Miracle-dz/UniFAR-FTUs huggingface dataset:
The CXCR4-Tropic Human Immunodeficiency Virus Envelope Promotes More-Efficient Gene Delivery to Resting CD4+ T Cells than the Vesicular Stomatitis Virus Glycoprotein G Envelope

ABSTRACT Current gene transfer protocols for resting CD4+ T cells include an activation step to enhance transduction efficiency. This step is performed because it is thought that resting cells are resistant to transduction by lentiviral-based gene therapy vectors. However, activating resting cells prior to transduction alters their physiology, with foreseeable and unforeseeable negative consequences. Thus, it would be desirable to transduce resting CD4+ T cells without activation. We recently demonstrated, contrary to the prevailing belief, that wild-type human immunodeficiency virus (HIV) integrates into resting CD4+ T cells. Based on that finding, we investigated whether a commonly used, vesicular stomatitis virus glycoprotein G (VSV-G)-pseudotyped lentiviral gene therapy vector could also integrate into resting CD4+ T cells. To investigate this, we inoculated resting CD4+ T cells with lentiviral particles that were pseudotyped with VSV-G or CXCR4-tropic HIV Env and assayed binding, fusion, reverse transcription, and integration. We found that the VSV-G-pseudotyped lentiviral vector failed to fuse to resting CD4+ T cells while HIV Env-pseudotyped lentiviral vectors fused, reverse transcribed, and integrated in resting cells. Our findings suggest that HIV Env could be used effectively for the delivery of therapeutic genes to resting CD4+ T cells and suggest that fusion may be the critical step restricting transduction of resting CD4+ T cells by lentiviral gene therapy vectors.
Covariation of Major and Minor Viral Capsid Proteins in Norovirus Genogroup II Genotype 4 Strains

ABSTRACT We report sequence hypervariability in the viral protein 1 (VP1) interaction domain of VP2 in the norovirus (NoV) genogroup II genotype 4 (GII.4) lineage on 3 levels: (i) the global evolution of pandemic/epidemic strains from the mid-1970s through post-2006, (ii) the local emergence of an epidemic strain, and (iii) an immunocompromised patient chronically shedding NoV. When a quantitative yeast two-hybrid assay was used, VP2 was found to interact with VP1 in a time-ordered, strain-dependent manner among 3 NoV GII.4 strains. Our findings suggest that VP1 and VP2 may covary in virus evolution and that sequence hypervariability of VP2 may be functionally driven. Further investigations are warranted.
Neutralization Resistance of Virological Synapse-Mediated HIV-1 Infection Is Regulated by the gp41 Cytoplasmic Tail

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) infection can spread efficiently from infected to uninfected T cells through adhesive contacts called virological synapses (VSs). In this process, cell-surface envelope glycoprotein (Env) initiates adhesion and viral transfer into an uninfected recipient cell. Previous studies have found some HIV-1-neutralizing patient sera to be less effective at blocking VS-mediated infection than infection with cell-free virus. Here we employ sensitive flow cytometry-based infection assays to measure the inhibitory potency of HIV-1-neutralizing monoclonal antibodies (MAb) and HIV-1-neutralizing patient sera against cell-free and VS-mediated infection. To various degrees, anti-Env MAbs exhibited significantly higher 50% inhibitory concentration (IC50s) against VS-mediated infection than cell-free infection. Notably, the MAb 17b, which binds a CD4-induced (CD4i) epitope on gp120, displayed a 72-fold reduced efficacy against VS-mediated inocula compared to cell-free inocula. A mutant with truncation mutation in the gp41 cytoplasmic tail (CT) which is unable to modulate Env fusogenicity in response to virus particle maturation but which can still engage in cell-to-cell infection was tested for the ability to resist neutralizing antibodies. The ΔCT mutation increased cell surface staining by neutralizing antibodies, significantly enhanced neutralization of VS-mediated infection, and had reduced or no effect on cell-free infection, depending upon the antibody. Our results suggest that the gp41 CT regulates the exposure of key neutralizing epitopes during cell-to-cell infection and plays an important role in immune evasion. Vaccine strategies should consider immunogens that reflect Env conformations exposed on the infected cell surface to enhance protection against VS-mediated HIV-1 spread.
Structure and Receptor Binding Specificity of Hemagglutinin H13 from Avian Influenza A Virus H13N6

