gebhart/patrepeval huggingface dataset:
Cellular transformation by cigarette smoke extract involves alteration of glycolysis and mitochondrial function in esophageal epithelial cells (2009)

Cigarette-smoking increases the risk of developing various types of human cancers including esophageal cancers. To test the effects of chronic cigarette smoke exposure directly on esophageal epithelium, cellular resistance to mainstream extract (MSE), or sidestream smoke extract (SSE) was developed in chronically exposed nonmalignant Het-1A cells. Anchorage-independent growth, in vitro invasion capacity and proliferation of the resistant cells increased compared with the unexposed, sensitive cells. An epithelial marker E-cadherin was down-regulated and mesenchymal markers N-cadherin and vimentin were up-regulated in the resistant cells. Het-1A cells resistant to MSE or SSE consumed more glucose, and produced more lactate than the sensitive cells. The increased anchorage-independent cell growth of the resistant cells was suppressed by a glycolysis inhibitor, 2-deoxy-D-glucose, indicating that these cells are highly dependent on the glycolytic pathway for survival. Decreased mitochondrial membrane potential and ATP production in the resistant cells indicate the presence of mitochondrial dysfunction induced by chronic exposure of cigarette smoke extract. Increased expression of nuclear genes in the glycolytic pathway and decreased levels of mitochondrial genes in the resistant cells support the notion that cigarette smoking significantly contributes to the transformation of nonmalignant esophageal epithelial cells into a tumorigenic phenotype.
A New Technique for Exarnining Blood (2016)

the result of disease. Because of the information these abnormalities convey to the physician, and because a sample of blood can be taken in almost any clinical setting, the complete blood count is one of the tests most frequently performed in the medical laboratory. The complete blood count includes measurement of the total quantity of red blood cells, white blood cells and their subtypes, and platelets. Each component of the blood has its own function. The primary role of the red blood cells is to carry and deliver oxygen to all parts of the body. White blood cells are essential components of the body's immune system. They fall into two main subgroups, the granulo cytes and the nongranulocytes?the lymphocytes and monocytes. Granu locytes and monocytes ingest foreign invaders, such as bacteria, and are also involved in the inflammatory re sponse against infection. The recog- nition of antigens and the production of antibodies are important functions of the lympho cytes. In various disease states the granulocytes and the nongranulocytes vary independently, often in inverse proportion to each other (Wintrobe 1981); for this reason, it is important for the physician to know the absolute numbers of white blood cells in each subgroup rather than just the total number. The platelets are the body's first line of defense against bleeding; they are small fragments of cytoplasm with no distinct nucleus. An accurate blood count can be the first step toward a specific diagnosis; for example, a reduction below the normal number of platelets may be the result of the infiltration of the bone marrow by cancerous cells, as in the case of leukemia, or of dysfunction of the immune
A statistical algorithm for assessing cellular alignment (2012)

Current statistical techniques for analyzing cellular alignment data in the fields of biomaterials and tissue engineering are limited because of heuristic and less quantitative approaches. For example, generally a cutoff degree limit (commonly 20 degrees) is arbitrarily defined within which cells are considered "aligned." The effectiveness of a patterned biomaterial in guiding the alignment of cells, such as neurons, is often critical to predict relationships between the biomaterial design and biological outcomes, both in vitro and in vivo. This becomes particularly important in the case of peripheral neurons, which require precise axon guidance to obtain successful regenerative outcomes. To address this issue, we have developed a protocol for processing cellular alignment data sets, which implicitly determines an "angle of alignment." This was accomplished as follows: cells "aligning" with an underlying, anisotropic scaffold display uniformly distributed angles up to a cutoff point determined by how effective the biomaterial is in aligning cells. Therefore, this fact was then used to determine where an alignment angle data set diverges from a uniform distribution. This was accomplished by measuring the spacing between the collected, increasingly ordered angles and analyzing their underlying distributions using a normalized cumulative periodogram criterion. The proposed protocol offers a novel way to implicitly define cellular alignment, with respect to various anisotropic biomaterials. This method may also offer an alternative to assess cellular alignment, which could offer improved predictive measures related to biological outcomes. Furthermore, the approach described can be used for a broad range of cell types grown on 2D surfaces, but would not be applicable to 3D scaffold systems in the present format.
On the behavior of responsive loads in the presence of DFACTS devices (2012)

