gebhart/patrepeval huggingface dataset:
Immortalization of Primary Human Epithelial Cells by Cloned Cervical Carcinoma DNA Containing Human Papillomavirus Type 16 E6/E7 Open Reading Frames (1989)

Primary human epithelial cells were transfected with a subgenomic fragment of DNA cloned from a cervical carcinoma, containing the putative transforming genes E6 and E7 from the human papillomavirus type 16 prototype. Several immortalized cell lines were generated, all retaining tumour DNA and expressing the viral genes, suggesting that either one or both of these genes is sufficient for the immortalization of primary human genital keratinocytes.
Engineered Synthetic Pathway for Isopropanol Production in Escherichia coli (2007)

A synthetic pathway was engineered in Escherichia coli to produce isopropanol by expressing various combinations of genes from Clostridium acetobutylicum ATCC 824, E. coli K-12 MG1655, Clostridium beijerinckii NRRL B593, and Thermoanaerobacter brockii HTD4. The strain with the combination of C. acetobutylicum thl (acetyl-coenzyme A [CoA] acetyltransferase), E. coli atoAD (acetoacetyl-CoA transferase), C. acetobutylicum adc (acetoacetate decarboxylase), and C. beijerinckii adh (secondary alcohol dehydrogenase) achieved the highest titer. This strain produced 81.6 mM isopropanol in shake flasks with a yield of 43.5% (mol/mol) in the production phase. To our knowledge, this work is the first to produce isopropanol in E. coli, and the titer exceeded that from the native producers.
Oleic acid-induced mucosal injury in developing piglet intestine (1993)

A role for luminal nutrients, in particular products of lipid digestion, in the pathogenesis of mucosal injury to developing intestine has been postulated. We evaluated changes in mucosal permeability and light and electron microscopic histology induced by luminal perfusion with the long-chain fatty acid oleate in developing piglet intestine as a function of age and concentration of the fatty acid. 51Cr-labeled EDTA plasma-to-lumen clearance was measured in jejunum and ileum of 1-day-, 3-day-, 2-wk-, and 1-mo-old piglets during sequential perfusion with saline control (20 min); 0, 1, 5, and 10 mM oleic acid/10 mM taurocholate in saline (20 min); and normal saline (60 min). The jejunum of piglets < or = 2 wk showed significantly greater increases in mucosal permeability compared with 1-mo-old animals after perfusion with oleic acid. This effect was dependent on the luminal concentration of the fatty acid and was associated with mucosal injury evident under light and electron microscopy. In contrast, the overall response in ileum was more attenuated compared with jejunum. Thus oleic acid, a common dietary fatty acid, induces dose- and age-dependent injury in developing piglet intestine. Investigation of the mechanisms of this injury may provide the basis for dietary modifications directed at decreasing the risk of mucosal injury during enteral feeding in neonatal intestine.
Computer-Aided Software Engineering in a distributed workstation environment (1984)

Computer-Aided Software Engineering environments are becoming essential for complex software projects, just as CAD systems have become essential for complex hardware projects. DSEE, the DOMAIN Software Engineering Environment, is a distributed, production quality, software development environment that runs on Apollo workstations. DSEE provides source code control, configuration management, release control, advice management, task management, and user-defined dependency tracking with automatic notification. DSEE incorporates some of the best ideas from existing systems. This paper describes DSEE, contrasts it other systems, and discusses some of the technical issues involved in the construction of a highly-reliable, safe, efficient, and distributed development environment.
Daily melatonin intake resets circadian rhythms of a sighted man with non‐24‐hour sleep‐wake syndrome who lacks the nocturnal melatonin rise (1997)

