gebhart/patrepeval huggingface dataset:
Intratumoral bidirectional transitions between epithelial and mesenchymal cells in triple‐negative breast cancer (2017)

Epithelial-mesenchymal transition (EMT) and its reverse process, mesenchymal-epithelial transition MET, are crucial in several stages of cancer metastasis. Epithelial-mesenchymal transition allows cancer cells to move to proximal blood vessels for intravasation. However, because EMT and MET processes are dynamic, mesenchymal cancer cells are likely to undergo MET transiently and subsequently re-undergo EMT to restart the metastatic process. Therefore, spatiotemporally coordinated mutual regulation between EMT and MET could occur during metastasis. To elucidate such regulation, we chose HCC38, a human triple-negative breast cancer cell line, because HCC38 is composed of epithelial and mesenchymal populations at a fixed ratio even though mesenchymal cells proliferate significantly more slowly than epithelial cells. We purified epithelial and mesenchymal cells from Venus-labeled and unlabeled HCC38 cells and mixed them at various ratios to follow EMT and MET. Using this system, we found that the efficiency of EMT is approximately an order of magnitude higher than that of MET and that the two populations significantly enhance the transition of cells from the other population to their own. In addition, knockdown of Zinc finger E-box-binding homeobox 1 (ZEB1) or Zinc finger protein SNAI2 (SLUG) significantly suppressed EMT but promoted partial MET, indicating that ZEB1 and SLUG are crucial to EMT and MET. We also show that primary breast cancer cells underwent EMT that correlated with changes in expression profiles of genes determining EMT status and breast cancer subtype. These changes were very similar to those observed in EMT in HCC38 cells. Consequently, we propose HCC38 as a suitable model to analyze EMT-MET dynamics that could affect the development of triple-negative breast cancer.
Monolithic silicon-on-nothing photonic crystal pressure sensor (2017)

We present a single-mask process that combines isotropic and anisotropic etching with selective removal of passivation layers followed by hydrogen annealing to yield monolithic crystalline silicon (c-Si) devices. The process is demonstrated by creating pressure sensors that combine photonic crystal (PC) mirror pressure-sensing diaphragms with silicon-on-nothing (SON) reference cavities. The first generation sensors were tested with fiber-optic readout and showed high sensitivity. The single-mask process has sufficient flexibility for application-specific optimization of the PC, diaphragm, and cavity. The monolithic silicon structure gives the sensor potential for good stability. The simple process, robust structure, and integration of all critical components simplifies packaging, which could lead to low-cost mass production.
Replication strategy of human hepatitis B virus (1987)

To study the replication strategy of the human hepatitis B virus, the 5' end of the RNA pregenome and the initiation sites of DNA plus and minus strands have been mapped. The RNA pregenome was found to be terminally redundant by 120 nucleotides; it is initiated within the pre-C region and may also function as mRNA for synthesis of the major core protein and the hepatitis B virus reverse transcriptase. The hepatitis B virus DNA minus strand is initiated within the direct repeat sequence DR1, it contains a terminal redundancy of up to eight nucleotides, and its synthesis does not require any template switch. The DNA plus strand is primed by a short oligoribonucleotide probably derived from the 5' end of the RNA pregenome, and its synthesis is initiated close to the direct repeat sequence DR2. For its elongation to pass the discontinuity in the DNA minus strand an intramolecular template switch occurs using the terminal redundancy of this template. Thus, the route of reverse transcription and DNA replication of hepatitis B viruses is fundamentally different from that of retroviruses.
Data‐Driven Facial Simulation (2020)

