Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of bovine leukemia virus in beef cattle kept in the Central Coast Regions of Vietnam

Bovine leukemia virus (BLV) is the etiologic agent of enzootic bovine leucosis. Our previous study showed the BLV existence in cattle kept in the Red River Delta Region of Vietnam. However, no positive samples were identified in beef cattle. Besides, information related to the BLV circulation in the remained parts of Vietnam is limited. Therefore, we tested the existence of BLV in 48 beef cattle kept in the Central Coast Regions. Nested PCR targeting the BLV-env-gp51 confirmed the prevalence of 14.6% in investigated regions. Phylogenetic analysis suggested the co-existence of genotypes 1 and 10. The close relationship between strains found in Vietnam, Thailand, Myanmar, and China was revealed suggesting the possibility of BLV transmission through the movement of live cattle.
Differential Hypothalamic-pituitary-adrenal Response to Stress among Rat Strains: Methodological Considerations and Relevance for Neuropsychiatric Research

The hormones of the hypothalamic-pituitary-adrenal (HPA) axis, particularly glucocorticoids (GCs), play a critical role in the behavioral and physiological consequences of exposure to stress. For this reason, numerous studies have described differences in HPA function between different rodent strains/lines obtained by genetic selection of certain characteristics not directly related to the HPA axis. These studies have demonstrated a complex and poorly understood relationship between HPA function and certain relevant behavioral characteristics. The present review first remarks important methodological considerations regarding the evaluation and interpretation of resting and stress levels of HPA hormones. Then, it presents works in which differences in HPA function between Lewis and Fischer rats were explored as a model for how to approach other strain comparisons. After that, differences in the HPA axis between classical strain pairs (e.g. High and Low anxiety rats, Roman high- and low-avoidance, Wistar Kyoto versus Spontaneously Hypertensive or other strains, Flinder Sensitive and Flinder Resistant lines) are described. Finally, after discussing the relationship between HPA differences and relevant behavioral traits (anxiety-like and depression-like behavior and coping style), an example for main methodological and interpretative concerns and how to test strain differences is offered.
ISG15 Is a Novel Regulator of Lipid Metabolism during Vaccinia Virus Infection

The functions of ISG15 are continuously expanding, and growing evidence supports its role as a relevant modulator of cell metabolism. In this work, we highlight how the absence of ISG15 impacts macrophage lipid metabolism in the context of viral infections and how poxviruses modulate metabolism to ensure successful replication. Our results open the door to new advances in the comprehension of macrophage immunometabolism and the interaction between VACV and the host. ABSTRACT Interferon-stimulated gene 15 (ISG15) is a 15-kDa ubiquitin-like modifier that binds to target proteins in a process termed ISGylation. ISG15, first described as an antiviral molecule against many viruses, participates in numerous cellular processes, from immune modulation to the regulation of genome stability. Interestingly, the role of ISG15 as a regulator of cell metabolism has recently gained strength. We previously described ISG15 as a regulator of mitochondrial functions in bone marrow-derived macrophages (BMDMs) in the context of Vaccinia virus (VACV) infection. Here, we demonstrate that ISG15 regulates lipid metabolism in BMDMs and that ISG15 is necessary to modulate the impact of VACV infection on lipid metabolism. We show that Isg15−/− BMDMs demonstrate alterations in the levels of several key proteins of lipid metabolism that result in differences in the lipid profile compared with Isg15+/+ (wild-type [WT]) BMDMs. Specifically, Isg15−/− BMDMs present reduced levels of neutral lipids, reflected by decreased lipid droplet number. These alterations are linked to increased levels of lipases and are independent of enhanced fatty acid oxidation (FAO). Moreover, we demonstrate that VACV causes a dysregulation in the proteomes of BMDMs and alterations in the lipid content of these cells, which appear exacerbated in Isg15−/− BMDMs. Such metabolic changes are likely caused by increased expression of the metabolic regulators peroxisome proliferator-activated receptor-γ (PPARγ) and PPARγ coactivator-1α (PGC-1α). In summary, our results highlight that ISG15 controls BMDM lipid metabolism during viral infections, suggesting that ISG15 is an important host factor to restrain VACV impact on cell metabolism. IMPORTANCE The functions of ISG15 are continuously expanding, and growing evidence supports its role as a relevant modulator of cell metabolism. In this work, we highlight how the absence of ISG15 impacts macrophage lipid metabolism in the context of viral infections and how poxviruses modulate metabolism to ensure successful replication. Our results open the door to new advances in the comprehension of macrophage immunometabolism and the interaction between VACV and the host.
Neural differentiation protocols: how to choose the correct approach

