Miracle-dz/UniFAR-FTUs huggingface dataset:
An Amino Acid Polymorphism within the HIV-1 Nef Dileucine Motif Functionally Uncouples Cell Surface CD4 and SERINC5 Downregulation

A contributing factor to HIV-1 persistence is evasion of the host immune response. HIV-1 uses the Nef accessory protein to evade the antiviral roles of the adaptive and intrinsic innate immune responses. ABSTRACT Serine incorporator 5 (SERINC5) reduces the infectivity of progeny HIV-1 virions by incorporating into the outer host-derived viral membrane during egress. To counter SERINC5, the HIV-1 accessory protein Nef triggers SERINC5 internalization by engaging the adaptor protein 2 (AP-2) complex using the [D/E]xxxL[L/I]167 Nef dileucine motif. Nef also engages AP-2 via its dileucine motif to downregulate the CD4 receptor. Although these two Nef functions are related, the mechanisms governing SERINC5 downregulation are incompletely understood. Here, we demonstrate that two primary Nef isolates, referred to as 2410 and 2391 Nef, acquired from acutely HIV-1 infected women from Zimbabwe, both downregulate CD4 from the cell surface. However, only 2410 Nef retains the ability to downregulate cell surface SERINC5. Using a series of Nef chimeras, we mapped the region of 2391 Nef responsible for the functional uncoupling of these two antagonistic pathways to the dileucine motif. Modifications of the first and second x positions of the 2410 Nef dileucine motif to asparagine and aspartic acid residues, respectively (ND164), impaired cell surface SERINC5 downregulation, which resulted in reduced infectious virus yield in the presence of SERINC5. The ND164 mutation additionally partially impaired, but did not completely abrogate, Nef-mediated cell surface CD4 downregulation. Furthermore, the patient infected with HIV-1 encoding 2391 Nef had stable CD4+ T cell counts, whereas infection with HIV-1 encoding 2410 Nef resulted in CD4+ T cell decline and disease progression. IMPORTANCE A contributing factor to HIV-1 persistence is evasion of the host immune response. HIV-1 uses the Nef accessory protein to evade the antiviral roles of the adaptive and intrinsic innate immune responses. Nef targets SERINC5, a restriction factor which potently impairs HIV-1 infection by triggering SERINC5 removal from the cell surface. The molecular determinants underlying this Nef function remain incompletely understood. Recent studies have found a correlation between the extent of Nef-mediated SERINC5 downregulation and the rate of disease progression. Furthermore, single-residue polymorphisms outside the known Nef functional motifs can modulate SERINC5 downregulation. The identification of a naturally occurring Nef polymorphism impairing SERINC5 downregulation in this study supports a link between Nef downregulation of SERINC5 and the rate of plasma CD4+ T cell decline. Moreover, the observed functional impairments of this polymorphism could provide clues to further elucidate unknown aspects of the SERINC5 antagonistic pathway via Nef.
Thymoquinone-entrapped chitosan-modified nanoparticles: formulation optimization to preclinical bioavailability assessments

Abstract The major limitation with the oral administration of most of the phytochemicals is their low aqueous solubility and bioavailability. Thymoquinone (THQ) is one of the most widely used phytochemicals used to treat a variety of diseases. However, strong lipophilic characteristics limit its clinical application. Therefore, this study was aimed to design novel chitosan (C) modified polycaprolactone (PL) nanoparticles (NPs) for improved oral bioavailability of THQ. THQ-CPLNPs was optimized 33-Box–Behnken design. After that, the optimized THQ-CPLNPs was characterized by different parameters. THQ-CPLNPs showed the size, PDI, and ZP of 182.32 ± 6.46 nm, 0.179 ± 0.012, and +21.36 ± 1.22 mV, respectively. The entrapment and loading capacity were found to be 79.86 ± 4.36%, and 13.45 ± 1.38%, respectively. THQ-CPLNPs exhibited burst release in initial 2 h followed by prolonged release up to 24 h in simulated intestinal fluids. THQ-CPLNPs showed excellent mucoadhesion properties which were further confirmed with the intestinal permeation study as well as confocal microscopy. The study revealed higher permeation of THQ-CPLNPs compared to neat THQ suspension (THQ-S). Moreover, in vivo gastric irritation study revealed good compatibility of THQ-CPLNPs with the gastric mucosa. Furthermore, pharmacokinetic results depicted ∼3.53-fold improved oral bioavailability of THQ from THQ-CPLNPs than THQ-S. Therefore, from the findings, it was concluded that the prepared polymeric NPs could be an effective delivery system for improved oral bioavailability of THQ.
“Medical treatments are also part of God’s gift”: Holy water attendants’ perspectives on a collaboration between spiritual and psychiatric treatment for mental illness in Ethiopia

