gebhart/patrepeval huggingface dataset:
DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways (2008)

The assembly of large recombinant DNA encoding a whole biochemical pathway or genome represents a significant challenge. Here, we report a new method, DNA assembler, which allows the assembly of an entire biochemical pathway in a single step via in vivo homologous recombination in Saccharomyces cerevisiae. We show that DNA assembler can rapidly assemble a functional D-xylose utilization pathway (approximately 9 kb DNA consisting of three genes), a functional zeaxanthin biosynthesis pathway (approximately 11 kb DNA consisting of five genes) and a functional combined D-xylose utilization and zeaxanthin biosynthesis pathway (approximately 19 kb consisting of eight genes) with high efficiencies (70-100%) either on a plasmid or on a yeast chromosome. As this new method only requires simple DNA preparation and one-step yeast transformation, it represents a powerful tool in the construction of biochemical pathways for synthetic biology, metabolic engineering and functional genomics studies.
Cognate interactions between helper T cells and B cells. VI. TGF-beta inhibits B cell activation and antigen-specific, physical interactions between Th and B cells. (1991)

TGF-beta is a 25-kDa homodimeric protein that has been shown to have multiple roles in the regulation of lymphocyte activation. Previous studies have shown that TGF-beta is an inhibitor of numerous T and B lymphocyte activities. This study shows that TGF-beta is able to inhibit Th- and mitogen-induced murine B cell proliferation, as well as mitogen-induced B cell cycle entry and immunoglobulin secretion. Acridine orange analysis established that TGF-beta inhibits the LPS-induced B cell transition from G0 to G1A phase of the cell cycle. Evaluation of the effects of TGF-beta on the interactions between Th and B cells showed that TGF-beta inhibited antigen-specific Th-B cell physical interactions. Flow cytometric data showed that the ability of TGF-beta to interfere with the formation of Th-B cell conjugates was not due to decreased expression of IgD, IgM, class I, class II, LFA-1, or ICAM1 by the B cell. Taken together, these data establish that TGF-beta is able to act at multiple sites within the immune system.
Warts in primary schoolchildren: prevalence and relation with environmental factors (2009)

One-third of primary schoolchildren have warts. This study does not find support for generally accepted wart prevention recommendations, such as wearing protective footwear in communal showers and swimming pool changing areas. Rather, recommendations should focus on ways to limit the transmission of wart viruses within families and school classes.
Process optimization tweaking tool (POTT) and its application in controlling oxidation thickness (1989)

This computer utility extracts process data from a manufacturing statistical process control database, calculates oxidation times appropriate to recenter the thickness to the desired process mean, and inserts the values of new oxidation times directly into furnace oxidation recipes resident in the main BTU host computer so that production furnace recipes downloaded to the furnace controller automatically contain the new oxidation times. The major attributes of POTT are summarized and its application in controlling oxidation thickness for silicon integrated-circuit fabrication as well as results obtained using two different retargeting strategies are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Elastin as a random‐network elastomer: A mechanical and optical analysis of single elastin fibers (1981)

Abstract The physical properties of single, 5–8‐μm diameter, water‐swollen elastin fibers have been investigated on a microtest apparatus attached to a polarizing microscope. Analysis of the mechanical and optical properties at extensions below 100% indicate that the elastic modulus ( G ) has a value of 4.1 × 10 5 N m −2 , the average molecular weight of chains between crosslinks is in the range of 6000–7100, and the stress optical coefficient ( C ′) is 1 × 10 −9 m 2 N −1 at 24°C. Analysis of the temperature dependence of the stress optical coefficient indicates that the polarizability of the random link decreases with increasing temperature, with an apparent activation energy for this process of the order of 1.6 kcal/mol. Analysis of the non‐Gaussian mechanical and optical properties at extensions above about 100% suggest that the chains between crosslinks contain approximately 10 “effective” random links, with each link consisting of 7–8 amino acid residues. These parameters for the random chains in the elastin network have been used to predict the dimensions of other random proteins. The close correlation of these predictions with published values for the dimensions of a series of proteins in solution in 6 M guanidinium hydrochloride provides an independent test of the appropriateness of our analysis.
Comments on "Principal component extraction using recursive least squares learning" (1996)

In the above paper, (Bannour and Azimi-Sanjadi, 1995) we point out and correct flaws in the proofs of the orthonormal property of the optimal weight vectors of a two-layer linear auto-associative network used for sequentially extracting the principal components of a stationary vector stochastic process.
MCM—L:多层PCB的一个动态演变 (1994)