Abstract In Visual Effects, the creation of realistic facial performances is still a challenge that the industry is trying to overcome. Blendshape deformation is used to reproduce the action of different groups of muscles, which produces realistic static results. However, this is not sufficient to generate believable and detailed facial performances of animated digital characters. To increase the realism of facial performances, it is possible to enhance standard facial rigs using physical simulation approaches. However, setting up a simulation rig and controlling material properties according to the performance is not an easy task and could take a lot of time and iterations to get it right. We present a workflow that allows us to generate an activation map for the fibres of a set of superficial patches we call pseudo‐muscles . The pseudo‐muscles are automatically identified using k‐means to cluster the data from the blendshape targets in the animation rig and compute the direction of their contraction (direction of the pseudo‐muscle fibres). We use an Extended Position–Based Dynamics solver to add physical simulation to the facial animation, controlling the behaviour of simulation through the activation map. We show the results achieved using the proposed solution on two digital humans and one fantastic cartoon character, demonstrating that the identified pseudo‐muscles approximate facial anatomy and the simulation properties are properly controlled, increasing the realism while preserving the work of animators.
Modeling heterogeneity and dependence for analysis of neuronal data (2007)

In this paper, we describe two types of neuroscience problems which challenge the typical statistical models assumed for analyzing neuronal data. This offers an opportunity for new modeling and statistical inference. In the first problem, the data are spatial neural counts which are often over-dispersed and spatially correlated so that a standard Poisson regression model is inadequate. In the second problem, the data are averaged electroencephalograph signals recorded during muscle fatigue, where a time series AR(1) regression model cannot fully capture all the variation and correlation structure in the data. It is shown that an additional parameter has to be included in the modeling of the correlation structure and that the role of the parameter differs from one channel to the other. We propose appropriate generalized models for these data, develop statistical procedures under the generalized models, and apply these procedures to the real data that motivated this paper. The effect of mis-specification of a correlation structure is also investigated.
Green Rocket Propulsion by Reaction of Al and Mg Powders and Water (2004)

The efficacy of using aluminum-water and magnesium-water as propellants for underwater thruster applications has been investigated by the authors. The theoretical specific impulse for both reactant systems is high, and the products of reaction (alumina, magnesia, and hydrogen) are environmentally benign. The attractiveness of these systems as “green” propellants has been commented on previously, however, no practical experimentation with these systems has been made. The present work describes the testing of a linear combustor with magnesium-water and aluminum-water under conditions of pressure and oxidizer-fuel ratios and with a metal powder feed system that could be employed in actual rocket engines. Measurements of off-design specific impulse are compared with theoretical predictions that take into account two-phase losses. Measurements of heat fluxes available to vaporize regeneratively the liquid water oxidizer are presented as well. Perhaps of most importance, observations of the degree of product oxide accumulation in the combustor are presented. These measurements and observations are used to determine the effectiveness of these two metal fuel systems as practical green propellants.
A model for irreversible adsorption hysteresis (1988)

Abstract A model is proposed which is capable of describing non‐linear irreversible adsorption hysteresis with a single set of coefficients. The model is predicated on the assumption that two types of adsorption sites are present on the sorbent. At the first type of sites, solutes are irreversibly adsorbed in an amount related to the highest concentration at which the sorbent was exposed. Adsorption at the other sites is completely reversible and non‐hysteretic. The total adsorption is the sum of the two. However, when the equilibrium concentration is decreased, only the reversible component desorbs. Experimental protocol and mathematical techniques are presented for calibrating and verifying the model. The model is capable of predicting continuous flow column behavior based upon batch isotherm data.
A Primate Model of Cognitive Dysfunction in Parkinson's Disease (1995)