In Ethiopia, traditional and spiritual treatments, such as holy water, are used by people with mental disorders instead of, or alongside, psychiatric services. Collaborations between traditional and psychiatric providers may increase access to evidence-based treatments and address human rights abuses. This study aimed to explore the perspectives of holy water attendants on a novel collaboration between holy water and psychiatric care, at St Mary’s Clinic, Entoto, Ethiopia, and to characterize the users of this service. Semi-structured interviews were conducted with 14 holy water attendants, who run group houses for holy water residents and are paid by family members. A thematic analysis was conducted. Socio-demographic and clinical data were extracted from the records of all service users who had attended the clinic. A total of 174 individuals have attended the clinic in the three years since it opened. The majority were diagnosed with schizophrenia. Holy water attendants provide a partial gatekeeping role to psychiatric care, selecting which of their clients they think will benefit and, for these individuals, facilitating attendance to the clinic and antipsychotic medication adherence. Psychiatric care was felt to be compatible with holy water by some, but not all, attendants. However, family members often had the “final say” in individuals attending the clinic, in some cases putting up strong resistance to using psychiatric care. A novel collaboration is acceptable to some holy water attendants and may increase access to psychiatric care amongst people with mental illness living at a holy water site in Ethiopia.
In vitro assembly of nuclear envelope in tobacco cultured cells

ABSTRACT The coordinated regulation of the nucelar envelope (NE) reassembly during cell division is an essential event. However, there is little information on the molecular components involved in NE assembly in plant cells. Here we developed an in vitro assay of NE assembly using tobacco BY-2 cultured cells. To start the NE assembly reaction, the demembranated nuclei and the S12 fraction (cytosol and microsomes) were mixed in the presence of GTP and ATP nucleotides. Time–course analysis indicated that tubule structures were extended from the microsomal vesicles that accumulated on the demembranated nuclei, and finally sealed the NE. Immunofluorescence confirmed that the assembled membrane contains a component of nuclear pore complex. The efficiency of the NE assembly is significantly inhibited by GTPγS that suppresses membrane fusion. This in-vitro assay system may elucidate the role of specific proteins and provide important insights into the molecular machinery of NE assembly in plant cells.
Mitochondria transfer from early stages of erythroblasts to their macrophage niche via tunnelling nanotubes

Adult erythropoiesis entails a series of well‐coordinated events that produce mature red blood cells. One of such events is the mitochondria clearance that occurs cell‐autonomously via autophagy‐dependent mechanisms. Interestingly, recent studies have shown mitochondria transfer activities between various cell types. In the context of erythropoiesis, macrophages are known to interact closely with the early stages of erythroblasts to provide a specialized niche, termed erythroblastic islands (EBI). However, whether mitochondria transfer can occur in the EBI niche has not been explored. Here, we report that mitochondria transfer in the EBI niche occurs in vivo. We observed mitochondria transfer activities from the early stages of erythroblasts to macrophages in the reconstituted in vitro murine EBI via different modes, including tunnelling nanotubes (TNT). Moreover, we demonstrated that Wiskott‐Aldrich syndrome protein (WASp) in macrophages mediates TNT formation and mitochondria transfer via the modulation of F‐actin filamentation, thus promoting mitochondria clearance from erythroid cells, to potentially enhance their differentiation. Taken together, our findings provide novel insight into the mitochondria clearance machineries that mediate erythroid maturation.
3D bioprinting and microscale organization of vascularized tissue constructs using collagen‐based bioink

