gebhart/patrepeval huggingface dataset:
Enzyme engineering reaches the boiling point (1998)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
An enzymic method for the trace iodination of immunoglobulins and other proteins (1969)

1. A method is described for the trace iodination of immunoglobulins and other serum proteins by a system consisting of lactoperoxidase, hydrogen peroxide and iodide. 2. gammaG immunoglobulin that had been labelled to a specific radioactivity of 5muc/mug. by use of carrier-free [(125)I]iodide gave no evidence of denaturation when analysed by electrophoresis and density-gradient ultracentrifugation. 3. Tryptic hydrolysis and peptide ;mapping' of a completely characterized peptide radioiodinated by this method showed that the [(125)I]iodide was bound to tyrosyl residues. 4. Proteins differ in their susceptibility to iodination by this method. Human gammaG immunoglobulin, for example, is iodinated more than ten times as readily as is human alpha(2)-macroglobulin under the same conditions. 5. Lactoperoxidase catalyses the iodination of proteins much more readily than does horseradish peroxidase.
On the capacity of a twisted-wire pair: Gaussian model (1990)

The performance of a twisted-pair channel is assumed to be dominated by near-end crosstalk (NEXT) from other pairs in the same cable. Both intrabuilding local and central office loop channels can be modeled as NEXT-dominated channels. The capacity of this type of channel is found, using a Gaussian model. It is shown that the capacity is independent of the transmitted power spectral density. The results also indicate that present systems operate far below theoretical capacity. The capacity of a twisted-pair channel with both NEXT and white Gaussian noise present is also addressed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Aerosol Matrixassisted Laser DesorptionIonization Mass Spectrometry: I.Effect of Solvent on Ion Signal (1996)

The effects of methanol, ethanol, propan-2-ol and acetonitrile on the aerosol matrix-assisted laser desorption/ionization (MALDI) ion signal of bradykinin, bovine insulin and myoglobin were examined. The effect of these solvents mixed with water was also studied. The aerosol MALDI ion signal for each analyte depends on the solvent, but the solvent dependence is different for the matrices 4-nitroaniline and α-cyano-4-hydroxycinnamic acid. The data suggest that matrix–analyte–solvent interactions are an important consideration for the aerosol MALDI ion signal. It appears that the ion signal is the result of a competition between solvent polarity and volatility. The solvent polarity affects matrix–analyte interactions whereas solvent volatility affects the aerosol drying process.
Human milk oligosaccharides: prebiotics and beyond (2009)

Human milk oligosaccharides (HMO) are complex glycans that are present at very high concentrations in human milk but not in infant formula. The significant energy expended by mothers to make these complex glycans suggests they must be important. How do maternal HMOs benefit the breast-fed infant? How are HMOs synthesized in the human mammary gland? How can we provide formula-fed infants with HMOs or HMO-like glycans? This article reviews current knowledge and open questions on the biosynthesis and functions of HMOs.
Massive cluster impact ionization on a four sector tandem mass spectrometer (1995)

Abstract High energy gycerol cluster ions from an electrohydrodynamic ion gun have been used as a primary ion beam to generate secondary ions of proteins with molecular weights up to 29 kDa and oligonucleotides. The technique not only demonstrated good performance in the picomole/nanomole range for the desorbtion of highly polar and fragile molecules such as proteins and deoxyoligonucleotides, but it also allowed the observation of a non‐covalent complex in the form of a deoxyoligonucleotide duplex. We have also shown that it is feasible to carry out structural analysis of oligonucleotides by collisional activation in a four sector tandem instrument.
Germline genetic polymorphisms may influence chemotherapy response and disease outcome in osteosarcoma (2011)

This pilot study represents the most comprehensive study to date examining the role of genetic polymorphisms in osteosarcoma. Although small and retrospective, it shows that several polymorphisms appear to significantly influence toxicity and clinical outcome. These deserve prospective validation in the hope of optimizing treatment for resistant disease and reducing the late effects burden.
Carbon nanotube/carbon fiber hybrid multiscale composites (2002)

