gebhart/patrepeval huggingface dataset:
Characterization of the mmsAB operon of Pseudomonas aeruginosa PAO encoding methylmalonate-semialdehyde dehydrogenase and 3-hydroxyisobutyrate dehydrogenase. (1992)

A 5417-base pair (bp) region of Pseudomonas aeruginosa PAO chromosomal DNA containing the mmsAB operon and an upstream regulatory gene (mmsR) has been cloned and characterized. The operon contains two structural genes involved in valine metabolism: mmsA, which encodes methylmalonate-semialdehyde dehydrogenase; and mmsB, which encodes 3-hydroxyisobutyrate dehydrogenase. mmsA and mmsB share the same orientation and are separated by a 16-bp noncoding region. The transcriptional start site for the operon has been pinpointed to a cytidine residue located 77 bp from the translational start site of the operon. mmsR is located on the opposite strand and begins 134 bp from the translational start site of mmsA. MmsR has been identified as a member of the XylS/AraC family of transcriptional regulators and appears to act as a positive regulator of the mmsAB operon. Sequence comparison of MmsA to other proteins in the data bases revealed that MmsA belongs to the aldehyde dehydrogenase (NAD+) superfamily. MmsB shares a 44% amino acid identity with 3-hydroxyisobutyrate dehydrogenase from rat liver. Mutants with insertionally inactivated mmsR, mmsA, and mmsB grow slowly on valine/isoleucine medium and exhibit reduced enzyme activity in cell-free extracts compared to P. aeruginosa PAO.
Clinical Aspects of Cytomegalovirus Antiviral Resistance in Solid Organ Transplant Recipients (2012)

Despite advances in the prophylaxis and acute treatment of cytomegalovirus (CMV), it remains an important pathogen affecting the short- and long-term clinical outcome of solid organ transplant. The emergence of CMV resistance in a patient reduces the clinical efficacy of antiviral therapy, complicates therapeutic and clinical management decisions, and in some cases results in loss of the allograft and/or death of the patient. There is increasing use of antiviral prophylaxis after transplant with little expansion in the range of antiviral agents effective in treatment of CMV. Further understanding is needed of the risk factors for development of CMV antiviral resistance and of therapeutic strategies for treating patients infected with resistant viruses. We review the current status of CMV resistance in solid organ transplant recipients, and provide diagnostic and therapeutic suggestions for the clinician in managing antiviral resistance.
A unified object-oriented toolkit for discrete contextual computer vision (1997)

This paper describes a new general-purpose contextual architecture which provides a unified framework for efficiently combining all types and levels of context in discrete computer vision applications, by organising the multidimensional search space in best-first order along each dimension. It then implements an efficient 'lazy evaluation' algorithm, which searches from the most probable vertex outwards, and guarantees to find solutions in absolute best-first order. The architecture has been designed and built as a C++ class library, and utilised within a demonstrator which implements full contextual constraints for optical character recognition of hand-printed postal addresses. Preliminary evaluation of the demonstrator suggests the system has the potential to achieve genuinely remarkable performance compared with previous context systems: its memory requirements are an order of magnitude less than an equivalent trie-based dictionary; its search speed is at least an order of magnitude faster than the trie, and actually get faster as the dictionary size increases; and its error rate is virtually zero, even when an OCR system with appalling performance is simulated. Using this architecture it appears to be possible to build real-time solutions to large-scale contextual vision problems which have previously been beyond the bounds of computational feasibility.
Band Structure, Phonon Scattering, and the Performance Limit of Single-Walled Carbon Nanotube Transistors (2005)

Semiconducting single-walled carbon nanotubes are studied in the diffusive transport regime. The peak mobility is found to scale with the square of the nanotube diameter and inversely with temperature. The maximum conductance, corrected for the contacts, is linear in the diameter and inverse temperature. These results are in good agreement with theoretical predictions for acoustic phonon scattering in combination with the unusual band structure of nanotubes. These measurements set the upper bound for the performance of nanotube transistors operating in the diffusive regime.
Solid Phase Microextraction for Determining the Distribution of Chemicals in Aqueous Matrices (1997)

