gebhart/patrepeval huggingface dataset:
HPLC analysis of brain and plasma for octanoic and decanoic acids. (1989)

Two methods are described for determination of octanoic and decanoic acids in plasma and brain homogenate by "high-performance" liquid chromatography with ultraviolet detection. Analysis of the underivatized acids had a detection limit of only 50 mg/L, but formation of the p-bromophenacyl ester increased the sensitivity by 100-fold, to a detection limit of 0.5 mg/L. The latter procedure gave interassay coefficients of variation of 4.1% and 4.8% for octanoic and decanoic acids, respectively. The corresponding intra-assay values were 3.95% and 4.7% (n = 6). The derivative method, applied to samples of plasma from children receiving a medium-chain triglyceride (MCT) diet, gave values in agreement with results by gas-liquid chromatography. Results have also been obtained for samples from mice, either treated with the medium-chain triglyceride diet or given infusions of sodium octanoate.
Maternal reproductive history and birth characteristics in childhood acute lymphoblastic leukemia (1991)

Using birth-registration data, a case-control study was done to investigate the possible associations of childhood acute lymphoblastic leukemia (ALL) with birth characteristics and maternal reproductive history. The data included cases born and diagnosed in Minnesota since 1969. Matched analyses were conducted using 337 cases and 1336 birth year-matched controls. There was a statistically significant increased odds of ALL for birth to older (greater than 35 years) mothers (odds ratio (OR) = 2.14, 95% confidence interval (CI) = 1.28, 3.58), older fathers (OR = 1.62, 95% CI = 1.14, 2.30), mothers with at least a high school education (OR = 1.61, 95% CI = 1.05, 2.48), and larger intervals (greater than 5 years) between the birth of the proband and the preceding sibling (OR = 1.86, 95% CI = 1.12, 3.09). The increased odds of ALL for birth by Caesarean section approached significance (OR = 1.42, P = 0.06). No overall association was found for: gender, race, paternal education, fetal-loss history, birth order, prenatal care history, pregnancy complications, inducement of labor, multiple birth, gestational age, or birth weight. Age at diagnosis was an important effect modifier of some analyses. For cases diagnosed before age 2 years, there was a 2.7-fold increased odds of ALL if the last pregnancy had resulted in a fetal loss (P = 0.03). For cases diagnosed before age 4 years, birth weight greater than 3800 g was associated with a significant 2.05-fold increased odds of ALL. These data strengthen the hypothesis that prenatal events may play a causative role in childhood ALL, particularly in those cases diagnosed at a younger age.
Chronic lymphocytic leukemia: molecular heterogeneity revealed by high-throughput genomics (2013)

Chronic lymphocytic leukemia (CLL) has been consistently at the forefront of genetic research owing to its prevalence and the accessibility of sample material. Recently, genome-wide technologies have been intensively applied to CLL genetics, with remarkable progress. Single nucleotide polymorphism arrays have identified recurring chromosomal aberrations, thereby focusing functional studies on discrete genomic lesions and leading to the first implication of somatic microRNA disruption in cancer. Next-generation sequencing (NGS) has further transformed our understanding of CLL by identifying novel recurrently mutated putative drivers, including the unexpected discovery of somatic mutations affecting spliceosome function. NGS has further enabled in-depth examination of the transcriptional and epigenetic changes in CLL that accompany genetic lesions, and has shed light on how different driver events appear at different stages of disease progression and clonally evolve with relapsed disease. In addition to providing important insights into disease biology, these discoveries have significant translational potential. They enhance prognosis by highlighting specific lesions associated with poor clinical outcomes (for example, driver events such as mutations in the splicing factor subunit gene SF3B1) or with increased clonal heterogeneity (for example, the presence of subclonal driver mutations). Here, we review new genomic discoveries in CLL and discuss their possible implications in the era of precision medicine.
Fanfare (Available only in Special Structural Issue) (2000)