Conference Abstract| July 01 1995 A Primate Model of Cognitive Dysfunction in Parkinson's Disease P Collins; P Collins 1Department of Experimental Psychology, University of Cambridge, Cambridge CB2 3EB Search for other works by this author on: This Site PubMed Google Scholar LS Wilkinson; LS Wilkinson 1Department of Experimental Psychology, University of Cambridge, Cambridge CB2 3EB Search for other works by this author on: This Site PubMed Google Scholar BJ Everitt; BJ Everitt 1Department of Experimental Psychology, University of Cambridge, Cambridge CB2 3EB Search for other works by this author on: This Site PubMed Google Scholar TW Robbins; TW Robbins 1Department of Experimental Psychology, University of Cambridge, Cambridge CB2 3EB Search for other works by this author on: This Site PubMed Google Scholar AC Roberts AC Roberts 1Department of Experimental Psychology, University of Cambridge, Cambridge CB2 3EB Search for other works by this author on: This Site PubMed Google Scholar Clin Sci (Lond) (1995) 89 (s33): 48P–49P. https://doi.org/10.1042/cs089048Pc Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation P Collins, LS Wilkinson, BJ Everitt, TW Robbins, AC Roberts; A Primate Model of Cognitive Dysfunction in Parkinson's Disease. Clin Sci (Lond) 1 July 1995; 89 (s33): 48P–49P. doi: https://doi.org/10.1042/cs089048Pc Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu nav search search input Search input auto suggest search filter All ContentAll JournalsClinical Science Search Advanced Search This content is only available as a PDF. © 1995 The Biochemical Society and the Medical Research Society1995 Article PDF first page preview Close Modal You do not currently have access to this content.
Switching of Receptor Binding Poses between Closely Related Enteroviruses (2022)

Echoviruses, for which there are currently no approved vaccines or drugs, are responsible for a range of human diseases, for example echovirus 11 (E11) is a major cause of serious neonatal morbidity and mortality. Decay-accelerating factor (DAF, also known as CD55) is an attachment receptor for E11. Here, we report the structure of the complex of E11 and the full-length ectodomain of DAF (short consensus repeats, SCRs, 1-4) at 3.1 Å determined by cryo-electron microscopy (cryo-EM). SCRs 3 and 4 of DAF interact with E11 at the southern rim of the canyon via the VP2 EF and VP3 BC loops. We also observe an unexpected interaction between the N-linked glycan (residue 95 of DAF) and the VP2 BC loop of E11. DAF is a receptor for at least 20 enteroviruses and we classify its binding patterns from reported DAF/virus complexes into two distinct positions and orientations, named as E6 and E11 poses. Whilst 60 DAF molecules can attach to the virion in the E6 pose, no more than 30 can attach to E11 due to steric restrictions. Analysis of the distinct modes of interaction and structure and sequence-based phylogenies suggests that the two modes evolved independently, with the E6 mode likely found earlier.
The influence of heat treatment on the properties of shape memory fibers. II. Tensile properties, dimensional stability, recovery force relaxation, and thermomechanical cyclic properties (2008)

Abstract Shape memory fibers (SMFs) were prepared via a melt spinning process. The fibers were subject to different heat treatments to eliminate internal stress and structure deficiency caused during the melt spinning process. The influences of heat treatments on the SMF thermal properties, molecular orientation, tensile properties, dimensional stability, recovery force relaxation, and thermomechanical cyclic properties were studied. It was found that the heat treatments increased soft segment crystallinity and phase separation while decreased molecular orientation. The low‐temperature heat treatment increased the breaking elongation, shape fixity ratios, and decreased boiling water shrinkage while shape recovery ratios were decreased. High‐temperature treatment increased both the shape recovery ratios, fixity ratios, recovery stress stability and at the same time decreasing the fiber mechanical strength. The results from differential scanning calorimetry, molecular orientation apparatus, and cyclic tensile testing were used to illustrate the mechanism governing the mechanical properties and shape memory effect. To obtain comprehensive outstanding properties, the SMF is expected to be treated at a high temperature because of the hard segment high glass transition temperature. Unfortunately, the heat treatment could not be conducted at a too high temperature because the SMF became too tacky and soft due to the melting of the soft segment phase. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
Dependence of the Electrically Controlled Birefringence on Applied Frequency in a Nematic Liquid Crystal (1981)

