gebhart/patrepeval huggingface dataset:
Chlamydial gene encoding a 70-kilodalton antigen in Escherichia coli: analysis of expression signals and identification of the gene product (1989)

In an attempt to identify chlamydial genes whose native promoters allow them to be expressed in Escherichia coli, we isolated and characterized a chlamydial gene identified by screening a library of chlamydial DNA with antichlamydial antibodies. This gene encodes a 70-kilodalton immunoreactive polypeptide in E. coli hosts. Sequence analysis of the 5' portion of the gene identified its product as the chlamydial homolog of the E. coli ribosomal protein S1. The site of transcription initiation of the mRNA in chlamydiae was determined, and its putative promoter regions were identified. These regions apparently do not function efficiently in E. coli; in vitro transcripts generated by using E. coli RNA polymerase did not start at the authentic chlamydial initiation site. Several in vitro transcripts both larger and smaller than the authentic transcript were seen; presumably, these transcripts result from adventitious promoterlike elements in adjacent chlamydial DNA and may be responsible for the expression of the gene in E. coli.
Forced-Path Execution for Android Applications on x86 Platforms (2013)

We present a code analysis framework that performs scalable forced-path execution of Android applications in commodity hardware. Our goal is to reveal the full application functional behavior for large commercial applications without access to source code. We do so by identifying code blocks and API calls that are deemed sensitive and provide a security report to an analyst regarding the functionality of the Android application that is under inspection. We show that our approach is scalable by allowing for the execution of each software component by numerous instances of execution modules. Each execution instance exercises a different code path through the application call-graph leading to full code and state space coverage and exposing any hidden or unwanted functionality. The output is a list of API calls, parameter values, component call graphs, and control flow graphs. We show how this can be leveraged for automated policy enforcement of runtime functionality.
Alexithymia in Fibromyalgia Patients and Its Impact on the Quality of Life (2016)

Objective: Alexithymia, a personal trait characterized by difficulty in identifying feelings, is common among chronic pain patients. In our study, we aimed to assess alexithymia in patients with fibromyalgia (FM), to determine its association with clinical parameters and depression, and to analyze its impact on the quality of life.Methods: A total of 70 patients with FM and 40 age- and sex-matched healthy controls were included in the study. Alexithymia was assessed using the 20-item Toronto Alexithymia Scale (TAS-20). The Fibromyalgia Impact Questionnaire (FIQ) was used for measuring disease severity. The quality of life was evaluated using the Nottingham Health Profile (NHP) and depression by the Beck Depression Scale (BDS). The Visual Analog Scale (VAS) was used for determining pain severity.Results: The prevalence of alexithymia was 24.29% in FM patients and 7.5% in controls. It was higher in patients with FM than in controls [Odds ratio (OR)=3.96, confidence interval (CI) 95% (1.08–14.48)] (p=0.028). FM patients scored significantly higher in TAS-20 than the controls (p<0.01). TAS-20 was found to be correlated with FIQ, BDS, and pain, sleep, social isolation, and emotional reaction subgroups of NHP (r: 0.257, 0.503, 0.276, 0.260, 0.649, and 0.303 r espectively) (p<0.05).Conclusion: Alexithymia is common among FM patients and associated with disease severity, depression, and poor quality of life with respect to pain, sleep, and emotional and social functions. The assessment of the presence of alexithymia will help us find new treatment strategies in FM patients who are nonresponsive to conventional therapies.
Radiation exposure and associated risks to operating-room personnel during use of fluoroscopic guidance for selected orthopaedic surgical procedures. (1983)

Because of the increased use of fluoroscopic guidance techniques in certain orthopaedic surgical procedures, surgeons and other operating-room personnel who are involved in these procedures are voicing growing concern over possible associated radiation health hazards. Using thin-layer lithium fluoride chips for thermoluminescence dosimetry, we directly measured the radiation exposure encountered by the primary surgeon during seven operative procedures that were done utilizing fluoroscopic guidance techniques. Dosimetry studies were also carried out using a tissue-equivalent phantom model to determine the directions of maximum scatter radiation. These studies indicated that the standard protective apron that is commonly worn during the use of fluoroscopy provides adequate protection to most of the body; however, the surgeon is exposed to significant levels of scatter radiation to the head, neck, and hands, Dosimetry studies showed that positioning the fluoroscopic beam vertically to the fracture site of the supine patient, with the x-ray source posterior to the patient, provided the lowest levels of scatter radiation to the surgeon in the normal working position.
Status Of CuInSe2 Solar Cells (1985)

