gebhart/patrepeval huggingface dataset:
Common pathway signature in lung and liver fibrosis (2016)

Fibrosis, a progressive accumulation of extracellular matrix components, encompasses a wide spectrum of distinct organs, and accounts for an increasing burden of morbidity and mortality worldwide. Despite the tremendous clinical impact, the mechanisms governing the fibrotic process are not yet understood, and to date, no clinically reliable therapies for fibrosis have been discovered. Here we applied Regeneration Intelligence, a new bioinformatics software suite for qualitative analysis of intracellular signaling pathway activation using transcriptomic data, to assess a network of molecular signaling in lung and liver fibrosis. In both tissues, our analysis detected major conserved signaling pathways strongly associated with fibrosis, suggesting that some of the pathways identified by our algorithm but not yet wet-lab validated as fibrogenesis related, may be attractive targets for future research. While the majority of significantly disrupted pathways were specific to histologically distinct organs, several pathways have been concurrently activated or downregulated among the hepatic and pulmonary fibrosis samples, providing new evidence of evolutionary conserved pathways that may be relevant as possible therapeutic targets. While future confirmatory studies are warranted to validate these observations, our platform proposes a promising new approach for detecting fibrosis-promoting pathways and tailoring the right therapy to prevent fibrogenesis.
Evolutionary data sampling for user movement classification (2015)

Smartphones are nowadays used for recognizing people's daily activities and habits, by collecting and analysing user activity information in real-time. In order to demonstrate this methodology, we have developed GPSTracker <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> a prototype application for Android phones, which collects position, speed, altitude and time information and performs real-time classification of user's movement. The GPSTracker application also uses geo-location information abouts Points Of Interest (POIs) such as bus or metro routes, parks and stadiums in order to improve the set of features used for the classification of a type of movement. In this work, we use evolutionary algorithms, in order to reduce the number of samples required for training our classifier, without loosing in classification accuracy. The resulting model, a) is able to provide personalized solutions, tuned to each individual users movement abilities, b) better adapts to unbalanced training data, due to the generation of training samples from the existing ones, c) performs an initial sampling of the training data, which reduces requirements for computational resources and improves the classification performance.
Development of Novel Tools to Study and Combat Pathogenic Microbial Biofilms (2014)

University of Minnesota M.S. thesis. 2014. Major: Microbial Engineering. Advisor: Christine Salomon. 1 computer file (PDF); 82 pages.
A Simple Design and Simulation of Full Bridge LLC Resonant DC-DC Converter for Pv Applications (2015)

This paper deals with the design and simulation of full bridge LLC resonant converter suitable for photovoltaic applications. LLC converter has several desired features such as high efficiency, low electromagnetic interference (EMI) and high power density. This paper provides a detailed practical design aspect of full bridge LLC resonant converter. The LLC converter is implemented with a full-bridge on the primary side and a full-bridge rectifier on the secondary side. It includes designing the transformer turns ratio and selecting the components such as resonant inductor, resonant capacitor and magnetizing inductor. Also performance parameters such as voltage gain and output voltage ripple are calculated. Simulation of LLC resonant converter is carried out using MATLAB / SIMULINK and the results are verified.
Mechanical Property Testing of Irradiated Zircaloy Cladding Under Reactor Transient Conditions (2002)

Specimen geometries have been developed to determine the mechanical properties of irradiated Zircaloy cladding subjected to the mechanical conditions and temperatures associated with reactivity-initiated accidents (RIA) and loss-of-coolant accidents (LOCA). Miniature ring-stretch specimens were designed to induce both uniaxial and plane-strain states of stress in the transverse (hoop) direction of the cladding. Also, longitudinal tube specimens were also designed to determine the constitutive properties in the axial direction. Finite-element analysis (FEA) and experimental parameters and results were closely coupled to optimize an accurate determination of the stress-strain response and to induce fracture behavior representative of accident conditions. To determine the constitutive properties, a procedure was utilized to transform measured values of load and displacement to a stress-strain response under complex loading states. Additionally, methods have been developed to measure true plastic strains in the gauge section and the initiation of failure using real-time data analysis software. Strain rates and heating conditions have been selected based on their relevance to the mechanical response and temperatures of the cladding during the accidents.
Absolute Analysis of Particulate Materials by Laser-Induced Breakdown Spectroscopy (1997)

