gebhart/patrepeval huggingface dataset:
Unusual nucleotide sequences at the 5' end of actin genes in Dictyostelium discoideum. (1979)

The nucleotide sequences at the 5' end of one actin cDNA and six actin genomic clones from Dictyostelium have been determined. The amino acid sequences derived from the nucleotide sequences show strong conservation for six of the seven genes relative to the NH2-terminal region of Physarum actin. The region 5' to the AUG initiating codon is greater than 90% A+T residues in all of the genes.
Uptake and deacylation of bacterial lipopolysaccharides by macrophages from normal and endotoxin-hyporesponsive mice (1985)

Macrophages are thought to play a central role in the responses of animals to gram-negative bacterial lipopolysaccharides (LPS). Since nothing is known about the metabolism of LPS by these cells, we studied the uptake and deacylation of radiolabeled LPS by thioglycolate-elicited peritoneal macrophages from normal (C3H/HeN) and LPS-hyporesponsive (C3H/HeJ) mice. Macrophages from both kinds of mice took up and deacylated LPS that were added to the culture medium. Opsonization of the LPS with anti-LPS immunoglobulin G antibodies greatly increased LPS uptake; the opsonized LPS also underwent deacylation at rates that were directly related to the amount of cell-associated LPS. An analysis of the fatty acid composition of the cell-associated LPS indicated that the cells have one or more acyloxyacyl hydrolases that remove the non-hydroxylated fatty acids that are normally substituted to the hydroxyl groups of (glucosamine-linked) 3-hydroxytetradecanoate residues in lipid A; we also found evidence for deacylation of 3-hydroxytetradecanoate from the glucosamine backbone. LPS deacylation by macrophages from C3H/HeN and C3H/HeJ mice was qualitatively and quantitatively similar. Nonopsonized LPS are able to stimulate LPS-responsive cells; in these studies we established that animal cells can deacylate nonopsonized LPS, thus raising the possibility that LPS metabolism may play a role in modulating cellular stimulation.
Multispectral labeling of antibodies with polyfluorophores on a DNA backbone and application in cellular imaging (2011)

Most current approaches to multiantigen fluorescent imaging require overlaying of multiple images taken with separate filter sets as a result of differing dye excitation requirements. This requirement for false-color composite imaging prevents the user from visualizing multiple species in real time and disallows imaging of rapidly moving specimens. To address this limitation, here we investigate the use of oligodeoxyfluoroside (ODF) fluorophores as labels for antibodies. ODFs are short DNA-like oligomers with fluorophores replacing the DNA bases and can be assembled in many colors with excitation at a single wavelength. A DNA synthesizer was used to construct several short ODFs carrying a terminal alkyne group and having emission maxima of 410-670 nm. We developed a new approach to antibody conjugation, using Huisgen-Sharpless cycloaddition, which was used to react the alkynes on ODFs with azide groups added to secondary antibodies. Multiple ODF-tagged secondary antibodies were then used to mark primary antibodies. The set of antibodies was tested for spectral characteristics in labeling tubulin in HeLa cells and revealed a wide spectrum of colors, ranging from violet-blue to red with excitation through a single filter (340-380 nm). Selected sets of the differently labeled secondary antibodies were then used to simultaneously mark four antigens in fixed cells, using a single image and filter set. We also imaged different surface tumor markers on two live cell lines. Experiments showed that all colors could be visualized simultaneously by eye under the microscope, yielding multicolor images of multiple cellular antigens in real time.
<i>Propionibacterium acnes</i> Resistance: A Worldwide Problem (2003)

Antibiotic therapy directed against Propionibacterium acnes has been a mainstay of treatment for more than 40 years. Despite years of widespread use of systemic tetracyclines and erythromycin, change in P. acnes sensitivity to antibiotics was not seen until the early 1980s. The first clinically relevant changes in P. acnes antibiotic sensitivity were found in the USA shortly after the introduction of topical formulations of erythromycin and clindamycin. By the late 1980s, P. acnes strains with very high MIC levels for erythromycin and elevated MICs for tetracycline were increasingly found in the UK and the USA. Mutations in the genes encoding the 23S and 16S subunits of ribosomal RNA were first identified in the UK and also seen in a recent survey from clinics in Europe, Japan, Australia and the USA. In addition, strains were found in which these known mutations could not be identified, indicating that as yet unidentified resistance mechanisms have evolved. These findings indicate the need to develop strategies to minimize the use of antibiotics in acne therapy.
The Human Gut Microbiome (2013)