Bioprinting three‐dimensional (3D) tissue equivalents have progressed tremendously over the last decade. 3D bioprinting is currently being employed to develop larger and more physiologic tissues, and it is of particular interest to generate vasculature in biofabricated tissues to aid better perfusion and transport of nutrition. Having an advantage over manual culture systems by bringing together biological scaffold materials and cells in precise 3D spatial orientation, bioprinting could assist in placing endothelial cells in specific spatial locations within a 3D matrix to promote vessel formation at these predefined areas. Hence, in the present study, we investigated the use of bioprinting to generate tissue‐level capillary‐like networks in biofabricated tissue constructs. First, we developed a bioink using collagen type‐1 supplemented with xanthan gum (XG) as a thickening agent. Using a commercial extrusion‐based multi‐head bioprinter and collagen‐XG bioink, the component cells were spatially assembled, wherein the endothelial cells were bioprinted in a lattice pattern and sandwiched between bioprinted fibroblasts layers. 3D bioprinted constructs thus generated were stable, and maintained structural shape and form. Post‐print culture of the bioprinted tissues resulted in endothelial sprouting and formation of interconnected capillary‐like networks within the lattice pattern and between the fibroblast layers. Bioprinter‐assisted spatial placement of endothelial cells resulted in fabrication of patterned prevascularized constructs that enable potential regenerative applications in the future.
DISTRIBUTION OF HEAVY METALS IN NATUNA COASTAL WATERS

ABSTRACTThe study of Pb, Cd, Cu, Hg, and As and Fe in Natuna coastal waters, Riau Islands was conducted in November 2012. Water and sediment samples were collected from 35 stations by purposive sampling method and those heavy metals were analysed using Atomic Absorption Spectrophotometer, flame type (FAAS). The results showed that concentrations of total Pb, Cd, Cu, Hg, and As in surface water were below instrument detection limit (2 µg/L for Pb, Cd, and Cu; 0.02 µg/L for Hg and As). Moreover, the concentration of metal Fe in surface water was 0.021-0.054 mg/L. Concentrations of Pb and Cu in sediment were 0.05-22.67 mg/kg and 3.77-11.00 mg/kg, respectively, at which the highest concentrations were found near Binjai Estuary. Those concentrations were significantly below the standard levels set by CCME (2002) and ANZECC/ARMCANZ (2000). Concentration of Fe in sediment varied from 751.13-2309.12 mg/kg and showed similar spatial distribution to Cu-in-sediment. No standard level for Fe in waters was available. Generally, it can be concluded that Natuna coastal water was still uncontaminated. Keywords: heavy metals, iron metal, Natuna coastal waters.
Efficient and Rapid Divergent Synthesis of Ethylene Oxide-Containing Dendrimers through Catalyst-Free Click Chemistry

Third and fourth generation ethylene oxide-containing dendrimers containing triazole units were prepared divergently through metal-free Huisgen 1,3-dipolar cycloaddition (“click”) reaction between activated disubstituted alkyne and terminal azide groups. The growth of the dendrimers was achieved in high yield with minimal purification effort and without the participation of toxic metal or excess of reagents. Preliminary in vitro testing on different cell lines indicates that this series of dendrimers is very promising for bio-related applications.
Phospho‐regulation, nucleotide binding and ion access control in potassium‐chloride cotransporters

Potassium‐coupled chloride transporters (KCCs) play crucial roles in regulating cell volume and intracellular chloride concentration. They are characteristically inhibited under isotonic conditions via phospho‐regulatory sites located within the cytoplasmic termini. Decreased inhibitory phosphorylation in response to hypotonic cell swelling stimulates transport activity, and dysfunction of this regulatory process has been associated with various human diseases. Here, we present cryo‐EM structures of human KCC3b and KCC1, revealing structural determinants for phospho‐regulation in both N‐ and C‐termini. We show that phospho‐mimetic KCC3b is arrested in an inward‐facing state in which intracellular ion access is blocked by extensive contacts with the N‐terminus. In another mutant with increased isotonic transport activity, KCC1Δ19, this interdomain interaction is absent, likely due to a unique phospho‐regulatory site in the KCC1 N‐terminus. Furthermore, we map additional phosphorylation sites as well as a previously unknown ATP/ADP‐binding pocket in the large C‐terminal domain and show enhanced thermal stabilization of other CCCs by adenine nucleotides. These findings provide fundamentally new insights into the complex regulation of KCCs and may unlock innovative strategies for drug development.
Discrepancies Between Beliefs and Practices on Sleep as a Factor of Insomnia and Negative Feelings