The paper studies a constrained economic dispatch problem in electricity networks with price-dependent demand, and in which the transmission lines are potentially instrumented with DFACTS devices with a view to mitigating system congestion. Specifically, the network objective concerns the joint adjustment of consumption profiles in response to the electricity price and the design of variable reactance (DFACTS settings) that lead to a form of welfare optimization. To this end, the paper introduces an iterative minimization approach that seeks to optimize the constrained dispatch objective through successive (iterative) adjustments of consumption profiles at the responsive loads based on the difference between the price estimated by the loads and the price resulting from the economic dispatch. Simulations demonstrating the efficiency of the proposed approach in the presence of two different types of DFACTS devices are presented on the IEEE 14-bus system. In particular, the numerical findings provide a quantitative understanding of how the presence of DFACTS lead to reduced locational marginal prices and increased demand accommodation capacity in networks of responsive loads.
Super Fine Jet Underfill Dispense Technique for Robust Micro Joint in Direct Bonded Heterogeneous Integration (DBHi) Silicon Bridge Packages (2022)

Heterogeneous integration is becoming a key technical approach to extend Moore’s law. A new packaging technology named Direct Bonded Heterogeneous Integration (DBHi) with Si-bridge has recently been proposed [1] [2]. The DBHi package uses mixed pitch interconnections. Standard pitch bumps (150 μm) connect processor chips to a laminate substrate, while fine pitch bumps (75 μm) connect the processor chips to a bridge chip. In the assembly process of this new package, the chip-bridge joining is performed first, then the bridged chips assembly is joined to the laminate. However, during joining of the bridged chips to the laminate, a critical thermo-mechanical stress is generated in the micro joint on the small bridge chip due to the coefficient of thermal expansion (CTE) mismatch between silicon and laminate. In addition, dispensing capillary underfill from the edge of the bridge chip is not possible because the space from the edge of the bridge chip for underfill supply is limited to 250 μm maximum distance due to the standard pitch bumps located near the bridge chip. In this paper, the chip-bridge joining and encapsulating processes for the micro joint are investigated, and material properties of both conventional non-conductive pastes (NCPs) and a capillary underfill (CUF) which can be dispensed by a fine jet dispense tool are compared. We demonstrate a fine jet underfill dispensing technique which significantly increases the bridge micro joint robustness. The jetted micro dots fly through the high-aspect narrow gap (150 μm-width and 800 μm-depth) between the two processor chips, and land directly on the surface of the bridge chip and then flow into the micro joint area by capillary force. The flying dot size and shape of underfill jetting are measured experimentally and monitored by a high-speed camera. The diameter was about 100 μm with an elongated tail. This assembly method provided improved assembly yields and excellent reliability performance of the DBHi modules.
High field-gradient dysprosium tips for magnetic resonance force microscopy (2012)

Magnetic resonance force microscopy (MRFM) is based on measuring the attonewton-scale force between nuclear or electronic spins and a magnetic tip. The force is directly proportional to the magnetic field gradient generated by the tip, making a high moment nanoscale magnet desirable. Dysprosium, with a bulk magnetization 70% higher than iron, is a suitable candidate for such a tip. We have performed MRFM to quantitatively characterize two Dy nanomagnets. We find that magnetic field gradients as high as 6 MT/m (60 G/nm) can be generated, a 40% enhancement compared to our previous FeCo tips.
Sequence-dependent force response during peeling of single-stranded DNA from graphite (2010)

