gebhart/patrepeval huggingface dataset:
The BANYULS gene encodes a DFR‐like protein and is a marker of early seed coat development (1999)

Mutations in the BANYULS (BAN) gene lead to precocious accumulation of anthocyanins in immature seed coat in Arabidopsis. The ban -1 allele has been isolated from a collection of T-DNA transformants and found to be tagged by the integrative molecule. The sequencing of wild-type and two independent mutant alleles confirmed the identity of the gene. Analysis of the full-length cDNA sequence revealed an open reading frame encoding a 342 amino acid protein which shared strong similarities with DFR and other enzymes of the phenylpropanoid biosynthesis pathway. BAN expression was restricted to the endothelium of immature seeds at the pre-globular to early globular stages of development as predicted from the maternal inheritance of the phenotype, and therefore represents a marker for early differentiation and development of the seed coat. BAN is probably involved in a metabolic channelling between the production of anthocyanins and pro-anthocyanidins in the seed coat.
Dynamics of Coalescence of Plugs with a Hydrophilic Wetting Layer Induced by Flow in a Microfluidic Chemistrode (2009)

This manuscript analyzes the dynamics of coalescence of an incoming aqueous plug with a wetting layer above a hydrophilic surface in the chemistrode. The chemistrode is a recently described (Chen, D.; Du, W.; Liu, Y.; Liu, W.; Kuznetsov, A.; Mendez, F. E.; Philipson, L. H.; Ismagilov, R. F. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 16843-16848) microfluidic analogue of an electrode, but operating at the chemical rather than electrical level, developed with the aim of capturing local stimulus-response processes in chemistry and biology. The chemistrode consists of open-ended V-shaped microfluidic channels that can be brought into contact with a chemical or biological hydrophilic substrate. The chemistrode relies on multiphase aqueous/fluorous flow and uses plugs to achieve high temporal resolution of stimulation and sampling. Coalescence of the incoming plugs, containing the stimuli, with the liquid in the wetting layer is required for chemical exchange to take place in the chemistrode. Here, we investigate the system with triethyleneglycol mono[1H,1H-perfluorooctyl]ether RfOEG as the surfactant. This surfactant was necessary to prevent nonspecific absorption of proteins to the aqueous fluorous interface and to ensure biocompatibility of the system, but too much surfactant increased the barrier for coalescence. In this system, coalescence was controlled by the capillary number. At a higher value of the capillary number, coalescence took more time, and deformation of the interface of the incoming plug and the wetting layer was more significant. Above a critical capillary number, coalescence did not occur between the incoming plug and the wetting layer. The critical capillary number was an increasing function of surface tension but was independent of viscosity ratio. Coalescence was surprisingly reproducible, presumably because film rupture during coalescence was reliably initiated at the hydrophilic substrate. These results are useful in rational operation of the chemistrode and also provide an experimental description of deformation, film drainage, and coalescence of surfactant-coated droplets in an external flow field.
Engineering Escherichia coli for efficient conversion of glucose to pyruvate (2004)

Escherichia coli TC44, a derivative of W3110, was engineered for the production of pyruvate from glucose by combining mutations to minimize ATP yield, cell growth, and CO2 production (DeltaatpFH DeltaadhE DeltasucA) with mutations that eliminate acetate production [poxB::FRT (FLP recognition target) DeltaackA] and fermentation products (DeltafocA-pflB DeltafrdBC DeltaldhA DeltaadhE). In mineral salts medium containing glucose as the sole carbon source, strain TC44(DeltafocA-pflB DeltafrdBC DeltaldhA DeltaatpFH DeltaadhE DeltasucA poxB::FRT DeltaackA) converted glucose to pyruvate with a yield of 0.75 g of pyruvate per g of glucose (77.9% of theoretical yield; 1.2 g of pyruvate liters(-1).h(-1)). A maximum of 749 mM pyruvate was produced with excess glucose. Glycolytic flux was >50% faster for TC44 producing pyruvate than for the wild-type W3110 during fully aerobic metabolism. The tolerance of E. coli to such drastic changes in metabolic flow and energy production implies considerable elasticity in permitted pool sizes for key metabolic intermediates such as pyruvate and acetyl-CoA. In strain TC44, pyruvate yield, pyruvate titer, and the rate of pyruvate production in mineral salts medium were equivalent or better than previously reported for other biocatalysts (yeast and bacteria) requiring complex vitamin feeding strategies and complex nutrients. TC44 offers the potential to improve the economics of pyruvate production by reducing the costs of materials, product purification, and waste disposal.
Detection of HCV RNA by the asymmetric gap ligase chain reaction. (1994)