Effects of daily melatonin intake on the circadian rhythms of sleep and wakefulness, rectal temperature and plasma cortisol were examined in a sighted man who had suffered from the non-24-hour sleep-wake syndrome. The subject lacked the nocturnal melatonin rise in plasma, but showed robust circadian rhythms in rectal temperature and plasma cortisol. The sleep-wake rhythm free-ran with a period longer than 24 hours. Daily melatonin intake at 21:00 h concentrated sleep episodes in the nocturnal period (24:00-8:00 h), and increased the length of the episodes. A single oral dose (3 mg) of melatonin increased plasma melatonin levels to about 1300 pg/mL within one hour and remained at pharmacological levels for approximately 6 hours. The trough of rectal temperature and the circadian rise of plasma cortisol were fixed to the early morning. A higher dose of melatonin (6 mg) did not improve the general feature. After the cessation of melatonin intake, the sleep-wake rhythm began to free-run together with the circadian rhythms in rectal temperature and plasma cortisol. It is concluded that daily intake of melatonin at early night time resets the circadian rhythms in a sighted man who lacked the nocturnal melatonin rise and showed free-running circadian rhythms in routine life.
Ion/Ion Proton-Transfer Kinetics:  Implications for Analysis of Ions Derived from Electrospray of Protein Mixtures (1998)

Protein ions of different mass and charge but similar mass-to-charge ratios are shown to undergo significantly different rates of differential neutralization, defined as the rate of change of charge with time, upon initiation of reactions with oppositely charged ions in the quadrupole ion trap. Overlapping charge state distributions arising from mixtures of ions of dissimilar charge are separated on the mass-to-charge scale at short reactions times. It is also demonstrated that the time frame for near total neutralization, defined as charge reduction to the 1+ ion, is relatively insensitive to initial charge state. It is shown, for example, that the (M + 11H)(11+)-(M + 22H)22+ ions derived from horse skeletal muscle apomyoglobin yield the (M + H)+ ion as the major ion/ion reaction product over the same reaction period that largely converts doubly protonated bradykinin to the singly protonated species. Less than 25% of the bradykinin ions are expected to be totally neutralized when roughly 7% of the myoglobin ions are expected to be totally neutralized. The phenomenon of significantly different initial differential neutralization rates for ions of dissimilar charge, and the relative insensitivity to ion charge for total neutralization, can be used to advantage in strategies for protein ion mixture analysis.
Treatment of Tardive Dyskinesia (1997)

Although the new generation of atypical antipsychotic agents could some day eliminate concerns about tardive dyskinesia (TD), this disorder remains a significant clinical problem for both patients and physicians. Fortunately, many, if not most, cases of TD are mild. For patients with mild to moderate TD, therapeutic efforts are primarily directed at minimizing neuroleptic exposure or, when possible, changing to atypical agents. Most cases of TD do not seem to progress, suggesting that the risk of remaining on typical neuroleptics is probably small. Patients with moderate to severe forms of TD present greater challenges. These patients frequently require medication to suppress their dyskinesias. A variety of suppressive agents have been tried with limited success. No treatment strategy has emerged that is clearly superior or even successful in most patients. Increasing doses of typical neuroleptics may be useful for short-term suppression; however, the long-term efficacy and risk of this strategy have not been studied carefully. Data on atypical neuroleptics are scant. Clozapine's short-term suppressive effects seem, at best, weak, but patients may improve with long-term treatment. Medications with relatively few side effects that may have suppressive efficacy for some patients include calcium channel blockers, adrenergic antagonists, and vitamin E. Gamma-amino-butyric acid agonists agents and dopamine depleters are frequently useful, but have troubling side effects of their own. A variety of other medications have been employed, but are not well studied. For patients with tardive dystonia, anticholinergic agents or botulinum toxin has been particularly effective. Efforts to understand the neurobiology of TD may shed light on this persistent clinical conundrum.
Micellar enzymology (1986)

Experimental approaches to modelling the enzymatic function of biological membranes are discussed. Emphasis is given to pseudohomogeneous systems such as proteolipid complexes and enzymes in organic solvents; the latter are solubilized with phospholipids or synthetic surfactants. Methods for producing and studying such micellar systems are considered. The key research problems of micellar enzymology are formulated and its relation to enzyme membranology is discussed. Finally, the new potentialities are noted of applied enzymology (biotechnology) offered by application of a colloidal solution of water in organic solvents as a microheterogeneous medium for enzymatic reactions.
Non-albicansoralcandidosis in HIV-positive patients (1999)

