Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptive Mutations in a Human Immunodeficiency Virus Type 1 Envelope Protein with a Truncated V3 Loop Restore Function by Improving Interactions with CD4

ABSTRACT We previously reported that a human immunodeficiency virus type 1 (HIV-1) clade B envelope protein with a severely truncated V3 loop regained function after passage in tissue culture. The adapted virus, termed TA1, retained the V3 truncation, was exquisitely sensitive to neutralization by the CD4 binding site monoclonal antibody b12 and by HIV-positive human sera, used CCR5 to enter cells, and was completely resistant to small molecule CCR5 antagonists. To examine the mechanistic basis for these properties, we singly and in combination introduced each of the 5 mutations from the adapted clone TA1 into the unadapted envelope. We found that single amino acid changes in the C3 region, the V3 loop, and in the fusion peptide were responsible for imparting near-normal levels of envelope function to TA1. T342A, which resulted in the loss of a highly conserved glycosylation site in C3, played the primary role. The adaptive amino acid changes had no impact on CCR5 antagonist resistance but made virus more sensitive to neutralization by antibodies to the CD4 binding site, modestly enhanced affinity for CD4, and made TA1 more responsive to CD4 binding. Specifically, TA1 was triggered by soluble CD4 more readily than the parental Env and, unlike the parental Env, could mediate entry on cells that express low levels of CD4. In contrast, TA1 interacted with CCR5 less efficiently and was highly sensitive to antibodies that bind to the CCR5 N terminus and ECL2. Therefore, enhanced utilization of CD4 is one mechanism by which HIV-1 can overcome mutations in the V3 region that negatively affect CCR5 interactions.
Noninvasive assessment of arterial stiffness by pulse wave analysis

Pulse wave evaluation is an effective method for arteriosclerosis screening. The pulse wave comprises two displacement components, the incident wave ε<sub>i</sub>(t) and the reflected wave ε<sub>r</sub>(t). Because the amplitude of the reflected wave changes markedly with arterial stiffness, analysis of this wave is useful for evaluation of such stiffness. In this paper, a noninvasive method for extracting the reflected component from a pulse wave is proposed. First, the pulse wave ε<sub>i</sub>(t) + ε<sub>r</sub>(t) and blood flow velocity <sub>i</sub>(t) - u<sub>r</sub>(t) were measured at the common carotid artery. A new approach is used to estimate the displacement wave ε<sub>i</sub>(t) - ε<sub>r</sub>(t), in which a transform of the conservation of mass, an elastic tube model, and a Voigt model for a viscoelastic body are applied to blood flow velocity data. Twice the amplitude of the reflected wave [TARW; 2ε<sub>r</sub>(t)] was obtained by subtracting the amplitude of the calculated displacement wave from that of the observed pulse wave. This method was applied to subjects aged from their 20s to 60s to evaluate differences in the reflected component. The results indicate moderate correlation between age and TARW (R<sup>2</sup> = 0.65). To evaluate the validity of this method for screening arterial stiffness, we compared TARW with existing diagnostic indices pulse wave velocity (PWV) and cardio-ankle vascular index (CAVI). TARW was moderately correlated with PWV (R<sup>2</sup> = 0.48) and CAVI (R<sup>2</sup> = 0.71). Therefore, this new method has potential for diagnosing arterial stiffness.
Cellular Vimentin Regulates Construction of Dengue Virus Replication Complexes through Interaction with NS4A Protein