Recent advances in parallel genomic processing and computational mapping have been applied to the native human microbial environment to provide a new understanding of the role of the microbiome in health and disease. In particular, studies of the distal gut microbiome have proposed that changes in gut microbiota are related to obesity, the metabolic syndrome, and Western diet. We examined the changes in the distal gut microbiome composition as it relates to the lean and obese phenotypes, particularly after surgical weight loss. A PubMed search of publications from January 1, 2005, through December 31, 2012, used the search terms weight, obesity, microbiome, and bariatric surgery. We included studies that provided information on subjects' weight and/or body mass index and a formal assessment of the microbiome. Certain bacteria, specifically the archaeon Methanobrevibacter smithii, have enhanced ability to metabolize dietary substrate, thereby increasing host energy intake and weight gain. With weight loss, there is a decrease in the ratio of Firmicutes to Bacteroidetes phyla. One major finding from microbial sequencing analyses after Roux-en-Y gastric bypass is the comparative overabundance of Proteobacteria in the distal gut microbiome, which is distinct from the changes seen in weight loss without Roux-en-Y gastric bypass. This review provides the practicing surgeon with (1) an update on the state of a rapidly innovating branch of clinical bioinformatics, specifically, the microbiome; (2) a new understanding of the microbiome changes after Roux-en-Y gastric bypass and weight loss; and (3) a basis for understanding further clinical applications of studies of the distal gut microbiome, such as in Crohn disease, ulcerative colitis, and infectious colitis.
Negative Regulators of Hemopoiesis and Stroma Function in Patients with Myelodysplastic Syndrome (2000)

The mechanism that leads to hemopoietic failure in patients with myelodysplastic syndrome (MDS) is not well understood. There is evidence, however, that regulatory molecules such as tumor necrosis factor (TNF)-alpha, Fas (CD95), and Fas-ligand, which negatively affect hemopoiesis by way of apoptosis are upregulated. Here we analyzed marrow samples from 80 patients with MDS in regard to TNF-alpha and Fas-ligand levels and a possible correlation with various disease parameters and risk factors. TNF-alpha levels were elevated in comparison to samples from normal marrow donors, however, no significant correlation with FAB subtype, cytogenetic risk group or score by the International Prognostic Scoring System (IPSS) was observed. However, there was an inverse correlation between the cytogenetic risk category (low, intermediate, high) and levels of soluble Fas-ligand. The major source of TNF-alpha were mononuclear (non-stromal) cells which appeared to produce TNF-alpha at maximum levels. Limiting dilution analysis of CD34+ precursor cells showed that individually assayed cells, removed from companion cells that presumably provided negative signals such as TNF-alpha or Fas-ligand, were able to generate progressively increasing numbers of colonies. Stromal layers derived from MDS marrow did not have an inhibitory effect. In fact, higher colony numbers were obtained from both normal and MDS marrow derived hemopoietic precursors propagated on irradiated stromal layers from MDS marrow than on stromal layers from normal marrow. These results show that substantial numbers of normal hemopoietic precursors persist in MDS marrow. However, differentiation into mature cells is inhibited by negative signals originating from accessory or abnormal hemopoietic precursors in the non-adherent marrow fraction.
Hybrid organic/inorganic complementary circuits (1996)

The transfer characteristics of hybrid complementary inverters with n-channel a-Si transistors and p-channel organic transistors are described. These inverters can operate at supply voltages as low as 7 V. Such circuit schemes may be useful in low-cost, low-power applications.
Improving the mechanical properties of single-walled carbon nanotube sheets by intercalation of polymeric adhesives (2003)

Organic polymers, such as poly(vinyl alcohol), poly(vinyl pyrrolidone), and poly(styrene), were intercalated into single-walled carbon nanotube sheets by soaking the sheets in polymer solutions. Even for short soak times, significant polymer intercalation into existing free volume was observed. Tensile tests on intercalated sheets showed that the Young’s modulus, strength, and toughness increased by factors of 3, 9, and 28, respectively, indicating that the intercalated polymer enhances load transmission between nanotubes.
Site-directed analysis of the functional domains in the factor Xa inhibitor tick anticoagulant peptide: identification of two distinct regions that constitute the enzyme recognition sites (1992)