The owners of the Milwaukee Brewers baseball team decided in the late 1980s that their current home, the 50-year-old County Stadium, could no longer offer the facilities that attract crowds to baseball games; a new stadium had to be built. Key to the new ballpark design is a retractable roof that will allow play in the open on natural grass whenever possible but also provide protection from the rain and, early and late in the season, snow. From the beginning, the designers looked for a way to integrate the baseball diamond shape into the design of the stadium and its roof. Other baseball parks with retractable roofs have either a rectangular or a circular geometry. The designers came up with a unique fan configuration that would rotate about a pivot base at home plate. The retractable roof would be combined with an 80 ft (24 m) high wall around the outfield that could be opened for ventilation. Unlike other retractable roofs, Miller Park’s roof can expand and contract with movement joints above its mechanism, so it does not need to rely on the design of the seating structure to accommodate the movements of the roof. The stadium’s completion is set for April 2001, when the Brewers will play the opening game of the season in their new home.
The Composition of Coding Joints Formed in V(D)J Recombination Is Strongly Affected by the Nucleotide Sequence of the Coding Ends and Their Relationship to the Recombination Signal Sequences (1997)

V(D)J recombination proceeds in two stages. Precise cleavage at the border of the conserved recombination signal sequences (RSSs) and the coding ends results in flush double-stranded signal ends and coding ends terminating in hairpins. In the second stage, the signal and coding ends are processed into signal and coding joints. Coding ends containing certain nucleotide homopolymers affect the efficiency of V(D)J recombination. In this study, we have tested the effect of small changes in coding-end nucleotide composition on the frequency of coding- and signal joint formation. Furthermore, we have determined the sequences of coding joints resulting from recombination of coding ends with different compositions. We found that the presence of two T nucleotides 5' of both RSSs, but not a single T, reduces the frequency of signal joint formation, i.e., interferes with the cleavage stage of V(D)J recombination. However, coding-joint processing is sensitive even to a single T. Both the sequence of the coding ends and the particular RSS (12-mer or 23-mer) with which the coding end is associated affect the final composition of the coding joints. Thus, the presence of P nucleotides, the conservation of one undeleted coding end, the formation of joints without any deletions, and the template-dependent insertion of nucleotides are strongly influenced by the coding-end nucleotide composition and/or RSS association. The implications of these results with respect to the processing of coding ends are discussed.
Estimating cache misses and locality using stack distances (2003)

Cache behavior modeling is an important part of modern optimizing compilers. In this paper we present a method to estimate the number of cache misses, at compile time, using a machine independent model based on stack algorithms. Our algorithm computes the stack histograms symbolically, using data dependence distance vectors and is totally accurate when dependence distances are uniformly generated. The stack histogram models accurately fully associative caches with LRU replacement policy, and provides a very good approximation for set-associative caches and programs with non-constant dependence distances.The stack histogram is an accurate, machine-independent metric of locality. Compilers using this metric can evaluate optimizations with respect to memory behavior. We illustrate this use of the stack histogram by comparing three locality enhancing transformations: tiling, data shackling and the product-space transformation. Additionally, the stack histogram model can be used to compute optimal parameters for data locality transformations, such as the tile size for loop tiling.
Protection of non‐obese diabetic mice from autoimmune diabetes by Escherichia coli heat‐labile enterotoxin B subunit (2005)

Autoimmune diabetes in the non-obese diabetic (NOD) mouse is associated with development of inflammation around the islets at around 4-5 weeks of age, which may be prolonged until frank diabetes begins to occur around 12 weeks of age. Although many interventions can halt disease progression if administration coincides with the beginning of the anti-beta cell response, very few are able to prevent diabetes development once insulitis is established. Here we describe a strategy which blocks cellular infiltration of islets and prevents diabetes. Intranasal treatment with the B-subunit of Escherichia coli heat labile enterotoxin (EtxB), a protein that binds GM1 ganglioside (as well as GD1b, asialo-GM1 and lactosylceramide with lower affinities), protected NOD mice from developing diabetes in a receptor-binding dependent manner. Protection was associated with a significant reduction in the number of macrophages, CD4(+) T cells, B cells, major histocompatibility complex class II(+) cells infiltrating the islets. Despite this, treated mice showed increased number of interleukin-10(+) cells in the pancreas, and a decrease in both T helper 1 (Th1) and Th2 cytokine production in the pancreatic lymph node. Disease protection was also transferred with CD4(+) splenocytes from treated mice. Taken together, these results demonstrated that EtxB is a potent immune modulator capable of blocking diabetes.
Ac induces homologous recombination at the maize P locus. (1991)