CuInSe2 has unique optical and electronic properties which make it a prime candidate for low-cost high efficiency thin-film polycrystalline solar cells. Within a decade of the first experiments with thin-film solar cells efficiencies had exceeded 10% and already pre-commercialization efforts are underway. The status and prospects of single junction CuInSe2 based solar cells are reviewed and the potential extension into multijunction configurations considered.
Truncation of type IV pilin induces mucoidy in <i><scp>P</scp>seudomonas aeruginosa</i> strain PAO579 (2013)

Abstract Pseudomonas aeruginosa is a Gram negative, opportunistic pathogen that uses the overproduction of alginate, a surface polysaccharide, to form biofilms in vivo. Overproduction of alginate, also known as mucoidy, affords the bacterium protection from the host's defenses and facilitates the establishment of chronic lung infections in individuals with cystic fibrosis. Expression of the alginate biosynthetic operon is primarily controlled by the alternative sigma factor AlgU (AlgT/σ 22 ). In a nonmucoid strain, AlgU is sequestered by the transmembrane antisigma factor MucA to the cytoplasmic membrane. AlgU can be released from MucA via regulated intramembrane proteolysis by proteases AlgW and MucP causing the conversion to mucoidy. Pseudomonas aeruginosa strain PAO579, a derivative of the nonmucoid strain PAO1, is mucoid due to an unidentified mutation ( muc‐23 ). Using whole genome sequencing, we identified 16 nonsynonymous and 15 synonymous single nucleotide polymorphisms (SNP). We then identified three tandem single point mutations in the pilA gene (PA4525), as the cause of mucoidy in PAO579. These tandem mutations generate a premature stop codon resulting in a truncated version of PilA (PilA 108 ), with a C‐terminal motif of phenylalanine‐threonine‐phenylalanine ( FTF ). Inactivation of pilA 108 confirmed it was required for mucoidy. Additionally, algW and algU were also required for mucoidy of PAO579. Western blot analysis indicated that MucA was less stable in PAO579 than nonmucoid PAO1 or PAO381. The mucoid phenotype and high P algU and P algD promoter activities of PAO579 require pilA 108 , algW , algU , and rpoN encoding the alternative sigma factor σ 54 . We also observed that RpoN regulates expression of algW and pilA in PAO579. Together, these results suggest that truncation in type IV pilin in P. aeruginosa strain PAO579 can induce mucoidy through an AlgW/AlgU‐dependent pathway.
Assessment of early diabetic renal changes with hyperpolarized [1‐<sup>13</sup>C]pyruvate (2012)

Hyperpolarized (13) C-MRI shows promise in the diagnosis and monitoring of early renal changes associated with diabetes, with the pyruvate/lactate ratio as an imaging biomarker for regional renal changes.
Kinetic and Chemical Mechanism of <i>Mycobacterium tuberculosis</i> 1-Deoxy-<scp>d</scp>-xylulose-5-phosphate Isomeroreductase (2004)

1-Deoxy-D-xylulose-5-phosphate (DXP) isomeroreductase catalyzes the isomerization and reduced nicotinamide adenine dinucleotide phosphate- (NADPH-) dependent reduction of DXP to generate 2-C-methylerythritol 4-phosphate (MEP) in the first committed step of the MEP pathway of isoprenoid biosynthesis. We have cloned the gene encoding the Mycobacterium tuberculosis DXP isomeroreductase, expressed the protein in Escherichia coli, and purified the enzyme to homogeneity using conventional column chromatography methods. DXP isomeroreductase is a metal ion-activated enzyme displaying superior specificity for Co(2+), good specificity for Mn(2+), and poor specificity for Mg(2+). Although NADPH is preferred over reduced nicotinamide adenine dinucleotide (NADH) about 100-fold as evaluated by the relative k(cat)/K(m) values, the maximum turnover numbers are similar, suggesting that the 2'-phosphate of NADPH contributes predominantly to binding and not to catalysis. While k(cat) was independent of pH in the region 6.0 <or= pH <or= 8.75, k(cat)/K(act)(Mn)2+ decreased at low pH as two enzymatic groups with pK(a) values of 7.4 are protonated. These groups likely represent carboxylate groups that coordinate the divalent metal ion in the active site. The results also support an electrostatic role for the divalent metal ion in catalysis. The results of product inhibition studies and isotope effects suggest that the enzyme utilizes a steady-state random mechanism. Significant isotope effects were observed with [4S-(2)H]NAD(P)H, establishing that the enzyme promotes transfer of the C(4)-proS hydride of the reduced pyridine nucleotide. The magnitude of these primary deuterium kinetic isotope effects varied with metal ion and reduced pyridine nucleotide identities. The results are discussed in terms of significant differences in the commitment factors for the various metal ions and pyridine nucleotides.
Self--administered cough cardiopulmonary resuscitation (c-CPR) in patients threatened by MAS events of cardiovascular origin. (1998)

