gebhart/patrepeval huggingface dataset:
Structurally Mapping the Diverse Phenotype of Adeno-Associated Virus Serotype 4 (2006)

The adeno-associated viruses (AAVs) can package and deliver foreign DNA into cells for corrective gene delivery applications. The AAV serotypes have distinct cell binding, transduction, and antigenic characteristics that have been shown to be dictated by the capsid viral protein (VP) sequence. To understand the contribution of capsid structure to these properties, we have determined the crystal structure of AAV serotype 4 (AAV4), one of the most diverse serotypes with respect to capsid protein sequence and antigenic reactivity. Structural comparison of AAV4 to AAV2 shows conservation of the core beta strands (betaB to betaI) and helical (alphaA) secondary structure elements, which also exist in all other known parvovirus structures. However, surface loop variations (I to IX), some containing compensating structural insertions and deletions in adjacent regions, result in local topological differences on the capsid surface. These include AAV4 having a deeper twofold depression, wider and rounder protrusions surrounding the threefold axes, and a different topology at the top of the fivefold channel from that of AAV2. Also, the previously observed "valleys" between the threefold protrusions, containing AAV2's heparin binding residues, are narrower in AAV4. The observed differences in loop topologies at subunit interfaces are consistent with the inability of AAV2 and AAV4 VPs to combine for mosaic capsid formation in efforts to engineer novel tropisms. Significantly, all of the surface loop variations are associated with amino acids reported to affect receptor recognition, transduction, and anticapsid antibody reactivity for AAV2. This observation suggests that these capsid regions may also play similar roles in the other AAV serotypes.
Identification and localization of the cytokine SDF1 and its receptor, CXC chemokine receptor 4, to regions of necrosis and angiogenesis in human glioblastoma. (2000)

Glioblastoma multiforme (GBM) tumors display extensive histomorphological heterogeneity, with great variability in the extent of invasiveness, angiogenesis, and necrosis. The identification of genes associated with these phenotypes should further the molecular characterization, permitting better definition of glioma subsets that may ultimately lead to better treatment strategies. Therefore, we performed a differential mRNA display analysis comparing six GBM-derived primary cell cultures from patients having tumors with varied histomorphological features. We identified stromal cell-derived factor 1 (SDF1) as a gene with varied expression. SDF1 (cytokine) and CXC chemokine receptor 4 (CXCR4) interactions are implicated in modulating cell migration. They are also implicated in modulating the immune response in AIDS patients by macrophage-mediated T-cell apoptosis. GBM patients also fail to mount an immune response, although their tumors are seemingly exposed to immune cells in regions of angiogenesis, where the blood-brain barrier is absent, or in areas of necrosis. To determine whether the expression and localization of SDF1 and CXCR4 are consistent with such a role in these brain tumors, immunohistochemical analyses of these proteins were performed on normal brain and astrocytomas (grades II-IV). In normal brain tissue, low levels of SDF1 (0.5+) were observed in astrocytic processes, in neurons, and in the occasional phagocytic cells around vessels. CXCR4 expression was negative in brain tissue but was observed in phagocytic cells within the vessel lumen. In tumors, SDF1 and CXCR4 expression was colocalized when both were expressed, and SDF1 and CXCR4 expression increased with increasing tumor grade (from 0.5+ to 6+). Additionally, CXCR4 was expressed in neovessel endothelial cells. The proteins were expressed in regions of angiogenesis and degenerative, necrotic, and microcystic changes. Those tumors displaying greater amounts of these features had greater staining intensity of the proteins. The expression of SDF1 and CXCR4 did not colocalize with the proliferation marker MIB-1. Thus, our data suggest that SDF1 and CXCR4 expressions: (a) increase with increasing grade; (b) colocalize to regions within these tumors where their interaction may contribute to angiogenesis and/or modulation of the immune response; and (c) may serve to characterize subsets of GBMs.
Oligomerization and activation of caspase-9, induced by Apaf-1 CARD (2002)