Solid phase microextraction (SPME) can be applied to measure the distribution of chemicals in different speciation states. The standard SPME apparatus and procedures can be applied to measure free concentrations of a target compound spiked into pure water and spiked into water containing another pseudophase, such as dissolved humic organic matter (HOM). Based on a comparison of results obtained for the two samples, the partitioning of the target analyte between water and the pseudophase is calculated. The samples investigated in the present study were from heavily contaminated coal wastewater containing dissolved organic polymers with properties similar to those of HOM. External calibration provides information about freely dissolved analytes. After calibration of the SPME signal by addition of an internal standard (e.g., a deuterated surrogate), the results indicate the total concentration of the target analyte in the sample due to the identical partitioning of the internal standard. The concentration determined in this way coincides well with data obtained from liquid−liquid extraction (LLE). Both methods, SPME with internal calibration and LLE, measure total concentration, composed of a freely dissolved portion and a portion that is reversibly bound onto a pseudophase (HOM).
A vehicle occupant counting system based on near-infrared phenomenology and fuzzy neural classification (2000)

We undertook a study to determine if the automatic detection and counting of vehicle occupants is feasible. In the present paper, we report our findings regarding the appropriate sensor phenomenology and arrangement for the task. We propose a novel system based on fusion of near-infrared imaging signals and demonstrate its adequacy with theoretical and experimental arguments. We also propose a fuzzy neural network classifier to operate upon the fused near-infrared imagery and perform the occupant detection and counting function. We demonstrate experimentally that the combination of fused near-infrared phenomenology and fuzzy neural classification produces a robust solution to the problem of automatic vehicle occupant counting. We substantiate our argument by providing comparative experimental results for vehicle occupant counters based on visible, single near-infrared, and fused near-infrared bands. Our proposed solution can find a more general applicability as the basis for a reliable face detector both indoors and outdoors.
Gene transfer with herpes simplex vectors. (1999)

In developing any viral gene delivery vector there are two fundamental problems which need to be addressed. Firstly, replication disabled vectors which will be safe for clinical use must be constructed, and secondly, strategies for obtaining appropriate transgene expression in vector transduced cells must be devised. In this review, the progress which has been made in developing herpes simplex virus (HSV)-based gene delivery vectors is discussed, as are the experimental results which have been obtained using these vectors for gene delivery in tissue culture cells and animal models.
Counterflow Gradient Focusing in Free-Flow Electrophoresis for Protein Fractionation (2020)

With its ability to continuously separate and collect charged analytes, free-flow electrophoresis (FFE) has become a useful tool for the purification and real-time analysis of biological mixtures. This work presents a new free-flow counterflow gradient focusing (FF-CGF) mechanism that uses a novel velocity gradient to counterbalance electrophoretic migration. This counterflow gradient is created by simply introducing fluid flow through the sidewalls of the FFE chamber. The theoretical foundation and device design for FF-CGF are provided in this work, followed by implementation and validation, with a detailed discussion on future opportunities and challenges. Initial results show promise, with the potential to improve FFE resolution and offer versatility. Compared to existing focusing techniques, such as free-flow isotachophoresis and isoelectric focusing, no complex buffer compositions are required.
In situ nucleoprotein structure at the SV40 major late promoter: melted and wrapped DNA flank the start site. (1989)

New in situ probing methods have been developed and used to probe the nucleoprotein structures at the SV40 major late promoter in infected monkey cells. The region that contains the three proximal transcription elements was probed with DNase I and micrococcal nuclease in transcriptionally active, permeabilized cells, and with the single-strand selective reagent KMnO4 in intact cells. The downstream element is included in a region of enhanced DNase I reactivity at 10- to 11-bp intervals for approximately 140 bp, presumably because of DNA wrapping around a specifically positioned nucleosome particle. The two other proximal DNA elements appear to be mostly melted, with a protecting factor bound primarily to the template DNA strand. The protecting factor directly borders the wrapped particle. These observations provide an initial description of parts of the biological transcription machinery and suggest that the SV40 major late promoter elements are part of a higher order nucleoprotein complex that involves wrapped and melted DNA.
Therapeutic Protein and Peptide Formulation and Delivery (1997)

