gebhart/patrepeval huggingface dataset:
Molecular Validation of LpxC as an Antibacterial Drug Target in <i>Pseudomonas aeruginosa</i> (2006)

LpxC [UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc deacetylase] is a metalloamidase that catalyzes the first committed step in the biosynthesis of the lipid A component of lipopolysaccharide. A previous study (H. R. Onishi, B. A. Pelak, L. S. Gerckens, L. L. Silver, F. M. Kahan, M. H. Chen, A. A. Patchett, S. M. Galloway, S. A. Hyland, M. S. Anderson, and C. R. H. Raetz, Science 274:980-982, 1996) identified a series of synthetic LpxC-inhibitory molecules that were bactericidal for Escherichia coli. These molecules did not inhibit the growth of Pseudomonas aeruginosa and were therefore not developed further as antibacterial drugs. The inactivity of the LpxC inhibitors for P. aeruginosa raised the possibility that LpxC activity might not be essential for all gram-negative bacteria. By placing the lpxC gene of P. aeruginosa under tight control of an arabinose-inducible promoter, we demonstrated the essentiality of LpxC activity for P. aeruginosa. It was found that compound L-161,240, the most potent inhibitor from the previous study, was active against a P. aeruginosa construct in which the endogenous lpxC gene was inactivated and in which LpxC activity was supplied by the lpxC gene from E. coli. Conversely, an E. coli construct in which growth was dependent on the P. aeruginosa lpxC gene was resistant to the compound. The differential activities of L-161,240 against the two bacterial species are thus the result primarily of greater potency toward the E. coli enzyme rather than of differences in the intrinsic resistance of the bacteria toward antibacterial compounds due to permeability or efflux. These data validate P. aeruginosa LpxC as a target for novel antibiotic drugs and should help direct the design of inhibitors against clinically important gram-negative bacteria.
Effects of Bovine Immunoglobulins on Immune Function, Allergy, and Infection (2018)

This review aims to provide an in depth overview of the current knowledge of the effects of bovine immunoglobulins on the human immune system. The stability and functional effects of orally ingested bovine immunoglobulins in milk products are described and potential mechanisms of action are discussed. Orally ingested bovine IgG (bovine IgG) can be recovered from feces, ranging from very low levels up to 50% of the ingested IgG that has passed through the gastrointestinal tract. In infants the recovered levels are higher than in adults most likely due to differences in stomach and intestinal conditions such as pH. This indicates that bovine IgG can be functionally active throughout the gastrointestinal tract. Indeed, a large number of studies in infants and adults have shown that bovine IgG (or colostrum as a rich source thereof) can prevent gastrointestinal tract infections, upper respiratory tract infections, and LPS-induced inflammation. These studies vary considerably in target group, design, source of bovine IgG, dosage, and endpoints measured making it hard to draw general conclusions on effectiveness of bovine immunoglobulin rich preparations. Typical sources of bovine IgG used in human studies are serum-derived IgG, colostrum, colostrum-derived IgG, or milk-derived immunoglobulins. In addition, many studies have used IgG from vaccinated cows, but studies using IgG from nonimmunized animals have also been reported to be effective. Mechanistically, bovine IgG binds to many human pathogens and allergens, can neutralize experimental infection of human cells, and limits gastrointestinal inflammation. Furthermore, bovine IgG binds to human Fc receptors which, enhances phagocytosis, killing of bacteria and antigen presentation and bovine IgG supports gastrointestinal barrier function in <i>in vitro</i> models. These mechanisms are becoming more and more established and explain why bovine IgG can have immunological effects <i>in vivo</i>. The inclusion of oral bovine immunoglobulins in specialized dairy products and infant nutrition may therefore be a promising approach to support immune function in vulnerable groups such as infants, children, elderly and immunocompromised patients.
A kernel-based integration of genome-wide data for clinical decision support (2009)

For both cancer sites the prediction of all outcomes improved when more than one genome-wide data set was considered. This suggests that integrating multiple genome-wide data sources increases the predictive performance of clinical decision support models. This emphasizes the need for comprehensive multi-modal data. We acknowledge that, in a first phase, this will substantially increase costs; however, this is a necessary investment to ultimately obtain cost-efficient models usable in patient tailored therapy.
Regression Testing of Database Applications (2002)

