gebhart/patrepeval huggingface dataset:
Computational prediction of chemically synthesizable organic structure directing agents for zeolites (2013)

We describe a computational procedure to predict chemically synthesizable organic structure directing agents (OSDAs) for zeolites. To identify these structure-directing agents, we apply transformations from organic chemistry to a library of available reagents. The compounds are scored based upon stability under synthesis conditions, rigidity, volume, geometric compatibility, and energy of interaction with the target zeolite. We illustrate the method on the three zeolites AEI, ITE, and STF. This method can be used to search for novel, perhaps cheaper or more effective, OSDAs to synthesize known zeolites. The method also has the potential to identify OSDAs that will allow the synthesis of novel, perhaps even theoretically predicted, zeolites.
Damage formed by electron cyclotron resonance plasma etching on a gallium arsenide surface (1990)

Radiation damage induced on a gallium arsenide surface by electron cyclotron resonance (ECR) plasma etching is studied. The number of displaced atoms (displaced atom density) formed by exposure to ECR plasma is determined quantitatively by Rutherford backscattering spectrometry aligned spectra. The density increases with increasing microwave power. The amount of increase of displaced atom density from the undamaged virgin surface ΔDda is 2.9×1015 and 4.4×1015 atoms/cm2 at microwave power of 500 W (ion current density, Ii: 0.80 mA/cm2) and 800 W (Ii: 2.00 mA/cm2), respectively. The reflection high-energy electron diffraction study shows that an amorphous layer is formed on the surface at 800 W (Ii: 2.00 mA/cm2). The effect of bias power and chamber pressure on the damage is also studied. The increase of damage (ΔDda: 3.2×1015 atom/cm2) from ECR plasma etching with an rf bias of 15 W is less by a factor of 2 than damage of reactive ion etching (ΔDda: 6.9×1015 atom/cm2) when compared at an ion current density of 1.17 mA/cm2. Low-damage anisotropic etching can be achieved by ECR plasma etching.
Automatic initialization for 3D bone registration (2008)

In image-guided bone surgery, sample points collected from the surface of the bone are registered to the preoperative CT model using well-known registration methods such as Iterative Closest Point (ICP). These techniques are generally very sensitive to the initial alignment of the datasets. Poor initialization significantly increases the chances of getting trapped local minima. In order to reduce the risk of local minima, the registration is manually initialized by locating the sample points close to the corresponding points on the CT model. In this paper, we present an automatic initialization method that aligns the sample points collected from the surface of pelvis with CT model of the pelvis. The main idea is to exploit a mean shape of pelvis created from a large number of CT scans as the prior knowledge to guide the initial alignment. The mean shape is constant for all registrations and facilitates the inclusion of application-specific information into the registration process. The CT model is first aligned with the mean shape using the bilateral symmetry of the pelvis and the similarity of multiple projections. The surface points collected using ultrasound are then aligned with the pelvis mean shape. This will, in turn, lead to initial alignment of the sample points with the CT model. The experiments using a dry pelvis and two cadavers show that the method can align the randomly dislocated datasets close enough for successful registration. The standard ICP has been used for final registration of datasets.
Association of interferon regulatory factor-1, nucleophosmin, nuclear factor-kappaB, and cyclic AMP response element binding with acquired resistance to Faslodex (ICI 182,780). (2002)

