gebhart/patrepeval huggingface dataset:
Optimising Bacterial DNA Extraction from Faecal Samples: Comparison of Three Methods (2011)

Culture independent methods are used widely in diagnostic laboratories for infectious disease Isolation of genomic DNA from clinical samples is the first and important step in the procedure. Several procedures for extracting DNA from faecal samples have been described, including different mechanical cell disruptors. To our knowledge, the use of TissueLyser as a mechanical disruptor on faecal samples before DNA extraction has not been previously described. The purpose of the study was to implement a method for preparing faecal samples for optimal DNA extraction. Thus, three different procedures for extracting DNA from human faeces were compared. This was done either by using the mechanical disrupter by Mini BeadBeater 8, or the TissueLyser both followed by DNA purification using QIAamp DNA stool MiniKit, in comparison with DNA extractions using QIAamp DNA stool MiniKit without any prior mechanical disruption, according to manufacturer's instructions. The obtained DNA from the three procedures was analysed by DGGE, and the number of bands was compared between each procedure. There was no significant difference between the numbers of bacterial bands obtained from DGGE when using a TissueLyser or Mini BeadBeater 8, so the two different mechanical cell disruptors can be used comparably when isolating bacterial DNA from faecal samples. The QIAamp DNA stool MiniKit alone resulted in a reduced number of bands compared to the two mechanical disruption methods.
TERATOGENIC COMPOUNDS OF VERATRUM CALIFORNICUM (DURAND): I. PREPARATION AND CHARACTERIZATION OF FRACTIONS AND ALKALOIDS FOR BIOLOGIC TESTING (1966)

The isolation and identification of four known alkaloids (jervine, veratrosine, pseudojervine, and isorubijervine) was achieved from teratogenic fractions of Veratrum californicum. Two additional alkaloids, not previously reported and herein designated alkaloids X and V, were also isolated from these fractions and partially characterized.
Imidazole acetol phosphate aminotransferase in Zymomonas mobilis: molecular genetic, biochemical, and evolutionary analyses (1995)

hisH encodes imidazole acetol phosphate (IAP) aminotransferase in Zymomonas mobilis and is located immediately upstream of tyrC, a gene which codes for cyclohexadienyl dehydrogenase. A plasmid containing hisH was able to complement an Escherichia coli histidine auxotroph which lacked the homologous aminotransferase. DNA sequencing of hisH revealed an open reading frame of 1,110 bp, encoding a protein of 40,631 Da. The cloned hisH product was purified from E. coli and estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis to have a molecular mass of 40,000 Da. Since the native enzyme had a molecular mass of 85,000 Da as determined by gel filtration, the active enzyme species must be a homodimer. The purified enzyme was able to transaminate aromatic amino acids and histidine in addition to histidinol phosphate. The existence of a single protein having broad substrate specificity was consistent with the constant ratio of activities obtained with different substrates following a variety of physical treatments (such as freeze-thaw, temperature inactivation, and manipulation of pyridoxal 5'-phosphate content). The purified enzyme did not require addition of pyridoxal 5'-phosphate, but dependence upon this cofactor was demonstrated following resolution of the enzyme and cofactor by hydroxylamine treatment. Kinetic data showed the classic ping-pong mechanism expected for aminotransferases. Km values of 0.17, 3.39, and 43.48 mM for histidinol phosphate, tyrosine, and phenylalanine were obtained. The gene structure around hisH-tyrC suggested an operon organization. The hisH-tyrC cluster in Z. mobilis is reminiscent of the hisH-tyrA component of a complex operon in Bacillus subtilis, which includes the tryptophan operon and aroE. Multiple alignment of all aminotransferase sequences available in the database showed that within the class I superfamily of aminotransferases, IAP aminotransferases (family I beta) are closer to the I gamma family (e.g., rat tyrosine aminotransferase) than to the I alpha family (e.g., rat aspartate aminotransferase or E. coli AspC). Signature motifs which distinguish the IAP aminotransferase family were identified in the region of the active-site lysine and in the region of the interdomain interface.
Foliar nutrients and induced susceptibility: genetic mechanisms of Douglas-fir resistance to western spruce budworm defoliation (2004)