采用现有元器件封装技术的表面安装设计正很快接近基片(substrate,以下同)密度限制。一个可能的解决办法是使用多芯片模块(MCM)或更确切地说,是层压基片的改型,称作(MCM-L)。MCM-L技术还处于初期,它要从现有表面安装技术(SMT)中吸取优点,并突破现有技术。从设计和制造角度看,MCM-L是多层印制板(PCB)应用中元器件组装的下一个合乎逻辑的步聚。
Overview of the trastuzumab (Herceptin) anti-HER2 monoclonal antibody clinical program in HER2-overexpressing metastatic breast cancer. Herceptin Multinational Investigator Study Group. (1999)

The recombinant humanized anti-HER2 monoclonal antibody trastuzumab (Herceptin; Genentech, San Francisco, CA) was evaluated in human clinical trials for treatment of women with metastatic breast cancer who have tumors that overexpress HER2. The trastuzumab clinical program consisted of a series of phase I, phase II, and phase III clinical trials. Clinical experience with this novel biologic has been obtained in more than 1,000 women with HER2-overexpressing metastatic breast cancer. Two pivotal trials were performed to evaluate trastuzumab efficacy and safety: (1) trastuzumab in combination with chemotherapy as first-line therapy and (2) trastuzumab as a single agent in second- and third-line chemotherapy. Preliminary results of the pivotal clinical trials that have been presented at national meetings are summarized below. The data suggest that trastuzumab will be an important new treatment option for women with HER2-overexpressing metastatic breast cancer.
Electroluminescent diodes from a single component emitting layer of dendritic macromolecules (1996)

Organic LEDs based on dendrimer materials are reported (see the figure for an example; a dot represents phenylene). Single‐organic‐layer devices have been produced using structurally welldefined dendritic modules. Although the efficiency of the devices is still low, this work provides a basis for a systematic strategy for tuning the properties of the active layers of organic LEDs. magnified image
Levodopa pharmacokinetics and pharmacodynamics in fluctuating parkinsonian patients (1986)

We investigated levodopa intravenous infusion rates, plasma concentrations, and clinical responses in 23 parkinsonian patients with a fluctuating response to the drug. There was a linear relationship between rate of levodopa infusion and plasma concentration when carbidopa was coadministered. Minimum-therapeutically effective plasma concentrations of levodopa ranged from 3 to 12 nmol/ml. The duration, but not the magnitude, of clinical response was linearly related to plasma concentrations. The clinical response lagged behind the rise and fall of plasma levodopa. There was no evidence of idiosyncratic pharmacokinetic or pharmacodynamic responses to levodopa to explain the fluctuating response.
Oplophorus oxyluciferin and a model luciferin compound biologically active with Oplophorus luciferase (1975)

The luciferin of the bioluminescent decapod shrimp, Oplophorus gracilorostris, was purified and studied with respect to u.v. spectrum, fluorescence spectrum, mass spectrum and luminescent cross-reaction with the enzyme luciferase of the bioluminescent ostracod, Cypridina hilgendorfii. On the basis of these results, an empirical formula C10H13N3O3 and an imidazo [1,2-a]pyrazin-3-one structure are proposed for luciferin. Of three model luciferin compounds, 3-hydroxy-2-methylimidazo[1,2-a]pyridine is biologically active with both Oplophorus and Cypridina luciferase, indicating that a pyrazine structure is not essential for biological activity with Cypridina luciferase.
Molecular Cloning of PCR Products (2001)

It is often desirable to clone PCR products to establish a permanent source of cloned DNA for hybridization studies, to obtain high-quality DNA sequencing results, or to separate products when PCR amplification yields a complex mixture. The efficiency of direct cloning of PCR products can be improved by generating suitable ends on the amplified fragments. This unit describes the strategies for generating and manipulating suitable ends on the PCR fragments.
An intelligent listening framework for capturing encounter notes from a doctor-patient dialog (2009)

The work here encouraged us that the goal is reachable, so we conclude with proposed next steps.Some challenging steps include acquiring a corpus of doctor-patient conversations, exploring a workable microphone setup, performing user interface research, and developing a multi-speaker version of our tools.
Lateral-driven continuous dielectrophoretic microseparators for blood cells suspended in a highly conductive medium (2008)

