gebhart/patrepeval huggingface dataset:
The Rabbit Ileal Lipid‐Binding Protein Gene Cloning and Functional Expression of the Recombinant Protein (1996)

A bile-acid-binding protein of Mr 14000 has been previously identified by photoaffinity labeling in rabbit ileal brush border membrane vesicles [Kramer et al. (1993) J. Biol. Chem. 268, 18035-18046]. This peripheral membrane-associated protein was purified and identified as an ileal lipid-binding protein. It was further shown to be identical to the cytosolic 14-kDa bile-acid-binding protein from the same tissue. Starting with sequence information from tryptic fragments, we cloned and sequenced the gene and its transcript. It has four exons (123, 176, 90, 115 bp) and three introns (1372, 2291, 3137 bp) and a similar structure as the genes from other members of the fatty-acid-binding protein family. The deduced protein has 128 amino acid residues and a calculated molecular mass of 14404 Da. It exhibits high similarity to its human (83%), mouse (77%), rat (76%) and porcine (72%) counterparts. Furthermore, the recombinant protein was produced in Escherichia coli and shown to be identical to native protein from ileal tissue. Functionality of the recombinant protein was demonstrated by labeling with various photoaffinity derivatives of bile acids. Ranking of the photolabeling efficiency of these probes towards the recombinant protein was comparable to the respective ranking towards the native protein. Polyclonal antibodies that were raised in hens against the recombinant protein, specifically recognized the ileal lipid-binding protein in the brush border membrane and cytosol from rabbit ileum. In contrast, no labeling was observed with jejunal tissue. Our results suggest a specific role of the membrane-associated ileal lipid-binding protein for the process of ileal bile acid uptake.
Backpropagation and adaptive resonance theory in predicting suicidal risk (1998)

The ability of backpropagation and adaptive resonance theory (ART) neural networks to predict the probability of complete suicide, within a two year span, in major psychiatric patients was investigated. Variables associated with suicide risk were collected from the files of 161 hospitalized psychiatric patients with a 10 year or greater history of illness. 84 patients were hospitalized due to suicide attempts and 77 had no previous suicide attempts or ideations. Suicide attempts were rated as medically serious suicide attempts (MSSA) or non-MSSA and used for training the systems. The ability of the neural networks was evaluated by screening the extremes of the suicidal spectrum (1) 54 records of patients who committed suicide and (2) 150 records of patients who never had suicidal thoughts. The records were taken from 3 hospitals, in various geographic regions in Israel. Neither neural network system is reliable in predicting suicide, however, records from one hospital, Gehah Hospital, were better identified than those from the two other hospitals (p < 0.05 for PPV; p < 0.01 for specificity). At present, neural networks are not reliable instruments for evaluating suicidal risk due to the significant number of false positive results. When low risk was indicated reliability was greater (NPV = 75.28%, specificity = 97.10% with ART; NPV = 91.76%, specificity = 95.12% with backpropagation). However, PPV, NPV and specificity rates of both systems achieved with Gehah Hospital records suggest that using a direct-subjective questionnaire may produce better results in the future. ART and backpropagation performed similarly in all measurements.
Evolution of a Novel, Orally Bioavailable Series of PI3Kδ Inhibitors from an Inhaled Lead for the Treatment of Respiratory Disease (2016)

A four-step process of high-quality modeling of existing data, deconstruction, identification of replacement cores, and an innovative synthetic regrowth strategy led to the rapid discovery of a novel oral series of PI3Kδ inhibitors with promising selectivity and excellent in vivo characteristics.
(Invited) Electrical Performance Improvement in 300mm Ge-Based Devices (2021)