Sudden cardiac death caused by cardiac arrhythmia's or asystolies in patients with coronary heart disease can often be avoided if resuscitation is administered immediately, preferably before the patient loses consciousness. In cases when rapid help is not available usually death occurs. We have studied a method of cardiopulmonary resuscitation (CPR) which can be self--administered by patients trained in recognizing imminent arrival of life-threatening Morgani Adams Stokes (MAS) events. The recent study comprised the three methods of investigation in three separate groups of patients: the first group underwent invasive procedures (20 pts), the second non invasive Doppler studies (31 pts) and the third in-and outhospital clinical observations (115 pts). The results indicate that evoked coughing can effectively prevent fainting and maintaining consciousness until conventional CPR help becomes available.
Magnetically uniform and tunable Janus particles (2011)

Magnetic particles serve as an important tool for a variety of biomedical applications but often lack uniformity in their magnetic responsiveness. For quantitative analysis studies, magnetic particles should ideally be monodisperse and possess uniform magnetic properties. Here we fabricate magnetically uniform Janus particles with tunable magnetic properties using a spin-coating and thermal evaporation method. The resulting 2 μm ferromagnetic particles exhibited a 4% magnetic response variability, and the 10 μm ferromagnetic particles exhibited a 1% size variability and an 8% magnetic response variability. Furthermore, by reducing the film thickness, the particle behavior was tuned from ferromagnetic to superparamagnetic.
Eight years of single-molecule localization microscopy (2014)

Super-resolution imaging by single-molecule localization (localization microscopy) provides the ability to unravel the structural organization of cells and the composition of biomolecular assemblies at a spatial resolution that is well below the diffraction limit approaching virtually molecular resolution. Constant improvements in fluorescent probes, efficient and specific labeling techniques as well as refined data analysis and interpretation strategies further improved localization microscopy. Today, it allows us to interrogate how the distribution and stoichiometry of interacting proteins in subcellular compartments and molecular machines accomplishes complex interconnected cellular processes. Thus, it exhibits potential to address fundamental questions of cell and developmental biology. Here, we briefly introduce the history, basic principles, and different localization microscopy methods with special focus on direct stochastic optical reconstruction microscopy (dSTORM) and summarize key developments and examples of two- and three-dimensional localization microscopy of the last 8 years.
A Tricatecholic Receptor for Carbohydrate Recognition:  Synthesis and Binding Studies (2007)

A new tripodal receptor bearing three catechol subunits on a benzene platform has been synthesized in four steps from 1,3,5-triethylbenzene and pyrogallol. The binding ability of the tricatecholic receptor was investigated toward several monosaccharides in CDCl3, where multiple equilibria were detected, and compared to that of a previously reported trisureidic receptor of analogous structure. Association constants were measured by 1H NMR titrations, and the corresponding affinities were assessed through the BC50 parameter, a binding descriptor univocally defining the affinity of a host for a guest in multi-equilibrium systems. Results show that the tripodal catecholic receptor binds the octyl glycosides with affinities ranging from 0.87 to 5.2 mM and with a 6-fold selectivity factor for the alpha-mannoside over the beta-glucoside. Although the affinity for glycosides was not appreciably improved with respect to the ureidic receptor, a significant change in selectivity was obtained by the H-bonding group replacement.
Humanized antibody to the alpha4beta7 integrin for induction of remission in ulcerative colitis (2009)

