gebhart/patrepeval huggingface dataset:
Novel retroviral vector transferring a suicide gene and a selectable marker gene with enhanced gene expression by using a tetracycline-responsive expression system (1996)

A retroviral vector for the enhanced expression of the herpes simplex virus thymidine kinase (HSV tk) gene was developed by using a tetracycline-responsive expression system (TRES). The two components of the TRES, the chimeric transactivator (tTA) and the corresponding tTA-binding cis element (tetO), were both incorporated into a retroviral vector and resulted in high levels of tk gene expression from tetO in target cells. Amphotropic virus supernatants from stable producer cells, generated by the retroviral vector containing the TRES, gave titers of 10(4) to 10(5) G418-resistant CFU/ml on murine NIH 3T3 cells. The retroviral vector (G1tTA-[tetOTkINa]R), in which tetO was used in the opposite orientation relative to viral transcription, was capable of transducing tk and neo genes into murine NIH 3T3 cells to yield a high level of tk gene expression. TK enzyme activity in NIH 3T3 cells transduced by this vector was 417-fold higher than in control cells. This increased TK activity was returned to basal levels in the presence of tetracycline. The level of tk gene expression driven by tetO from G1tTA-[tetOTkINa]R vector in NIH 3T3 cells was fourfold higher at both the mRNA level and the TK enzyme level than that produced by the long terminal repeat of G1Tk1SvNa, the vector being used in the ongoing brain tumor gene therapy trial. Retroviral vectors containing the TRES may be useful therefore in achieving higher levels of tk gene expression, which should facilitate gene therapy approaches in the treatment of cancer.
Photoacoustic ocular imaging (2010)

We developed a photoacoustic ocular imaging device and demonstrated its utility in imaging the deeper layers of the eye including the retina, choroid, and optic nerve. Using safe laser intensity, the photoacoustic system was able to visualize the blood distribution of an enucleated pig's eye and an eye of a living rabbit. Ultrasound images, which were simultaneously acquired, were overlaid on the photoacoustic images to visualize the eye's anatomy. Such a system may be used in the future for early detection and improved management of neovascular ocular diseases, including wet age-related macular degeneration and proliferative diabetic retinopathy.
Parallel skeletons for structured composition (1995)

In this paper, we propose a straightforward solution to the problems of compositional parallel programming by using skeletons as the uniform mechanism for structured composition. In our approach parallel programs are constructed by composing procedures in a conventional base language using a set of high-level, pre-defined, functional, parallel computational forms known as skeletons. The ability to compose skeletons provides us with the essential tools for building further and more complex application-oriented skeletons specifying important aspects of parallel computation. Compared with the process network based composition approach, such as PCN, the skeleton approach abstracts away the fine details of connecting communication ports to the higher level mechanism of making data distributions conform, thus avoiding the complexity of using lower level ports as the means of interaction. Thus, the framework provides a natural integration of the compositional programming approach with the data parallel programming paradigm.
A typology of blockchain recordkeeping solutions and some reflections on their implications for the future of archival preservation (2017)

This paper presents a synthesis of original research documenting several cases of the application of blockchain technology to land transaction, medical, and financial record keeping. Using a thematic synthesis of the cases, the paper describes a typology of blockchain solutions for managing current records representing three distinct design patterns. It then considers the different types of solutions in relation to implications for recordkeeping and long-term preservation of authentic records.
Epigenetic modification of SOCS-1 differentially regulates STAT3 activation in response to interleukin-6 receptor and epidermal growth factor receptor signaling through JAK and/or MEK in head and neck squamous cell carcinomas (2006)

Signal transducer and activator of transcription 3 (STAT3) has been reported to be activated by interleukin-6 receptor (IL-6R) or epidermal growth factor receptor (EGFR) in head and neck squamous cell carcinomas (HNSCC), which may have important implications for responsiveness to therapeutics targeted at EGFR, IL-6R, or intermediary kinases. Suppressor of cytokine signaling-1 (SOCS-1) has been implicated recently in the negative regulation of IL-6R/Janus-activated kinase (JAK)-mediated activation of STAT3, suggesting that SOCS-1 could affect alternative activation of STAT3 by EGFR, IL-6R, and associated kinases. We investigated whether epigenetic modification of SOCS-1 affects STAT3 activation in response to IL-6R-, EGFR-, JAK-, or mitogen-activated protein kinase/extracellular signal-regulated kinase kinase (MEK)-mediated signal activation. STAT3 was predominantly activated by IL-6R via Jak1/Jak2 in HNSCC lines UMSCC-9 and UMSCC-38 in association with transcriptional silencing of SOCS-1 by hypermethylation. In UMSCC-11A cells with unmethylated SOCS-1, STAT3 activation was regulated by both EGFR and IL-6R via a JAK-independent pathway involving MEK. Pharmacologic inhibitors of JAK and MEK and expression of SOCS-1 following demethylation or transient transfection inhibited STAT3 activation and cell proliferation and induced cell apoptosis in corresponding cell lines. Hypermethylation of SOCS-1 was found in about one-third of human HNSCC tissues, making it a potentially relevant marker for STAT-targeted therapy in HNSCC patients. We conclude that SOCS-1 methylation status can differentially affect STAT3 activation by IL-6R and EGFR through JAK or MEK in different HNSCC and response to pharmacologic antagonists. Identifying the potential factors and the regulatory pathways in STAT3 activation has important implications for the development and selection of molecularly targeted therapy in HNSCC.
Measurement of tracheal temperature is not a reliable index of total respiratory heat loss in mechanically ventilated patients (2000)