ABSTRACT Dengue virus (DENV) interacts with host cellular factors to construct a more favorable environment for replication, and the interplay between DENV and the host cellular cytoskeleton may represent one of the potential antiviral targeting sites. However, the involvement of cellular vimentin intermediate filaments in DENV replication has been explored less. Here, we revealed the direct interaction between host cellular vimentin and DENV nonstructural protein 4A (NS4A), a known component of the viral replication complex (RC), during DENV infection using tandem affinity purification, coimmunoprecipitation, and scanning electron microscopy. Furthermore, the dynamics of vimentin-NS4A interaction were demonstrated by using confocal three-dimensional (3D) reconstruction and proximity ligation assay. Most importantly, we report for the first time the discovery of the specific region of NS4A that interacts with vimentin lies within the first 50 amino acid residues at the cytosolic N-terminal domain of NS4A (N50 region). Besides identifying vimentin-NS4A interaction, vimentin reorganization and phosphorylation by calcium calmodulin-dependent protein kinase II occurs during DENV infection, signifying that vimentin reorganization is important in maintaining and supporting the DENV RCs. Interestingly, we found that gene silencing of vimentin by small interfering RNA induced a significant alteration in the distribution of RCs in DENV-infected cells. This finding further supports the crucial role of intact vimentin scaffold in localizing and concentrating DENV RCs at the perinuclear site, thus facilitating efficient viral RNA replication. Collectively, our findings implicate the biological and functional significance of vimentin during DENV replication, as we propose that the association of DENV RCs with vimentin is mediated by DENV NS4A.
Pancreatic Botryomycosis Caused by Viridans Streptococci: A Case Report

Botryomycosis is a chronic suppurative granulomatous disease of the skin viscera. It is known to mimic diseases such as actinomycosis and invasive carcinoma. Visceral botryomycosis is a rare entity compared with its cutaneous counterpart. It can be identified using staining techniques such as Gomori methenamine silver, periodic acid-Schiff Gram stain, histopathological examination, and aerobic culture of the lesion. Splendore-Hoeppli phenomenon is a characteristic feature of this disease. It responds to prolonged treatment with beta-lactams and surgery . There have been very few case reports on visceral botryomycosis across the world. We report a case of pancreatic botryomycosis caused by viridans streptococci in a patient with chronic calcific pancreatitis who was presumptively diagnosed as having carcinoma of the head of the pancreas.
PrP P102L and Nearby Lysine Mutations Promote Spontaneous In Vitro Formation of Transmissible Prions

ABSTRACT Accumulation of fibrillar protein aggregates is a hallmark of many diseases. While numerous proteins form fibrils by prion-like seeded polymerization in vitro, only some are transmissible and pathogenic in vivo. To probe the structural features that confer transmissibility to prion protein (PrP) fibrils, we have analyzed synthetic PrP amyloids with or without the human prion disease-associated P102L mutation. The formation of infectious prions from PrP molecules in vitro has required cofactors and/or unphysiological denaturing conditions. Here, we demonstrate that, under physiologically compatible conditions without cofactors, the P102L mutation in recombinant hamster PrP promoted prion formation when seeded by minute amounts of scrapie prions in vitro. Surprisingly, combination of the P102L mutation with charge-neutralizing substitutions of four nearby lysines promoted spontaneous prion formation. When inoculated into hamsters, both of these types of synthetic prions initiated substantial accumulation of prion seeding activity and protease-resistant PrP without transmissible spongiform encephalopathy (TSE) clinical signs or notable glial activation. Our evidence suggests that PrP's centrally located proline and lysine residues act as conformational switches in the in vitro formation of transmissible PrP amyloids. IMPORTANCE Many diseases involve the damaging accumulation of specific misfolded proteins in thread-like aggregates. These threads (fibrils) are capable of growing on the ends by seeding the refolding and incorporation of the normal form of the given protein. In many cases such aggregates can be infectious and propagate like prions when transmitted from one individual host to another. Some transmitted aggregates can cause fatal disease, as with human iatrogenic prion diseases, while other aggregates appear to be relatively innocuous. The factors that distinguish infectious and pathogenic protein aggregates from more innocuous ones are poorly understood. Here we have compared the combined effects of prion seeding and mutations of prion protein (PrP) on the structure and transmission properties of synthetic PrP aggregates. Our results highlight the influence of specific sequence features in the normally unstructured region of PrP that influence the infectious and neuropathogenic properties of PrP-derived aggregates.
Iterative reconstruction of the transducer surface velocity

