gebhart/patrepeval huggingface dataset:
Rosuvastatin Alone or With Extended‐Release Niacin: A New Therapeutic Option for Patients With Combined Hyperlipidemia (2004)

Combination therapy with a statin and niacin may provide optimal therapy for patients with combined hyperlipidemia and low levels of high-density lipoprotein (HDL) cholesterol. The authors assessed the efficacy and safety of rosuvastatin monotherapy, extended-release (ER) niacin monotherapy, or rosuvastatin and ER niacin combined therapy in patients with atherogenic dyslipidemia. In a 24-week, open-label, multicenter trial, men and women aged > or =18 years with fasting levels of total cholesterol > or =200 mg/dL, HDL cholesterol > or =45 mg/dL, triglycerides 200-800 mg/dL, and apolipoprotein B > or =110 mg/dL were randomly assigned to one of four treatment groups: rosuvastatin 10-40 mg, ER niacin 0.5-2 g, rosuvastatin 40 mg plus ER niacin 0.5-1 g, or rosuvastatin 10 mg plus ER niacin 0.5-2 g. Daily doses of rosuvastatin 40 mg monotherapy reduced low-density lipoprotein (LDL) cholesterol and non-HDL cholesterol levels significantly more than did either ER niacin 2 g monotherapy or rosuvastatin 10 mg combined with ER niacin 2 g. Addition of ER niacin 1 g to rosuvastatin 40 mg did not further reduce total or non-HDL cholesterol. Triglyceride reductions were similar among the four treatment groups. ER niacin mono- and combined therapy produced significantly greater rises in HDL cholesterol and apolipoprotein A-1 than did rosuvastatin monotherapy. Rosuvastatin monotherapy was better tolerated than ER niacin taken either alone or with rosuvastatin. In this study, rosuvastatin very effectively improved the three major lipoprotein-lipid abnormalities of combined hyperlipidemia.
Rapid SAGD Simulation Considering Geomechanics for Closed Loop Reservoir Optimization (2012)

While numerical modeling and coupling techniques have been continuously studied, analytical solution or proxy modeling for geomechanical coupling of the steam assisted gravity drainage (SAGD) has not been clearly addressed in the literature. Simulations aside, there is no particular study on the use of geomechanics in closed loop reservoir optimization. This research has been carried out to cover two major objectives; providing a low order model to work with real-time data, and also investigating high-resolution geomechanical-flow simulation to work with data assimilation algorithms for history matching and reservoir characterization. As the first step, a physics-based semi-analytical model was proposed based on the original Butler/Reis SAGD theory. The model was proposed for linear steam chamber geometry by modifying the variation of oil saturation in advance of the steam chamber. The model was then verified with the past experimental lab test results and numerical simulation results. Geomechanics was incorporated using the classical limit equilibrium theory. The linear geometry model was then replaced by circular geometry model to better simulate the rising and depletion stages of SAGD process. For the circular geometry model, a multiplier coefficient was defined to consider geomechanics called the geomechanical impact factor (GIF). The final version of the proposed model was used for history matching two SAGD projects, UTF phases A and B. The application of analytical models in automated history matching and reservoir characterization was further investigated using the extended Kalman filter (EKF). For this case, Butler/Reis theory and the GIF concept were combined with the EKF for history matching the heterogeneous reservoirs with uncertainty. Using synthetic data and stochastic reservoir realizations, it was shown how analytical models are helpful in reservoir characterization. While the analytical solution is placed at the centre of the optimization process, the second objective of this research was explored by applying the ensemble Kalman filter (EnKF) to link monitoring data to the simulator(s). For this reason, an iterative geomechanical-flow coupling code was developed and assembled with the EnKF. Through numerical simulations using synthetically generated data, the significance of considering geomechanical monitoring data in reservoir surveillance was examined.
Multiple-point simulation integrating wells, three-dimensional seismic data, and geology (2004)

