gebhart/patrepeval huggingface dataset:
Gene expression profiles associated with aging and mortality in humans (2009)

We investigated the hypothesis that gene expression profiles in cultured cell lines from adults, aged 57-97 years, contain information about the biological age and potential longevity of the donors. We studied 104 unrelated grandparents from 31 Utah CEU (Centre d'Etude du Polymorphisme Humain - Utah) families, for whom lymphoblastoid cell lines were established in the 1980s. Combining publicly available gene expression data from these cell lines, and survival data from the Utah Population Database, we tested the relationship between expression of 2151 always-expressed genes, age, and survival of the donors. Approximately 16% of 2151 expression levels were associated with donor age: 10% decreased in expression with age, and 6% increased with age. Cell division cycle 42 (CDC42) and CORO1A exhibited strong associations both with age at draw and survival after draw (multiple comparisons-adjusted Monte Carlo P-value < 0.05). In general, gene expressions that increased with age were associated with increased mortality. Gene expressions that decreased with age were generally associated with reduced mortality. A multivariate estimate of biological age modeled from expression data was dominated by CDC42 expression, and was a significant predictor of survival after blood draw. A multivariate model of survival as a function of gene expression was dominated by CORO1A expression. This model accounted for approximately 23% of the variation in survival among the CEU grandparents. Some expression levels were negligibly associated with age in this cross-sectional dataset, but strongly associated with inter-individual differences in survival. These observations may lead to new insights regarding the genetic contribution to exceptional longevity.
Optimizing alpha executables on Windows NT with spike (1998)

Vol. 9 No. 4 1997 3 Spike is a performance tool developed by DIGITAL to optimize Alpha executables on the Windows NT operating system. This optimization system has two main components: the Spike Optimizer and the Spike Optimization Environment. The Spike Optimizer reads in an executable, optimizes the code, and writes out the optimized version. The Optimizer uses profile feedback from previous runs of an application to guide its optimizations. Profile feedback is not commonly used in practice because it is difficult to collect, manage, and apply profile information. The Spike Optimization Environment provides a user-transparent profile feedback system that solves most of these problems, allowing a user to easily optimize large applications composed of many executables and dynamic link libraries (DLLs). Optimizing an executable image after it has been compiled and linked has several advantages. The Spike Optimizer can see the entire image and perform interprocedural optimizations, particularly with regard to code layout. The Optimizer can use profile feedback easily, because the executable that is profiled is the same executable that is optimized; no awkward mapping of profile data back to the source language takes place. Also, Spike can be used when the sources to an application are not available, which is beneficial when DIGITAL is working with independent software vendors (ISVs) to tune applications. Applications can be loosely classified into two categories: loop-intensive programs and call-intensive programs. Conventional compiler technology is well suited to loop-intensive programs. The important loops in a program in this category are within a single procedure, which is typically the unit of compilation. The control flow is predictable, and the compiler can use simple heuristics to determine the frequently executed parts of the procedure. Spike is designed for large, call-intensive programs; it uses interprocedural optimization and profile feedback. In call-intensive programs, the important loops span multiple procedures, and the loop bodies contain procedure calls. Consequently, optimizations on the loops must be interprocedural. The control flow is Optimizing Alpha Executables on Windows NT with Spike Robert S. Cohn David W. Goodwin P. Geoffrey Lowney
Altered expression of imprinted genes in Wilms tumors (2010)

Overexpression of insulin-like growth factor 2 (IGF2), an imprinted gene located on chromosome 11p15, has been reported as a characteristic feature in various embryonal tumors, including Wilms tumor (WT). Recent studies specified loss of imprinting (LOI) in a differential methylated region (DMR) of the IGF2/H19 cluster or loss of heterozygosity (LOH), respectively, uniparental disomy (UPD) being responsible for this overexpression. However, the role of other imprinted genes in the genesis of WT is still unknown. In the current study, we analyzed transcriptional activity of the imprinted genes IGF2, H19, NNAT, DLK1, RTL1, MEG3, and MEST as well as the methylation status of the DMR of the IGF2/H19 cluster in a panel of 32 WTs. Except for H19, we detected massive overexpression of all genes in the majority of WTs compared to normal renal tissue, which was most prominent for the paternally expressed genes IGF2, NNAT, and MEST. Alterations of the H19DMR were found in two-thirds of the WTs. Moreover, we have seen a strong correlation between the transcriptional activity of IGF2, NNAT and MEST and LOI/LOH of H19DMR, which was inverse for H19. Expression of DLK1, RTL1 and MEG3 does not correlate with LOI/LOH of H19DMR. Altogether, our findings suggest that over-expression of imprinted genes is common in WTs and correlates at least for some imprinted genes with LOI of H19DMR. Thus, it may be speculated that alterations of the DNA modification machinery drive erroneous setting of methylation marks in imprinting regions throughout the genome, which leads to the concomitant activation of imprinted genes in blastomagenesis.
Production in vitro of mouse early pregnancy factor and purification to homogeneity (1984)

