gebhart/patrepeval huggingface dataset:
VisExpress: Visual exploration of differential gene expression data (2015)

Biologists are keen to understand how processes in cells react to environmental changes. Differential gene expression analysis allows biologists to explore functions of genes with data generated from different environments. However, these data and analysis lead to unique challenges since tasks are ill-defined, require implicit domain knowledge, comprise large volumes of data, and are, therefore, of explanatory nature. To investigate a scalable visualization-based solution, we conducted a design study with three biologists specialized in differential gene expression analysis. We stress our contributions in three aspects: first, we characterize the problem domain for exploring differential gene expression data and derive task abstractions and design requirements. Second, we investigate the design space and present an interactive visualization system, called VisExpress. Third, we evaluate the usefulness of VisExpress via a Pair Analytics study with real users and real data and report on insights that were gained by our experts with VisExpress.
Auto‐calibration of drive condition for cholesteric liquid crystal displays (2012)

Abstract Dynamic drive scheme (DDS) is known widely as passive matrix addressing that obtains both high‐speed re‐writing and a high contrast ratio in the field of cholesteric liquid crystal displays (LCDs). However, DDS has a serious problem in that the proper drive condition is very narrow and it is largely influenced by individual differences in LCDs that arise during their production. We have developed a new auto‐calibration system that adjusts both the contrast ratio and color balance automatically using capacitances of effective pixels and temperature compensation models that utilize the physical properties of cholesteric LCDs. We have managed to optimize the driving conditions between 5 and 35 °C with this method, and obtained both stable and high‐quality color images where the reflectance is 36%, contrast ratio is 8, and NTSC ratio is 20%. This auto‐calibration system has been able to greatly improve the production yield of cholesteric LCDs and made it possible to make practical use of cholesteric LCDs.
Catheter Tip Tracking and Visualisation with a Single Receiver Coil (2003)

S. Zuehlsdorff, S. Ferrari, R. Umathum, S. Volz, W. Semmler, M. Bock German Cancer Research Center, Heidelberg, Germany Synopsis A catheter design is proposed to perform active catheter tip tracking and visualization of the distal catheter end simultaneously. A small tracking coil and an extended twisted pair coil are connected in series and mounted near the end of a catheter. With the help of a special miniature detune circuitry the tracking coil can be switched off during MR imaging using a very small DC current. For the interleaved tracking experiment the DC current is not applied and the MR signal is predominantly received by the tracking coil.
Team IHMC's Lessons Learned from the DARPA Robotics Challenge: Finding Data in the Rubble (2016)

This article presents a retrospective analysis of Team IHMC's experience throughout the DARPA Robotics Challenge (DRC), where we took first or second place overall in each of the three phases. As an extremely demanding challenge typical of DARPA, the DRC required rapid research and development to push the boundaries of robotics and set a new benchmark for complex robotic behavior. We present how we addressed each of the eight tasks of the DRC and review our performance in the Finals. While the ambitious competition schedule limited extensive experimentation, we will review the data we collected during the approximately three years of our participation. We discuss some of the significant lessons learned that contributed to our success in the DRC. These include hardware lessons, software lessons, and human‐robot integration lessons. We describe refinements to the coactive design methodology that helped our designers connect human–machine interaction theory to both implementation and empirical data. This approach helped our team focus our limited resources on the issues most critical to success. In addition to helping readers understand our experiences in developing on a Boston Dynamics Atlas robot for the DRC, we hope this article will provide insights that apply more widely to robotics development and design of human–machine systems.
Graves' Disease with Markedly Elevated Serum Immunoglobulin E (1989)

A 37-year-old female with Graves' disease was reported. An abnormally high concentration of serum IgE was observed by radioimmuno-sorbent test before treatment. Laboratory findings showed no evidence of atopic diseases or other known diseases with hyperglobulinemia E. There is no reported case of Graves' disease associated with remarkably elevated plasma IgE level. In the present patient, a further elevation of serum IgE concentration was observed when the dose of methimazole reached about 500 mg in total. Allergic mechanism may be the cause of this phenomenon. Serum IgE level was decreased gradually after replacement of methimazole by propylthiouracil. IgE level was not parallel with thyroid functions, and even when her thyroid function was normalized after subtotal thyroidectomy, IgE concentration was still increased around 900 IU/ml. The mechanism of hyperglobulinemia E in this case was discussed.
Write process modeling in MLC flash memories using renewal theory (2015)