There are two significant challenges in building a reservoir model integrating all available information. One challenge is that wells and seismic data measure the reservoir at different scales of resolution. The other challenge lies in how to account for conceptual geological knowledge with resolution at multiple scales.In this paper, we present a case study of integrating well data, seismic data, and conceptual geologic models. The well and seismic data are of good quality, but conventional well-seismic data calibration indicates that the seismic data are unable to fully differentiate sand from shale. The reason for this poor well-seismic data calibration is that well log and seismic data measure the reservoir at different scales. Well logs are able to differentiate sand from shale, whereas seismic data are better at detecting larger scale depositional geometries.A new workflow is presented to deal with this problem. First, principal component analysis clustering is used to identify characteristic patterns of certain depositional facies, from which sandy and shaly channels are interpreted. Next, multiple-point geostatistical simulation is performed to build a depositional-facies model, which integrates both hard and soft data but also incorporates realistic depositional-facies geometries provided by our geological knowledge of this reservoir. Finally, different lithofacies (sand and shale) indicators and corresponding petrophysical properties are simulated honoring the limited well data.The results show that not only are the geological features better reproduced, but also is the uncertainty about the reservoir significantly reduced because of a better integration of corresponding three-dimensional seismic data.
Polyamine analogue induction of programmed cell death in human lung tumor cells. (1996)

The naturally occurring polyamines putrescine, spermidine, and spermine are required for cell growth. Based on this requirement, several polyamine analogues that interfere with polyamine function and metabolism have been synthesized as antineoplastic agents. The symmetrically substituted N1,N12-bis(ethyl)spermine (BESpm), and unsymmetrically substituted N1-ethyl-N11-[(cyclopropyl)methyl]-4, 8-diazaundecane (CPENSpm) have previously been shown to cause rapid cytotoxicity of NCI H157 cells, with concurrent high induction of the polyamine catabolic enzyme spermidine/spermine N1-acetyltransferase. However, the precise mechanism(s) of the cytotoxic action of the compounds is not known. We now demonstrate that treatment with either BESpm or CPENSpm results in morphological and biochemical changes consistent with the activation of programmed cell death pathways, and that the unsymmetrically substituted CPENSpm more rapidly activates the death program. These studies suggest that the cell type-specific cytotoxicity of these polyamine analogues may be a result of their ability to selectively activate the cell death pathway in sensitive phenotypes and indicate that the relationship between the structure of the polyamine analogues and the ability to induce programmed cell death should be investigated.
Isotope dilution-gas chromatography/mass spectrometry and liquid chromatography/electrospray ionization-tandem mass spectrometry for the determination of triiodo-L-thyronine in serum (1999)

Isotope dilution-gas chromatography/mass spectrometry (ID-GC/MS) and isotope dilution-liquid chromatography/tandem mass spectrometry (ID-LC/MS/MS) methods have been developed for an determination of triiodothyronine (T3) in serum and their potential as candidate reference methods investigated. In both methods, (13)C(9)-T3 was used as internal standard. Sample pretreatment consisted of deproteinization, extraction and high performance liquid chromatography (HPLC) purification. Conversion of serum thyroxine (T4) to T3 was controlled by adding (13)C(6)-T4. For GC/MS, T3 and (13)C(9)-T3 were converted to the N,O-di-heptafluorobutyryl (HFB) methyl ester derivatives and monitored at m/z 844 and 853. For LC/MS with electrospray ionization, the transitions m/z 652/661 to 606/614 were monitored. For use of the methods as candidate reference methods, special attention was paid to the calibration and the measurement protocol (duplicate analysis of each sample on three occasions). Evaluation of the ID-GC/MS and ID-LC/MS/MS methods showed the absence of interference by reverse T3 and T4, a limit of detection of 100 pg (GC/MS) and 18 pg (LC/MS), a recovery of 100 +/- 1.5% (95% confidence interval) and good precision (the total coefficient of variation, n = 6, was typically 1.5%). In addition to the recovery study, the accuracy of the methods was proven by method comparison (ID-GC/MS vs. LC/MS/MS) on three sera, showing a maximum deviation of 1.1%. Finally, the ID-GC/MS method was applied for measurement of 10 different human sera with a T3 concentration range from 0.6 to 7.3 ng/mL.
Molecular analysis of deletions in human chromosome 3p21 and the role of resident cancer genes in disease (2007)