Recombinant tick anticoagulant peptide (rTAP) is a highly selective inhibitor of blood coagulation factor Xa. rTAP has been characterized kinetically as a slow, tight-binding, competitive inhibitor of the enzyme. We used an approach consisting of both recombinant, site-directed mutagenesis and solid-phase chemical synthesis to generate 31 independent mutations in rTAP to identify those regions of the molecule which contribute to the specific, high-affinity binding interaction with factor Xa. Our results demonstrate that the four amino-terminal residues of rTAP constitute the primary recognition determinant necessary for the formation of the high-affinity enzyme-inhibitor complex. The Arg residue in position three is probably not interacting with the S1-specificity pocket of factor Xa in a substrate-like manner since substitution at this position with a D-Arg amino acid produced only a modest decrease in affinity (5-fold). An additional domain in the rTAP molecule located between residues 40 and 54 was identified as a probable secondary binding determinant. Interestingly, this region in rTAP shares significant amino acid sequence homology with a sequence in prothrombin immediately amino-terminal to the factor Xa cleavage site that generates meizothrombin. These observations indicate that specific segments within two different regions of the rTAP molecule contribute to the potent binding interaction between rTAP and factor Xa.
Lattice generation with accurate word boundary in WFST framework (2012)

This paper presents an algorithm to generate the speech recognition lattice with accurate word boundary in weighted finite-state transducer (WFST) decoding framework. In traditional WFST lattice generation algorithms, the transformation from context-dependent phone lattice to word lattice does not yield accurate time boundaries between words. Meanwhile, this lattice is not a Standard Lattice Format nor is it compatible with existing toolkits. The lattice without word boundary can only be used in the area where the word boundary is not needed. In this paper, we propose a lexicon matching algorithm based on token passing to transform the phone lattice to the word lattice. This algorithm generates standard lattices with accurate word boundary. The experiments show that the proposed lattice generation algorithm has an good lattice quality and good algorithm efficiency.
PRD-based global-mean-time signaling for high-speed chip-to-chip communications (2002)

A chip-to-chip signaling scheme employs partial response detection (PRD) combined with the zero-delay time delivery of a global timing reference, or global mean time (GMT). High-output-impedance drivers and higher termination resistances for signal transmission reduce driver power to the 10 mW range while maintaining a data rate of 500Mb/s. The resulting intersymbol interference (ISI) is eliminated by the PRD receivers, a type of auto-zero-comparator. Signal lines are segmented and pipelined by PRD buffers to limit the segment lengths to below Lmax=cT/2, where c is the effective velocity of signal propagation and T is the bit time. Segmentation reduces the driver power considerably.
Molecular reconstruction of complex hydrocarbon mixtures: An application of principal component analysis (2010)

Abstract Three methods for reconstruction of the detailed molecular composition of complex hydrocarbon mixtures, based on their global properties, are compared: a method based on the Shannon entropy criterion, an artificial neural network and a multiple linear regression model. In spite of the broad range of naphthas included in the training set, the application range of the last two methods proved to be limited. Principal component analysis allowed to identify their three‐dimensional ellipsoidal application range. In this subspace, the artificial neural network is more accurate than the multiple linear regression model and the Shannon entropy method. However, outside its application range, the performance of the neural network, as well as the regression model, decreases drastically. In contrast, the performance of the Shannon entropy method is not influenced by the characteristics of the considered naphtha, but rather depends on the number of available commercial indices. The Shannon entropy method yields comparable results to the artificial neural network, provided that a sufficient amount of distillation data is available to supply information on the carbon number distribution. Combining the reconstruction methods with a fundamental simulation model illustrates the necessity of having accurate feedstock reconstruction methods since they allow to capture the full power of fundamental simulation models for the simulation of industrial processes. © 2010 American Institute of Chemical Engineers AIChE J, 2010
Transcriptional Control of the Stearoyl-CoA Desaturase-1 Gene by Polyunsaturated Fatty Acids1 (1994)