Abstract Detailed studies on the dependence of the ECB effect on the applied frequency have been made in a nematic liquid crystal MBBA. It is found experimentally that, when the applied voltage is just above the threshold voltage, there are strong dependences of both the delay time and the mean deformation angle of the molecular director subjected to a constant voltage setup on the applied frequency. Those applied frequency dependences of the ECB effect can be interpreted in terms of the dielectric alignment in an electrically conducting nematic liquid crystal. We have measured the capacitance of the deformed liquid crystal cell varying the applied frequency. The experimental results are compared with the Gruler and Cheung theoretical prediction, and good agreements are obtained between them when the applied voltage is just above the threshold voltage.
Identification of green note compounds in malt whisky using multidimensional gas chromatography (2002)

Abstract We studied green note compounds in malt whisky using multidimensional GC–MS–olfactometry (MDGC–MS–O). Two aldehydes and three alcohols were shown to contribute to the green note: E , Z ‐2,6‐nonenal and E ‐2‐nonenal, and 1‐octen‐3‐ol, 4‐hepten‐1‐ol and nonan‐2‐ol, respectively. Malt whiskies with high green note scores organoleptically contained more of the aldehydes and nonan‐2‐ol than those with low scores. This is the first time that E , Z ‐2,6‐nonadienal, 1‐octen‐3‐ol, and 4‐hepten‐1‐ol have been identified in malt whisky. These compounds are related to lipid oxidation and degradation, and formation may be due to the action of lipoxygenase. In addition, MDGC–MS–O was effective in examining small amounts of compounds in malt whisky, which contains many volatiles, since this method enables the volatiles in a complicated matrix to be highly resolved without the influence of large amounts of volatiles. Copyright © 2002 John Wiley &amp; Sons, Ltd.
Structure, Constitution, and General Characteristics of Wrought Ferritic Stainless Steels (1977)

High chromium-ferritic stainless steels have good general corrosion and pitting resistance and are resistant to stress-corrosion cracking. Despite these desirable properties, the alloys have found little use as materials of construction. This lack of use is a result of significant losses in ductility, toughness, and corrosion resistance when these alloys are subjected to moderate or high temperatures. Names given to the phenomena causing loss in properties include 475°C, sigma phase, and high-temperature embrittlement. This publication summarizes the literature describing the causes, the cures, and the limitations imposed on alloys when these problems occur. The most seriously limiting problem—high temperature embrittlement and loss or corrosion resistance—is discussed in considerable detail. The key role that interstitial carbon and nitrogen play on notch sensitivity and loss of ductility and corrosion resistance following a high-temperature exposure as in welding is defined. Good aswelded properties, the absence of which has severely restricted the use of ferritic stainless steels, depend on controlling interstitial carbon and nitrogen. The publication describes three methods that are being used for interstitial control. It is now possible to produce ferritic stainless steels which are tough and which have excellent corrosion resistance and ductility in the as-welded conditions. Several new high-chromium ferritic alloys with these desirable properties are being produced commercially.
Optical flow vs Bspline image registration for respiratory motion modeling (2012)

Respiratory motion modeling is a key approach that has the potential to improve the efficiency of radiation therapy, especially in the thorax and the abdomen areas. Such modeling may help delivering lower dose to the healthy tissues and higher, more concentrated dose to the tumor target under breathing-induced motion. These respiratory models under investigation here relate the respective organs and tumors motion to an external acquired respiratory signal. The first step for building such models consists in extracting the tumor and healthy tissues motion using a four dimensional computed tomography (4D CT) image registration algorithm. The efficacy of the registration algorithm directly affects the accuracy and the robustness of the derived respiratory motion models. In this study, we compared and evaluated the use of two registration algorithms, namely the elastic Bspline and the optical flow, for the process of building the patient specific respiratory motion model. From the same datasets of 10 4D CT patients acquisitions carried out with an external respiratory signal, two different patient specific models were built, one for each registration approach. Similar performance in accuracy was obtained using the two different registration algorithms with however an advantage for the Bspline approach with respect to the computational time involved in building the model.
High-bandwidth address translation for multiple-issue processors (1996)