To identify genes associated with survival from antiestrogens, both serial analysis of geneexpression and gene expression microarrays were used to explore the transcriptomes of antiestrogen-responsive (MCF7/LCC1) and -resistant variants(MCF7/LCC9) of the MCF-7 human breast cancer cell line. Structure of the gene microarray expression data was visualized at the top level using a novel algorithm that derives the first three principal components,fitted to the antiestrogen-resistant and -responsive gene expression data, from Fisher's information matrix. The differential regulation of several candidate genes was confirmed. Functional studies of the basal expression and endocrine regulation of transcriptional activation of implicated transcription factors were studied using promoter-reporter assays. The putative tumor suppressor interferon regulatory factor-1 is down-regulated in resistant cells, whereas its nucleolar phosphoprotein inhibitor nucleophosmin is up-regulated. Resistant cells also up-regulate the transcriptional activation of cyclic AMP response element (CRE) binding and nuclear factor kappaB (NFkappaB) while down-regulating epidermal growth factor receptor protein expression. Inhibition of NFkappaB activity by ICI 182,780 is lost in resistant cells, but CRE activity is not regulated by ICI 182,780 in either responsive or resistant cells. Parthenolide, a potent and specific inhibitor of NFkappaB, inhibits the anchorage-dependent proliferation of antiestrogen-resistant but not antiestrogen-responsive cells. This observation implies a greater reliance on their increased NFkappaB signaling for proliferation in cells that have survived prolonged exposure to ICI 182,780. These data from serial analysis of gene expression and gene microarray studies implicate changes in a novel signaling pathway, involving interferon regulatory factor-1, nucleophosmin, NFkappaB, and CRE binding in cell survival after antiestrogen exposure. Cells can up-regulate some estrogen-responsive genes while concurrently losing the ability of antiestrogens to regulate their expression. Signaling pathways that are not regulated by estrogens also can be up-regulated. Thus, some breast cancer cells may survive antiestrogen treatment by bypassing specific growth inhibitory signals induced by antagonist-occupied estrogen receptors.
Clioquinol down-regulates mutant huntingtin expression<i>in vitro</i>and mitigates pathology in a Huntington's disease mouse model (2005)

In investigating the role of metal ions in the pathogenesis of Huntington's disease, we examined the effects of clioquinol, a metal-binding compound currently in clinical trials for Alzheimer's disease treatment, on mutant huntingtin-expressing cells. We found that PC12 cells expressing polyglutamine-expanded huntingtin exon 1 accumulated less mutant protein and showed decreased cell death when treated with clioquinol. This effect was polyglutamine-length-specific and did not alter mRNA levels or protein degradation rates. Clioquinol treatment of transgenic Huntington's mice ( R6 / 2 ) improved behavioral and pathologic phenotypes, including decreased huntingtin aggregate accumulation, decreased striatal atrophy, improved rotarod performance, reduction of weight loss, normalization of blood glucose and insulin levels, and extension of lifespan. Our results suggest that clioquinol is a candidate therapy for Huntington's disease and other polyglutamine-expansion diseases.
Two Distinct Pathways for Trehalose Assimilation in the Yeast<i>Saccharomyces cerevisiae</i> (2004)

The yeast Saccharomyces cerevisiae can synthesize trehalose and also use this disaccharide as a carbon source for growth. However, the molecular mechanism by which extracellular trehalose can be transported to the vacuole and degraded by the acid trehalase Ath1p is not clear. By using an adaptation of the assay of invertase on whole cells with NaF, we showed that more than 90% of the activity of Ath1p is extracellular, splitting of the disaccharide into glucose. We also found that Agt1p-mediated trehalose transport and the hydrolysis of the disaccharide by the cytosolic neutral trehalase Nth1p are coupled and represent a second, independent pathway, although there are several constraints on this alternative route. First, the AGT1/MAL11 gene is controlled by the MAL system, and Agt1p was active in neither non-maltose-fermenting nor maltose-inducible strains. Second, Agt1p rapidly lost activity during growth on trehalose, by a mechanism similar to the sugar-induced inactivation of the maltose permease. Finally, both pathways are highly pH sensitive and effective growth on trehalose occurred only when the medium was buffered at around pH 5.0. The catabolism of trehalose was purely oxidative, and since levels of Ath1p limit the glucose flux in the cells, batch cultures on trehalose may provide a useful alternative to glucose-limited chemostat cultures for investigation of metabolic responses in yeast.
A 160 dB Equivalent Dynamic Range Auto-Scaling Interface for Resistive Gas Sensors Arrays (2007)

