gebhart/patrepeval huggingface dataset:
Make the right measurement: Discovery of an allosteric inhibition site for p300-HAT (2019)

Histone acetyltransferases (HATs) and histone deacetylases (HDACs) catalyze the dynamic and reversible acetylation of proteins, an epigenetic regulatory mechanism associated with multiple cancers. Indeed, HDAC inhibitors are already approved in the clinic. The HAT paralogs p300 and CREB-binding protein (CBP) have been implicated in human pathological conditions including several hematological malignancies and androgen receptor-positive prostate cancer. Others have reported CoA-competitive inhibitors of p300 and CBP with cell-based activity. Here, we describe 2 compounds, CPI-076 and CPI-090, discovered through p300-HAT high throughput screening screening, which inhibit p300-HAT via binding at an allosteric site. We present the high resolution (1.7 and 2.3 Å) co-crystal structures of these molecules bound to a previously undescribed allosteric site of p300-HAT. Derivatization yielded actionable structure-activity relationships, but the full-length enzymatic assay demonstrated that this allosteric HAT inhibitor series was artifactual, inhibiting only the HAT domain of p300 with no effect on the full-length enzyme.
Low-Energy, High-Performance Lossless 8×8 SOA Switch (2015)

We demonstrate the first monolithically-integrated active-passive lossless 8×8 SOA switch. A wide IPDR of 14.5dB for penalty <1dB is achieved. The switch paths through the device exhibit excellent uniformity.
A multipath channel model for mobile-radio communications (2003)

A model for the mobile radio channel is proposed that is intended to apply to wideband signals in the 900 MHz band. The model is specified by a two-variable impulse response h/sub x/(t), where x represents the location of the receiver. The model consists of two submodels, one describing the direct line-of-sight path, and the other the signal that reaches the receiver over simple reflections. This geometric model is spatially stationary but time-invariant. Time variation is the result of the receiver's motion that alters the point x. Moreover the model is based on physical reasoning and places no restriction on the transmitted signal.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Chemical synthesis, expression and product assessment of a gene coding for biologically active human tumour necrosis factor α (1989)

A gene encoding human tumour necrosis factor alpha (TNF-alpha) has been chemically synthesized, cloned and expressed to yield a biologically active protein in Escherichia coli. The 480-bp gene was assembled by enzymic ligation of 32 oligonucleotides, cloned directly into M13mp18 for sequence verification and expressed in the broad host range high-level expression vector pMMB66EHST. Expressed recombinant TNF-alpha was shown to have the correct molecular weight, processed N-terminal sequence, antibody cross-reactivity and tumour cell killing activity. The expression product of the synthetic gene has been purified to homogeneity by a two-step ion-exchange procedure and the purified material shown to be active.
Synergistic activation of the insulin gene by a LIM-homeo domain protein and a basic helix-loop-helix protein: building a functional insulin minienhancer complex. (1992)

The distal portion of the rat insulin I gene 5'-flanking DNA contains two sequence elements, the Far and FLAT elements, that can function in combination, but not separately, as a beta-cell-specific transcriptional enhancer. We have isolated several cDNAs encoding proteins that bind to the FLAT element. Two of these cDNAs, cdx-3 and lmx-1, represent homeo box containing mRNAs with restricted patterns of expression. The protein encoded by lmx-1 also contains two amino-terminal cysteine/histidine-rich "LIM" domains. Both cdx-3 and lmx-1 can activate transcription of a Far/FLAT-linked gene when expressed in a normally non-insulin-producing fibroblast cell line. Furthermore, in fibroblasts expressing transfected beta-cell lmx-1, the addition of the Far-binding, basic helix-loop-helix protein shPan-1 (the hamster equivalent of human E47) causes a dramatic synergistic activation. ShPan-1 causes no activation in fibroblasts expressing transfected cdx-3 or the related LIM-homeodomain protein isl-1. Deletion of one or both of the LIM domains from the 5' end of the lmx-1 cDNA removes this synergistic interaction with shPan-1 without any loss of basal transcriptional activation. We conclude that beta-cell lmx-1 functions by binding to the FLAT element and interacting through the LIM-containing amino terminus with shPan-1 bound at the Far element. These proteins form the minimal components for a functional minienhancer complex.
Level of anti‐mouse‐antibody response induced by bi‐specific monoclonal antibody OC/TR in ovarian‐carcinoma patients is associated with longer survival (1999)