ABSTRACT Interspecies transmission (host switching/jumping) of influenza viruses is a key scientific question that must be addressed. In addition to the vigorous research on highly pathogenic avian influenza viruses (HPAIVs), studies of the mechanism of interspecies transmission of low-pathogenic avian influenza viruses (LPAIVs) could also provide insights into host tropism and virulence evolution. Influenza A viruses harboring hemagglutinin (HA) H13 (e.g., H13N6) are LPAIVs. In this study, soluble H13 HA glycoprotein was purified, and its receptor binding activity was characterized. The results revealed that H13 exclusively binds the avian α2-3-linked sialic acid receptor; no binding to the mammalian α2-6-linked sialic acid receptor was detected. Furthermore, the molecular basis of the H13 receptor binding specificity was revealed by comparative analysis of the crystal structures of both receptor-bound H13 and H5 HAs, which might be contributed by the hydrophobic residue V186. Work with an H13N186 mutant confirmed the importance of V186 in the receptor binding specificity of H13 HA, which shows that the mutant protein reduced the binding of an avian receptor analog but increased the binding of a human receptor analog. Detailed structural analysis also demonstrated that the conserved binding sites of the recently well-studied broadly neutralizing human monoclonal antibodies targeting the HA2 domain are found in H13. Our results expand our understanding of virulence evolution, receptor binding preference, and species tropism of the LPAIVs and HPAIVs.
Novel cis-Acting Element within the Capsid-Coding Region Enhances Flavivirus Viral-RNA Replication by Regulating Genome Cyclization

ABSTRACT cis-Acting elements in the viral genome RNA (vRNA) are essential for the translation, replication, and/or encapsidation of RNA viruses. In this study, a novel conserved cis-acting element was identified in the capsid-coding region of mosquito-borne flavivirus. The downstream of 5′ cyclization sequence (5′CS) pseudoknot (DCS-PK) element has a three-stem pseudoknot structure, as demonstrated by structure prediction and biochemical analysis. Using dengue virus as a model, we show that DCS-PK enhances vRNA replication and that its function depends on its secondary structure and specific primary sequence. Mutagenesis revealed that the highly conserved stem 1 and loop 2, which are involved in potential loop-helix interactions, are crucial for DCS-PK function. A predicted loop 1-stem 3 base triple interaction is important for the structural stability and function of DCS-PK. Moreover, the function of DCS-PK depends on its position relative to the 5′CS, and the presence of DCS-PK facilitates the formation of 5′-3′ RNA complexes. Taken together, our results reveal that the cis-acting element DCS-PK enhances vRNA replication by regulating genome cyclization, and DCS-PK might interplay with other cis-acting elements to form a functional vRNA cyclization domain, thus playing critical roles during the flavivirus life cycle and evolution.
Respiratory Syncytial Virus (RSV) Pulmonary Infection in Humanized Mice Induces Human Anti-RSV Immune Responses and Pathology

ABSTRACT Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract disease, which causes high rates of morbidity and mortality in infants and the elderly. Models of human RSV pulmonary disease are needed to better understand RSV pathogenesis and to assess the efficacy of RSV vaccines. We assessed the RSV-specific human innate, humoral, and cellular immune responses in humanized mice (mice with a human immune system [HIS mice]) with functional human CD4+ T and B cells. These mice were generated by introduction of HLA class II genes, various human cytokines, and human B cell activation factor into immunodeficient NOD scid gamma (NSG) mice by the use of an adeno-associated virus vector, followed by engraftment of human hematopoietic stem cells. During the first 3 days of infection, HIS mice lost more weight and cleared RSV faster than NSG mice. Human chemokine (C-C motif) ligand 3 (CCL3) and human interleukin-1β (IL-1β) expression was detected in the RSV-infected HIS mice. The pathological features induced by RSV infection in HIS mice included peribronchiolar inflammation, neutrophil predominance in the bronchioalveolar lavage fluid, and enhanced airway mucus production. Human anti-RSV IgG and RSV-neutralizing antibodies were detected in serum and human anti-RSV mucosal IgA was detected in bronchioalveolar lavage fluid for up to 6 weeks. RSV infection induced an RSV-specific human gamma interferon response in HIS mouse splenocytes. These results indicate that human immune cells can induce features of RSV lung disease, including mucus hyperplasia, in murine lungs and that HIS mice can be used to elicit human anti-RSV humoral and cellular immunity. IMPORTANCE Infections with respiratory syncytial virus (RSV) are common and can cause severe lung disease in infants and the elderly. The lack of a suitable animal model with disease features similar to those in humans has hampered efforts to predict the efficacy of novel anti-RSV therapies and vaccines for use in humans. A murine model consisting of mice with a human immune system (HIS mice) could be useful for assessment of RSV disease and anti-RSV responses specific to humans. This study investigates an HIS mouse model to imitate human RSV disease and immune responses. We found that RSV lung infection in HIS mice results in an RSV-specific pathology that mimics RSV disease in humans and induces human anti-RSV immune responses. This model could be useful for better understanding of human RSV disease and for the development of RSV therapies.
A Viral Nonstructural Protein Regulates Bluetongue Virus Trafficking and Release