As device feature size continues to scale, new device architecture and dielectric materials with engineered properties are becoming essential in overcoming the issues in scaled CMOS devices such as short channel effects. Some of the recent innovations device makers are exploring for better electrostatic control and improved performance are the introduction of new device architecture such as gate all around devices (nanowires/nanosheets), and channel engineering such as high mobility channel materials (Ge and III-V). Ge is particularly attractive for use as a channel material for P-type MOSFETs due to its high hole mobility and Si VLSI high volume manufacturing (HVM) compatibility. However, there are couple significant remaining challenges to integrating Ge into 300mm Si VLSI HVM which are a stable gate-stack formation and integration of Ge on Si (1-5). In this talk, advances in Ge gate stack engineering will be discussed. Using Si compatible technologies we have demonstrated scaled EOT by engineering both the interface and high-k formation. Reference Swaminathan, Y. Oshima, M. Kelly, P.C. McIntyre, Appl. Phys. Lett., 95, 032907 (2009). Zhang, M. Gunji, S. Thombare, P.C. McIntyre, IEEE Electr. Device. L. , 34 , 736 (2013). H Lee, T. Nishimura, C. Lu, S. Kabuyanagi, A. Toriumi, IEDM , 32.5.1 (2014). S. Goley, M. K. Hudait, Materials , 2301 (2014). Xie, S. Deng, M. Shaekers, D. Lin, M. Caymax, A. Delabie, X-P Qu, Y-L. Jiang, D. Dedytsche, C. Detavernier, Semicond. Sci. Technol. 074012 (2012)
Enzyme-Linked Immunosorbent Spot Assay Analysis of Peripheral Blood Lymphocyte Reactivity to Donor HLA-DR Peptides (2002)

Chronic allograft dysfunction, which is the most common cause of late allograft failure, is in part caused by an ongoing immune response orchestrated by T lymphocytes primed by the indirect pathway of allorecognition. The low frequencies of such T cells have made it difficult to study indirect alloreactivity by using currently available assays. The development of a sensitive, clinically useful method of measuring indirect alloreactivity among human renal transplant recipients was thus attempted. Furthermore, in a pilot immunologic study, the contribution of the indirect pathway was studied in two groups of renal transplant recipients, i.e., patients with no prior acute rejection episodes and stable renal function ("stable" patients) and patients with at least one previous episode of biopsy-proven acute rejection, who were thus at risk for the development of chronic rejection ("high-risk" patients). The frequencies of type 1 T helper (interferon-gamma-producing) and type 2 T helper (interleukin-5- and -10-producing) peripheral blood lymphocytes reactive with a panel of synthetic peptides (corresponding to sequences from donor HLA-DR molecules) were determined for renal transplant recipients and normal control subjects by using an enzyme-linked immunosorbent spot assay (ELISPOT). Among recipients of DR-mismatched allografts, a cut-off value of 60 interferon-gamma spots/10(6) cells significantly (P = 0.02) separated stable patients (creatinine concentration, 1.1 +/- 0.3 mg/dl) from high-risk patients (creatinine concentration, 2.3 +/- 1.7 mg/dl). This is the first demonstration that the enzyme-linked immunosorbent spot assay can be used to monitor indirect alloreactivity to donor HLA-DR peptides among renal transplant recipients. These data provide the rationale for the prospective study of indirect alloreactivity among transplant recipients, to allow predictions of which patients would be at risk for the development of chronic rejection and thus allow appropriate planning of future interventions.
Prevention of dewetting during annealing of FePt films for bit patterned media applications (2012)

We investigated different fabrication methods for (002) textured high anisotropy L10-FePt thin continuous films. While depositing at elevated temperature or post-annealing yields discontinuous or very rough films unsuitable for bit patterned media (BPM) fabrication, post-annealing with an additional SiO2 cap layer results in smooth continuous L10-FePt thin films that can be used for patterning. The SiO2 layer can be removed after annealing without significantly damaging the FePt, thus allowing additional deposition of lower anisotropy layers for forming exchange coupled composite or other layered BPM structures.
Fatigue Life Extension of AA2024 Specimens and Integral Structures by Laser Shock Peening (2018)

The goal of the present study is to understand the effects of laser shock peening (LSP)-induced residual stresses on the fatigue crack propagation (FCP) behaviour of the commonly used aircraft aluminium alloy AA2024 in T3 heat treatment condition. LSP treatment was performed using a pulsed Nd:YAG laser on compact tensile C(T)50-specimens with a thickness of 2.0 mm. LSP-treated specimens reveal a significant retardation of the fatigue crack propagation. The fatigue crack retardation effect can be correlated with the compressive residual stresses introduced by LSP throughout the entire specimen thickness. A possible application of the LSP process on a component like panel with three welded stringers representing a part of a fuselage structure was performed as well. The skin-stringer AA2024-AA7050 Tjoints were realised through stationary shoulder friction stir welding (SSFSW), a variant of the conventional friction stir welding process. In this relatively new process, the shoulder does not rotate and therefore does not contribute to the heat generation. Consequently, a reduced and more homogeneous heat input leads to a less affected microstructure and better mechanical properties. The efficiency of the LSP process has been demonstrated resulting in an increase of 200 – 400% in fatigue lifetime.
Histone H3 K56 Hyperacetylation Perturbs Replisomes and Causes DNA Damage (2008)