We have analyzed the statistical thermodynamics of peeling single-stranded DNA (ssDNA) from the surface of graphite. Using recently measured parameters, we represent ssDNA as a polymer chain strongly adsorbed to a frictionless substrate using the freely jointed chain, wormlike chain, and rotational isomeric state models. All three models predict steady peeling force under force control, in agreement with single-molecule experiments. We predict that, for finite-length chains, the force response has measurable spikes under displacement control. These force spikes carry information about the underlying sequence of ssDNA, which might thus be measurable with a sufficiently stiff loading system. For the freely jointed chain model, under force control, we have obtained several exact closed-form results and provide relations between the measured peel force and the underlying adhesion free energy.
Optical spectroscopy noninvasively monitors response of organelles to cellular stress (2005)

Fast and noninvasive detection of cellular stress is extremely useful for fundamental research and practical applications in medicine and biology. We discovered that light scattering spectroscopy enables us to monitor the transformations in cellular organelles under thermal stress. At the temperatures triggering expression of heat shock proteins, the refractive index of mitochondria increase within 1 min after the onset of heating, indicating enhanced metabolic activity. At higher temperatures and longer exposures, the organelles increase in size. This technique provides an insight into metabolic processes within organelles larger than 50 nm without exogenous staining and opens doors for noninvasive real-time assessment of cellular stress.
An optical device for measuring bending strain to 5000 microstrain and compatible with optical fiber installations (2005)

An optical sensor is described which can be attached to a structure and used as a gage for measuring bending strain. This device can be adjusted to maximize the gage factor for predetermined strain ranges. The sensor consists of glass capillaries coated on the outer surfaces with an optical absorbing layer followed by a reflecting layer. A mechanical strengthening layer can be included to extend the range of strain response. A source laser beam from an optical fiber is injected into one end of the gage. The light remaining in the beam after traveling through the gage is collected via another optical fiber. The optically active layer is adjusted during manufacture to provide a predetermined gage factor. For a given thickness of the absorber layer, the detected light is proportional to the amount of bending. Thus, by rigidly affixing the sensor to a structural member, the strain experienced by the member can be monitored.
Reactivity of quinone imine and quinone diimine metabolites of the antitumor drug amsacrine and related compounds to nucleophiles (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactivity of quinone imine and quinone diimine metabolites of the antitumor drug amsacrine and related compounds to nucleophilesHo H. Lee, Brian D. Palmer, and William A. DennyCite this: J. Org. Chem. 1988, 53, 26, 6042–6047Publication Date (Print):December 1, 1988Publication History Published online1 May 2002Published inissue 1 December 1988https://pubs.acs.org/doi/10.1021/jo00261a010https://doi.org/10.1021/jo00261a010research-articleACS PublicationsRequest reuse permissionsArticle Views391Altmetric-Citations15LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The thoracic veins and ablation for atrial fibrillation. (2010)

The last decade has witnessed a revolution in the management of paroxysmal atrial fibrillation (PAF). Fundamental to these changes has been the understanding that the thoracic veins, which include the pulmonary veins and superior vena cava, represent the initiating trigger site for atrialf ibrillation (AF). In this article, we discuss the rationale for ablation around the thoracic veins for managing patients with PAF. We describe a selection of appropriate patients for venous isolation procedures, particularly in the context of the Indian subcontinent and then go on to explain ablation approaches that optimize safety and efficacy with the complex procedures. Although this article is targeted for interventional electrophysiologists beginning these procedures the rational, initial patient selection for referral and follow up of post ablation patients will be relevant to all practicing cardiologists.
New 5′ Regions of the Murine and Human Genes for DNA (Cytosine-5)-methyltransferase (1996)

