gebhart/patrepeval huggingface dataset:
Crystal structure of human recombinant interleukin‐4 at 2.25 Å resolution (1992)

The crystal structure of human recombinant interleukin-4 (IL-4) has been solved by multiple isomorphous replacement, and refined to an R factor of 0.218 at 2.25 A resolution. The molecule is a left-handed four-helix bundle with a short stretch of beta sheet. The structure bears close resemblance to other cytokines such as granulocyte-macrophage colony stimulating factor (GM-CSF). Although no sequence similarity of IL-4 to GM-CSF and other related cytokines has been previously postulated, structure-based alignment of IL-4 and GM-CSF revealed that the core of the molecules, including large parts of all four helices and extending over half of the molecule, has 30% sequence identity. This may have identified regions which are not only important to maintain structure, but could also play a role in receptor binding.
Thermoelectric Energy Harvesting of Human Body Heat for Wearable Sensors (2013)

The study of thermoelectric energy harvesting on people presented in this paper shows that although power generation is affected by many factors such as ambient temperature, wind speed, clothing thermal insulation, and a person's activity, it does not directly depend on metabolic rate as shown in the experiment. The relevant thermal properties of humans measured at different ambient conditions are reported. Several thermopiles are either attached with a strap directly to the skin or integrated into garments in different locations on human body, and power generation is extensively studied at different ambient conditions. Textile covering thermopiles is found not to essentially decrease power generation. Therefore, a hidden energy harvester is integrated into an office-style shirt and tested on people in real life. It generated power in 5-0.5 mW range at ambient temperatures of 15 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">°</sup> C-27 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">°</sup> C, respectively. The thermoelectric shirt with such an energy harvester produces more energy during nine months of use (if worn 10 h/day) than the energy stored in alkaline batteries of the same thickness and weight.
Developing a High Density Pt/Alumina Hermetic Feedthrough (2012)

Typically, hermetic feedthroughs for implantable devices, such as pacemakers, use a alumina ceramic insulator brazed to a platinum wire pin. This combination of material has a long history in implantable devices and has been approved by the FDA for implantable hermetic feedthroughs. The growing demand for increased input/output (I/O) hermetic feedthroughs for implantable neural stimulator applications could be addressed by developing a new, cofired platinum/alumina multilayer ceramic technology in a configuration that supports 300 plus I/Os, which is not commercially available. Seven platinum powders with different particle sizes were used to develop different conductive cofire inks to control the densification mismatch between platinum and alumina. Firing profile (ramp rate, burn- out and holding times) and firing atmosphere and concentrations (hydrogen (wet/dry), air, neutral, vacuum) were also optimized. Platinum and alumina exhibit the alloy formation reaction in a reduced atmosphere. Formation of any compound can increase the bonding of the metal/ceramic interface, resulting in enhanced hermeticity. The feedthrough fabricated in a reduced atmosphere demonstrated significantly superior performance than that of other atmospheres. A composite structure of tungsten/platinum ratios graded thru the via structure (pure W, 50/50 W/Pt, 80/20 Pt/W and pure Pt) exhibited the best performance in comparison to the performance of other materials used for ink metallization. Studies on the high temperature reaction of platinum and alumina, previously unreported, showed that, at low temperatures in reduced atmosphere, Pt3Al or Pt8Al21 with a tetragonal structure would be formed. Cubic Pt3Al is formed upon heating the sample to temperatures above 1350 °C. This cubic structure is the equilibrium state of Pt-Al alloy at high temperatures. The alumina dissolves into the platinum ink and is redeposited as a surface coating. This was observed on both cofired samples and pure platinum thin films coated on a 99.6 Wt% alumina and fired at 1550 °C. Different mechanisms are proposed to describe this behavior based on the size of the platinum particle.
Profiling Human Serum Antibodies with a Carbohydrate Antigen Microarray (2009)