Deacetylation of histone H3 K56, regulated by the sirtuins Hst3p and Hst4p, is critical for maintenance of genomic stability. However, the physiological consequences of a lack of H3 K56 deacetylation are poorly understood. Here we show that cells lacking Hst3p and Hst4p, in which H3 K56 is constitutively hyperacetylated, exhibit hallmarks of spontaneous DNA damage, such as activation of the checkpoint kinase Rad53p and upregulation of DNA-damage inducible genes. Consistently, hst3 hst4 cells display synthetic lethality interactions with mutations that cripple genes involved in DNA replication and DNA double-strand break (DSB) repair. In most cases, synthetic lethality depends upon hyperacetylation of H3 K56 because it can be suppressed by mutation of K56 to arginine, which mimics the nonacetylated state. We also show that hst3 hst4 phenotypes can be suppressed by overexpression of the PCNA clamp loader large subunit, Rfc1p, and by inactivation of the alternative clamp loaders CTF18, RAD24, and ELG1. Loss of CTF4, encoding a replisome component involved in sister chromatid cohesion, also suppresses hst3 hst4 phenotypes. Genetic analysis suggests that CTF4 is a part of the K56 acetylation pathway that converges on and modulates replisome function. This pathway represents an important mechanism for maintenance of genomic stability and depends upon proper regulation of H3 K56 acetylation by Hst3p and Hst4p. Our data also suggest the existence of a precarious balance between Rfc1p and the other RFC complexes and that the nonreplicative forms of RFC are strongly deleterious to cells that have genomewide and constitutive H3 K56 hyperacetylation.
Rocky Mountain spotted fever vaccine in an animal model (1983)

Formalin-killed, purified Rickettsia rickettsii vaccine was evaluated in a guinea pig model of R. rickettsii infection. Vaccinated guinea pigs were partially protected by the vaccine when challenged with virulent, viable rickettsiae. Greater protection was observed when higher doses of vaccine were given and when frequent booster injections were administered. Stimulation of cell-mediated immunity to the vaccine antigens was variable and also appeared to be achieved more reproducibly with booster vaccinations. Serum antibody was elicited by high doses of vaccine and by booster vaccinations. The presence of serum antibody was useful in predicting immunity to challenge with R. rickettsii.
Latency-Associated Peptide Identifies a Novel CD4+CD25+ Regulatory T Cell Subset with TGFβ-Mediated Function and Enhanced Suppression of Experimental Autoimmune Encephalomyelitis (2008)

CD4(+)CD25(+) regulatory T cells (Tregs) are essential for maintaining self-tolerance and immune homeostasis. Here we characterize a novel subset of CD4(+)CD25(+) Tregs that express latency-associated peptide (LAP) on their cell surface (CD4(+)CD25(+)LAP(+) cells). CD4(+)CD25(+)LAP(+) cells express elevated levels of Foxp3 and Treg-associated molecules (CTLA4, glucocorticoid-induced TNFR-related gene), secrete TGFbeta, and express both cell surface TGFbeta and surface receptors for TGFbeta. In vitro, the suppressive function of CD4(+)CD25(+)LAP(+) cells is both cell contact and soluble factor dependent; this contrasts with CD4(+)CD25(+)LAP(-) cells, which are mainly cell contact dependent. In a model of experimental autoimmune encephalomyelitis, CD4(+)CD25(+)LAP(+) cells exhibit more potent suppressive activity than CD4(+)CD25(+)LAP(-) cells, and the suppression is TGFbeta dependent. We further show that CD4(+)CD25(+)LAP(+) cells suppress myelin oligodendrocyte glycoprotein-specific immune responses by inducing Foxp3 and by inhibiting IL-17 production. Our findings demonstrate that CD4(+)CD25(+) Tregs are a heterogeneous population and that the CD4(+)CD25(+) subset that expresses LAP functions in a TGFbeta-dependent manner and has greater in vivo suppressive properties. Our work helps elucidate the ambiguity concerning the role of TGFbeta in CD4(+)CD25(+) Treg-mediated suppression and indicates that LAP is an authentic marker able to identify a TGFbeta-expressing CD4(+)CD25(+) Treg subset.
Understanding cracking behavior of glass from its response to hydrostatic compression (2020)