The ligase chain reaction (LCR) and the gap ligase chain reaction (gLCR) are exponential amplification techniques for the detection of DNA sequences in a sample. Both techniques depend on the enzyme, DNA ligase, to join adjacent probes annealed to a DNA molecule. However, DNA ligase joins DNA inefficiency on an RNA target. Consequently, LCR and gLCR cannot amplify RNA efficiency. RNA detection methods using LCR or gLCR require a cDNA synthesis step. The carryover of four dNTPs from the cDNA reaction inhibits gLCR. Although LCR can use cDNA reaction products directly, background generated by blunt-end ligation does not allow the high sensitivity typically needed for HIV or HCV detection. The asymmetric gap ligase chain reaction (AGLCR) is a modification of gLCR that allows for the detection of RNA by using < or = 3 of the 4 nucleotides in the cDNA step and the gLCR step. Fewer than 50 copies of synthetic RNA transcript can be reproducibly detected. HCV, an RNA virus with no DNA intermediate, was chosen as the initial RNA model system. HCV antibody-positive and normal samples were analyzed, and the results were found to correlate with the results obtained using nested RNA-PCR. AGLCR provides a new nucleic acid amplification technique that can aid in the diagnosis of disease when the detection of RNA is critical.
γ-Tocopherol Is Metabolized Faster than α-Tocopherol in Young Japanese Women (2018)

To elucidate the characteristics of γ-tocopherol metabolism, serum concentrations of α- and γ-tocopherol, and urinary excretion of their metabolites after ingestion of α- or γ-tocopherol, major isoforms in our diet, were compared. Six healthy Japanese women (age 22.7±1.7 y old, BMI 21.4±0.9) ingested 134 mg of α- or γ-tocopherol, and blood and urine were collected until 72 h later. After α-tocopherol intake, the serum concentration of α-tocopherol increased at 12-24 h, and urinary excretion of 2,5,7,8-tetramethyl-2(2'-carboxyethyl)-6-hydroxychroman (α-CEHC), an α-tocopherol metabolite, increased at 12-36 h. However, after γ-tocopherol intake, the serum concentration of γ-tocopherol increased at 6-12 h, and excretion of 2,7,8-trimethyl-2(2'-carboxyethyl)-6-hydroxychroman (γ-CEHC), a γ-tocopherol metabolite, increased at 3-12 h. The area under the curve from 0 to 72 h and serum maximal concentration of γ-tocopherol were lower than those of α-tocopherol. The time to maximal concentration of γ-tocopherol was faster than that of α-tocopherol. The ratio of urinary excretion of carboxyethyl-hydroxychroman to tocopherol intake was 2.9% for α-CEHC and 7.7% for γ-CEHC. These results revealed that γ-tocopherol is metabolized faster than α-tocopherol in healthy young women.
Sterility, mechanical properties, and molecular stability of polylactide internal-fixation devices treated with low-temperature plasmas (1996)

The effect of low-temperature plasma on sterility, molecular, mechanical, and crystalline properties of poly (L-lactide), poly (L/D-lactide) and poly (L/DL-lactide) was investigated. Polymers were treated for 15 and 30 min at 100 W with nitrogen, argon, oxygen, and carbon dioxide plasma. All polymers treated with oxygen or carbon dioxide plasma were rendered sterile after 15 min of treatment. Only 70% of the samples treated under similar conditions with nitrogen or argon plasma were sterile. Extension of the exposure time to 30 min and increasing power to 200 W did not improve sterilization efficiency. Plasma sterilization, under the conditions used, caused no significant decrease or increase in overall molecular weight or polydispersity of the polylactides used. In most instances the effect of plasma sterilization was to slightly increase the overall molecular weight of the polymers studied. Treatment with argon plasma led to a more consistent increase in molecular weight than did treatment with nitrogen, oxygen, or carbon dioxide. Analysis of the surface (skin) of a poly(L-lactide) injection-molded rod following plasma sterilization indicated an increase in molecular weight as related to the interior (core) of the rod. Comparison of Mark-Houwink plots for the surface and interior of poly(L-lactide) injection-molded rods following plasma sterilization indicated an increase in chain branching for the surface relative to the interior of the rod. Generally the highly crystalline poly(L-lactide) was less susceptible to change upon plasma treatment than was the less crystalline poly(L/D-lactide) and poly(L/DL-lactide). The mechanical properties (shear strength, bending strength, and moduli) of the polylactides were not affected by plasma treatment. The overall melting temperature and the heat of melting of polylactides studied were not affected by plasma treatment. The melting temperature of the skin of the samples was about 1 degree C higher than the melting temperature of the core due to the chain orientation upon injection-molding. Plasma treatment of the polylactides reduced the melting temperature of the skin by 3 degrees C to 5 degrees C due to the crosslinking or branching at the surface layer.
Chlamydia pneumoniae sp. nov. for Chlamydia sp. Strain TWAR (1989)

