gebhart/patrepeval huggingface dataset:
ype Graph-Partitioning Algorithms* (1993)

In this paper we present a very efficient graph partitioning scheme Quick-Cut that uses the basic strat- egy of the Kernighan-Lin (I<-L) algorithm to swap pairs of nodes to improve an existing partition of a graph G. The main feature of Quick-Cut is a neighborhood strategy that is based on the result (obtained in this pa- per) that it is not necessary to search more than a certain subset of d2 node pairs to find the node pair with the max- imum swap gain. Here d is the maximum node degree of G. We also use an improved data structure, viz., balanced trees, to store the nodes in the two part,itions. Due to the new search strategy and dat,a struct,ure, Quick-Cut has a worst-case time complexity of O(max(ed, elog n)), and an average-case complexity of O(e1og n), where e is the number of edges of G. The K-L algorithm, on the other hand, has a time complexity of O(n2 log n.), where n is the number of nodes of G. Another contribution of this paper is the presentation of efficient node-pair scanning meth- ods for obtaining the best, node pair to swap in the I<-L algorithm. We have implemented Quick-Cut, I<-L, and its various enhancements suggested here. The results ob- tained from using these different algorithms to partition a number of random and other well-defined graphs show that Quick-Cut is the fastest, and that it is faster than the I<-L algorithm by factors of 5 to 50. Thus Quick-Cut can serve as the basis for very fast VLSI part,itioning and layout tools.
Submucosal gland secretions in airways from cystic fibrosis patients have normal [Na+] and pH but elevated viscosity (2001)

Fluid and macromolecule secretion by submucosal glands in mammalian airways is believed to be important in normal airway physiology and in the pathophysiology of cystic fibrosis (CF). An in situ fluorescence method was applied to measure the ionic composition and viscosity of freshly secreted fluid from airway glands. Fragments of human large airways obtained at the time of lung transplantation were mounted in a humidified perfusion chamber and the mucosal surface was covered by a thin layer of oil. Individual droplets of secreted fluid were microinjected with fluorescent indicators for measurement of [Na(+)], [Cl(-)], and pH by ratio imaging fluorescence microscopy and viscosity by fluorescence recovery after photobleaching. After carbachol stimulation, 0.1--0.5 microl of fluid accumulated in spherical droplets at gland orifices in approximately 3--5 min. In gland fluid from normal human airways, [Na(+)] was 94 +/- 8 mM, [Cl(-)] was 92 +/- 12 mM, and pH was 6.97 +/- 0.06 (SE, n = 7 humans, more than five glands studied per sample). Apparent fluid viscosity was 2.7 +/- 0.3-fold greater than that of saline. Neither [Na(+)] nor pH differed in gland fluid from CF airways, but viscosity was significantly elevated by approximately 2-fold compared to normal airways. These results represent the first direct measurements of ionic composition and viscosity in uncontaminated human gland secretions and indicate similar [Na(+)], [Cl(-)], and pH to that in the airway surface liquid. The elevated gland fluid viscosity in CF may be an important factor promoting bacterial colonization and airway disease.
Melanization in albino mice transformed by introducing cloned mouse tyrosinase gene (1990)

We introduced a mouse tyrosinase minigene, mg-Tyrs-J, in which the authentic genomic 5' non-coding flanking sequence was fused to a mouse tyrosinase cDNA, into fertilized egges of albino mice. Of the 25 animals that developed from the injected eggs, four mice exhibited pigmented hair and eyes. Histological analysis of the transgenic mice revealed that the melanogenesis was restricted to hair bulbs and eyes. These results suggest that this minigene encodes active tyrosinase protein and that its 5' flanking region contains the sequences regulating expression of mouse tyrosinase gene. This is the first report of a successful expression of tyrosinase gene and of pigment production in transgenic mice.
A highly scalable vertical gate (VG) 3D NAND Flash with robust program disturb immunity using a novel PN diode decoding structure (2011)

A novel PN diode decoding method for 3D NAND Flash is proposed. The PN diodes are fabricated self-aligned at the source side of the Vertical Gate (VG) 3D NAND architecture. Contrary to the previous 3D NAND approaches, there is no need to fabricate plural string select (SSL) transistors inside the array, thus enabling a highly symmetrical and scalable cell structure. A novel three-step programming pulse waveform is integrated to implement the program-inhibit method, capitalizing on that the PN diodes can prevent leakage of the self-boosted channel potential. A large program-disturb-free window >5V is demonstrated.
Induced Pluripotent Stem Cell Therapy Ameliorates Hyperoxia-Augmented Ventilator-Induced Lung Injury through Suppressing the Src Pathway (2014)