In this paper an integrated wide-dynamic-range interface circuit for resistive gas-sensors arrays is presented. The proposed device consists of a multiscale transresistance continuous time amplifier followed by a 13-bit incremental A/D converter. The circuit selects automatically the scale to use for each measurement and includes two digital-to-analog converters for the calibration of offset and gain of each scale. The proposed interface circuit achieves a measurement accuracy almost always better than 0.1 % over a sensor resistance range of more than 5 decades [100 Omega-20 MOmega], leading to an equivalent dynamic range of about 160 dB. The chip has been realized with a 0.35 mum CMOS technology and occupies an area of 3.1 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> consuming 6 mW from a 3.3 V power supply.
Lipophilic Pyridinium Bisphosphonates: Potent γ<i>δ</i> T Cell Stimulators (2009)

Chain gang: Lipophilic pyridinium bisphosphonates containing long alkyl chains (see picture, P red, N blue, C orange, H gray) stimulate human γδ T cells expressing the Vγ2Vδ2 T cell receptor. Stimulation with such compounds is more potent than with zoledronate, which is active against breast and prostate cancer. The lipophilic bisphosphonates bind poorly to bone and are thus less likely to cause side effects associated with bisphosphonates in clinical use. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Evaluation of CD4-CD4i Antibody Architectures Yields Potent, Broadly Cross-Reactive Anti-Human Immunodeficiency Virus Reagents (2009)

The envelope glycoprotein of human immunodeficiency virus type 1 (HIV-1) has several adaptations that allow the virus to evade antibody neutralization. Nevertheless, a few broadly cross-reactive neutralizing antibodies as well as reagents containing portions of CD4, the HIV receptor, have demonstrated partial efficacy in suppressing viral replication. One type of reagent designed for improved HIV neutralization fuses the CD4 D1-D2 domains to the variable regions of an antibody recognizing the CD4-induced (CD4i) coreceptor binding site on the gp120 portion of the HIV envelope spike. We designed, expressed, purified, and tested the neutralization potencies of CD4-CD4i antibody reagents with different architectures, antibody combining sites, and linkers. We found that fusing CD4 to the heavy chain of the CD4i antibody E51 yields a bivalent reagent including an antibody Fc region that expresses well, is expected to have a long serum half-life, and has comparable or greater neutralization activity than well-known broadly neutralizing anti-HIV antibodies. A CD4 fusion with the anti-HIV carbohydrate antibody 2G12 also results in a potent neutralizing reagent with more broadly neutralizing activity than 2G12 alone.
Spin-transfer torque magnetic random access memory (STT-MRAM) (2013)

Spin-transfer torque magnetic random access memory (STT-MRAM) is a novel, magnetic memory technology that leverages the base platform established by an existing 100+nm node memory product called MRAM to enable a scalable nonvolatile memory solution for advanced process nodes. STT-MRAM features fast read and write times, small cell sizes of 6F 2 and potentially even smaller, and compatibility with existing DRAM and SRAM architecture with relatively small associated cost added. STT-MRAM is essentially a magnetic multilayer resistive element cell that is fabricated as an additional metal layer on top of conventional CMOS access transistors. In this review we give an overview of the existing STT-MRAM technologies currently in research and development across the world, as well as some specific discussion of results obtained at Grandis and with our foundry partners. We will show that in-plane STT-MRAM technology, particularly the DMTJ design, is a mature technology that meets all conventional requirements for an STT-MRAM cell to be a nonvolatile solution matching DRAM and/or SRAM drive circuitry. Exciting recent developments in perpendicular STT-MRAM also indicate that this type of STT-MRAM technology may reach maturity faster than expected, allowing even smaller cell size and product introduction at smaller nodes.
The Use of Fibrin Tissue Adhesive to Reduce Blood Loss and the Need for Blood Transfusion After Total Knee Arthroplasty. A Prospective, Randomized, Multicenter Study* (1999)

The use of fibrin tissue adhesive in total knee arthroplasty seems to be an effective and safe means with which to reduce blood loss and blood-transfusion requirements. Furthermore, the importance of these findings was enhanced by a significant reduction in blood loss, in the postoperative decrease in the level of hemoglobin, and in blood-transfusion requirements despite preoperative thromboprophylaxis with low-molecular-weight heparin.
Improved delivery through biological membranes. 4. Prodrugs of L-DOPA (1977)