Database applications features such as Structured Query Language or SQL, exception programming, integrity constraints, and table triggers pose difficulties for maintenance activities; especially for regression testing that follows modifications to database applications. In this work, we address these difficulties and propose a two-phase regression testing methodology. In phase 1, we explore control flow and data flow analysis issues of database applications. Then, we propose an impact analysis technique that is based on dependencies that exist among the components of database applications. This analysis leads to selecting test cases from the initial test suite for regression testing the modified application. In phase 2, further reduction in the regression test cases is performed by using reduction algorithms. We present two such algorithms. The Graph Walk algorithm walks through the control flow graph of database modules and selects a safe set of test cases to retest. The Call Graph Firewall algorithm uses a firewall for the inter-procedural level. Finally, a maintenance environment for database applications is described. Our experience with this regression testing methodology shows that the impact analysis technique is adequate for selecting regression tests and that phase 2 techniques can be used for further reduction in the number of theses tests.
Novel markers for poor prognosis in head and neck cancer (2004)

Head and neck cancer (HNSCC) is one of the most distressing human cancers, causing pain and affecting the basic survival functions of breathing and swallowing. Mortality rates have not changed despite recent advances in radiotherapy and surgical treatment. We have compared the expression of over 13,000 unique genes in 7 cases of matched HNSCC and normal oral mucosa. Of the 1,260 genes that showed statistically significant differences in expression between normal and tumor tissue at the mRNA level, the three top ranking of the top 5% were selected for further analysis by immunohistochemistry on paraffin sections, along with the tumor suppressor genes p16 and p53, in a total of 62 patients including 55 for whom >4-year clinical data was available. Using univariate and multivariate survival analysis, we identified SPARC/osteonectin as a powerful independent prognostic marker for short disease-free interval (DFI) (p < 0.002) and poor overall survival (OS) (p = 0.018) of HNSCC patients. In combination with other ECM proteins found in our analysis, PAI-1 and uPA, the association with DFI and OS became even more significant (p < 0.001). Our study represents the first instance of SPARC as an independent prognostic marker in HNSCC.
A controlled clinical trial to assess the effect of a calcium channel blocker on the progression of coronary atherosclerosis. (1990)

To determine whether calcium channel blockers influence the progression of coronary atherosclerosis, 383 patients age 65 years or less with 5-75% stenoses in at least four coronary artery segments were selected at random within 1 month of coronary arteriography to participate in double-blind therapy with a placebo or nicardipine 30 mg three times daily. Coronary events (5 deaths, 22 myocardial infarctions, and 28 unstable anginas) occurred in 28 of 192 nicardipine patients and 23 of 191 placebo patients (p = NS). At 24 months coronary arteriography was repeated in 335 patients. Progression, defined as a 10% or more worsening in diameter stenosis, measured quantitatively, was found in 147 of 1,153 lesions (12.7%) in 168 nicardipine patients and in 170 of 1,170 lesions (14.5%) in 167 placebo patients (p = NS). Ninety-two nicardipine patients (55%) and 95 placebo patients (57%) had progression at one or more sites (p = NS). Regression, that is, an improvement by 10% or more in diameter stenosis, was seen in 140 of 2,323 lesions (6.0%) overall, with no significant intergroup difference. Among the 217 patients with 411 stenoses of 20% or less in the first study, such minimal lesions progressed in only 15 of 99 nicardipine patients compared with 32 of 118 placebo patients (15% versus 27%, p = 0.046). In this subgroup, 16 of 178 minimal lesions in nicardipine patients and 38 of 233 minimal lesions in placebo patients progressed (p = 0.038). By stepwise logistic-regression analysis, baseline systolic blood pressure (p = 0.04) and the change in systolic blood pressure between baseline and 6 months (p = 0.002) correlated with progression of minimal lesions. This suggested blood pressure reduction may account for the beneficial action of nicardipine. These results suggested nicardipine has no effect on advanced coronary atherosclerosis but may retard the progression of minimal lesions.
Histochemical Application Of A Peroxidase DNAzyme with a Covalently Attached Hemin Cofactor (2010)