The data suggest that iPSC-based therapy is capable of partially suppressing acute inflammatory and oxidant responses that occur during hyperoxia-augmented VILI through the inhibition of Src-dependent signaling pathway.
Synergistic interaction between oxaliplatin and SN-38 in human gastric cancer cell lines in vitro (2005)

The interaction between CPT-11 and oxaliplatin, a new platinum derivative that has a great antitumor activity against colon cancer, has not been determined in gastric cancer cells. In this study, we investigated in vitro cytotoxic activity of oxaliplatin alone or in combination with SN-38, an active metabolite of CPT-11, using different exposure schedules in three human gastric cancer cell lines (AZ-521, MKN-45, and NUGC-4). Cytotoxicity was determined by WST-1 assay. Different treatment schedules of the two drugs were compared and evaluated for synergism, additivity, or antagonism with a quantitative method based on the median-effect principle of Chou and Talalay. Cell cycle perturbation was evaluated by flow cytometry. In 24-h exposure, simultaneous administration of oxaliplatin and SN-38 showed a synergistic effect in AZ-521 and NUGC-4 cells, and an additive effect in MKN-45 cells. Greater than additive effects were observed in all of the cell lines when cells were treated with oxaliplatin followed by SN-38, whereas such effects were observed only in NUGC-4 cells in the reverse sequence. Flow cytometric analyses at IC(50) indicated that apoptosis was most prominent in simultaneous exposures with accumulation of cells in both G(0)/G(1) and S phases. These results suggest that SN-38 may kill the cells recovering from the G(1) block produced by oxaliplatin as they progress into the S phase. Simultaneous administration appears most active in gastric cancer cell lines. These results may provide important information for a clinical trial of oxaliplatin and CPT-11 combination for patients with gastric cancer.
Use of a Subcutaneous Glucose Sensor To Detect Decreases in Glucose Concentration Prior to Observation in Blood (1996)

The development of a hypoglycemic alarm system using a subcutaneous glucose sensor implies that a decrease in blood glucose is rapidly followed by a decrease in the signal generated by the sensor. In a first set of experiments the linearity and the kinetics of the response of sensors implanted in the subcutaneous tissue of normal rats were investigated during a progressive increase in plasma glucose concentration: the sensitivities determined between 5 and 10 mM and between 10 and 15 mM were not significantly different, and a 5-10 min delay in the sensor's response was observed. In a second set of experiments, performed in diabetic rats, the kinetics of the decrease in subcutaneous glucose concentration following insulin administration was monitored during a decrease in plasma glucose level, from 15 to 3 mmol/L. During the 20 first min following insulin administration, the sensor monitored glucose concentration in subcutaneous tissue with no lag time. Subsequently, the decrease in the estimation of subcutaneous glucose concentration preceded that of plasma glucose. This phenomenon was not observed when the same sensors were investigated in vitro during a similar decrease in glucose concentration and may be due to a mechanism occurring in vivo, such as the effect of insulin on glucose transfer from the interstitial space to the cells surrounding the sensor. It reinforces the interest of the use of implantable glucose sensors as a part of a hypoglycemic alarm.
Transferrin-adriamycin conjugates which inhibit tumor cell proliferation without interaction with DNA inhibit plasma membrane oxidoreductase and proton release in K562 cells. (1991)

Conjugates of adriamycin crosslinked to transferrin with glutaraldehyde inhibit proliferation of transformed cells. Conjugates of this type inhibit oxidoreductase activity in the plasma membrane of K562 cells, and the inhibition of electron transport is found at concentrations ten times lower than concentrations of free adriamycin which inhibit electron transport and cell growth. The transferrin-adriamycin conjugate inhibits ferricyanide reduction, diferric transferrin reduction and plasma membrane NADH oxidase activity stimulated by transferrin. Activation of proton release from the K562 cells by diferric transferrin also is inhibited by the conjugate, and conjugate kills cells more effectively than free adriamycin. Since the conjugate does not transfer adriamycin to the nucleus, the growth control may be based on inhibition of the transferrin regulated redox system and Na+/H+ antiport activity at the plasma membrane.
Suppression, subversion and escape: the role of regulatory T cells in cancer progression (2012)