Early pregnancy factor (EPF) has been produced in vitro by culture of oestrous mouse oviducts and ovaries in RPMI, with the addition of prolactin and mouse embryo culture medium. The pooled harvested medium was then subjected to immunoabsorption, electrofocusing and gel filtration. A fraction was isolated with pI 6.83 and molecular weight 21 000 which was responsible for 90% of the recovered biological activity. It appeared to be homogeneous when analysed by high-performance gel-permeation chromatography. SDS treatment showed that the molecule could be split into 3 peptides of molecular weights 10 500, 7200 and 3400, the first having activity equivalent to the EPF component EPF-A from the oviduct, while the last two combined to give activity corresponding with the ovarian component EPF-B.
Using Nanoparticles to Enable Simultaneous Radiation and Photodynamic Therapies for Cancer Treatment (2006)

This paper describes research into a new approach to cancer treatment through a combination of radiation and photodynamic therapies. The assumption is that supplementing conventional radiation therapy with photodynamic therapy (PDT) will enable the use of lower doses of radiation. Under this concept, scintillation or persistent luminescence nanoparticles with attached photosensitizers such as porphyrins are used as an in vivo agent for photodynamic therapy. The nanoparticle PDT agents are delivered to the treatment site. Upon exposure to ionizing radiation such as X-rays, the nanoparticles emit scintillation or persistent luminescence, which, in turn, activates the photosensitizers; as a consequence, singlet oxygen (1O2) is produced. Studies have shown that 1O2 can be effective in killing cancer cells. This is the conventional way in which PDT can augment the effectiveness of ionizing radiation. The innovation described in this study involves the use of in vivo luminescent nanoparticles so that an external light source is not required to support PDT. Consequently, application of the therapy can be more localized and the potential of damage to healthy cells is reduced. This new modality will provide an efficient, low-cost approach to PDT while still offering the benefits of augmented radiation therapy at lower doses.
Assay, Purification, and Partial Characterization of Choline Monooxygenase from Spinach (1995)

The osmoprotectant glycine betaine is synthesized via the path-way choline -> betaine aldehyde -> glycine betaine. In spinach (Spinacia oleracea), the first step is catalyzed by choline monooxygenase (CMO), and the second is catalyzed by betaine aldehyde dehydrogenase. Because betaine aldehyde is unstable and not easily detected, we developed a coupled radiometric assay for CMO. [14C]Choline is used as substrate; NAD+ and betaine aldehyde dehydrogenase prepared from Escherichia coli are added to oxidize [14C]betaine aldehyde to [14C]glycine betaine, which is isolated by ion exchange. The assay was used in the purification of CMO from leaves of salinized spinach. The 10-step procedure included polyethylene glycol precipitation, polyethyleneimine precipitation, hydrophobic interaction, anion exchange on choline-Sepharose, dimethyldiethanolamine-Sepharose, and Mono Q, hydroxyapatite, gel filtration, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Following gel filtration, overall purification was about 600-fold and recovery of activity was 0.5%. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed a polypeptide with a molecular mass of 45 kD. Taken with the value of 98 kD estimated for native CMO (R. Brouquisse, P. Weigel, D. Rhodes, C.F. Yocum, A.D. Hanson [1989] Plant Physiol 90: 322-329), this indicates that CMO is a homodimer. CMO preparations were red-brown, showed absorption maxima at 329 and 459 nm, and lost color upon dithionite addition, suggesting that CMO is an iron-sulfur protein.
NetMHCstab – predicting stability of peptide–MHC‐I complexes; impacts for cytotoxic T lymphocyte epitope discovery (2013)