The maize P gene conditions red phlobaphene pigmentation to the pericarp and cob. Starting from two unstable P alleles which carry insertions of the transposable element Ac, we have derived 51 P null alleles; 47 of the 51 null alleles have a 17-kb deletion which removes the 4.5-kb Ac element and 12.5 kb of P sequences flanking both sides of Ac. The deletion endpoints lie within two 5.2-kb homologous direct repeats which flank the P gene. A P allele which contains the direct repeats, but does not have an Ac insertion between the direct repeats, shows very little sporophytic or gametophytic instability. The apparent frequency of sporophytic mutations was not increased when Ac was introduced in trans. Southern analysis of DNA prepared from the pericarp tissue demonstrates that the deletions can occur premeiotically, in the somatic cells during development of the pericarp. Evidence is presented that the deletions occurred by homologous recombination between the two direct repeats, and that the presence of an Ac element at the P locus is associated with the recombination/deletion. These results add another aspect to the spectrum of activities of Ac: the destabilization of flanking direct repeat sequences.
Biocatalysis in the Pharmaceutical and Biotechnology Industries (2006)

Because enzyme-catalyzed reactions exhibit higher enantioselectivity, regioselectivity, substrate specificity, and stability, they require mild conditions to react while prompting higher reaction efficiency and product yields. Biocatalysis in the Pharmaceutical and Biotechnology Industries examines the use of catalysts to produce fine chemic
Selective amplification of an mRNA and related pseudogene for a human ADP-ribosylation factor, a guanine nucleotide-dependent protein activator of cholera toxin. (1990)

ADP-ribosylation factors (ARFs) are approximately 20-kDa proteins that act as GTP-dependent allosteric activators of cholera toxin. With deoxyinosine-containing degenerate oligonucleotide primers corresponding to conserved GTP-binding domains in ARFs, the polymerase chain reaction (PCR) was used to amplify simultaneously from human DNA portions of three ARF genes that include codons for 102 amino acids, with intervening sequences. Amplification products that differed in size because of differences in intron sizes were separated by agarose gel electrophoresis. One amplified DNA contained no introns and had a sequence different from those of known ARFs. Based on this sequence, selective oligonucleotide probes were prepared and used to isolate clone psi ARF 4, a putative ARF pseudogene, from a human genomic library in lambda phage EMBL3. Reverse transcription-PCR was then used to clone from human poly(A)+ RNA the cDNA corresponding to the expressed homolog of psi ARF 4, referred to as human ARF 4. It appears that psi ARF 4 arose during human evolution by integration of processed ARF 4 mRNA into the genome. Human ARF 4 differs from previously identified mammalian ARFs 1, 2, and 3. Hybridization of ARF 4-specific oligonucleotide probes with human, bovine, and rat RNA revealed a single 1.8-kilobase mRNA, which was clearly distinguished from the 1.9-kilobase mRNA for ARF 1 in these tissues. The PCR provides a powerful tool for investigating diversity in this and other multigene families, especially with primers targeted at domains believed to have functional significance.
Development and Qualification of a Pharmacodynamic Model for the Pronounced Inoculum Effect of Ceftazidime against Pseudomonas aeruginosa (2008)

Evidence is mounting in support of the inoculum effect (i.e., slow killing at large initial inocula [CFUo]) for numerous antimicrobials against a variety of pathogens. Our objectives were to (i) determine the impact of the CFUo of Pseudomonas aeruginosa on ceftazidime activity and (ii) to develop and validate a pharmacokinetic/pharmacodynamic (PKPD) mathematical model accommodating a range of CFUo. Time-kill experiments using ceftazidime at seven concentrations up to 128 mg/liter (MIC, 2 mg/liter) were performed in duplicate against P. aeruginosa PAO1 at five CFUo from 10(5) to 10(9) CFU/ml. Samples were collected over 24 h and fit by candidate models in NONMEM VI and S-ADAPT 1.55 (all data were comodeled). External model qualification integrated data from eight previously published studies. Ceftazidime displayed approximately 3 to 4 log(10) CFU/ml net killing at 10(6.2) CFUo and concentrations of 4 mg/liter (or higher), less than 1.6 log(10) CFU/ml killing at 10(7.3) CFUo, and no killing at 10(8.0) CFUo for concentrations up to 128 mg/liter. The proposed mechanism-based model successfully described the inoculum effect and the concentration-independent lag time of killing. The mean generation time was 28.3 min. The effect of an autolysin was assumed to inhibit successful replication. Ceftazidime concentrations of 0.294 mg/liter stimulated the autolysin effect by 50%. The model was predictive in the internal cross-validation and had excellent in silico predictive performance for published studies of P. aeruginosa ATCC 27853 for various CFUo. The proposed PKPD model successfully described and predicted the pronounced inoculum effect of ceftazidime in vitro and integrated data from eight literature studies to support translation from time-kill experiments to in vitro infection models.
Assembly of double-shelled rotaviruslike particles by simultaneous expression of recombinant VP6 and VP7 proteins (1991)

