gebhart/patrepeval huggingface dataset:
Structure of the RWJ-51084–bovine pancreatic β-trypsin complex at 1.8 Å (1999)

The three-dimensional structure of bovine pancreatic trypsin complexed with the inhibitor RWJ-51084 has been determined at 1.8 A resolution. These crystals belong to the trigonal space group P3(1)21, with unit-cell parameters a = b = 53.43, c = 107.76 A. The refined R and R(free) values are 0.175 and 0.237, respectively. The carbonyl group bonded to the benzothiazole group of the inhibitor is covalently linked to the hydroxyl O atom of Ser195, forming a tetrahedral intermediate hemiketal structure. The other carbonyl O atom of the inhibitor forms a hydrogen bond with the Gln192 side-chain amide group. The benzothiazole group is oriented with the aromatic N atom of RWJ-51084 accepting a hydrogen bond from His57 NE2. The arginine side chain of the inhibitor extends into the deep and narrow pocket of the S1 specificity site of trypsin, forming a network of hydrogen bonds.
ChemInform Abstract: A Lewis Acid‐Catalyzed Procedure for the Conversion of 2‐Methoxyethoxymethyl Ethers to Carboxylic Esters. (1988)

Abstract The 2‐methoxyethoxymethyl ethers (I) are selectively cleaved with acetic anhydride (II) in the presence of ferric chloride, producing the acetates (III).
Antihyperglycemic effect of equol, a daidzein derivative, in cultured L6 myocytes and ob/ob mice (2013)

The hypoglycemic effect of equol is related to increased GLUT4 translocation to the plasma membrane via AMPK activation. In addition, equol suppresses the fasting blood glucose level and gene expression of hepatic enzymes related to glucose metabolism. These results strongly suggest that equol has antidiabetic potential.
Low-Dose Linaclotide (72 μg) for Chronic Idiopathic Constipation: A 12-Week, Randomized, Double-Blind, Placebo-Controlled Trial (2017)

Once-daily linaclotide 72 μg significantly improved CIC symptoms in both men and women with a low rate of discontinuation due to diarrhea over 12 weeks of treatment.
Cerebrospinal Fluid in Neurology and Psychiatry. Edited By H. McConnell and J. Bianchine. London: Chapman & Hall. 1994. 322 pp. £45.00. (1995)

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3-[5-(4-Chlorophenyl)-1-(4-methoxyphenyl)-1H-pyrazol-3-yl]propionic acid and the corresponding methyl ester (2009)

The synthesis of 3-[5-(4-chlorophenyl)-1-(4-methoxyphenyl)-1H-pyrazol-3-yl]propionic acid, C(19)H(17)ClN(2)O(3), (I), and its corresponding methyl ester, methyl 3-[5-(4-chlorophenyl)-1-(4-methoxyphenyl)-1H-pyrazol-3-yl]propionate, C(20)H(19)ClN(2)O(3), (II), is regiospecific. However, correct identification of the regioisomer formed by spectroscopic techniques is not trivial and single-crystal X-ray analysis provided the only means of unambiguous structure determination. Compound (I) crystallizes with Z' = 2. The propionic acid groups of the two crystallographically unique molecules form a hydrogen-bonded dimer, as is typical of carboxylic acid groups in the solid state. Conformational differences between the methoxybenzene and pyrazole rings give rise to two unique molecules. The structure of (II) features just one molecule in the asymmetric unit and the crystal packing makes greater use than (I) of weak C-H...A interactions, despite the lack of any functional groups for classical hydrogen bonding.
Tango: Declarative Semantics for Multiagent Communication Protocols (2021)