Ultrasound arrays used for medical imaging consist of many elements placed closely together. Ideally, each element vibrates independently. However, because of mechanical coupling, crosstalk between neighboring elements may occur. To quantify the amount of crosstalk, the transducer velocity distribution should be measured. In this work, a method is presented to reconstruct the velocity distribution from far-field pressure field measurements acquired over an arbitrary surface. The distribution is retrieved from the measurements by solving an integral equation, derived from the Rayleigh integral of the first kind, using a conjugate gradient inversion scheme. This approach has the advantages that it allows for arbitrary transducer and pressure field measurement geometries, as well as the application of regularization techniques. Numerical experiments show that measuring the pressure field along a hemisphere enclosing the transducer yields significantly more accurate reconstructions than measuring along a parallel plane. In addition, it is shown that an increase in accuracy is achieved when the assumption is made that all points on the transducer surface vibrate in phase. Finally, the method has been tested on an actual transducer with an active element of 700 × 200 μm which operates at a center frequency of 12.2 MHz. For this transducer, the velocity distribution has been reconstructed accurately to within 50 μm precision from pressure measurements at a distance of 1.98 mm (=16λ0) using a 200-μm-diameter needle hydrophone.
Strategien zur Behandlung der Limbusstammzellinsuffizienz

Background: Stem cells are the ultimate source of the rapidly self-renewing corneal epithelium and are located in the basal layer of the limbal epithelium. A variety of diseases can compromise the stem cell pool, causing an entity called limbal stem cell deficiency. Several therapeutic strategies should be taken into account. Methods and results: Ocular surface defence should be restored prior to any kind of stem cell transplantation to assure a sufficient and stable tearfilm. Surgical strategies comprise superficial keratectomy with or without amniotic membrane transplantation, conjunctival-limbal autograft and keratolimbal allograft transplantation. A damaged limbal and corneal stroma can be reconstructed by amniotic membrane as a biological substrate. First encouraging results have been reported using tissue bio-engineered limbal epithelium on amniotic membrane for corneal surface reconstruction. Conclusion: The correct diagnosis and a restored ocular surface defence are a prerequisite for subsequent transplantation of limbal stem cells. Optimal patient selection for the respective surgical approach and systemic immunosuppression protocols to improve allograft survival need to be further investigated.
Immunization with Live Attenuated Influenza Viruses That Express Altered NS1 Proteins Results in Potent and Protective Memory CD8+ T-Cell Responses

ABSTRACT The generation of vaccines that induce long-lived protective immunity against influenza virus infections remains a challenging goal. Ideally, vaccines should elicit effective humoral and cellular immunity to protect an individual from infection or disease. Cross-reactive T- and B-cell responses that are elicited by live virus infections may provide such broad protection. Optimal induction of T-cell responses involves the action of type I interferons (IFN-I). Influenza virus expressed nonstructural protein 1 (NS1) functions as an inhibitor of IFN-I and promotes viral growth. We wanted to examine the priming of CD8+ T-cell responses to influenza virus in the absence of this inhibition of IFN-I production. We generated recombinant mouse-adapted influenza A/PR/8/34 viruses with NS1 truncations and/or deletions that also express the gp33-41 epitope from lymphocytic choriomeningitis virus. Intranasal infection of mice with the attenuated viruses primed long-lived T- and B-cell responses despite significantly reduced viral replication in the lungs compared to wild-type virus. Antigen-specific CD8+ T cells expanded upon rechallenge and generated increased protective memory T-cell populations after boosting. These results show that live attenuated influenza viruses expressing truncated NS1 proteins can prime protective immunity and may have implications for the design of novel modified live influenza virus vaccines.
Nonhuman Primate Models for Translational Research in Endometriosis

Endometriosis, defined as the ectopic presence of endometrial-like cells, is associated with infertility and pelvic pain in women. Whereas pathogenesis and spontaneous evolution of endometriosis are still poorly understood, recurrences after surgical therapy or after medical treatment are common. Spontaneous endometriosis occurs only in women and in nonhuman primates (NHPs). Inbred rhesus monkeys kept in colonies offer an attractive preclinical model to study the inheritance of spontaneous endometriosis. Baboons with spontaneous or induced endometriosis appear to be the best NHP model to study pathogenesis, pathophysiology, spontaneous evolution and new medical treatment options. In baboons, induction of endometriosis after intrapelvic injection of menstrual endometrium leads to biological changes in peritoneal cavity and in endometrium. This induction process may allows the study of cause-effect relationships which may lead to the discovery of new biomarkers for the development of new non-invasive diagnostic tests and drugs that may prevent or treat endometriosis.
Comparison of 3-D synthetic aperture phased-array ultrasound imaging and parallel beamforming