Two online surveys were conducted in Japan to develop and validate the Sleep Belief-Practice Index (SBPI) scales, a pair of new scales designed to measure beliefs (SBPI-B) and practices (SBPI-P) on sleep and its environment. Their discrepancies (SBPI-D) were calculated as differences between SBPI-B and -P. In Survey 1 (N = 400), survey data of the pilot version of the scales were entered into an exploratory factor analysis to obtain a meaningful set of scale items. In Survey 2 (N = 2952), survey data were entered into a confirmatory factor analysis and then correlation analyses to confirm associations of SBPI-D with insomnia and positive and negative feelings. Furthermore, participants were categorized into four groups according to the degree and combination of sleep beliefs and practices to compare the status of insomnia and positive and negative feelings by the groups. As a result of factor analyses, we obtained 13 common item scales of SBPI-B and -P. SBPI-D was positively correlated with insomnia and negative feelings. In addition, the group with high-scoring beliefs in SBPI-B and low-scoring practices in SBPI-P showed the most severe insomnia and negative feelings among the four groups. These results suggest that the belief-practice discrepancy about sleep can explain one aspect of insomnia.
Evaluation of candidate template beam models for a matched TrueBeam treatment delivery system

Abstract Purpose To explore candidate RayStation beam models to serve as a class‐specific template for a TrueBeam treatment delivery system. Methods Established validation techniques were used to evaluate three photon beam models: a clinically optimized model from the authors’ institution, the built‐in RayStation template, and a hybrid consisting of the RayStation template except substituting average MLC parameter values from a recent IROC survey. Comparisons were made for output factors, dose profiles from open fields, as well as representative VMAT test plans. Results For jaw‐defined output factors, each beam model was within 1.6% of expected published values. Similarly, the majority (57–66%) of jaw‐defined dose curves from each model had a gamma pass rate >95% (2% / 3 mm, 20% threshold) when compared to TrueBeam representative beam data. For dose curves from MPPG 5.a MLC‐defined fields, average gamma pass rates (1% / 1 mm, 20% threshold) were 92.9%, 85.1%, and 86.0% for the clinical, template, and hybrid models, respectively. For VMAT test plans measured with a diode array detector, median dose differences were 0.6%, 1.3%, and 1.1% for the clinical, template, and hybrid models, respectively. For in‐phantom ionization chamber measurements with the same VMAT test plans, the average percent difference was −0.3%, −1.4%, and −1.0% for the clinical, template, and hybrid models, respectively. Conclusion Beam model templates taken from the vendor and aggregate results within the community were both reasonable starting points, but neither approach was as optimal as a clinically tuned model, the latter producing better agreement with all validation measurements. Given these results, the clinically optimized model represents a better candidate as a consensus template. This can benefit the community by reducing commissioning time and improving dose calculation accuracy for matched TrueBeam treatment delivery systems.
Clinical MR imaging in Parkinson’s disease: How useful is the swallow tail sign?

With conventional MRI, no Parkinson's disease (PD)‐specific abnormalities can be detected. However, there is a critical need for accompanying neuroimaging markers to guide the diagnosis. With high‐resolution susceptibility‐weighted MRI (SWI) sequences, the imaging of nigrosome‐1 (N1) is possible. The so‐called swallow tail sign (STS) has been proposed as a suitable neuroimaging marker for the diagnosis of PD.
An 8-gene DNA methylation signature predicts the recurrence risk of cervical cancer