ABSTRACT Bluetongue virus (BTV), a nonenveloped insect-borne virus, is released from infected cells by multiple pathways. Unlike other nonenveloped viruses, in addition to cell lysis the newly synthesized virus particles also appear to use a unique “budding” process. The nonstructural protein NS3, the only membrane protein encoded by BTV in infected cells, has been implicated in this process, since it appears to interact not only with the outermost viral capsid protein VP2 but also with a component of the cellular ESCRT pathway. However, to date it had not been possible to obtain direct evidence for the involvement of NS3 in BTV morphogenesis due to the lack of a genetic system that would allow introducing the targeted mutation in NS3 gene. In this study, we have used the recently developed T7 transcript-based reverse genetics system for BTV to introduce mutations in the sequence of NS3 into the viral genome and have investigated the effect of these mutations in the context of a replicating virus. While certain NS3 mutations exhibited drastic effects on newly synthesized virus release, others had less pronounced effects. In particular, mutations of two residues in the Tsg101 binding motif, the putative L domain of NS3, altered normal virus egress patterns and left nascent particles tethered to the cellular membrane, apparently arrested in the process of budding. In cells infected with a mutant virus that was incapable of an NS3-VP2 interaction, no budding particles were visualized. These data suggest that NS3 may act like the membrane protein of enveloped viruses and is responsible for intracellular trafficking and budding of virus particles. NS3 is thus a bridge between the maturing virion particles and cellular proteins during virus egress.
Alterações eletrocardiográficas e sua relação com os fatores de risco para doença isquêmica do coração em população da área metropolitana de São Paulo

OBJETIVO: A doenca isquemica do coracao apresenta altas taxas de mortalidade e e a mais prevalente entre as doencas cardiovasculares. E uma doenca multifatorial, cuja prevencao depende do controle dos fatores de risco. O eletrocardiograma de repouso pode ser utilizado para detectar manifestacoes da doenca isquemica do coracao quando o individuo ainda e assintomatico. O objetivo do estudo foi o de analisar a relacao entre as anormalidades eletrocardiograficas e os fatores de risco para doenca isquemica do coracao em uma populacao adulta residente na area metropolitana de Sao Paulo. METODOS: Realizou-se um estudo transversal com populacao do municipio de Cotia (SP). A amostra constou de 1067 individuos com idade acima de 20 anos, de ambos os sexos. Os dados foram obtidos por meio de entrevista com utilizacao de um questionario padronizado. As variaveis estudadas foram: sexo, idade, tabagismo, atividade fisica, indice de massa corporea, relacao cintura/quadril, pressao arterial, diabetes melito, dislipidemia (colesterol total, LDL-colesterol, HDL-colesterol e triglicerides) e alteracoes eletrocardiograficas. As alteracoes eletrocardiograficas foram agrupadas em tres categorias: alteracoes de repolarizacao ventricular (ARV), sobrecarga do ventriculo esquerdo (SVE) e alteracoes nao relacionadas a isquemia miocardia ou sem alteracoes (NRI). RESULTADOS: A populacao de estudo era predominantemente jovem, sendo 79% abaixo de 50 anos, com idade de 39,8 anos ± 13,2 anos. Cerca de 59,3% dos individuos eram do sexo feminino. O eletrocardiograma mostrou que 9,5% da populacao apresentava ARV e 3,3% apresentava SVE. O sexo feminino, a idade de risco (acima de 65 anos para mulheres e acima de 55 anos para homens), a presenca de diabetes, hipertensao arterial, colesterol total ³ a 200 mg/dl, LDL-colesterol ³ a 130 mg/dl, triglicerides acima de 200 mg/dl, indice de massa corporea indicativo de sobrepeso ou obesidade (³25 Kg/m2),relacao cintura/quadril alterada correlacionaram-se positivamente com ARV. O sexo masculino, diabetes, hipertensao arterial e o tabagismo foram correlacionados positivamente com SVE. Na presenca de ARV no ECG encontramos uma razao de chance de 3,54 para a ocorrencia do diagnostico de hipertensao sistolica e de 1,83 para colesterol total ³ a 200 mg/dl. Na presenca de SVE no ECG, a razao de chance para a ocorrencia do diagnostico de hipertensao sistolica observada foi de 5,92. Dos tres fatores de risco correlacionados as alteracoes eletrocardiograficas associadas a isquemia miocardia, dois sao controlaveis e ligados a condicoes nutricionais (hipertensao e colesterol ³ a 200 mg/dl), o que demonstra a importância da sua deteccao precoce. Em estudos epidemiologicos e de intervencao nutricional, o eletrocardiograma, metodo simples e de baixo custo, pode auxiliar na identificacao de fatores de risco cardiovascular. Seria importante que estas informacoes fossem confirmadas por estudos prospectivos que incluissem a determinacao dos valores preditivos do ECG nesta situacao.
Quantifying the Early Immune Response and Adaptive Immune Response Kinetics in Mice Infected with Influenza A Virus