Major histocompatibility complex class I (MHC-I) molecules play an essential role in the cellular immune response, presenting peptides to cytotoxic T lymphocytes (CTLs) allowing the immune system to scrutinize ongoing intracellular production of proteins. In the early 1990s, immunogenicity and stability of the peptide-MHC-I (pMHC-I) complex were shown to be correlated. At that time, measuring stability was cumbersome and time consuming and only small data sets were analysed. Here, we investigate this fairly unexplored area on a large scale compared with earlier studies. A recent small-scale study demonstrated that pMHC-I complex stability was a better correlate of CTL immunogenicity than peptide-MHC-I affinity. We here extended this study and analysed a total of 5509 distinct peptide stability measurements covering 10 different HLA class I molecules. Artificial neural networks were used to construct stability predictors capable of predicting the half-life of the pMHC-I complex. These predictors were shown to predict T-cell epitopes and MHC ligands from SYFPEITHI and IEDB to form significantly more stable MHC-I complexes compared with affinity-matched non-epitopes. Combining the stability predictions with a state-of-the-art affinity predictions NetMHCcons significantly improved the performance for identification of T-cell epitopes and ligands. For the HLA alleles included in the study, we could identify distinct sub-motifs that differentiate between stable and unstable peptide binders and demonstrate that anchor positions in the N-terminal of the binding motif (primarily P2 and P3) play a critical role for the formation of stable pMHC-I complexes. A webserver implementing the method is available at www.cbs.dtu.dk/services/NetMHCstab.
Use of Methotrexate-Based Peptide Substrates to Characterize the Substrate Specificity of Prostate-Specific Membrane Antigen (PSMA) (2004)

Prostate-Specific Membrane Antigen (PSMA) is a glutamate carboxypeptidase II that is highly expressed by both normal and malignant prostate epithelial cells and by the neovasculature of many tumor types but is not expressed by endothelial cells in normal tissue. PSMA possesses the hydrolytic properties of an N-acetylated alpha-linked acidic dipeptidase (NAALADase) and also functions as a pteroyl poly-gamma-glutamyl carboxypeptidase (i.e., folate hydrolase). Therefore, PSMA can be targeted for activation of peptide-based prodrugs within the extracellular fluid of prostate cancers. In this study, methotrexate-based peptide analogs were evaluated to identify PSMA selective substrates that are also stable to nonspecific hydrolysis in human and mouse plasma. These methotrexate analogs were also characterized for in vitro toxicity against PSMA and nonPSMA producing human cancer cell lines. Analogs containing gamma-linked glutamate residues were most efficiently hydrolyzed by PSMA, but were unstable in plasma. Analogs containing both alpha- and gamma-linked acidic amino acids were less efficiently hydrolyzed by PSMA but were most stable in plasma. Analogs were 5-10 fold more selectively toxic in vitro in the presence of active PSMA. These studies have identified PSMA selective, plasma stable peptide substrates that can be incorporated into prodrugs targeted for activation by PSMA within prostate cancer sites.
Ideal spatial adaptation by wavelet shrinkage (1994)

SUMMARY With ideal spatial adaptation, an oracle furnishes information about how best to adapt a spatially variable estimator, whether piecewise constant, piecewise polynomial, variable knot spline, or variable bandwidth kernel, to the unknown function. Estimation with the aid of an oracle offers dramatic advantages over traditional linear estimation by nonadaptive kernels; however, it is a priori unclear whether such performance can be obtained by a procedure relying on the data alone. We describe a new principle for spatially-adaptive estimation: selective wavelet reconstruction. We show that variable-knot spline fits and piecewise-polynomial fits, when equipped with an oracle to select the knots, are not dramatically more powerful than selective wavelet reconstruction with an oracle. We develop a practical spatially adaptive method, RiskShrink, which works by shrinkage of empirical wavelet coefficients. RiskShrink mimics the performance of an oracle for selective wavelet reconstruction as well as it is possible to do so. A new inequality in multivariate normal decision theory which we call the oracle inequality shows that attained performance differs from ideal performance by at most a factor of approximately 2 log n, where n is the sample size. Moreover no estimator can give a better guarantee than this. Within the class of spatially adaptive procedures, RiskShrink is essentially optimal. Relying only on the data, it comes within a factor log 2 n of the performance of piecewise polynomial and variableknot spline methods equipped with an oracle. In contrast, it is unknown how or if piecewise polynomial methods could be made to function this well when denied access to an oracle and forced to rely on data alone.
Mucosal or Parenteral Administration of Microsphere-Associated Bacillus anthracis Protective Antigen Protects against Anthrax Infection in Mice (2002)