In intensive care unit (ICU) mechanically ventilated patients, total respiratory heat loss was twice as much with either hydrophobic or hydroscopic HME than with the HH. This suggests that a much greater amount of heat was extracted from the respiratory tract by the HMEs than by the HH. Tracheal temperature, although simple to measure in ICU patients, does not appear to be a reliable estimate of total respiratory heat loss.
Network Synchrony in the Nucleus AccumbensIn Vivo (2001)

Nucleus accumbens neurons show membrane potential fluctuations between a very negative resting membrane potential and periodical plateau depolarizations. Because action potential firing occurs only during the depolarized state, the control of transitions between states is important for information processing within this region, with an impact on accumbens-related behaviors. It has been proposed that ensembles of active neurons in the nucleus accumbens could be based on a population of cells depolarizing simultaneously into the UP state. In this study, in vivo intracellular recordings from accumbens neurons were performed simultaneously with local field potential recordings to examine whether the nucleus accumbens can exhibit synchronization of membrane potential states in a population of neurons. These simultaneous recordings indicated that local field potential shifts occurred synchronously with transitions to the UP state. Furthermore, manipulations that evoked prolonged plateau depolarizations also evoked field potentials of similar duration. Such signals likely occurred because of simultaneous membrane potential changes in a population of neurons. Together with our previous studies, these results suggest that membrane potential states in the nucleus accumbens can be synchronized by synaptic inputs from the hippocampus.
Microbial Mannanases: An Overview of Production and Applications (2007)

Microbial mannanases have become biotechnologically important since they target the hydrolysis of complex polysaccharides of plant tissues into simple molecules like manno-oligosaccharides and mannoses. The role of mannanases in the paper and pulp industry is well established and recently they have found application in the food and feed technology, coffee extraction, oil drilling and detergent industry. Mannanses are enzymes produced mainly from microorganisms but mannanases produced from plants and animals have also been reported. Bacterial mannanases are mostly extracellular and can act in a wide range of pH and temperature, though acidic and neutral mannanases are more common. This review will focus on complex mannan structure and the microbial enzyme complex involved in its complete breakdown, mannanase sources, production conditions and their applications in the commercial sector. The reference to plant and animal mannanases has been made to complete the overview. However, the major emphasis of the review is on the microbial mannanases.
[An experimental quantitative assessment of the efficiency of Borrelia persica transmission by Ornithodoros papillipes ticks. 1. 2 forms of borreliemia in guinea pigs]. (1990)

Experimental borreliosis in guinea pigs caused by ticks' bites assumed two forms--typical and mild, the latter being encountered in 40% of cases. Mild form significantly differs from the typical one in some indices of borreliemia: intensity, duration, time of onset and cessation, absence of fluctuations in the number of borrelia. The form is not easily diagnosed by the analysis of animal blood preparations, which should be taken into consideration in experimental and clinical practice. In mild form of borreliemia the agent should be searched for in the blood of guinea pigs daily from days 6 to 12 after the infection, with the following control till day 20.
Action of agonists and antagonists at muscarinic receptors present on ileum and atria in vitro (1985)

The action of 'selective' agonists and antagonists at muscarinic receptors mediating ileal contractions, and the rate and force of atrial contractions has been assessed. The effect of nicotinic receptor stimulation, catecholamine release and acetylcholinesterase (AChE) action on muscarinic activity has also been assessed. The nicotinic actions of carbachol did not affect its agonist potency nor the antagonist affinity data obtained when this agonist was used in atrial and ileal preparations. Antagonist data indicated that muscarinic receptors mediating the rate and force of atrial contractions did not differ. Differences in agonist potencies at these two muscarinic receptors were attributable to either differences in intrinsic efficacy or susceptibility to the action of acetylcholinesterase. The small differences in agonist potency observed between atrial and ileal muscarinic receptors were considered not sufficient to indicate receptor heterogeneity. The pirenzepine affinity data indicated that all three receptors are of the M2 type. Affinity data using secoverine and 4-diphenyl-acetoxy-N-methyl piperidine methiodide indicated that ileal and atrial muscarinic receptors differ. Data obtained using gallamine, pancuronium and stercuronium cannot be regarded as indicative of receptor affinity since the antagonism is not competitive; it did nonetheless corroborate the conclusion that ileal and atrial muscarinic receptors are different.
RDOCK: Refinement of rigid‐body protein docking predictions (2003)