Under sharp contact loading, glass deforms elastically and then plastically in the form of densification, shear flow, and network structure changes, which interplay with each other and lead to stress/residual stress buildup and cracking. Vickers indentation is often used to study the deformation and cracking behavior of glass; however, it is not easy to delineate the individual contribution of each deformation mode under indentation due to experimental difficulties associated with in situ investigations at a local scale (tens of microns) under nonuniform stresses. Given the stress field under an indenter is largely compressive, hydrostatic compression and decompression in a diamond anvil cell (DAC) were used in this work to help understand the response of glass to indentation during the loading and unloading process. To this end, an optical microscopy technique was developed to measure the volume of glass under pressure in the DAC by using argon as a pressure transmitting medium. This provided the densification and recovery of glass under hydrostatic compression and decompression. In situ Brillouin light scattering experiments were carried out at the same time to measure the elastic response of glass to pressure. A few multicomponent glasses with vastly different indentation cracking behaviors were selected for study in this work. Our experiments reveal that glass with a high ability to undergo reversible structure changes in response to hydrostatic compression and decompression shows a high cracking resistance under sharp contact loading.
Chitin for the Replacement of Fluoropolymers in the Assembly of Electrochemical Devices (2018)

Chitin and graphene/chitin composite films were prepared using ionic liquid processing and tested as separators and electrodes, respectively, in a supercapacitor to demonstrate the construction and function of an energy storage device which is constructed solely from bio-based polymer materials. The dry films possessed high thermal (Td = 265 and 246 °C) and mechanical (tensile strength = 5(1) and 1.7(2) MPa) stabilities. Once soaked in an aqueous electrolyte (2 M (NH4)2SO4) for use in a supercapacitor test cell, the device reached a peak capacitance value of 2.4 F/g. This work demonstrates a first step towards a scalable method for the preparation and assembly of biorenewable electrochemical devices, which avoid the use of unsustainable fluoropolymers and solvents, and is poised to be an important part of environmentally-sustainable economies.
Realizing a Two-Dimensional Ordered Array of Ferritin Molecules Directly on a Solid Surface Utilizing Carbonaceous Material Affinity Peptides (2007)

A two-dimensional hexagonally close-packed (2D-HCP) array of ferritin molecules with a nanoparticle core was fabricated directly on a carbonaceous solid substrate by genetically modifying the outer surface of the ferritin with carbonaceous materials-specific binding peptides. The displayed peptides endowed ferritins with a specific protein-substrate interaction and masked the strong nonspecific interaction. The specific interaction was weak enough to allow ferritins to be rearranged as well as an attractive protein-protein interaction that could be adjusted by selecting the buffer conditions. This method not only produced 2D-HCP arrays of ferritin but also 2D-ordered arrays of independent inorganic nanoparticles after protein elimination that can be applied to floating gate memories.
Automatic Formal Verification of Fused-Multiply-Add FPUs (2005)

In this paper we describe a fully-automated methodology for formal verification of fused-multiply-add floating point units (FPU). Our methodology verifies an implementation FPU against a simple reference model derived from the processor's architectural specification, which may include all aspects of the IEEE specification including denormal operands and exceptions. Our strategy uses a combination of BDD- and SAT-based symbolic simulation. To make this verification task tractable, we use a combination of case-splitting, multiplier isolation, and automatic model reduction techniques. The case-splitting is defined only in terms of the reference model, which makes this approach easily portable to new designs. The methodology is directly applicable to multi-GHz industrial implementation models (e.g., HDL or gate-level circuit representations) that contain all details of the high-performance transistor-level model, such as aggressive pipelining, clocking, etc. Experimental results are provided to demonstrate the computational efficiency of this approach.
Database security (1990)