We conducted greenhouse defoliation experiments with clones of interior Douglas-fir (Pseudotsuga menziesii var. glauca (Beissn.) Franco) over 3 years to assess the role of foliar nutrients as a resistance mechanism to western spruce budworm (Choristoneura occidentalis Freeman) defoliation. The grafted clones were derived from mature trees (i.e., ortets) that showed resistance or susceptibility to budworm defoliation in the forest. Current-year foliage was analyzed for concentrations of nitrogen (N), sugars (sucrose + fructose + glucose), phosphorus (P), potassium (K), magnesium (Mg), calcium (Ca), manganese (Mn), copper (Cu), iron (Fe), and zinc (Zn). We computed rank correlations between foliar nutrient levels in the ortets and their corresponding clones to test the null hypothesis that foliar chemistry does not have a genetic basis (H 0 1). Foliar concentrations of sugars and P were under genetic control to some degree, but concentrations of other nutrients were not. We used analysis of variance to test the null hypotheses that foliar chemistry does not change in response to budworm defoliation (H 0 2) and that it is not different between resistant and susceptible clones (H 0 3). We rejected H 0 2 for sugars, P, K, Mn, and Zn; defoliation by the budworm changed levels of these nutrients and had divergent effects on concentrations of P, K, and Zn in resistant clones. We concluded that induced susceptibility, whereby defoliation alters foliar nutrients to make trees more favorable for insect feeding, appears to be an important determinant of Douglas-fir resistance to the western spruce budworm. Failure to reject H 0 3 implies that previously reported differences between the foliar nutrient levels in resistant Douglas-firs and those in susceptible Douglas-firs in the forest are probably caused by induced susceptibility.
Genome-Level Longitudinal Expression of Signaling Pathways and Gene Networks in Pediatric Septic Shock (2007)

We have conducted longitudinal studies focused on the expression profiles of signaling pathways and gene networks in children with septic shock. Genome-level expression profiles were generated from whole blood-derived RNA of children with septic shock (n=30) corresponding to day one and day three of septic shock, respectively. Based on sequential statistical and expression filters, day one and day three of septic shock were characterized by differential regulation of 2,142 and 2,504 gene probes, respectively, relative to controls (n=15). Venn analysis demonstrated 239 unique genes in the day one dataset, 598 unique genes in the day three dataset, and 1,906 genes common to both datasets. Functional analyses demonstrated time-dependent, differential regulation of genes involved in multiple signaling pathways and gene networks primarily related to immunity and inflammation. Notably, multiple and distinct gene networks involving T cell- and MHC antigen-related biology were persistently downregulated on both day one and day three. Further analyses demonstrated large scale, persistent downregulation of genes corresponding to functional annotations related to zinc homeostasis. These data represent the largest reported cohort of patients with septic shock subjected to longitudinal genome-level expression profiling. The data further advance our genome-level understanding of pediatric septic shock and support novel hypotheses.
An In Vivo/In Vitro Study of Allyl Alcohol Toxicity Using Enzyme Inhibitors (1993)

The aim of this study was to verify an in vitro model of hepatotoxicity, designed to assess the production of reactive species from biologically-inert chemicals through their metabolic transformation. One example is allyl alcohol, which produces acrolein through the action of the enzyme alcohol dehydrogenase. Acrolein is a highly hepatotoxic aldehyde which is detoxified to acrylic acid by aldehyde dehydrogenase (ALDH). A deficiency of this enzyme, common in some Asian populations, can give rise to pathological conditions of hepatotoxicity. Isolated rat hepatocytes were incubated with allyl alcohol with and without cyanamide, a known inhibitor of ALDH. The toxicity of allyl alcohol, assessed on the basis of release of glutamic-oxaloacetic transaminase (GOT), glutamic-pyruvic transaminase (GPT) and lactate dehydrogenase (LDH) into the culture medium, was dramatically increased by the addition of cyanamide. In vivo, the same treatment scheme was used in rats treated with allyl alcohol with or without cyanamide pretreatment. It was also demonstrated that allyl alcohol toxicity is dramatically enhanced by the addition of an aldehyde dehydrogenase inhibitor, as shown by plasma levels of hepatic enzymes (GOT, GPT and LDH) and by histological findings. We believe that this in vitro model, involving the use of enzyme inhibitors, could be useful for verification of the hypothesis that hepatotoxins, such as acrolein, are produced from some pharmaceutical and other chemical compounds.
3,3′‐Diiodo‐BINOL‐Fused Maleimides as Chiral Hypervalent Iodine(III) Organocatalysts (2013)

Abstract Original and readily available 3,3′‐diiodo‐BINOL‐fused maleimides were designed as hypervalent iodine(III) organocatalysts. They were used in intermolecular oxidation reactions at the α‐position of ketones. The expected products were obtained with yields and enantiomeric excesses that were comparable to the best reported values achieved using structurally different organocatalysts.
Cancer Biomarkers Defined by Autoantibody Signatures to Aberrant O-Glycopeptide Epitopes (2010)