Specimens from HIV-positive patients with oral candidosis were taken for culture, species identification and azole susceptibility testing, which was correlated with treatment outcome. Of 921 specimens, 95 yielded non-albicans species, mainly from patients with low CD4 lymphocyte counts and extensive previous azole exposure. Most non-albicans isolates were from specimens co-infected with Candida albicans, complicating the interpretation of in-vitro susceptibility results, which accurately predicted antifungal failure when the non-albicans species was isolated alone. Eighty-five non-albicans isolates were resistant to fluconazole in vitro. Of 149 courses of azole therapy prescribed, 115 failed to clear non-albicans candidosis clinically. Culture media that discoloured in the presence of non-albicans colonies might, therefore, guide therapy.
Monitoring heart rate variability to assess experimentally induced pain using the analgesia nociception index (2015)

ANI did not allow a differentiation of painful, nonpainful or sham stimuli in alert volunteers. Therefore, ANI does not exclusively detect nociception, but may be modified by stress and emotion. Thus, we conclude that ANI is not a specific, robust measure for assessment of pain intensity.
Approaching cancer pain relief (2001)

Pain is defined as an unpleasant experience-it is subjective and achieving pain relief is achieving a change in the patient's experience. There needs to be an adequate concept of a human person (an ecological model will be discussed) and a logical process for approaching pain relief in an individual patient (e.g. the plan used in the Sydney Institute of Palliative Medicine). Communication with the patient is critical to get a grasp of him or her as a person, their environment, personal experience and cultural background. Then encourage him or her to tell the story of the cancer saga as they perceive it, listening carefully for the matters which may have given rise to acute distress (for example, delay in diagnosis) and how they adjusted to this. The individual is conveying a great deal about him or herself as they tell their story. Next the story of the treatment and their experience of it, and then the response of their tumour to it--then the story of their pain: when it began, its characteristics, how it evolved, what factors worsen the pain, what relieves it, etc. This is followed by careful clinical examination to clarify what could be the most likely mechanism(s) responsible for the noxious stimulus. Some investigation (e.g. X-ray) may be justified to assist clarification--but not before making a clinical diagnosis (best guess) and commencing treatment with drugs or other logical measures with some local action--depending on the most probable mechanism. Paracetamol/non-steroidal anti-inflammatory drugs (NSAIDs) etc may be logical. Threshold factors should be attended to--comfort, concern always, or anxiolytic or antidepressant drugs if the patient is pathologically anxious or depressed. The opioid drugs--with morphine still as the gold standard--should be appropriately used. This involves careful calibration of dose (below sedative level) normally with an immediate-release, preparation--and, in the case of morphine, specific counselling concerning 'myths' to ventilate fears of dying, fears of addiction, fear of tolerance, etc. It is irresponsible to use an opioid without assessing the prior state of the bowel (? loaded) or without prescribing a laxative. When neuropathic pain does not respond to a correctly calibrated opioid, it may be necessary to add certain antidepressants, anticonvulsants, gabapentin, steroid, etc. A system must be set in place for evaluation of pain relief: relief is usually possible.
fAST refresh using mass query optimization (2002)

Automatic summary tables (ASTs), more commonly known as materialized views, are widely used to enhance query performance, particularly for aggregate queries. Such queries access a huge number of rows to retrieve aggregated summary data while performing multiple joins in the context of a typical data warehouse star schema. To keep ASTs consistent with their underlying base data, the ASTs are either immediately synchronized or fully recomputed. This paper proposes an optimization strategy for simultaneously refreshing multiple ASTs, thus avoiding multiple scans of a large fact table (one pass for AST computation). A query stacking strategy detects common sub-expressions using the available query matching technology of DB2. Since exact common sub-expressions are rare, the novel query sharing approach systematically generates common subexpressions for a given set of "related" queries, considering different predicates, grouping expressions, and sets of base tables. The theoretical framework, a prototype implementation of both strategies in the IBM DB2 UDB/UWO database system, and performance evaluations based on the TPC/R data schema are presented in this paper.
4-Gbps Uncompressed Video Transmission over a 60-GHz Orbital Angular Momentum Wireless Channel (2013)