We present a simple and effective algorithm RDOCK for refining unbound predictions generated by a rigid-body docking algorithm ZDOCK, which has been developed earlier by our group. The main component of RDOCK is a three-stage energy minimization scheme, followed by the evaluation of electrostatic and desolvation energies. Ionic side chains are kept neutral in the first two stages of minimization, and reverted to their full charge states in the last stage of brief minimization. Without side chain conformational search or filtering/clustering of resulting structures, RDOCK represents the simplest approach toward refining unbound docking predictions. Despite its simplicity, RDOCK makes substantial improvement upon the top predictions by ZDOCK with all three scoring functions and the improvement is observed across all three categories of test cases in a large benchmark of 49 non-redundant unbound test cases. RDOCK makes the most powerful combination with ZDOCK2.1, which uses pairwise shape complementarity as the scoring function. Collectively, they rank a near-native structure as the number-one prediction for 18 test cases (37% of the benchmark), and within the top 4 predictions for 24 test cases (49% of the benchmark). To various degrees, funnel-like energy landscapes are observed for these 24 test cases. To the best of our knowledge, this is the first report of binding funnels starting from global searches for a broad range of test cases. These results are particularly exciting, given that we have not used any biological information that is specific to individual test cases and the whole process is entirely automated. Among three categories of test cases, the best results are seen for enzyme/inhibitor, with a near-native structure ranked as the number-one prediction for 48% test cases, and within the top 10 predictions for 78% test cases. RDOCK is freely available to academic users at http://zlab.bu.edu/ approximately rong/dock.
A High Density Programmable Logic Array Chip (1979)

A programmable logic array (PLA) chip design using special array folding techniques and an on-chip bus structure has been developed. It overcomes the sparseness in conventional large PLA configurations. The design is a masterslice FET chip personalized for the particular application during processing. Software algorithms are used to map conventional PLA formats into the new structure. The techniques used provide improved logic function and performance for an FET array technology. Included are descriptions of the PLA architecture and the circuitry that was used.
Agent behavior and agent models in unregulated markets (2001)

Mobile-agent systems show significant promise as the most effective way to harness the power of the Internet and the massive collection of information and opportunity that the Internet holds. However the efficient organization and control of these systems remains one of a number of unsolved problems with this approach to network computing. This paper examines a mobile-agent system with specific focus on environment sensing, preemptive load balancing and open agent markets. Agent behaviour is studied with actual agent systems using progressively sophisticated agent migration strategies.It is shown that actual modeling shows interesting and difficult to predict behaviour in the agent systems. It is shown that mobile agents with relatively simple migration strategies can cause loads in self-regulating agent markets to oscillate. It is further shown that using Autoregressive modeling to predict the market behaviour can allow individual agents to significantly outperform other agents. However the fidelity of the model is critical to the success of the agents. The criticality of good agent strategies and actual agent system modeling is thus highlighted.
Relative contribution of cytochromes P‐450 and flavin‐containing monoxygenases to the metabolism of albendazole by human liver microsomes (2000)

We conclude that the production of ABS in human liver is mediated via both FMO and CYP, principally CYP3A4, with the CYP component being the major contributor.
A 1.8-GHz CMOS low-phase-noise voltage-controlled oscillator with prescaler (1995)

The implementation of the two high-frequency building blocks for a low-phase-noise 1.8-GHz frequency-synthesizing PLL in a standard 0.7-/spl mu/m CMOS process is discussed. The VCO uses on-chip bondwires, instead of spiral inductors, for low noise and low power. The design of these bondwire inductors is discussed in great detail. A general formula for the theoretical limit of the phase noise of LC-tuned oscillators is presented. The design of a special LC-tank allows a trade-off between noise and power. The realized VCO has a phase noise of -115 dBc/Hz at 200 kHz from the 1.8-GHz carrier and consumes 8 mA from a 3-V supply. The prescaler has a fixed division ratio of 128 and uses an enhanced ECL-alike high-frequency D-flipflop. Its power consumption is 28 mW.
Formation of Novel Polymeric Nanoparticles (2001)

We have found that not only block copolymers but also ionomers can self-assemble in a selective solvent to form surfactant-free nanoparticles. The self-assembly can be induced by chemical reaction, polymer-polymer complexation, and microphase inversion in addition to the temperature. A recently developed microwave method for the preparation of uniform surfactant-free polymeric nanoparticles is also reviewed. Our results have revealed that for a given dispersion, the particle surface area occupied per stabilizer (surfactant, polymer chains, and ionic groups) is close to a constant.
Maximum likelihood and discriminative training of direct translation models (2002)