Autoantibodies to cancer antigens hold promise as biomarkers for early detection of cancer. Proteins that are aberrantly processed in cancer cells are likely to present autoantibody targets. The extracellular mucin MUC1 is overexpressed and aberrantly glycosylated in many cancers; thus, we evaluated whether autoantibodies generated to aberrant O-glycoforms of MUC1 might serve as sensitive diagnostic biomarkers for cancer. Using an antibody-based glycoprofiling ELISA assay, we documented that aberrant truncated glycoforms were not detected in sera of cancer patients. An O-glycopeptide microarray was developed that detected IgG antibodies to aberrant O-glycopeptide epitopes in patients vaccinated with a keyhole limpet hemocyanin-conjugated truncated MUC1 peptide. We detected cancer-associated IgG autoantibodies in sera from breast, ovarian, and prostate cancer patients against different aberrent O-glycopeptide epitopes derived from MUC1. These autoantibodies represent a previously unaddressed source of sensitive biomarkers for early detection of cancer. The methods we have developed for chemoenzymatic synthesis of O-glycopeptides on microarrays may allow for broader mining of the entire cancer O-glycopeptidome.
Tetraethylammonium Derivatives (1981)

Derivatives of tetraethylammonium ion (TEA+) were synthesized in which one ethyl group was replaced by a C6, C8, C10, C12, C14, or C16 side chain. These TEA+ derivatives were tested for duration of sensory block of the rat infraorbital (trigeminal) nerve. The duration of sensory anesthesia increased exponentially from 1.2 hours to 388 hours as chain length increased from C2-C12, while C12, C14, and C16 all produced a similar reversible block of 17--20 days. The block duration of C12 was correlated with C12 bound to the infraorbital nerve; C12 not bound by the nerve was quantitatively excreted by the kidneys. These data, along with the lack of observable microscopic toxicity, suggests that TEA+ derivatives may be a useful new class of ultralong-acting local anesthetics.
Retinal oxygen tension and the electroretinogram during arterial occlusion in the cat. (1995)

Ventilation with 100% O2 during occlusion increased the PO2 across most of the retina and partially restored the LERG b-wave, but the tissue near the vitreous was still sometimes anoxic. The illumination status seemed to make little difference. Inspiration of elevated O2 might be beneficial in treating retinal vascular occlusive disease, although it alone cannot completely maintain retinal function.
Functional Studies on the p10 Gene of Autographa californica Nuclear Polyhedrosis Virus Using a Recombinant Expressing a p10-beta-Galactosidase Fusion Gene (1988)

The beta-galactosidase gene (lacZ) of Escherichia coli was inserted in phase with the coding sequence of the Autographa californica nuclear polyhedrosis virus (AcMNPV) late-expressed Mr 10,000 (p10) gene. The fusion gene was inserted into the AcMNPV genome by cotransfection of a recombinant plasmid pAcR159Z, consisting of the EcoRI P fragment-containing pBR325-derived plasmid pAcR159 and the lacZ insert in the p10 gene, and wild-type AcMNPVDNA. Infection of Spodoptera frugiperda cells by the resulting recombinant AcMNPV/p10Z-2 showed high level expression of a p10-lacZ fusion protein, but no synthesis of p10. Therefore, the p10 gene is dispensable for virus replication and the p10 promoter is effective in driving the expression of foreign genes. Cells infected with AcMNPV/p10Z recombinants resembled those infected with wild-type AcMNPV in the amounts of polyhedrin synthesized and polyhedra formed, although p10 was absent. The nucleus and cytoplasm of AcMNPV/p10Z-2-infected cells lacked the fibrous structures that are associated with p10 in wild-type AcMNPV-infected cells. Instead, large granular structures were observed that were found by immunogold labelling to contain the lacZ gene product. The electron-dense 'spacers', thought to be precursors of the polyhedron membrane, were absent from cells infected by the recombinant virus and the polyhedra did not have a membrane. The recombinant AcMNPV/p10Z-2 was at least twice as virulent for second instar S. exigua larvae than was wild-type AcMNPV. The increased virulence of the recombinant is an important property for the control of insects.
Binding of lipopeptide to CD14 induces physical proximity of CD14, TLR2 and TLR1 (2005)