Existing licensed anthrax vaccines are administered parenterally and require multiple doses to induce protective immunity. This requires trained personnel and is not the optimum route for stimulating a mucosal immune response. Microencapsulation of vaccine antigens offers a number of advantages over traditional vaccine formulations, including stability without refrigeration and the potential for utilizing less invasive routes of administration. Recombinant protective antigen (rPA), the dominant antigen for protection against anthrax infection, was encapsulated in poly-L-lactide 100-kDa microspheres. Alternatively, rPA was loosely attached to the surfaces of microspheres by lyophilization. All of the microspheric formulations were administered to A/J mice with a two-dose schedule by either the intramuscular route, the intranasal route, or a combination of these two routes, and immunogenicity and protective efficacy were assessed. An intramuscular priming immunization followed by either an intramuscular or intranasal boost gave optimum anti-rPA immunoglobulin G titers. Despite differences in rPA-specific antibody titers, all immunized mice survived an injected challenge consisting of 10(3) median lethal doses of Bacillus anthracis STI spores. Immunization with microencapsulated and microsphere-associated formulations of rPA also protected against aerosol challenge with 30 median lethal doses of STI spores. These results show that rPA can be encapsulated and surface bound to polymeric microspheres without impairing its immunogenicity and also that mucosal or parenteral administration of microspheric formulations of rPA efficiently protects mice against both injected and aerosol challenges with B. anthracis spores. Microspheric formulations of rPA could represent the next generation of anthrax vaccines, which could require fewer doses because they are more potent, are less reactogenic than currently available human anthrax vaccines, and could be self-administered without injection.
Multipoint linkage-disequilibrium mapping narrows location interval and identifies mutation heterogeneity (2003)

Single-nucleotide polymorphism (SNP) genotypes were recently examined in an 890-kb region flanking the human gene CYP2D6. Single-marker and haplotype-based analyses identified, with genomewide significance (P < 10-7), a 403-kb interval displaying strong linkage disequilibrium (LD) with predicted poor-metabolizer phenotype. However, the width of this interval makes the location of causal variants difficult: for example, the interval contains seven known or predicted genes in addition to CYP2D6. We have developed the Bayesian fine-mapping software coldmap, which, applied to these genotype data, yields a 95% location interval covering only 185 kb and establishes genomewide significance for a causal locus within the region. Strikingly, our interval correctly excludes four SNPs, which individually display association with genomewide significance, including the SNP showing strongest LD (P < 10-34). In addition, coldmap distinguishes homozygous cases for the major CYP2D6 mutation from those bearing minor mutations. We further investigate a selection of SNP subsets and find that previously reported methods lead to a 38% savings in SNPs at the cost of an increase of <20% in the width of the location interval.
Genes for Growth Hormone, Chorionic Somatomammotropin, and Growth Hormone-Like Gene on Chromosome 17 in Humans (1980)

The human genes for growth hormone (GH), chorionic somatomammotropin (CSH), and a third growth hormone-like gene (GHL) have been located on chromosome 17 in humans. DNA fragments of 2.6, 2.8, and 9.5 kilobase pairs containing GH, CSH, and GHL, respectively, were identified in human genomic DNA, and a 7.5-kilobase DNA fragment related to growth hormone DNA sequences was found in mouse cells. In somatic hybrids of human and mouse cells containing reduced numbers of human chromosomes, but a normal complement of mouse chromosomes, the mouse, 7.5-kolobase DNA fragment was always present, whereas the 2.6-, 2.8-, and 9.5-kilobase human fragments were present only when human chromosome 17 was also present.
The K1 capsule is the critical determinant in the development of Escherichia coli meningitis in the rat. (1992)