A flexible communication protocol is necessary to build a decentralized multiagent system whose member agents are not coupled to each other's decision making. Information-based protocol languages capture a protocol in terms of causality and integrity constraints based on the information exchanged by the agents. Thus, they enable highly flexible enactments in which the agents proceed asynchronously and messages may be arbitrarily reordered. However, the existing semantics for such languages can produce a large number of protocol enactments, which makes verification of a protocol property intractable. This paper formulates a protocol semantics declaratively via inference rules that determine when a message emission or reception becomes enabled during an enactment, and its effect on the local state of an agent. The semantics enables heuristics for determining when alternative extensions of a current enactment would be equivalent, thereby helping produce parsimonious models and yielding improved protocol verification methods.
The MAR databases: development and implementation of databases specific for marine metagenomics (2017)

We introduce the marine databases; MarRef, MarDB and MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation. These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/.
OPTIMAL ESTIMATION OF LINEAR FILTERING FOR ENHANCED LISTENING (2010)

The intelligibility of a speech signal describes the proportion of meaningful speech that can be understood by a listener. The intelligibility is degraded when there is noise present in the listening environment. We present a method to filter the far-end speech signal using knowledge of the near-end noise in order to optimise the Speech Intelligibility Index (SII) of the system. In most applications it is not reasonable to simply amplify the speech signal, hence the optimisation will be constrained in terms of output power. In order to improve the efficiency and accuracy of the optimisation an estimate for the SII is found that we are able to differentiate. The optimisation results from the differentiable estimate for SII are compared to those found with the original SII measurement. Along with an increase in convergence speed, due to the concave nature of the SII estimate there is a small improvement in intelligibility increase over the original SII measurement.
Highly dispersed nickel and palladium nanoparticle silica aerogels: sol–gel processing of tethered metal complexes and application as catalysts in the Mizoroki–Heck reaction (2006)

Highly dispersed Ni and Pd silica aerogels were prepared through sol–gel processes. They have been synthesized by tethering the metal to the silica matrix with the use of the complexing silanes AEAPTS [N-(aminoethyl)aminopropyl]trimethoxysilane or TRIAMIN [N-((aminoethyl)aminoethyl)aminopropyl]trimethoxysilane. The gels were dried with scCO2 to afford the aerogels. High metal dispersion and small particle sizes were observed through HRTEM and XRD measurements. The organic groups were removed by oxidation and/or pyrolysis. The Pd reduced aerogels containing 15–17% of palladium are good recoverable catalysts in the Mizoroki–Heck reaction.
In silico Design, Synthesis, and Screening of Novel Deoxyhypusine Synthase Inhibitors Targeting HIV‐1 Replication (2014)

Abstract The human enzyme deoxyhypusine synthase (DHS) is an important host cell factor that participates in the post‐translational hypusine modification of eukaryotic initiation factor 5A (eIF‐5A). Hypusine‐modified eIF‐5A plays a role in a number of diseases, including HIV infection/AIDS. Thus, DHS represents a novel and attractive drug target. So far, four crystal structures are available, and various substances have been tested for inhibition of human DHS. Among these inhibitors, N ‐1‐guanyl‐1,7‐diaminoheptane (GC7) has been co‐crystallized in the active site of DHS. However, despite its potency, GC7 is not selective enough to be used in drug applications. Therefore, new compounds that target DHS are needed. Herein we report the in silico design, chemical synthesis, and biological evaluation of new DHS inhibitors. One of these inhibitors showed dose‐dependent inhibition of DHS in vitro, as well as suppression of HIV replication in cell cultures. Furthermore, the compound exhibited no cytotoxic effects at active concentrations. Thus, this designed compound demonstrated proof of principle and represents a promising starting point for the development of new drug candidates to specifically interfere with DHS activity.
ChemInform Abstract: 2‐Oxo‐tetrahydro‐1,8‐naphthyridines as Selective Inhibitors of Malarial Protein Farnesyltransferase and as Antimalarials. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Transketolase a of Escherichia coli K12 (1995)