We demonstrate successful transmission of 4-Gbps uncompressed video over a 60-GHz orbital angular momentum (OAM) wireless channel. Matlab simulation was employed to support the experimental work and to generate the holographic masks used. Matlab coding is a unique approach which can produce any desired shape on copper or dielectric plates by mean of a commercial routing tool. We believe this is the first reported transmission of 4-Gbps uncompressed video over the 60-GHz OAM wireless channel. Good agreement was achieved between the simulated and measured results. Practical opportunities for multi-gigabit future wireless communications are available.
Comparison of the Electrochemical Behavior of the High Molecular Mass Cadmium Proteins in Arabidopsis thaliana and in Vegetable Plants on Using Preparative Native Continuous Polyacrylamide Gel Electrophoresis (PNC‐PAGE) (2005)

Abstract In Arabidopsis cytosol (supernatant) and in supernatants of vegetable plants high molecular mass cadmium proteins with molecular mass 200 kDa were isolated by using p reparative n ative c ontinuous p oly a crylamide g el e lectrophoresis (PNC‐PAGE). Because of a different electrochemical behavior of the Cd proteins in Arabidopsis and endive supernatants on using the same PAGE method, it is concluded that the high molecular mass cadmium proteins of Arabidopsis and endive possess different isoelectric points. Consequently, different chemical structures of the Cd proteins with molecular mass 200 kDa are present in Arabidopsis thaliana and in endive. During the electrophoretic separation of vegetable metalloproteins by using the Model 491 Prep Cell from BioRad , electroanalytical processes like electrode reactions may play an important role.
Piezoelectric self-sensing system for tactile intraoperative brain tumor delineation in neurosurgery (2009)

Mechanical characteristics of tumor and healthy tissue in the brain differ but slightly. The task of designing a system that is able to differentiate tissue dignity with high sensitivity is of great importance in neurosurgery. Even when localization of tumor by use of preoperative imaging techniques provides the surgeon with valuable information to decide where and what to resect, the brain shift due to change in pressure during skull opening demands the surgeon to define the limits of the tumor using tactile and visual differentiation. This paper contains a general description of the tactile sensor system based on a piezoelectric bimorph. The main parts of the measurement system are described and the selection of the electrical parameters for tactile differentiation is justified. Results are discussed for a series of measurements at different concentrations in gelatin phantoms.
LDP Specification (2001)

The architecture for Multi Protocol Label Switching (MPLS) is described in RFC 3031. A fundamental concept in MPLS is that two Label Switching Routers (LSRs) must agree on the meaning of the labels used to forward traffic between and through them. This common understanding is achieved by using a set of procedures, called a label distribution protocol, by which one LSR informs another of label bindings it has made. This document defines a set of such procedures called LDP (for Label Distribution Protocol) by which LSRs distribute labels to support MPLS forwarding along normally routed paths.
Targeted Therapies in Combination with Chemotherapy in Non–Small Cell Lung Cancer (2006)

With rare exceptions, attempts to combine so-called targeted agents with standard cytotoxic chemotherapy in advanced non-small cell lung cancer have yielded disappointing results. The reasons underlying these spectacular failures are not always fully understood, but certainly the lack of careful patient selection is a major contributing factor. In addition, recent preclinical and clinical studies indicate that antagonism may exist between the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors and chemotherapy primarily in tumor cells with wild-type EGFR. By contrast, tumor cells harboring somatic mutations in EGFR experience massive apoptosis when exposed to the EGFR tyrosine kinase inhibitors. Therefore, in theory, mutant tumor cells should exhibit enhanced cell kill when treated with concomitant chemotherapy and EGFR tyrosine kinase inhibitors akin to what is observed with chemotherapy and trastuzumab in breast cancer. Clinical data from the recently completed TRIBUTE trial support the latter possibility. Ideally, future studies of EGFR tyrosine kinase inhibitors and other targeted drugs will use careful patient selection criteria based on well-characterized and validated predictive markers. However, in the absence of such biomarkers, clinical judgment, common sense, and innovative clinical trial design are necessary to avoid undue delay in drug development.
Reactive Oxygen Species–Activated Ca/Calmodulin Kinase IIδ Is Required for Late I Na Augmentation Leading to Cellular Na and Ca Overload (2011)