Apaf-1 facilitates the proteolytic activation of procaspase-9 and maintains the hyperactive state of the processed caspase-9. The underlying molecular mechanisms for these activities remain poorly characterized. Here we report that the isolated Apaf-1 caspase recruitment domain (CARD) forms a large hetero-oligomer with the active caspase-9. The catalytic activity of caspase-9 is significantly enhanced in this complex, demonstrating that Apaf-1 CARD allosterically up-regulates caspase-9 activity. Point mutations that inactivate the interactions between Apaf-1 CARD and the prodomain of caspase-9 also abolished the formation of this complex. Based on these observations, we discuss the implications of this complex on the observed Apaf-1 function.
Genetic Immunization with Lung-Targeting Macroaggregated Polyethyleneimine-Albumin Conjugates Elicits Combined Systemic and Mucosal Immune Responses (2000)

Genetic immunization is a novel form of vaccination in which transgenes are delivered into the host to produce the foreign protein within host cells. Although systemic immune responses have been relatively easy to induce by genetic immunization, the induction of regional and mucosal immunity has often been more challenging. To address the problem of eliciting mucosal immunity in the lung, we utilized macroaggregated albumin to target plasmid DNA to the lung. Macroaggregated albumin is trapped in the lung after i. v. injection, and it is routinely used in radiolabeled form as an imaging modality to evaluate pulmonary blood flow. To couple DNA to this targeting agent, polyethyleneimine (a polycation that binds DNA and enhances transfection) was conjugated to serum albumin, and the conjugate was aggregated by heating to produce particles of 25-100 microm. The resulting particles bound plasmid DNA avidly, and when injected i.v. in mice, the particles distributed in the peripheral lung tissue in the alveolar interstitium. Particle-bound luciferase plasmid transfected a variety of cell lines in vitro, and after i.v. injection, gene expression was detected exclusively in the lung. Using human growth hormone as the encoded foreign Ag for immunization, i.v. injection of the particle-bound plasmid elicited both pulmonary mucosal and systemic immune responses, whereas naked DNA injected either i.v. or i.m. elicited only systemic responses. Thus, particle-bound plasmid DNA may have utility for genetic immunization by intravascular delivery to the lung and potentially to other organs and tissues.
Clinical experience with plasmid DNA- and modified vaccinia virus Ankara-vectored human immunodeficiency virus type 1 clade A vaccine focusing on T-cell induction (2006)

Candidate human immunodeficiency virus type 1 (HIV-1) vaccines focusing on T-cell induction, constructed as pTHr.HIVA DNA and modified vaccinia virus Ankara (MVA).HIVA, were delivered in a heterologous prime-boost regimen. The vaccines were tested in several hundred healthy or HIV-1-infected volunteers in Europe and Africa. Whilst larger trials of hundreds of volunteers suggested induction of HIV-1-specific T-cell responses in <15 % of healthy vaccinees, a series of small, rapid trials in 12-24 volunteers at a time with a more in-depth analysis of vaccine-elicited T-cell responses proved to be highly informative and provided more encouraging results. These trials demonstrated that the pTHr.HIVA vaccine alone primed consistently weak and mainly CD4(+), but also CD8(+) T-cell responses, and the MVA.HIVA vaccine delivered a consistent boost to both CD4(+) and CD8(+) T cells, which was particularly strong in HIV-1-infected patients. Thus, whilst the search is on for ways to enhance T-cell priming, MVA is a useful boosting vector for human subunit genetic vaccines.
Use of tactile feedback to control exploratory movements to characterize object compliance (2012)

Humans have been shown to be good at using active touch to perceive subtle differences in compliance. They tend to use highly stereotypical exploratory strategies, such as applying normal force to a surface. We developed similar exploratory and perceptual algorithms for a mechatronic robotic system (Barrett arm/hand system) equipped with liquid-filled, biomimetic tactile sensors (BioTac(®) from SynTouch LLC). The distribution of force on the fingertip was measured by the electrical resistance of the conductive liquid trapped between the elastomeric skin and a cluster of four electrodes on the flat fingertip surface of the rigid core of the BioTac. These signals provided closed-loop control of exploratory movements, while the distribution of skin deformations, measured by more lateral electrodes and by the hydraulic pressure, were used to estimate material properties of objects. With this control algorithm, the robot plus tactile sensor was able to discriminate the relative compliance of various rubber samples.
Photonic analog-to-digital converters (2007)