ABSTRACT Seasonal and pandemic influenza A virus (IAV) continues to be a public health threat. However, we lack a detailed and quantitative understanding of the immune response kinetics to IAV infection and which biological parameters most strongly influence infection outcomes. To address these issues, we use modeling approaches combined with experimental data to quantitatively investigate the innate and adaptive immune responses to primary IAV infection. Mathematical models were developed to describe the dynamic interactions between target (epithelial) cells, influenza virus, cytotoxic T lymphocytes (CTLs), and virus-specific IgG and IgM. IAV and immune kinetic parameters were estimated by fitting models to a large data set obtained from primary H3N2 IAV infection of 340 mice. Prior to a detectable virus-specific immune response (before day 5), the estimated half-life of infected epithelial cells is ∼1.2 days, and the half-life of free infectious IAV is ∼4 h. During the adaptive immune response (after day 5), the average half-life of infected epithelial cells is ∼0.5 days, and the average half-life of free infectious virus is ∼1.8 min. During the adaptive phase, model fitting confirms that CD8+ CTLs are crucial for limiting infected cells, while virus-specific IgM regulates free IAV levels. This may imply that CD4 T cells and class-switched IgG antibodies are more relevant for generating IAV-specific memory and preventing future infection via a more rapid secondary immune response. Also, simulation studies were performed to understand the relative contributions of biological parameters to IAV clearance. This study provides a basis to better understand and predict influenza virus immunity.
Vaccine-Induced Cellular Responses Control Simian Immunodeficiency Virus Replication after Heterologous Challenge

ABSTRACT All human immunodeficiency virus (HIV) vaccine efficacy trials to date have ended in failure. Structural features of the Env glycoprotein and its enormous variability have frustrated efforts to induce broadly reactive neutralizing antibodies. To explore the extent to which vaccine-induced cellular immune responses, in the absence of neutralizing antibodies, can control replication of a heterologous, mucosal viral challenge, we vaccinated eight macaques with a DNA/Ad5 regimen expressing all of the proteins of SIVmac239 except Env. Vaccinees mounted high-frequency T-cell responses against 11 to 34 epitopes. We challenged the vaccinees and eight naïve animals with the heterologous biological isolate SIVsmE660, using a regimen intended to mimic typical HIV exposures resulting in infection. Viral loads in the vaccinees were significantly less at both the peak (1.9-log reduction; P < 0.03) and at the set point (2.6-log reduction; P < 0.006) than those in control naïve animals. Five of eight vaccinated macaques controlled acute peak viral replication to less than 80,000 viral RNA (vRNA) copy eq/ml and to less than 100 vRNA copy eq/ml in the chronic phase. Our results demonstrate that broad vaccine-induced cellular immune responses can effectively control replication of a pathogenic, heterologous AIDS virus, suggesting that T-cell-based vaccines may have greater potential than previously appreciated.
Effect of Sleep Deprivation on Functional Connectivity of EEG Channels