Pluripotent stem cells in neural differentiation: characterization and potential: The establishment and use of pluripotent stem cells (PSCs), including embryonic (ESCs) and induced (iPSCs), constitutes a major scientific breakthrough of the last decades. Human PSCs hold the potential to deliver regenerative therapies in many diseases, including neurological ones. The general approach is to produce functioning human neurons and glial cells in vitro, to be later implanted in the diseased nervous system, replacing dysfunctional or dead cells. In addition, human and other animal-sourced PSCs make useful and dynamic in vitro models for neurodevelopmental, neurodegenerative and psychiatric disorders, enabling researchers to continuously produce normal and diseased neurons to investigate basic mechanistic questions, which can eventually lead to new therapeutics. Therefore, the development of efficient protocols to induce neural differentiation in ESCs and iPSCs is currently a major effort in the field (Mertens et al., 2016).
BTB domains: A structural view of evolution, multimerization, and protein–protein interactions

Broad‐complex, Tramtrack, and Bric‐à‐brac/poxvirus and zinc finger (BTB/POZ) is a conserved domain found in many eukaryotic proteins with diverse cellular functions. Recent studies revealed its importance in multiple developmental processes as well as in the onset and progression of oncological diseases. Most BTB domains can form multimers and selectively interact with non‐BTB proteins. Structural studies of BTB domains delineated the presence of different interfaces involved in various interactions mediated by BTBs and provided a basis for the specific inhibition of distinct protein‐interaction interfaces. BTB domains originated early in eukaryotic evolution and progressively adapted their structural elements to perform distinct functions. In this review, we summarize and discuss the structural principles of protein‐protein interactions mediated by BTB domains based on the recently published structural data and advances in protein modeling. We propose an update to the structure‐based classification of BTB domain families and discuss their evolutionary interconnections.
Molecular insights of 2,6‐dichlorobenzoquinone‐induced cytotoxicity in zebrafish embryo: Activation of ROS‐mediated cell cycle arrest and apoptosis

2,6‐dichloro‐1,4‐benzoquinone (2,6‐DCBQ), as an emerging disinfection by‐product, has been frequently detected in waters, posing potential health risk on public health. Although some studies have pointed out that 2,6‐DCBQ exposure can induce cytotoxicity, limited information is available for underlying mechanism for 2,6‐DCBQ‐induced cytotoxicity. To explore this mechanism, we assessed the levels of reactive oxygen species (ROS), acridine orange (AO) staining, and the mRNA transcriptions of genes (Chk2, Cdk2, Ccna, Ccnb and Ccne) involved in cell‐cycle and genes (p53, bax, bcl‐2 and caspase 3) involved in apoptosis in zebrafish embryo, after exposed to different concentrations (10, 30, 60, 90 and 120 μg/L) of 2,6‐DCBQ for 72 h. Our results indicated that 2,6‐DCBQ exposure induced ROS generation and cell apoptosis, and disturbed the mRNA transcription of genes related to cell cycle and apoptosis in zebrafish embryo. Moreover, we also found that 30 ~ 60 μg/L 2,6‐DCBQ is the important transition from cell‐cycle arrest to cell apoptosis. These results provided novel insight into 2,6‐DCBQ‐induced cytotoxicity.
Disturbed Sleep is Not Good for the Heart: A Narrative Review

