gebhart/patrepeval huggingface dataset:
Development and Field Demonstration of DSRC-Based V2I Traffic Information System for the Work Zone (2010)

This report describes the architecture, functionality and the field demonstration of a newly developed dedicated&#13;\nshort-range communication (DSRC)-based Vehicle to Infrastructure (V2I) communication system for improving&#13;\ntraffic efficiency and safety in the work-zone related congestion buildup on US roadways. The goal was to develop&#13;\na portable system that can be easily deployed at a work zone site to acquire and communicate important travel&#13;\ninformation, e.g., travel time (TT) and start of congestion (SoC) location to the driver. By providing this&#13;\ninformation, i.e., SoC location and TT, drivers can make informed decisions on route choice and be prepared for&#13;\nupcoming congestion. The system is composed of a portable road-side unit (RSU) that can engage the on board&#13;\nunits (OBUs) of the traveling vehicles using DSRC technology to acquire necessary traffic data (speed, time, and&#13;\nlocation). From the acquired data, the RSU periodically estimates the SoC location and TT that are broadcast to all&#13;\nvehicles in its coverage range. An OBU receiving the broadcast message calculates the distance to the SoC&#13;\nlocation. The distance to the SoC location and TT are then relayed to the driver, who can make smart decisions&#13;\nregarding whether to seek an alternate route and when to expect a sudden speed reduction. Results from the field&#13;\ndemonstration have shown that the developed system can adapt to changing work-zone environments smoothly&#13;\nunder various congestion patterns on the road.
Synthesis of Trifunctional PNA−Benzophenone Derivatives for Mitochondrial Targeting, Selective DNA Binding, and Photo-Cross-Linking (2003)

Mutations in mitochondrial DNA (mtDNA) cause a variety of human pathologies. In many patients, mutated and wild-type mtDNAs coexist in the same cell, a situation termed mtDNA heteroplasmy. In the absence of standard therapies for these disorders, a genetic strategy for treatment has been proposed whereby replication of mutated mtDNA is inhibited by the selective hybridization of a nucleic acid derivative, allowing propagation of the wild-type genome and correction of the associated defects. To allow for selective binding under physiological conditions, peptide nucleic acids (PNA) are being used. Two other problems, however, have to be resolved: mitochondrial import and attachment of the PNA to the target DNA to inhibit replication. Mitochondrial localization can be achieved by the addition of a caged lipophilic cation and addition of a photo-cross-linking reagent should facilitate covalent attachment. We therefore report the synthesis of benzophenone-PNA derivatives carrying a triphenylphosphonium moiety and demonstrate irreversible binding selectivity between two DNA molecules that differ by a single nucleotide.
Pulsed Magnetic Fields Applied to a Transferred Arterial Loop Support the Rat Groin Composite Flap (2004)

Pulsed magnetic fields have been shown to stimulate neovascularization in the authors' laboratory. The rat groin composite flap was used to create a prospective randomized trial to test the effectiveness of these pulsed magnetic fields. The skin paddle to this flap is highly consistent, and the authors proposed using the flap to study how pulsed magnetic fields affect composite flap survival when the dominant vessel to the flap is divided and flap survival becomes dependent on a transferred vessel loop. Forty-three rats had the tail artery microsurgically anastomosed to the femoral artery and placed between the groin musculature and the abdominal skin. Pulsed magnetic energy of 1 gauss was applied for 8 (n = 14) or 12 (n = 8) weeks to the experimental groups. Control groups were treated in a comparable manner for 8 (n = 16) or 12 (n = 5) weeks. After the 8 or 12 weeks, all groups had an 8 x 4-cm skin flap raised, and the superficial epigastric artery, the main feeding vessel, was ligated. After 5 days, the total area of the flap and the area of necrosis were traced onto velum paper for each rat. The percent survival was calculated per rat, and a mean survival percentage was calculated per group. The experimental animals treated with pulsed magnetic fields for 8 weeks had statistically significant improved flap survival over the control animals. The study provides evidence that pulsed magnetic energy stimulates angiogenesis and suggests a possible use of this modality to create island vascular flaps in otherwise random vascular territories.
NetAdapt: Platform-Aware Neural Network Adaptation for Mobile Applications (2018)