Carbon nanotubes were grown directly on carbon fibers using chemical vapor deposition. When embedded in a polymer matrix, the change in length scale of carbon nanotubes relative to carbon fibers results in a multiscale composite, where individual carbon fibers are surrounded by a sheath of nanocomposite reinforcement. Single-fiber composites were fabricated to examine the influence of local nanotube reinforcement on load transfer at the fiber/matrix interface. Results of the single-fiber composite tests indicate that the nanocomposite reinforcement improves interfacial load transfer. Selective reinforcement by nanotubes at the fiber/matrix interface likely results in local stiffening of the polymer matrix near the fiber/matrix interface, thus, improving load transfer.
Temperature measurement within myocardium during in vitro RF catheter ablation (2000)

While most commercial ablation units and research systems can provide catheter tip temperature during ablation, they do not provide information about the temperature change inside the myocardium, which determines the lesion size. We present the details of a flow simulation and temperature measurement system, which allows the monitoring of the temperature change inside the myocardium during in vitro radio frequency (RF) cardiac catheter ablation at different blood flow rates to which the catheter site may be exposed. We set up a circulation system that simulated different blood flow rates of 0 to 5 L/min at 37 degrees C. We continuously measured the temperature at the catheter tip using the built-in thermistor and inside the myocardium using a three-thermocouple probe. The system provides a means for further study of the temperature inside myocardium during RF catheter ablation under different flow conditions and at different penetration depths.
Exploring Chemical Modifications for siRNA Therapeutics: A Structural and Functional Outlook (2009)

Abstract RNA interference (RNAi) is a post‐transcriptional gene silencing mechanism induced by small interfering RNAs (siRNAs) and micro‐RNAs (miRNAs), and has proved to be one of the most important scientific discoveries made in the last century. The robustness of RNAi has opened up new avenues in the development of siRNAs as therapeutic agents against various diseases including cancer and HIV. However, there had remained a lack of a clear mechanistic understanding of messenger RNA (mRNA) cleavage mediated by Argonaute2 of the RNA‐induced silencing complex (RISC), due to inadequate structural data. The X‐ray crystal structures of the Argonaute (Ago)–DNA–RNA complexes reported recently have proven to be a breakthrough in this field, and the structural details can provide guidelines for the design of the next generation of siRNA therapeutics. To harness siRNAs as therapeutic agents, the prudent use of various chemical modifications is warranted to enhance nuclease resistance, prevent immune activation, decrease off‐target effects, and to improve pharmacokinetic and pharmacodynamic properties. The focus of this review is to interpret the tolerance of various chemical modifications employed in siRNAs toward RNAi by taking into account the crystal structures and biochemical studies of Ago–RNA complexes. Moreover, the challenges and recent progress in imparting druglike properties to siRNAs along with their delivery strategies are discussed.
Glycosylated hemoglobins in heterozygotes and homozygotes for hemoglobin C with or without diabetes. (1984)

Glycosylated hemoglobin in red blood cell hemolysates of five patients homozygous for CC, 18 patients with SC condition, and 13 patients heterozygous for Hb C with or without insulin-dependent diabetes mellitus were separated by Bio-Rex 70 chromatography. The various glycosylated components were identified by analysis of the hemoglobin components for ketoamine and phosphate, in vitro glycosylation studies, and by the quantitative differences in the minor components between the participants with and without diabetes. The percentages of Hb A1a + b, Hb A1c, and Hb C1c were significantly increased in the Hb C heterozygote with diabetes. Similarly, the percentages of Hb S1a + b and Hb S1c were elevated in the SC patient with diabetes. It was noteworthy that the levels of these components became normal after adequate control of diabetes. Moreover, the levels of Hb C1c in the CC participants and Hb S1c (Hb S1c/total Hb S) in the SC patients were significantly higher than the Hb S1c levels previously reported in patients with sickle cell anemia. These findings might reflect the fact that CC and SC patients have less severe hemolytic anemia. Moreover, the relative proportions of Hb A1c and Hb C1c were nearly the same in Hb C heterozygotes, which indicated that Hb A and Hb C were glycosylated in vivo to approximately the same extent.
Compression loading-induced stress responses in intervertebral disc cells encapsulated in 3D collagen constructs (2016)