More than 60% of cancer patients injected with intact murine monoclonal antibody (MAb) develop a humoral response against the antigen even after a single dose. Analysis of a series of 35 ovarian-cancer patients entered in phase-I and -II clinical studies of T-cells retargeted with the bi-specific F(ab′)2 OC/TR revealed: (i) a detectable human anti-mouse antibody (HAMA) response in 31/35 (88%) patients, with high HAMA levels (≥150 ng/ml) in 18/31 (58%) cases by the end of the treatment; (ii) no correlation between HAMA levels and the form of delivery of the mAb (OC/TR bound to T cells or bound plus soluble), time schedule or cumulative dose; (iii) an association between high HAMA levels and favorable clinical parameters and response to immunotherapy; and (iv) a significantly longer median survival probability in patients with high HAMA levels than in patients with lower HAMA levels, even when the sub-group of non-responder patients was considered. Evaluation of the anti-idiotypic response in HAMA-positive sera indicated that 11/17 sera showed high-titer (>6000) binding of OC/TR, as evaluated by a specific radioimmunoassay, and 15/18 and 16/16 sera specifically inhibited the binding of the MOv18 and anti-CD3 parental MAbs to ovarian-carcinoma cells and T lymphocytes respectively. Of 7 patients evaluated for duration of the HAMA response, 5 showed stable or even increased HAMA levels. The long-lasting HAMA response maintained an anti-idiotypic component, directed mainly against the αCD3 idiotype of bi-MAb OC/TR in 2 out of 3 cases tested. Int. J. Cancer (Pred. Oncol.) 84:62–68, 1999. © 1999 Wiley-Liss, Inc.
Physiological response of <i>Clostridium carboxidivorans</i> during conversion of synthesis gas to solvents in a gas‐fed bioreactor (2012)

Clostridium carboxidivorans P7 is one of three microbial catalysts capable of fermenting synthesis gas (mainly CO, CO(2) , and H(2) ) to produce the liquid biofuels ethanol and butanol. Gasification of feedstocks to produce synthesis gas (syngas), followed by microbial conversion to solvents, greatly expands the diversity of suitable feedstocks that can be used for biofuel production beyond commonly used food and energy crops to include agricultural, industrial, and municipal waste streams. C. carboxidivorans P7 uses a variation of the classic Wood-Ljungdahl pathway, identified through genome sequence-enabled approaches but only limited direct metabolic analyses. As a result, little is known about gene expression and enzyme activities during solvent production. In this study, we measured cell growth, gene expression, enzyme activity, and product formation in autotrophic batch cultures continuously fed a synthetic syngas mixture. These cultures exhibited an initial phase of growth, followed by acidogenesis that resulted in a reduction in pH. After cessation of growth, solventogenesis occurred, pH increased and maximum concentrations of acetate (41 mM), butyrate (1.4 mM), ethanol (61 mM), and butanol (7.1 mM) were achieved. Enzyme activities were highest during the growth phase, but expression of carbon monoxide dehydrogenase (CODH), Fe-only hydrogenases and two tandem bi-functional acetaldehyde/alcohol dehydrogenases were highest during specific stages of solventogenesis. Several amino acid substitutions between the tandem acetaldehyde/alcohol dehydrogenases and the differential expression of their genes suggest that they may have different roles during solvent formation. The data presented here provide a link between the expression of key enzymes, their measured activities and solvent production by C. carboxidivorans P7. This research also identifies potential targets for metabolic engineering efforts designed to produce higher amounts of ethanol or butanol from syngas. .
Collagen matrix duraplasty for cranial and spinal surgery: a clinical and imaging study (2007)

When used as a dural onlay graft, collagen matrix had a 100% CSF containment rate but might be associated with occult radiological abnormalities.
Microvascularization of the human digit as studied by corrosion casting (2004)

