gebhart/patrepeval huggingface dataset:
Functional Characterization of DNase X, a Novel Endonuclease Expressed in Muscle Cells (2000)

The activation of endonucleases resulting in the degradation of genomic DNA is one of the most characteristic changes in apoptosis. Here, we report the characterization of a novel endonuclease, termed DNase X due to its X-chromosomal localization. The active nuclease is a 35 kDa protein with 39% identity to DNase I. When incubated with isolated nuclei, recombinant DNase X was capable of triggering DNA degradation at internucleosomal sites. Similarly to DNase I, the nuclease activity of DNase X was dependent on Ca(2+) and Mg(2+) and inhibited by Zn(2+) ions or chelators of bivalent cations. Overexpression of DNase X caused internucleosomal DNA degradation and induction of cell death associated with increased caspase activation. Despite the presence of two potential caspase cleavage sites, DNase X was processed neither in vitro nor in vivo by different caspases. Interestingly, after initiation of apoptosis DNase X was translocated from the cytoplasm to the nuclear compartment and aggregated as a detergent-insoluble complex. Abundant expression of DNase X mRNA was detected in heart and skeletal muscle cells, suggesting that DNase X may be involved in apoptotic or other biological events in muscle tissues.
Association of Dietary Phosphorus Intake and Phosphorus to Protein Ratio with Mortality in Hemodialysis Patients (2010)

Higher dietary phosphorus intake and higher dietary phosphorus to protein ratios are each associated with increased death risk in MHD patients, even after adjustments for serum phosphorus, phosphate binders and their types, and dietary protein, energy, and potassium intakes.
Does integrated behavioral health care reduce mental health disparities for Latinos? Initial findings. (2013)

Integrated behavioral health care (IBHC) is a model of mental health care service delivery that seeks to reduce stigma and service utilization barriers by embedding mental health professionals into the primary care team. This study explored whether IBHC service referrals, utilization, and outcomes were comparable for Latinos and non-Latino White primary care patients. Data for the current study were collected from 793 consecutive patients (63.8% Latino; <i>M</i> age = 29.02 years [<i>SD</i> = 17.96]; 35.1% under 18 years; 65.3% women; 54.3% uninsured) seen for behavioral health services in 2 primary care clinics during a 10.5 month period. The most common presenting concerns were depression (21.6%), anxiety (18.5%), adjustment disorder (13.0%), and externalizing behavior problems (9.8%). Results revealed that while Latino patients had significantly lower self-reported psychiatric distress, significantly higher clinician-assigned global assessment of functioning scores, and fewer received a psychiatric diagnosis at their initial visit compared to non-Latino White patients, both groups had comparable utilization rates, comparable and clinically significant improvements in symptoms (Cohen's <i>d</i> values > .50), and expressed high satisfaction with integrated behavioral services. These data provide preliminary evidence suggesting integration of behavioral health services into primary care clinics may help reduce mental health disparities for Latinos.
Crystal Structure of FMN-Dependent Nitroreductase from <i>Escherichia </i><i>c</i><i>oli</i> B:  A Prodrug-Activating Enzyme<sup>,</sup> (2000)

The FMN-dependent flavoprotein nitroreductase from Escherichia coli B (NTR) is used in cancer chemotherapy to activate a range of prodrugs. The crystal structure of this enzyme has been determined, using molecular replacement methods and refined at 2.06 A resolution. The recombinant 24-kDa enzyme was crystallized in the tetragonal space group P4(1)2(1)2, with unit cell dimensions of a = b = 57.74 A and c = 275.51 A and two molecules in the asymmetric unit. The structure has a final R factor of 20.3% (R(free) = 26.7%), for all data between the resolution ranges of 10-2.06 A, and includes 4453 protein atoms, 230 water molecules, and 2 flavin mononucleotide (FMN) molecules. The functional unit is a homodimer, which forms the asymmetric unit in the crystal structure. The tertiary structures of these two monomers and their subunit interactions are nearly identical. The molecular replacement search model, the crystal structure of the major NAD(P)H:FMN oxidoreductase of Vibrio fisheri (FRase 1), was selected on the basis of its high sequence identity to that of NTR. The final superposition of these two enzymes revealed a very similar overall fold, with variation in the structures focused around surface loops and helices near the FMN cofactor. Helix G is implicated in substrate specificity and is better resolved in the present NTR structure than in the previously reported FRase 1 structure. The FMN binding pocket is also well-resolved, showing the presence of two channels leading into the active site. The amino acid side chains and main chain atoms interacting with the FMN are well-ordered. The structure of the substrate binding pocket has been used to examine substrate specificity and enzyme kinetics for prodrugs used in antibody-directed enzyme prodrug therapy (ADEPT) and gene-directed enzyme prodrug therapy (GDEPT).
2'-Deoxy-2'-fluoro- -D-arabinonucleic acid (2'F-ANA) modified oligonucleotides (ON) effect highly efficient, and persistent, gene silencing (2006)

