gebhart/patrepeval huggingface dataset:
Disposable real-time microPCR device: lab-on-a-chip at a low cost (2006)

We have designed, fabricated and tested a real-time micro polymerase chain reaction (microPCR) system. It consists of a microscope glass cover slip placed on top of a micromachined silicon chip integrated with a heater and a temperature sensor. A single microL of a sample containing DNA was placed on the glass and encapsulated with mineral oil to prevent the evaporation of water, thus forming a virtual reaction chamber (VRC). The PCR chip required half a second to heat up from 72 to 94 degrees C and two seconds to cool from 94 to 55 degrees C, corresponding to a cooling rate of -20 K s(-1). The real-time PCR yield was determined by a fluorescence method. The melting curve analysis method as well as capillary electrophoresis was performed to determine the purity of the PCR product. As the glass slip is disposable, cross-contamination from sample to sample is eliminated. The total cost of running the PCR is given by the value of the cover slip and its treatment.
7-Deaza-2-phenyladenines: structure-activity relationships of potent A1 selective adenosine receptor antagonists (1990)

A series of derivatives of 7-deazapurines with varying substituents in the 2-, 6-, and 9-position was synthesized in an attempt to improve the adenosine receptor affinity and A1 or A2 selectivity. The adenosine receptor affinities were assessed by measuring the inhibition of [3H]-(R)-N6-(phenylisopropyl) adenosine (R-PIA) binding to rat brain A1 and inhibition of [3H]-5'-(N-ethylcarboxamido)adenosine (NECA) binding to rat striatum A2 adenosine receptors. A selected set of compounds representing the main structural variations was further examined in adenosine receptor coupled adenylate cyclase assays. All tested compounds antagonized the inhibition of adenylate cyclase elicited by interaction of R-PIA with A1 receptors in rat fat cell membranes and the activation of adenylate cyclase elicited by interaction of NECA with A2 receptors of pheochromocytoma PC12 cell membranes. The results indicate that 7-deazahypoxanthines have a potential for A2 selectivity, while all 7-deazaadenines are A1 selective. Introduction of a phenyl residue in the 2-position of 7-deazaadenines increases A1 activity tremendously. 2-(p-Chlorophenyl)-7,8-dimethyl-9-phenyl-7-deazaadenine (29) is potent and specific for the A1 receptors of rat brain (Ki = 122 nM), having no affinity for the A2 receptors of rat striatum. The compound has low activity at the A2 receptors of rat PC12 cell membranes where it appears to act as a noncompetitive inhibitor. A 1-phenylethyl substituent at the 9-position was found to be superior to a phenyl residue in terms of A1 affinity. The most potent A1 antagonist in the present series is the highly A1 selective (790-fold) (R)-7,8-dimethyl-2-phenyl-9-(1-phenylethyl)-7-deazaadenine (31, Ki = 4.7 nM), which is 30-35 times more potent at A1 receptors than its S enantiomer. The solubility of six of the potent 7-deaza-2-phenyladenines was determined by means of an A1 binding assay. Chloro substitution of the 2-phenyl ring appeared to improve the solubility as well as the solubility over A1 affinity ratio of 9-phenyl- and 9-(1-phenylethyl)-substituted 7-deazadenines.
Fabrication of microlasers and microresonator optical switches (1989)

We have microfabricated low-threshold, high-speed vertical-cavity lasers and optical switches by optimizing the mirror design, crystal growth, and ion etching of microresonators. By minimizing the sidewall ion damage in electrically pumped microlasers, we have defined large arrays of 3-μm-diam surface-emitting devices with threshold currents below 1.5 mA. Ion beam etching was also used to define 0.5–1.5 μm wide all-optical microresonator switches with recovery times as low as 30 ps and controlling energies as low as 0.6 pJ.
Research Papers : Electronic Imeging System with Silver Halide Photography Emulation (2000)

본 논문은 은염사진의 노광, 현삼, 인화 공정과 각종 사진 기법을 전자화상시스템에서 구현한 Emulation 기능에 관한 것이다. 이는 기술적 성숙기에 있는 은염 방식의 사진 기술의 디지털화를 시도한 것으로서, 이를 위해 전자화상시스템의 구성하고, 은염사진과 디지털사진의 화상 형성 과정과 특성을 분석하고 실험을 수행하였다. 은염사진의 현상 인화 공정 등 각 공정의 모델링 및 분석을 수행하고, 전자 화상의 입출력 특성과 영상처리 기법과 비교하였으며, 스튜디오 및 야외 실사를 통한 은염필름과 CCD 촬상소자의 성능 분석 결과를 제시한다. 나아가서, 전자화상의 Emulation 기능의 설계에 대해 제안한다.
On the dehydration of (R)‐lactate in the fermentation of alanine to propionate by Clostridium propionicum (1984)