This paper presents the functional interdependences among electroencephalograph (EEG) signals collected from human subjects undergoing a controlled experiment over a period of 36 h of sleep deprivation. The EEG signals were recorded from 19 electrodes spread all over the scalp. The interdependence among the signals was measured using synchronization likelihood (SL), which measures the dynamical (both linear and nonlinear) interdependence between two or more nonstationary time series. A network structure was evolved based on these SL values. The EEG signal being nonstationary, instead of the frequency bands, the connectivity was evaluated at various intrinsic modes known as intrinsic mode functions (IMFs). These IMFs were generated using empirical mode decomposition. It was observed that the connectivity of the networks exhibits definite patterns at specific IMFs with increase in sleep deprivation at successive stages of the experiment. The results were validated using subjective assessment and audiovisual response tests.
Antimicrobial Efficacy of Endomethasone and Sealapex Sealers against Specific Endodontic Pathogens

Background: Antimicrobial efficacy is one of the desired properties of root canal sealer to eliminate the residual microorganisms from complex root canal system unaffected by chemomechanical preparation and intracanal medication. The aim of the study is to compare the antimicrobial effects of two different sealers, i.e. zinc oxide based Endomethasone and calcium hydroxide based Sealapex against E. faecalis, S. aureus and C. albicans which are considered most resistant microorganisms in the oral cavity. Methods: Agar diffusion method was used in this study. The sealers were prepared according to manufacturer’s instruction and placed in prepared wells 36 agar plates inoculated with E. faecalis, S. aureus and C. albicans . All plates were incubated for 5 days at 370C. The zone of inhibition of each sealer was measured after 24 hours, 48 hours and 5 days interval in order to evaluate the antimicrobial efficacy in different time duration. Statistical analysis was performed by ANOVA, independent sample ‘t’ test and paired ‘t’ test as applicable. P value <0.05 was considered as statistically significant. Results: Endomethasone produced largest zone of inhibition at all-time interval than that of Sealapex against all tested microorganisms. However, the zone of inhibition of Endomethasone reduced significantly after 48 hours. The antimicrobial efficacy of Sealapex gradually increased at all times interval. Conclusion: The antimicrobial efficacy of Endomethasone against E. faecalis, S. aureus and C. albicans is higher than that of Sealapex. DOI: http://dx.doi. org/10.3329/cdcj.v10i2. 16317 City Dent. Coll. J Volume-10, Number-2, July-2013
On the hardware implementation efficiency of SHA-3 candidates

The most well known and officially used hash function is the Secure Hash Algorithm-1 (SHA-1) and Secure Hash Algorithm-2 (SHA-2). In recent years serious attacks have been published against SHA-1. This led the National Institute of Standard and Technology (NIST) to organize an effort to develop a modern and more secure hash algorithms through a hash function competition for usage in the following years in the near future. The selected new hash function will be called SHA-3. This paper deals with the hardware implementation efficiency of SHA-3 candidates, which is one of the most critical issues, regarding the adoption of the SHA-3 standard. Comparisons, in terms of hardware terms are given in detail, through this work.
Cleavage Activation of the Human-Adapted Influenza Virus Subtypes by Matriptase Reveals both Subtype and Strain Specificities

ABSTRACT Cleavage activation of the hemagglutinin (HA) precursor is an essential step in the influenza virus replication cycle that is driven by host cell proteases. HA cleavage activation is required for virus-endosome membrane fusion and the subsequent release of the influenza virus genome into the cytoplasm. Previous studies have determined that HA cleavage is most likely driven by either membrane-bound or extracellular trypsin-like proteases that reside in the respiratory tract. However, there is still uncertainty regarding which proteases are critical for HA cleavage in vivo. Therefore, further investigation of HA cleavage activation is needed in order to gain insight into the critical proteases involved. Matriptase is a member of the type II transmembrane serine protease family that is highly expressed in a membrane-bound form throughout the respiratory tract. One feature of matriptase is that, once activated, the catalytic domain is secreted into the extracellular space and so serves as a functional extracellular protease. In this study, we have determined that the secreted, catalytic domain of matriptase has the ability to cleave and activate HA from the influenza virus H1 subtype but not the H2 and H3 subtypes. Furthermore, matriptase selectively cleaved the HA of particular strains within the H1 subtype, revealing both subtype and H1 strain specificity. Matriptase was also found to activate thrombolytic zymogens that have been shown to cleave and activate the influenza virus HA. Our data demonstrate that matriptase has the ability to cleave HA directly or indirectly by activating HA-cleaving zymogens.