Transketolase A was purified to apparent homogeneity from recombinant Escherichia coli K12 cells carrying the homologous cloned tktA gene on a pUC19-derived plasmid. These recombinant cells exhibited a transketolase activity in crude extracts of up to 9.7 U/mg compared to < or = 0.1 U/mg in wild-type cells. Transketolase A was purified from crude extracts of a recombinant strain by successive ammonium sulfate precipitations and two anion-exchange chromatography steps (Q-Sepharose FF, Fractogel EMD-DEAE column) and afforded an apparently homogeneous protein band on SDS/PAGE. The enzyme, both in its active and apoform, had a molecular mass of 145,000 Da (+/- 10,000 Da), judged by gel-filtration chromatography. Subunits of 73,000 Da (+/- 2000 Da) were determined on SDS/PAGE, thus, transketolase A most likely forms a homodimer. N-terminal amino acid sequencing of the protein verified the identity with the cloned gene tktA. The specific activity of the purified enzyme, determined at 30 degrees C with the substrates xylulose 5-phosphate (donor of C2 compound) and ribose 5-phosphate (acceptor) at an optimal pH (50 mM glycylglycine, pH 8.5), was 50.4 U/mg. Km values for the substrates xylulose 5-phosphate and ribose 5-phosphate were 160 microM and 1.4 mM, respectively. Km values for the other physiological substrates of transketolase A were 90 microM for erythrose 4-phosphate (best acceptor substrate), 2.1 mM for D,L-glyceraldehyde 3-phosphate, 1.1 mM for fructose 6-phosphate, and 4 mM for sedoheptulose 7-phosphate. Hydroxypyruvate served as alternative donor (Km = 18 mM). Unphosphorylated acceptor compounds were formaldehyde (Km = 31 mM), glycolaldehyde (14 mM), D,L-glyceraldehyde (10 mM) and D-erythrose (150 mM). The enzyme was competitively inhibited by D-arabinose 5-phosphate (K = 6 mM at a concentration of 2.5 mM D-arabinose 5-phosphate) or by the chelating agent EDTA. The inactive apoform of transketolase A was yielded by dialysis against buffer containing 10 mM EDTA, thus removing the cofactors thiamine diphosphate and divalent cations. The reconstitution of the apoenzyme proceded faster in the presence of manganese ions (Kd = 7 microM at 10 microM thiamine diphosphate) than with other divalent cations.
Structural Basis of Zika Virus Specific Neutralization in Subsequent Flavivirus Infections (2020)

Zika virus (ZIKV), a mosquito-borne human flavivirus that causes microcephaly and other neurological disorders, has been a recent focus for the development of flavivirus vaccines and therapeutics. We report here a 4.0 Å resolution structure of the mature ZIKV in complex with ADI-30056, a ZIKV-specific human monoclonal antibody (hMAb) isolated from a ZIKV infected donor with a prior dengue virus infection. The structure shows that the hMAb interactions span across the E protein dimers on the virus surface, inhibiting conformational changes required for the formation of infectious fusogenic trimers similar to the hMAb, ZIKV-117. Structure-based functional analysis, and structure and sequence comparisons, identified ZIKV residues essential for neutralization and crucial for the evolution of highly potent E protein crosslinking Abs in ZIKV. Thus, this epitope, ZIKV's "Achilles heel", defined by the contacts between ZIKV and ADI-30056, could be a suitable target for the design of therapeutic antibodies.
Mechanical and structural changes in diabetic rat peripheral nerve collagens (2003)

An underlying mechanism for ultrastructural changes in collagens of the peripheral nerve tissue of diabetic animals may be an increase in endoneurial fluid pressure observed with prolonged diabetic neuropathy. We hypothesize that the extracellular matrix of both the endoneurium and epineurium remodel in response to the modified chemical and mechanical environment present in diabetic peripheral neuropathy. Our approach involves quantitative comparisons of mechanical properties, image analysis, and content (collagens I, III and IV) analysis of healthy and diabetic sciatic nerve collagens from Sprague-Dawley rats. Experimental data for these three comparative approaches were obtained via uniaxial mechanical testing, atomic force microscopy, and in situ immunohistochemistry, respectively. Atomic force microscopy (AFM) revealed larger collagen fibrils in both endoneurium and epineurium. Mechanical tests revealed slight stiffening of the tissues. Both of these results suggest that the extracellular matrix of both the endoneurium and epineurium remodel in the presence in diabetic peripheral neuropathy, and suggest that mechanical factors may play a role in the permanence of these changes.
Automated test case generation for spreadsheets (2002)