We have developed a new data acquisition approach followed by a suitable data analysis for Laser-induced breakdown spectroscopy. It provides absolute concentrations of elements in particulate materials (e.g., industrial dusts and soils). In contrast to the known calibration procedures (based on the ratio of spectral lines), which are applicable only when one component is constant, this approach requires no constant constituent and results in absolute (rather than relative) concentrations. Thus, the major drawback of this analytical method, namely, the signals' instability (especially when particulate materials are concerned) is partially solved. Unlike the commonly used integrated data acquisition, we use a sequence of signals from single breakdown events. We compensate for pulse to pulse fluctuations in an intrinsic way, and the final results do not depend on the presence of any constant component. Extended linear calibration curves are obtained, and limits of detection are improved by 1 order of magnitude relative to previous methods applied to the same samples (e.g., detection limit of 10(-12) g of Zn in aerosol samples). The proposed compensation for pulse variations is based on the assumption that they can be described as a multiplicative effect for both the spectral peaks and a component of the baseline. In other words, we assume that the same fluctuation pattern observed in the spectral peaks is present in the baseline as well. This assumption is shown to hold and is utilized in the proposed method. In addition, a proper data-filtering process, which eliminates ill-conditioned spectra, is shown to partially compensate for problems due to the nature of analysis of particulate materials.
Gummy and conductive silicone rubber fingers: Importance of vulnerability analysis (2002)

Abstract. Vulnerability evaluation of various biometric systems should be conducted and its results should be available to potential users. Summary Biometrics is utilized in individual authentication techniques which identify individuals by checking physiological or behavioral characteristics, such as fingerprints, faces, voice, iris patterns, signatures, etc. Biometric systems are said to be convenient because they need neither something to memorize such as passwords nor something to carry about such as ID tokens [1]. In spite of that, a user of biometric systems would get into a dangerous situation when her/his biometric data are abused. For example, you cannot change your fingerprints while you can change your passwords or ID tokens when they are compromised. Therefore, biometric systems must protect the information for biometrics against abuse, and they must also prevent fake biometrics. We focus on fingerprint systems since they have become widespread as authentication terminals for PCs or mobile terminals. A fingerprint system has
c-Jun N-Terminal Kinase 1 Is Required for Toll-Like Receptor 1 Gene Expression in Macrophages (2007)

The regulation of innate immune responses to pathogens occurs through the interaction of Toll-like receptors (TLRs) with pathogen-associated molecular patterns and the activation of several signaling pathways whose contribution to the overall innate immune response to pathogens is poorly understood. We demonstrate a mechanism of control of murine macrophage responses mediated by TLR1/2 heterodimers through c-Jun N-terminal kinase 1 (JNK1) activity. JNK controls tumor necrosis factor alpha production and TLR-mediated macrophage responses to Borrelia burgdorferi, the causative agent of Lyme disease, and the TLR1/TLR2-specific agonist PAM(3)CSK(4). JNK1, but not JNK2, activity regulates the expression of the tlr1 gene in the macrophage cell line RAW264.7, as well as in primary CD11b(+) cells. We also show that the proximal promoter region of the human tlr1 gene contains an AP-1 binding site that is subjected to regulation by the kinase and binds two complexes that involve the JNK substrates c-Jun, JunD, and ATF-2. These results demonstrate that JNK1 regulates the response to TLR1/2 ligands and suggest a positive feedback loop that may serve to increase the innate immune response to the spirochete.
Interfacial Engineering of Ultrathin Metal Film Transparent Electrode for Flexible Organic Photovoltaic Cells (2014)