A third species, Chlamydia pneumoniae, is proposed for the genus Chlamydia. This bacterium is a human respiratory pathogen, which has been referred to as the TWAR strain of Chlamydia. Species identification is based on ultrastructural differences in the elementary bodies, deoxyribonucleic acid analysis, and serology.
<title>Automated video surveillance: teaching an old dog new tricks</title> (1993)

The automated video surveillance market is booming with new players, new systems, new hardware and software, and an extended range of applications. This paper reviews available technology, and describes the features required for a good automated surveillance system. Both hardware and software are discussed. An overview of typical applications is also given. A shift towards PC-based hybrid systems, use of parallel processing, neural networks, and exploitation of modern telecomms are introduced, highlighting the evolution modern video surveillance systems.
Contrast Agents and Applications to Assess Tumor Angiogenesis In Vivo by Magnetic Resonance Imaging (2006)

Angiogenesis plays a key role in the development of cancer and is precondition for tumor growth, invasion and spread. Therefore, numerous angiogenesis inhibitors have been developed, of which some show potential to defeat cancer in preclinical and clinical trials. However, response to antiangiogenic treatments is often delayed and marked by high interindividual variability making a closely mashed and efficient observation of the patient necessary. Therefore, surrogate markers which specifically catch early response to tumor therapy are highly desirable. Functional parameters like relative blood volume, perfusion and vessel permeability can be assessed using T1 and T2*-weighted dynamic contrast-enhanced (DCE) MRI. Various reports are available on this topic but results are controversial. During antiangiogenic therapies some authors describe pronounced changes in blood volume: others find effects only on vessel permeability or perfusion. These conflictive observations can be attributed to the different tumor models, therapies, measurement techniques and contrast agents (CA). Particularly the choice of the optimal CA is considered to be essential for a successful characterization of tumor angiogenesis. Often therapy effects on vessel permeability only become apparent, when blood pool CA are used. This article reviews the current state of DCE and molecular MRI of angiogenesis. Besides a general introduction of the different measurement and postprocessing methods and its previous applications, design, structure and use of different types of CA are the main focus of this article. Keywords: MRI, angiogenesis, contrast agent, gadolinium-chelate, blood pool, albumin, dendrimer
The protein coded by the PP2216 gene ofPseudomonas putidaKT2440 is an acyl-CoA dehydrogenase that oxidises only short-chain aliphatic substrates (2005)

A gene (PP2216) that codes for an acyl-CoA dehydrogenase was cloned from Pseudomonas putida strain KT2240 and over-expressed in Escherichia coli, and the recombinant enzyme purified and characterised. The enzyme is tetrameric with one FAD per subunit of molecular mass 40,500 Da. An anaerobic titration with sodium dithionite showed that the enzyme accepts two electrons. A similar titration with butyryl-CoA showed that reduction by this substrate was incomplete with 4.5 mol butyryl-CoA added per mol enzyme FAD; the equilibrium was used to calculate that the oxidation-reduction potential of the enzyme at pH 7 and 25 degrees C is 5+/-5 mV versus the standard hydrogen electrode. The enzyme shows catalytic activity with butyryl-CoA, valeryl-CoA and hexanoyl-CoA, and very low activity with heptanoyl-CoA and octanoyl-CoA; it fails to oxidise propionyl-CoA. These properties resemble those of short-chain acyl-CoA dehydrogenases from other sources. The enzyme is inactive with the CoA derivatives of all phenylalkanoates that were tested (side chains 3-8 carbon atoms) indicating that in contrast to an earlier suggestion, the enzyme is not involved in the beta-oxidation of aromatic compounds.
Toll-like Receptor 4 Is Expressed on Intestinal Stem Cells and Regulates Their Proliferation and Apoptosis via the p53 Up-regulated Modulator of Apoptosis (2012)