Lipoproteins or lipopeptides (LP) are bacterial cell wall components detected by the innate immune system. For LP, it has been shown that TLR2 is the essential receptor in cellular activation. However, molecular mechanisms of LP recognition are not yet clear. We used a FLAG-labeled derivative of the synthetic lipopeptide N-palmitoyl-S-[2,3-bis(palmitoyloxy)-(2R,S)-propyl]-(R)-cysteinyl-seryl-(lysyl)(3)-lysine (Pam(3)CSK(4)) to study the roles of CD14, TLR2 and TLR1 in binding and signaling of LP and their molecular interactions in human cells. The activity of Pam(3)CSK(4)-FLAG was TLR2 dependent, whereas the binding was enabled by CD14, as evaluated by flow cytometry and confocal microscopy. Using FRET and FRAP imaging techniques to study molecular associations, we could show that after Pam(3)CSK(4)-FLAG binding, CD14 and Pam(3)CSK(4)-FLAG associate with TLR2 and TLR1, and TLR2 is targeted to a low-mobility complex. Thus, LP binding to CD14 is the first step in the LP recognition, inducing physical proximity of CD14 and LP with TLR2/TLR1 and formation of the TLR2 signaling complex.
OR Practice—A Scenario Approach to Capacity Planning (1989)

Production capacity has always been one of the most important strategic variables for the major automobile companies. Decisions by individual companies concerning the overall level of capacity, the type of facility (e.g., the level of flexibility), and the location of that capacity (e.g., in the United States or abroad) are discussed in great detail in the popular business press. In this paper, we describe a model developed for General Motors to aid in making decisions about capacity for four of their auto lines. The model incorporates elements of scenario planning, integer programming, and risk analysis. All the input and output is done using Lotus 1-2-3. Although the presentation is motivated by the particular application in the auto industry, the model represents a general purpose approach that is applicable to a wide variety of decisions under risk. An example in this paper uses actual data, appropriately transformed to ensure confidentiality.
Effective Production of Glycosyl-steviosides byα-1,6 Transglucosylation of Dextrin Dextranase (1994)

Dextrin dextranase (EC 2.4.1.2; DDase), which is produced by Acetobacter capsulatus ATCC 11894, acted on a mixture of stevioside and starch hydrolysate with isoamylase, so that the enzyme was found to convert stevioside to predominantly mono-glucosyl-stevioside (SG1) and di-glucosyl-stevioside (SG2), and little of the stevioside initially added remained. SG1 was separated into two compounds (SG1a and SG1b) by reversed-phase high-pressure liquid chromatography. The structures of SG1a, SG1b, and SG2 were analyzed and concluded to be 13-O-(6-alpha-glucosyl-2-beta-glucosyl-beta-glucosyl)-19-O-beta-glucosyl -steviol, 13-O-[(6-alpha-glucosyl)(2-beta-glucosyl)-beta-glucosyl]-19-O- glucosyl-steviol, and 13-O-[(6-alpha-glucosyl)(6-alpha-glucosyl-2-beta- glucosyl)-beta-glucosyl]-19-O-beta-glucosyl-steviol, respectively. During the reaction for production of glycosyl-steviosides, DDase catalyzes transglucosylations from glucosyl donor compounds to stevioside to be SG1a and SG1b, and to SG1b to be SG2 rapidly forming alpha-1,6 glucosidic linkages. However transglucosylation to SG1a to be SG2 rarely occurred, and the conversions among stevioside and these glycosyl-steviosides were catalyzed by the action of DDase to transfer alpha-1,6 linked glucosyl residues, forming alpha-1,6 linkages.
Addition of Sodium Bicarbonate to Lidocaine Decreases the Duration of Peripheral Nerve Block in the Rat (2000)

With 1% commercial lidocaine without epinephrine, sodium bicarbonate decreases the degree and duration of block. However, in solutions with epinephrine, sodium bicarbonate hastens onset, without effecting degree or duration.
Regulation of the Rapamycin and FKBP-Target 1/Mammalian Target of Rapamycin and Cap-dependent Initiation of Translation by the c-Abl Protein-tyrosine Kinase (2000)

The c-Abl protein-tyrosine kinase is activated by ionizing radiation and certain other DNA-damaging agents. The rapamycin and FKBP-target 1 (RAFT1), also known as FKBP12-rapamycin-associated protein (FRAP, mTOR), regulates the p70S6 kinase (p70(S6k)) and the eukaryotic initiation factor 4E (eIF4E)-binding protein 1 (4E-BP1). The present results demonstrate that c-Abl binds directly to RAFT1 and phosphorylates RAFT1 in vitro and in vivo. c-Abl inhibits autophosphorylation of RAFT1 and RAFT1-mediated phosphorylation p70(S6k). The functional significance of the c-Abl-RAFT1 interaction is further supported by the finding that eIF4E-dependent translation in mouse embryo fibroblasts from Abl(-/-) mice is significantly higher than that compared in wild-type cells. The results also demonstrate that exposure of cells to ionizing radiation is associated with c-Abl-mediated binding of 4E-BP1 to eIF4E and inhibition of translation. These findings with the c-Abl tyrosine kinase represent the first demonstration of a negative physiologic regulator of RAFT1-mediated 5' cap-dependent translation.
Development of Self-Setting Calcium Phosphate Cements (1991)