Carbohydrate antigen arrays (glycan arrays) have been recently developed for the high-throughput analysis of carbohydrate macromolecule interactions. When profiling serum, information about experimental variability, interindividual biological variability, and intraindividual temporal variability is critical. In this report, we describe the characterization of a carbohydrate antigen array and assay for profiling human serum. Through optimization of assay conditions and development of a normalization strategy, we obtain highly reproducible results with a within-experiment coefficient of variation (CV) of 10.8% and an overall CV (across multiple batches of slides and days) of 28.5%. We also report antibody profiles for 48 human subjects and evaluate for the first time the effects of age, race, sex, geographic location, and blood type on antibody profiles for a large set of carbohydrate antigens. We found significant dependence on age and blood type of antibody levels for a variety of carbohydrates. Finally, we conducted a longitudinal study with a separate group of 7 serum donors to evaluate the variation in anti-carbohydrate antibody levels within an individual over a period ranging from 3 to 13 weeks and found that, for nearly all antigens on our array, antibody levels are generally stable over this period. The results presented here provide the most comprehensive evaluation of experimental and biological variation reported to date for a glycan array and have significant implications for studies involving human serum profiling.
Characterization and Effects of the Replicated Flowering Time Gene FLC in Brassica rapa (2002)

Functional genetic redundancy is widespread in plants and could have an important impact on phenotypic diversity if the multiple gene copies act in an additive or dosage-dependent manner. We have cloned four Brassica rapa homologs (BrFLC) of the MADS-box flowering-time regulator FLC, located at the top of chromosome 5 of Arabidopsis thaliana. Relative rate tests revealed no evidence for differential rates of evolution and the ratios of nonsynonymous-to-synonymous substitutions suggest BrFLC loci are not under strong purifying selection. BrFLC1, BrFLC2, and BrFLC3 map to genomic regions that are collinear with the top of At5, consistent with a polyploid origin. BrFLC5 maps near a junction of two collinear regions to Arabidopsis, one of which includes an FLC-like gene (AGL31). However, all BrFLC sequences are more closely related to FLC than to AGL31. BrFLC1, BrFLC2, and BrFLC5 cosegregate with flowering-time loci evaluated in populations derived by backcrossing late-flowering alleles from a biennial parent into an annual parent. Two loci segregating in a single backcross population affected flowering in a completely additive manner. Thus, replicated BrFLC genes appear to have a similar function and interact in an additive manner to modulate flowering time.
Regioselective [5,5]-Sigmatropic Rearrangement Reactions of Aryl Hydrazides (2006)

[reaction: see text] N,N'-Aryl hydrazides with substituents at the ortho or meta positions undergo highly regioselective [5,5]-sigmatropic rearrangement reactions to furnish benzidines in good to excellent isolated yields. The presence of single substituent at either the ortho or meta position provides sufficient bias, effectively suppressing the formation of diphenylene, the major byproduct of the conventional benzidine rearrangement reaction.
Identification of novel mutations that confer drug resistance in the human immunodeficiency virus polymerase gene. (1994)

We generated variants of the human immunodeficiency virus type 1 (HIV-1) that are resistant to 2',3'-dideoxycytidine (ddC) and 2',3'-didehydro-3'-deoxythymidine (d4T) by in vitro selection in MT-4 cells. Portions of flanking protease and integrase sequences as well as the complete reverse transcriptase (RT) open-reading frame of these viruses were cloned and sequenced, using polymerase chain reaction (PCR)-based methods. Mutations were observed at amino acid position 65 (Lys-->Arg; AAA-->AGA) when ddC was employed in the selection procedure and at site 50 (Ile-->Thr; ATT-->ACT) when d4T was used. We confirmed the ability of these mutations to confer diminished sensitivity for these compounds by site-directed mutagenesis, in which these mutations were inserted into the pol gene of infectious recombinant HXB2-D DNA. Viruses that contained the site 65 mutation possessed approximately 5-10 fold resistance against ddC when compared with wild-type HXB2-D. The site 50 mutation conferred approximately 30-fold resistance to d4T in these same assays. Similar results were obtained using primary cord blood lymphocytes in drug resistance assays, indicating that these mutations could confer drug resistance in more than one cell type and that the respective mutations could be expressed in cells of primary origin. No cross-resistance against 3'-azido-3'-deoxythymidine (AZT) was noted for either the site 65 or 50 mutations.
Protein Kinase C and A3Adenosine Receptor Activation Inhibit Presynaptic Metabotropic Glutamate Receptor (mGluR) Function and Uncouple mGluRs from GTP-Binding Proteins (1998)