Various classes of transient derivatives of L-Dopa have been synthesized, systematically protecting one or more of the main sites of metabolism in the molecule: the carboxy function, the amino, and/or the catechol system. The derivatives studied include carboxy esters, phenol esters, amides, peptides, and various combinations of these functions. A number of these derivatives effectively prevent the metabolism of L-Dopa prior to and/or during the absorption process, resulting in a significantly better bioavailability of the drug. In vivo studies using dogs showed up to 2.5-fold increase in L-Dopa blood levels. The metabolism as well as toxicity aspects of the prodrugs is also discussed.
Error-resilient transcoding for video over wireless channels (2000)

We describe a method to maintain quality for video transported over wireless channels. The method is built on three fundamental blocks. First, we use a transcoder that injects spatial and temporal resilience into an encoded bitstream. The amount of resilience is tailored to the content of the video and the prevailing error conditions, as characterized by bit error rate. Second, we derive analytical models that characterize how corruption propagates in a video that is compressed using motion-compensated encoding and subjected to bit errors. Third, we use rate distortion theory to compute the optimal allocation of bit rate among spatial resilience, temporal resilience, and source rate. Furthermore, we use the analytical models to generate the resilience rate distortion functions that are used to compute the optimal resilience. The transcoder then injects this optimal resilience into the bitstream. Simulation results show that using a transcoder to optimally adjust the resilience improves video quality in the presence of errors while maintaining the same input bit rate.
Outcomes Evaluation Following Bilateral Breast Reconstruction Using Latissimus Dorsi Myocutaneous Flaps (2010)

The demand for bilateral breast reconstruction has recently increased. Although numerous options exist, the latissimus dorsi myocutaneous flap remains a popular technique. The benefits of additional autologous coverage are evident; however, donor site morbidity does exist. The purpose of this report is to evaluate our experience with bilateral latissimus dorsi breast reconstructions, focusing on donor site morbidity and patient satisfaction. All patients who underwent bilateral latissimus dorsi breast reconstruction at Emory University Hospital, were evaluated and included in the series. Data points queried included patient demographics, risk factors, radiation therapy, timing of the procedure (immediate or delayed), type of procedure (latissimus dorsi only, latissimus dorsi with expander, latissimus dorsi with implant), and outcomes. Outcomes included >1 additional operation, any breast and any donor-site complications. A patient satisfaction survey was performed evaluating outcomes such as aesthetic results, general satisfaction, morbidities, and functional assessment. Comparisons were made using radiation therapy, timing of reconstruction, and type of reconstruction as variables. Eighty-three patients underwent bilateral latissimus dorsi breast reconstruction with an average follow-up of 2.3 years. The method of reconstruction included latissimus dorsi with expander (n = 54), latissimus dorsi only (n = 17), and latissimus dorsi with implant (n = 12). Breast complications occurred in 34% of the patients with radiation therapy being a significant risk factor. The average number of secondary operations was 2.3 with the expander group resulting in an increased need for additional procedures. Overall patient satisfaction was 3.93/5, with the average symmetry score being 3.82/5, shape 3.84/5, nipple position 3.92/5, and inframammary fold (IMF) position 4/5. The majority of patients (n = 28/37) reported no pain (0/5) at the time of the survey. Most patients (n = 33/37) reported no impairment in daily activities, however, some did report impairment in physical activity, decreased range of motion (ROM), and pain. The latissimus dorsi remains a reliable option for bilateral breast reconstruction. Although patient satisfaction with this approach remains high, functional impairment can occur and needs to be appropriately discussed.
How Smart, Connected Products Are Transforming Competition (2014)