Regulatory T cells (T(regs) ) are crucial in mediating immune homeostasis and promoting the establishment and maintenance of peripheral tolerance. However, in the context of cancer their role is more complex, and they are thought to contribute to the progress of many tumours. As cancer cells express both self- and tumour-associated antigens, T(regs) are key to dampening effector cell responses, and therefore represent one of the main obstacles to effective anti-tumour responses. Suppression mechanisms employed by T(regs) are thought to contribute significantly to the failure of current therapies that rely on induction or potentiation of anti-tumour responses. This review will focus on the current evidence supporting the central role of T(regs) in establishing tumour-specific tolerance and promoting cancer escape. We outline the mechanisms underlying their suppressive function and discuss the potential routes of T(regs) accumulation within the tumour, including enhanced recruitment, in-situ or local proliferation, and de-novo differentiation. In addition, we review some of the cancer treatment strategies that act, at least in part, to eliminate or interfere with the function of T(regs) . The role of T(regs) is being recognized increasingly in cancer, and controlling the function of these suppressive cells in the tumour microenvironment without compromising peripheral tolerance represents a significant challenge for cancer therapies.
Development of a Three-Dimensional Transmigration Assay for Testing Cell–Polymer Interactions for Tissue Engineering Applications (2001)

The ability of synthetic or natural scaffolds to support invasion of cells from surrounding tissue is a key parameter for tissue engineering (TE). In this study, the migration of fibroblasts, chondrocytes, and osteoblasts into biodegradable polymer scaffolds was evaluated using a novel, three-dimensional (3-D) transmigration assay. This assay is based on a cell-populated contracted collagen lattice with a biodegradable polymer scaffold implanted at the center of the collagen gel. Cell migration into the scaffolds was assessed both quantitatively and qualitatively following various time lengths in culture using image analysis. Chondrocytes, incorporated within the collagen lattice, migrated into polymer scaffolds, when cultured both statically or in a rotating bioreactor. However, the bioreactor cultures resulted in a significantly greater cell invasion as compared to static cultures. There was a cell density-dependent osteoblast migration from collagen lattice into polymer scaffold, when tested in the transmigration assay. In addition, polymer scaffolds, treated with or without recombinant human platelet-derived growth factor (rh-PDGF-BB) were evaluated for fibroblast migration. The presence of rh-PDGF-BB resulted in significantly greater fibroblast invasion as compared to untreated scaffolds. Our studies suggest that the transmigration model provides a rapid system for testing cell invasion of potential scaffolds for tissue engineering applications.
Inhibitors of Protein Methyltransferases and Demethylases (2017)

Post-translational modifications of histones by protein methyltransferases (PMTs) and histone demethylases (KDMs) play an important role in the regulation of gene expression and transcription and are implicated in cancer and many other diseases. Many of these enzymes also target various nonhistone proteins impacting numerous crucial biological pathways. Given their key biological functions and implications in human diseases, there has been a growing interest in assessing these enzymes as potential therapeutic targets. Consequently, discovering and developing inhibitors of these enzymes has become a very active and fast-growing research area over the past decade. In this review, we cover the discovery, characterization, and biological application of inhibitors of PMTs and KDMs with emphasis on key advancements in the field. We also discuss challenges, opportunities, and future directions in this emerging, exciting research field.
Triamcinolone Acetonide as an Adjuvant in the Surgical Treatment of Retinal Detachment With Proliferative Vitreoretinopathy (2007)

