gebhart/patrepeval huggingface dataset:
Construction of a food-grade host/vector system forLactococcus lactisbased on the lactose operon (1995)

A plasmid-based food-grade vector system was developed for Lactococcus lactis by exploiting the genes for lactose metabolism. L. lactis MG5267 is a plasmid-free strain containing the entire lactose operon as a chromosomal insertion. The lacF gene was deleted from this strain by a double cross-over homologous recombination event. The lacF-deficient strain produced a Lac- phenotype on indicator agar. A cloned copy of the lacF gene expressed on a plasmid was capable of complementing the lacF-deficient strain resulting in a Lac+ phenotype. This stably maintained system fits the requirements of a self-selecting vector system and has the potential to be exploited in the food industry.
Graphene-assisted control of coupling between optical waveguides (2012)

The unique properties of optical waveguides electrically controlled by means of graphene layers are investigated. We demonstrate that, thanks to tunable losses induced by graphene layers, a careful design of silicon on silica ridge waveguides can be used to explore passive PT-symmetry breaking in directional couplers. We prove that the exceptional point of the system can be probed by varying the applied voltage and we thus propose very compact photonic structures which can be exploited to control coupling between waveguides and to tailor discrete diffraction in arrays.
Chromatinized templates reveal the requirement for the LEDGF/p75 PWWP domain during HIV-1 integration in vitro (2007)

Integration is an essential step in the retroviral lifecycle, and the lentiviral integrase binding protein lens epithelium-derived growth factor (LEDGF)/p75 plays a crucial role during human immunodeficiency virus type 1 (HIV-1) cDNA integration. In vitro, LEDGF/p75 stimulates HIV-1 integrase activity into naked target DNAs. Here, we demonstrate that this chromatin-associated protein also stimulates HIV-1 integration into reconstituted polynucleosome templates. Activation of integration depended on the LEDGF/p75-integrase interaction with either type of template. A differential requirement for the dominant DNA and chromatin-binding elements of LEDGF/p75 was however observed when using naked DNA versus polynucleosomes. With naked DNA, the complete removal of these N-terminal elements was required to abate cofactor function. With polynucleosomes, activation mainly depended on the PWWP domain, and to a lesser extent on nearby AT-hook DNA-binding motifs. GST pull-down assays furthermore revealed a role for the PWWP domain in binding to nucleosomes. These results are completely consistent with recent ex vivo studies that characterized the PWWP and integrase-binding domains of LEDGF/p75 as crucial for restoring HIV-1 infection to LEDGF-depleted cells. Our studies therefore establish novel in vitro conditions, highlighting chromatinized DNA as target acceptor templates, for physiologically relevant studies of LEDGF/p75 in lentiviral cDNA integration.
Proton transfer in methylmalonyl-CoA epimerase from Propionibacterium shermanii. The reaction of (2R)-methylmalonyl-CoA in tritiated water (1983)

The reaction catalysed by methylmalonyl-CoA epimerase from Propionibacterium shermanii was studied in tritiated water, in the direction with (2R)-methylmalonyl-CoA as substrate, under 'irreversible' conditions. After partial reaction, even when most of the substrate had been converted into product (isolated as propionyl-CoA) essentially no solvent tritium appeared in residual (2R)-methylmalonyl-CoA. The product, however, did contain tritium, and the specific radioactivity of the (2S)-epimer was deduced to be 0.33 times that of the solvent. These results provide further support for the mechanism proposed for the epimerase-catalysed reaction in the accompanying paper [Leadlay & Fuller (1983) Biochem. J. 213, 635-642], in which two enzyme bases act respectively as proton donor and acceptor. The observed low discrimination against solvent tritium entering the product can be accounted for by a mechanism in which the release of product is slow, and the re-protonation step on the enzyme is reversible, without leading to isotopic exchange with the solvent.
Synthesis and characterization of UTD-1, a novel zeolite molecular sieve (1995)

We recently discovered that bis(pentamethylcyclopentadienyl)cobalt(III)hydroxide,Cp * 2 CoOH can function as a structure directing agent for the synthesis of zeolite molecular sieves. This complex has been used to prepare several new phases including the novel zeolite UTD-1. This high silica molecular sieve has been caracterized
6-Deoxy-13-hydroxy-8,11-dione-dihydrogranaticin B, an Intermediate in Granaticin Biosynthesis, from Streptomyces sp. CPCC 200532 (2014)

