gebhart/patrepeval huggingface dataset:
Characterization of oncogene-induced senescence and the role of the senescence-associated secretory phenotype in pilocytic astrocytoma (2017)

Variations in proliferation caused by oncogene-induced senescence (OIS) are proposed to cause the benign but unpredictable growth behaviour of pilocytic astrocytoma (PA). In PA OIS is induced by aberrant MAPK pathway activation. The senescence-associated secretory phenotype (SASP), a set of cytokines, growth factors and proteases, regulates the OIS state. We here characterize the key SASP factors in PA and investigate their functional significance as growth regulators and potential targets.
Hexanor–cucurbitacin D, a degraded cucurbitacin from Begoniatuberhybrida var. alba (1970)

A compound isolated from Begoniatuberhybrida has been shown to have the structure of hexanor–cucurbitacin D (3). Its diacetate is identical to the neriodate cleavage product of cucurbitacin B diacetate.
Extracting and compensating dispersion mismatch in ultrahigh-resolution Fourier domain OCT imaging of the retina (2012)

We present a numerical approach to extract the dispersion mismatch in ultrahigh-resolution Fourier domain optical coherence tomography (OCT) imaging of the retina. The method draws upon an analogy with a Shack-Hartmann wavefront sensor. By exploiting mathematical similarities between the expressions for aberration in optical imaging and dispersion mismatch in spectral / Fourier domain OCT, Shack-Hartmann principles can be extended from the two-dimensional paraxial wavevector space (or the x-y plane in the spatial domain) to the one-dimensional wavenumber space (or the z-axis in the spatial domain). For OCT imaging of the retina, different retinal layers, such as the retinal nerve fiber layer (RNFL), the photoreceptor inner and outer segment junction (IS/OS), or all the retinal layers near the retinal pigment epithelium (RPE) can be used as point source beacons in the axial direction, analogous to point source beacons used in conventional two-dimensional Shack-Hartman wavefront sensors for aberration characterization. Subtleties regarding speckle phenomena in optical imaging, which affect the Shack-Hartmann wavefront sensor used in adaptive optics, also occur analogously in this application. Using this approach and carefully suppressing speckle, the dispersion mismatch in spectral / Fourier domain OCT retinal imaging can be successfully extracted numerically and used for numerical dispersion compensation to generate sharper, ultrahigh-resolution OCT images.
Protecting PUF Error Correction by Codeword Masking (2013)

Abstract. One of the main applications of Physical Unclonable Functions (PUFs) is unique key generation. While the advantages of PUFbased key extraction and embedding have been shown in several papers, physical attacks on it have gained only little interest until now. In this work, we demonstrate the feasibility of a differential power analysis attack on the error correction module of a secure sketch. This attack can also be applied to code-offset fuzzy extractors because they build upon secure sketches. We propose a codeword masking scheme to protect key generation algorithms used for PUFs. Our proposed countermeasure enables masking of linear Error-Correcting Codes (ECCs) without impact on their error correction capabilities while keeping the overhead low. This is achieved by random masking codewords, which can be efficiently generated by the ECC’s encoding function. Further, it allows to consistently protect the PUF-based key generation process and can provide the masked key and its mask to a subsequent crypto module which implements masking as well. We demonstrate the practical protection of our codeword masking scheme by attacking a masked secure sketch implementation. We emphasize that, besides protecting code-offset algorithms, the proposed masking scheme can also be applied to index-based syndrome coding and other security-critical error correction modules.
Ion-Exchange Membranes for the Fabrication of Reverse Electrodialysis Device (2021)