In an effort to push the envelope of system performance, microprocessor designs are continually exploiting higher levels of instruction-level parallelism, resulting in increasing bandwidth demands on the address translation mechanism. Most current microprocessor designs meet this demand with a multi-ported TLB. While this design provides an excellent hit rate at each port, its access latency and area grow very quickly as the number of ports is increased. As bandwidth demands continue to increase, multi-ported designs will soon impact memory access latency.We present four high-bandwidth address translation mechanisms with latency and area characteristics that scale better than a multiported TLB design. We extend traditional high-bandwidth memory design techniques to address translation, developing interleaved and multi-level TLB designs. In addition, we introduce two new designs crafted specifically for high-bandwidth address translation. Piggyback ports are introduced as a technique to exploit spatial locality in simultaneous translation requests, allowing accesses to the same virtual memory page to combine their requests at the TLB access port. Pretranslation is introduced as a technique for attaching translations to base register values, making it possible to reuse a single translation many times.We perform extensive simulation-based studies to evaluate our designs. We vary key system parameters, such as processor model, page size, and number of architected registers, to see what effects these changes have on the relative merits of each approach. A number of designs show particular promise. Multi-level TLBs with as few as eight entries in the upper-level TLB nearly achieve the performance of a TLB with unlimited bandwidth. Piggyback ports combined with a lesser-ported TLB structure, e.g., an interleaved or multi-ported TLB, also perform well. Pretranslation over a single-ported TLB performs almost as well as a same-sized multi-level TLB with the added benefit of decreased access latency for physically indexed caches.
A 1.2V, 2.4GHz Fully Integrated Linear CMOS Power Amplifier with Efficiency Enhancement (2006)

A 2.4GHz power amplifier is implemented with standard thin-oxide transistors in a 1.2V, 0.13 mum CMOS process. The output matching network is fully integrated on chip. The PA transmits up to 24dBm linear power with 25% drain efficiency at -1dB compression point. When driven into saturation, it transmits 27dBm peak power with 32% drain efficiency. A technique for enhancing average efficiency is proposed and demonstrated. This technique does not degrade instantaneous efficiency at peak power and maintains constant power gain with power back-off
The connexin mimetic peptide Gap27 improves cell motility in human skin models despite raised glucose, insulin and IGFBP-5 (2012)

In chronic non-healing diabetic wounds Connexin43 (Cx43) is upregulated at the wound edge compared to ‘normal’ skin wounds. Reduced Cx43 expression/function is associated with improved wound closure rates, consistent with our data to date showing that the Cx43 channel blocker, Gap27, increases scrape-wound closure rates in human skin models. Insulin Growth Factor-I (IGF-I) also stimulates skin wound healing whilst its actions can be attenuated by IGF binding protein 5 (IGFBP-5). The IGF-I:IGFBP-5 ratio is altered in diabetic skin and maybe of clinical significance.<br/>
Sugar, Uric Acid, and the Etiology of Diabetes and Obesity (2013)

The intake of added sugars, such as from table sugar (sucrose) and high-fructose corn syrup has increased dramatically in the last hundred years and correlates closely with the rise in obesity, metabolic syndrome, and diabetes. Fructose is a major component of added sugars and is distinct from other sugars in its ability to cause intracellular ATP depletion, nucleotide turnover, and the generation of uric acid. In this article, we revisit the hypothesis that it is this unique aspect of fructose metabolism that accounts for why fructose intake increases the risk for metabolic syndrome. Recent studies show that fructose-induced uric acid generation causes mitochondrial oxidative stress that stimulates fat accumulation independent of excessive caloric intake. These studies challenge the long-standing dogma that "a calorie is just a calorie" and suggest that the metabolic effects of food may matter as much as its energy content. The discovery that fructose-mediated generation of uric acid may have a causal role in diabetes and obesity provides new insights into pathogenesis and therapies for this important disease.