Objective This study examined the predictive utility of DNA methylation for cervical cancer recurrence. Methods DNA methylation and RNA expression data for patients with cervical cancer were downloaded from The Cancer Genome Atlas. Differentially methylated genes (DMGs) and differentially expressed genes were screened and extracted via correlation analysis. A support vector machine (SVM)-based recurrence prediction model was established using the selected DMGs. Cox regression analysis and receiver operating characteristic curve analysis were used for self-evaluation. The Gene Expression Omnibus (GEO) database was applied for external validation. Functional enrichment was determined using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. Results An eight-gene DNA methylation signature identified patients with a high risk of recurrence (area under the curve = 0.833). The SVM score was an independent risk factor for recurrence (hazard ratio [HR] = 0.418; 95% confidence interval [CI] = 0.26–0.67). The independent GEO database analysis further supported the result. Conclusion An eight-gene DNA methylation signature predictive of cervical cancer recurrence was identified in this study, and this signature may help identify patients at high risk of recurrence and improve clinical treatment.
Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

ABSTRACT New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies’ composition varies with time during the early onset of symptoms, which implicates viral evolution during infection. Network analysis of co-occurring SNPs revealed the most abundant non-synonymous SNP 22,638 in the S glycoprotein RBD region and 28,144 in the ORF8 region. Furthermore, SARS-CoV-2 variations differ in an individual’s respiratory tissue (nose, throat, BALF, or sputum), suggesting independent compartmentalization of SARS-CoV-2 populations in patients. The positive selection analysis of the SARS-CoV-2 genome uncovered the positive selected amino acid G251V on ORF3a. Alternative allele frequency spectrum (AAFS) of all variants revealed that ORF8 could bear alternate alleles with high frequency. Overall, the results show the quasispecies’ profile of SARS-CoV-2 in the respiratory tract in the first two months after the outbreak.
Cocaine Augments Dopamine-Mediated Inhibition of Neuronal Activity in the Dorsal Bed Nucleus of the Stria Terminalis

The dorsal region of the bed nucleus of the stria terminalis (dBNST) receives substantial dopaminergic input which overlaps with norepinephrine input implicated in stress responses. Using ex vivo fast scan cyclic voltammetry in male C57BL6 mouse brain slices, we demonstrate that electrically stimulated dBNST catecholamine signals are of substantially lower magnitude and have slower uptake rates compared with caudate signals. Dopamine terminal autoreceptor activation inhibited roughly half of the catecholamine transient, and noradrenergic autoreceptor activation produced an ∼30% inhibition. Dopamine transporter blockade with either cocaine or GBR12909 significantly augmented catecholamine signal duration. We optogenetically targeted dopamine terminals in the dBNST of transgenic (TH:Cre) mice of either sex and, using ex vivo whole-cell electrophysiology, we demonstrate that optically stimulated dopamine release induces slow outward membrane currents and an associated hyperpolarization response in a subset of dBNST neurons. These cellular responses had a similar temporal profile to dopamine release, were significantly reduced by the D2/D3 receptor antagonist raclopride, and were potentiated by cocaine. Using in vivo fiber photometry in male C57BL/6 mice during training sessions for cocaine conditioned place preference, we show that acute cocaine administration results in a significant inhibition of calcium transient activity in dBNST neurons compared with saline administration. These data provide evidence for a mechanism of dopamine-mediated cellular inhibition in the dBNST and demonstrate that cocaine augments this inhibition while also decreasing net activity in the dBNST in a drug reinforcement paradigm. SIGNIFICANCE STATEMENT The dorsal bed nucleus of the stria terminalis (dBNST) is a region highly implicated in mediating stress responses; however, the dBNST also receives dopaminergic inputs from classically defined drug reward pathways. Here we used various techniques to demonstrate that dopamine signaling within the dBNST region has inhibitory effects on population activity. We show that cocaine, an abused psychostimulant, augments both catecholamine release and dopamine-mediated cellular inhibition in this region. We also demonstrate that cocaine administration reduces population activity in the dBNST, in vivo. Together, these data support a mechanism of dopamine-mediated inhibition within the dBNST, providing a means by which drug-induced elevations in dopamine signaling may inhibit dBNST activity to promote drug reward.