DNA (cytosine-5)-methyltransferases (EC 2.1.1.37) maintain patterns of methylated cytosine residues in the mammalian genome; faithful maintenance of methylation patterns is required for normal development of mice, and aberrant methylation patterns are associated with certain human tumors and developmental abnormalities. The organization of coding sequences at the 5'-end of the murine and human DNA methyltransferase genes was investigated, and the DNA methyltransferase open reading frame was found to be longer than previously suspected. Expression of the complete open reading frame by in vitro transcription-translation and by transfection of expression constructs into COS7 cells resulted in the production of an active DNA methyltransferase of the same apparent mass as the endogenous protein, while translation from the second in-frame ATG codon produced a slightly smaller but fully active protein. Characterization of mRNA 5' sequences and the intron-exon structure of the 5' region of the murine and human genes indicated that a previously described promoter element (Rouleau, J., Tanigawa, G., and Szyf, M. (1992) J. Biol. Chem. 267, 7368-7377) actually lies in an intron that is more than 5 kilobases downstream of the transcription start sites.
A delay model for router microarchitectures (2001)

This article introduces a router delay model that takes into account the pipelined nature of contemporary routers and proposes pipelines matched to the specific flow control method employed. Given the type of flow control and router parameters, the model returns router latency in technology-independent units and the number of pipeline stages as a function of cycle time. We apply this model to derive realistic pipelines for wormhole and virtual-channel routers and compare their performance. Contrary to the conclusions of previous models, our results show that the latency of a virtual channel router doesn't increase as we scale the number of virtual channels up to 8 per physical channel. Our simulation results also show that a virtual-channel router gains throughput of up to 40 % over a wormhole router.
QnA (2004)

The growing use of Instant Messaging for social and work-related communication has created a situation where incoming messages often become a distraction to users while they are performing important tasks. Staying on task at the expense of responsiveness to IM buddies may portray the users as impolite or even rude. Constantly attending to IM, on the other hand, may prevent users from performing tasks efficiently, leaving them frustrated. In this paper we present a tool that augments a commercial IM client by automatically increasing the salience of incoming messages that may deserve immediate attention, helping users decide whether or not to stay on task.
Correlating the microstructure of thin films of poly[5,5-bis(3-dodecyl-2-thienyl)-2,2-bithiophene] with charge transport: Effect of dielectric surface energy and thermal annealing (2008)

Poly[5,${5}^{\ensuremath{'}}$-bis(3-dodecyl-2-thienyl)-2,${2}^{\ensuremath{'}}$-bithiophene] (PQT-12) is a conjugated polymer that shows promising performance $(\ensuremath{\mu}&gt;0.1\text{ }{\text{cm}}^{2}/\text{V}\text{ }\text{s})$ as a semiconductor for thin-film electronics. The electrical properties of PQT-12 thin films can vary by over 3 orders of magnitude depending on the chemistry of the substrate onto which they are deposited and on annealing conditions. The highest mobility is obtained in films annealed on a dielectric treated with a self-assembled monolayer of octadecyltrichlorosilane (OTS). Polymeric thin films were processed from either a solution of dissolved PQT-12 molecules in 1,2-dichlorobenzene or from a nanoparticle dispersion of the polymer in the same solvent (nPQT-12). In addition, the substrate surface chemistry was altered by spin coating on a bare ${\text{SiO}}_{2}$ dielectric or on ${\text{SiO}}_{2}$ treated with OTS. The microstructure of the two forms of polymer, as characterized using specular and grazing x-ray diffraction in addition to rocking curves, was compared and correlated with the electrical performance of the films as active layers in thin-film transistors. As-spun films of nPQT-12 are always more crystalline than those of PQT-12, independent of substrate chemistry. Consequently, carrier mobility in as-spun films is higher in nPQT-12 than in PQT-12. The presence of the OTS monolayer at the polymer/dielectric interface increases crystallinity of both PQT-12 and nPQT-12, without significantly affecting their texture. After annealing, the mobility in PQT-12 films and nPQT-12 films is comparable. Annealing causes the polymer films on OTS to undergo crystallite growth in the direction normal to the substrate. In nPQT-12, growth of the crystalline coherence length in the $\ensuremath{\pi}\text{\ensuremath{-}}\ensuremath{\pi}$ stacking direction (i.e., parallel to the substrate and in the direction of charge transport) occurs as well. The mobility increase in nPQT-12 on OTS upon annealing is thus attributed to the higher crystallinity of the film. In PQT-12 films deposited on OTS on the other hand, annealing causes a decrease in the out-of-plane misorientation of neighboring crystallites without any significant grain growth in the plane of the film. The mobility increase in PQT-12 on OTS upon annealing is attributed to a better intergrain connectivity, in agreement with electrical modeling of the transistor characteristics using a mobility edge model.
Vertical Transmission of Human Immunodeficiency Virus Type 1: Seroreactivity by Maternal Antibodies to the Carboxy Region of the gp41 Envelope Glycoprotein (1997)