Cells protect themselves from stresses through a cellular stress response. In the interverebral disc, such response was also demonstrated to be induced by various environmental stresses. However, whether compression loading will cause cellular stress response in the nucleus pulposus cells (NPCs) is not well studied. By using an in vitro collagen microencapsulation model, we investigated the effect of compression loading on the stress response of NPCs. Cell viability tests, and gene and protein expression experiments were conducted, with primers for the heat shock response (HSR: HSP70, HSF1, HSP27 and HSP90), and unfolded protein response (UPR: GRP78, GRP94, ATF4 and CHOP) genes and an antibody to HSP72. Different gene expression patterns occurred due to loading type throughout experiments. Increasing the loading strain for a short duration did not increase the stress response genes significantly, but over longer durations, HSP70 and HSP27 were upregulated. Longer loading durations also resulted in a continuous upregulation of HSR genes and downregulation of UPR genes, even after load removal. The rate of apoptosis did not increase significantly after loading, suggesting that stress response genes might play a role in cell survival following mechanical stress. These results demonstrate how mechanical stress might induce and control the expression of HSR and UPR genes in NPCs.
Genetic Requirements for Salmonella -Induced Cytopathology in Human Monocyte-Derived Macrophages (2002)

Infection of human macrophages with Salmonella enterica serovar Typhimurium or Salmonella enterica serovar Dublin produces delayed cytotoxicity characterized by cell detachment and associated apoptosis. Using a site-specific mutant in the SpvB active site, we verify that the ADP-ribosylation activity of SpvB is required for delayed cytotoxicity in human macrophages infected with Salmonella: SipB and the type III protein secretion system (TTSS) encoded by Salmonella pathogenicity island 1 (SPI1) are not involved, whereas the SPI2 TTSS is absolutely required for SpvB-dependent cytotoxicity. Furthermore, we show that infection of macrophage cultures with wild-type or sipB mutant bacteria led to a complete loss of polymerized actin in over half of the cells after 24 h. In contrast, macrophages infected with the spvB or SPI2 (ssaV or ssaJ) mutant strain retained normal F-actin filaments, despite similar numbers of intracellular bacteria. We conclude that SpvB and a functional SPI2 TTSS are essential for Salmonella-induced delayed cytotoxicity of human macrophages.
Post-placement C-slow retiming for the xilinx virtex FPGA (2003)

C-slow retiming is a process of automatically increasing the throughput of a design by enabling fine grained pipelining of problems with feedback loops. This transformation is especially appropriate when applied to FPGA designs because of the large number of available registers. To demonstrate and evaluate the benefits of C-slow retiming, we constructed an automatic tool which modifies designs targeting the Xilinx Virtex family of FPGAs. Applying our tool to three benchmarks: AES encryption, Smith/Waterman sequence matching, and the LEON 1 synthesized microprocessor core, we were able to substantially increase the total throughput. For some parameters, throughput is effectively doubled.
Potential Therapeutic Roles for Inhibition of the PI3K/Akt/mTOR Pathway in the Pathophysiology of Diabetic Retinopathy (2011)

Novel therapeutics such as inhibitors of PI3K/Akt/mTOR pathway presents a unique opportunity for the management of diabetic retinopathy (DR). Second generation mTOR inhibitors have the prospect to be efficacious in managing various stages of disease progression in DR. During early stages, the mTOR inhibitors suppress HIF-1α, VEGF, leakage, and breakdown of the blood-retinal barrier. These mTOR inhibitors impart a pronounced inhibitory effect on inflammation, an early component with diverse ramifications influencing the progression of DR. These inhibitors suppress IKK and NF-κB along with downstream inflammatory cytokines, chemokines, and adhesion molecules. In proliferative DR, mTOR inhibitors suppress several growth factors that play pivotal roles in the induction of pathological angiogenesis. Lead mTOR inhibitors in clinical trials for ocular indications present an attractive treatment option for chronic use in DR with favorable safety profile and sustained ocular pharmacokinetics following single dose. Thereby, reducing dosing frequency and risk associated with chronic drug administration.
L-AP4 inhibits calcium currents and synaptic transmission via a G- protein-coupled glutamate receptor (1992)