All the enzymes of the pathway of (S)-alanine fermentation to acetate and propionate were detected in cell-free extracts of Clostridium propionicum . Among these (S)-glutamate dehydrogenase (NAD), (R)-lactate dehydrogenase (NAD) and propionate CoA-transferase were purified to apparent homogeneity. Their structures were presumably alpha 6, alpha 2 and alpha 4, respectively. The latter enzyme was specific for short-chain monocarboxylic acids with a pronounced preference for (R)-lactate over the (S)-enantiomer. The key step of the pathway, the dehydration of (R)-lactate required acetyl phosphate and CoASH under anaerobic conditions. It was inhibited by hydroxylamine, arsenate, azide (1 mM each) or by 0.1 mM 2,4-dinitrophenol. Thus it closely resembled the dehydration of (R)-2-hydroxyglutarate in Acidaminococcus fermentans , although an activation was not necessary.
Identification of a biomarker panel using a multiplex proximity ligation assay improves accuracy of pancreatic cancer diagnosis (2009)

A multiplex panel assaying CA19-9, OPN and CHI3L1 in plasma improves accuracy of pancreatic cancer diagnosis. A panel assaying CEA and CA125 in plasma can predict survival for this clinical cohort of pancreatic cancer patients.
A new class of HIV-1 specific 6-substituted acyclouridine derivatives: synthesis and anti-HIV-1 activity of 5- or 6-substituted analogs of 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) (1991)

A series of novel acyclouridine derivatives substituted at both the C-5 and C-6 positions were synthesized for the purpose of improving the activity of a recently reported HIV-1-specific lead, 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT). Preparation of C-6 substituted derivatives was carried out based on the following three methods: (1) LDA (lithium diisopropylamide) lithiation of a thymine derivative (4) and subsequent reaction with electrophiles, (2) an addition-elimination reaction of HEPT or its 6-(phenylsulfinyl) derivative (10), or (3) palladium-catalyzed cross-coupling between a 6-iodo derivative (16) and terminal alkynes. Following the methods, 21 C-6 substituted analogues were synthesized. Among these, 6-(cyclohexylthio) (8), 6-phenoxy (13), and 6-benzyl (27) derivatives showed anti-HIV-1 (HTLV-IIIB) activity with EC50 values of 8.2, 85, and 23 microM, respectively. Preparation of C-5 substituted derivatives was based on either LTMP (lithium 2,2,6,6-tetramethylpiperidide) lithiation of 6-(phenylthio)uracil derivative 37 or the above mentioned palladium-catalyzed cross-coupling of a 5-iodo-6-(phenylthio)uracil derivative (38). Following these methods, 11 C-5 substituted analogues were synthesized. Some 5-substituted derivatives (5-I, 44; 5-CH = CPh2, 49; 5-CH = CHPh (Z), 54; and 5-CH = CH2, 55) were more active than HEPT, but their selectivity indices (SI = CC50/EC50) were lower than that of HEPT. Compound 8 was also evaluated against another HIV-1 strain (HTLV-IIIRF) and HIV-2 strains (LAV-2ROD and LAV-2EHO). Only HTLV-IIIRF was as sensitive as HTLV-IIIB.
New anticancer agents: taxol, camptothecin analogs, and anthrapyrazoles. (1992)

Taxol, an agent with a unique mechanism of action, has been shown to be highly active in patients with refractory ovarian cancer and may well have significant activity in other malignancies such as breast and lung cancer. The camptothecin analogs, another unique class of agents, have demonstrated antitumor activity in phase I and II trials. Finally, the anthrapyrazoles are intercalating agents with clinical activity in breast cancer and a toxicity profile that may permit increased dose intensity using colony-stimulating factor support. While this review focuses on these three drug classes, a number of other agents with apparently unique mechanisms of antitumor activity and unusual dose-limiting toxicities are in earlier development. These include antimetabolites; inhibitors of DNA, RNA, or protein synthesis; differentiating agents; agents that inhibit tumor growth by binding to growth factors; and agents whose mechanism of action is best classified as unknown.
Determination of the Chromophore Structures in the Photoinduced Reaction Cycle of Phytochrome (2004)