This paper presents lateral-driven continuous dielectrophoretic (DEP) microseparators for separating red and white blood cells suspended in highly conductive dilute whole blood. The continuous microseparators enable the separation of blood cells based on the lateral DEP force generated by a planar interdigitated electrode array placed at an angle to the direction of flow. The simplified line charge model that we developed for the theoretical analysis was verified by comparing it with simulated and measured results. Experimental results showed that the divergent type of microseparator can continuously separate out 87.0% of the red blood cells (RBCs) and 92.1% of the white blood cells (WBCs) from dilute whole blood within 5 min simply by using a 2 MHz, 3 Vp-p AC voltage to create a gradient electric field in a medium that conducts at 17 mS cm(-1). Under the same conditions, the convergent type of microseparator could separate out 93.6% of the RBCs and 76.9% of the WBCs. We have shown that our lateral-driven continuous DEP microseparator design is practical for the continuous separation of blood cells without the need to control the conductivity of the suspension medium, overcoming critical drawbacks of DEP microseparators.
Role of thioredoxin in the response of normal and transformed cells to histone deacetylase inhibitors (2005)

This study examines the basis of resistance and sensitivity of normal and transformed cells to histone deacetylase inhibitor (HDACi)-induced cell death, specifically the role of caspases and thioredoxin (Trx). An important attribute of HDACis is that they induce cancer cell death at concentrations to which normal cells are relatively resistant, making them well suited for cancer therapy. The mechanism underlying this selectivity has not been understood. In this study we found that the HDACi suberoylanilide hydroxamic acid (SAHA) and MS-275, a benzamide, cause an accumulation of reactive oxygen species (ROS) and caspase activation in transformed but not normal cells. Inhibition of caspases does not block HDACi-induced cell death. These studies provide a possible mechanism that can explain why normal but not certain transformed cells are resistant to HDACi-induced cell death. The HDACi causes an increase in the level of Trx, a major reducing protein for many targets, in normal cells but not in transformed cells. The SAHA-induced increase in Trx activity in normal cells is associated with no increase in ROS accumulation. Transfection of transformed cells with Trx small interfering RNA caused a marked decrease in the level of Trx protein with an increase in ROS, a decrease in cell proliferation, and an increase in sensitivity to SAHA-induced cell death. Thus, Trx, independent of the caspase apoptotic pathway, is an important determinant of resistance of cells to HDACi-induced cell death.
Electrochemical Synthesis of Methanol from  CO 2 in High‐Pressure Electrolyte (1997)

We synthesized from and on a copper cathode in the high‐pressure system. Methanol was the only product of reduction detected in the electrolytic solution, with a maximum current efficiency for methanol production of 40% at a current density of 9 mA/cm2 and potential of −1.1 V vs. Ag/AgCl. This is the highest efficiency yet reported for methanol production at this current density. Current‐potential curves shifted in the positive potential direction with increasing temperature and with increasing pressure up to approximately 60 atm. When the applied potential is more negative than about −1.2 V vs. Ag/AgCl, the current density decreases dramatically with time. Electrolyte conductivity in this system increases with increasing temperature, increasing concentration of LiCl, and decreasing pressure.
Expression of a conserved cell-type-specific protein in nerve terminals coincides with synaptogenesis. (1991)

Contact of axons with target territories results in the formation of synapses, specific junctional complexes that may represent a final stage of neuronal maturation. Synaptosomal-associated protein 25 (SNAP-25) is a component of particular nerve terminals recently identified in rodent brain. To evaluate the structure and regulation of molecular components of the synapse, we investigated the expression of SNAP-25 in the developing chicken nervous system. Analysis of SNAP-25 cDNA clones demonstrated that the chicken homologue is identical in amino acid sequence to the mouse protein. In chicken retina and neural tube, the onset of SNAP-25 mRNA and protein expression was found to correspond to the time of synaptogenesis. These results suggest that SNAP-25 plays a role in the physiology of mature nerve terminals and that its expression may be regulated by specific cell-cell interactions occurring during synapse formation.
Fibroblasts, myofibroblasts, and wound contraction (1994)

clinical case reconstructed by Guido
Cytokine Response To Respiratory Syncytial Virus Stimulation Of Human (1994)