The AP4 (2-amino-4-phosphonobutyrate) receptor is a presynaptic glutamate receptor that inhibits transmitter release via an unknown mechanism. We examined the action of L-AP4 on voltage-dependent calcium currents and excitatory synaptic transmission on cultured olfactory bulb neurons using whole-cell voltage-clamp methods. In neurons dialyzed with GTP, L-AP4 inhibited high-threshold calcium currents evoked in barium solutions. The inhibition was irreversible in the presence of GTP-gamma-S and blocked by removing intracellular Mg2+ or by preincubation with pertussis toxin (PTX), consistent with the involvement of a PTX-sensitive G-protein. Dialysis with staurosporine or buffering of intracellular calcium to pCa less than 8 did not block the action of L-AP4, suggesting that protein phosphorylation or release of intracellular calcium stores was not involved in calcium current inhibition under these experimental conditions. PTX also blocked the L-AP4-induced inhibition of monosynaptic EPSPs evoked by intracellular stimulation of cultured mitral cells. These results suggest that the presynaptic AP4 receptor is a G-protein-coupled glutamate receptor, and that inhibition of calcium influx by a membrane-delimited action of a G-protein may account for L-AP4-induced presynaptic inhibition.
Mitochondrial damage elicits a TCDD-inducible poly(ADP-ribose) polymerase-mediated antiviral response (2017)

The innate immune system senses RNA viruses by pattern recognition receptors (PRRs) and protects the host from virus infection. PRRs mediate the production of immune modulatory factors and direct the elimination of RNA viruses. Here, we show a unique PRR that mediates antiviral response. Tetrachlorodibenzo-p-dioxin (TCDD)-inducible poly(ADP ribose) polymerase (TIPARP), a Cysteine3 Histidine (CCCH)-type zinc finger-containing protein, binds to Sindbis virus (SINV) RNA via its zinc finger domain and recruits an exosome to induce viral RNA degradation. TIPARP typically localizes in the nucleus, but it accumulates in the cytoplasm after SINV infection, allowing targeting of cytoplasmic SINV RNA. Redistribution of TIPARP is induced by reactive oxygen species (ROS)-dependent oxidization of the nuclear pore that affects cytoplasmic-nuclear transport. BCL2-associated X protein (BAX) and BCL2 antagonist/killer 1 (BAK1), B-cell leukemia/lymphoma 2 (BCL2) family members, mediate mitochondrial damage to generate ROS after SINV infection. Thus, TIPARP is a viral RNA-sensing PRR that mediates antiviral responses triggered by BAX- and BAK1-dependent mitochondrial damage.
3D analysis of facial morphology (2004)

Dense surface models can be used to analyze 3D facial morphology by establishing a correspondence of thousands of points across each 3D face image. The models provide dramatic visualizations of 3D face-shape variation with potential for training physicians to recognize the key components of particular syndromes. We demonstrate their use to visualize and recognize shape differences in a collection of 3D face images that includes 280 controls (2 weeks to 56 years of age), 90 individuals with Noonan syndrome (NS) (7 months to 56 years), and 60 individuals with velo-cardio-facial syndrome (VCFS; 3 to 17 years of age). Ten-fold cross-validation testing of discrimination between the three groups was carried out on unseen test examples using five pattern recognition algorithms (nearest mean, C5.0 decision trees, neural networks, logistic regression, and support vector machines). For discriminating between individuals with NS and controls, the best average sensitivity and specificity levels were 92 and 93% for children, 83 and 94% for adults, and 88 and 94% for the children and adults combined. For individuals with VCFS and controls, the best results were 83 and 92%. In a comparison of individuals with NS and individuals with VCFS, a correct identification rate of 95% was achieved for both syndromes. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/suppmat/index.html.
Leukocyte Telomere Length Is Unrelated to Cognitive Performance Among Non-Demented and Demented Persons: An Examination of Long Life Family Study Participants (2020)