To be effective in vivo, antisense oligonucleotides (AS ON) should be nuclease resistant, form stable ON/RNA duplexes and support ribonuclease H mediated heteroduplex cleavage, all with negligible non-specific effects on cell function. We report herein that AS ONs containing a 2'-deoxy-2'-fluoro-beta-D-arabinonucleic acid (2'F-ANA) sugar modification not only meet these criteria, but have the added advantage of maintaining high intracellular concentrations for prolonged periods of time which appears to promote longer term gene silencing. To demonstrate this, we targeted the c-MYB protooncogene's mRNA in human leukemia cells with fully phosphorothioated 2'F-ANA-DNA chimeras (PS-2'FANA-DNA) and compared their gene silencing efficiency with AS ON containing unmodified nucleosides (PS-DNA). When delivered by nucleofection, chemically modified ON of both types effected a >90% knockdown of c-MYB mRNA and protein expression, but the PS-2'F-ANA-DNA were able to accomplish this at 20% of the dose of the PS-DNA, and in contrast to the PS-AS DNA, their silencing effect was still present after 4 days after a single administration. Therefore, our data demonstrate that PS-2'F-ANA-DNA chimeras are efficient gene silencing molecules, and suggest that they could have significant therapeutic potential.
Silicon phosphorus nitride, the first ternary compound in the silicon-phosphorus-nitrogen system (1993)

The novel compound SiPN3 has been prepared by reacting hexachloro-N-silylphosphinimine Cl3Si-N=PC13 with liquid ammonia a t -78 "C followed by subsequent removal of the ammonium chloride byproduct and annealing of the resulting polymeric imide at 800 "C for 12 h.The compound has been characterized by elemental analysis and 29Si and 31P MAS-NMR, as well as X-ray powder diffraction methods.The powder data suggest a defect Wurtzite type structure which is closely related to the structures of SizNzO and SiZNzNH.(Rietveld analysis data: space group CmcB1, 2 = 4, a = 902.4(4)pm, b = 527.5(2)pm, c = 469.8(2)pm; 44 reflections observed; scan range 10" < 279 < 81"; germanium monochromator, Cu Kal, R(wp) = 0.047, R(l,h,k,l) = 0.071.)At 920 "C SiPN3 decomposes into Si3N4, P4, and Nz.The Si3N4 obtained on pyrolysis of SiPN3 consists of a pure a-phase and has an extremely low oxygen content.
Impact of epidermal growth factor receptor (EGFR) kinase mutations, <i>EGFR</i> gene amplifications, and <i>KRAS</i> mutations on survival of pancreatic adenocarcinoma (2007)

The incidence of somatic mutations in the tyrosine kinase domains of EGFR was very low and the increased gene copy number of EGFR did not significantly influence survival.
Evaluation of Large Aberrations Using a Lateral-Shear Interferometer Having Variable Shear (1975)

A variable shear lateral shearing interferometer consisting of two holographically produced crossed diffraction gratings is used to test nonrotationally symmetric wavefronts having aberrations greater than 100 wavelengths and slope variations of more than 400 wavelengths/diameter. Comparisons are made with results of Twyman-Green interferometric tests for wavefront aberrations of up to thirty wavelengths. The results indicate that small wavefront aberrations can be measured as accurately with the lateral-shear interferometer as with the Twyman-Green interferometer and that aberrations that cannot be measured at all with a Twyman-Green interferometer can be measured to about 1% accuracy or better.
Dynamic programming for detecting, tracking, and matching deformable contours (1995)