Data from one trial suggests that MLN-02 may be effective for induction of clinical response and remission in patients with moderately severe ulcerative colitis. Adverse events appear to be similar to placebo, although immunogenicity may be an issue. Further trials are needed to confirm the results of this study and to define the optimal dose and frequency of administration of MLN-02.
Novel Poly(<i>p</i>-phenylenevinylene)s with an Electron-Withdrawing Cyanophenyl Group (2002)

Novel poly(p-phenylenevinylene) derivatives with an electron-withdrawing cyanophenyl group on the polymer backbone, poly[2-(2‘-ethylhexyloxy)-5-(4‘-cyanophenyl)-1,4-phenylenevinylene] (PEHCNPV) and poly[2-dimethyloctylsilyl-5-(4‘-cyanophenyl)-1,4-phenylenevinylene] (PSi8CNPV), were synthesized via the Gilch polymerization. These polymers were completely soluble in common organic solvents and showed good thermal stability up to 400 °C. Surprisingly, they showed very high glass transition temperatures (above 180 °C), indicating that electroluminescenece (EL) devices constructed from these polymers should have good thermal stability. The presence of the electron-withdrawing cyanophenyl group lowered the HOMO and LUMO energy levels of PEHCNPV and PSi8CNPV relative to those of common PPV derivatives. Light-emitting diodes (LEDs) with the configuration ITO/PEDOT/polymer/LiF/Al were fabricated using the novel polymers. The LED devices based on PEHCNPV and PSi8CNPV exhibited maximum electroluminescence at 546 and 513 nm, respectively. In particular, the LED device containing PSi8CNPV emitted pure green light with a CIE (Commission Internationale de L'Eclairage) chromaticity coordinate of (0.330, 0.599), which is very close to that of the standard green (0.30, 0.60) used for high definition television (HDTV), a maximum external quantum efficiency of 0.67%, and a maximum brightness of 2900 cd/m2.
Electrical characteristics of Si3N4/Si/GaAs metal-insulator-semiconductor capacitor (1991)

We report on the electrical characteristics of an as-grown Si3N4/Si/n-GaAs metal-insulator-semiconductor capacitors. The GaAs layer is grown by molecular beam epitaxy and both the Si3N4 and the 10 Å Si layers are deposited using silane in a vacuum connected ultrahigh vacuum chemical vapor deposition chamber driven by an electron cyclotron resonance plasma source. The current-voltage characteristics of the Si3N4 films at high fields can be best represented by Fowler–Nordheim tunneling indicative of the high quality of the films. Hole inversion of the n-GaAs layer is clearly seen in the quasi-static capacitance-voltage curve. Despite past reports on the presence of a large amount of bulk traps in Si3N4, a hysteresis of less than 100 meV is observed in the high-frequency capacitance-voltage curves with a bias voltage swing of ±4 V. From the high-low capacitance method we estimated the interface trap density to be of the order of 4×1011 eV−1 cm−2 and from the conductance measurements we found a value of 1012 eV−1 cm−2.
Discovery of Potent and Centrally Active 6-Substituted 5-Fluoro-1,3-dihydro-oxazine β-Secretase (BACE1) Inhibitors via Active Conformation Stabilization (2018)

β-Secretase (BACE1) has an essential role in the production of amyloid β peptides that accumulate in patients with Alzheimer's disease (AD). Thus, inhibition of BACE1 is considered to be a disease-modifying approach for the treatment of AD. Our hit-to-lead efforts led to a cellular potent 1,3-dihydro-oxazine 6, which however inhibited hERG and showed high P-gp efflux. The close analogue of 5-fluoro-oxazine 8 reduced P-gp efflux; further introduction of electron withdrawing groups at the 6-position improved potency and also mitigated P-gp efflux and hERG inhibition. Changing to a pyrazine followed by optimization of substituents on both the oxazine and the pyrazine culminated in 24 with robust Aβ reduction in vivo at low doses as well as reduced CYP2D6 inhibition. On the basis of the X-ray analysis and the QM calculation of given dihydro-oxazines, we reasoned that the substituents at the 6-position as well as the 5-fluorine on the oxazine would stabilize a bioactive conformation to increase potency.
TDP2–Dependent Non-Homologous End-Joining Protects against Topoisomerase II–Induced DNA Breaks and Genome Instability in Cells and In Vivo (2013)