One of the most prominent roles of metabotropic glutamate receptors (mGluRs) in the CNS is to serve as presynaptic receptors that inhibit transmission at glutamatergic synapses. Previous reports suggest that the presynaptic effect of group II mGluRs at corticostriatal synapses can be inhibited by activators of protein kinase C (PKC). We now report that activation of PKC inhibits the ability of group II and group III mGluRs to regulate transmission at three major synapses in the hippocampal formation. Thus, this effect may be a widespread phenomenon that occurs at glutamatergic synapses throughout the CNS. We also report that this response is not limited to PKC-activating phorbol esters but that activation of A3 adenosine receptors induces a PKC-dependent inhibition of group III mGluR function at the Schaffer collateral-CA1 synapse. In addition to inhibiting mGluR modulation of excitatory synaptic transmission, we found that activation of PKC reduces inhibition of forskolin-stimulated cAMP accumulation by group II and group III mGluRs, suggesting that the effect of PKC on mGluR signaling is not specific to their effects on neurotransmitter release. This led us to test the hypothesis that PKC acts upstream from effector proteins regulated by mGluRs and acts at the level of the receptor or GTP-binding protein. Interestingly, we found that PKC inhibited mGluR-induced increases in [35S]-GTPgammaS binding in cortical synaptosomes. These data suggest that PKC-induced inhibition of mGluR signaling may be mediated by the inhibition of coupling of mGluRs to GTP-binding proteins.
Development of a high-throughput microwave imaging system for concealed weapons detection (2016)

A video-rate microwave imaging aperture for concealed threat detection can serve as a useful tool in securing crowded, high foot traffic environments. Realization of such a system presents two major technical challenges: 1) implementation of an electrically large antenna array for capture of a moving subject, and 2) fast image reconstruction on cost-effective computing hardware. This paper presents a hardware-efficient multistatic array design to address the former challenge, and a compatible fast imaging technique to address the latter. Prototype hardware which forms a partition of an imaging aperture is discussed. Using this hardware, it is shown that the proposed array design can be used to form high-fidelity 3D images, and that the presented image reconstruction technique can form an image of a human-sized domain in ≤0.1s with low cost computing hardware.
On using rectangle packing for SOC wrapper/TAM co-optimization (2003)

The testing time for a system-on-chip (SOC) is determined to a large extent by the design of test wrappers and the test access mechanism (TAM). Wrapper/TAM co-optimization is therefore necessary for minimizing SOC testing time. We recently proposed an exact technique for co-optimization based on a combination of integer linear programming (ILP) and exhaustive enumeration. However, this approach is computationally expensive for large SOCs, and it is limited to fixed-width test buses. We present a new approach for wrapper/TAM co-optimization based on generalized rectangle packing, also referred to as two-dimensional packing. This approach allows us to decrease testing time by reducing the mismatch between a core's test data needs and the width of the TAM to which it is assigned. We apply our co-optimization technique to an academic benchmark SOC and three industrial SOCs. Compared to the ILP-based technique, we obtain lower or comparable testing times for two out of the three industrial SOCs. Moreover, we obtain more than two orders of magnitude decrease in the CPU time needed for wrapper/TAM co-design.
A security analysis of the NTP protocol version 2 (2002)