This paper demonstrates that synthetic aperture imaging (SAI) can be used to achieve real-time 3-D ultrasound phased-array imaging. It investigates whether SAI increases the image quality compared with the parallel beamforming (PB) technique for real-time 3-D imaging. Data are obtained using both simulations and measurements with an ultrasound research scanner and a commercially available 3.5- MHz 1024-element 2-D transducer array. To limit the probe cable thickness, 256 active elements are used in transmit and receive for both techniques. The two imaging techniques were designed for cardiac imaging, which requires sequences designed for imaging down to 15 cm of depth and a frame rate of at least 20 Hz. The imaging quality of the two techniques is investigated through simulations as a function of depth and angle. SAI improved the full-width at half-maximum (FWHM) at low steering angles by 35%, and the 20-dB cystic resolution by up to 62%. The FWHM of the measured line spread function (LSF) at 80 mm depth showed a difference of 20% in favor of SAI. SAI reduced the cyst radius at 60 mm depth by 39% in measurements. SAI improved the contrast-to-noise ratio measured on anechoic cysts embedded in a tissue-mimicking material by 29% at 70 mm depth. The estimated penetration depth on the same tissue-mimicking phantom shows that SAI increased the penetration by 24% compared with PB. Neither SAI nor PB achieved the design goal of 15 cm penetration depth. This is likely due to the limited transducer surface area and a low SNR of the experimental scanner used.
An analytical formulation for phase noise in MEMS oscillators

In recent years, there has been much interest in the design of low-noise MEMS oscillators. This paper presents a new analytical formulation for noise in a MEMS oscillator encompassing essential resonator and amplifier nonlinearities. The analytical expression for oscillator noise is derived by solving a second-order nonlinear stochastic differential equation. This approach is applied to noise modeling of an electrostatically addressed MEMS resonator-based square-wave oscillator in which the resonator and oscillator circuit nonlinearities are integrated into a single modeling framework. By considering the resulting amplitude and phase relations, we derive additional noise terms resulting from resonator nonlinearities. The phase diffusion of an oscillator is studied and the phase diffusion coefficient is proposed as a metric for noise optimization. The proposed nonlinear phase noise model provides analytical insight into the underlying physics and a pathway toward the design optimization for low-noise MEMS oscillators.
New Insights into the Nonconserved Noncoding Region of the Subtype-Determinant Hemagglutinin and Neuraminidase Segments of Influenza A Viruses

ABSTRACT The noncoding regions (NCRs) of the eight-segmented viral RNAs (vRNAs) of influenza A virus consist of the highly conserved promoter region and the nonconserved segment-specific NCRs at both the 3′ and 5′ ends. The roles of the segment-specific NCRs of the eight segments have been extensively studied. However, the diversities in the same region of the two subtype-determinant hemagglutinin (HA) and neuraminidase (NA) segments have received little attention. In this study, we bioinformatically analyzed all available NCRs of HA and NA vRNAs of influenza A viruses and found that nucleotides in the segment-specific NCRs of HA and NA vRNAs are subtype specific and vary significantly in sequence and length at both the 3′ and 5′ ends among different subtypes. We then systematically studied the biological significance of the HA subtype-specific NCRs (HA ssNCRs) of the common HA subtypes (H1 to H7 and H9) in the context of the WSN (H1N1) reverse genetics system. We found that the HA ssNCRs play a critical role in HA vRNA virion incorporation. Upon HA vRNA incorporation, the 3′-end HA ssNCR plays a more critical role than the 5′-end HA ssNCR, and no stringent compatibility between the two ends is required. Furthermore, our data imply that, in addition to a particular nucleotide(s), the length of the HA ssNCR is involved in regulating HA vRNA incorporation efficiency. These results provide new insights into the HA segment virion incorporation that is critical for the emergence of epidemic and pandemic influenza A virus strains. IMPORTANCE The nonconserved noncoding regions (NCRs) of the vRNAs of influenza A virus have been extensively studied, whereas the diversities in the nonconserved NCRs of the two subtype-determinant segments hemagglutinin (HA) and neuraminidase (NA) have received little attention. In this study, we bioinformatically analyzed all available NCRs of HA and NA vRNAs and discovered that the HA and NA vRNAs contain key subtype signatures in the NCRs. Our functional studies of the HA subtype-specific NCRs (HA ssNCRs) of the common HA subtypes in the context of WSN virus (H1N1) demonstrated that the HA ssNCR modulates virus replication efficiency by influencing HA segment virion incorporation. Moreover, we revealed important features of the HA ssNCR in determining HA vRNA incorporation efficiency. These data not only show new genetic characteristics of influenza A viruses, but also provide further evidence for understanding the selective genome packaging of influenza virus required for the emergence of epidemic and pandemic influenza virus strains.
The Human Cytomegalovirus UL36 Gene Controls Caspase-Dependent and -Independent Cell Death Programs Activated by Infection of Monocytes Differentiating to Macrophages