A key impediment to developing respiratory syncytial virus (RSV) vaccines is a lack of understanding of enhanced disease that occurred in children who received a formalin-inactivated RSV (FI-RSV) vaccine. Studies in mice have suggested that the FI-RSV vaccine induces a TH2 and live RSV induces a TH1 memory T cell response. In this study, the cytokine mRNA response of peripheral blood mononuclear cells (PBMC) from adults and children with and without previous RSV infection was characterized using a semiquantitative polymerase chain reaction (PCR). PBMC from 22 subjects previously infected with RSV usually had RSV-specific increases in TH1 cytokine-specific mRNA (interferon-gamma [IFN-gamma] mRNA, 20; interleukin [IL]-2 mRNA, 12; IL-5 mRNA, 6; and IL-4 mRNA, 0). PBMC from RSV antibody-negative children had no RSV-specific increases in IFN-gamma, IL-2, or IL-4 mRNA; 1 of 7 had an increase in IL-5 mRNA. These data indicate that naturally acquired RSV induces a TH1 memory T cell response.
Endothelin-binding inhibitors, BE-18257A and BE-18257B. II. Structure determination. (1991)

The structures of novel endothelin-binding inhibitors, BE-18257A and BE-18257B, were elucidated by spectral analyses and chemical studies. Both inhibitors were found to have a cyclic pentapeptide structure containing three D-form amino acid residues, namely, the structures of BE-18257A and BE-18257B were elucidated to be cyclo(-D-Glu-L-Ala-D-Val-L-Leu-D-Trp-) and cyclo(-D-Glu-L-Ala-allo-D-Ile-L-Leu-D-Trp-), respectively.
Construction of nondefective adenovirus type 5 bearing a 2.8-kilobase hepatitis B virus DNA near the right end of its genome (1985)

A novel helper-free adenovirus type 5 (Ad5) vector system, which utilizes a cloning site 0.2 kilobase (kb) from the right end of the genome, has been developed. To construct a nondefective Ad5 bearing the 2.8-kb DNA fragment of hepatitis B virus (HBV) at this site, we deleted the 2.1-kb nonessential E3 fragment from cloned DNA covering the right one-fourth of the Ad5 genome (76 to 100 map units), inserted the HBV DNA into this site, ligated the recombinant DNA to the rest of the Ad5 genome, and transfected the ligated DNA into human embryo kidney cells. Most of the recovered virus clones had only the E3 deletion and no HBV insertion, suggesting that a homologous recombination occurs between transfected DNAs in these cells. The isolated Ad5 virus bearing the HBV DNA (Ad5-HBL) grew without helper virus in HeLa cells as efficiently as wild-type Ad5, although the 1.9-kb major E4 transcript was detected only poorly in the early phase in the Ad5-HBL-infected cells, suggesting that the HBV DNA inserted upstream of the E4 promoter reduces the E4 transcript. HBV mRNAs transcribed from the inserted DNA were at least as abundant as Ad5 early mRNAs in the late phase of Ad5-HBL infection, but the HBV surface antigen was barely detectable in the infected-cell lysate and culture medium. This result suggests that HBV mRNAs can be transcribed from the inserted genes but no protein can be translated from the HBV mRNAs, presumably because of the translational suppression of cellular mRNAs caused by adenovirus in its late phase.
Catalytic Markovnikov and anti‐Markovnikov Functionalization of Alkenes and Alkynes: Recent Developments and Trends (2004)

The regioselective functionalization of terminal alkenes and alkynes is of utmost importance for the synthesis of a wide variety of organic products. Based on the original observation by Vladimir Markovnikov-the pioneer of this field of research-in the 19th century, the possible regioisomeric products are classified as Markovnikov or anti-Markovnikov products. Contrary to traditional belief, it is nowadays possible to control the regiochemistry of various additions of nucleophiles to alkenes and alkynes by applying different transition-metal catalysts. Recent developments in this area of selective functionalization of alkenes and alkynes are reviewed.
Restriction fragment length polymorphism analysis using IS6110 as an epidemiological marker in tuberculosis (1991)

The mycobacterial insertion sequence IS6110 has been shown to be present in multiple copies in the chromosome of Mycobacterium tuberculosis. IS6110 restriction fragment length polymorphism analysis of strains isolated from patients who developed tuberculosis showed identical patterns over a 2- to 3-year period. In contrast, a high degree of polymorphism was observed between strains of the M. tuberculosis complex isolated from different patients. This study demonstrates that the presence of IS6110 does not induce in vivo major genomic rearrangements over a 2- to 3-year period and confirms its use as a valuable epidemiological marker in tuberculosis.
Increased cellular expression of matrix proteins that regulate mineralization is associated with calcification of native human and porcine xenograft bioprosthetic heart valves. (1997)