The aim of this study was to describe microcirculation in the human digit, focusing on the vascular patterns of its cutaneous and subcutaneous areas. We injected a functional supranumerary human thumb (Wassel type IV) with a low-viscosity acrylic resin through its digital artery. The tissues around the vessels were then digested in hot alkali and the resulting casts treated for scanning electron microscopy. We concentrated on six different areas: the palmar and dorsal side of the skin, the eponychium, the perionychium, the nail bed and the nail root. On the palmar side, many vascular villi were evident: these capillaries followed the arrangement of the fingerprint lines, whereas on the dorsal side they were scattered irregularly inside the dermal papillae. In the hypodermal layer of the palmar area, vascular supports of sweat glands and many arteriovenous anastomoses were visible, along with glomerular-shaped vessels involved in thermic regulation and tactile function. In the eponychium and perionychium, the vascular villi followed the direction of nail growth. In the face of the eponychium in contact with the nail, a wide-mesh net of capillaries was evident. In the nail bed, the vessels were arranged in many longitudinal trabeculae parallel to the major axis of the digit. In the root of the nail, we found many columnar vessels characterized by multiple angiogenic buttons on their surface.
Automatic compilation to a coarse-grained reconfigurable system-opn-chip (2003)

The rapid growth of device densities on silicon has made it feasible to deploy reconfigurable hardware as a highly parallel computing platform. However, one of the obstacles to the wider acceptance of this technology is its programmability. The application needs to be programmed in hardware description languages or an assembly equivalent, whereas most application programmers are used to the algorithmic programming paradigm. SA-C has been proposed as an expression-oriented language designed to implicitly express data parallel operations. The Morphosys project proposes an SoC architecture consisting of reconfigurable hardware that supports a data-parallel, SIMD computational model. This paper describes a compiler framework to analyze SA-C programs, perform optimizations, and automatically map the application onto the Morphosys architecture. The mapping process is static and it involves operation scheduling, processor allocation and binding, and register allocation in the context of the Morphosys architecture. The compiler also handles issues concerning data streaming and caching in order to minimize data transfer overhead. We have compiled some important image-processing kernels, and the generated schedules reflect an average speedup in execution times of up to 6× compared to the execution on 800 MHz Pentium III machines.
Incidence of tooth loss among elderly Iowans. (1988)

This study investigated the 18-month incidence of tooth loss in a random sample of 451 dentate noninstitutionalized Iowans aged 65 and older residing in two rural counties. They had a mean of 19.0 teeth at baseline and lost an average of 0.4 teeth during the subsequent 18 months. Twenty-one per cent of the population lost at least one tooth. Four people had all their teeth extracted. Of the teeth present at baseline, 1.9 per cent subsequently were extracted. The highest incidence of tooth loss occurred among mandibular molars (3.7 per cent), followed by maxillary premolars and canines (3.1 per cent each). The best predictors of tooth loss were previous coronal and root caries.
A Short Synthesis of a Pyrrole Derivative Having a Chiral Substituent (1988)

Optically active pyrrole derivative 4 with a pyrrolidinyl group derived from L-proline has been prepared by a three-step sequence in 48% overall yield from N-benzyloxycarbonyl-L-prolyl chloride (1).
Mobile Augmented Reality: Placing Labels Based on Gaze Position (2016)

The arrangement of Augmented Reality (AR) labels on mobile displays can cause problems when the labels over populate the screen space. This can result in occlusion, not only of real scene, but also of other labels annotating the scene. We are developing view management systems that arrange and display AR content based on user attention. We present a pilot user study that tests speed and accuracy on a simple information retrieval task on simulated AR scenarios. We varied the presentation in two ways: a naive approach and a gaze-based approach. The results did not show statistical differences between the two methods, yet results from this study provide valuable insight for subsequent studies.
Lymphocytes bearing the γδ T cell receptor in acute Brucella melitensis infection (1993)