Reverse electrodialysis (RED) is an effective way to generate power by mixing two different salt concentrations in water using cation-exchange membranes (CEM) and anion-exchange membranes (AEM). The RED stack is composed of an alternating arrangement of the cation-exchange membrane and anion-exchange membrane. The RED device acts as a potential candidate for fulfilling the universal demand for future energy crises. Here, in this article, we demonstrate a procedure to fabricate a reverse electrodialysis device using laboratory-scale CEM and AEM for power production. The active area of the ion-exchange membrane is 49 cm<sup>2</sup>. In this article, we provide a step-by-step procedure for synthesizing the membrane, followed by the stack's assembly and power measurement. The measurement conditions and net power output calculation have also been explained. Furthermore, we describe the fundamental parameters that are taken into consideration for obtaining a reliable outcome. We also provide a theoretical parameter that affects the overall cell performance relating to the membrane and the feed solution. In short, this experiment describes how to assemble and measure RED cells on the same platform. It also contains the working principle and calculation used for estimating the net power output of the RED stack using CEM and AEM membranes.
Model Reduction Captures Stochastic Gamma Oscillations on Low-Dimensional Manifolds (2021)

Gamma frequency oscillations (25-140 Hz), observed in the neural activities within many brain regions, have long been regarded as a physiological basis underlying many brain functions, such as memory and attention. Among numerous theoretical and computational modeling studies, gamma oscillations have been found in biologically realistic spiking network models of the primary visual cortex. However, due to its high dimensionality and strong non-linearity, it is generally difficult to perform detailed theoretical analysis of the emergent gamma dynamics. Here we propose a suite of Markovian model reduction methods with varying levels of complexity and apply it to spiking network models exhibiting heterogeneous dynamical regimes, ranging from nearly homogeneous firing to strong synchrony in the gamma band. The reduced models not only successfully reproduce gamma oscillations in the full model, but also exhibit the same dynamical features as we vary parameters. Most remarkably, the invariant measure of the coarse-grained Markov process reveals a two-dimensional surface in state space upon which the gamma dynamics mainly resides. Our results suggest that the statistical features of gamma oscillations strongly depend on the subthreshold neuronal distributions. Because of the generality of the Markovian assumptions, our dimensional reduction methods offer a powerful toolbox for theoretical examinations of other complex cortical spatio-temporal behaviors observed in both neurophysiological experiments and numerical simulations.
Relações educacionais entre o Design e a Engenharia: um panorama nacional e internacional (2020)

Este artigo sintetiza uma parte da tese de doutorado intitulada “A contribuição do pensamento do Design na formação do Engenheiro: o espaço do Fab Lab como experiência transversal” e apresenta como objeto de estudo uma análise comparativa referente à inserção do ensino de Design nos cursos superiores de Engenharia, em um panorama nacional (no Brasil) e interna-cional (em outros países). Foi realizada uma investigação exploratória e des-critiva dividida em duas etapas. Primeiramente foi feito um levantamento de como o Design está sendo inserido nos cursos de graduação em Engenharia e depois, foi pesquisado como o Design e a Engenharia estão convivendo em cursos integrados; nos dois casos estão sendo considerados os panoramas nacionais e internacionais. A pesquisa teve uma função importante para a visualização da situação atual da educação em Engenharia e foi fundamental para se perceber a lacuna existente e quantas oportunidades e espaços ainda existem para serem explorados.
Three Dimensional Sketch for a Landscape Using Morse Theory and Reeb Graphs (2012)

The theoretical procedure for making a three dimensional landscape sketch is proposed in this paper. At the first stage, the critical points such as summits, ravine bottoms and passes are allocated by a user. These critical points construct fundamental properties of the mountain that a user tries to draw. Applying Morse theory to these critical points, the landscape of the mountain is defined as a sequence of a CW-complex that explains how the surface structure of the mountain changes when the mountain is formed from the bottom to the top step by step. The CW-complex is then concreted by obtaining skeletons from the Reeb graph of the mountain. The skeleton consisting of contour lines is modified without changing its topological structure by giving ranges and ravines. These lines constitute a series of continuous critical points and become invariants as well as summits, ravine bottoms and passes. At the final step, the system automatically generates a proposed landscape from the skeleton using Nurbs lines and surfaces or polygon meshes. By rendering the landscape, a user can change its shape by modifying ranges and ravines until the user satisfies it.
Blood Flow in Cerebral Aneurysms: Comparison of Phase Contrast Magnetic Resonance and Computational Fluid Dynamics - Preliminary Experience (2008)