A generally applicable method has been developed for fabricating highly transparent ultrathin Ag films on both glass and plastic substrates using the self-assembled monolayer modified ZnO/Ag/ZnO tri-layer structure. The resulting films show remarkably low surface roughness with very high transparency (>80% between 400 and 600 nm) and low surface resistance (8.61 Ω/□). With an inverted architecture, the devices based on the SAM modified tri-layer UTMF electrode show superior performance and mechanical properties than those using ITO electrode on both glass and plastic substrates. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to 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.
Robust Physical-World Attacks on Machine Learning Models. (2017)

Deep neural network-based classifiers are known to be vulnerable to adversarial examples that can fool them into misclassifying their input through the addition of small-magnitude perturbations. However, recent studies have demonstrated that such adversarial examples are not very effective in the physical world--they either completely fail to cause misclassification or only work in restricted cases where a relatively complex image is perturbed and printed on paper. In this paper we propose a new attack algorithm--Robust Physical Perturbations (RP2)-- that generates perturbations by taking images under different conditions into account. Our algorithm can create spatially-constrained perturbations that mimic vandalism or art to reduce the likelihood of detection by a casual observer. We show that adversarial examples generated by RP2 achieve high success rates under various conditions for real road sign recognition by using an evaluation methodology that captures physical world conditions. We physically realized and evaluated two attacks, one that causes a Stop sign to be misclassified as a Speed Limit sign in 100% of the testing conditions, and one that causes a Right Turn sign to be misclassified as either a Stop or Added Lane sign in 100% of the testing conditions.
Out of The Box: Strategies for Achieving Profits Today and Growth Tomorrow Through Web Services (2002)

Anyone in search of an exhaustive treatment of the role of technology in enabling loose 'process networks', should turn to John Hagel's Out Of The Box. - Financial Times. Managers are understandably skeptical of the promises of new technologies. Now, leading business strategist John Hagel III has a refreshing message for managers burned by over-hyped technologies yet pressured to find innovative ways to deliver more value with fewer resources. Out of the Box tackles the most fundamental business issue facing managers today: how to continue to create value as competition intensifies. The book's practical advice will enable companies of all sizes to realize bottom-line savings quickly with modest investment, and create leveraged growth platforms for long-term competitiveness. For any manager who must envision and execute the next IT/business strategy, and the strategy after that, this book will prove to be a rich source of new ideas and a landmark in shaping their thinking.
Ringsubstitutionen und Folgereaktionen an Aromaten‐Metall‐π‐Komplexen I (1962)

Abstract Schwermetall‐Aromaten‐π‐Komplexe besitzen aromatischen Charakter. Dies zeigt sich unter anderem daran, daß viele solche Verbindungen aromatischen Substitutionsreaktionen zugänglich sind. Es wird eine Übersicht über Substitutions‐ und Folgereaktionen an derartigen Systemen gegeben.
Coma induced by abuse of γ-hydroxybutyrate (GBH or liquid ecstasy): a case report (1997)

Objective: To investigate if the incidence of disorders of spermatogenesis and testicular tissue morphology have changed in middle aged Finnish men over 10 years.Design: Two necropsy series completed in 1981 and in 1991.
Reestablishment of the Endothelial Lining by Endothelial Cell Therapy Stabilizes Experimental Abdominal Aortic Aneurysms (2013)

Our study demonstrates the potential of restoring the endothelial lining to control AAA dynamics and designates ECs as an efficient therapy to stop AAA expansion.
Analysis of a head-mounted display-type multifocus display system using a laser scanning method (2011)