Maternal antibodies against the envelope glycoprotein of human immunodeficiency virus type 1 (HIV-1) have previously been suggested to be important in influencing the rate of vertical transmission. In this study, serum antibody responses in mothers who did or did not transmit HIV-1 infection to their children were measured against the carboxy region of the transmembrane envelope glycoprotein gp41. Results indicate significantly higher binding reactivity of nontransmitter mothers compared with transmitters to three peptides spanning amino acids 771-810 and 841-856. In addition, high neutralization titers in maternal sera against HIV-1(MN) were associated with a nontransmission status. This is the initial report demonstrating a correlation between maternal antibody binding to epitopes within the carboxy region of gp41 envelope glycoprotein and lack of vertical transmission. Immunodetection that identifies antibodies to these regions in gp41 could therefore be considered a strategy to assess the risk of vertical transmission of HIV-1.
Abstract B34: Targeted destruction of endogenous K-RAS using an Affinity directed PROtein Missile (AdPROM) (2020)

Abstract K-RAS is one of the most frequently mutated oncogenes in cancer. Yet there are no effective strategies to target K-RAS for inhibition. Our laboratory has developed an Affinity-directed PROtein Missile (AdPROM) system for targeted proteolysis of endogenous proteins. Here, we show that we can achieve a robust degradation of endogenous K-RAS and mutant K-RAS from different cell lines in a targeted manner using our AdPROM system. We are currently assessing the impact of the targeted destruction of K-RAS and mutant K-RAS in cell signaling and proliferation. Citation Format: Sascha O. M. Roth, Thomas J. Macartney, Agnieszka Konopacka, Markus Queisser, Gopal P. Sapkota. Targeted destruction of endogenous K-RAS using an Affinity directed PROtein Missile (AdPROM) [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr B34.
CHANGE IN RETINAL SENSITIVITY DUE TO EXCISION OF CHOROIDAL NEOVASCULARIZATION AND ITS INFLUENCE ON VISUAL ACUITY OUTCOME (1999)

In most cases, excision of CNV does not improve central retinal sensitivity, and patients have poor visual outcome. In some cases, however, postoperative sensitivity in the bed of CNV is preserved and visual outcome is relatively good. Better or worse preoperative retinal sensitivity does not predict better or worse visual acuity outcome, respectively.
Notes: Kluyveromyces lactis Maintains Saccharomyces cerevisiae Intron-Encoded Splicing Signals (1989)

The actin (ACT) gene from the budding yeast Kluyveromyces lactis was cloned, and the nucleotide sequence was determined. The gene had a single intron 778 nucleotides in length which possessed the highly conserved splicing signals found in Saccharomyces cerevisiae introns. We demonstrated splicing of heterologous ACT transcripts in both K. lactis and S. cerevisiae.
Improved EDC performance for different duobinary modulation formats with optical filtering (2008)

Nonlinear EDC including nonlinear Volterra based equalizer and MLSE are investigated and compared for different duobinary formats with optical filtering at 43Gb/s data rate.