regulates the expression of dsRNA1, whereas dsRNAs 1 to 3 have no obvious impact on the biological traits of the host fungus including morphologies and virulence. This study indicates that PfHV1 dsRNA3 is a special type of satellite-like nucleic acid that has substantial sequence homology with the host viral genome without encapsidation in a coat protein, which broadens the definition of fungal satellite.
Biallelic structural variations within FGF12 detected by long-read sequencing in epilepsy

This study demonstrates biallelic intragenic structural variations and a homozygous single-nucleotide variant in FGF12 cause epilepsy as a new loss-of-function mechanism of FGF12 in humans. We discovered biallelic intragenic structural variations (SVs) in FGF12 by applying long-read whole genome sequencing to an exome-negative patient with developmental and epileptic encephalopathy (DEE). We also found another DEE patient carrying a biallelic (homozygous) single-nucleotide variant (SNV) in FGF12 that was detected by exome sequencing. FGF12 heterozygous recurrent missense variants with gain-of-function or heterozygous entire duplication of FGF12 are known causes of epilepsy, but biallelic SNVs/SVs have never been described. FGF12 encodes intracellular proteins interacting with the C-terminal domain of the alpha subunit of voltage-gated sodium channels 1.2, 1.5, and 1.6, promoting excitability by delaying fast inactivation of the channels. To validate the molecular pathomechanisms of these biallelic FGF12 SVs/SNV, highly sensitive gene expression analyses using lymphoblastoid cells from the patient with biallelic SVs, structural considerations, and Drosophila in vivo functional analysis of the SNV were performed, confirming loss-of-function. Our study highlights the importance of small SVs in Mendelian disorders, which may be overlooked by exome sequencing but can be detected efficiently by long-read whole genome sequencing, providing new insights into the pathomechanisms of human diseases.
Sex, T Cells, and the Microbiome in Natural ABO Antibody Production in Mice

Background. “Natural” ABO antibodies (Abs) are produced without known exposure to A/B carbohydrate antigens, posing significant risks for hyperacute rejection during ABO-incompatible transplantation. We investigated anti-A "natural" ABO antibodies versus intentionally induced Abs with regard to the need for T-cell help, the impact of sex, and stimulation by the microbiome. Methods. Anti-A was measured by hemagglutination assay of sera from untreated C57BL/6 wild-type (WT) or T cell–deficient mice of both sexes. Human ABO-A reagent blood cell membranes were injected intraperitoneally to induce anti-A Abs. The gut microbiome was eliminated by maintenance of mice in germ-free housing. Results. Compared with WT mice, CD4+ T-cell knockout (KO), major histocompability complex–II KO, and αβ/γδ T-cell receptor KO mice produced much higher levels of anti-A nAbs; females produced dramatically more anti-A nAbs than males, rising substantially with puberty. Sensitization with human ABO-A reagent blood cell membranes did not induce additional anti-A in KO mice, unlike WT. Sex-matched CD4+ T-cell transfer significantly suppressed anti-A nAbs in KO mice and rendered mice responsive to A-sensitization. Even under germ-free conditions, WT mice of several strains produced anti-A nAbs, with significantly higher anti-A nAbs levels in females than males. Conclusions. Anti-A nAbs were produced without T-cell help, without microbiome stimulation, in a sex- and age-dependent manner, suggestive of a role for sex hormones in regulating anti-A nAbs. Although CD4+ T cells were not required for anti-A nAbs, our findings indicate that T cells regulate anti-A nAb production. In contrast to anti-A nAbs, induced anti-A production was T-cell dependent without a sex bias.
Exploring the third-generation tetracycline resistance of multidrug-resistant livestock-associated methicillin-resistant Staphylococcus aureus ST9 across healthcare settings in China

Abstract Background The overuse of antibiotics in livestock is contributing to the burden of antimicrobial resistance in humans, representing a One Health challenge. Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has recently become a growing concern, and ST9 is the major LA-MRSA lineage in China and has emerged in clinical settings. Methods Antimicrobial susceptibility testing was used to evaluate the tetracycline resistance of ST9 MRSA collections, and gene cloning experiments were performed to explore the resistance mechanisms. Whole-genome sequencing and comparative genomics were used to analyse the genetic features of clinical ST9 isolates. A phylogenetic tree was constructed to investigate the relationship of human- and livestock-derived ST9 isolates. Results Clinical ST9 isolates were found to possess several types of resistance genes and resistance-related mutations and were multidrug-resistant. Notably, all clinical ST9 isolates were resistant to third-generation tetracyclines. Cloning experiments showed that both the acquisition of the tetracycline resistance gene tet(L)/tet(63) and a mutation in the rpsJ gene contributed to third-generation tetracycline resistance. Phylogenetic analysis showed that the ST9 isolates collected in healthcare systems were probably transmitted from livestock. The ST9 lineage underwent multiple interspecies recombination events and gained many resistance elements. Furthermore, the resistance to third-generation tetracyclines may have evolved under tetracycline pressure in livestock. Conclusions The evolution of ST9 MRSA in livestock and transmission of this clone between humans and livestock highlight the importance of establishing control strategies with the One Health approach to reduce the burden of antibiotic resistance.
A Pilot Phase I Trial of Allogeneic Umbilical Cord Tissue-Derived Mesenchymal Stromal Cells in Neonates With Hypoxic-Ischemic Encephalopathy