This paper reviews recent studies on self-setting calcium phosphate cements (CPC). Discussions are focused on the cement setting reactions, the products formed, the effects of the products on properties of the cement, and in vivo characteristics of CPC. Although cementation can occur in systems based on several different mixtures, data in the literature at present indicate that mixtures of tetracalcium phosphate and dicalcium phosphate (or dicalcium phosphate dihydrate) may be most desirable because they produce cements that have greater strengths and contain nearly pure hydroxyapatite. The strengths of CPC are considerably lower than ceramic calcium phosphate biomaterial and are also lower than some of the dental cements. On the other hand, the combination of self-setting capability and high biocompatibility makes CPC a unique biomaterial. Near perfect adaptation of the cement to the tissue surfaces in a defect, and an optimum resorption rate followed by new bone formation are some of the distinctive advantages of CPC. In its present state CPC appears to be suitable for a number of applications. Much remains to be done to further improve its properties to meet the requirements for different applications.
Anti-invasive, antitumorigenic, and antimetastatic activities of the PHSCN sequence in prostate carcinoma. (2000)

Using naturally serum-free SU-ECM basement membranes as invasion substrates showed that plasma fibronectin was necessary to stimulate invasion by DU 145 human and metastatic MATLyLu (MLL) rat prostate carcinoma cells. This activity mapped to the PHSRN sequence, which induced invasion through alpha5beta1 integrin. PHSCN, a competitive inhibitor, blocked both PHSRN- and serum-induced invasion. Acetylated, amidated PHSCN (Ac-PHSCN-NH2) was 30-fold more potent; however, Ac-HSPNC-NH2 was inactive. Rats receiving injections s.c. with 100,000 MLL cells were treated systemically by i.v. injection three times weekly with 1 mg of either Ac-PHSCN-NH2 or Ac-HSPNC-NH2 beginning 24 h later, three times weekly with 1 mg of Ac-PHSCN-NH2 beginning only after surgery to remove large (2 cm) MLL tumors, or were left untreated. MLL tumors grew rapidly in Ac-HSPNC-NH2-treated and in untreated rats. MLL tumor growth in rats treated with Ac-PHSCN-NH2 beginning 1 day after MLL cell injection was reduced by 99.9% during the first 16 days of treatment, although subsequent tumor growth occurred. MLL tumor cryosections immunostained with anti-PECAM-1 showed that Ac-PHSCN-NH2 inhibited neovascularization by 12-fold during this time. Whether initiated after MLL cell injection or only after MLL tumor removal, Ac-PHSCN-NH2 treatment reduced the numbers of MLL lung colonies and micrometastases by 40- to >100-fold, whereas Ac-HSPNC-NH2 was inactive. Thus, Ac-PHSCN-NH2 may be a potent antitumorigenic and antimetastatic agent for postsurgical use prior to extensive metastasis.
Role of Navigation in Total Hip Arthroplasty (2009)

Current uses of computed tomography-based and imageless navigation systems for total hip arthroplasty include proper placement of the acetabular component, measurement of limb-length changes, enablement of minimally invasive surgery, and proper placement of components for hip resurfacing procedures. This article provides an overview of the rationale for computer-assisted surgery in total hip arthroplasty and hip resurfacing. The experience of the senior author (M.L.S.) with computer-assisted surgery for hip arthroplasty has demonstrated improved position of the acetabular component as compared with the position attainable with use of mechanical instruments, maintenance of appropriate position of the acetabular component during minimally invasive surgery, and appropriate positioning of the femoral and acetabular components during the learning curve for hip resurfacing procedures.
Synthesis of fagaronine (1988)

Alkaloids fagaronine ( I ), dihydrofagaronine ( XXV ) and oxyfagaronine ( XXVI ) were synthesized from 2,3-dihydroxynaphthalene ( II ) and 2-bromo-4,5-dimethoxybenzaldehyde ( XI ), the key synthetic steps being the preparation of 2-hydroxy-3-methoxy-5-nitronaphthalene ( VI ) by partial methylation of 2,3-dihydroxy-5-nitronaphthalene ( V ) and formation of benzo[ c ]phenanthridone XXI by photocyclization of amide XVI .