This paper reviews over 30 years of work on photonic analog-to-digital converters. The review is limited to systems in which the input is a radio-frequency (RF) signal in the electronic domain and the output is a digital version of that signal also in the electronic domain, and thus the review excludes photonic systems directed towards digitizing images or optical communication signals. The state of the art in electronic ADCs, basic properties of ADCs and properties of analog optical links, which are found in many photonic ADCs, are reviewed as background information for understanding photonic ADCs. Then four classes of photonic ADCs are reviewed: 1) photonic assisted ADC in which a photonic device is added to an electronic ADC to improve performance, 2) photonic sampling and electronic quantizing ADC, 3) electronic sampling and photonic quantizing ADC, and 4) photonic sampling and quantizing ADC. It is noted, however, that all 4 classes of "photonic ADC" require some electronic sampling and quantization. After reviewing all known photonic ADCs in the four classes, the review concludes with a discussion of the potential for photonic ADCs in the future.
The Control of Drug Release from Conventional Melt Granulation Matrices (1987)

Sustained release potassium chloride tablets were prepared using a melt granulation formulation in a Baker Perkins Granulator. Parts of the validation for this manufacturing process are highlighted in this paper including granulation end point temperature, incorporation of extragranular excipients, amount of wax in the formulation, granule cooling rate and scale of the operation. A number of other factors have been studied which are not Included here although they are no less important. The release of potassium chloride from tablets was found to be dependent on the wax level and the amount of extragranular excipients (“wicklng agent”). Within the controlled production process, any variation in granulation end point temperature and granule cooling rate should not have any significant effect.
Potential clinical utility of high-density lipoprotein-mimetic peptides (2006)

Peptides that sequester lipoprotein lipid hydroperoxides release a series of high-density lipoprotein-associated antioxidant enzymes such as paraoxonase from inhibition and protect apoA-I from oxidative damage that would impair cholesterol efflux.
Multianalyte Detection Using a Capillary-Based Flow Immunosensor (1998)

A highly sensitive, dual-analyte detection system using capillary-based immunosensors has been designed for explosive detection. This model system consists of two capillaries, one coated with antibodies specific for 2,4,6-trinitrotoluene (TNT) and the other specific for hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) combined into a single device. The fused silica capillaries are prepared by coating anti-TNT and anti-RDX antibodies onto the silanized inner walls using a hetero-bifunctional crosslinker. After immobilization, the antibodies are saturated with a suitable fluorophorelabeled antigen. A "T" connector is used to continuously flow the buffer solution through the individual capillaries. To perform the assay, an aliquot of TNT or RDX or a mixture of the two analytes is injected into the continuous flow stream. In each capillary, the target analyte displaces the fluorophore-labeled antigen from the binding pocket of the antibody. The labeled antigen displaced from either capillary is detected downstream using two portable spectrofluorometers. The limits of detection for TNT and RDX in the multi-analyte formate are 44 fmol (100 microliters of 0.1 ng/ml TNT solution) and 224 fmol (100 microliters of 0.5 ng/ml RDX solution), respectively. The entire assay for both analytes can be performed in less than 3 min.
Comparison of Protein Force Fields for Molecular Dynamics Simulations (2008)

In the context of molecular dynamics simulations of proteins, the term "force field" refers to the combination of a mathematical formula and associated parameters that are used to describe the energy of the protein as a function of its atomic coordinates. In this review, we describe the functional forms and parameterization protocols of the widely used biomolecular force fields Amber, CHARMM, GROMOS, and OPLS-AA. We also summarize the ability of various readily available noncommercial molecular dynamics packages to perform simulations using these force fields, as well as to use modern methods for the generation of constant-temperature, constant-pressure ensembles and to treat long-range interactions. Finally, we finish with a discussion of the ability of these force fields to support the modeling of proteins in conjunction with nucleic acids, lipids, carbohydrates, and/or small molecules.
Hybrid image and signal processing III; Proceedings of the Meeting, Orlando, FL, Apr. 23, 24, 1992 (1990)