Factors regulating the proliferation and apoptosis of intestinal stem cells (ISCs) remain incompletely understood. Because ISCs exist among microbial ligands, immune receptors such as toll-like receptor 4 (TLR4) could play a role. We now hypothesize that ISCs express TLR4 and that the activation of TLR4 directly on the intestinal stem cells regulates their ability to proliferate or to undergo apoptosis. Using flow cytometry and fluorescent in situ hybridization for the intestinal stem cell marker Lgr5, we demonstrate that TLR4 is expressed on the Lgr5-positive intestinal stem cells. TLR4 activation reduced proliferation and increased apoptosis in ISCs both in vivo and in ISC organoids, a finding not observed in mice lacking TLR4 in the Lgr5-positive ISCs, confirming the in vivo significance of this effect. To define molecular mechanisms involved, TLR4 inhibited ISC proliferation and increased apoptosis via the p53-up-regulated modulator of apoptosis (PUMA), as TLR4 did not affect crypt proliferation or apoptosis in organoids or mice lacking PUMA. In vivo effects of TLR4 on ISCs required TIR-domain-containing adapter-inducing interferon-β (TRIF) but were independent of myeloid-differentiation primary response-gene 88 (MYD88) and TNFα. Physiological relevance was suggested, as TLR4 activation in necrotizing enterocolitis led to reduced proliferation and increased apoptosis of the intestinal crypts in a manner that could be reversed by inhibition of PUMA, both globally or restricted to the intestinal epithelium. These findings illustrate that TLR4 is expressed on ISCs where it regulates their proliferation and apoptosis through activation of PUMA and that TLR4 regulation of ISCs contributes to the pathogenesis of necrotizing enterocolitis.
Mapping of the Active Site of Recombinant Human Erythropoietin (1997)

Recombinant human erythropoietin (rHuEPO) variants have been constructed to identify amino acid residues important for biological activity. Immunoassays were used to determine the effect of each mutation on rHuEPO folding. With this strategy, we could distinguish between mutations that affected bioactivity directly and those that affected bioactivity because the mutation altered rHuEPO conformation. Four regions were found to be important for bioactivity: amino acids 11 to 15, 44 to 51, 100 to 108, and 147 to 151. EPO variants could be divided into two groups according to the differential effects on EPO receptor binding activity and in vitro biologic activity. This suggests that rHuEPO has two separate receptor binding sites. Mutations in basic residues reduced the biologic activity, whereas mutations in acidic residues did not. This suggests that electrostatic interactions between rHuEPO and the human EPO receptor may involve positive charges on rHuEPO.
Cellular packet communications (1990)

The future of third-generation wireless networking is discussed. The vision of the third generation is a single set of standards that can meet a wide range of wireless access applications. Third-generation systems, in harmony with broadband integrated services digital networks, will use shared resources to convey many information types. A single network architecture will serve its users efficiently in many environments, including moving vehicles, indoor and outdoor public areas, residences, offices, and factories. A study of a switching architecture, referred to as a cellular packet switch, and a packet transmission technique, referred to as a packet reservation multiple access is discussed. By means of a design example, it is shown how these techniques can work together to meet some of the demands of third-generation systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
[Complications during and after surgical removal of mandibular third molars. Impact of patient related and anatomical factors]. (2008)

The estimation of possible intra- and postoperative complications for surgical removal of third molars in the mandible poses a frequent dilemma in oral surgery. In the present study, the influence of the patient's age and gender, a reduced mouth opening, and the anatomical position of the tooth in the mandible on intra- and postoperative complications were evaluated. In a total of 120 surgically removed third molars, 9.2% intraoperative complications occurred, mainly bleeding. Factors influencing the risk for intraoperative complications were a male patient, a reduced mouth opening, and distally angulated teeth. Postoperative complications were encountered in 6.7%, mainly dry sockets. For this group, a female gender, a higher age, and distally angulated teeth were identified as risk parameters. As most of the patient- and anatomy-related factors are set parameters when evaluating possible risk factors for third molar surgery, only the timepoint of surgery can be influenced by the surgeon. Regarding the increase in intra- and postoperative complications for third molar removal in higher age groups, the prophylactic third molar surgery between the age of 18 and 25 seems justified.
The inactivation of Fe-S cluster containing hydro-lyases by superoxide. (1993)