CFD simulations using inflow boundary conditions measured with pcMRI yield main features of intra-aneurysmal velocity patterns corresponding to intra-aneurysmal measurements performed with pcMRI. Thus, pcMRI may become a valuable complementary technique to CFD simulations to obtain in-vivo reference data for the study of aneurysmal hemodynamics. More data is needed to compare and fully explore the capabilities of both methods.
Analysis of DNA mismatch repair gene expression and mutations in thyroid tumours. (2006)

Alterations of DNA mismatch repair genes, primarily demonstrated in hereditary nonpolyposis colorectal carcinomas, were reported to be of relevance for the progression of several sporadic tumours. In this study, the expression and mutations of MLH1, MSH2, PMS1 and PMS2 in a panel of thyroid tumours, including nodular hyperplasia, follicular adenomas and carcinomas, were investigated. The expressions of MLH1, MSH2 and PMS1 were generally higher in malignant tumours than in benign lesions (p < 0.01). This observation can find potential diagnostic application in the differentiation of follicular adenomas from follicullar carcinomas of the thyroid. No point mutations in the DNA mismatch repair genes MSH2 (exon 12, 13) and MLH1 (exon 15, 16) were found.
Spectrally resolved fluorescence lifetime imaging of Nile red for measurements of intracellular polarity (2015)

Spectrally resolved confocal microscopy and fluorescence lifetime imaging have been used to measure the polarity of lipid-rich regions in living HeLa cells stained with Nile red. The emission peak from the solvatochromic dye in lipid droplets is at a shorter wavelength than other, more polar, stained internal membranes, and this is indicative of a low polarity environment. We estimate that the dielectric constant, ϵ , is around 5 in lipid droplets and 25<ϵ<40 in other lipid-rich regions. Our spectrally resolved fluorescence lifetime imaging microscopy (FLIM) data show that intracellular Nile red exhibits complex, multiexponential fluorescence decays due to emission from a short lifetime locally excited state and a longer lifetime intramolecular charge transfer state. We measure an increase in the average fluorescence lifetime of the dye with increasing emission wavelength, as shown using phasor plots of the FLIM data. We also show using these phasor plots that the shortest lifetime decay components arise from lipid droplets. Thus, fluorescence lifetime is a viable contrast parameter for distinguishing lipid droplets from other stained lipid-rich regions. Finally, we discuss the FLIM of Nile red as a method for simultaneously mapping both polarity and relative viscosity based on fluorescence lifetime measurements.
Simple Derivation of the Electron-Nucleus Contact Hyperfine Interaction (1962)

A simple derivation is given of the Fermi formula for the contact hyperfine interaction energy between the magnetic moment of a nucleus and that of the surrounding electrons. Considerably fewer mathematical and more physical arguments are used than in previous derivations. It is shown that the contact hyperfine field at the nucleus is necessarily equal to the magnetic induction in the interior of a sphere possessing a uniform electronic magnetization. The simplifications achieved in the present derivation do not seem to result in a loss of rigor, and they do not require the introduction of essentially new assumptions.
Survey and perspectives of social touch in HCI (2017)

Touch is one of the primary channel of non-verbal communication. It is used to convey emotions and to establish bounds between people. Its use has already been considered in HCI to interact with devices, but it has rarely been used for direct emotional communication between individuals. This article presents a literature review of social touch in human-computer interaction. Based at the cross-section of psychology, HCI, emotions and haptics research communities, we first review the role and importance of social touch for communicating emotions. We then discuss existing and emerging technologies to perform social touch and finally we present new perspectives for interfaces in HCI.
Cumulant-based blind identification of linear multi-input-multi-output systems driven by colored inputs (1997)