Anticancer topoisomerase "poisons" exploit the break-and-rejoining mechanism of topoisomerase II (TOP2) to generate TOP2-linked DNA double-strand breaks (DSBs). This characteristic underlies the clinical efficacy of TOP2 poisons, but is also implicated in chromosomal translocations and genome instability associated with secondary, treatment-related, haematological malignancy. Despite this relevance for cancer therapy, the mechanistic aspects governing repair of TOP2-induced DSBs and the physiological consequences that absent or aberrant repair can have are still poorly understood. To address these deficits, we employed cells and mice lacking tyrosyl DNA phosphodiesterase 2 (TDP2), an enzyme that hydrolyses 5'-phosphotyrosyl bonds at TOP2-associated DSBs, and studied their response to TOP2 poisons. Our results demonstrate that TDP2 functions in non-homologous end-joining (NHEJ) and liberates DSB termini that are competent for ligation. Moreover, we show that the absence of TDP2 in cells impairs not only the capacity to repair TOP2-induced DSBs but also the accuracy of the process, thus compromising genome integrity. Most importantly, we find this TDP2-dependent NHEJ mechanism to be physiologically relevant, as Tdp2-deleted mice are sensitive to TOP2-induced damage, displaying marked lymphoid toxicity, severe intestinal damage, and increased genome instability in the bone marrow. Collectively, our data reveal TDP2-mediated error-free NHEJ as an efficient and accurate mechanism to repair TOP2-induced DSBs. Given the widespread use of TOP2 poisons in cancer chemotherapy, this raises the possibility of TDP2 being an important etiological factor in the response of tumours to this type of agent and in the development of treatment-related malignancy.
Stabilization procedures based on fuzzy inference algorithms for PWM drives (2002)

The problem of instability areas of the general purpose drive system with PWM inverter and an induction motor was investigated. The first task of detection of instability (or excessive angular velocity oscillations with a poor damping factor) was solved in the drive system without velocity feedback and without velocity signal. The fuzzy inference based algorithm uses for processing only one signal from power circuit-inverter supply current signal, and two other signals from the control circuit of the inverter. It activates the adequate reference frequency correcting procedure. The improvement of stability is achieved only by the influence on the reference frequency signal.
Central nervous system complications of coronary artery bypass graft surgery: prospective analysis of 421 patients. (1983)

A prospective analysis of 421 patients undergoing coronary artery bypass graft (CABG) surgery as the sole cardiac procedure was carried out to assess the frequency of central nervous system (CNS) complications. In all, 451 variables were assessed in each patient. Stroke occurred in 5.2% but was severe in only 2%. Prolonged encephalopathy occurred in 11.6% but usually resolved before discharge. No statistically significant pre- or intraoperative risk variables for CNS complications were found; specifically, age or pump times in excess of two hours were not significant factors. Postoperative use of an intraaortic balloon pump and pressor agents were significantly correlated with prolonged encephalopathy. The frequency of CNS injury in CABG surgery is similar to that in other forms of open heart surgery, and there has been little change in the frequency of CNS complications over the past seven years. Possible mechanisms of CNS damage during CABG surgery are discussed.
Pitch quantization in low bit-rate speech coding (1999)

This paper describes a new pitch quantization method for low bit-rate speech coding systems. The logarithm of the pitch period is quantized in a combination of two uniform quantizers, one working directly on logarithmic pitch values and the other working on the difference between current and previous logarithmic pitch. The best of the two output values is transmitted to the receiver. This scheme can exploit: both redundancy in the signal and properties of the ear to achieve an efficient quantization. Listening tests show that the proposed scheme allows the pitch parameter to be quantized using 4 bits, with no degradation in audible quality.
Evaluation of the service execution environment and the service development environment for AIN (2003)

The feasibility of the scenario processor in the service logic execution environment (SLEE), which is ideal for a service/vendor independent environment, is evaluated. It is shown how to shorten the introduction of new telephone services considerably by using a new software engineering model based on the concept of scenario. The conclusions draw from comprehensive testing done to establish a design for the advance intelligent network (AIN) on a testbed system using the proposed architecture.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>