The network time protocol (NTP) is being used throughout the Internet to provide an accurate time service. The author examines the security requirements of such a service, analyzes version 2 of the NTP protocol to determine how well it meets these requirements, and suggests improvements where appropriate. Five types of security attacks on a time service are possible. An attacker could cause a nontime server to impersonate a time server (masquerade), an attacker could modify some (or all) time messages sent by a time server (modification), an attacker could resend a time server's time messages (replay), an attacker could intercept a time server's time messages and delete them (denial of service), and an attacker could delay the time messages by, for example, deliberately flooding the network, thereby introducing large transmission delays (delay).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Integrated micro-liquid dosing system (2002)

An integrated micro-liquid dosing system consisting of a micropump and a microliquid flow sensor is demonstrated. The dosing system allows accurate dosing of liquid in the microliter regime and can easily be integrated with components such as mixers and detectors in micro-liquid handling systems. The liquid pump is of the reciprocating type with a thermopneumatic actuator. The microliquid flow sensor is based on the thermal anemometer type. Both pump and flow sensor are realized in a 3-in
Experimental oleic acid-induced cholelithiasis in the rabbit associated with increased biliary 5α-deoxycholic acid (1972)

Research Article| June 01 1972 Experimental oleic acid-induced cholelithiasis in the rabbit associated with increased biliary 5α-deoxycholic acid P A Kyd; P A Kyd Search for other works by this author on: This Site PubMed Google Scholar I A D Bouchier I A D Bouchier Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1972) 128 (1): 169–172. https://doi.org/10.1042/bj1280169 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation P A Kyd, I A D Bouchier; Experimental oleic acid-induced cholelithiasis in the rabbit associated with increased biliary 5α-deoxycholic acid. Biochem J 1 June 1972; 128 (1): 169–172. doi: https://doi.org/10.1042/bj1280169 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1972 London: The Biochemical Society1972 Article PDF first page preview Close Modal You do not currently have access to this content.
DNA-Encoding to Improve Performance and Allow Parallel Evaluation of the Binding Characteristics of Multiple Antibodies in a Surface-Bound Immunoassay Format (2011)

High affinity capture agents against protein targets are essential components for immunoassays, regardless of specific analysis format. Here, we describe the use of DNA-encoded antibodies for rapidly screening the kinetic and equilibrium binding properties of twelve commercial antibodies in a parallel analysis format using a multiplexed array of microring optical resonators. We show that DNA-encoding offers advantages in terms of antigen binding capacity, compared to covalently tethered antibodies; we also demonstrate that this linkage modality facilitates the rapid self-assembly of multiplexed arrays on account of complementarity between the DNA sequences on the antibodies and sensor array, respectively. Furthermore, DNA-encoded antibodies also allow for sensor array regeneration and reprogramming, as chaotropic agents can be used to disrupt the DNA-DNA duplexes that link the capture agents to the sensor without harming the underlying DNA on the surface, which can subsequently be reloaded with antibodies either targeting the same or different antigens.
Two-dimensional stimulated resonance Raman spectroscopy of molecules with broadband x-ray pulses (2012)

Expressions for the two-dimensional stimulated x-ray Raman spectroscopy (2D-SXRS) signal obtained using attosecond x-ray pulses are derived. The 1D- and 2D-SXRS signals are calculated for trans-N-methyl acetamide (NMA) with broad bandwidth (181 as, 14.2 eV FWHM) pulses tuned to the oxygen and nitrogen K-edges. Crosspeaks in 2D signals reveal electronic Franck-Condon overlaps between valence orbitals and relaxed orbitals in the presence of the core-hole.
Molecular chaperones in the kidney: distribution, putative roles, and regulation (2000)