In the write process of multilevel per cell (MLC) flash memories, an iterative approach is used to mitigate the monotonicity problem. The monotonicity in programming is considered to be the major restriction in MLC flash. In this paper, we are mostly concerned with deriving a mathematical model for iterative programming using the framework of “renewal processes”. Then, we approximate the maximum number of steps in iterative programming, and obtain the voltage distribution in flash due to iterative programming. Moreover, the obtained results help us to accurately analyze the effect of inter-cell interference (ICI) in this type of memory. Finally, we obtain a more precise voltage distribution for the symbol states in flash memory. Simulation results show the effect of varying the step size in the iterative programming and the effect of ICI on the information rate.
Complex Flow Generation and Development in a Full-Scale Turbofan Inlet (2017)

The future of aviation relies on the integration of airframe and propulsion systems to increase fuel efficiency and improve the aerodynamic performance of aircraft. This need brings design challenges, such as the ingestion of non-uniform flows by turbofan engines. In this work, we seek to understand the behavior of a complex distorted inflow in a full-scale engine rig. A 21-inch diameter distortion screen previously designed is used to mimic the behavior of an adverse inlet flow encountered by a hybrid wing body type of aircraft. Three measurement planes along the inlet of the research engine are selected for the acquisition of data using particle image velocimetry at a duct diameter Reynolds number of 2.6 million. The resulting mean velocity profiles, velocity gradients and turbulent stresses are analyzed in order to describe the evolution of the flow along the inlet of the turbofan engine and as it approaches the fan face. As flow develops downstream, the vortex present in the profile migrates clockwise, opposite to the rotation of the fan, and towards the spinner of the engine. The turbulent stresses indicate that the center of the vortex meanders around a preferred location, and that location tightens as flow gets closer to the fan, yielding a smaller radius mean vortex near the fan. An analysis of velocity gradients shows the influence of the distortion screen in the flow, mainly in the streamwise direction, where signature features of the distortion device are observed, as an effect from the wakes of the vanes. The results obtained shed light onto the aerodynamics of swirling flows representative of distorted turbofan inlets, while further advancing the understanding of the complex vane technology presented herein for advanced ground testing of swirling inflows.
18F-FPPRGD2 PET/CT: Pilot Phase Evaluation of Breast Cancer Patients (2014)

Data from this pilot phase study suggest that (18)F- FPPRGD2 2-fluoropropionyl labeled PEGylated dimeric RGD peptide (PEG3-E[c{RGDyk}]2) is a safe PET radiopharmaceutical agent. Evaluation of (18)F- FPPRGD2 2-fluoropropionyl labeled PEGylated dimeric RGD peptide (PEG3-E[c{RGDyk}]2) in participants with breast cancer demonstrated significant uptake in the primary lesion and in the metastases. Larger cohorts are required to confirm these preliminary findings.
In Vitro Selection, Structural Characteristics, and Photocleavage of an Isoalloxazine Binding Rna Aptamer (1997)

Abstract ABSTRACT: An RNA motif which binds FMN was isolated by in vitro selection of an RNA library. The secondary structure of this RNA contains an internal loop forming an isoalloxazine binding site through non-canonical base pairing. Irradiation with light in presence of FMN induces photocleavage at G.U base pairs outside the aptamer binding site.
Intracellular Calcium Responses Encode Action Potential Firing in Spinal Cord Lamina I Neurons (2020)

