gebhart/patrepeval huggingface dataset:
Inducible expression of amplified human beta interferon genes in CHO cells. (1984)

Plasmid DNA containing the human beta-interferon (IFN-beta) gene and mouse dihydrofolate reductase cDNA was transfected into dihydrofolate reductase-negative Chinese hamster ovary cells. Dihydrofolate reductase-positive transformants were obtained, and cells containing amplified copies of mouse dihydrofolate reductase were selected by exposure to increasing methotrexate concentrations. These cells were found to express high levels of human IFN-beta after polyriboinosinic acid-polyribocytidylic acid superinduction or NDV infection; this was a result of coamplification of the IFN-beta gene. Levels of expression of 1 U/cell per day were achieved on superinduction, giving corresponding titers of up to 10(10) U/liter medium in culture supernatants. Constitutive production of IFN-beta rates of about 0.5% of superinduced rates was observed; cells producing these levels of IFN-beta had acquired resistance to cytotoxic antiviral effects of IFN-beta. Two forms of human IFN-beta were produced; a major glycosylated 23,000-dalton form and an unglycosylated 18,500-dalton form. The latter had greatly reduced antiviral activity. IFN-beta production was very sensitive to cellular growth rate; the highest levels were produced by density-arrested cultures. Regulation of IFN-beta production by polyriboinosinic acid-polyribocytidylic acid or by cell density effects required the presence of DNA sequences 5' to the IFN-beta-coding sequences; replacement of these sequences with the simian virus 40 early promoter resulted in uninducible, density-independent production of IFN-beta.
Ki-67 immunostaining in 322 primary breast cancers: Associations with clinical and pathological variables and prognosis (1997)

Cell-proliferation markers are very important in the clinical management of cancer patients, and the identification of Ki-67 (a monoclonal antibody that recognizes proliferating cells) can make it easier to define the level of proliferative activity. This study investigated the associations between the Ki-67 levels measured by means of immunohistochemistry, and other clinical and pathological variables and prognosis in 322 breast-cancer patients. A significant association was found (p < 0.001) between Ki-67 values and tumor size, nodal status, estrogen and progesterone receptor status; multivariate analysis showed that Ki-67 levels were associated with disease-free and overall survival, thus confirming that it is an independent prognostic variable. Various statistical approaches were used in an attempt to establish the best cut-off point for dividing patients into groups at high or low risk of relapse but, in this series, we could find no evidence leading to a single "best" cut-off point. We conclude that the quantitative level of Ki-67 could be used as a prognostic factor in breast-cancer patients.
Design and implementation of multi-frequency magnetic field generator producing sinusoidal current waveform for biological researches (2016)

Recently, induction heating systems are being widely used in many applications, and wireless power transmission systems are being introduced into commercially available electrical vehicles. These applications use time varying magnetic fields (under 100 kHz) which are in close proximity of the human body. Therefore, it should be discussed an influence of the time varying magnetic fields around 100 kHz to the human body. This paper presents design and implementation of a magnetic field generator for biological research. While conventional magnetic field generators only produce one frequency component, this paper discusses a multi-frequency range magnetic field generator with frequencies of 200 Hz and 20 kHz. In addition, actual systems with the inverter circuits for the purpose of biological evaluation are presented.
The use of bootstrapping when using propensity‐score matching without replacement: a simulation study (2014)

Propensity-score matching is frequently used to estimate the effect of treatments, exposures, and interventions when using observational data. An important issue when using propensity-score matching is how to estimate the standard error of the estimated treatment effect. Accurate variance estimation permits construction of confidence intervals that have the advertised coverage rates and tests of statistical significance that have the correct type I error rates. There is disagreement in the literature as to how standard errors should be estimated. The bootstrap is a commonly used resampling method that permits estimation of the sampling variability of estimated parameters. Bootstrap methods are rarely used in conjunction with propensity-score matching. We propose two different bootstrap methods for use when using propensity-score matching without replacementand examined their performance with a series of Monte Carlo simulations. The first method involved drawing bootstrap samples from the matched pairs in the propensity-score-matched sample. The second method involved drawing bootstrap samples from the original sample and estimating the propensity score separately in each bootstrap sample and creating a matched sample within each of these bootstrap samples. The former approach was found to result in estimates of the standard error that were closer to the empirical standard deviation of the sampling distribution of estimated effects.
Heat Resistance of Xerophilic Fungi Based on Microscopical Assessment of Spore Survival (1970)