The problem of segmenting an image into separate regions and tracking them over time is one of the most significant problems in vision. Terzopoulos et al. (1987) proposed an approach to detect the contour regions of complex shapes, assuming a user selected initial contour not very far from the desired solution. We propose to further explore the information provided by the user's selected points and apply an optimal method to detect contours which allows a segmentation of the image. The method is based on dynamic programming (DP), and applies to a wide variety of shapes. It is exact and not iterative. We also consider a multiscale approach capable of speeding up the algorithm by a factor of 20, although at the expense of losing the guaranteed optimality characteristic. The problem of tracking and matching these contours is addressed. For tracking, the final contour obtained at one frame is sampled and used as initial points for the next frame. Then, the same DP process is applied. For matching, a novel strategy is proposed where the solution is a smooth displacement field in which unmatched regions are allowed while cross vectors are not. The algorithm is again based on DP and the optimal solution is guaranteed. We have demonstrated the algorithms on natural objects in a large spectrum of applications, including interactive segmentation and automatic tracking of the regions of interest in medical images.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Pathway-specific regulation of the synthesis of anticoagulantly active heparan sulfate. (1994)

L cells and endothelial cells synthesize a heparan sulfate (HS) subpopulation, HSact, that exhibits anticoagulant activity due to a specific monosaccharide sequence; the remaining heparan sulfate, HSinact, lacks this region of defined structure and is anticoagulantly inactive. HSact biosynthesis was examined in these two cell types by stably expressing epitope-tagged rat ryudocan (ryudocan12CA5), which possesses three glycosaminoglycan (GAG) acceptor sites. Both HSact and HSinact were present on ryudocan12CA5 isolated from L cells and endothelial cells; thus, a core protein with a unique primary sequence initiates the synthesis of both GAGs. The expression in L cells of ryudocan12CA5 variants containing a single functional GAG acceptor site demonstrated that each of the three acceptor regions initiates the synthesis of both types of GAGs to a similar extent. Most importantly, in both cell types total HSact generation declined as a function of ryudocan12CA5 overexpression even though HSinact production increased linearly as a function of this variable. This discordant relationship is a general property of the biosynthetic machinery since in both cell types HSact production was reduced to an equal extent on protein cores of either exogenous or endogenous origins. The suppression of HSact generation was also observed with a secreted form of core protein lacking transmembrane and cytoplasmic domains or by a GAG acceptor site mutated form of core protein incapable of augmenting GAG synthesis. These results suggest that elevated intracellular levels of core protein saturate the capacity of a critical component of the HSact biosynthetic machinery. This critical component is not a member of the common set of biosynthetic enzymes involved in the production of HSact and HSinact since no structural changes were observed in either GAG during overexpression of core protein. Based upon the above data, we conclude that increased intracellular levels of ryudocan probably act by saturating the capacity of components which regulate HSact production by coordinating the function of biosynthetic enzymes.
Reinfection of virus free mice with mouse mammary tumour virus (1989)

BR6/Icrf mice carrying a milk-transmitted mammary tumour virus (MMTV) develop tumours after several pregnancies. If the mice are freed from MMTV, no tumours develop. In the experiments described in this paper, MMTV was reintroduced into MMTV-free mice by foster nursing, which was least effective if the pups were exposed to the virus only during the first week of life. Exposure for even a short time after that age led to a tumour incidence similar to that found in normally infected mice. Reinfection was also achieved by injection of MMTV-containing milk into weanling or pregnant mice, and was then transmitted naturally to the next generation.
Search strategy using LHC pileup interactions as a zero bias sample (2018)

Due to a limited bandwidth and a large proton-proton interaction cross section relative to the rate of interesting physics processes, most events produced at the Large Hadron Collider (LHC) are discarded in real time. A sophisticated trigger system must quickly decide which events should be kept and is very efficient for a broad range of processes. However, there are many processes that cannot be accommodated by this trigger system. Furthermore, there may be models of physics beyond the standard model (BSM) constructed after data taking that could have been triggered, but no trigger was implemented at run time. Both of these cases can be covered by exploiting pileup interactions as an effective zero bias sample. At the end of high-luminosity LHC operations, this zero bias dataset will have accumulated about $1\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$ of data from which a bottom line cross section limit of $\mathcal{O}(1)\text{ }\text{ }\mathrm{fb}$ can be set for BSM models already in the literature and those yet to come.
The function of TLR2 during staphylococcal diseases (2013)