Various papers on hybrid image and signal processing are presented. The topics addressed include: optical matrix-vector laboratory data for finite element problems, solving ill-posed algebra problems using the bimodal optical computer, robust texture extractors for real-time pyramidal architectures, modified algorithm for scanning tomographic acoustic microscopy, identifying metal surfaces in color images, interpolative vector quantization, and moving image signal processing by Markovian random walk approach. Also discussed are: parallel optical pyramidal image processing, optical laboratory realization of distortion invariant filters, hybrid methods to compute image moments, hybrid techniques for postal address location, automatic visual inspection system for IC bonding wires, image processing on hypercube multiprocessors, interactive three-dimensional display and analysis, flexible mask subtraction for digital topography, least squares filtering via systolic array and light scattering for testing roughness of formed surfaces.
AmniSure Placental Alpha Microglobulin-1 Rapid Immunoassay versus Standard Diagnostic Methods for Detection of Rupture of Membranes (2005)

The purpose of this study was to compare the AmniSure rapid immunoassay with standard methods for diagnosing rupture of fetal membranes. Patients presenting with signs/symptoms of membrane rupture between 15 and 42 weeks of gestation were invited to participate. Standard/control methods were performed to establish a diagnosis and compare it with AmniSure results. AmniSure performance metrics and their 95% confidence intervals were calculated. A total of 203 patients agreed to participate. Discrepancies between the control method and AmniSure were noted in seven cases. In these cases, true positives and negatives were determined by retesting with the control method and AmniSure and by noting sonographic evidence of low amniotic fluid. In the final analysis, the AmniSure diagnostic test demonstrated a sensitivity of 98.9%, specificity of 100%, positive predictive value of 100%, and a negative predictive value of 99.1%. AmniSure is highly accurate in diagnosing fetal membrane rupture.
BH4 domain of antiapoptotic Bcl-2 family members closes voltage-dependent anion channel and inhibits apoptotic mitochondrial changes and cell death (2000)

A change of mitochondrial membrane permeability is essential for apoptosis, leading to translocation of apoptogenic cytochrome c and apoptosis-inducing factor into the cytoplasm. We recently showed that the Bcl-2 family of proteins regulate cytochrome c release and the mitochondrial membrane potential (Deltapsi) by directly modulating the activity of the voltage-dependent anion channel (VDAC) through binding. Here we investigated the biochemical role of the conserved N-terminal homology domain (BH4) of Bcl-x(L), which has been shown to be essential for inhibition of apoptosis, with respect to the regulation of mitochondrial membrane permeability and found that BH4 was required for Bcl-x(L) to prevent cytochrome c release and Deltapsi loss. A study using VDAC liposomes revealed that Bcl-x(L), but not Bcl-x(L) lacking the BH4 domain, inhibited VDAC activity. Furthermore, BH4 oligopeptides of Bcl-2 and Bcl-x(L), but not mutant peptides, were able to inhibit both VDAC activity on liposomes even in the presence of Bax and apoptotic Deltapsi loss in isolated mitochondria. It was also shown that the BH4 domain, fused to the protein transduction domain of HIV TAT protein (TAT-BH4), efficiently prevented apoptotic cell death. These results indicate that the BH4 of Bcl-2/Bcl-x(L) is essential and sufficient for inhibiting VDAC activity, which in turn prevents apoptotic mitochondrial changes, and for preventing apoptotic cell death. Finally, the data suggest that the TAT-BH4 peptide is potentially useful as a therapeutic agent for diseases caused by accelerated apoptosis.
Glutathione-s-transferase M1 and T1 polymorphisms and associations with type 1 diabetes age-at-onset (2005)