Maladaptive plasticity of neurons in lamina I of the spinal cord is a lynchpin for the development of chronic pain, and is critically dependent on intracellular calcium signaling. However, the relationship between neuronal activity and intracellular calcium in these neurons is unknown. Here we combined two-photon calcium imaging with whole-cell electrophysiology to determine how action potential firing drives calcium responses within subcellular compartments of male rat spinal cord lamina I neurons. We found that single action potentials generated at the soma increase calcium concentration in the somatic cytosol and nucleus, and these calcium responses invade dendrites and dendritic spines by active backpropagation. Calcium responses in each compartment were dependent on voltage-gated calcium channels, and somatic and nuclear calcium responses were amplified by release of calcium from ryanodine-sensitive intracellular stores. Grouping single action potential-evoked calcium responses by neuron type demonstrated their presence in all defined types, as well as a high degree of similarity in calcium responses between neuron types. With bursts of action potentials, we found that calcium responses have the capacity to encode action potential frequency and number in all compartments, with action potential number being preferentially encoded. Together, these findings indicate that intracellular calcium serves as a readout of neuronal activity within lamina I neurons, providing a unifying mechanism through which activity may regulate plasticity, including that seen in chronic pain.<b>SIGNIFICANCE STATEMENT</b> Despite their critical role in both acute pain sensation and chronic pain, little is known of the fundamental physiology of spinal cord lamina I neurons. This is especially the case with respect to calcium dynamics within these neurons, which could regulate maladaptive plasticity observed in chronic pain. By combining two-photon calcium imaging and patch-clamp electrophysiological recordings from lamina I neurons, we found that action potential firing induces calcium responses within the somatic cytosol, nucleus, dendrites, and dendritic spines of lamina I neurons. Our findings demonstrate the presence of actively backpropagating action potentials, shifting our understanding of how these neurons process information, such that calcium provides a mechanism for lamina I neurons to track their own activity.
Wieloczęstotliwościowe zabezpieczenie admitancyjne (2016)

Wydawnictwo SIGMA-NOT wydaje czasopisma fachowe informujące swoich czytelników o najnowszych osiągnięciach naukowych i nowoczesnych rozwiązaniach technicznych w Polsce i na świecie, popularyzuje problemy techniczne oraz poszerza wiedzę i kulturę techniczną.
Yeast mannan genetics controls the molecular specificity of anti-carbohydrate antibodies cross-reactive to the HIV envelope (2009)

Immunologically self carbohydrates protect the human immunodeficiency virus type -1 (HIV-1) surface glycoprotein, gp120 from antibody recognition. However, one broadly neutralising antibody, 2G12, can protect against primary viral challenge by direct recognition of these "self" glycans on gp120.
Data from Adaptive Prediction Model in Prospective Molecular Signature–Based Clinical Studies (2023)

&lt;div&gt;Abstract&lt;p&gt;Use of molecular profiles and clinical information can help predict which treatment would give the best outcome and survival for each individual patient, and thus guide optimal therapy, which offers great promise for the future of clinical trials and practice. High prediction accuracy is essential for selecting the best treatment plan. The gold standard for evaluating the prediction models is prospective clinical studies, in which patients are enrolled sequentially. However, there is no statistical method using this sequential feature to adapt the prediction model to the current patient cohort. In this article, we propose a reweighted random forest (RWRF) model, which updates the weight of each decision tree whenever additional patient information is available, to account for the potential heterogeneity between training and testing data. A simulation study and a lung cancer example are used to show that the proposed method can adapt the prediction model to current patients' characteristics, and, therefore, can improve prediction accuracy significantly. We also show that the proposed method can identify important and consistent predictive variables. Compared with rebuilding the prediction model, the RWRF updates a well-tested model gradually, and all of the adaptive procedure/parameters used in the RWRF model are prespecified before patient recruitment, which are important practical advantages for prospective clinical studies. &lt;i&gt;Clin Cancer Res; 20(3); 531–9. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Simultaneous inhibition of Sirtuin 3 and cholesterol homeostasis targets acute myeloid leukemia stem cells by perturbing fatty acid β-oxidation and inducing lipotoxicity (2023)