Although Escherichia coli strains possessing the K1 capsule are predominant among isolates from neonatal E. coli meningitis and most of these K1 isolates are associated with a limited number of 0 lipopolysaccharide (LPS) types, the basis of this association of K1 and certain 0 antigens with neonatal E. coli meningitis is not clear. The present study examined in experimental E. coli bacteremia and meningitis in newborn and adult rats whether or not the K1 capsule and/or O-LPS antigen are critical determinants in the development of meningitis. Rats received subcutaneously at K1 E. coli strain (018+K1+) or mutants lacking either the K1 capsule (018+K1-) or 0 side-chain (018-K1+). 12-24 h later, blood and cerebrospinal fluid (CSF) specimens were obtained for quantitative cultures. The isolation of E. coli from CSF was observed in both newborn and adult rats infected with K1+ strains regardless of LPS phenotype (018+ or 18-) who also developed a high degree of bacteremia (e.g., greater than 10(4) CFU/ml of blood). In contrast, none of the newborn and adult rats infected with 018+K1- and developing bacteremia of greater than 10(4) were found to have positive CSF cultures. These findings indicate that the presence of the K1 capsule and a high degree of bacteremia are key determinants in the development of E. coli meningitis, suggesting that there may be specific binding sites present in the brain which have an affinity for the K1 capsule and thus may be responsible for the entry of K1-encapsulated E. coli into the meninges.
In vivo identification of sialic acid as the ocular receptor for Pseudomonas aeruginosa (1986)

In vivo bacterial adherence of Pseudomonas aeruginosa to the immature ocular epithelium was mediated by a sialic (N-acetylneuraminic) acid (NANA) receptor. Saturation of binding sites on the bacterial surface by NANA prevented attachment of the organism to the epithelial cell membrane receptor. Additionally, a significant number of animals receiving NANA-treated organisms were protected from septicemia and death. In vivo protection studies showed excellent correlation with scanning electron microscopy, in that the number of adherent organisms at the corneal surface decreased dramatically in the presence of NANA. These studies exhibit a strong correlation with clinical cases of human infant ocular infection.
Developmental and Metabolic Effects of Disruption of the Mouse CTP:Phosphoethanolamine Cytidylyltransferase Gene (Pcyt2) (2007)

The CDP-ethanolamine pathway is responsible for the de novo biosynthesis of ethanolamine phospholipids, where CDP-ethanolamine is coupled with diacylglycerols to form phosphatidylethanolamine. We have disrupted the mouse gene encoding CTP:phosphoethanolamine cytidylyltransferase, Pcyt2, the main regulatory enzyme in this pathway. Intercrossings of Pcyt2(+/-) animals resulted in small litter sizes and unexpected Mendelian frequencies, with no null mice genotyped. The Pcyt2(-/-) embryos die after implantation, prior to embryonic day 8.5. Examination of mRNA expression, protein content, and enzyme activity in Pcyt2(+/-) animals revealed the anticipated 50% decrease due to the gene dosage effect but rather a 20 to 35% decrease. [(14)C]ethanolamine radiolabeling of hepatocytes, liver, heart, and brain corroborated Pcyt2 gene expression and activity data and showed a decreased rate of phosphatidylethanolamine biosynthesis in heterozygotes. Total phospholipid content was maintained in Pcyt2(+/-) tissues; however, this was not due to compensatory increases in the decarboxylation of phosphatidylserine. These results establish the necessity of Pcyt2 for murine development and demonstrate that a single Pcyt2 allele in heterozygotes can maintain phospholipid homeostasis.
Haloacetylated Enol Ethers, 19: Synthesis of 3-(2-Thienyl)- and 3-(2-Furyl)-5-trihalomethyl Substituted Azoles (2005)

Heterocyclization of 1,1,1-trifluoro[chloro]-4-methoxy-4-[2-tienyl]-3-buten-2-one and 1,1,1-trifluoro[chloro]-4-methoxy-4-[2-furyl]-3-buten-2-ones into isoxazoles and pyrazoles derivatives as a new type of trihalomethylated bicyclic heterocycles is reported.