Type 1 diabetes (T1D) is an autoimmune disease characterized by pancreatic beta cell destruction involving auto-reactive T-cells, pro-inflammatory cytokines, reactive oxygen species (ROS) and loss of insulin. Monozygotic twin studies show a 20-60% concordance with T1D indicating there may be an environmental component to the disease. Glutathione (GSH) is the major endogenous antioxidant produced by the cell. GSH participates directly in the neutralization of free radicals and plays a role in the immune response. Glutathione-s-transferases (GSTs) conjugate GSH to free-radicals or xenobiotics. GST activity depletes GSH levels and may either detoxify or enhance the toxicity of a compound. Glutathione-s-transferase mu 1 (GSTM1) and glutathione-s-transferase theta 1 (GSTT1) have polymorphic homozygous deletion (null) genotypes resulting in complete absence of enzyme activity. GSTM1 and GSTT1 null genotypes in Caucasian populations have frequencies of approximately 40-60% and 15-20%, respectively. GST null genotypes have been associated with susceptibility to cancer and protection against chronic pancreatitis. The aim of this study was to investigate associations with GSTM1 and GSTT1 polymorphisms in a group T1D patients and control subjects 0-35 years old who participated in the Combined Swedish Childhood Diabetes Registry and Diabetes Incidence Study (1986-1988). Results show that the presence of the GSTM1 and not the null genotype (OR, 2.13 95% CI, 1.23-3.70, p-value, 0.007, Bonferroni corrected p-value, 0.035) may be a susceptibility factor in T1D 14-20 years old. These results suggest that the GSTM1 null genotype is associated with T1D protection and T1D age-at-onset and that susceptibility to T1D may involve GST conjugation.
Porous Poly(DL-lactic- co -glycolic acid)/Calcium Phosphate Cement Composite for Reconstruction of Bone Defects (2006)

Calcium phosphate (Ca-P) cements are injectable, self-setting ceramic pastes generally known for their favorable bone response. Ingrowth of bone and subsequent degradation rates can be enhanced by the inclusion of macropores. Initial porosity can be induced by CO(2) foaming during setting of the cement, whereas secondary porosity can develop after hydrolysis of incorporated poly(DL-lactic- co-glycolic acid) (PLGA) microparticles. In this study, we focused on the biological response to porous PLGA/Ca-P cement composites. Pre-set composite discs of four formulations (4 wt% or 15 wt% PLGA microparticles and low or high CO(2) induced porosity) were implanted subcutaneously and in cranial defects in rats for 12 weeks. Histological analysis of the explanted composites revealed that bone and fibrous tissue ingrowth was facilitated by addition of PLGA microparticles (number average diameter of 66 +/- 25 microm). No adverse tissue reaction was observed in any of the composites. Significant increases in composite density due to bone ingrowth in cranial implants were found in all formulations. The results suggest that the PLGA pores are suitable for bone ingrowth and may be sufficient to enable complete tissue ingrowth without initial CO(2) induced porosity. Finally, bone-like mineralization in subcutaneous implants suggests that, under appropriate conditions and architecture, porous PLGA/Ca-P cement composites can exhibit osteoinductive properties. These PLGA/Ca-P composites are a promising scaffolding material for bone regeneration and bone tissue engineering.
Restricted Authentication and Encryption for Cyber-physical Systems (2009)

Cyber-physical systems (CPS) are characterized by the close linkage of computational resources and physical devices. These systems can be deployed in a number of critical infrastructure settings. As a result, the security requirements of CPS are different than traditional computing architectures. For example, critical functions must be identified and isolated from interference by other functions. Similarly, lightweight schemes may be required, as CPS can include devices with limited computing power. One approach that offers promise for CPS security is the use of lightweight, hardware-based authentication. Specifically, we consider the use of Physically Unclonable Functions (PUFs) to bind an access request to specific hardware with device-specific keys. PUFs are implemented in hardware, such as SRAM, and can be used to uniquely identify the device. This technology could be used in CPS to ensure locationbased access control and encryption, both of which would be desirable for CPS implementations. The submitted manuscript has been authored by a contractor of the U.S. Government under contract DE-AC05-00OR22725. Accordingly, the U.S. Government retains a nonexclusive, royaltyfree license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes. 1
Fifteen-Year Survival in Prostate Cancer<subtitle>A Prospective, Population-Based Study in Sweden</subtitle> (1997)

Patients with localized prostate cancer have a favorable outlook following watchful waiting, and the number of deaths potentially avoidable by radical initial treatment is limited. Without reliable prognostic indicators, an aggressive approach to all patients with early disease would entail substantial overtreatment. In contrast, patients with locally advanced or metastatic disease need trials of aggressive therapy to improve their poor prognosis.