Free [Ca](i) and a functional SR are required for ROS activation of CaMKII. ROS-activated CaMKIIδ enhances late I(Na), which may lead to cellular Na and Ca overload. This may be of relevance in hear failure, where enhanced ROS production meets increased CaMKII expression.
Redox Regulation of Fos and Jun DNA-Binding Activity in Vitro (1990)

The proto-oncogenes c-fos and c-jun function cooperatively as inducible transcription factors in signal transduction processes. Their protein products, Fos and Jun, form a heterodimeric complex that interacts with the DNA regulatory element known as the activator protein-1 (AP-1) binding site. Dimerization occurs via interaction between leucine zipper domains and serves to bring into proper juxtaposition a region in each protein that is rich in basic amino acids and that forms a DNA-binding domain. DNA binding of the Fos-Jun heterodimer was modulated by reduction-oxidation (redox) of a single conserved cysteine residue in the DNA-binding domains of the two proteins. Furthermore, a nuclear protein was identified that reduced Fos and Jun and stimulated DNA-binding activity in vitro. These results suggest that transcriptional activity mediated by AP-1 binding factors may be regulated by a redox mechanism.
Nonequilibrium fluctuation-induced transport (1994)

Ratchetlike devices can rectify symmetric, unbiased nonequilibrium noise resulting in fluctuation-induced currents. We study some simple models to investigate the dependence of a nonequilibrium steady-state current on the characteristic features of the ratchet and the applied noise. It turns out that the magnitude and the direction of the induced current depend not only on the shape of the ratchet, but also on the statistics of the fluctuations.
Collagen-binding proteoglycan fibromodulin can determine stroma matrix structure and fluid balance in experimental carcinoma (2007)

Research on the biology of the tumor stroma has the potential to lead to development of more effective treatment regimes enhancing the efficacy of drug-based treatment of solid malignancies. Tumor stroma is characterized by distorted blood vessels and activated connective tissue cells producing a collagen-rich matrix, which is accompanied by elevated interstitial fluid pressure (IFP), indicating a transport barrier between tumor tissue and blood. Here, we show that the collagen-binding proteoglycan fibromodulin controls stroma structure and fluid balance in experimental carcinoma. Gene ablation or inhibition of expression by anti-inflammatory agents showed that fibromodulin promoted the formation of a dense stroma and an elevated IFP. Fibromodulin-deficiency did not affect vasculature but increased the extracellular fluid volume and lowered IFP. Our data suggest that fibromodulin controls stroma matrix structure that in turn modulates fluid convection inside and out of the stroma. This finding is particularly important in relation to the demonstration that targeted modulations of the fluid balance in carcinoma can increase the response to cancer therapeutic agents.
Efficient anomaly detection in dynamic, attributed graphs: Emerging phenomena and big data (2013)

When working with large-scale network data, the interconnected entities often have additional descriptive information. This additional metadata may provide insight that can be exploited for detection of anomalous events. In this paper, we use a generalized linear model for random attributed graphs to model connection probabilities using vertex metadata. For a class of such models, we show that an approximation to the exact model yields an exploitable structure in the edge probabilities, allowing for efficient scaling of a spectral framework for anomaly detection through analysis of graph residuals, and a fast and simple procedure for estimating the model parameters. In simulation, we demonstrate that taking into account both attributes and dynamics in this analysis has a much more significant impact on the detection of an emerging anomaly than accounting for either dynamics or attributes alone. We also present an analysis of a large, dynamic citation graph, demonstrating that taking additional document metadata into account emphasizes parts of the graph that would not be considered significant otherwise.
Optically-processed routing for fast packet switching (1990)

Electronic routing control of photonic switches is considered. The types of network architectures and routing strategies that the authors think are best-suited to optical processing are proposed, and a generic optical routing processor is described. Address-encoding schemes for optically controlling a photonic switching node are presented. The results of several experiments that have demonstrated optical control of a photonic switching node are reported. Potential applications of these photonic switching architectures are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>