This work proposes an algorithm, called NetAdapt, that automatically adapts a pre-trained deep neural network to a mobile platform given a resource budget. While many existing algorithms simplify networks based on the number of MACs or weights, optimizing those indirect metrics may not necessarily reduce the direct metrics, such as latency and energy consumption. To solve this problem, NetAdapt incorporates direct metrics into its adaptation algorithm. These direct metrics are evaluated using empirical measurements, so that detailed knowledge of the platform and toolchain is not required. NetAdapt automatically and progressively simplifies a pre-trained network until the resource budget is met while maximizing the accuracy. Experiment results show that NetAdapt achieves better accuracy versus latency trade-offs on both mobile CPU and mobile GPU, compared with the state-of-the-art automated network simplification algorithms. For image classification on the ImageNet dataset, NetAdapt achieves up to a 1.7$\times$ speedup in measured inference latency with equal or higher accuracy on MobileNets (V1&amp;V2).
Ligand-Induced Conformational Transitions in Escherichia coli Phosphofructokinase 2:  Evidence for an Allosteric Site for MgATP2- (1998)

The binding of ligands to phosphofructokinase 2 (Pfk-2) from Escherichia coli induces changes in the fluorescence emission properties of its single tryptophan residue, Trp88, suggesting that upon binding the protein undergoes a conformational change. This fluorescence probe was used to determine the presence of an allosteric site for MgATP2- in the enzyme. Fructose 6-phosphate (fructose-6-P), the first substrate that binds to the enzyme with an ordered bi-bi mechanism, increases the fluorescence up to 30%. The saturation curve for this compound is hyperbolic with a Kd of 6 microM. The titration of Pfk-2 with MgATP2- causes a quenching of fluorescence of about 30% of its initial value, with a blue shift of 7 nm in the emission maximum. The response is cooperative with a Kd of 80 microM and a Hill coefficient of 2. The interaction of MgATP2- cannot take place at the active site in the absence of fructose-6-P, due to the ordered kinetic mechanism. Addition of compounds that bind to the catalytic site of Pfk-2, such as ATP4- or Mg-AMP-PNP, did not produce significant changes in the fluorescence spectrum of Trp88. However, in the absence of Mg2+, the addition of ATP4- to the enzyme-fructose-6-P complex shows a hyperbolic increase of fluorescence of 8%. Acrylamide steady-state quenching experiments for different enzyme-ligand complexes of Pfk-2, indicate that the tryptophan in the enzyme-MgATP2- complex is exposed to a much smaller extent to the solvent than in the free enzyme or in the enzyme-fructose-6-P complex. The effect of the binding of fructose-6-P or MgATP2- on the polarization fluorescence of the emission of Trp88 in Pfk-2 indicates changes in the local mobility of the Trp88 in both enzyme complexes. The average lifetime for Trp88 in Pfk-2 was found to be unusually large, approximately 7.7 ns, and did not vary significantly with the ligation state of the enzyme, which demonstrates that the quenching or enhancement of fluorescence induced by the ligands is mainly due to the complex formation with Pfk-2. These results demonstrate the presence of an allosteric site for MgATP2- in Pfk-2 from E. coli, responsible for the inhibition of the enzyme activity by this ligand.
A Comparison of Injections of Botulinum Toxin and Topical Nitroglycerin Ointment for the Treatment of Chronic Anal Fissure (1999)

Although treatment with either topical nitroglycerin or botulinum toxin is effective as an alternative to surgery for patients with chronic anal fissure, botulinum toxin is the more effective nonsurgical treatment.
Radical Polymerization Initiated from a Solid Substrate. 2. Study of the Grafting Layer Growth on the Silica Surface by in situ Ellipsometry (1999)

Kinetics of the grafting free radical polymerization of styrene from the surface of Si wafers with a top silica layer was studied by in situ ellipsometric measurements of the grafted amount (A). Wafers uncovered and covered by physisorbed azo- or peroxide macroinitiator or covalently bonded with the substrate azo-initiator were used. Additional initiator of the same chemical nature was added to the bath solution (bulk). It was found that the grafted amount approaches a plateau value depending on the rate of grafting polymerization. At low rates, the plateau A values are on the order of 1−2 mg/m2, whereas at high rates, they are typically 10−15 mg/m2. Two kinetic regimes were studied where (1) the surface-attached chains terminate by chain transfer to the bulk or (2) the grafted chains terminate with the bulk free radicals. The rate of polymerization for the both regimes is linearly proportional to the surface density of the initiator. Within regime 2, the rate of polymerization has inverse square root dependence on the concentration of the initiator in the bulk. Two models were applied to explain the kinetics, which provide good agreement with the experimental data.
An Update on Methotrexate Pharmacogenetics in Rheumatoid Arthritis (2008)