An improved viable counting technique was developed to facilitate study of the heat resistance of fungal spores. Spores were heated and subsequently incubated in the same medium. After germination, hyphae and germ tubes were stained with lactofuchsin, and the germinated spores were counted with the aid of a microscope. A number of xerophilic strains were examined, mostly isolates from spoiled highmoisture prunes. Of these, ascospores of Aspergillus chevalieri, A. mangini, and Xeromyces bisporus were the most heat-resistant. A decimal reduction curve obtained for A. chevalieri was specified by a z value of 23 F and an F(180) of 2.2 min.
Influence of the subendothelial basement membrane components on fibrin assembly. Evidence for a fibrin binding site on type IV collagen. (1988)

Effective repair of a vascular injury depends on establishment of a stable fibrin patch at the injury site. Data presented in this study demonstrate that structural modification of fibrin occurs as a result of fibrin interaction with naturally occurring components of the vascular basement membrane and subendothelial structures. Of the basement membrane components, type IV collagen produces the greatest structural modification, generating thick fibrin fibers; a 3-fold increase in the fiber mass/length ratio occurs when type IV collagen is increased from 0 to 100 ng/ml. Laminin and dermatan sulfate decrease the fibrin fiber mass/length ratio resulting in thinner fibers. However, the overall effect of the basement membrane on fibrin is to increase the fibrin fiber diameter. Electrophoretic light scattering and the binding of type IV collagen by fibrinogen-Sepharose further establish the interaction between type IV collagen and fibrinogen. Incorporation of laminin with type IV collagen onto coated surfaces decreases the ability of type IV collagen to bind fibrinogen. These studies emphasize that the final fibrin structure is influenced by the milieu in which the clot is assembled.
Class I Major Histocompatibility Complexes Loaded by a Periodate Trigger (2009)

Class I major histocompatibility complexes (MHCs) present peptide ligands on the cell surface for recognition by appropriate cytotoxic T cells. The unstable nature of unliganded MHC necessitates the production of recombinant class I complexes through in vitro refolding reactions in the presence of an added excess of peptides. This strategy is not amenable to high-throughput production of vast collections of class I complexes. To address this issue, we recently designed photocaged MHC ligands that can be cleaved by a UV light trigger in the MHC bound state under conditions that do not affect the integrity of the MHC structure. The results obtained with photocaged MHC ligands demonstrate that conditional MHC ligands can form a generally applicable concept for the creation of defined peptide-MHCs. However, the use of UV exposure to mediate ligand exchange is unsuited for a number of applications, due to the lack of UV penetration through cell culture systems and due to the transfer of heat upon UV irradiation, which can induce evaporation. To overcome these limitations, here, we provide proof-of-concept for the generation of defined peptide-MHCs by chemical trigger-induced ligand exchange. The crystal structure of the MHC with the novel chemosensitive ligand showcases that the ligand occupies the expected binding site, in a conformation where the hydroxyl groups should be reactive to periodate. We proceed to validate this technology by producing peptide-MHCs that can be used for T cell detection. The methodology that we describe here should allow loading of MHCs with defined peptides in cell culture devices, thereby permitting antigen-specific T cell expansion and purification for cell therapy. In addition, this technology will be useful to develop miniaturized assay systems for performing high-throughput screens for natural and unnatural MHC ligands.
Palladium Catalysts for the Suzuki Cross-Coupling Reaction: An Overview of Recent Advances (2004)

This review with 206 references covers the literature published until March 2004 on the development and applications of new efficient catalyst systems for the Suzuki palladium-catalysed cross-coupling reaction of organoboron compounds with organic electrophiles. Where possible, the relative advantages of the new catalyst systems in this synthetically very important carbon-carbon bond forming reaction have been compared. 1 Introduction 2 Palladacycle Complexes as Catalyst Precursors 3 Catalyst Systems Composed of Pd(0) or Pd(II) Derivatives and Electron-Rich and/or Bulky Phosphine Ligands 4 Catalyst Systems Composed of Pd(0) or Pd(II) Derivatives and N-Heterocyclic Carbene Ligands 5 Water-Soluble Catalyst Precursors 6 Ligandless Catalyst Precursors 7 Other Novel Pd Catalyst Precursors 8 Conclusions
Method for grafting poly(acrylic acid) onto nylon 6,6 using amine end groups on nylon surface (2002)

Abstract Several methods have been developed for grafting materials to the surface of polymers to alter their surface characteristics. This article reports a procedure for grafting poly(acrylic acid) (PAA) onto nylon 6,6 films via the naturally occurring amine end groups of nylon 6,6 using N ‐hydroxy‐succinimide in conjunction with 1‐ethyl‐3‐ (3‐dimethylaminopropyl)carbodiimide hydrochloride (EDC) facilitated amidazation. Reaction conditions were investigated with respect to PAA molecular weight, activator concentrations, reaction temperature, and time. X‐ray photoelectron spectroscopy showed that surface coverage of more than 50% was consistently achieved for 250 kD PAA. The maximum grafting occurred at room temperature with a large excess of EDC with a reaction time of 30 min. The same level of grafting can be achieved using smaller amounts of EDC at 60 °C. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 719–728, 2002; DOI 10.1002/pola.10149
Web Host Access Tool: A Support Vector Machine Approach (2006)