The enzyme horseradish peroxidase is routinely used in immunohistochemistry to facilitate the chromogenic oxidation of 3,3'-diaminobenzidine, producing an insoluble brown precipitate marking the location and quantity of a tissue protein. In an effort to develop non-protein reagents for tissue diagnostics, we have developed a peroxidase DNAzyme construct that can be used as a chromogenic functional group in immunohistochemistry assays. The DNAzyme is based on a reported 18-mer G-quadruplex-forming DNA sequence, PS2.M, and has been covalently linked to its catalytically active moiety, hemin, to avoid the high background signal associated with the use of free hemin in histochemical studies. The activity of the covalent construct is maintained under conditions where G-quadruplex formation is unfavored and where the noncovalent DNAzyme-hemin complex has no activity.
Automatic registration of brain magnetic resonance images based on Talairach reference system (2004)

The suggested registration method can be applied to any MR images for functional studies. It can also be applied to patients unless their brains are highly deformed or have a highly deformed CC.
A Scalable Bootstrap for Massive Data (2014)

Summary The bootstrap provides a simple and powerful means of assessing the quality of estimators. However, in settings involving large data sets—which are increasingly prevalent—the calculation of bootstrap-based quantities can be prohibitively demanding computationally. Although variants such as subsampling and the m out of n bootstrap can be used in principle to reduce the cost of bootstrap computations, these methods are generally not robust to specification of tuning parameters (such as the number of subsampled data points), and they often require knowledge of the estimator's convergence rate, in contrast with the bootstrap. As an alternative, we introduce the ‘bag of little bootstraps’ (BLB), which is a new procedure which incorporates features of both the bootstrap and subsampling to yield a robust, computationally efficient means of assessing the quality of estimators. The BLB is well suited to modern parallel and distributed computing architectures and furthermore retains the generic applicability and statistical efficiency of the bootstrap. We demonstrate the BLB's favourable statistical performance via a theoretical analysis elucidating the procedure's properties, as well as a simulation study comparing the BLB with the bootstrap, the m out of n bootstrap and subsampling. In addition, we present results from a large-scale distributed implementation of the BLB demonstrating its computational superiority on massive data, a method for adaptively selecting the BLB's tuning parameters, an empirical study applying the BLB to several real data sets and an extension of the BLB to time series data.
Effects of simvastatin and atorvastatin on inflammation markers in plasma (2002)

Atorvastatin reduced the liver-derived acute-phase reactants, CRP and SAA, whilst the effect of simvastatin was small or absent. Small and inconsistent effects were seen for both statins on plasma levels of IL-6 and ICAM-1.
Navigating Users Based on Estimation of Interest Vectors with Utility Function (2008)

In large-scale trade shows, there are two kinds of connections dependent on interests of attendees: connections between attendees and booths, and that between booths and booths. The large-scale-ness, however, prevents the establishment of these connections because each attendee cannot obtain the entire information on all of his interesting booths. In this paper, we propose a personal navigation system to promote establishment of these connections by providing the information of unvisited booths which are interesting to each attendee. The proposed system numerically estimates each user's interest from the history of visited booths and recommends unvisited booths according to his estimated interest through a mobile device and RFID tags installed in booths. By recommending booths with a floor map, their locations, his current position, and quantitative bases of recommendation, each attendee can select and visit one of recommended booths according to these satisfaction levels and locations.
Interleukin-6 fused to an anti-idiotype antibody in a vaccine increases the specific humoral immune response against CA125+ (MUC-16) ovarian cancer. (2003)