We report in this paper that highly purified Escherichia coli dihydroxy-acid dehydratase, fumarase A, fumarase B, and mammalian aconitase are inactivated by O2- with second order rate constants in the range of 10(6) to 10(7) M-1 s-1. Each of these enzymes belongs to the hydro-lyase class and contains catalytically active [4Fe-4S] clusters. Simultaneous with inactivation by O2- is the release of iron from their clusters. Our working hypothesis is O2- inactivates these enzymes by oxidizing their clusters to an unstable oxidation state, and cluster degradation follows. Consistent with this hypothesis is our observation that spinach dihydroxy-acid dehydratase, a member of the hydro-lyase class that has a catalytically active [2Fe-2S] cluster, is not inactivated and does not lose iron in the presence of O2-. Porcine fumarase, a member of the hydro-lyase class that does not contain an Fe-S cluster, is also not inactivated by O2-. We also report the rate constants for the inactivation of E. coli dihydroxy-acid dehydratase, fumarase A, fumarase B, and mammalian aconitase by O2 are close to 2 x 10(2) M-1 s-1, and the rate constants for the inactivation of E. coli dihydroxy-acid dehydratase and mammalian aconitase by H2O2 are about 10(3) M-1 s-1. E. coli dihydroxy-acid dehydratase has been reported previously to be inactivated in vivo when cells are grown in hyperbaric O2, presumably due to the increased O2- generated under these conditions. We report here that E. coli fumarase A, fumarase B, and aconitase are also inactivated in vivo by hyperbaric O2. Thermodynamic parameters for the oxidation of the cluster of aconitase by O2- and O2 are calculated.
Synthesis of β-Enantiomers of N4-Hydroxy-3′-Deoxy-Pyrimidine Nucleosides and Their Evaluation against Bovine Viral Diarrhoea Virus and Hepatitis C Virus in Cell Culture (2004)

N4-Hydroxycytidine (NHC) was recently reported to have anti-pestivirus and anti-hepacivirus activity. It is thought that this nucleoside acts as a weak alternative substrate for the hepatitis C virus (HCV) polymerase. In addition to NHC, 3'-deoxyuridine (3'-dU) was found to inhibit bovine diarrhoea virus (BVDV) production by 1 log10 at 37.2 microM. These initial findings prompted the synthesis of beta-D and beta-L analogues of (i) base-modified 3'-deoxy-NHC; (ii) 3'-deoxyuridine; and 3'-deoxycytidine. The antiviral activity of these 42 nucleosides was evaluated against BVDV and HCV bicistronic replicon in cell culture. Among the NHC analogues, the antiviral activity observed for the beta-L-3'-deoxy-5-fluoro-derivative 1-(3-deoxy-beta-L-erythro-pentofuranosyl)-5-fluoro-4-hydroxyaminopyrimidin-2(1H)-one and the beta-D-3'-deoxy-5-iodo-derivative 1-(3-deoxy-beta-D-erythro-pentofuranosyl)-5-iodocytosine in the replicon system (1 log10 reduction at 100 microM) was due to the concomitant toxicity towards intracellular ribosomal RNA levels (CC90 equal or lower than the EC90). In conclusion, none of the newly synthesized derivatives exhibited enhanced antiviral activity compared to the parent nucleoside NHC.
Prognostic value of quantitative reverse transcription-polymerase chain reaction in lymph node-negative esophageal cancer patients. (2001)

QRT-PCR offers significant benefits over standard RT-PCR and identifies node-negative patients at high risk for recurrence.
Relevance of tumor microenvironment for progression, therapy and drug development (2004)

Tumor interstitium exhibits a microenvironment that differs from corresponding normal tissues. Tumor phenotype shows, for example, an elevated intracellular pH (pHi), a lowered extracellular pH (pHe), a low oxygen concentration and low glucose levels. These differences are caused by cell biological (so called intrinsic) factors, e.g. a higher acidification rate, as well as by more systemic (extrinsic) factors, e.g. poor tumor vascularization. They represent important factors for invasiveness, immune suppression and proliferation, and they imply possibilities for diagnosis, prognosis and therapy. We have developed an experimental data-based computer model, which has simulated the potential role of metabolic effects on tumor progression. We show an experiment on cellular metabolism demonstrating the immunosuppressive impact of low pHe on peripheral blood mononuclear cells. Finally, we review important findings on the tumor microenvironment leading to possibilities for therapy which are currently evolving and which promise higher effectiveness for cancer therapy.