Search engines are an integral part of web information gathering and retrieval process, but they are significantly dependent upon the words or word phrases input by the end user. The search engine usually contributes no additional semantic data toward the information acquisition process. This paper presents an intelligent search agent "Web host access tool" (WHAT) based on support vector machines (SVM), which introduces the notion of queries conducted within a specific contextual meaning. Given a context and associated keywords that personalize the search history and preferences of the user, WHAT performs more intelligent resource filtering than conventional search engines, providing more relevant results while filtering the irrelevant references. Search results obtained in the form of text from different search engines are processed by the SVM based word classifier that arrange the results obtained according to user preference obtained from previous search processes. The text materials are processed by Latent Semantic Indexing (LSI) for creating a document matrix that gives the probability of a word occurrence in a specified context. For simplicity, this paper considers 5 different contexts: business, education, entertainment, news and information and tourism. The LSI coefficients were used by SVM to yield confidence levels for each search result and according to that the results were sorted and presented to the end user. As an alternative, least square support vector machines (LS-SVM) are also studied in this paper. The system is updated by the user that provides feedback regarding the search relevance, based on which the LSI coefficients are updated to ensure increased relevance in future searches. Three different types of kernel function were considered in this paper -Linear. Radial basis function (RBF) and polynomial kernel. Results claim that Linear SVM perform better than the others, not only in terms of classification accuracy but also in terms of training speed.
Readily Available Unprotected Amino Aldehydes (2006)

We report a new class of bench-stable compounds that contain seemingly incompatible functional groups: an aldehyde and an unprotected secondary amine. The thermodynamic driving force to undergo condensation between these two functionalities is offset by a high barrier imposed on this process by the aziridine ring strain. The resulting amino aldehydes exist as dimers and in the solid state. They are stable to epimerization and contain two orthogonal reaction centers, namely, an amine/aziridine and an aldehyde. Their ability to act as linchpins has been evaluated in complex heterocycle synthesis. For instance, pentacyclic frameworks can be made in one simple operation using N-benzyltryptamine as the reaction partner. Construction of other molecular skeletons with minimal use of protecting group manipulations should be feasible.
Regulating Innovation: High Frequency Trading in Dark Pools (2017)

Federal statutes regulate risk-taking by financial market intermediaries including the broker-dealers who execute trades and the securities exchange and clearinghouse platforms where trading occurs. For almost a century, these statutes have enforced norms that encourage disclosure, transparency, and fairness. In modern markets, innovation, and technology challenge these core principles of regulation. The engineering of computer-driven automated trade execution, the development of algorithmic trading, and the introduction of high frequency trading strategies accompany a number of important shifts in financial market intermediation. 
First, a universe of private trading platforms known as alternative trading systems (ATSs) increasingly compete with and displace conventional exchanges. ATSs include a small group of platforms known as “dark pools” that engender critical benefits. Dark pools mitigate information leakage, enabling institutional investors to execute large block trade transactions without fear that imitators will replicate or that predators may prey on their trades. 
Second, dark pools intermediate trading with limited regulatory oversight. These private pools function in a manner similar to conventional securities exchanges and clearinghouse platforms; yet, dark pools are subject to a lighter-touch regulatory framework. As a result, hidden dark pool trades enjoy reduced regulatory, compliance, and transaction costs. Unsurprisingly, the volume of dark pool transactions has grown exponentially, eclipsing conventional trading venues’ market share and redefining the balance of power in the financial market ecosystem. 
Third, fragmentation has fractured trading markets. The transition from a small body of actors with quasi-monopolistic power to a diverse body of trading venues challenges antiquated notions regarding financial intermediaries’ role in facilitating price discovery, identifying market manipulation, and employing best practices for ensuring fairness and protecting the integrity of financial markets. 
This Article argues that gaps in governance, contentious conflicts of interest, and increasingly intense fragmentation in trading markets create a growing source of underexplored concerns. An examination of the current regulatory framework reveals noteworthy perils including the potential for high volatility and significant market disruption. These concerns necessitate exploring ex ante the various enforcement measures, regulations, governance protocols, and information gathering tools already employed in markets to mitigate systemic risk concerns. This Article cautions regulators and commentators to emphasize dynamic, sustainable macroprudential regulatory solutions.
Programmable cells: Interfacing natural and engineered gene networks (2004)