Anti-idiotypic (Id) monoclonal antibodies can serve as surrogate for tumor-associated antigens in vaccination strategies. The murine anti-Id monoclonal antibody ACA125 that mimics the CA125 carbohydrate antigen expressed on ovarian cancer cells induces an anti-anti-Id antibody (Ab3) response that is associated with prolonged survival of ovarian cancer patients. To increase the Ab3 antibody response, we evaluated two strategies in a mouse model: (a) coinjection of human interleukin (IL)-6 together with the fusion protein chACA125, which consists of the anti-Id ACA125 single-chain Fv antibody joined to the human IgG1 CH2/CH3 domain; and (b) injection of the fusion protein chACA125-IL-6, which consists of the ACA125 single-chain Fv fused to human IL-6 via the IgG1 CH2/CH3 domain. Vaccination of mice with the chACA125-IL-6 fusion protein resulted in higher titers of anti-CA125 (Ab3) antibodies compared with application of the chACA125 antibody with or without systemic coadministration of IL-6. Application of the chACA125-IL-6 fusion protein did not elicit detectable antihuman IL-6 antibody titers, whereas coinjection of human IL-6 did. Taken together, these data suggest that the chACA125-IL-6 fusion protein directly stimulates ACA125-specific B cells via the IL-6 domain, whereas coinjection of IL-6 leads to an overall immune stimulation. Antigen-IL-6 fusion proteins will improve vaccination regimens and anticancer immunotherapeutic strategies by increasing the antigen-specific humoral immune response.
Cost–benefit, cost‐effectiveness and cost–utility analyses of periodontitis prevention (2005)

It is suggested that economic parameters as well as patient-centred outcomes be included in clinical trials. These data are essential for the appropriate allocation of resources for preventive measures on an individual patient and population base.
Computer simulation techniques to design Xenon- 124 solid target for iodine-123 production (2008)

I in the form of sodium iodide is used most commonly for the measurement of thyroid uptake and thyroid imaging. In addition, radioiodinated compounds have been widely employed in the detection of cardiological, neurological and oncological diseases (1). Among the various types of nuclear reactions for producing I, the following reactions are favored due to the absence of I and I impurities: I production system via Xe gas target technology has been constructed and installed in Cyclotron and Nuclear Medicine Department of Nuclear Research Centre for Agriculture and Medicine (NRCAM). One of the major problems in this system is the highly expensive cost of the enriched Xe gas. Therefore, saving this gas inside the system is very important. Unfortunately, by accidental rupture of the window foil or bad function of O-rings, the whole Xenon gas will escape from the system immediately. In this paper, by using computer codes, Alice91, SRIM and doing some calculations, it has been tried to demonstrate the latest effort for feasibility study of producing I with the above mentioned reactions, but using Xe solid target instead.
Modulation of protein C inhibitor activity (1994)

Protein C inhibitor (PCI), antithrombin, and heparin cofactor II are members of the serine proteinase inhibitor (serpin) superfamily that inhibit proteinases at rates which increase in the presence of the glycosaminoglycan heparin. These studies were undertaken to understand how PCI activity is modulated by various substances that are found in or interact with the vascular endothelium/basement membrane. The effects of antithrombin-heparin, thrombomodulin, vitronectin and leukocyte elastase on PCI-thrombin and PCI-activated protein C (APC) interactions were investigated. Antithrombin, which does not inhibit APC but which does bind to heparin/heparan sulphate with higher affinity than PCI, caused only a small decrease in the inhibition rate of PCI-APC in the presence of unfractionated heparin. Thrombomodulin, a chondroitin sulphate-containing proteoglycan, accelerated PCI inhibition of thrombin and APC. PCI-thrombin in the presence or absence of heparin bound plastic absorbed vitronectin, but neither PCI alone nor PCI-APC bound. Vitronectin also decreased the inhibition rate of PCI-thrombin and PCI-APC in the presence of low concentrations of heparin. Leukocyte elastase proteolytically inactivated PCI in a reaction that was accelerated by heparin. Overall, these results indicate that PCI activity is modulated by these endothelial cell/basement membrane-based substances in similar ways as other heparin-binding serpins, especially antithrombin.
Bis(ditertiaryphosphine) complexes of rhodium(I). Synthesis, spectroscopy, and activity for catalytic hydrogenation (1979)