Sleep-related breathing disorders, including obstructive sleep apnea (OSA) and central sleep apnea (CSA), have a major impact on cardiovascular function. It has shown an association with hypertension, coronary artery disease, cardiac arrhythmias, sudden cardiac death, and congestive heart failure (CHF). This review focuses on highlighting the relationship between sleep apnea and CHF. We discuss the underlying pathophysiology, which involves the mechanical, neurohormonal, and inflammatory mechanisms; in addition, the similarities and differentiating clinical features of OSA in patients with CHF and without CHF. We have also discussed several treatment strategies, including weight loss, continuous positive airway pressure (CPAP), supplemental oxygen therapy, theophylline, acetazolamide, mandibular advancement device, and hypoglossal nerve stimulation (HGNS). We conclude that since there are several overlapping clinical features in patients with OSA with Heart Failure (HF) and without HF, early detection and treatment are crucial to decrease the risk of HF, coronary artery disease, and stroke.
Technical approaches and challenges to study AMPA receptors in oligodendrocyte lineage cells: Past, present, and future

Receptors for α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid (AMPARs) are ligand‐gated ionotropic receptors for glutamate that is a major excitatory neurotransmitter in the central nervous system. AMPARs are located at postsynaptic sites of neuronal synapses where they mediate fast synaptic signaling and synaptic plasticity. Remarkably, AMPARs are also expressed by glial cells. Their expression by the oligodendrocyte (OL) lineage cells is of special interest because AMPARs mediate fast synaptic communication between neurons and oligodendrocyte progenitor cells (OPCs), modulate proliferation and differentiation of OPCs, and may also be involved in regulation of myelination. On the other hand, during pathological conditions, AMPARs may mediate damage of the OL lineage cells. In the present review, we focus on the technical approaches that have been used to study AMPARs in the OL lineage cells, and discuss future perspectives of AMPAR research in these glial cells.
A Paul trap configuration to simulate intense non-neutral beam propagation over large distances through a periodic focusing quadrupole magnetic field

This paper considers an intense non-neutral charged particle beam propagating in the z-direction through a periodic focusing quadrupole magnetic field with transverse focusing force, −κq(s)[xex−yey], on the beam particles. Here, s=βbct is the axial coordinate, (γb−1)mbc2 is the directed axial kinetic energy of the beam particles, qb and mb are the charge and rest mass, respectively, of a beam particle, and the oscillatory lattice coefficient satisfies κq(s+S)=κq(s), where S is the axial periodicity length of the focusing field. The particle motion in the beam frame is assumed to be nonrelativistic, and the Vlasov-Maxwell equations are employed to describe the nonlinear evolution of the distribution function fb(x,y,x′,y′,s) and the (normalized) self-field potential ψ(x,y,s)=qbφ(x,y,s)/γb3mbβb2c2 in the transverse laboratory-frame phase space (x,y,x′,y′), assuming a thin beam with characteristic radius rb≪S. It is shown that collective processes and the nonlinear transverse beam dynamics can be simulated in a compact Paul trap configuration in which a long non-neutral plasma column (L≫rp) is confined axially by applied dc voltages V=const on end cylinders at z=±L, and transverse confinement in the x−y plane is provided by segmented cylindrical electrodes (at radius rw) with applied oscillatory voltages ±V0(t) over 90° segments. Here, V0(t+T)=V0(t), where T=const is the oscillation period, and the oscillatory quadrupole focusing force on a particle with charge q and mass m near the cylinder axis is −mκq(t)[xex−yey], where κq(t)≡8qV0(t)/πmrw2. This paper considers an intense non-neutral charged particle beam propagating in the z-direction through a periodic focusing quadrupole magnetic field with transverse focusing force, −κq(s)[xex−yey], on the beam particles. Here, s=βbct is the axial coordinate, (γb−1)mbc2 is the directed axial kinetic energy of the beam particles, qb and mb are the charge and rest mass, respectively, of a beam particle, and the oscillatory lattice coefficient satisfies κq(s+S)=κq(s), where S is the axial periodicity length of the focusing field. The particle motion in the beam frame is assumed to be nonrelativistic, and the Vlasov-Maxwell equations are employed to describe the nonlinear evolution of the distribution function fb(x,y,x′,y′,s) and the (normalized) self-field potential ψ(x,y,s)=qbφ(x,y,s)/γb3mbβb2c2 in the transverse laboratory-frame phase space (x,y,x′,y′), assuming a thin beam with characteristic radius rb≪S. It is shown that collective processes and the nonlinear transverse beam dynamics can be simulated .
Using natural killer cell‐derived exosomes as a cell‐free therapy for leukemia