A phenotypical analysis carried out by indirect immunofluorescence and two-color cytofluorometry showed that the number of lymphocytes bearing the gamma delta T cell receptor (TcR) heterodimer was dramatically increased in the blood of six children with Brucella melitensis infection. Most in vivo expanded gamma delta T cells reacted with a monoclonal antibody which identifies V delta 2 gene products and a significant proportion expressed CD25 and HLA-DR activation antigens. In addition, whereas only a few gamma delta T lymphocytes were CD8+, nearly all were CD4-. Highly enriched populations of both alpha beta and gamma delta T cells were obtained by negative immunoselection from three subjects with brucellosis sampled during convalescence. Despite the different form of their TcR, the proliferation of these two major T cell subsets in response to a mitogenic anti-CD3 monoclonal reagent (OKT3) was optimal. In contrast, alpha beta, but not gamma delta, T lymphocytes proliferated vigorously in response to the antigenic stimulus elicited by heat-killed Brucella. Further studies are, therefore, needed to determine whether the selective expansion of the gamma delta T cell subpopulation observed during the clinical course of the infection is driven by antigenic determinant(s) borne by the pathogen in vivo or is due to host-derived stimuli, such as autologous heat-shock proteins expressed on the surface of the infected cells.
XI. Bibliography on piezoelectricity and pyroelectricity of polymers 1986-1987 (1988)

Abstract Abstract A bibliography on piezoelectricity and pyroelectricity of polymers is presented which includes 185 references published principally during 1986 and 1987. Research papers, reports, conference presentations, and patents are covered. A chronological bibliography is given, followed by an alphabetical list of all authors and a Key-Word-in- Context Index to all titles.
Nematic Liquid Crystal Spatial Light Modulators for Laser Beam Steering (2004)

Laser beam control is important in many applications. Phase modulating spatial light modulators (SLMs) can be used to electronically alter the phase distribution of an optical wave-front and thus change the direction and shape of a laser beam. Physical constraints set limitations to the SLM and an ideal phase distribution can usually not be realised. In order to understand how such components can be used for non-mechanical beam control three nematic liquid crystal (NLC) SLMs have been thoroughly characterised and modelled. The pixel structure and phase quantisation give a discrepancy between ideal and realised phase distributions. The impact on beam steering capability was examined by measurements and simulations of the intensity distribution in the far-field. In two of the studied SLMs the pixel period was shorter than the thickness of the LC layer giving the optical phase shift. This results in a so-called “fringing field”, which was shown to degrade the phase modulation and couple light between polarisation modes. The deformation of the LC was simulated and a finite-difference time-domain (FDTD) algorithm was used to calculate how polarised light propagates through the optically anisotropic SLM. Non-mechanical beam steering and tracking in an optical free-space communication link were demonstrated. Continual optimisation of the steering angle was achieved by feedback from a video camera. The optical properties of the SLM in the time period right after a voltage update were studied. It was shown how light is redistributed between orders during the switching from one blazed grating to another. By appropriate choice of the blazed gratings the effects on the diffraction efficiency can be minimised. The detailed knowledge of the SLM structure and its response to electronic control makes it possible to predict and optimise the device performance in future systems.
Review of current guidelines related to the diagnosis and treatment of rhinosinusitis (2008)

Accurate diagnosis of rhinosinusitis with recommended treatments should standardize management. However, these recommendations are guidelines and the clinician's judgment is highly important.
Immunosuppressive activity of T cell clones generated from human T cells stimulated with autologous TPHA cells. (1987)

T cell clones were generated from human T cells stimulated with autologous phytohemagglutinin (PHA)-activated T (TPHA) cells. Characterization of three T cell clones originated from donor SF and one from donor JM showed that they proliferated when stimulated with autologous TPHA cells, non-T cells, and peripheral blood mononuclear cells, but did not proliferate when stimulated with allogeneic TPHA cells, non-T cells, and mononuclear cells, with autologous and allogeneic resting T cells, and with PHA. These results in conjunction with the blocking of the proliferation by anti-histocompatibility leukocyte antigen class II monoclonal antibodies indicate that these class II antigens are involved in the proliferation of T cell clones stimulated with autologous lymphoid cells. The four T cell clones are cytotoxic neither to autologous lymphoid cells nor to a panel of cultured human cell lines. The four T cell clones display immunosuppressive activity, since they inhibit the proliferation of autologous and allogeneic cells stimulated with antigens and mitogens and the secretion of immunoglobulin by B cells stimulated with pokeweed mitogen in presence of T cells. Furthermore, the four T cell clones display differential inhibitory activity on the proliferation of cultured human cell lines. The immunosuppressive activity is species-specific, since the T cell clones do not inhibit the proliferation of murine cells. The suppression is mediated by a factor(s) with an apparent m.w. of 13,000 to 16,000. The suppressor activity is labile at alkaline pH and is lost following incubation with pronase (100 U/ml) for 30 min at 37 degrees C.
High abrasion resistance laminated Sendust VTR heads (1992)