Abstract Hypoxic ischemic encephalopathy (HIE) in neonates causes increased mortality and long-term morbidity in surviving babies. Hypothermia (HT) has improved outcomes, however, mortality remains high with ~half of surviving babies developing neurological impairment in their first years. We previously explored the use of autologous cord blood (CB) to determine if CB cells could lessen long-term damage to the brain. However, the feasibility of CB collection from sick neonates limited the utility of this approach. Allogeneic cord tissue mesenchymal stromal cells (hCT-MSC), cryopreserved and readily available, have been shown to ameliorate brain injury in animal models of HIE. We, therefore, conducted a pilot, phase I, clinical trial to test the safety and describe the preliminary efficacy of hCT-MSC in neonates with HIE. The study treated infants with moderate to severe HIE, treated with HT, with 1 or 2 doses of 2 million cells/kg/dose of hCT-MSC given intravenously. The babies were randomized to receive 1 or 2 doses with the first dose during HT and the second dose 2 months later. Babies were followed for survival and development with scoring of Bayley’s at 12 postnatal months. Six neonates with moderate (4) or severe (2) HIE were enrolled. All received 1 dose of hCT-MSC during HT and 2 received a 2nd dose, 2 months later. hCT-MSC infusions were well tolerated although 5/6 babies developed low titer anti-HLA antibodies by 1 year of age. All babies survived, with average to low-average developmental assessment standard scores for ages between 12 and 17 postnatal months. Further study is warranted.
Exploring the Predictors of the Discrepancy Between Quantitative Flow Ratio and Fractional Flow Reserve Measurements

Background: Quantitative flow ratio is a novel technology for the functional assessment of intermediate coronary stenoses. The authors sought to explore the influence of diabetes mellitus on the application of quantitative flow ratio and predictors of discrepancies between quantitative flow ratio and fractional flow reserve. Methods: Quantitative flow ratio was calculated in 224 patients (317 vessels) who underwent fractional flow reserve measurement by professional technicians blinded to fractional flow reserve value. Patients were divided into the diabetes mellitus group and the non-diabetes mellitus group. The diagnostic performance of quantitative flow ratio was assessed using fractional flow reserve as a reference. Results: Good correlation and agreement between quantitative flow ratio and fractional flow reserve can be found in the diabetes mellitus group (r = 0.834, P < .001; mean difference: 0.007 ± 0.108). Prior myocardial infarction showed a statistically significant association with increased classification discrepancy between quantitative flow ratio and fractional flow reserve [odds ratio 3.16 (95% confidence interval: 1.29-7.75), P = . 01]. The area under the receiver-operating characteristic curve of quantitative flow ratio showed no significant difference in diabetes mellitus and non-diabetes mellitus groups, hemoglobin A1c ≥ 7% and hemoglobin A1c < 7% groups, diabetic duration ≥ 10 years and diabetic duration < 10 years groups (area under receiver-operating characteristic curve: 0.90 (95% confidence interval: 0.84-0.94) vs. 0.92 (95% confidence interval: 0.87-0.96), P = . 54; 0.89 (95% confidence interval: 0.81-0.95) vs. 0.92 (95% confidence interval: 0.81-0.97), P = . 65; 0.88 (95% confidence interval: 0.79-0.94) vs. 0.89 (95% confidence interval: 0.79-0.96), P = . 83; respectively). Conclusions: Clinical application of quantitative flow ratio is not limited to diabetic patients. The relationship between prior myocardial infarction and quantitative flow ratio needs to be further developed.
A Comprehensive, Affordable, Open-Source Hardware-Software Solution for Flexible Implementation of Complex Behaviors in Head-Fixed Mice