Within this unique LLFS cohort, a group of families assembled on the basis of exceptional survival, LTL is unrelated to cognitive ability for individuals with and without cognitive impairment. LTL does not change in the context of degenerative disease for these individuals who are biologically younger than the general population.
Interpretable credit model development via artificial neural networks (2007)

Abstract Poor credit granting decisions are coming back to haunt providers of loan finance. Past poor credit granting decisions are in part due to the Equal Credit Opportunity Act (1975). This act requires lenders to explain the decision to grant or refuse credit. As a result, models such as artificial neural networks, which offer improved ability to identify poor credit risks but which do not offer easy explanations of why a loan applicant has scored badly, remain unused. This paper investigates whether these models can be interpreted so that explanations for credit application rejection can be provided. The results indicate that while the artificial neural networks can be used (with caution) to develop credit scoring models, the limitations imposed by the credit granting process make their use unlikely until interpretation techniques are developed that are more robust and that can interpret multiple hidden‐layer artificial neural networks. Copyright © 2008 John Wiley &amp; Sons, Ltd.
Surface Antigens on Transplantable Tumor Cell Lines Producing Mouse Type C Viruses (1977)

A variety of transplantable mouse tumor lines were shown to contain murine type C viruses and virus-associated antigens. The type of virus isolated and antigens detected could not invariably be correlated with the original method of tumor induction, but testing of the majority of tumor lines for infectious virus at various levels of in vivo or in vitro passage yielded isolates that were consistent in tissue culture host range for each tumor. In contrast, during the course of in vivo transplantation, some of the lines underwent considerable change in the pattern of virus-associated cell-surface antigens. When the transplanted tumor lines were placed into culture, all showed some alteration in the detectable surface antigens. Upon retransplantation and passage of the cultured cells in mice, the surface antigens gradually returned to the original in vivo patterns and occasionally acquired additional type C virus-associated antigens not detected in the original tumor line. To test for association of antigens with infectious virus, appropriate tissue culture cell lines were infected with the viruses isolated from the tumors. In these infected indicator cells, some new virus-associated cell-surface and virion evelope antigens were detected, but the complete array of antigens found in the original tumor lines was not acquired. These findings indicated the presence of several different type C viruses in long transplanted cell lines and demonstrated that environmental and host cell factors may have major influences on expression of virus-associated antigens.
Synthesis of Double C-Glycoside Analogue of sTn (2005)

A sTn double C-glycoside, sTn analogue 2, was synthesized using samarium chemistry developed in our laboratory. Complications in the oxidation reaction affording aldehyde acceptor were overcome by double protection of amide and the use of a room-temperature ionic liquid as solvent. Studies are underway to conjugate the sTn double C-glycoside hapten 2 to KLH carrier protein for biological evaluation as a vaccine.
Activation of Various Fe‐Based Precursors on Carbon Black and Graphite Supports to Obtain Catalysts for the Reduction of Oxygen in Fuel Cells (1997)

Three synthetic paths have been used to prepare iron‐based catalysts for the electrochemical reduction of oxygen in solid polymer fuel cells. The catalyst precursor used in the first synthetic path was a dispersion of on carbon black (Vulcan) that was reduced at 600°C in . The second synthetic path involved a method to intercalate that was first used with graphite and then extended to Vulcan. The oxidized iron was reduced by either heating the resulting materials at 600°C in or by reacting them at room temperature with K‐naphthalene in a nonaqueous solution. In the third synthetic path, Fe particles were generated directly on Vulcan by the reduction in a nonaqueous solution of with triethylborohydride. All these iron containing materials were then activated at 1000°C in the presence of acetonitrile in order to transform them into active catalysts for reduction. The best catalyst was obtained by extending the intercalation method of to carbon black (Vulcan) and then reducing the oxidized iron with K‐naphthalene. Based on electrochemical and physicochemical analysis (mostly scanning electron microscopy and x‐ray diffraction analysis) it is suggested that iron is included or intercalated in the carbon black particles. The higher catalytic activity of this material compared to the others is explained by the progressive release of the iron from the carbon black particles and its reaction with acetonitrile during the final thermal activation step at 1000°C.