Information technology is revolutionizing products, from appliances to cars to mining equipment. Products once composed solely of mechanical and electrical parts have become complex systems combining hardware, sensors, electronics, and software that connect through the internet in myriad ways. These “smart, connected products” offer exponentially expanding opportunities for new functionality, far greater reliability, and capabilities that cut across and transcend traditional product boundaries. The changing nature of products is disrupting value chains, argue Michael Porter and PTC CEO James Heppelmann, and forcing companies to rethink nearly everything they do, from how they conceive, design, and source their products; to how they manufacture, operate, and service them; to how they build and secure the necessary IT infrastructure. Smart, connected products raise a broad set of new strategic choices for companies about how value is created and captured, how to work with traditional partners and what new partnerships will be required, and how to secure competitive advantage as the new capabilities reshape industry boundaries. For many firms, smart, connected products will force the fundamental question: “What business am I in?” This article provides a framework for developing strategy and achieving competitive advantage in a smart, connected world.
Tempo And Beat Estimation Of Musical Signals. (2004)

[TODO] Add abstract here.
High sensitivity pixel technology for a 1/4-inch PAL 430 k pixel IT-CCD (2002)

A new pixel technology has been developed for a 1/4-inch 430 k (PAL) pixel IT-CCD (Inter-line Transfer Charge Coupled Device). The new pixel has a thin light shield made of tungsten silicide film and an inner-layer optical micro-lens pre-defined by BPSG flow. This process technology can reduce the pixel size to 22.6 /spl mu/m/sup 2/ with improved sensitivity and reduced smear value. The sensitivity is increased by 30% and the smear value is reduced by 6dB compared to a conventional pixel technology. These characteristics are comparable to a conventional 1/3-inch 560 k pixel IT-CCD with the pixel size of 33.6 /spl mu/m/sup 2/.
Network Convergence: Where is the Value? (2002)

The entire telecommunications industry is going through very difficult times. Rapidly changing technology, lack of good business models, and lack of visibility in the near-term for renewed growth all create an uncertain environment. Yet, the global Internet is becoming a multi-service network infrastructure that can potentially replace existing disparate voice and data networks. Although it is widely believed in the telecommunications industry that network convergence of voice, data, video, and images is an industry driver, not much attention has yet been paid to a key proposition: what value does network convergence bring to business and residential customers? This paper explains how different industries are converging; the technological, economic and regulatory forces that are at play and how the various customer segments can benefit from network convergence. While technological advancement is transforming industry and business models rapidly, one question keeps coming back to haunt managers: Where is the business value? We illustrate the value proposition of convergence (for various players) by first explaining the paradigm shifts happening across industries and then highlighting the "high velocity spiral" of knowledge dissemination theory that is fueled by convergence.
PI3K therapy reprograms mitochondrial trafficking to fuel tumor cell invasion (2015)

Molecular therapies are hallmarks of "personalized" medicine, but how tumors adapt to these agents is not well-understood. Here we show that small-molecule inhibitors of phosphatidylinositol 3-kinase (PI3K) currently in the clinic induce global transcriptional reprogramming in tumors, with activation of growth factor receptors, (re)phosphorylation of Akt and mammalian target of rapamycin (mTOR), and increased tumor cell motility and invasion. This response involves redistribution of energetically active mitochondria to the cortical cytoskeleton, where they support membrane dynamics, turnover of focal adhesion complexes, and random cell motility. Blocking oxidative phosphorylation prevents adaptive mitochondrial trafficking, impairs membrane dynamics, and suppresses tumor cell invasion. Therefore, "spatiotemporal" mitochondrial respiration adaptively induced by PI3K therapy fuels tumor cell invasion, and may provide an important antimetastatic target.
Results from the microminiature thermionic converter demonstration testing program (2002)

Research is in progress to develop microminiature thermionic converters (MTCs) using semiconductor integrated circuit (IC) fabrication methods. The use of IC techniques allows the fabrication of MTCs with an emitter to collector spacing of several microns or less and with emitter and collector materials that will have work functions ranging from 1 eV to 2 eV. Theory predicts that the small emitter to collector spacing and highly emissive low work function electrodes should allow the conversion of heat energy to relatively large electrical current densities (up to tens of Amps/cm/sup 2/) at relatively high conversion efficiencies (15-25%). Tests of prototype MTCs have demonstrated energy conversion at several emitter temperatures. The power generated is less than expected because of less than optimal emission characteristics encountered with the low work function materials used for the first MTC prototypes. Efforts to improve electrode emission characteristics are in progress.