High-performance laminated sputtered Sendust (LSS) video heads with high abrasion resistance have been realized by using a newly developed CaO-TiO/sub 2/-NiO ceramic substrate. For acceptable head abrasion for practical use of 15 mu m, head life is more than 1000 h at more than 20 m/s relative tape-head speed. Low magnetostriction Sendust films provide high reproduce voltage for the head. The LSS head, with CaO-TiO/sub 2/-NiO substrate, has sufficient performance for use as high-definition television (HDTV) video tape recorder (VTR) heads.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Measuring soluble salts in soils via portable x-ray fluorescence spectrometry (2013)

Soil scientists have been using the same quantification methods for soluble salts for decades. Yet they have long struggled with an effective method for quantifying gypsum content, because current methods are fraught with problems. Saline soil has been historically defined as soil containing salts more soluble than gypsum (e.g., various combinations of Na+, Mg2+, Ca2+, K+, Cl-, SO42-, HCO3- and CO32-) to the extent that soil fertility is severely reduced across a wide array of climates and geological settings. Since salinity is not germane to specific soil characteristics such as texture or parent material, it can be challenging to predict salt concentrations within a profile. Given the success of previous studies using portable x-ray fluorescence (PXRF) as a tool for measuring soil characteristics, the evaluation of soluble salts in soil with PXRF seems timely. Not only does this newer technology offer more accurate, quantifiable data to investigators, it produces results in-situ, in seconds. Recent enhancements to PXRF spectrometers have provided better detection limits especially for lighter elements such as S and Cl, a key component of gypsum and other salts. Thus, this research aimed to test the effectiveness of PXRF as a means of directly quantifying gypsum and salinity in soils. A total of 102 soil samples containing a wide variety of gypsum (~2–95%) and 122 samples with various salt concentrations were subjected to both traditional laboratory analysis (thermogravimetry and electrical conductivity, respectively) and elemental analysis via PXRF. Simple and multiple linear regression were used to establish the relationship between the two data sets. Log transformation of some data sets was necessary to normalize the data. Using simple linear regression between laboratory and PXRF data, an R2 of 0.88 was produced for the gypsum data, and an R2 of 0.839 was produced for salinity data. Similarly, simple linear regression for laboratory-quantified gypsum vs. PXRF S produced an R2 of 0.91. Multiple linear regression of laboratory quantified gypsum vs. both PXRF S and Ca produced an R2 of 0.91, and 0.8669 for laboratory determined EC (dS m-1) vs. PXRF Cl, S, Ca, and K. No significant differences were observed between model generation and validation data sets. Overall, PXRF shows great promise for the direct quantification of soluble salts in soils.
Efficient signal processing in MIMO radars (2011)

An efficient way to process data of MIMO radars by means of FFT is here discussed. However, MIMO radars are here shown to suffer a discontinuous phase history across all the channels, due to their geometry, especially in the short-range. In turn, this would prevent the FFT-based algorithm to work correctly. Consequently, it is here shown that data of MIMO radars have to be pre-processed in order to allow an efficient FFT-based focalization. For this purpose a sub-optimal algorithm is presented, discussed and tested against real data gathered by the JRC MIMO radar system.
Using CART to generate partially synthetic public use microdata (2005)

To limit disclosure risks, one approach is to release partially synthetic, public use microdata sets. These comprise the units originally surveyed, but some collected values, for example sensitive values at high risk of disclosure or values of key identifiers, are replaced with multiple imputations. This article presents and evaluates the use of classification and regression trees to generate partially synthetic data. Two potential applications of CART are studied via simulation: (i) generate synthetic data for sensitive variables; and, (ii) generate synthetic data for variables that are key identifiers. 1