The chromophore structures in the parent states Pr and Pfr as well as in the photocycle intermediate Lumi-R of oat phytochrome phyA are determined by comparison of the experimental resonance Raman spectra with calculated Raman spectra that have been obtained by density functional theory calculations (B3LYP) using scaled force fields. The spectra were calculated for various tetrapyrrole geometries including more than twenty different methine bridge isomers. For the parent states Pr and Pfr the best agreement in terms of vibrational frequencies, isotopic shifts, and Raman intensities was achieved with the ZZZasa and ZZEssa geometry, respectively. For the first intermediate Lumi-R, the chromophore geometry is concluded to be the ZZEasa configuration. These finding imply that the primary step of the photoactivation of phytochrome is the Z/E isomerization of the C-D methine bridge double bond, whereas the single bond remains in the anti conformation. The subsequent transition to the physiologically active state Pfr includes a (partial) single bond rotation of the A-B methine bridge.
Protective Effect of Vaccination with Toxoplasma Lysate Antigen and CpG as an Adjuvant against Toxoplasma gondii in Susceptible C57BL/6 Mice (2005)

Infection with the intracellular protozoan parasite Toxoplasma gondii causes serious public health problems to both humans and livestock and of great economic impact worldwide. Oligodeoxynucleotides (ODN) which contain immunostimulatory CG motifs (CpG ODN) can promote Th1 responses, an adjuvant activity that is desirable for vaccination against intracellular pathogens. We investigated the feasibility of using CpG as an adjuvant combined with Toxoplasma lysate antigen (TLA) as a vaccine against toxoplasmosis. Genetically susceptible C57BL/6 mice were vaccinated with TLA with or without CpG ODN as an adjuvant and then challenged with 85 cysts of the moderately virulent RRA (Beverley) strain of T. gondii. Prior to challenge infection, immunization with TLA plus CpG ODN directed cellular and humoral immunity toward a Th1 pattern, characterized by enhanced INF gamma production by splenic cells in response to TLA, and enhanced production of toxoplasma-specific IgG and IgG (2a) antibodies. Consequently, CpG/TLA-treated mice showed prolonged survival and 64% reduction in brain parasite burden compared to non-CpG/TLA treated group. Our results suggest that CpG ODN would provide a stable and effective adjuvant for use in vaccination against toxoplasmosis.
Global epidemiology of haemoglobin disorders and derived service indicators (2008)

To demonstrate a method for using genetic epidemiological data to assess the needs for equitable and cost-effective services for the treatment and prevention of haemoglobin disorders. We obtained data on demographics and prevalence of gene variants responsible for haemoglobin disorders from online databases, reference resources, and published articles. A global epidemiological database for haemoglobin disorders by country was established, including five practical service indicators to express the needs for care (indicator 1) and prevention (indicators 2-5). Haemoglobin disorders present a significant health problem in 71% of 229 countries, and these 71% of countries include 89% of all births worldwide. Over 330,000 affected infants are born annually (83% sickle cell disorders, 17% thalassaemias). Haemoglobin disorders account for about 3.4% of deaths in children less than 5 years of age. Globally, around 7% of pregnant women carry b or a zero thalassaemia, or haemoglobin S, C, D Punjab or E, and over 1% of couples are at risk. Carriers and at-risk couples should be informed of their risk and the options for reducing it. Screening for haemoglobin disorders should form part of basic health services in most countries.
Expression of the Erythropoietin Gene (1986)

Injection of cobalt into rats resulted in erythropoietin (EPO) mRNA accumulation in the kidney. The same response was obtained upon bleeding. No EPO mRNA was detected in the spleen, salivary gland, or thymus following cobalt injection or bleeding. In some animals, but not in others, EPO mRNA was also expressed in the liver in response to cobalt injection. Time course studies showed that message appearance begins sometime between 3 and 6 h after cobalt injection. This correlated very well with the EPO concentration in the circulation; EPO levels in the circulation were the same as those of controls at 3 h but increased to six- to sevenfold that of controls by 6 h after cobalt injection. The mature EPO mRNA in the rat and mouse comigrated with the 18S rRNA, indicating that it is about 1,850 nucleotides in length.
Effect of treatment of shell vial cell cultures with dimethyl sulfoxide and dexamethasone for detection of cytomegalovirus (1988)