Abstract Experiments that take advantage of head-fixed behavioral tasks have been a staple of systems neuroscience research for half a century. More recently, rodents came to the forefront of these efforts, primarily because of the rich experimental possibilities afforded by modern genetic tools. There is, however, a considerable barrier to entering this field, requiring expertise in engineering, hardware and software development, and significant time and financial commitment. Here, we present a comprehensive, open-source hardware and software solution to implement a head-fixed environment for rodent behaviors (HERBs). Our solution provides access to three frequently used experimental frameworks (two-alternative forced choice, Go-NoGo, or passive sensory stimulus presentation) in a single package. The required hardware can be built at a relatively low cost compared with commercially available solutions, from off-the-shelf components. Our graphical user interface-based software provides great experimental flexibility and requires no programming experience for either installation or use. Furthermore, an HERBs takes advantage of motorized components that allow the precise, temporal separation of behavioral phases (stimulus presentation, delays, response window and reward). Overall, we present a solution that will allow laboratories to join the growing community of systems neuroscience research at a substantially lower cost of entry.
A unified hybrid transformer for joint MRI sequences super-resolution and missing data imputation

Objective. High-resolution multi-modal magnetic resonance imaging (MRI) is crucial in clinical practice for accurate diagnosis and treatment. However, challenges such as budget constraints, potential contrast agent deposition, and image corruption often limit the acquisition of multiple sequences from a single patient. Therefore, the development of novel methods to reconstruct under-sampled images and synthesize missing sequences is crucial for clinical and research applications. Approach. In this paper, we propose a unified hybrid framework called SIFormer, which utilizes any available low-resolution MRI contrast configurations to complete super-resolution (SR) of poor-quality MR images and impute missing sequences simultaneously in one forward process. SIFormer consists of a hybrid generator and a convolution-based discriminator. The generator incorporates two key blocks. First, the dual branch attention block combines the long-range dependency building capability of the transformer with the high-frequency local information capture capability of the convolutional neural network in a channel-wise split manner. Second, we introduce a learnable gating adaptation multi-layer perception in the feed-forward block to optimize information transmission efficiently. Main results. Comparative evaluations against six state-of-the-art methods demonstrate that SIFormer achieves enhanced quantitative performance and produces more visually pleasing results for image SR and synthesis tasks across multiple datasets. Significance. Extensive experiments conducted on multi-center multi-contrast MRI datasets, including both healthy individuals and brain tumor patients, highlight the potential of our proposed method to serve as a valuable supplement to MRI sequence acquisition in clinical and research settings.
Use of Traditional and Proteomic Methods in the Assessment of a Preclinical Model of Preeclampsia

Recent studies have demonstrated downregulation of breast cancer resistance protein (BCRP/ABCG2) in placenta obtained from women with preeclampsia (PE). BCRP is highly expressed in placenta and plays an important role in preventing xenobiotics from entering the fetal compartment. Although PE is often therapeutically managed with drugs that are substrates of BCRP, there are limited studies on the impact of PE on fetal drug exposure. Due to ethical concerns, use of preclinical models is an important approach. Thus, by using proteomic and traditional methods, we characterized transporter changes in an immunologic rat model of PE to determine its utility and predictive value for future drug disposition studies. PE was induced by daily administration of low-dose endotoxin (0.01–0.04 mg/kg) to rats on gestational days (GD) 13–16, urine was collected, and rats were sacrificed on GD17 or GD18. PE rats shared similar phenotype to PE patients, including proteinuria, and increased levels of tumor necrosis factor α and interleukin 6. Transcript and protein levels of Bcrp were significantly downregulated in placenta of PE rats on GD18. multidrug resistance 1a, multidrug resistance 1b, and organic anion transporting polypeptide 2B1 mRNA were also decreased in PE. Proteomics revealed activation of various hallmarks of PE including immune activation, oxidative stress, endoplasmic reticulum stress and apoptosis. Overall, our results demonstrated that the immunologic PE rat model exhibits numerous similarities to human PE along with dysregulation of placental transporters. Therefore, this model may be useful in examining the impact of PE on the maternal and fetal disposition of BCRP substrates. SIGNIFICANCE STATEMENT Fully characterizing preclinical models of disease is necessary to determine their validity to human conditions. Combining traditional and proteomic methods of model characterization, we identified numerous phenotypic similarities between our model of preeclampsia and human disease. The alignment with human pathophysiological changes allows for more confident use of this preclinical model.
Functional assays to screen and select monoclonal antibodies that target Yersinia pestis