Natural killer (NK) cells are components of the innate immune system which play a pivotal role in cancer cell surveillance. Despite promising results in clinical trials, the use of NK‐based therapies is limited due to unsatisfactory efficiencies and safety issues. In recent years, exosomes have emerged as a powerful, natural therapeutic tool. Since exosomes are known to carry cargos that reflect the cellular makeup of their cell of origin, we were prompted to test whether NK‐derived exosomes (NKexo) maintain the anti‐leukemia capacity of NK‐cells. We found NK92MI‐cells to secrete large amounts of 100–200 nm cap‐shaped particles expressing exosomal and NK biomarkers (CD63, CD81, CD56). We demonstrated that NKexo exert a potent, selective, anti‐leukemia effect on all leukemia cell‐lines tested. Furthermore, NKexo eliminated leukemia cells isolated from patients with acute and chronic leukemia and inhibited hematopoietic colony growth. While leukemia cells were targeted and severely affected by NKexo, healthy B‐cells remained unaffected, indicating a selective effect. This selectivity was further confirmed by demonstrating that NKexo were specifically taken up by leukemic cells but not by healthy B‐cells. Our in vivo data support our in vitro and ex vivo findings and demonstrate improved human‐CD45+ leukemia blast counts and overall survival in NKexo treated humanized acute myeloid leukemia (HL‐60) xenograft mice thus supporting the assumption that NKexo possess an anti‐leukemia effect. Pending further analyses, our findings provide the pre‐clinical evidence needed to test the NKexo approach in future pre‐clinical and clinical studies to ultimately develop an acellular “off‐the‐shelf” product to treat leukemia.
Effective doses for common paediatric diagnostic general radiography examinations at a major Australian paediatric hospital and the communication of associated radiation risks

Health professionals in paediatric medical imaging are routinely required to communicate radiation risks to carers and patients. Effective dose alone cannot be used to specify and communicate the radiation risk for an individual as risks are dependent on many factors including age and patient sex. In this study, we estimated typical effective doses for 20 commonly performed paediatric general radiography examinations using the weight‐based imaging protocols employed at a major Australian specialist paediatric hospital. Effective doses were used to estimate and categorise associated age‐based stochastic risks with commonly used risk terminology to facilitate communication of risk.
The Phylogenetic Limits to Diversity-Dependent Diversification

Abstract While the theory of micro-evolution by natural selection assigns a crucial role to competition, its role in macroevolution is less clear. Phylogenetic evidence for a decelerating accumulation of lineages suggests a feedback of lineage diversity on diversification. However, does this feedback only occur between close relatives, or do distant relatives also influence each other’s diversification? In other words: are there phylogenetic limits to this diversity-dependence? Islands form ideal systems to answer these questions because their boundedness facilitates an overview of all potential competitors. The DAISIE (Dynamic Assembly of Island biota through Speciation Immigration and Extinction) framework allows for testing the presence of diversity-dependence on islands given phylogenetic data on colonization and branching times. The current inference models in DAISIE assume that this diversity-dependence only applies within a colonizing clade, i.e., all mainland species can colonize and diversify independently from one another. We term this clade-specific (CS) diversity-dependence. Here we introduce a new DAISIE model that assumes that diversity-dependence applies to all island species of a taxonomic group regardless of their mainland ancestry, i.e., diversity-dependence applies both to species within the same clade and between different clades established by different mainland species. We call this island-wide (IW) diversity-dependence. We present a method to compute a likelihood for this model given phylogenetic data on colonization and branching events and use likelihood ratio bootstrapping to compare it to the likelihood of the CS model in order to overcome biases known for standard model selection. We apply it to the diversification of Eleutherodactylus frogs on Hispaniola. Across the Greater Antilles archipelago, this radiation shows repeated patterns of diversification in ecotypes that are similar across clades. This could be suggestive of overlapping niche space and hence between-clade interactions, i.e., IW diversity-dependence. But it could also be suggestive of only within-clade interactions because between-clade interactions would have blocked the same ecotype from re-appearing. We find that the CS model fits the data much better than the IW model, indicating that different colonizations while resulting in similar ecotypes, are sufficiently distinct to avoid interacting strongly. We argue that non-overlapping distributions between clades (both spatially and in terms of ecotypes) cannot be used as evidence of CS diversity-dependence, because this pattern may be a consequence of IW diversity-dependence. By contrast, by using phylogenetic data rather than distributional data our method does allow for inferring the phylogenetic limits to diversity-dependent diversification. We discuss possibilities for future extensions and applications of our modelling approach. [Adaptive radiation; birth-death model; Caribbean; diversity-dependence; Eleutherodactylus; island biogeography. ]
Two Cases of Familial Mediterranean Fever Involving MEFV Variants: The Importance of Differentiating the Diagnosis from COVID-19