The blind identification problem of a linear multi-input-multi-output (MIMO) system is widely noticed by many researchers in diverse fields due to its relevance to blind signal separation. However, such a problem is ill-posed and has no unique solution. Therefore, we can only find a solution of the problem within an equivalence class. We address the blind identification problem of the linear MIMO system driven by unobservable colored inputs using higher order statistics (HOS), particularly the fourth-order cumulants, of the outputs, where the unobservable inputs are mutually independent but temporally colored linear processes. We first define the set, which is denoted by S, of stable scalar transfer functions and then define the notion of a generalized permutation matrix (which is abbreviated by a g-matrix) over S. Then, it is shown that the transfer function matrix of an unknown system is identified only up to post-multiplication by a g matrix. This result is applied to identifying FIR systems for blind signal separation.
Pharmacological management of polycystic kidney disease (2014)

Given the accumulated knowledge, it is currently uncertain whether drugs will become available in the near future to significantly change the course of the relentlessly progressing polycystic kidney disease.
Accurate round-trip delay-time estimator for simultaneous identification of multiple SAW ID tags (2013)

In this paper an iterative method of accurate round-trip delay-time (RTDT) estimation is presented. Using this method, it is possible to take imperfections like amplitude and phase distortions into account and avoid biased RTDT estimates. Those accurate RTDT estimates are a prerequisite for precise grid estimation of pulse position coded surface acoustic wave tags as a fundament for further identification and the possibility of a grid refinement and/or larger reading ranges.
CD34-positive cells isolated from cryopreserved peripheral-blood progenitor cells can be expanded ex vivo and used for transplantation with little or no toxicity. (1996)

These data demonstrate that CD34 cells can successfully be selected from cryopreserved material, expanded ex vivo on a large scale, and safely reinfused following myeloablative conditioning regimens.
Improving accuracy of microarray classification by a simple multi-task feature selection filter (2011)

Leveraging information from the publicly accessible data repositories can be very useful when training a classifier from a small-sample microarray data. To achieve this, we proposed a multi-task feature selection filter that borrows strength from auxiliary microarray data. It uses Kruskal-Wallis test on auxiliary data and ranks genes based on their aggregated p-values. The top-ranked genes are selected as features for the target task classifier. The multi-task filter was evaluated on microarray data related to nine different types of cancers. The results showed that the multi-task feature selection is very successful when applied in conjunction with both single-task and multi-task classifiers.
Modified Auditory Brainstem Responses (MABR): Part I - Rationale and Normative Study (1987)

Binaural, rapid rate, ABR stimulation at four intensity levels (MABR) as well as ABR at two intensity levels were carried out in 35 normal subjects. Latency and amplitude relationship with stimulus intensity of wave V of the MABR was extensively studied in these subjects. MABR recording is a rapid, sensitive, non-invasive screening method readily done at the intensive care bedside. Less than 10 minutes is required in addition to the ABR examination time. Normality of the MABR potentials implies a high degree of peripheral auditory and brainstem functional integrity, augmenting information gained with standard ABR technique. Only clinical trials can decide if MABR sensitivity will exceed that of the ABR and prove helpful to diagnosis and patient care.
Fostering Language and Literacy Learning: Strategies to Support the Many Ways Children Communicate (2012)

Early literacy instruction is receiving increasing emphasis. Many teachers of young children recognize that skills such as identifying and forming letters and practicing oral language skills are important (Helm &amp; Katz, 2010). At the same time, teachers also report feeling pressure to focus on intensive drill and practice of isolated skills such as letter recognition (Jeynes, 2006). Framing early literacy learning as direct instruction of isolated skills typically results in a very narrow approach to learning to read and communicate clearly. In contrast to a narrow approach, National Association for the Education of Young Children (NAEYC) recommends a broad range of language and literacy experiences be provided for young children in early childhood programs. This article identifies ways teachers of young children can provide a range of language and literacy experiences and creates a meaningful context for explicit language and literacy instruction. It begins with a discussion of the relationship between culture and development that has informed recent understandings of early literacy. Four intentional teaching strategies--share personal stories, foster peer cross talk, vary group structures, and engage children in recording and representing their ideas--are described here. (Contains 1 table and 3 figures.)
Measurements of dark current in a CCD imager during light exposures (2008)