A marketable protein formulation must be safe to administer, remain physically, chemically, and biologically stable during the recommended shelf life, induce minimal local irritation, and meet the specific clinical and delivery needs. Achieving this goal is an evolutionary process involving many disciplines in process sciences, pharmacokinetics, toxicology, and clinical studies. With this scope in mind, this review will focus on protein stability and analytical tools for characterization which are critical to formulation development, demonstration of process robustness, and establishment of rational specifications. Of particular importance are the recent changes in the FDA requirements 1 that have allowed for a shift from showing in vivo biological equivalence in humans to demonstrating physical-chemical, bioactivity, and pharmacokinetic equivalence in animal models; this calls for greater understanding of the physical-biochemical stability of the protein using sensitive and specific analytical tools. In addition to providing a summary of the common protein degradation pathways in this
Signaling at Purinergic P2X Receptors (2008)

P2X receptors are membrane cation channels gated by extracellular ATP. Seven P2X receptor subunits (P2X(1-7)) are widely distributed in excitable and nonexcitable cells of vertebrates. They play key roles in inter alia afferent signaling (including pain), regulation of renal blood flow, vascular endothelium, and inflammatory responses. We summarize the evidence for these and other roles, emphasizing experimental work with selective receptor antagonists or with knockout mice. The receptors are trimeric membrane proteins: Studies of the biophysical properties of mutated subunits expressed in heterologous cells have indicated parts of the subunits involved in ATP binding, ion permeation (including calcium permeability), and membrane trafficking. We review our current understanding of the molecular properties of P2X receptors, including how this understanding is informed by the identification of distantly related P2X receptors in simple eukaryotes.
Conformational Regulation of Integrin Structure and Function (2002)

Integrins are a structurally elaborate family of heterodimers that mediate divalent cation-dependent cell adhesion in a wide range of biological contexts. The inserted (I) domain binds ligand in the subset of integrins in which it is present. Its structure has been determined in two alternative conformations, termed open and closed. In striking similarity to signaling G proteins, rearrangement of a Mg(2+)-binding site is linked to large conformational movements in distant backbone regions. Mutations have been used to stabilize either the closed or open structures. These show that the snapshots of the open conformation seen only in the presence of a ligand or a ligand mimetic represent a high-affinity, ligand-binding conformation, whereas those of the closed conformation correspond to a low-affinity conformation. The C-terminal alpha-helix moves 10 A down the side of the domain in the open conformation. Locking in the conformation of the preceding loop is sufficient to increase affinity for ligand 9000-fold. This C-terminal "bell-rope" provides a mechanism for linkage to conformational movements in other domains. The transition from the closed to open conformation has been implicated in fast (<1 s) regulation of integrin affinity in response to activation signals from inside the cell. Recent integrin structures and functional studies reveal interactions between beta-propeller, I, and I-like domains in the headpiece, and a critical role for integrin EGF domains in the stalk region. These studies suggest that the headpiece of the integrin faces down toward the membrane in the inactive conformation and extends upward in a "switchblade"-like opening motion upon activation. These long-range structural rearrangements of the entire integrin molecule involving multiple interdomain contacts appear closely linked to conformational changes in the I domain, which result in increased affinity and competence for ligand binding.
Supporting developers with natural language queries (2010)

The feature list of modern IDEs is steadily growing and mastering these tools becomes more and more demanding, especially for novice programmers. Despite their remarkable capabilities, IDEs often still cannot directly answer the questions that arise during program comprehension tasks. Instead developers have to map their questions to multiple concrete queries that can be answered only by combining several tools and examining the output of each of them manually to distill an appropriate answer. Existing approaches have in common that they are either limited to a set of predefined, hardcoded questions, or that they require to learn a specific query language only suitable for that limited purpose. We present a framework to query for information about a software system using guided-input natural language resembling plain English. For that, we model data extracted by classical software analysis tools with an OWL ontology and use knowledge processing technologies from the Semantic Web to query it. We use a case study to demonstrate how our framework can be used to answer queries about static source code information for program comprehension purposes.
国家作用的变化：测量、机会与问题 (2001)