Dystrophic mineralization remains the leading cause of stenotic or regurgitant failure in native human and porcine bioprosthetic heart valves. We hypothesized that cellular expression of noncollagenous matrix proteins (osteopontin, osteocalcin, and osteonectin) that regulate skeletal mineralization may orchestrate valvular calcification. Porcine bioprosthetic heart valves and native human heart valves obtained during replacement surgery were analyzed for cells, matrix proteins that regulate mineralization, and vessels. Cell accumulation and calcification were correlated for both valve types (rho = 0.75, P = 0.01, native; rho = 0.42, P = 0.08, bioprosthetic). Osteopontin expression correlated with cell accumulation (rho = 0.58, P = 0.04) and calcification (rho = 0.52, P = 0.06) for bioprosthetic valves. Osteocalcin expression correlated with calcification (rho = 0.77, P = 0.04) and cell accumulation (rho = 0.69, P = 0.07) in native valves. Comparisons of calcified versus noncalcified native and bioprosthetic valves for averaged total matrix protein mRNA signal score revealed increased noncollagenous proteins mRNA levels in calcified valves (P = 0.07, group I vs. group II; P = 0.02, group III vs. group IV). When stratified according to positive versus negative mRNA signal status, both calcified bioprosthetic valves (P = 0.03) and calcified native valves (P = 0.01) were significantly more positive for noncollagenous proteins mRNA than their noncalcified counterparts. Local cell-associated expression of proteins regulating mineralization suggests a highly coordinated mechanism of bioprosthetic and native valve calcification analogous to physiologic bone mineralization. Modulation of cellular infiltration or cellular expression of matrix proteins that regulate mineralization, may offer an effective therapeutic approach to the prevention of valve failure secondary to calcification.
P2X7 receptor-mediated Nlrp3-inflammasome activation is a genetic determinant of macrophage-dependent crescentic glomerulonephritis (2012)

P2RX7, a mediator of IL-1β and IL-18 processing and release, is a ligand-gated cation channel that is expressed by macrophages. In experimental Crgn, P2RX7 deficiency attenuates renal injury, but the underlying mechanism is unknown. Here, we show that P2RX7 levels and the expression of several genes belonging to the Nlrp3-inflammasome pathway are up-regulated in the macrophages of the WKY rat, a strain uniquely susceptible to macrophage-dependent NTN. Importantly, following P2RX7 activation, WKY BMDMs produce markedly increased levels of active caspase-1, IL-1β, and IL-18 when compared with the NTN-resistant LEW rat BMDMs. P2RX7 and active IL-1β, IL-18, and caspase-1 protein levels were markedly increased in the WKY nephritic glomeruli 4 days following induction of NTN, and the use of a P2RX7 antagonist reduced the levels of secreted active IL-1β. Interestingly, the post-translational control of P2RX7-mediated inflammasome activation is under the genetic regulation of two previously identified Crgn quantitative trait loci in the BMDMs and nephritic glomeruli of the WKY rat. In conclusion, we propose a novel mechanism, whereby genetically determined P2RX7 levels in macrophages regulate Nlrp3-inflammasome activation and susceptibility to Crgn.
Regioselective O-Derivatization of Quercetin via Ester Intermediates. An Improved Synthesis of Rhamnetin and Development of a New Mitochondriotropic Derivative (2010)

The regioselective synthesis of several quercetin (3,3',4',5,7-pentahydroxy flavone) tetraesters bearing a single free OH on 5-C was achieved in good yield by proper choice of reaction conditions using common esterification procedures. Tetracetylated quercetin with the free OH on 7-C was selectively obtained instead via imidazole-promoted deacylation of the corresponding pentaester. Unambiguous structural characterization of the two isomeric tetraacetyl quercetin derivatives was obtained by combined HSQC and HMBC 2D-NMR analysis. These molecules can be used as starting materials for the regioselective synthesis of other derivatives. High yield syntheses of the natural polyphenol rhamnetin (7-O-methylquercetin) and of the new mitochondriotropic compound 7-(4-triphenylphosphoniumbutyl) quercetin iodide are reported as examples.