article Database security Share on Authors: Teresa F. Lunt Computer Science Laboratory, SRI International, Menlo Park, California Computer Science Laboratory, SRI International, Menlo Park, CaliforniaView Profile , Eduardo B. Fernandez Dept. of Computer Engineering, Florida Atlantic University, Boca Raton, Florida Dept. of Computer Engineering, Florida Atlantic University, Boca Raton, FloridaView Profile Authors Info & Claims ACM SIGMOD RecordVolume 19Issue 4Dec. 1990 pp 90–97https://doi.org/10.1145/122058.122069Published:01 December 1990 21citation3,007DownloadsMetricsTotal Citations21Total Downloads3,007Last 12 Months74Last 6 weeks19 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Multimaterial multifunctional fiber devices (2009)

Recent discoveries have enabled the integration of metals, insulators and semiconductors structures into extended length of polymer fibers. The challenges and opportunities associated with this new class of fiber devices will be presented.
In Reply: Dominance of Ossicular Route in Sound Transmission (2016)

We reported that the degree of conductive hearing loss resulting from a tympanic membrane (TM) perforation would be expected with the size of perforation and pneumatization of middle ear and mastoid, not location of perforation. This result was conflicted with previous study that revealed the influence of location of TM perforation on the severity of hearing loss in 1970
Low-density polymer thin film formation in supercritical carbon dioxide (2003)

We report a method for producing stable low-density polymer films by using supercritical carbon dioxide (scCO2). Two different molecular weight polystyrene films with various thicknesses were exposed to scCO2 along the density fluctuation ridge in P–T phase diagram. The swollen structures could be then frozen by flash evaporation of CO2 without forming additional voids. X-ray reflectivity data clearly showed that exposure to scCO2 could be used to produce uniform low-density films of about 2Rg thick or less, where Rg is radius of polymer gyration.
45-cm long compression-molded polymer-based optical bus (1993)

We report the formation of an optical bus using compression-molding technique. The linear dimension of such a waveguide is well beyond that of a microlithographically defined waveguide. Theoretical calculation based on the effective index method was used to determine the optimal dimension of the molding tool design for single- and multimode waveguides. A molded photolime gel-based polymer optical bus with a linear dimension of 45 cm was fabricated and then tested at 0.6328-μm wavelength. Waveguide propagation loss from 0.5 to 2 dB/cm was determined using the two prism method. As a result of this long interconnection distance, board-to-board optical interconnects through backplane can be realized using the technology.
Animal Toxins Influence Voltage-Gated Sodium Channel Function (2014)

Voltage-gated sodium (Nav) channels are essential contributors to neuronal excitability, making them the most commonly targeted ion channel family by toxins found in animal venoms. These molecules can be used to probe the functional aspects of Nav channels on a molecular level and to explore their physiological role in normal and diseased tissues. This chapter summarizes our existing knowledge of the mechanisms by which animal toxins influence Nav channels as well as their potential application in designing therapeutic drugs.
Spectral selective mid-infrared detector on a silicon platform (2009)

We report the design, fabrication, and characterization of spectral selective mid-infrared PbTe photodetector pixels monolithically integrated on a silicon platform. We demonstrate spectral selectivity with a peak responsivity of 65.4 V/W.
Learning to use a brain-machine interface: Model, simulation and analysis (2009)

This paper presents a model of the learning process occurring during operation of a closed-loop brain-machine interface. The model consists of a population of simulated cortical neurons, a decoder that transforms neural activity into motor output, a feedback controller whose role is to reduce the error based on an error-descent algorithm, and an open-loop controller whose parameters are updated based on the corrections made by the feedback controller. We present evidence of the convergence of the internal model to the decoder's inverse model and use global sensitivity analysis to study the convergence's dependence on the parameters of the overall learning model. This model can be used as a simulation tool that predicts the outcome of closed-loop BMI experiments.
Laminin and Fibronectin Treatment Leads to Generation of Dendritic Cells with Superior Endocytic Capacity (2010)

These studies underline the importance of including ECM components in in vitro studies investigating DC biology and DC-T cell interaction. Within the context of antigen specific DC induced T cell proliferation, inclusion of ECM proteins could lead to development of more sensitive assays.