Novel cellular behaviors and characteristics can be obtained by coupling engineered gene networks to the cell's natural regulatory circuitry through appropriately designed input and output interfaces. Here, we demonstrate how an engineered genetic circuit can be used to construct cells that respond to biological signals in a predetermined and programmable fashion. We employ a modular design strategy to create Escherichia coli strains where a genetic toggle switch is interfaced with: (i) the SOS signaling pathway responding to DNA damage, and (ii) a transgenic quorum sensing signaling pathway from Vibrio fischeri. The genetic toggle switch endows these strains with binary response dynamics and an epigenetic inheritance that supports a persistent phenotypic alteration in response to transient signals. These features are exploited to engineer cells that form biofilms in response to DNA-damaging agents and cells that activate protein synthesis when the cell population reaches a critical density. Our work represents a step toward the development of "plug-and-play" genetic circuitry that can be used to create cells with programmable behaviors.
Farnesol production from <i>Escherichia coli</i> by harnessing the exogenous mevalonate pathway (2010)

Farnesol (FOH) production has been carried out in metabolically engineered Escherichia coli. FOH is formed through the depyrophosphorylation of farnesyl pyrophosphate (FPP), which is synthesized from isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) by FPP synthase. In order to increase FPP synthesis, E. coli was metabolically engineered to overexpress ispA and to utilize the foreign mevalonate (MVA) pathway for the efficient synthesis of IPP and DMAPP. Two-phase culture using a decane overlay of the culture broth was applied to reduce volatile loss of FOH produced during culture and to extract FOH from the culture broth. A FOH production of 135.5 mg/L was obtained from the recombinant E. coli harboring the pTispA and pSNA plasmids for ispA overexpression and MVA pathway utilization, respectively. It is interesting to observe that a large amount of FOH could be produced from E. coli without FOH synthase by the augmentation of FPP synthesis. Introduction of the exogenous MVA pathway enabled the dramatic production of FOH by E. coli while no detectable FOH production was observed in the endogenous MEP pathway-only control.
Chemical mechanical polishing: the impact of a new technology on an industry (2002)

Chemical Mechanical Polishing (CMP), a technology born in IBM Confidential culture, has remained true to its heritage not only because of its significant competitive advantage, but because of the history of its birth in the semiconductor industry. In spite of this heritage, CMP has grown from its invention in 1984, to one of the fastest growing segments of the semiconductor equipment industry. In 1997 the growth rate of CMP equipment averaged 30% in comparison with the rest of the semiconductor equipment market. The factors that enabled this dynamic growth include both the technical advantages of CMP and the history of its development and subsequent spread into the industry. The growth of CMP technology has spawned new business and supplier networks as well as new fields of study. As the science of CMP evolves, it continues to borrow from several diverse technical fields and has created a new science within semiconductors.
Analysis of short tandem repeat polymorphisms by electrospray ion trap mass spectrometry (2000)

The application of electrospray ionization (ESI) ion trap mass spectrometry (MS) to the analysis of short tandem repeats (STRs or microsatellites) is described. Several equine dinucleotide STR loci were chosen as a model system to evaluate ESI ion trap as a routine instrument for rapid and reliable genoytping. With the use of specific primers STR loci were amplified from different blood samples having allele sizes between 60 and 100 bp. A new purification method based on reversible binding of PCR products to magnetic particles has proven to be directly compatible with ESI ion trap MS analysis. The sense and antisense strands of the PCR products with concentrations of approximately 100 fmol/microliter were measured with a mass accuracy of 0.01%. The simplicity of the purification method and the capability for automated handling together with the precise sizing of PCR products by ESI ion trap MS facilitate the large scale analysis of polymorphic STRs. Moreover, mixtures of different allele length as obtained for heterozygous samples could accurately be assigned as well as a C-->G switch between the two strands of a PCR product.
A Single Intracellular Cysteine Residue Is Responsible for the Activation of the Olfactory Cyclic Nucleotide-gated Channel by NO (2000)

The activation of cyclic nucleotide-gated (CNG) channels is the final step in olfactory and visual transduction. Previously we have shown that, in addition to their activation by cyclic nucleotides, nitric oxide (NO)-generating compounds can directly open olfactory CNG channels through a redox reaction that results in the S-nitrosylation of a free SH group on a cysteine residue. To identify the target site(s) of NO, we have now mutated the four candidate intracellular cysteine residues Cys-460, Cys-484, Cys-520, and Cys-552 of the rat olfactory rCNG2 (alpha) channel into serine residues. All mutant channels continue to be activated by cyclic nucleotides, but only one of them, the C460S mutant channel, exhibited a total loss of NO sensitivity. This result was further supported by a similar lack of NO sensitivity that we found for a natural mutant of this precise cysteine residue, the Drosophila melanogaster CNG channel. Cys-460 is located in the C-linker region of the channel known to be important in channel gating. Kinetic analyses suggested that at least two of these Cys-460 residues on different channel subunits were involved in the activation by NO. Our results show that one single cysteine residue is responsible for NO sensitivity but that several channel subunits need to be activated for channel opening by NO.