Rhodium(I)–bis(ditertiaryphosphine) complexes of the general formula [Formula: see text]n = 1–4, and (+)-diop (diop = 2,3-O-isopropylidene 2,3-dihydroxy-1,4-bis(diphenylphosphino)butane) have been prepared by treating [Rh(cyclooctene) 2 Cl] 2 with the appropriate ditertiaryphosphine. The n = 1 and n = 4 and diop species are five-coordinate in the solid state and in non-polar solvents, while the n = 2 and 3 species contain ionic chloride. The cationic complexes [Formula: see text] were prepared from the [Formula: see text] species by adding AgX (X = SbF 6 , PF 6 , BF 4 ). Reaction of the chloro complexes with borohydride has yielded the hydrides, [Formula: see text] for the n = 2 and 3 diphosphines, and for (+)-diop. 1 H and 31 P nmr, as well as visible spectral data, are presented: a solvent-dependent deshielding of ortho protons of the phenyl groups is observed in some of the complexes, and the ligand CH 2 protons are coupled to the rhodium in the Rh(Ph 2 PCH 2 PPh 2 ) 2 + cation; the P atom in this bis(diphenylphosphino) ligand shows an usual high field shift on coordination to rhodium.Preliminary kinetic data for catalytic hydrogenation of methylenesuccinic acid show that the cationic and hydrido complexes are more active than the corresponding chloro complexes, and that activity generally increases with increasing chain length of the diphosphine.
Comparative Influence of Surface Tungstate Species and Bulk Amorphous WO<sub>3</sub> Particles on the Acidity and Catalytic Activity of Tungsten Oxide Supported on Silica (2015)

Catalysts based on tungsten oxide supported on silica and containing up to 2.5 W atoms nm–2 were studied for the purpose of establishing quantitative relationships between the nature and abundance of surface species, acidity, and catalytic activity. Synthesis conditions that maximize the formation of amorphous WO3 were adopted to assess its influence on the overall acidity and activity. The results were compared to those of conventionally prepared catalysts. The catalysts’ structure was characterized by FTIR, Raman, and UV spectroscopies. The acidity of the solids was monitored by adsorption of 2,6-dimethylpyridine followed by FTIR, and their catalytic activity was tested for the reaction of propan-2-ol dehydration. A methodology for quantitation of W species (WOx surface species, amorphous or crystalline WO3 particles) detected following calcination at 673 or 773 K was developed. For both calcination temperatures, surface W species were first formed with initial W addition. Their abundance increased with increasing W content up to ca. 0.7 atom W nm–2 and levels off for higher W surface densities. The leveling off was concomitant with the detection and rapid development of amorphous or crystalline WO3 phase (catalysts calcined respectively at 673 or 773 K). The comparison of W speciation in both series indicated that amorphous WO3 phase is quantitatively transformed to crystalline WO3 on increasing the calcination temperature from 673 to 773 K. The observed development of Brønsted acidity of the solids was associated with W deposition. The abundance of these acid sites correlated directly with the catalytic activity. The study of structure–activity relationship showed that all W species were active. Modeling of the results permitted an estimation of the intrinsic activity of each W species. The values thus obtained suggest that amorphous WO3 particles exhibit the highest activity per surface W atom.
A DFT-based residual-excited linear predictive coder (RELP) for 4.8 and 9.6kb/s (2005)

The proposed RELP system is based on a DFT (discrete Fourier transform) of the linear prediction residual. The base-band Fourier coefficients, derived from frequencies 0 to 800 Hz, are transmitted to the receiver. For encoding, the Fourier coefficients are converted to polar representation re <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">iφ</sup> . The quantization accuracy of both magnitude and phase angle is controlled by an adaptive-bit assignment algorithm. At the receiver, the non-transmitted Fourier coefficients are replaced by base-band coefficients which have been frequency-shifted pitch-synchronously. In the 4.8 kb/s version, the spectral translation algorithm is controlled only by the transmitted pitch frequency. In the 9.6 kb/s version, however, additional information for reconstruction of the harmonic structure in the high-frequency region is computed at the transmitter. Audio tapes of both versions are presented.