Epithelial cancers inflict a heavy human and social burden. It was estimated [Tyczynski JE, Bray F, Parkin DM. Lung cancer in Europe in 2000: epidemiology, prevention, and early detection. Lancet Oncol 2003;4:45-55 (Review)] that in Europe, in the year 2000, 347 000 persons died of lung cancer alone, the deadliest cancer disease. Loss of heterozygosity and large homozygous deletions of the human chromosome region 3p21 are especially frequent in epithelial cancers of several organs. In fact, 3p21 is a very peculiar region of the genome harbouring, tightly clustered, several types of cancer-causing genes (CCG) (Lerman MI, Minna JD. The 630 kb lung cancer homozygous deletion region on human chromosome 3p21.3: identification and evaluation of the resident candidate tumour suppressor genes. The International Lung Cancer Chromosome 3p21.3 Tumor Suppressor Gene Consortium. Cancer Res 2000;60:6116-33). Current results show that, unlike it was thought initially, many tumour suppressor genes (TSG) are located close by even in small genomic regions. They may be involved, perhaps with varying role, in different types of tumour, and may be influenced by the genetic background of different human populations as well as by environmental pollutants (cigarette smoking, professional exposure). This review will discuss methods of molecular analysis of genomic deletions to uncover CCG at 3p21, will summarize the present knowledge regarding the TSGs located in this region, and will describe a possible model of epithelial cancer pathogenesis.
Etiology and treatment of chemotherapeutic agent extravasation injuries: a review. (1987)

While extravasation from intravenous (IV) lines is common and usually benign, leakage of certain drugs can cause severe skin ulceration. These ulcerogenic drugs can be conveniently divided into two categories, depending on whether they bind to DNA. Chemotherapeutic agents such as doxorubicin, which bind to DNA, are especially prone to cause severe extravasation skin ulcers. These ulcers are often chronic and progressive. Neither clinical nor experimental studies have shown an antidote to doxorubicin extravasation, which is best prevented by careful technique. If extravasation is suspected, the infusion should be immediately stopped. In the event of extravasation, elevation and ice are the currently recommended treatment. While small ulcerations may on occasion heal, large ulcerations require surgical excision for relief of pain and salvage of underlying tissues.
Chemotactic requirements of bovine leukocytes (1982)

A system was described for studying bovine leukotaxis. Chemotaxis was readily observed toward bovine serum activated by zymosan of agarose. However, bacterial culture filtrates and peptides, which were potent chemotaxins for leukocytes from other species, failed to affect bovine leukotaxis. Using conditions suitable for studying binding to leukocytes from other species, specific binding of a radiolabeled chemotactic peptide to bovine leukocytes was not apparent. These data indicate that bovine leukocytes have chemotactic requirements distinct from those of other species.
Backwards-Compatible Bounds Checking for Arrays and Pointers in C Programs (1997)

This paper presents a new approach to enforcing array bounds and pointer checking in the C language. Checking is rigorous in the sense that the result of pointer arithmetic must refer to the same object as the original pointer (this object is sometimes called the &amp;apos;intended referent&amp;apos;). The novel aspect of this work is that checked code can inter-operate without restriction with unchecked code, without interface problems, with some effective checking, and without false alarms. This &amp;quot;backwards compatibility&amp;quot; property allows the overheads of checking to be confined to suspect modules, and also facilitates the use of libraries for which source code is not available. The paper describes the scheme, its prototype implementation (as an extension to the GNU C compiler), presents experimental results to evaluate its effectiveness, and discusses performance issues and the effectiveness of some simple optimisations. 1 Introduction and related work C is unusual among programming languages in pro...
Characterization of an ATP-dependent DNA ligase encoded by Haemophilus influenzae (1997)