Spreadsheet languages, which include commercial spreadsheets and various research systems, have had a substantial impact on end-user computing. Research shows, however, that spreadsheets often contain faults. Thus, in previous work, we presented a methodology that assists spreadsheet users in testing their spreadsheet formulas. Our empirical studies have shown that this methodology can help end-users test spreadsheets more adequately and efficiently; however, the process of generating test cases can still represent a significant impediment. To address this problem, we have been investigating how to automate test case generation for spreadsheets in ways that support incremental testing and provide immediate visual feedback. We have utilized two techniques for generating test cases, one involving random selection and one involving a goal-oriented approach. We describe these techniques, and report results of an experiment examining their relative costs and benefits.
Robust tracking of spatial related components (2008)

This paper introduces a hierarchical approach for multi-component tracking, where the object-to-be-tracked is modeled as a group of spatial related parts. We propose to use a robust particle filtering framework for tracking the individual components and outline how the spatial coherency between the parts can be efficiently integrated by analyzing a two-level hierarchy of particle filters. Including spatial information allows to handle common tracking problems like occlusions, clutter or blur. Furthermore, the dynamic calculation of particle set uncertainties allows a dynamic adaption of stiffness values for the spatial model to e. g. force occluded parts to stay in spatial relation. The experimental section proves the robustness of the proposed tracker on challenging sequences of the VIVID-PETS database.
Influence of waveguide effects on pulse-delay measurements of material dispersion in optical fibres (1979)

The effect of the waveguide structure on pulse-delay measurements of material dispersion in optical fibres is examined. It is shown that waveguide dispersion has only a small influence on the measured values and introduces an uncertainty in the wavelength of zero material dispersion of order ±3 nm.
Underwater 3D Surface Measurement Using Fringe Projection Based Scanning Devices (2015)

In this work we show the principle of optical 3D surface measurements based on the fringe projection technique for underwater applications. The challenges of underwater use of this technique are shown and discussed in comparison with the classical application. We describe an extended camera model which takes refraction effects into account as well as a proposal of an effective, low-effort calibration procedure for underwater optical stereo scanners. This calibration technique combines a classical air calibration based on the pinhole model with ray-based modeling and requires only a few underwater recordings of an object of known length and a planar surface. We demonstrate a new underwater 3D scanning device based on the fringe projection technique. It has a weight of about 10 kg and the maximal water depth for application of the scanner is 40 m. It covers an underwater measurement volume of 250 mm × 200 mm × 120 mm. The surface of the measurement objects is captured with a lateral resolution of 150 μm in a third of a second. Calibration evaluation results are presented and examples of first underwater measurements are given.
Transcriptional control of the fibronectin gene in chick embryo fibroblasts transformed by Rous sarcoma virus. (1983)

Rous sarcoma virus transformed-chick embryo fibroblasts contain decreased amounts of the adhesive protein fibronectin that results from a lowering of fibronectin mRNA levels (Fagan, J.B., Sobel, M.E., Yamada, K.M., de Crombrugghe, B., and Pastan, I. (1981) J. Biol. Chem. 256, 520-525). In the present study, nuclei isolated from chick embryo fibroblasts (CEF) and Rous sarcoma virus transformed-chick embryo fibroblasts (RSV-CEF) were used to measure relative rates of fibronectin RNA synthesis. [32P]RNA was synthesized by preinitiated endogenous RNA polymerases in nuclei, and the radioactive RNA was subsequently hybridized to DNA fragments spanning approximately 40 kilobase pairs (approximately 85%) of the fibronectin gene. Transformation of CEF by RSV resulted in a 7- to 8-fold reduction in the amount of 32P-labeled nuclear RNA hybridizing with fibronectin DNA sequences when the nuclei were incubated for either 3.5 or 45 min. These results indicate that decreased transcription and not reduced RNA stability plays a major role in lowering fibronectin mRNA levels in RSV-CEF. When nuclear RNA was transcribed in the presence of Sarkosyl, diminished RNA synthesis was still observed suggesting that reduced fibronectin transcription in RSV-CEF is not due to a block in RNA chain elongation. Our data indicate that transcriptional regulation of the fibronectin gene is an important mechanism of lowering steady state levels of fibronectin mRNA in RSV-CEF.
1.3-.MU.m InGaAlAs-BH laser with Cl2/N2 ECR plasma etched mesas (2004)