ABSTRACT Yersinia pestis is a gram-negative bacterium that causes plague in animals and humans. Depending on the route of disease transmission, the bacterium can cause an acute, often fatal disease that has a narrow window for treatment with antibiotics. Additionally, antibiotic resistant strains have been identified, emphasizing the need for novel treatments. Antibody therapy is an appealing option that can direct the immune system to clear bacterial infections. Advances in biotechnology have made both engineering and producing antibodies easier and more affordable. In this study, two screening assays were optimized to evaluate the ability of antibodies to promote phagocytosis of Y. pestis by macrophages and to induce a cytokine signature in vitro that may be predictive of protection in vivo. We evaluated a panel of 21 mouse monoclonal antibodies targeting either the anti-phagocytic capsule F1 protein or the LcrV antigen, which is part of the type 3 secretion system that facilitates translocation of virulence factors into the host cell, using two functional assays. Anti-F1 and anti-LcrV monoclonal antibodies both increased bacterial uptake by macrophages, with greater uptake observed in the presence of antibodies that were protective in the mouse pneumonic plague model. In addition, the protective anti-F1 and anti-LcrV antibodies produced unique cytokine signatures that were also associated with in vivo protection. These antibody-dependent characteristics from in vitro functional assays will be useful in down-selecting efficacious novel antibodies that can be used for treatment of plague.
Rutin modified selenium nanoparticles reduces cell oxidative damage induced by H2O2 by activating Nrf2/HO-1 signaling pathway

Oxidative damage of neurons is one of the key pathological markers of Alzheimer’s disease (AD), which eventually leads to neuronal apoptosis and loss. Nuclear factor E2-related factor 2 (Nrf2) is a key regulator of antioxidant response and is considered to be an important therapeutic target for neurodegenerative diseases. In this study, the selenated derivative of antioxidant rutin (Se-Rutin) was synthesized with sodium selenate (Na2SeO3) as raw material by a simple electrostatic-compound in situ selenium reduction method. The effects of Se-Rutin on H2O2 induced oxidative damage in Pheochromocytoma PC12 cells were evaluated by cell viability, apoptosis, reactive oxygen species level and the expression of antioxidant response element (Nrf2). The results showed that H2O2 treatment significantly increased the level of apoptosis and reactive oxygen species, while the level of Nrf2 and HO-1 decreased. However, Se-Rutin significantly reduced H2O2 induced apoptosis and cytotoxicity, and increased the expression of Nrf2 and HO-1, both of which were better than that of pure rutin. Therefore, the activation of Nrf2/HO-1 signaling pathway may be the basis of Se-Rutin’s anti-oxidative damage to AD.
Quantum simulator to emulate lower-dimensional molecular structure

Bottom-up quantum simulators have been developed to quantify the role of various interactions, dimensionality, and structure in creating electronic states of matter. Here, we demonstrated a solid-state quantum simulator emulating molecular orbitals, based solely on positioning individual cesium atoms on an indium antimonide surface. Using scanning tunneling microscopy and spectroscopy, combined with ab initio calculations, we showed that artificial atoms could be made from localized states created from patterned cesium rings. These artificial atoms served as building blocks to realize artificial molecular structures with different orbital symmetries. These corresponding molecular orbitals allowed us to simulate two-dimensional structures reminiscent of well-known organic molecules. This platform could further be used to monitor the interplay between atomic structures and the resulting molecular orbital landscape with submolecular precision. Description Editor’s summary There is considerable interest in developing tunable quantum simulators of many-body Hamiltonians that use weakly conducting or insulating surfaces. Using patterned cesium atoms and surface confinement of electrons on indium–tin surfaces, Sierda et al. created artificial molecular orbitals that were strongly decoupled from the bulk bands, emulating a series of well-known planar organic molecules. This system serves as a versatile platform with which to emulate quantum chemistry on a surface and provides new ways to look at the interplay between structure and molecular orbitals. This will have relevance for quantum and organic chemistry, solid-state physics, and many-body physics. —Yury Suleymanov Artificial atoms created from cesium ions on an InSb(110) surface can be used to emulate the molecular orbitals of organic molecules.
Cellular RNA levels define heterotrophic substrate-uptake rate sub-guilds in activated sludge microbial communities

A heterotrophic-specialist model was proposed previously to divide wastewater treatment plant (WWTP) heterotrophs into sub-guilds of consumers of readily or slowly degradable substrates (RDS or SDS, respectively). The substrate degradation rate model coupled to metabolic considerations predicted that RNA and polyhydroxyalkanoate (PHA) levels would be positively correlated in the activated sludge communities with high RNA and PHA occurring in RDS-consumers, and low RNA with no PHA accumulation occurring in SDS-consumers because their external substrates are always present. This prediction was verified in previous studies and in the current one. Thus, RNA and PHA levels were used as biomarkers of the RDS- and SDS-consumer sub-guilds for cell sorting using flow cytometry of samples from three WWTPs. Subsequently, 16S rRNA gene amplicon sequencing revealed that the sorted groups were highly similar over time and among WWTPs, and demonstrated a clear segregation by RNA levels. Predicted ecophysiological traits based on 16S rRNA phylogeny suggested that the high-RNA population showed RDS-consumer traits such as higher rrn copy numbers per genome. Using a mass-flow immigration model, it appeared that the high-RNA populations exhibited high immigration rates more frequently than low-RNA populations, but the differences in frequencies were less with increasing solids residence times.