We consider translating natural language sentences into a formal language using direct translation models built automatically from training data. Direct translation models have three components: an arbitrary prior conditional probability distribution, features that capture correlations between automatically determined key phrases or sets of words in both languages, and weights associated with these features. The features and the weights are selected using a training corpus of matched pairs of source and target language sentences to maximize the entropy or a new discrimination measure of the resulting conditional probability model. We report results in the air travel information system domain and compare the two methods of training.
In situ hybridization protocol for enhanced detection of gene expression in the planarian Schmidtea mediterranea (2013)

The modifications we present here provide significant improvements in signal intensity and signal sensitivity for WISH and FISH in planarians. Additionally, these modifications might be of widespread utility for whole-mount FISH in other model organisms.
Yield Management Enhanced Advanced Process Control System (YMeAPC)—Part I: Description and Case Study of Feedback for Optimized Multiprocess Control (2010)

In today's competitive semiconductor manufacturing environment, improving fab productivity and reducing cost requires that all systems work collaboratively towards production, quality and cost targets. Equipment engineering systems (EES), including advanced process control have risen to the top as key enablers for maximizing fab productivity, however these systems have been hindered as they focus on equipment and process, rather than fab-wide, metrics. Extending EES into the yield management space allows for leveraging yield prediction information as feedback into closing the loop around the fab to better achieve productivity goals. With this added capability of yield prediction, EES can: 1) predict yield excursions as well as excursion sources (leveraging virtual metrology technology), thereby avoiding costly post mortem yield recovery activities; 2) improve EES capabilities such as maintenance management and scheduling/dispatch; and 3) utilize yield prediction information as feedback to all levels of control in the fab, from individual processes up through factory-level controllers so that processes can be continuously tuned to meet yield and device performance targets without resorting to design changes to slower products. Case studies of application of this feedback information illustrate that benefits can be achieved from straight-forward applications, however these benefits can be expanded (especially) as more complex scheduling and control solutions are implemented. Realizing this type of yield-enhanced EES solution (YMeAPC) in a cost-effective manner requires fab-wide adherence to standards and best practices for component integration, event-based control system operation, and user interface management.
Involvement of eicosanoids in the pathogenesis of pancreatic cancer: The roles of cyclooxygenase-2 and 5-lipoxygenase (2014)

The interplay between inflammation and cancer progression is a growing area of research. A combination of clinical, epidemiological, and basic science investigations indicate that there is a relationship between inflammatory changes in the pancreas and neoplastic progression. Diets high in ω-6 polyunsaturated fatty acids provide increased substrate for arachidonic acid metabolism by cyclooxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX) to form eicosanoids. These eicosanoids directly contribute to pancreatic cancer cell proliferation. Both COX-2 and 5-LOX are upregulated in multiple cancer types, including pancreatic cancer. In vitro studies using pancreatic cancer cell lines have demonstrated upregulation of COX-2 and 5-LOX at both the mRNA and protein levels. When COX-2 and 5-LOX are blocked via a variety of mechanisms, cancer cell proliferation is abrogated both in vitro and in vivo. The mechanism of COX-2 has been shown to include effects on apoptosis as well as angiogenesis. 5-LOX has been implicated in apoptosis. The use of COX-2 and 5-LOX inhibitors in clinical studies in patients with pancreatic cancer has been limited. Patient enrollment has been restricted to those with advanced disease which makes evaluation of these drugs as chemopreventive agents difficult. COX-2 and 5-LOX expression have been shown to be present during the early neoplastic changes of pancreatic cancer, well before progression to invasive disease. This indicates that the ideal role for these interventions is early in the disease process as preventive agents, perhaps in patients with chronic pancreatitis or hereditary pancreatitis.
Electron Microscopy in Biology (1991)

Abstract Transmission electron microscopy is one of the most important and widely used forms of microscopy in biomedical research. Electron Microscopy in Molecular Biology : A Practical Approach was published in 1987, and contained techniques relating specifically to nucleic acids and proteins. The present volume provides detailed protocols for a wide range of procedures relating to the electron microscopy of tissues, cells, and their components with the emphasis on biomedical applications. The fundamental methods for specimen preparation, tissue fixation, embedding, and sectioning are covered in depth and are followed by the more specialist techniques of freeze-substitution, immunogold labelling, autoradiography, and enzyme histochemistry. Although the technical details in the book relate mainly to tissues and cells, many of the procedures can be adapted for isolated organelles and membrane fractions, viral particles, macromolecular assemblies, and large proteins. This is a broadly based compilation of the most important specimen preparation techniques and their applications. It will be of interest to researchers and advanced students working in almost every biomedical discipline, plus technicians in electron microscopy units.