Simultaneous coinfection of Spodoptera frugiperda cells with baculovirus recombinants containing the genes for VP6 and VP7 of bovine rotavirus strain C486 resulted in the production of spherical particles resembling smooth, double-shelled rotavirus. These particles were predominantly located in the cell culture supernatant instead of being cell associated. Pretreatment of infected-cell culture supernatants with CaCl2, prior to particle purification, was found to enhance the smooth appearance of the particles. The authenticity of the proteins making up the particles was demonstrated by their reactivity with antiserum specific for double-shelled C486 rotavirus.
[Personal experience in clinical use of low power laser therapy]. (1995)

The results of our own clinical trials regarding therapeutical effects of low power lasers in the treatment of some diseases of motional system, skin and lesions of peripheral circulation were presented in the paper. The laser therapy was used in over 320 patients in period of last 3 years. The infra-red laser (wave-length 904 nm, mean power 4 mW) was used. The procedures were performed daily, for 5 days a week in 2 stages: the scan of sore region (3-min.) and the irradiation of trigger points (2-3 min. each). As a result of 10-25 procedures a significant clinical improvement in 65-90% patients was obtained. On the base of obtained results one can conclude that low-power laser therapy could make a useful supplementary method of treatment of overloading syndrome of motional system, postthrombotic syndrome, lymphatic edema and trophic lesions of skin.
The p53 Tumor Suppressor Gene Inhibits Angiogenesis by Stimulating the Production of Thrombospondin (1994)

The proteins encoded by most human tumor suppressor genes are transcription factors or components of signal transduction pathways (Levine 1993). These tumor suppressors impose their antineoplastic phenotype on cells by modulating the expression of other genes. It is the proteins encoded by these suppressor-regulated genes, acting as effector molecules for the suppressor genes, that directly alter the cell or its environment in such a way as to make progression toward malignancy less likely. For example, it is the p53-regulated p21 protein that actually implements the p53-induced cell-cycle block by binding to and inhibiting cyclin/cdk complexes (El-Deiry et al. 1993). We have sought effector proteins that implement phenotypes induced by tumor suppressor genes by studying secreted molecules that regulate new blood vessel growth (neovascularization or angiogenesis), reasoning that they may provide insight into suppressor gene action and simultaneously serve as a starting point for the development of nongenotoxic anticancer therapies.
Dynamic Changes in Gene Expression During Human Trophoblast Differentiation (2003)

The genetic program that directs human placental differentiation is poorly understood. In a recent study, we used DNA microarray analyses to determine genes that are dynamically regulated during human placental development in an in vitro model system in which highly purified cytotrophoblast cells aggregate spontaneously and fuse to form a multinucleated syncytium that expresses placental lactogen, human chorionic gonadotropin, and other proteins normally expressed by fully differentiated syncytiotrophoblast cells. Of the 6918 genes present on the Incyte Human GEM V microarray that we analyzed over a 9-day period, 141 were induced and 256 were downregulated by more than 2-fold. The dynamically regulated genes fell into nine distinct kinetic patterns of induction or repression, as detected by the K-means algorithm. Classifying the genes according to functional characteristics, the regulated genes could be divided into six overall categories: cell and tissue structural dynamics, cell cycle and apoptosis, intercellular communication, metabolism, regulation of gene expression, and expressed sequence tags and function unknown. Gene expression changes within key functional categories were tightly coupled to the morphological changes that occurred during trophoblast differentiation. Within several key gene categories (e.g., cell and tissue structure), many genes were strongly activated, while others with related function were strongly repressed. These findings suggest that trophoblast differentiation is augmented by "categorical reprogramming" in which the ability of induced genes to function is enhanced by diminished synthesis of other genes within the same category. We also observed categorical reprogramming in human decidual fibroblasts decidualized in vitro in response to progesterone, estradiol, and cyclic AMP. While there was little overlap between genes that are dynamically regulated during trophoblast differentiation versus decidualization, many of the categories in which genes were strongly activated also contained genes whose expression was strongly diminished. Taken together, these findings point to a fundamental role for simultaneous induction and repression of mRNAs that encode functionally related proteins during the differentiation process.
Relative Contributions of Cystathionine β-Synthase and γ-Cystathionase to H2S Biogenesis via Alternative Trans-sulfuration Reactions (2009)