Outcomes for patients with acute myeloid leukemia (AML) remain poor due to the inability of current therapeutic regimens to fully eradicate disease-initiating leukemia stem cells (LSC). Previous studies have demonstrated that oxidative phosphorylation (OXPHOS) is an essential process that is targetable in LSC. Sirtuin 3 (SIRT3), a mitochondrial deacetylase with a multi-faceted role in metabolic regulation, has been shown to regulate OXPHOS in cancer models; however, it has not yet been studied in the context of LSC. Thus, we sought to identify if SIRT3 is important for LSC function. Using RNAi and a SIRT3 inhibitor (YC8-02), we demonstrate that SIRT3 is a critical target for the survival of primary human LSC but is not essential for normal human hematopoietic stem and progenitor cell function. In order to elucidate the molecular mechanisms by which SIRT3 is essential in LSC we combined transcriptomic, proteomic, and lipidomic approaches, showing that SIRT3 is important for LSC function through the regulation of fatty acid oxidation (FAO) which is required to support OXPHOS and ATP production in human LSC. Further, we discovered two approaches to further sensitize LSC to SIRT3 inhibition. First, we found that LSC tolerate the toxic effects of fatty acid accumulation induced by SIRT3 inhibition by upregulating cholesterol esterification. Disruption of cholesterol homeostasis sensitizes LSC to YC8-02 and potentiates LSC death. Second, SIRT3 inhibition sensitizes LSC to the BCL-2 inhibitor venetoclax. Together, these findings establish SIRT3 as a regulator of lipid metabolism and potential therapeutic target in primitive AML cells.
Simplified model of an FSK-to-ASK direct-detection system using a Fabry-Perot demodulator (1990)

Design guidelines are presented for a direct-detection optical transmission system in which an FSK (frequency-shift-keyed) signal is converted to ASK (amplitude-shift-keyed format) by a tunable Fabry-Perot filter demodulator/demultiplexer. The analysis gives an estimated set of conditions for the proper Fabry-Periot (FP) bandwidth and tone frequency deviation that reduces the system power penalities. This is accomplished by calculating the tonal power transmitted through the FP; this simplifying assumption neglects pattern dependences but provides a simple, useful expression for predicting regions of rapidly increasing power penalties. The generated curves agree well with experimental results for three different systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lys05 (2012)

Lys05 is a previously undescribed dimeric chloroquine which more potently accumulates in the lysosome and blocks autophagy compared with HCQ. Lys05 produced more potent antitumor activity as a single agent both in vitro and in vivo in multiple human cancer cell lines and xenograft models compared with HCQ. Initial structure-activity relationship studies demonstrated that the increased activity associated with Lys05 was due to the bivalent aminoquinoline rings, C7-Chlorine, and a short triamine linker. While lower doses of Lys05 were well tolerated and associated with antitumor activity, at the highest dose tested, Lys05 produced Paneth cell dysfunction and intestinal toxicity, similar to what can be observed in mice and humans with genetic defects in the autophagy gene ATG16L1. Lys05 is therefore a new lysosomal autophagy inhibitor that has potential to be developed further into a drug for cancer and other medical applications.
Nouvelles formulations d'enrobages pour la conservation des fruits tropicaux (2001)

Le transport et le stockage des fruits tropicaux sont difficiles car ceux-ci ne supportent pas les basses températures souvent utilisées pour les fruits tempérés pour ralentir leur mûrissement et allonger leur durée de vie. C'est pourquoi les fruits tropicaux sont souvent transportés par avion plutôt que par route ou bateau, ce qui est plus coûteux pour le consommateur. Les enrobages comestibles associés à des températures de stockage modérément basses représentent une alternative économique. L'utilisation d'enrobages polysaccharides sur les fruits entraîne une modification de l'atmosphère interne du fruit, avec relativement peu d'oxygène et des teneurs élevées en dioxyde de carbone dues à l'effet combiné de la perméabilité de l'enrobage et de la respiration du fruit. Cette atmosphère modifiée ralentit le processus de maturation. De plus, dans une atmosphère de stockage tous les fruits perdent de l'eau ce qui cause un flétrissement de la peau. Ceci peut être réduit en introduisant une barrière à l'évaporation de l'eau telle que la cire ou un enrobage gras comestible. Enfin, les enrobages peuvent contenir des composants antimicrobiaux ou agir comme barrière physique aux pathogènes, réduisant le pourrissement des fruits. Les formulations des enrobages consistent souvent en films composites faits de combinaisons d'ingrédients. Par exemple, on utilise un film d'ester de sucrose (SemperFresh) sur les loquats, les tangelos, les ananas et les bananes; on utilise aussi de la cire de carnauba sur les goyaves et les mangues, de l'huile minérale sur les limes et un film à base de cellulose (Nature Seal) sur les goyaves, les mangues et les oranges.
The Alloreactive and Self-Restricted CD4+ T Cell Response Directed Against a Single MHC Class II/Peptide Combination (2000)