Rheumatoid arthritis (RA) is a systemic inflammatory disorder that mainly affects the joints. When left untreated, the disease can result in irreversible joint damage with high morbidity and mortality. Disease-modifying antirheumatic drugs are the cornerstones of treatment in RA. Disease-modifying antirheumatic drugs not only ameliorate the clinical signs and symptoms of disease, but also prevent the radiographic progression of joint damage. Methotrexate is one such disease-modifying antirheumatic drug that has been used in the treatment of RA for over two decades with excellent long-term efficacy and safety. However, there is significant variability in patients' response to methotrexate, both in terms of efficacy and toxicity. At the present time, there are no reliable means of predicting, a priori, an individual patient's response to methotrexate. In this review, recent published literature on the pharmacogenetics of methotrexate in RA is highlighted. Pharmacogenetics may be a powerful tool for optimizing methotrexate therapy in patients with RA.
Human Engineered Heart Tissue as a Versatile Tool in Basic Research and Preclinical Toxicology (2011)

Human embryonic stem cell (hESC) progenies hold great promise as surrogates for human primary cells, particularly if the latter are not available as in the case of cardiomyocytes. However, high content experimental platforms are lacking that allow the function of hESC-derived cardiomyocytes to be studied under relatively physiological and standardized conditions. Here we describe a simple and robust protocol for the generation of fibrin-based human engineered heart tissue (hEHT) in a 24-well format using an unselected population of differentiated human embryonic stem cells containing 30-40% α-actinin-positive cardiac myocytes. Human EHTs started to show coherent contractions 5-10 days after casting, reached regular (mean 0.5 Hz) and strong (mean 100 µN) contractions for up to 8 weeks. They displayed a dense network of longitudinally oriented, interconnected and cross-striated cardiomyocytes. Spontaneous hEHT contractions were analyzed by automated video-optical recording and showed chronotropic responses to calcium and the β-adrenergic agonist isoprenaline. The proarrhythmic compounds E-4031, quinidine, procainamide, cisapride, and sertindole exerted robust, concentration-dependent and reversible decreases in relaxation velocity and irregular beating at concentrations that recapitulate findings in hERG channel assays. In conclusion this study establishes hEHT as a simple in vitro model for heart research.
Software distribution to PC clients in an enterprise network (1998)

Rockwell CACD and CCA divisions merged into Rockwell Avionics &amp;amp; Communications in March, 1997 (now Rockwell Collins), creating support issues for integrating and maintaining several networks that included Banyan, Novell, Microsoft NT and PC-NFS (Hummingbird’s Maestro). The combined total PC clients now number about 10,000, which include
Insulin-secreting activity of the traditional antidiabetic plant Viscum album (mistletoe) (1999)

Viscum album (mistletoe) has been documented as a traditional treatment of diabetes. In acute 20-min tests, 1-10 mg/ml aqueous extract of mistletoe evoked a stepwise 1.1- to 12.2-fold stimulation of insulin secretion from clonal pancreatic B-cells. This effect was abolished by 0.5 mM diazoxide and prior exposure to extract did not alter subsequent stimulation of insulin secretion induced by 10 mM L-alanine, thereby negating a detrimental effect on cell viability. The insulin-releasing effect of mistletoe extract was unaltered by 16.7 mM glucose, l-alanine (10 mM), 3-isobutyl-1-methylxanthine (IBMX) (1 mM), or a depolarising concentration of KCl (25 mM). The ability of extract to enhance insulin secretion did not depend upon the use of heat during extract preparation and was not mediated by lectins. These results demonstrate the presence of insulin-releasing natural product(s) in Viscum album which may contribute to the reported antidiabetic property of the plant.
Identification of Two Escherichia coli Pseudouridine Synthases That Show Multisite Specificity for 23S RNA (1998)