Staphylococcus aureus is a versatile pathogen causing a wide range of infections. It has been a major threat both in hospitals and in the community for decades. S. aureus is a pyogenic bacterium that elicits recruitment of polymorphonuclear leukocytes (neutrophils) to the site of infection. Neutrophils are among the first immune cells to migrate to an infection site attracted by chemoattractant gradients, usually initiated in response to inflammation. Neutrophil recruitment to an inflammation and/or infection site is a sophisticated process involving their interaction with endothelial and epithelial cells through adhesion molecules. Phagocytes have various receptors to detect pathogens, and they include Toll-like receptors (TLRs). TLRs have been extensively studied over the last 10 years and it is now established that they are critical during bacterial infections. However, the function of TLRs, and more particularly TLR2, during staphylococcal infections is still debated. In this review we will consider recent findings concerning the staphylococcal ligands sensed by TLR2 and more specifically the role of staphylococcal lipoproteins in TLR2 recognition. A new concept to emerge in recent years is that staphylococcal components must be phagocytosed and digested in the phagosome to be efficiently detected by the TLR2 of professional phagocytes. Neutrophils are an essential part of the immune response to staphylococcal infections, and in the second part of this review we will therefore describe the role of TLR2 in PMN recruitment in response to staphylococcal infections.
Andrés Trapiello y 'Los amigos del crimen perfecto' (2003). El género policíaco entre homenaje y distanciamiento (2006)

International audience
A One-Pass Algorithm for Overload Resolution in Ada (1982)

A simple method is presented for detecting ambiguities and finding the correct interpretations of expressions in the programming language Ada. Unlike previously reported solutions to this problem, which require multiple passes over a tree structure, the method described here operates in one bottom-up pass, during which a directed acyclic graph is produced. The correctness of this approach is demonstrated by a brief formal argument.
Stereochemistry of Aminocyclanols. Synthesis of cis Epimers via Oxazolines. The 2-Aminocyclopentanols<sup>*</sup> (1950)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemistry of Aminocyclanols. Synthesis of cis Epimers via Oxazolines. The 2-Aminocyclopentanols*G. E. McCasland and Donald Arthur SmithCite this: J. Am. Chem. Soc. 1950, 72, 5, 2190–2195Publication Date (Print):May 1, 1950Publication History Published online1 May 2002Published inissue 1 May 1950https://pubs.acs.org/doi/10.1021/ja01161a089https://doi.org/10.1021/ja01161a089research-articleACS PublicationsRequest reuse permissionsArticle Views255Altmetric-Citations19LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Genetic analysis of carcinogen enhancement of type 5 adenovirus transformation of cloned fischer rat embryo fibroblast cells (1993)