&lt;H4&gt;BACKGROUND AND OBJECTIVE&lt;/H4&gt; &lt;P&gt;To report the efficacy of intravitreal triamcinolone acetonide as an adjuvant in the surgical management of cases with advanced proliferative vitreoretinopathy (PVR).&lt;/P&gt; &lt;H4&gt;PATIENTS AND METHODS&lt;/H4&gt; &lt;P&gt;Patients with complicated rhegmatogenous retinal detachment and PVR grade C2 or greater were recruited for this interventional, noncomparative, prospective study. All patients underwent three-port pars plana vitrectomy, membrane peeling, laser photocoagulation, and silicone oil injection to reattach the retina followed by 0.1 mL (4 mg) of triamcinolone acetonide injected through the pars plana into the silicone oil. All patients had supplemental laser therapy around retinal breaks and retinectomy edges at 1 to 2 weeks postoperatively.&lt;/P&gt; &lt;H4&gt;RESULTS&lt;/H4&gt; &lt;P&gt;Patients included 15 males and 9 females, with an average age of 53.6 years (range: 15 to 84 years) and PVR grade C2 to PVR C9. The mean follow-up period was 11.0 months (range: 3 to 26 months). Twenty-one (87.5%) patients had attached retinas at the final followup visit. Visual acuity improved in all patients following surgery (&lt;I&gt;P&lt;/I&gt; &lt; .05).&lt;/P&gt; &lt;H4&gt;CONCLUSION&lt;/H4&gt; &lt;P&gt;Triamcinolone acetonide may have potential as an adjuvant in the treatment of retinal detachment with PVR. Further research is required to evaluate the efficacy of this adjuvant treatment.&lt;/P&gt; &lt;P&gt;[&lt;CITE&gt;Ophthalmic Surg Lasers Imaging&lt;/CITE&gt; 2007;38:365- 370.]&lt;/P&gt; &lt;H4&gt;AUTHORS&lt;/H4&gt; &lt;P&gt;From the Cardiff Eye Unit (RAC, AJ, ADL, KL), University Hospital of Wales, Cardiff, United Kingdom; the Department of Ophthalmology and Vision Science (GAP), University of Arizona College of Medicine, Tucson, Arizona; and South Texas Eye Consultants (TF), Corpus Christi, Texas.&lt;/P&gt; &lt;P&gt;Accepted for publication November 20, 2006.&lt;/P&gt; &lt;P&gt;Address correspondence to Gholam A. Peyman, MD, Department of Ophthalmology and Vision Science, University of Arizona College of Medicine, 655 North Alvernon Way, Suite 108, Tucson, AZ 85711.&lt;/P&gt;
Discovery of the mammalian insulin release modulator, hepoxilin B3, from the tropical red algae Platysiphonia miniata and Cottoniella filamentosa. (1990)

The insulin release enhancer, 10-hydroxy-11,12-trans-epoxy-5(Z),8(Z),14(Z)-icosatrienoic acid (hepoxilin B3), is a 12-lipoxygenase metabolite of arachidonic acid that has been found in various mammalian tissues. Although lipoxygenase pathways are well documented in terrestrial plants, this lipoxygenase product has never been isolated from the plant kingdom. Herein, we report the first isolation of this lipoxygenase product, hepoxilin B3, from two plants, the tropical red marine algae Platysiphonia miniata (C. Agardh) Børgesen and Cottoniella filamentosa Børgesen. Furthermore, through application of two-dimensional NMR methodology to the structural description of this algal natural product, we demonstrate the tremendous power of this technique in this chemical class.
Silicon RFCMOS SOI technology with above-IC MEMS integration for front end wireless applications (2008)

We describe a 0.18/0.5 um RF CMOS thick Silicon-On-Insulator (SOI) technology built on high resistivity (1 kOhm-cm) substrates. A high performance/high power RF MEMS contact switch can also be integrated in the technology through above-IC post-processing. This RFCMOS/MEMS integrated technology provides a platform for cost-effective monolithic integration of several RF RX/TX functions for next generation wireless system applications. The silicon SOI technology also includes the integration of a solid-state RF switch, and a RF power LDMOS transistor with good linear and saturated RF power characteristics in the frequency range between 0.8 GH - 2.4 GHz. We present measured results of MEMS and FET solid-state RF switches, RF power devices, as well as characterization data integrated power management circuits.
Model of visual contrast gain control and pattern masking (1997)

We have implemented a model of contrast gain and control in human vision that incorporates a number of key features, including a contrast sensitivity function, multiple oriented bandpass channels, accelerating nonlinearities, and a devisive inhibitory gain control pool. The parameters of this model have been optimized through a fit to the recent data that describe masking of a Gabor function by cosine and Gabor masks [J. M. Foley, "Human luminance pattern mechanisms: masking experiments require a new model," J. Opt. Soc. Am. A 11, 1710 (1994)]. The model achieves a good fit to the data. We also demonstrate how the concept of recruitment may accommodate a variant of this model in which excitatory and inhibitory paths have a common accelerating nonlinearity, but which include multiple channels tuned to different levels of contrast.
Valency of Antibody Binding to Enveloped Virus Particles as Determined by Surface Plasmon Resonance (2002)