A new granaticin analogue and its hydrolysis product were isolated from Streptomyces sp. CPCC 200532. Their structures were determined to be 6-deoxy-13-hydroxy-8,11-dione-dihydrogranaticins B (1) and A (2), respectively, by detailed analysis of spectroscopic data. Compound 1 was regarded as an intermediate in granaticin biosynthesis, as it was bioconvertable to granaticin B. Compared to granaticin B, 1 showed similar cytotoxicity against cancer cell line HCT116, but decreased cytotoxicity against cancer cell lines A549, HeLa, and HepG2. Compound 2 displayed lower cytotoxicity than 1 against all four cancer cell lines tested.
Nonlinear optimization method in camera calibration (2009)

In order to obtain much better camera calibration accuracy, the last and important step is the on-whole optimization of all the intrinsic and extrinsic parameters. However, almost no concrete or performable methods are given so far. And only the principle is given that the RMS error should be the minimum, but there are no detailed realization steps. Therefore, a concrete and performable nonlinear optimization method is proposed by adopting an iterative strategy. In this method, first, solve the initial camera intrinsic and extrinsic parameters without considering the distortion coefficients. Second, take the distortion coefficients into consideration and conduct the optimization steps, which is comparing the practical image coordinates and the calculated image coordinates based on the initial parameters to get better distortion coefficients, using the distortion coefficients to correct the distorted image coordinates, and then getting the better values of the intrinsic and extrinsic parameters. This is the process of the iteration. The experiment results show that the proposed iterative optimization method is very stable and efficient.
GaN Growth Using GaN Buffer Layer (1991)

High-quality gallium nitride (GaN) film was obtained for the first time using a GaN buffer layer on a sapphire substrate. An optically flat and smooth surface was obtained over a two-inch sapphire substrate. Hall measurement was performed on GaN films grown with a GaN buffer layer as a function of the thickness of the GaN buffer layer. For the GaN film grown with a 200 Å-GaN buffer layer, the carrier concentration and Hall mobility were 4×10 16 /cm 3 and 600 cm 2 /V·s, respectively, at room temperature. The values became 8×10 15 /cm 3 and 1500 cm 2 /V·s at 77 K, respectively. These values of Hall mobility are the highest ever reported for GaN films. The Hall measurement shows that the optimum thickness of the GaN buffer layer is around 200 Å.
Evaluation of the antimicrobial effect of photodynamic antimicrobial therapy in an in situ model of dentine caries (2009)

Photodynamic antimicrobial therapy (PACT) promotes bacterial death as a result of the photosensitization of microbial components. This study evaluated the effect of PACT on dentine caries produced in situ. Over the course of 14 d, 20 volunteers wore intra-oral devices containing human dentine slabs that were treated 10 times daily with a 40% sucrose solution. Afterwards, the antimicrobial effect of toluidine blue O, associated with 47 or 94 J cm(-2) of a light-emitting diode, was evaluated. Before and after the treatments, dentine samples were analysed with regard to the total number of microorganisms, total streptococci, mutans streptococci, and lactobacilli. Significant reductions in the bacterial count were observed for PACT with both energy densities tested, with the following values observed for 47 and 94 J cm(-2) of irradiation: for total streptococci, 3.45 and 5.18; for mutans streptococci, 3.08 and 4.16; for lactobacilli, 3.24 and 4.66; and for total microorganisms, 4.29 and 5.43, respectively. The control, treated with 94 J cm(-2) of irradiation alone, was also effective against all bacteria. To conclude, PACT was effective in killing oral microorganisms present in dentine caries produced in situ and may be a useful technique for eliminating bacteria from dentine carious lesions before restoration.
Solid-Phase PEGylation of Recombinant Interferon α-2a for Site-Specific Modification: Process Performance, Characterization, andin VitroBioactivity (2007)