We report that Haemophilus influenzae encodes a 268 amino acid ATP-dependent DNA ligase. The specificity of Haemophilus DNA ligase was investigated using recombinant protein produced in Escherichia coli. The enzyme catalyzed efficient strand joining on a singly nicked DNA in the presence of magnesium and ATP (Km = 0.2 microM). Other nucleoside triphosphates or deoxynucleoside triphosphates could not substitute for ATP. Haemophilus ligase reacted with ATP in the absence of DNA substrate to form a covalent ligase-adenylate intermediate. This nucleotidyl transferase reaction required a divalent cation and was specific for ATP. The Haemophilus enzyme is the first example of an ATP-dependent DNA ligase encoded by a eubacterial genome. It is also the smallest member of the covalent nucleotidyl transferase superfamily, which includes the bacteriophage and eukaryotic ATP-dependent polynucleotide ligases and the GTP-dependent RNA capping enzymes.
Cyclophosphamide cystitis in mice: Behavioural characterisation and correlation with bladder inflammation (1999)

The generation of transgenic 'knock-out' mice which lack genes relevant to pain is becoming increasing common. However, only one visceral pain model, the writhing test, is available in mice. The aim of this study was to adapt cyclophosphamide cystitis, a model of inflammatory visceral pain described in rats, for use in mice, and to characterise its behavioural effects. The toxic metabolites of systemically-administered cyclophosphamide are excreted in the urine, and induce bladder inflammation. We compared the effects of cyclophosphamide (100 and 300 mg/kg i.p., 4 h survival period) and vehicle (saline) in male mice on spontaneous behaviour (4 h continuous video-tape, and a 5-min Open Field test after 4 h). Involvement of the urinary bladder and other abdominal tissues was assessed by macroscopic examination and measurement of Evan's Blue plasma extravasation. Cyclophosphamide (300 mg/kg) produced significant changes in behaviour, including 22 +/- 6 min of 'crises' of visceral pain-related behaviour and a 53% reduction in activity, and also induced haemorrhage and substantial plasma extravasation in the bladder, but no change in other abdominal tissues. We conclude that cyclophosphamide cystitis has many advantages as a model of sub-acute, inflammatory visceral pain in mice. It does not require surgery or intubation, and we have found it to produce consistent, reproducible and quantifiable behavioural changes, which are significantly correlated with the degree of bladder inflammation in the absence of inflammation of other abdominal tissues. Copyright 1999 European Federation of Chapters of the International Association for the Study of Pain.
New generation of electro-anatomic mapping: full intracardiac ultrasound image integration (2008)

Surrogate electro-anatomic-derived geometries are used as the three-dimensional (3D) basis for mapping of cardiac arrhythmias. While merged computed tomography (CT) imaging may provide stellar pulmonary vein (PV) and left atrial (LA) anatomy, the applied scans must be obtained prior to ablation, and may not reflect physiologic conditions at the time of intervention. Patient-specific, ultrasound-derived 3D imaging has been developed as an alternative basis for new generation electro-anatomic mapping. An electro-anatomic sensor positioned at the tip of the phased-array intracardiac ultrasound catheter, provides the means to specify both location and orientation of each image as the 'context' for creating the 3D volumes for co-registration with electro-anatomic mapping. Specific anatomic details such as the pulmonary veins, membranous fossa, papillary muscles, or valve structures derived from real-time imaging can also be integrated into each segmented volume. This presentation reviews the basis and methods for this novel multi-modality image fusion for the creation of robust, nearly real-time anatomic images for guiding electro-anatomic mapping and ablation without requiring pre-acquired CT image sets, with accompanying limitations.
Rifampicin-impregnated central venous catheters: a meta-analysis of randomized controlled trials (2007)

The available evidence suggests that rifampicin/minocycline-impregnated CVCs are safe and effective in reducing the rate of catheter colonization and CRBSI. Further research should focus on the possible development of resistance and on pharmacoeconomic issues related to the use of rifampicin/minocycline-impregnated CVCs.
Understanding deep image representations by inverting them (2015)