We developed a dry etching process suitable for fabricating InGaAlAs laser mesa stripes. We used optimized Cl2/N2 ECR plasma for etching an InGaAlAs laser multilayer structure. This Cl2/N2 ECR plasma led to a uniform etching rate and an anisotropic profile using a nitrified side-protection mechanism. This smooth and anisotropic dry etching produced a well-matched interface for semi-insulated Fe-InP regrowth. It also enabled successfully fabricating an InGaAlAs buried heterostructure laser. The laser showed stable operation at 85°C and long-term reliability over 5000 hrs.
UL-DL duality for cell-free massive MIMO with per-AP power and information constraints (2023)

We derive a novel uplink-downlink duality principle for optimal joint precoding design under per-transmitter power and information constraints in fading channels. The information constraints model limited sharing of channel state information and data bearing signals across the transmitters. The main application is to cell-free networks, where each access point (AP) must typically satisfy an individual power constraint and form its transmit signal using limited cooperation capabilities. Our duality principle applies to ergodic achievable rates given by the popular hardening bound, and it can be interpreted as a nontrivial generalization of a previous result by Yu and Lan for deterministic channels. This generalization allows us to study involved information constraints going beyond the simple case of cluster-wise centralized precoding covered by previous techniques. Specifically, we show that the optimal joint precoders are, in general, given by an extension of the recently developed team minimum mean-square error method. As a particular yet practical example, we then solve the problem of optimal local precoding design in user-centric cell-free massive MIMO networks subject to per-AP power constraints.
Development and testing of intrinsic anti-fogging plastic scintillators for radiation portal monitors (RPMs) (Conference Presentation) (2019)

Radiation Portal Monitors (RPMs) based on polyvinyl toluene (PVT) scintillators have been in use since the 1970s. Recently it has been discovered that under certain conditions PVT scintillators can fog at low temperatures. In collaboration with researchers at national laboratories, Eljen Technology has developed methods for the production of Intrinsic Anti-Fogging Scintillators. The production methods have been scaled up to allow for castings of rods and large sheets of scintillators that are deployable in RPMs and other extreme locations. The work is ongoing. The presentation will focus on the properties of the new scintillators and on the ongoing testing results from exposure to extreme environmental conditions.
Mesenchymal stem cell therapy for attenuation of scar formation during wound healing (2012)

Scars are a consequence of cutaneous wound healing that can be both unsightly and detrimental to the function of the tissue. Scar tissue is generated by excessive deposition of extracellular matrix tissue by wound healing fibroblasts and myofibroblasts, and although it is inferior to the uninjured skin, it is able to restore integrity to the boundary between the body and its environment. Scarring is not a necessary process to repair the dermal tissues. Rather, scar tissue forms due to specific mechanisms that occur during the adult wound healing process and are modulated primarily by the inflammatory response at the site of injury. Adult tissue-derived mesenchymal stem cells, which participate in normal wound healing, are trophic mediators of tissue repair. These cells participate in attenuating inflammation in the wound and reprogramming the resident immune and wound healing cells to favor tissue regeneration and inhibit fibrotic tissue formation. As a result, these cells have been considered and tested as a likely candidate for a cellular therapy to promote scar-less wound healing. This review identifies specific mechanisms by which mesenchymal stem cells can limit tissue fibrosis and summarizes recent in vivo studies where these cells have been used successfully to limit scar formation.