'Solid-phase' PEGylation, in which a conjugation reaction attaches proteins to a solid matrix, has distinct advantages over the conventional, solution-phase process. We report a case study in which recombinant interferon (rhIFN) alpha-2a was adsorbed to a cation-exchange resin and PEGylated at the N-terminus by 5, 10, and 20 kDa mPEG aldehydes through reductive alkylation. After PEGylation, a salt gradient elution efficiently purified the mono-PEGylate of unwanted species such as unmodified IFN and unreacted PEG. Mono-PEGylation and purification were integrated into a single, chromatographic step. Depending on the molecular weight of the mPEG aldehyde, the mono-PEGylation yield ranged from 50 to 65%. Major problems associated with the solution-phase process such as random or uncontrollable multi-PEGylation and post-PEGylation purification difficulties were overcome. N-terminus sequencing and MALDI-TOF mass spectrophometry confirmed that the PEG molecule was conjugated only to the N-terminus. A cell proliferation study indicated reduced antiviral activity of the mono-PEGylate compared to that of the unmodified IFN. As higher molecular weight PEG was conjugated, in vitro bioactivity and antibody binding activity, as measured by a surface plasmon resonance biosensor, decreased. Nevertheless, trypsin resistance and thermal stability were considerably improved .
Routes of Transimission of Hepatitis C Virus in an Endemic Rural Area of Japan : Molecular Epidemiologic Study of Hepatitis C Virus Infection (1997)

We conducted an epidemiological study to investigate the routes of transmission of hepatitis C virus (HCV) infection in an area endemic for HCV. Subjects were the 857 adult inhabitants of K area, Japan. The prevalence of antibody to HCV (anti-HCV) was 26.3%. The HCV genotype 1b was the most prevalent (89.3%) among the anti-HCV positive subjects. Molecular evolutionary analysis, based on the nucleotide sequences of the HCV core region from 23 participants with type 1b, showed that the isolates were distributed into more than 1 group. Multivariate regression analysis demonstrated that an age over 40 years, a history of blood transfusion, the presence of antibody to hepatitis B core antigen (anti-HBc), or a history of surgery were each independently associated with the presence of anti-HCV. No significant differences in the presence of anti-HCV prevalence were observed between the wives of men positive for anti-HCV (33.3%) and age-matched women (36.4%), or between the husbands of women positive for anti-HCV (36.4%) and age-matched men (38.3%), from the same area. Findings suggest that the various strains of HCV type 1b were transmitted via medical procedures, not by the intrafamilial route.
Potent Antitumor Activity of an Auristatin-Conjugated, Fully Human Monoclonal Antibody to Prostate-Specific Membrane Antigen (2006)

Prostate-specific membrane antigen (PSMA) is the prototypic cell-surface marker of prostate cancer and provides an attractive target for monoclonal antibody (mAb) targeted therapies. In this study, a novel antibody-drug conjugate (ADC) was generated by linking a fully human PSMA mAb to monomethylauristatin E (MMAE), a potent inhibitor of tubulin polymerization. The PSMA ADC was evaluated for antitumor activity in vitro and in a mouse xenograft model of androgen-independent human prostate cancer. The PSMA ADC eliminated PSMA-expressing cells with picomolar potency and >700-fold selectivity in culture. When used to treat mice with established human C4-2 tumors, the PSMA ADC significantly improved median survival 9-fold relative to vehicle or isotype-matched ADC (P = 0.0018) without toxicity. Treatment effects were also manifest as significant (P = 0.0068) reduction in serum levels of prostate-specific antigen (PSA). Importantly, 40% of treated animals had no detectable tumor or measurable PSA at day 500 and could be considered cured. The findings support development of PSMA antibody-auristatin conjugates for therapy of prostate cancer.
ARTIFICIAL NEU ASED MULTIPLE FAULT DIAGNOSIS IN DIGITAL C (1998)

The paper describes a technique, based on the use of Artificial Neural Networks (ANNs), for the diagnosis of multiple faults in digital circuits. The technique utilises different quantities of randomly selected circuit test data derived from a fault truth table [I], which is constructed by inserting random single stuck-at faults in the circuit. The paper describes the diagnostic procedure using the technique, the ANN architecture and results obtained with example circuits. Our results demonstrate that when the test data selection procedure is guided by test vectors of the circuit a compact, efficient and flexible ANN architecture is achieved.
Thiol-Selective Fluorogenic Probes for Labeling and Release (2009)