ABSTRACT The cellular protease caspase-8 activates extrinsic apoptosis and also functions to promote monocyte-to-macrophage differentiation. Differentiation-induced alterations to antiviral caspase-8-dependent cell death pathways are unclear. Here, we show THP-1 monocyte-to-macrophage differentiation alters the specific cell death pathways activated in response to human cytomegalovirus (HCMV) infection. Employing viruses with mutations in UL36, the gene that encodes the viral inhibitor of caspase-8 activation (vICA), our data indicate that both caspase-dependent and -independent death pathways are activated in response to infection. Activation of caspase-dependent and -independent cell death responses restricted growth of vICA-deficient viruses, and vICA/pUL36 inhibited either response. Thus, these studies also reveal that the UL36 gene controls a caspase-independent cell death pathway. The impact of caspases on control of antiviral responses differed at early and late stages of macrophage differentiation. Early in differentiation, vICA-deficient virus-induced cell death was dependent on caspases and inhibited by the pan-caspase inhibitor z-VAD(OMe)-fluoromethyl ketone. In contrast, virus-induced death at late times of differentiation was caspase independent. Additional unlabeled and fluorescent inhibitors indicated that caspase-8 promoted death from within infected cells at early but not late stages of differentiation. These data highlight the multifunctional role of vICA/pUL36 as HCMV encounters various antiviral responses during macrophage differentiation.
Design and In Vivo Characterization of Immunoconjugates Targeting HIV gp160

ABSTRACT The envelope (Env) glycoprotein of HIV is expressed on the surface of productively infected cells and can be used as a target for cytotoxic immunoconjugates (ICs), in which cell-killing moieties, including toxins, drugs, or radionuclides, are chemically or genetically linked to monoclonal antibodies (MAbs) or other targeting ligands. Such ICs could be used to eliminate persistent reservoirs of HIV infection. We have found that MAbs which bind to the external loop of gp41, e.g., MAb 7B2, make highly effective ICs, particularly when used in combination with soluble CD4. We evaluated the toxicity, immunogenicity, and efficacy of the ICs targeted with 7B2 in mice and in simian-human immunodeficiency virus-infected macaques. In the macaques, we tested immunotoxins (ITs), consisting of protein toxins bound to the targeting agent. ITs were well tolerated and initially efficacious but were ultimately limited by their immunogenicity. In an effort to decrease immunogenicity, we tested different toxic moieties, including recombinant toxins, cytotoxic drugs, and tubulin inhibitors. ICs containing deglycosylated ricin A chain prepared from ricin toxin extracted from castor beans were the most effective in killing HIV-infected cells. Having identified immunogenicity as a major concern, we show that conjugation of IT to polyethylene glycol limits immunogenicity. These studies demonstrate that cytotoxic ICs can target virus-infected cells in vivo but also highlight potential problems to be addressed. IMPORTANCE It is not yet possible to cure HIV infection. Even after years of fully effective antiviral therapy, a persistent reservoir of virus-infected cells remains. Here we propose that a targeted conjugate consisting of an anti-HIV antibody bound to a toxic moiety could function to kill the HIV-infected cells that constitute this reservoir. We tested this approach in HIV-infected cells grown in the lab and in animal infections. Our studies demonstrated that these immunoconjugates are effective both in vitro and in test animals. In particular, ITs constructed with the deglycosylated A chain prepared from native ricin were the most effective in killing cells, but their utility was blunted because they provoked immune reactions that interfered with the therapeutic effects. We then demonstrated that coating of the ITs with polyethylene glycol minimized the immunogenicity, as has been demonstrated with other protein therapies.