Urine specimens submitted for the diagnosis of cytomegalovirus infection were inoculated into shell vials that had been pretreated with a combination of dimethyl sulfoxide (DMSO) and dexamethasone (DEX). The results were compared with those for inoculated shell vials which had received no drug treatment. Of 664 specimens, 100 (15%) were positive for cytomegalovirus. Of the 100 strains of cytomegalovirus, 88 (88%) were detected in both DMSO-DEX-treated and untreated shell vials. Of the remaining 12 positive specimens, 6 were detected with untreated shell vials exclusively and 6 were detected with DMSO-DEX-treated shell vials alone (not significant by the sign test). The median number of fluorescent foci was not significantly higher in DMSO-DEX-treated shell vials compared with that in untreated cultures (Wilcoxon signed-rank test; P = 0.1). DMSO-DEX-treated monolayers did not enhance the sensitivity detection of cytomegalovirus in shell vial cell cultures.
Enzyme-linked immunosorbent assay (ELISA): a practical tool for rapid diagnosis of viruses and other infectious agents. (1980)

Tissue culture techniques are inadequate to diagnose some viral infections. Thus, solid-phase immunoassays have been developed for the direct detection of viral antigens in clinical specimens. While radioimmunoassays (RIA) have attained widespread use, solid-phase enzyme-linked immunosorbent assays (ELISA) offer a number of advantages over RIA systems. ELISAs can be established with approximately the same sensitivity as radioimmunoassays without utilizing unstable, gamma-emitting isotopes. However, before ELISA systems can obtain widespread usage, a number of aspects of the test must be optimized. These include the preparation and use of reagents, the nature of the solid phase, the choice of enzyme, and the enzyme-antibody conjugation method. With the solving of these problems, ELISA should attain widespread usage for rapid diagnosis of a large number of infectious agents.
Fabrication and in vitro testing of polymeric delivery system for condensed DNA (2003)

Polyethylenimine (PEI) was combined with plasmid DNA and freeze dried following the addition of sucrose as a lyoprotectant and pore-forming agent. Freeze-dried PEI DNA condensates were dry mixed with granular polylactideglycolic acid (PLGA) then compression molded and sponged to encapsulated PEI DNA. A measurement of the elastic modulus indicated that 91 wt% sucrose substituted for 95 wt% sodium chloride as a porogen, resulting in PLGA sponges with a mechanical modulus of 100 kPa. The PEI DNA was retained (80%) within PLGA sponges prepared with sucrose during the leaching and subsequent 2-week release studies, whereas sodium chloride PLGA sponges caused the premature release (100%) of PEI DNA within 2 days. In vitro gene transfer studies with PEI DNA PLGA sponges established that adherent and infiltrating fibroblasts expressed reporter gene for 15 days compared with the short, 3-day expression mediated by direct gene of PEI DNA on cells in culture. The results demonstrate an approach to encapsulate condensed DNA in a PLGA sponge for the purpose of retaining DNA within the matrices and creating efficient gene transfer during tissue engineering.
The computer glossary : the complete illustrated dictionary (2001)

There are 1500 new and revised entries in this glossary, which provides computer users at all levels with clear explanations of computer terminology, concepts, jargon and technology.
Ultrafast polarization dynamics in biased quantum wells under strong femtosecond optical excitation (2003)

We observe ultrafast polarization dynamics in strongly internally biased InGaN/GaN multiple quantum wells during intense femtosecond optical excitation. In the case of strong enough excitation we demonstrate that the built-in bias field (on the order of MV/cm) can be completely screened by the carriers excited in spatially separated states. The removal of the initial strong bias leads to dynamical modification of the band structure, the electron and hole wave functions, and the absorption coefficient within the duration of the excitation pulse. We show that such an optically induced dynamical screening of the biased quantum well can be described in terms of discharging of a nanoscale capacitor driven by a femtosecond laser pulse. The electrostatic energy stored in the capacitor is released via THz emission. Due to its nonlinearity such a process may lead to emission of a THz pulse with bandwidth significantly exceeding that of the excitation pulse.
Inhibition of Cell Adhesion to Fibronectin by Oligopeptide-Substituted Polynorbornenes (2001)

Polynorbornenes substituted with two different peptide sequences from the RGD-containing integrin cell-binding domain of fibronectin are potent inhibitors of human foreskin fibroblast cell adhesion to fibronectin-coated surfaces. Ring-opening metathesis polymerization (ROMP) using Ru==CHPh(Cl)(2)(PCy(3))(DHIMes) (1) as an initiator produced polymers substituted with GRGDS and PHSRN peptide sequences. The inhibitory activity was quantified for these polymers and compared to the free peptides and GRGES-containing controls. A homopolymer substituted with GRGDS peptides was significantly more active than the free GRGDS peptide (IC(50) of 0.18 +/- 0.03 and 1.33 +/- 0.20 mM respectively), and the copolymer containing both GRGDS and PHSRN is the most potent inhibitor (IC(50) of 0.04 +/- 0.01 mM). These results demonstrate that significant enhancements of observed biological activity can be obtained from polymeric materials containing more than one type of multivalent ligand and that ROMP is a useful method to synthesize such well-defined copolymers.
Primary structures of PYY, [Pro34]PYY, and PYY-(3–36) confer different conformations and receptor selectivity (2000)