Thiol alkylation is a powerful technique for the labeling of proteins. We report a new class of highly reactive, selective, and fluorogenic probes for thiols in aqueous solution at neutral pH, based on the 7-oxanorbornadiene (OND) framework. The maleate moiety in 7-oxabicyclo[2.2.1]hept-2,5-diene-2,3-dicarboxylic acid esters serves as both a tunable electrophile and an intramolecular quencher of an attached dansyl fluorophore. Thiols have been found to add with high rates (second-order rate constants of 40-200 M(-1) s(-1)) to give adducts that exhibit enhancements of fluorescence intensity up to 180-fold. The resulting adducts are also versatile with respect to cleavage (release) reactions by two mechanisms. First, retro-Diels-Alder fragmentation occurs with half-lives from days to weeks at room temperature, and an epoxide derivative is also reported that is incapable of cycloreversion cleavage. Second, monoamide OND derivatives undergo rapid closure to succinimides upon thiol addition, providing a thiol-triggered mechanism for immediate alcohol release. Peptides and proteins containing free thiol groups were labeled with OND electrophiles with high chemoselectivity. Since the system is so easily assembled from readily accessible modules, various functional groups can be added to OND linkers to allow the attachment of other molecules of interest.
Induction of Angiogenic Cytokine Expression in Cultured RPE by Ingestion of Oxidized Photoreceptor Outer Segments (2003)

Ingestion by RPE of oxidized bovine POS stimulates expression of the chemotactic and angiogenic factors IL-8 and MCP-1 that have the capability to promote angiogenesis directly, or indirectly through the accumulation of immune cells such as macrophages, which themselves may release angiogenic promoters and degrade Bruch's membrane. This may be of significance in the development of exudative AMD.
Multicolor CRISPR labeling of chromosomal loci in human cells (2015)

The intranuclear location of genomic loci and the dynamics of these loci are important parameters for understanding the spatial and temporal regulation of gene expression. Recently it has proven possible to visualize endogenous genomic loci in live cells by the use of transcription activator-like effectors (TALEs), as well as modified versions of the bacterial immunity clustered regularly interspersed short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system. Here we report the design of multicolor versions of CRISPR using catalytically inactive Cas9 endonuclease (dCas9) from three bacterial orthologs. Each pair of dCas9-fluorescent proteins and cognate single-guide RNAs (sgRNAs) efficiently labeled several target loci in live human cells. Using pairs of differently colored dCas9-sgRNAs, it was possible to determine the intranuclear distance between loci on different chromosomes. In addition, the fluorescence spatial resolution between two loci on the same chromosome could be determined and related to the linear distance between them on the chromosome's physical map, thereby permitting assessment of the DNA compaction of such regions in a live cell.
Role of transforming growth factor β3 in lymphatic metastasis in breast cancer (1998)

Transforming growth factor-betas (TGFbetas) play a prominent role in tumour growth and metastasis by enhancing angiogenesis and suppressing immune surveillance. Despite the increased interest in the effect of TGFbetas on tumour progression, little is known about the importance of TGFbeta3 and its receptor CD105 in breast cancer. In the present study, we measured the plasma levels of TGFbeta3, CD105-TGFbeta3 complexes and TGFbeta1 in 80 patients with untreated early-stage breast cancer using an enhanced chemiluminescence ELISA method. Of the 80 patients, 14 were histologically confirmed as having axillary lymph node metastases, while the remainder had no evidence of lymph node involvement. The results showed that levels of both TGFbeta3 and CD105-TGFbeta3 complex were significantly elevated in patients with positive lymph nodes compared to those without node metastasis. Furthermore, the levels of both TGFbeta3 and CD105-TGFbeta3 complex correlated with lymph node status. The only patient who died of the disease had very high plasma levels of TGFbeta3 and CD105-TGFbeta3 complex and positive lymph nodes; this patient developed lung metastases within 2 years of diagnosis. No significant correlation was seen between either TGFbeta3 or CD105-TGFbeta3 complex levels and tumour stage, size or histological grade. Plasma TGFbeta1 levels were not correlated with node metastasis, tumour stage, grade or size. Our data suggest that plasma levels of TGFbeta3 and CD105-TGFbeta3 complex may be of prognostic value in the early detection of metastasis of breast cancer.
Structural and functional analysis of a bacterial cellulase by proteolysis (1989)