Thermal excitation of electrons is a major source of noise in Charge-Coupled Device (CCD) imagers. Those electrons are generated even in the absence of light, hence the name dark current. Dark current is particularly important for long exposure times and elevated temperatures. The standard procedure to correct for dark current is to take several pictures under the same condition as the real image, except with the shutter closed. The resulting dark frame is later subtracted from the exposed image. We address the question of whether the dark current produced in an image taken with a closed shutter is identical to the dark current produced in an exposure in the presence of light. In our investigation, we illuminated two different CCD chips to different intensities of light and measured the dark current generation. A surprising conclusion of this study is that some pixels produce a different amount of dark current under illumination. Finally, we discuss the implications that this has for dark frame image correction.
Neural network predicts sequence of TP53 gene based on DNA chip (2002)

The trained neural network is available for academic use by contacting steen@cbs.dtu.dk
Supplementary Table S3 from High-Throughput Functional Evaluation of Variants of Unknown Significance in <i>ERBB2</i> (2023)

&lt;p&gt;Raw data of Fig. 1C and Supplementary Fig. S2.&lt;/p&gt;
Antibody Interference with N-Acyl Homoserine Lactone-Mediated Bacterial Quorum Sensing (2006)

Many bacterial pathogens coordinate their virulence factor expression in a cell density-dependent manner. This population-dependent coordination of gene expression in bacteria has been termed "quorum sensing" (QS). N-Acyl homoserine lactones (AHLs) are used by over 70 Gram-negative bacterial species as autoinducers. Inhibition of QS signaling might represent a new target for antimicrobial therapy. Here we report the hapten design, synthesis, generation of monoclonal antibodies (mAbs) against AHLs, and the evaluation of these mAbs for their ability to blunt QS signaling and inhibit virulence factor expression in P. aeruginosa. The mAbs can be envisioned as a tool for future investigations into AHL-based QS, which may aid in gaining new insights into the pathogenesis of P. aeruginosa and may ultimately lead to the development of new strategies to combat bacterial diseases.
In silico prediction of drug‐binding strengths to human serum albumin (2003)

Drug binding to Human Serum Albumin (HSA) is an area of intense research. The pharmacokinetics and pharmacodynamics of drugs are strongly affected by their binding to this protein. In this article, the field is reviewed, as well as our models to predict drug-binding affinities to HSA from drug structure. The physiological role of HSA is described, as well as its influence in drug action. The crystal structures of this protein are discussed, emphasizing the two drug-binding sites and the fatty acids binding sites observed therein. The advantages of using high-performance affinity chromatography to rapidly screen drugs for HSA binding are explained. The different QSAR models for HSA binding of restricted families of drugs (both from other groups and our group) are enumerated. Finally, a detailed description of our general models to predict drug-binding strengths to HSA from structure is given. It is expected for these models to be useful in drug design and pharmaceutical research.
An Autonomous and Distributed Mobility Management Scheme in Mobile Core Networks (2015)

The 5th generation mobile and wireless communication systems are expected to accommodate exploding traffic, increasing number of devices, and heterogeneous applications driven by proliferation of IoT and M2M technologies. The centralized mobility management architecture in a current mobile core network cannot satisfy these emerging requirements. In this paper, we introduce novel architecture of distributed mobility management and an autonomous and adaptive mobility management scheme which distributes mobility management function on nodes in a mobile core network in accordance with mobility characteristics of UEs and a management policy. We adopt a biologically-inspired adaptation algorithm, called attractor selection, to accomplish adaptive selection taking into account multiple objectives. Through simulation experiments, we conrmed that our proposal could accomplish lower delay, higher load balancing, and lower C-plane overhead comparing to other methods including the current standard.
Irritable bowel syndrome: diagnosis and management (2006)

<i>Irritable bowel syndrome is often dismissed as just being a nuisance rather than anything more serious, but its symptoms can seriously diminish a patient9s quality of life. When the disease is better understood and treatment is tailored to the individual patient, it can often be rewarding to manage</i>