Image representations, from SIFT and Bag of Visual Words to Convolutional Neural Networks (CNNs), are a crucial component of almost any image understanding system. Nevertheless, our understanding of them remains limited. In this paper we conduct a direct analysis of the visual information contained in representations by asking the following question: given an encoding of an image, to which extent is it possible to reconstruct the image itself? To answer this question we contribute a general framework to invert representations. We show that this method can invert representations such as HOG more accurately than recent alternatives while being applicable to CNNs too. We then use this technique to study the inverse of recent state-of-the-art CNN image representations for the first time. Among our findings, we show that several layers in CNNs retain photographically accurate information about the image, with different degrees of geometric and photometric invariance.
Stromal Gene Signatures in Large-B-Cell Lymphomas (2008)

Survival after treatment of diffuse large-B-cell lymphoma is influenced by differences in immune cells, fibrosis, and angiogenesis in the tumor microenvironment.
Expression of CD45 alters phosphorylation of the lck-encoded tyrosine protein kinase in murine lymphoma T-cell lines. (1989)

CD45 is a family of high molecular weight leukocyte cell surface glycoproteins. Recently, two related subregions of the cytoplasmic domain of CD45 have been shown to have 30-40% amino acid identity with a human placental protein phosphotyrosine phosphatase, and CD45 isolated from human spleen was found to exhibit intrinsic protein phosphotyrosine phosphatase (EC 3.1.3.48) activity. In the present studies, we demonstrate that each of the known isoforms of murine CD45 has an equivalent basal level of protein phosphotyrosine phosphatase activity and establish that this enzymatic activity is associated with the cytoplasmic domain of the glycoprotein. Studies with three independent sets of well-characterized parental CD45+, mutant CD45-, and revertant CD45+ lymphoma cell lines indicate that loss of CD45 increases the phosphorylation of the src-related leukocyte-specific tyrosine protein kinase p56lck on tyrosine-505, a putative negative regulatory site. This suggests that CD45 may play a role in leukocyte growth regulation by altering the kinase activity of p56lck.
Oncologic, Endocrine & Metabolic Overview: Recent advances in implants for bone growth promotion (1994)

Devices intended for delivery of bone growth promoters should possess several properties. The device should have enough strength to hold the bone in place during the course of fixation, yet it should be biodegradable so that ultimately replacement by new bone will occur. This requires that the device has a certain level of porosity to allow for the ingrowth of new bone during the healing process. Many materials can be utilised for implants including naturally occurring materials (e.g., bone, fibrin, collagen) and synthetic materials (polymers, ceramics, metals). The appropriate material should be biocom-patible and not inhibit bone growth. Many approaches combining various active agents (e.g., bone morphogenic proteins, transforming growth factor, prostaglandins) with one of several synthetic or naturally occurring matrices have been examined. Several systems show promising initial results; however, the actual bone growth promoter release profiles required for efficacious treatment have not yet been established. In addition, the commercial viability of this type of device is highly dependent on the ability of the manufacturer to prepare the implants economically and reproducibly.
Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements (2004)

Extensive conformational sampling and calculations of vibrational coupling provide a quantitative basis for the structurally inhomogeneous spectra of the amide unit in aqueous solutions containing folded and unfolded state distributions of helices. Replica exchange molecular dynamics simulations of the capped helical peptide, AA(AAKAA)(3)AAY, is carried out over a range of temperatures, where the system populates the folded and unfolded states. This sampling defines a set of ensembles that characterizes the conformational variability for configurations identified by their fraction of helical content. The effects of hydrogen bonding, both internal and external (with water), and the coupling between amide-I modes are computed as a function of temperature and helical content. End-to-end distance and coupling distributions are also computed. The solvent H-bonding, which is present at all temperatures, shifts the amide-I band toward lower frequency compared with the unsolvated band. Upon thermal denaturation of the peptide, the amide-I band shifts to higher frequency because the increase in solvent H-bonding fails to compensate for the loss in internal (helical) H-bonds. The loss of uniformity of the mode coupling along the helix at higher temperatures accounts for the well-known thermal broadening of the amide IR spectrum. The calculated inhomogeneities of segments of the peptide predict experimental properties of isotope-edited helices.