CenA is an endo-beta 1,4-glucanase from the cellulolytic bacterium Cellulomonas fimi. It is a bifunctional enzyme comprising an amino-terminal cellulose-binding domain and a carboxyl-terminal catalytic domain joined by a short sequence of prolyl and threonyl residues (the Pro-Thr box). Additional structural and functional information was revealed by a detailed analysis of the products generated by proteolytic cleavage of a nonglycosylated form of CenA. An extracellular C. fimi protease attacked nonglycosylated CenA at the junctions between the Pro-Thr box and the two functional domains. A stable "core" peptide (p30), corresponding to the catalytic domain, remained after extensive proteolysis. p30 was resistant to further attack even in the presence of 2-mercaptoethanol plus urea or dithiothreitol, but treatment in the presence of sodium dodecyl sulfate allowed complete fragmentation to small peptides. Stable peptides, identical, or closely related to p30, were generated by alpha-chymotrypsin or papain. These results indicated that the catalytic domain adopts a tightly folded conformation affording protection from proteolytic attack. In contrast, the cellulose-binding domain showed a relatively loose conformation. Progressive proteolytic truncation from the amino terminus was apparent during incubation with alpha-chymotrypsin or papain, or with C. fimi protease under reducing conditions. Affinity for cellulose was retained by products missing up to 64 amino-terminal amino acids. The remaining carboxyl-proximal region of the cellulose-binding domain with affinity (47 amino acids) contained sequences highly conserved in analogous domains from other bacterial endo-beta 1,4-glucanases. By analogy with other systems, the properties of the Pro-Thr box are consistent with an elongated conformation. The results of this investigation suggest that CenA has a tertiary structure which resembles that of certain fungal cellulases.
Injectable Soft-Tissue Fillers: Clinical Overview (2006)

As there is no single injectable filler that has all of the desired characteristics, understanding the advantages and disadvantages of one filler over another is extremely helpful in guiding the patient to an informed decision. Although all of the reviewed injectable fillers are safe, the concepts of their long-term volume persistence and how they compare with each other remain largely anecdotal, with few prospective controlled clinical trials.
Intestinal absorption of aspirin. Influence of pH, taurocholate, ascorbate, and ethanol. (1981)

The small intestinal absorption of aspirin at pharmacological concentrations was studied in the unanesthetized rat by using a single-pass perfusion technique. The rate of aspirin absorption remained linear with its concentration (0.5 to 10 mM). Intestinal aspirin absorption increased as the concentration of hydrogen ion, sodium taurocholate, and ascorbic acid in the perfusate increased. Aspirin absorption did not change after ethanol addition. At pH 3.5 or 6.5, intestinal absorption of aspirin was greater than gastric absorption of the compound. Aspirin was not absorbed by the stomach at pH 6.5. These experiments indicate that aspirin can be absorbed to an appreciable extent in its ionized form by the small intestine but not by the stomach.
형제,자매 자료를 이용한 교육투자수익률 추정 (2009)

본 연구는 형제·자매 자료를 이용해 전통적인 임금함수를 통해 교육투자수익률을 추정한 연구들에서 간과한 두 가지 문제점을 고려하여 교육의 투자수익률을 추정한다. 본 연구의 실증분석에 사용된 자료는 『경제활동인구부가조사』이다. 본 연구의 실증분석 결과에 따르면, 형제·자매의 교육수준을 자신의 능력을 대변하는 변수로 통제할 때 교육투자수익률은 통제하지 않을 때와 비교해 약 41.7%~61.2% 정도 감소하였고, 측정오차를 감안했을 때 교육투자수익률은 측정오차를 고려하지 않을 때와 비교해 52.5%~83.6% 증가하였다. 그러나 종합적으로는 볼 때 선행 외국연구와는 달리 우리나라의 경우 능력의 누락에 따른 효과가 측정오차를 간과한 효과보다 커서 전통적인 임금함수를 통해 추정된 교육투자수익률은 상향편의를 갖는 것으로 나타났다.