The effect of exogenous fatty acids on expression of the stearoyl-CoA desaturase-1 (SCD1) gene was assessed both in vivo and ex vivo. Mice fed a fat-free diet or a diet containing a largely monounsaturated (18:1) fat, i.e., olive oil, expressed high levels of hepatic SCD1 mRNA. In contrast, in mice fed diets containing primarily polyunsaturated (18:2 and 18:3) fats, expression of the hepatic SCD1 message was markedly suppressed. Similar experiments with pure fatty acid esters showed that arachidonate (20:4) and linoleate (18:2) were far more potent in down-regulating expression of the hepatic SCD1 message than oleate (18:1), an end-product (as its CoA thioester) of the SCD1-catalyzed reaction. The reduction of hepatic SCD1 mRNA appears to be primarily due to inhibition of SCD1 gene transcription since polyunsaturated fatty acids caused a decrease in run-on transcription of the gene comparable to the decrease in message level. Consistent with the effects observed in vivo, unsaturated fatty acids suppressed the expression of SCD1 mRNA by rat hepatocytes cultured in serum-free medium. Suppression increased with degree of unsaturation with arachidonic (20:4) and eicosapentaenoic (20:5) acids, causing a > or = 90% reduction in the level of SCD1 message. Thus, the SCD1 gene, like the fatty acid synthase and S14 genes, undergoes coordinate transcriptional down-regulation in response to unsaturated fatty acids.
Cyclization of Geranylgeranyl Diphosphate to Taxa-4(5),11(12)-diene Is the Committed Step of Taxol Biosynthesis in Pacific Yew (1995)

The biosynthesis of taxol (paclitaxel) and related taxoids in Pacific yew (Taxus brevifolia) is thought to involve the cyclization of geranylgeranyl diphosphate to a taxadiene followed by extensive oxygenation of this diterpene olefin intermediate. A cell-free preparation from sapling yew stems catalyzed the conversion of [1-3H]geranylgeranyl diphosphate to a cyclic diterpene olefin that, when incubated with stem sections, was converted in good radiochemical yield to several highly functionalized taxanes, including 10-deacetyl baccatin III and taxol itself. Addition of the labeled olefin to a yew bark extract, followed by radiochemically guided fractionation, provided sufficient product to establish the structure as taxa-4(5),11(12)-diene by two-dimensional NMR spectroscopic methods. Therefore, the first dedicated step in taxol biosynthesis is the conversion of the universal diterpenoid precursor geranylgeranyl diphosphate to taxa-4(5),11(12)-diene, rather than to the 4(20),11(12)-diene isomer previously suggested on the basis of the abundance of taxoids with double bonds in these positions. The very common occurrence of taxane derivatives bearing the 4(20)-ene-5-oxy functional grouping, and the lack of oxygenated derivatives bearing a 4(5)-double bond, suggest that hydroxylation at C-5 of taxadiene with allylic rearrangement of the double bond is an early step in the conversion of this olefin intermediate to taxol.
Drug Latentiation (1962)

The biological effect of a drug is determined by many factors, all of which are influenced by the chemical structure of the compound. In the animal body the biological activity of a compound is not only a function of its effect at a particular site but also its ability to reach and be removed from the locus of action. Therefore, a knowledge of the physico-chemical properties of the com-pound which influence its absorption, its distribution in tissues, its enzymatic biotransformation and its excretion after enzymatic detoxification are essential for a complete understanding of the speed and duration of action, the relative toxicity and possible routes of administration. In any approach to drug design this total spectrum of biological activity must be considered since the various parts will undoubtedly influence the quantitative and qualitative pharmacolog-ical effect of the drug.
Fast Viability Assessment of Clostridium Spores: Survival in Extreme Environments (2010)