We synthesized PYY-(1-36) (nonselective between Y(1) and Y(2) receptor subtype agonists), [Pro(34)]PYY (selective for Y(1)), and PYY-(3-36) (selective for Y(2)) to determine whether solution conformation plays a role in receptor subtype selectivity. The three peptides exhibited the expected specificities in displacing labeled PYY-(1-36) from cells transfected with Y(1) receptors (dissociation constants = 0.42, 0.21, and 1,050 nM, respectively) and from cells transfected with Y(2) receptors (dissociation constants = 0.03, 710, and 0.11 nM, respectively) for PYY-(1-36), [Pro(34)]PYY, and PYY-(3-36). Sedimentation equilibrium analyses revealed that the three PYY analogs were 80-90% monomer at the concentrations used for the subsequent circular dichroism (CD) and (1)H-nuclear magnetic resonance (NMR) studies. CD analysis measured helicities for PYY-(1-36), [Pro(34)]PYY, and PYY-(3-36) of 42%, 31%, and 24%, suggesting distinct differences in secondary structure. The backbone (1)H-NMR resonances of the three peptides further substantiated marked conformational differences. These patterns support the hypothesis that Y(1) and Y(2) receptor subtype binding affinities depend on the secondary and tertiary solution state structures of PYY and its analogs.
Evaluation of Differentiation-Inducing Activity of Retinoids on Human Leukemia Cell Lines HL-60 and NB4. (1996)

Retinoids, including all-trans-retinoic acid (ATRA), its isomers, and fifty synthetic retinoids (retinobenzoic acids), were tested for differentiation-inducing activity on human leukemia cell lines HL-60 and NB4. Binding activity of typical retinoids to nuclear retinoic acid receptors (RARs) was also investigated. A good linear correlation between the ED50 values of differentiation-inducing activity towards HL-60 cells and those towards NB4 cells was found. Binding activities of retinoids to RAR alpha and RAR beta also correlated well to the differentiation-inducing activities.
Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0 (2009)

http://babylone.ulb.ac.be/popmusic
Detection of Salmonella spp. Using Microsphere-Based, Fiber-Optic DNA Microarrays (2005)

Salmonella spp. are one of the most problematic food pathogens in public health, as they are responsible for food poisoning associated with contamination of meat, poultry, and eggs. Thus, rapid and sensitive detection of Salmonella spp. is required to ensure food safety. In this study, a fiber-optic DNA microarray using microsphere-immobilized oligonucleotide probes specific for the Salmonella invA and spvB genes was developed for detection of Salmonella spp. Microarrays were prepared by randomly distributing DNA probe-functionalized microspheres (3.1-microm diameter) into microwells created by etching optical fiber bundles. Hybridization of the probe-functionalized microspheres to target DNA from Salmonella was performed and visualized using Cy3-labeled secondary probes in a sandwich-type assay format. In this study, 10(3)-10(4) cfu/mL of the target organism could be detected after 1-h hybridization without any additional amplification. The DNA microarray showed no cross-reactivity with other common food pathogens, including E. coli and Y. enterocolitica, and could even detect Salmonella spp. from cocktails of bacterial strains with only moderate loss of sensitivity due to nonspecific binding. This work suggests that fiber-optic DNA microarrays can be used for rapid and sensitive detection of Salmonella spp. Since fiber-optic microarrays can be prepared with different probes, this approach could also enable the simultaneous detection of multiple food pathogens.
Microfabrication by ion milling: The lathe technique (1994)

Several novel and unusual microstructures were made by focused ion beam milling. These microstructures include needles, hooks, forks, and similar shapes resulting from 360° access afforded to the ion beam by a rotation mounting device. The lengths of the microstructures are in the 10 μm range, and the thicknesses all in the 1–2 μm range. Similar procedures were used to make prototype stylus geometries for scanning probe microscopy applications. Resolution limits to the fabrication process come mainly from the grain structure of the material being sputtered. The ion beam is 0.3 μm in diameter, and 0.08 μm pixel resolution for ion beam location was used to generate the objects. Start-to-finish fabrication time for most of the objects made was ∼2 h without any effort to streamline the process.