Pretreatment of CREF cells with methyl methanesulfonate (MMS) before infection with the host-range cold-sensitive type 5 adenovirus (Ad5) mutant H5hr1 results in a dose-dependent carcinogen enhancement of viral transformation (CET). The properties of CET observed with H5hr1, which include both an MMS dose-dependent enhancement in the number of transformed foci and an increase in transformation frequency after correction for cell toxicity, are not observed in carcinogen-pretreated wild-type (wt) Ad5 (H5wt)-infected CREF cells. This study was conducted to determine the role of the viral E1A and E1B transforming genes of H5hr1 in mediating the unique CET phenotype of H5hr1. Coinfection of MMS-pretreated CREF cells with H5wt or H5sub309 (which displays a wt Ad5 phenotype) and H5hr1 resulted in a suppression of the unique CET phenotype that was directly related to the multiplicity of infection with wt Ad5. Suppression of the unique H5hr1 CET phenotype was also apparent in MMS-pretreated CREF cells coinfected with H5hr1 and an Ad5 mutant expressing either a wt 13S E1A-encoded 289 amino-acid (aa) protein and an intact wt E1B gene or a wt 13S E1A-encoded 289-aa protein and a 22S E1B-encoded 495-aa protein. In contrast, the unique H5hr1 CET phenotype was not suppressed in MMS-pretreated CREF cells coinfected with H5hr1 and Ad5 or Ad2 mutants expressing either a wt 12S E1A-encoded 243-aa protein and both wt E1B gene products or an intact wt E1A gene and a wt E1B 13S-encoded 175-aa protein. That genetic changes in both the E1A and E1B viral regions of H5hr1 were required to induce the unique CET phenotype was also indicated by the inability of a recombinant Ad5 containing the 0-4.5 map-unit region of H5hr1 and the 4.5-100 map-unit region of H5sub309 to display the H5hr1 unique CET phenotype. Direct confirmation of the requirement for both gene regions of H5hr1 to mediate its unique CET was obtained by generating CREF cells stably expressing a wt Ad5 E1A 13S-encoded 289-aa protein and a wt E1B 22S-encoded 495-aa protein. In these CREF transformants (which displayed a CREF-like morphology), transformation by H5hr1 was not reduced, but the unique CET phenotype after MMS pretreatment was eliminated. These results suggest that alterations in both the 13S-encoded E1A and 22S-encoded E1B gene products of H5hr1 contribute to its unique CET.
Part I. Bcl‐2 and bcl‐x <sub>L</sub> limit apoptosis upon infection with alphavirus vectors (2000)

Viral expression systems offer the ability to generate high levels of a particular protein within a relatively short period of time. In particular, alphavirus constructs based on Sindbis virus (SV) and Semliki Forest virus (SFV) are promising vehicles as they are cytoplasmic vectors with the potential for high expression levels. Two such alphavirus vectors were utilized during the current study to infect two commercially relevant cell lines, baby hamster kidney (BHK) and Chinese hamster ovary (CHO); the first was a fully competent SV derivative carrying the gene for chloramphenicol acetyltransferase (dsSV-CAT), while the second was a replication deficient SFV construct containing the human interleukin-12 (IL-12) p35 and p40 genes (SFV-IL-12). Since infection with these vectors induced apoptosis in both cell lines, the present effort was dedicated to determining the ability of anti-apoptosis genes to limit the cell death associated with these virus constructs. Infection with the dsSV-CAT vector resulted in the rapid death of BHK and CHO cells within 4 days, a phenomenon which was considerably delayed by stably overexpressing bcl-2 or bcl-x(L). In fact, cellular lifespans were doubled in both BHK-bcl2 and CHO-bclx(L) cells relative to the parental cell lines. Furthermore, the presence of these gene products provided increases of up to 2-fold in recombinant CAT production. Overexpression of bcl-2 and bcl-x(L) also altered the response of these cells upon infection with SFV-IL-12. While the parental cell lines were completely nonviable within 1 week, the BHK-bcl2, BHK-bclx(L), and CHO-bclx(L) cells each recovered from the infection, resuming exponential growth and regaining viabilities of over 90% by 9 days post-infection. Total IL-12 productivities were nearly doubled by Bcl-2 and Bcl-x(L) in the CHO cells, although this effect was apparently cell-line specific, as the native BHK cells were able to secrete more IL-12 than either of its transfected derivatives. Regardless, the presence of the anti-apoptosis genes allowed the production of IL-12 to be maintained, albeit at low levels, from each of the cell lines for the duration of the culture process. Therefore, overexpression of bcl-2 family members can have a significant impact on culture viabilities and recombinant protein production during alphavirus infections of mammalian cells.
Biologically Active 2,5-Disubstituted-1,3,4-Oxadiazoles (2009)

There are vast numbers of pharmacologically active heterocyclic compounds in regular clinical use. The presence of heterocyclic structures in diverse types of compounds is strongly indicative of the profound effects such structure exerts on physiologic activity, and recognition of this is abundantly reflected in efforts to find useful synthetic drugs. The 1,3,4-oxadiazole nucleus has emerged as one of the potential pharmacophore responsible for diverse pharmacological properties. Medical Literature is flooded with reports of a variety of biological activities of 2,5-Disubstituted-1,3,4-oxadiazoles. The present work is an attempt to summarize and enlist the various reports published on biologically active 2,5-disubstituted-1,3,4-oxadiazoles.