Bacterial endospores are formed in genera such as Bacillus and Clostridium in response to adverse environmental changes. Endospores have remarkable resistance to various extreme conditions and can remain dormant for extended periods of time. Clostridium spores are of particular interest due to their significant importance in several industries, such as food processing, wastewater treatment, pharmaceuticals, and health care. They are also the ideal candidates to study Panspermia and potential extraterrestrial life. However, to date, most endospore research has been conducted on Bacillus, and study of the anaerobic spore former, Clostridium, is not adequate. In this study, we have developed a general protocol to produce and purify Clostridium spores. Spectroscopy and microscopy based Endospore Viability Assay (Spectro EVA and Micro EVA) were developed and validated to assess the viability of Clostridium spores. Germinability was used as an indicator for spore viability. The basic principle of the two EVAs is to measure the release of a unique biomarker, dipicolinic acid (DPA), via germination as a proxy for endospore viability. In particular, a luminescence time-gated microscopy technique (Micro EVA) has been developed to enumerate germinable Clostridium endospores within an hour. Micro EVA is based on energy transfer from DPA to terbium ions doped in a solid matrix upon UV excitation. The distinctive emission and millisecond lifetime enables time-resolved imaging to achieve single endospore sensitivity. Comparing to traditional CFU cultivation, EVA probes the early stage of germination, resulting in a much faster detection rate (within 60 minutes) than CFU measurement (more than 3 days incubation). Micro EVA has also been successfully applied to quantify Clostridium spores in an extreme cold biosphere, Greenland ice core, and a hyper-arid biosphere, Atacama Desert, two Mars analogs on earth. The development of EVA provides a faster way to assess viability of Clostridium spores, which has significant importance in various industries. It also enables the determination of the limit and longevity of life, and provides insight on the search of extinct or extant life on Mars and other celestial bodies.
The transcription factor HIF-1α plays a critical role in the growth factor-dependent regulation of both aerobic and anaerobic glycolysis (2007)

Mammalian cells are believed to have a cell-intrinsic ability to increase glucose metabolism in response to hypoxia. Here we show that the ability of hematopoietic cells to up-regulate anaerobic glycolysis in response to hypoxia is dependent on receptor-mediated signal transduction. In the absence of growth factor signaling, hematopoietic cells fail to express hypoxia-inducible transcription factor (Hif-1alpha) mRNA. Growth factor-deprived hematopoietic cells do not engage in glucose-dependent anabolic synthesis and neither express Hif-1alpha mRNA nor require HIF-1alpha protein to regulate cell survival in response to hypoxia. However, HIF-1alpha is adaptive for the survival of growth factor-stimulated cells, as suppression of HIF-1alpha results in death when growing cells are exposed to hypoxia. Growth factor-dependent HIF-1alpha expression reprograms the intracellular fate of glucose, resulting in decreased glucose-dependent anabolic synthesis and increased lactate production, an effect that is enhanced when HIF-1alpha protein is stabilized by hypoxia. Together, these data suggest that HIF-1alpha contributes to the regulation of growth factor-stimulated glucose metabolism even in the absence of hypoxia.
Association between single nucleotide polymorphisms in deoxycytidine kinase and treatment response among acute myeloid leukaemia patients (2004)

Development of resistance to 1-beta-arabinofuranosylcytosine (AraC) is a major obstacle in the treatment of patients with acute myeloid leukaemia (AML). Deficiency of functional deoxycytidine kinase (dCK) plays an important role in AraC resistance in vitro. We screened 5378 bp sequences of the dCK gene, including all exons and the 5' flanking region, and identified two single nucleotide polymorphisms (SNPs) in the regulatory region (rSNPs) with high allele frequencies. These two rSNPs (-201C>T and -360C>G) formed two major haplotypes. Genotyping with sequencing and MassARRAY system among 122 AML patients showed that those with -360CG/-201CT and -360GG/-201TT compound genotypes (n = 41) displayed a favourable response to chemotherapy whereas those with -360CC/-201CC (n = 81) tended to have a poor response (P = 0.025). Moreover, real-time quantitative reverse transcriptase-polymerase chain reaction showed that patients with -360CG/-201CT and -360GG/-201TT genotypes expressed higher level of dCK mRNA compared to those with the -360CC/-201CC genotype (P = 0.0034). Luciferase-reporter assay showed that dCK 5' regulatory region bearing -360G/-201T genotype alone had an eight-fold greater transcriptional activation activity compared to that with -360C/-201C genotype, whereas co-transfection of both -360G/-201T and -360C/-201C constructs mimicked the heterozygous genotype, which exhibited a four-fold greater activity compared to that with -360C/-201C. These results indicate that rSNP haplotypes of dCK gene may serve as a genetic marker for predicting drug responsiveness, which will be beneficial in establishing more effective AML chemotherapeutic regimens.