In mammals, the two enzymes in the trans-sulfuration pathway, cystathionine beta-synthase (CBS) and cystathionine gamma-lyase (CSE), are believed to be chiefly responsible for hydrogen sulfide (H2S) biogenesis. In this study, we report a detailed kinetic analysis of the human and yeast CBS-catalyzed reactions that result in H2S generation. CBS from both organisms shows a marked preference for H2S generation by beta-replacement of cysteine by homocysteine. The alternative H2S-generating reactions, i.e. beta-elimination of cysteine to generate serine or condensation of 2 mol of cysteine to generate lanthionine, are quantitatively less significant. The kinetic data were employed to simulate the turnover numbers of the various CBS-catalyzed reactions at physiologically relevant substrate concentrations. At equimolar concentrations of CBS and CSE, the simulations predict that H2S production by CBS would account for approximately 25-70% of the total H2S generated via the trans-sulfuration pathway depending on the extent of allosteric activation of CBS by S-adenosylmethionine. The relative contribution of CBS to H2S genesis is expected to decrease under hyperhomocysteinemic conditions. CBS is predicted to be virtually the sole source of lanthionine, and CSE, but not CBS, efficiently cleaves lanthionine. The insensitivity of the CBS-catalyzed H2S-generating reactions to the grade of hyperhomocysteinemia is in stark contrast to the responsiveness of CSE and suggests a previously unrecognized role for CSE in intracellular homocysteine management. Finally, our studies reveal that the profligacy of the trans-sulfuration pathway results not only in a multiplicity of H2S-yielding reactions but also yields novel thioether metabolites, thus increasing the complexity of the sulfur metabolome.
Synthesis, Structure and Properties of N-Acetylated Derivatives of Methyl 5-Amino-1H-[1,2,4]triazole-3-carboxylate (2004)

Methyl 5-amino-1H-[1,2,4]triazole-3-carboxylate hydrochloride (1). and free ester (2). were obtained and 2 was reacted with Ac(2)O to give the acetylated products 3-6. Compounds 1-6 were studied using HPLC, GC-MS, FTIR and multinuclear NMR spectroscopy, including the cross-polarisation magic angle spinning (CPMAS) technique. The results of the acetylation of 2 were compared to those of the acetylation of 5-amino-1H-[1,2,4]triazole, and for 2 a significant decrease in the susceptibility to acetylation was found. The reaction of 2 with Ac(2)O at 20 degrees C, regardless of the amount and the concentration of the latter, including neat Ac(2)O, proceeds fully regioselectively and leads to one product: methyl 1-acetyl-5-amino-1H-[1,2,4]triazole-3-carboxylate (3). In sharp contrast to 5-amino-1H-[1,2,4]triazole, neither an additional monoacetylated isomer, whether annular or exocyclic, nor any diacetylated derivative could be detected. The diacetylation of 2 requires the process to be carried out in neat boiling Ac(2)O and, as in the case of 5-amino-1H-[1,2,4]triazole, gives two diacetylated isomers. These are methyl 1-acetyl-3-(acetylamino)-1H-[1,2,4]triazole-5-carboxylate (4) and 1-acetyl-5-(acetylamino)-1H-[1,2,4]triazole-3-carboxylate (5). Hypothetical pathways of their formation have been suggested. A mixture of 4 and 5 upon hydrolysis of the ring acetyl group gives the monoacetylated derivative methyl 5-(acetylamino)-1H-[1,2,4]triazole-3-carboxylate (6). The spectroscopic, structural and conformational characteristics of compounds 1-6 have been given and methods for their preparation have been provided.