The cellular basis for allograft rejection derives from the strong T cell response to cells bearing foreign MHC. While it was originally assumed that alloreactive T cells focus their recognition on the polymorphic residues that differ between syngeneic and allogeneic MHC molecules, studies with MHC class I-restricted CTL have shown that MHC-bound peptides play a critical role in allorecognition. It has been suggested that alloreactive T cells depend more strongly on interactions with the MHC molecule than with the associated peptide, but there is little evidence to support this idea. Here we have studied the alloreactive and self-restricted response directed against the class II H2-Ab molecule bound with a single peptide, Ep, derived from the H2-Ealpha chain. This MHC class II-peptide combination was a poor target and stimulator of alloreactive CD4+ T cell responses, indicating that MHC-bound peptides are as important for alloreactive CD4+ T cells as they are for alloreactive CTL. We also generated alloreactive T cells with exquisite specificity for the Ab/Ep complex, and compared their reactivity with self-restricted T cells specific for the same Ab/Ep complex. Our results showed that peptide-specific alloreactive T cells, as compared with self-restricted T cells, were more sensitive to peptide stimulation, but equally sensitive to amino acid substitutions in the peptide. These findings indicate that alloreactive and self-restricted T cells interact similarly with their MHC/peptide ligand.
Intake of myo-inositol hexaphosphate and urinary excretion of inositol phosphates in Wistar rats: Gavage vs. oral administration with sugar (2019)

Administration of InsP6 to rats leads to the excretion of a mixture of different InsPs. Rats more effectively absorb InsP6 when supplied without dietary components that interfere with its uptake, such as the Ca ion and sugar.
<title>Visualization of time-varying MRI data for MS lesion analysis</title> (2001)

Conventional methods to diagnose and follow treatment of Multiple Sclerosis require radiologists and technicians to compare current images with older images of a particular patient, on a slic-by-slice basis. Although there has been progress in creating 3D displays of medical images, little attempt has been made to design visual tools that emphasize change over time. We implemented several ideas that attempt to address this deficiency. In one approach, isosurfaces of segmented lesions at each time step were displayed either on the same image (each time step in a different color), or consecutively in an animation. In a second approach, voxel- wise differences between time steps were calculated and displayed statically using ray casting. Animation was used to show cumulative changes over time. Finally, in a method borrowed from computational fluid dynamics (CFD), glyphs (small arrow-like objects) were rendered with a surface model of the lesions to indicate changes at localized points.
Targeting the Mitotic Checkpoint for Cancer Therapy with NMS-P715, an Inhibitor of MPS1 Kinase (2010)

MPS1 kinase is a key regulator of the spindle assembly checkpoint (SAC), a mitotic mechanism specifically required for proper chromosomal alignment and segregation. It has been found aberrantly overexpressed in a wide range of human tumors and is necessary for tumoral cell proliferation. Here we report the identification and characterization of NMS-P715, a selective and orally bioavailable MPS1 small-molecule inhibitor, which selectively reduces cancer cell proliferation, leaving normal cells almost unaffected. NMS-P715 accelerates mitosis and affects kinetochore components localization causing massive aneuploidy and cell death in a variety of tumoral cell lines and inhibits tumor growth in preclinical cancer models. Inhibiting the SAC could represent a promising new approach to selectively target cancer cells.