We developed a head-mounted display (HMD)-type multifocus display system using a laser-scanning method to provide an accommodation effect for viewers. This accomplishment indicates that providing a monocular depth cue is possible through this multifocus system. In the system, the optical path is changed by a scanning action. To provide an accurate accommodation effect for the viewer, the multifocus display system is designed and manufactured in accordance with the geometric analysis of the system's scanning action. Using a video camera as a substitute for the viewer, correct focus adjustment without the scanning action problem is demonstrated. By analyzing the scanning action and experimental results, we are able to illustrate the formation of a viewpoint in an HMD-type multifocus display system using a laser-scanning method. In addition, we demonstrate that the accommodation effect could be provided independent of the viewing condition of the viewer.
A CMOS Capacitance Sensor for Cell Adhesion Characterization (2005)

We describe a CMOS capacitance sensor for measuring the capacitive coupling between living cells and the underlying substrate, a quantity that can be used to characterize cell adhesion strength and cell health. The capacitance sensor operates on the charge sharing principle, mapping sensed capacitance values to voltages. The sensor has been fabricated in a commercially available 0.5 /spl mu/m, 2-poly 3-metal CMOS technology. Experimental results are presented for bench tests using a micropositioned electrode and in vitro tests with cells cultured directly on the chip surface. The sensor achieves an empirical distance resolution of 3 nm and capacitance resolution of 135 aF. The sensors have been successfully used for long term monitoring of cell viability in vitro.
Octamer-based genome scanning distinguishes a unique subpopulation of <i>Escherichia coli</i> O157:H7 strains in cattle (1999)

Multilocus-genotyping methods have shown that Escherichia coli O157:H7 is a geographically disseminated clone. However, high-resolution methods such as pulse-field gel electrophoresis demonstrate significant genomic diversity among different isolates. To assess the genetic relationship of human and bovine isolates of E. coli O157:H7 in detail, we have developed an octamer-based genome-scanning methodology, which compares the distance between over-represented, strand-biased octamers that occur in the genome. Comparison of octamer-based genome-scanning products derived from >1 megabase of the genome demonstrated the existence of two distinct lineages of E. coli O157:H7 that are disseminated within the United States. Human and bovine isolates are nonrandomly distributed among the lineages, suggesting that one of these lineages may be less virulent for humans or may not be efficiently transmitted to humans from bovine sources. Restriction fragment length polymorphism analysis with lambdoid phage genomes indicates that phage-mediated events are associated with divergence of the lineages, thereby providing one explanation for the degree of diversity that is observed among E. coli O157:H7 by other molecular-fingerprinting methods.
Early Changes in Gene Expression Induced by Tobacco Smoke: Evidence for the Importance of Estrogen within Lung Tissue (2010)

Lung cancer is the leading cause of cancer deaths in the United States, surpassing breast cancer as the primary cause of cancer-related mortality in women. The goal of the present study was to identify early molecular changes in the lung induced by exposure to tobacco smoke and thus identify potential targets for chemoprevention. Female A/J mice were exposed to either tobacco smoke or HEPA-filtered air via a whole-body exposure chamber (6 h/d, 5 d/wk for 3, 8, and 20 weeks). Gene expression profiles of lung tissue from control and smoke-exposed animals were established using a 15K cDNA microarray. Cytochrome P450 1b1, a phase I enzyme involved in both the metabolism of xenobiotics and the 4-hydroxylation of 17beta-estradiol (E(2)), was modulated to the greatest extent following smoke exposure. A panel of 10 genes were found to be differentially expressed in control and smoke-exposed lung tissues at 3, 8, and 20 weeks (P < 0.001). The interaction network of these differentially expressed genes revealed new pathways modulated by short-term smoke exposure, including estrogen metabolism. In addition, E(2) was detected within murine lung tissue by gas chromatography-coupled mass spectrometry and immunohistochemistry. Identification of the early molecular events that contribute to lung tumor formation is anticipated to lead to the development of promising targeted chemopreventive therapies. In conclusion, the presence of E(2) within lung tissue when combined with the modulation of cytochrome P450 1b1 and other estrogen metabolism genes by tobacco smoke provides novel insight into a possible role for estrogens in lung cancer.
The cephalosporin C group (1967)