Familial Mediterranean fever (FMF) is an inherited autoinflammatory disease associated with the MEFV gene. FMF is common in Mediterranean peoples but not highly recognized in Japan. We herein report two cases of Japanese FMF patients who were diagnosed by genetic testing for the MEFV gene during the coronavirus disease 2019 (COVID-19) pandemic. Both patients presented with symptoms similar to COVID-19, which delayed the definitive diagnosis. Patients with a confirmed diagnosis of FMF may be eligible for physical, emotional, and financial benefits. Therefore, the COVID-19 pandemic highlights the importance of differentiating the diagnosis by genetic testing.
Deciphering RNA G-quadruplex function during the early steps of HIV-1 infection

Abstract G-quadruplexes (G4s) are four-stranded nucleic acid structures formed by the stacking of G-tetrads. Here we investigated their formation and function during HIV-1 infection. Using bioinformatics and biophysics analyses we first searched for evolutionary conserved G4-forming sequences in HIV-1 genome. We identified 10 G4s with conservation rates higher than those of HIV-1 regulatory sequences such as RRE and TAR. We then used porphyrin-based G4-binders to probe the formation of the G4s during infection of human cells by native HIV-1. The G4-binders efficiently inhibited HIV-1 infectivity, which is attributed to the formation of G4 structures during HIV-1 replication. Using a qRT-PCR approach, we showed that the formation of viral G4s occurs during the first 2 h post-infection and their stabilization by the G4-binders prevents initiation of reverse transcription. We also used a G4-RNA pull-down approach, based on a G4-specific biotinylated probe, to allow the direct detection and identification of viral G4-RNA in infected cells. Most of the detected G4-RNAs contain crucial regulatory elements such as the PPT and cPPT sequences as well as the U3 region. Hence, these G4s would function in the early stages of infection when the viral RNA genome is being processed for the reverse transcription step.
An attention-based recurrent learning model for short-term travel time prediction

With the advent of Big Data technology and the Internet of Things, Intelligent Transportation Systems (ITS) have become inevitable for future transportation networks. Travel time prediction (TTP) is an essential part of ITS and plays a pivotal role in congestion avoidance and route planning. The novel data sources such as smartphones and in-vehicle navigation applications allow traffic conditions in smart cities to be analyzed and forecast more reliably than ever. Such a massive amount of geospatial data provides a rich source of information for TTP. Gated Recurrent Unit (GRU) has been successfully applied to traffic prediction problems due to its ability to handle long-term traffic sequences. However, the existing GRU does not consider the relationship between various historical travel time positions in the sequences for traffic prediction. We propose an attention-based GRU model for short-term travel time prediction to cope with this problem enabling GRU to learn the relevant context in historical travel time sequences and update the weights of hidden states accordingly. We evaluated the proposed model using FCD data from Beijing. To demonstrate the generalization of our proposed model, we performed a robustness analysis by adding noise obeying Gaussian distribution. The experimental results on test data indicated that our proposed model performed better than the existing deep learning time-series models in terms of Root Mean Square Error (RMSE), Mean Absolute Error (MAE), Mean Absolute Percentage Error (MAPE), and Coefficient of Determination (R2).