A simple method is described for determining the valency of binding of immunoglobulin G to immobilized influenza A virus. Where there is a free Fab arm (monovalent binding), a second virus particle is captured. This is detected by surface plasmon resonance. The methodology should be applicable to all enveloped and nonenveloped viruses.
DNA Cleavage by Copper−ATCUN Complexes. Factors Influencing Cleavage Mechanism and Linearization of dsDNA (2005)

The reactivity of two [peptide-Cu] complexes ([GGH-Cu](-) and [KGHK-Cu](+)) toward DNA cleavage has been quantitatively investigated. Neither complex promoted hydrolytic cleavage, but efficient oxidative cleavage was observed in the presence of a mild reducing agent (ascorbate) and dioxygen. Studies with scavengers of ROS confirmed hydrogen peroxide to be an obligatory diffusible intermediate. While oxidative cleavage of DNA was observed for Cu(2+)(aq) under the conditions used, the kinetics of cleavage and reaction products/pathway were distinct from those displayed by [peptide-Cu] complexes. DNA cleavage chemistry is mediated by the H(2)O-dependent pathway following C-4'H abstraction from the minor groove. Such a cleavage path also provides a ready explanation for the linearization reaction promoted by [KGHK-Cu](+). Kinetic activities and reaction pathways are compared to published results on other chemical nucleases. Both [peptide-Cu] complexes were found to display second-order kinetics, with rate constants k(2) approximately 39 and 93 M(-1) s(-1) for [GGH-Cu](-) and [KGHK-Cu](+), respectively. Neither complex displayed enzyme-like saturation behavior, consistent with the relatively low binding affinity and residence time expected for association with dsDNA, and the absence of a prereaction complex. However, the intrinsic activity of each is superior to other catalyst systems, as determined from relative k(2) or k(cat)/K(m) values. Linearization of DNA was observed for [KGHK-Cu](+) relative to [GGH-Cu](-), consistent with the increased positive charge and longer residency time on dsDNA.
Compression of high-energy laser pulses below 5 fs (1997)

High-energy 20-fs pulses generated by a Ti:sapphire laser system were spectrally broadened to more than 250 nm by self-phase modulation in a hollow fiber filled with noble gases and subsequently compressed in a broadband high-throughput dispersive system. Pulses as short as 4.5 fs with energy up to 20-microJ were obtained with krypton, while pulses as short as 5 fs with energy up to 70 microJ were obtained with argon. These pulses are, to our knowledge, the shortest generated to date at multigigawatt peak powers.
Cross-linked redox gels containing glucose oxidase for amperometric biosensor applications (1990)

Oxidoreductases, such as glucose oxidase, can be electrically "wired" to electrodes by electrostatic complexing or by covalent binding of redox polymers so that the electrons flow from the enzyme, through the polymer, to the electrode. We describe two materials for amperometric biosensors based on a cross-linkable poly(vinylpyridine) complex of [Os-(bpy)2Cl]+2+ that communicates electrically with flavin adenine dinucleotide redox centers of enzymes such as glucose oxidase. The uncomplexed pyridines of the poly(vinylpyridine) are quaternized with two types of groups, one promoting hydrophilicity (2-bromoethanol or 3-bromopropionic acid), the other containing an active ester (N-hydroxysuccinimide) that forms amide bonds with both lysines on the enzyme surface and with an added polyamine cross-linking agent (triethylenetetraamine, trien). In the presence of glucose oxidase and trien this polymer forms rugged, cross-linked, electroactive films on the surface of electrodes, thereby eliminating the requirement for a membrane for containing the enzyme and redox couple. The glucose response time of the resulting electrodes is less than 10 s. The glucose response under N2 shows an apparent Michaelis constant, Km' = 7.3 mM, and limiting current densities, jmax, between 100 and 800 microA/cm2. Currents are decreased by 30-50% in air-saturated solutions because of competition between O2 and the Os(III) complex for electrons from the reduced enzyme. Rotating ring desk experiments in air-saturated solutions containing 10 mM glucose show that about 20% of the active enzyme is electrooxidized via the Os(III) complex, while the rest is oxidized by O2. These results suggest that only part of the active enzyme is in electrical contact with the electrode.