E. P. Abraham, Q. Rev. Chem. Soc., 1967, 21, 231 DOI: 10.1039/QR9672100231
Social Network Sensors for Early Detection of Contagious Outbreaks (2010)

Current methods for the detection of contagious outbreaks give contemporaneous information about the course of an epidemic at best. It is known that individuals near the center of a social network are likely to be infected sooner during the course of an outbreak, on average, than those at the periphery. Unfortunately, mapping a whole network to identify central individuals who might be monitored for infection is typically very difficult. We propose an alternative strategy that does not require ascertainment of global network structure, namely, simply monitoring the friends of randomly selected individuals. Such individuals are known to be more central. To evaluate whether such a friend group could indeed provide early detection, we studied a flu outbreak at Harvard College in late 2009. We followed 744 students who were either members of a group of randomly chosen individuals or a group of their friends. Based on clinical diagnoses, the progression of the epidemic in the friend group occurred 13.9 days (95% C.I. 9.9-16.6) in advance of the randomly chosen group (i.e., the population as a whole). The friend group also showed a significant lead time (p<0.05) on day 16 of the epidemic, a full 46 days before the peak in daily incidence in the population as a whole. This sensor method could provide significant additional time to react to epidemics in small or large populations under surveillance. The amount of lead time will depend on features of the outbreak and the network at hand. The method could in principle be generalized to other biological, psychological, informational, or behavioral contagions that spread in networks.
Gateable Skyrmion Transport via Field-induced Potential Barrier Modulation (2016)

We report on the influence of pinning potentials on current-driven skyrmion dynamics and demonstrate that skyrmions can be gated via either magnetic or electric fields. When encountering pinning potentials, skyrmions are well known to simply skirt around them. However, we show that skyrmions can be depinned much more easily when their driving force is oriented against the pinning site rather that the intuitive option of being oriented away. This observation can be exploited together with the normally undesirable Magnus force for the creation of a skyrmion diode. The phenomenon is explained by the increased skyrmion compression resulting from the spin transfer torque opposing the repulsive potential. The smaller skyrmion size then experiences a reduced pinning potential. For practical low-power device applications, we show that the same skyrmion compression can be recreated by applying either a magnetic or electric field. Our analysis provides an insight on the skyrmion dynamics and manipulation that is critical for the realization of skyrmion-based transistors and low-power memory.
The phenotypic spectrum of congenital Zika syndrome (2017)

In October 2015, Zika virus (ZIKV) outbreak the Brazilian Ministry of Health (MoH). In response, the Brazilian Society of Medical Genetics established a task force (SBGM-ZETF) to study the phenotype of infants born with microcephaly due to ZIKV congenital infection and delineate the phenotypic spectrum of this newly recognized teratogen. This study was based on the clinical evaluation and neuroimaging of 83 infants born during the period from July, 2015 to March, 2016 and registered by the SBGM-ZETF. All 83 infants had significant findings on neuroimaging consistent with ZIKV congenital infection and 12 had confirmed ZIKV IgM in CSF. A recognizable phenotype of microcephaly, anomalies of the shape of skull and redundancy of the scalp consistent with the Fetal Brain Disruption Sequence (FBDS) was present in 70% of infants, but was most often subtle. In addition, features consistent with fetal immobility, ranging from dimples (30.1%), distal hand/finger contractures (20.5%), and feet malpositions (15.7%), to generalized arthrogryposis (9.6%), were present in these infants. Some cases had milder microcephaly or even a normal head circumference (HC), and other less distinctive findings. The detailed observation of the dysmorphic and neurologic features in these infants provides insight into the mechanisms and timings of the brain disruption and the sequence of developmental anomalies that may occur after prenatal infection by the ZIKV.