新千年伊始，正是思考国家的作用、总结得失以启示未来的时候。国家权力在20世纪具有空前的破坏力，如希特勒和斯大林的独裁政权。但是强有力的国家也促进了经济增长，大大提高了人民的生活水准，使大众更能安然自在地追求自己所好。这种对比自然要引发一系列问题。国家领导人应行使多大权力?应当在什么情况下行使这些权力?过去的20年市场改革和民主化运动中施行的政策，哪些运转良好，哪些尚需调整？
Exisulind induction of apoptosis involves guanosine 3',5'-cyclic monophosphate phosphodiesterase inhibition, protein kinase G activation, and attenuated beta-catenin. (2000)

Sulindac sulfone (exisulind), although a nonsteroidal anti-inflammatory drug derivative, induces apoptosis in tumor cells by a mechanism that does not involve cyclooxygenase inhibition. SW480 colon tumor cells contain guanosine 3',5'-monophosphate (cGMP) phosphodiesterase (PDE) isoforms of the PDE5 and PDE2 gene families that are inhibited by exisulind and new synthetic analogues. The analogues maintain rank order of potency for PDE inhibition, apoptosis induction, and growth inhibition. A novel mechanism for exisulind to induce apoptosis is studied involving sustained increases in cGMP levels and cGMP-dependent protein kinase (PKG) induction not found with selective PDE5 or most other PDE inhibitors. Accumulated beta-catenin, shown to be a substrate for PKG, is decreased by exisulind, suggesting a mechanism to explain apoptosis induction in neoplastic cells harboring adenomatous polyposis coli gene mutations.
L‐Gulose or D‐gluco‐Hexodialdose from D‐Glucurono‐6,3‐lactone by Controlled Reductions (1980)

New reduction reactions with boranes in sugar chemistry permitted the first synthesis of anhydrous solid L-gulose (1) (with Et2BH). The same starting material can also yield anhydrous solid D-gluco-hexodialdose (2) (with 1. (EtBO)3 and 2. Et2BH).
Comparison of cyclosporin A and methotrexate in the treatment of psoriatic arthritis: a one-year prospective study. (1995)

To compare the effectiveness and toxicity of cyclosporin A (CsA) vs low-dose methotrexate (MTX) over a period of one year in the treatment of psoriatic arthritis (PsA) with peripheral involvement.Thirty-five patients with PsA were enrolled in a prospective, controlled, randomized trial. CsA was initially given in doses of 3 mg/kg/day to a maximum permitted dose of 5 mg/kg/day; MTX was given in oral doses of 2.5 mg every 12 hours for 3 consecutive doses each week up to a maximum dose of 15 mg/weekly. Clinical and laboratory evaluations were performed at entry and monthly thereafter.After 6 and 12 months the number of painful joints, the number of swollen joints, the Ritchie index, the duration of morning stiffness, grip strength, CRP, the patient's and the physician's assessment of PsA activity, as well as the PASI, were significantly improved in both treatment groups. ESR values were significantly reduced only in the MTX group (p < 0.01), which also showed a significantly increase of liver enzymes. The changes in the main clinical and laboratory parameters during the course of CsA or MTX treatment were not significantly different except for the AST and ALT levels (p < 0.05). After one year of therapy CsA and MTX were withdrawn in 41.2% and 27.8% of the patients respectively, but these differences were not statistically significant.Our one-year prospective trial shows that low-dose CsA and MTX are both effective in the treatment of PsA, but the differences in the tolerability of these drugs must be considered at the start of therapy.
Total skin electron beam therapy as palliative treatment for cutaneous manifestations of advanced, therapy-refractory cutaneous lymphoma and leukemia (2012)