Several putative Escherichia coli pseudouridine (Psi) synthases have been identified by iterative searching of genomic databases for ORFs homologous to known Psi synthases [Gustafsson et al. (1996) Nucleic Acids Res. 24, 3756-3762]. Of these, yceC and yfiI were proposed to encode Psi synthases which modify 23S rRNA. In the present work, yceC and yfiI were cloned and overexpressed in E. coli, and the encoded enzymes, YceC and YfiI, were purified to homogeneity. Both proteins converted Urd residues of rRNA to Psi, thus confirming their identities as Psi synthases. However, in in vitro experiments both enzymes extensively modified Urd residues of both 23S rRNA and 16S rRNA. Gene-disruption of yceCresulted in the absence of Psi modification at positions U955, 2504, and 2580 of 23S RNA, thus identifying these sites as in vivo targets for YceC. Likewise, yfiI disruption resulted in the absence of Psi modification at positions U1911, 1917, and possibly 1915 of 23S RNA. Disruption of yceC did not affect the growth under the conditions tested, whereas yfiI-disrupted cells showed a dramatic decrease in growth rate. Since YceC and YfiI hypermodify RNA in vitro, factors in addition to ribonucleotide sequence must contribute to the in vivo specificity of these enzymes.
Monoclonal Antibodies as Innovative Therapeutics (2008)

Monoclonal antibodies (mAbs) comprise the majority of protein candidates currently in clinical development because of their versatility as therapeutic agents. While traditionally associated with the biotechnology industry, mAb therapeutics are now being developed and marketed by most major pharmaceutical firms. A total of 21 products are approved in the US, with additional products marketed outside the US, and over 200 mAb candidates are currently undergoing clinical study. Benchmark data for mAb therapeutics, such as clinical development and US Food and Drug Administration approval times, approval success rates, and clinical phase transition probabilities, are critical for strategic planning purposes. Trends in these benchmarks for various types of mAbs, with an emphasis on those studied as anticancer and immunological therapeutics, are discussed.
Design of dynamic soundscape : mapping time to space for audio browsing with simultaneous listening (1996)

Thesis (M.S.)--Massachusetts Institute of Technology, Program in Media Arts & Sciences, 1996.
Quantitative evaluation of the development of tracheal submucosal glands in infants with cystic fibrosis and control infants. (1982)

The development of the tracheal submucosal glands has been determined quantitatively in 22 infants with cystic fibrosis and in 25 control infants, all under 4 months of age. In cross-sections of normal trachea significant relationships were found between postconceptional age (PCA) and gland area (P less than 0.001), submucosal area (P less than 0.02), tracheal airway diameter (P less than 0.05), and acinar diameter (P less than 0.001). In infants with cystic fibrosis the pattern of development was similar to that of the control infants. No statistically significant differences were found between three subgroups of infants with cystic fibrosis, which included those with meconium ileus with no lung infection, those with meconium ileus with lung infection, and those with lung infection and no history of meconium ileus. The normal pattern of development of tracheal submucosal glands in infants with cystic fibrosis was in contrast to the deficiency of normal maturation seen in the exocrine pancreas of these infants. The lumen fraction, an index of dilatation of acinar lumina, showed no significant relationship with PCA in either the control group or the group with cystic fibrosis. However, statistically significant dilatation of acini was observed in the tracheal submucosal glands of infants with cystic fibrosis (0.14, P less than 0.005).
A fast polymerase chain reaction-mediated strategy for introducing repeat expansions into CAG-repeat containing genes (1999)

We describe a simple method for expanding CAG trinucleotides in CAG-repeat containing genes which, in contrast to other techniques, leaves the original gene sequence intact. Here, we expanded the CAG stretches of a plasmid clone containing the cDNA of the SCA3/MJD gene from 22 CAG up to > 130 CAG repeats using polymerase chain reaction (PCR)-mediated mutagenesis. The method reported in this article requires minimal resources, is very fast, and enables to construct recombinant plasmids carrying large CAG expansions.
Insights into a plasma membrane signature (2001)