Molecular chaperones are intracellular proteins that prevent inappropriate intra- and intermolecular interactions of polypetide chains. A specific group of highly conserved molecular chaperones are the heat shock proteins (HSPs), many of which are constitutively expressed but most of which are inducible by diverse (in some cases specific) stress factors. HSPs, either alone or in cooperation with "partner" chaperones, are involved in cellular processes as disparate as correct folding and assembly of proteins, transport of proteins to specific intracellular locations, protein degradation, and preservation and restructuring of the cytoskeleton. The characteristic distribution of individual HSPs in the kidney, and their response to different challenges, suggests that a number of HSPs may fulfill specific, kidney-related functions. HSP72 and the osmotic stress protein 94 (Osp94) appear to participate in the adaptation of medullary cells to high extracellular salt and urea concentrations; the small HSPs (HSP25/27 and crystallins) may be involved in the function of mesangial cells and podocytes and contribute to the volume-regulatory remodeling of the cytoskeleton in medullary cells during changes in extracellular tonicity. HSP90 contributes critically to the maturation of steroid hormone receptors and may thus be a critical determinant of the aldosterone sensitivity of specific renal epithelial cells. Certain HSPs are also induced in various pathological states of the kidney. The observation that the expression of individual HSPs in specific kidney diseases often displays characteristic time courses and intrarenal distribution patterns supports the idea that HSPs are involved in the recovery but possibly also in the initiation and/or maintenance phases of these disturbances.
Distance between the Left Atrial Appendage and Mitral Annulus Evaluated by CARTO 3 Integrated Computed Tomography Imaging (2015)

The angiographic CT provided detailed information regarding the anatomy of the left atrium and distances between atrial structures. The LAA-MA was shorter than the other three lines with the CxA and CS situated at a distance.
Method Validation for Preparing Serum and Plasma Samples from Human Blood for Downstream Proteomic, Metabolomic, and Circulating Nucleic Acid-Based Applications (2014)

We validated serum and plasma collection methods suitable for downstream protein, metabolite, or free nucleic acid-based applications. Temperature and pre-centrifugation delay can influence analytic results, and laboratories and biobanks should systematically record these conditions in the scope of accreditation.
Regional Contraction patterns of the Left Ventricle during Ventricular Pacing (1977)

Ten mongrel dogs were used to assess regional myocardial function in response to electrical pacing from the inflow (RVI), outflow tracts (RVO), and apex (RVA) of the right ventricle and apex (LVA) and lateral wall (LVL) of the left ventricle. Straingauge arches were sutured to the epicardial segments of the apical and lateral walls of the left ventricle and their mechanical shortening was measured during right atrial (RA) and during ventricular pacing. The onset of shortening of two segments did not differ significantly in RA and RVI pacing, while the stimulation of RVA and LVA caused the initial contraction of the apical segment, and RVO and LVL pacing caused that of the lateral segment; i. e. RVA and RVO pacing resulted in left ventricular asynchrony of contraction similar to LVA and LVL pacing, respectively. Asynchrony of contraction was not accompanied by a uniform change in peak tension of regional myocardial segments, but pre-ejection tension rose and ejection tension fell at the pacing site. The reduction in mean aortic pressure inversely correlated with the prolongation of the time interval between the onset of shortening of two segments during left ventricular pacing. The decrease in cardiac performance observed during ventricular pacing was related to the severity of asynchrony rather than the direction of the ventricular depolarization or change in regional myocardial tension.
A synthetic inhibitor of the mitogen-activated protein kinase cascade. (1995)

Treatment of cells with a variety of growth factors triggers a phosphorylation cascade that leads to activation of mitogen-activated protein kinases (MAPKs, also called extracellular signal-regulated kinases, or ERKs). We have identified a synthetic inhibitor of the MAPK pathway. PD 098059 [2-(2'-amino-3'-methoxyphenyl)-oxanaphthalen-4-one] selectively inhibited the MAPK-activating enzyme, MAPK/ERK kinase (MEK), without significant inhibitory activity of MAPK itself. Inhibition of MEK by PD 098059 prevented activation of MAPK and subsequent phosphorylation of MAPK substrates both in vitro and in intact cells. Moreover, PD 098059 inhibited stimulation of cell growth and reversed the phenotype of ras-transformed BALB 3T3 mouse fibroblasts and rat kidney cells. These results indicate that the MAPK pathway is essential for growth and maintenance of the ras-transformed phenotype. Further, PD 098059 is an invaluable tool that will help elucidate the role of the MAPK cascade in a variety of biological settings.