For palliation of symptomatic cutaneous manifestations of advanced cutaneous lymphoma or leukemia, total skin electron beam therapy is an efficient and well tolerated considerable treatment option.
Application of preemphasis to achieve flat output OSNR in time-varying channels in cascaded EDFAs without equalization (2001)

In this paper, we present a new method for optical signal-to-noise ratio (OSNR) equalization of wavelength division multiplexed (WDM) channels at the end of a cascade of several erbium-doped fiber amplifiers (EDFAs) by use of preemphasis, as well as the proper choice of EDFA design parameters. Identical OSNR at the end of the cascade ensures better signal detection and quality of service. The dynamics of the equalizing method have been demonstrated by simulation for single- and double-stage amplifier designs using a numerical model incorporating time variation effects in EDFA. Calculations are based on the solution of a transcendental equation describing the dynamics of the reservoir, i.e., the total number of excited ions, for each EDFA. Traffic on eight WDM channels is modeled as statistically independent ON-OFF time-slotted sources. In addition, we investigate the effect of gain clamping of the first amplifier in the cascade-by implementing a ring laser and propagating the lasing power through the cascade-on the statistics of OSNR variation. We show that it is possible to achieve dynamic OSNR equalization for a WDM system by the use of preemphasis and an appropriate choice of EDFA parameters, without resorting to optical equalization filters. Most previous equalization methods are static with flat gain for a given inversion level in the amplifier. Changes in the input power (due to network reconfiguration or packetized traffic) will lead to a varying inversion level and hence non optimal equalization.
Reactivation of Mg acceptor in Mg-doped GaN by nitrogen plasma treatment (2000)

Mg-doped GaN films, grown by metalorganic chemical vapor deposition, were treated with a nitrogen plasma after a conventional rapid thermal annealing (RTA). The conductivity of the p-type GaN film was greatly enhanced by nitrogen plasma treatment, and exhibited a higher sheet hole concentration as well as lower sheet resistance than the RTA samples. A photoluminescence (PL) band which peaked at 3.27 eV was new, and a band at 2.95 eV was markedly attenuated in the plasma treated samples. PL measurements suggest that self-compensation in a Mg-doped GaN caused by the nitrogen vacancies is effectively reduced by the nitrogen plasma treatment, leading to an enhanced p-type conductivity. In addition, the plasma-treated sample revealed a drastic reduction in specific contact resistance by three orders of magnitude, compared with the RTA samples.
Novel Synthesis of Diketo-Acid Chondroitin-4-Sulfate as Coordination Biopolymer Precursor through Oxidation of Chondroitin-4-Sulfate by Alkaline Permanganate (2013)

Coordination biopolymer diketo-acid derivative of chondroitin-4-sulfate (DKA-CS) was prepared by the oxidation of CS with potassium permanganate in alkaline solution at pH's > 12. The chemical structure of the synthesized heterocyclic macromolecule (DKA-CS) has been characterized by elemental analysis and IR spectroscopy. The tendency of DKA-CS as a coordination biopolymer chelating agent for some metal ions has been examined. A tentative mechanism consistent with the experimental results for oxidation is suggested.
Sex Differences in Platelet Reactivity and Response to Low-Dose Aspirin Therapy (2006)

Women experienced the same or greater decreases in platelet reactivity after aspirin therapy, retaining modestly more platelet reactivity compared with men. However, most women achieved total suppression of aggregation in the direct COX-1 pathway, the putative mechanism for aspirin's cardioprotection.
Treatment of Hereditary Angioedema with a Vapor-Heated C1 Inhibitor Concentrate (1996)

Background. Hereditary angioedema results from a congenital deficiency of functional C1 inhibitor and is characterized by episodic bouts of edema, which may be life-threatening when they involve the larynx. We evaluated the effectiveness of a C1 inhibitor concentrate in the prevention and treatment of attacks of hereditary angioedema. The concentrate was vapor-heated to inactivate hepatitis and human immunodeficiency viruses.