The plasma membrane (PM) is an organized biological system that serves as a structural barrier and communication interface with the extracellular environment. Many basic questions regarding the PM as a system remain unanswered. In particular, we do not understand the scope of similarity and differences in protein expression at the PM. This study takes an initial step toward addressing these questions by comparing the PM proteomes of fibroblasts and mammary carcinoma cells. Three sets of proteins were revealed by the study. The first set comprises between 9 and 23% of all proteins at the PM and appears to be common to both fibroblasts and mammary carcinoma. A second group of proteins, comprising approximately 40% of the proteins at the PM, is tightly linked to cell lineage. The third set of proteins is unique to each cell line and is independent of cell lineage. It is reasonable to hypothesize then, that this third group of proteins is responsible for unique aspects of cell behavior. In an effort to find proteins linked to the metastatic phenotype, we identified several proteins that are uniquely expressed at the PM of the metastatic MDA-MB-435 cells. These proteins have functions ranging from cell adhesion to the regulation of translation and the control of oxidant stress.
Molecular cloning of a gene involved in lipooligosaccharide biosynthesis and virulence expression by Haemophilus influenzae type B (1991)

A wild-type Haemophilus influenzae type b (Hib) genomic DNA library was constructed in the plasmid shuttle vector pGJB103. A virulence-deficient lipooligosaccharide (LOS) mutant of Hib was used as a recipient for genetic transformation to screen this Hib genomic DNA library for genes involved in LOS expression. A recombinant plasmid containing a 7.8 kb PstI fragment of Hib DNA was shown to transform this LOS mutant to reactivity with a monoclonal antibody (mAb) specific for a wild-type LOS epitope. Transformation of two different virulence-deficient LOS mutants with a 4.4 kb BglII fragment of this recombinant plasmid yielded transformants which expressed LOS that bound the wild-type LOS-specific mAb and yielded profiles in sodium dodecyl sulphate/polyacrylamide gradient gel electrophoresis different from those of the original LOS mutants. These transformants with structurally altered LOS molecules also exhibited increased virulence in an animal model for invasive Hib disease. The virulence-transforming ability was further localized to a 1.8 kb BglII-AlwNI fragment of the Hib DNA insert. Nucleotide sequence analysis indicated the presence of a single large open reading frame within this fragment. This open reading frame contained 19 consecutive repeats of the tetramer CAAT near the 5' end. Linker insertion mutagenesis was used to demonstrate directly the involvement of this open reading frame in both LOS biosynthesis and virulence expression by Hib.
Dimerization-Induced Inhibition of Receptor Protein Tyrosine Phosphatase Function Through an Inhibitory Wedge (1998)

The function and regulation of the receptorlike transmembrane protein tyrosine phosphatases (RPTPs) are not well understood. Ligand-induced dimerization inhibited the function of the epidermal growth factor receptor (EGFR)-RPTP CD45 chimera (EGFR-CD45) in T cell signal transduction. Properties of mutated EGFR-CD45 chimeras supported a general model for the regulation of RPTPs, derived from the crystal structure of the RPTPalpha membrane-proximal phosphatase domain. The phosphatase domain apparently forms a symmetrical dimer in which the catalytic site of one molecule is blocked by specific contacts with a wedge from the other.
The GPIIb/IIIa (integrin αIIbβ3) odyssey: a technology-driven saga of a receptor with twists, turns, and even a bend (2008)

Starting 90 years ago with a clinical description by Glanzmann of a bleeding disorder associated with a defect in platelet function, technologic advances helped investigators identify the defect as a mutation(s) in the integrin family receptor, alphaIIbbeta3, which has the capacity to bind fibrinogen (and other ligands) and support platelet-platelet interactions (aggregation). The receptor's activation state was found to be under exquisite control, with activators, inhibitors, and elaborate inside-out signaling mechanisms controlling its conformation. Structural biology has produced high-resolution images defining the ligand binding site at the atomic level. Research on alphaIIbbeta3 has been bidirectional, with basic insights resulting in improved Glanzmann thrombasthenia carrier detection and prenatal diagnosis, assays to identify single nucleotide polymorphisms responsible for alloimmune neonatal thrombocytopenia, and the development of alphaIIbbeta3 antagonists, the first rationally designed antiplatelet agents, to prevent and treat thrombotic cardiovascular disease. The future looks equally bright, with the potential for improved drugs and the application of gene therapy and stem cell biology to address the genetic abnormalities. The alphaIIbbeta3 saga serves as a paradigm of rigorous science growing out of careful clinical observations of a rare disorder yielding both important new scientific information and improved diagnosis, therapy, and prevention of other disorders.