gebhart/patrepeval huggingface dataset:
Biophotonic tool for sensing the dynamics of H<sub>2</sub>O<sub>2</sub> extracellular release in stressed cells (2012)

Hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) is known to play a multifaceted role in cell physiology mechanisms involving oxidative stress and intracellular signal transduction. Therefore, the development of analytical tools providing information on the dynamics of H<sub>2</sub>O<sub>2</sub> generation remains of utmost importance to achieve further insight in the complex physiological processes of living cells and their response to environmental stress. In the present work we developed a novel optic biosensor that provides continuous real-time quantification of the dynamics of the hydrogen peroxide release from cells under oxidative stress conditions. The biosensor is based on the ultra-sensitive dark field optical detection of cytochrome <i>c</i> (cyt <i>c</i>) that exhibits a narrow absorption peaks in its reduced state (Fe(II)) at λ = 550 nm. In the presence of H<sub>2</sub>O<sub>2</sub> the ferrous heme group Fe(II) is oxidised into Fe(III) providing the spectroscopic information exploited in this approach. Extremely low limit-of-detection for H<sub>2</sub>O<sub>2</sub> down to the subnanomolar range is achieved by combining scattering substrates (eg. polystyrene beads) able to shelter cyt c and an inverted microscope in dark field configuration. The developed biosensor was able to perform real-time detection of H<sub>2</sub>O<sub>2</sub> extracellular release from human promyelocytic leukemia cells (HL-60) exposed to lipopolysaccaride (LPS) that elicits strong immune-response. This biosensing tool is currently being implemented to the real-time detection of superoxide anion (O<sub>2</sub>.<sup>-</sup>) and offers the possibility to extend to further oxidative stress biomarkers such as glutathione. More generally, multianalyte and dynamic informations might bring new insights to understand complex cellular metabolisms involved in oxidative-stress-related diseases and cytotoxic responses.
Molecular Mechanisms of Sepsis (2011)

In cancer, therapies are targeted at 6 important pathways. In sepsis, there is ongoing controversy regarding the number and relative roles of pathways that are activated or repressed and which are important in the progression from health to death. Adding to complexity, there is interaction of pathways, there are differences in temporal pattern of up and down-regulation of pathways and there are different responses of pathways to therapies of sepsis. In this review, we define four key pathways of sepsis: (1) inflammation and immunity, (2) coagulation and fibrinolysis, (3) apoptosis, and (4) endocrine. Each of these pathways can impair endothelial function, a unifying aspect of the pathophysiology of sepsis. There are few studies of interactions of pathways except for the interacttion of inflammation/immunity with coagulation/fibrinolysis. Successful treatment of cancer requires that cancer therapies interrupt several key pathways of cancer. Accordingly, we suggest that successful treatment of sepsis will require therapies that interrupt several key pathways of sepsis. Perhaps the paucity of approved therapies for sepsis is related in part to the underevaluation of novel pathways, to lack of understanding of interactions of pathways and to lack of interruption of key pathways of sepsis.
[Cloning expression and characterization of a multifunctional anticoagulated peptide gene in E. Coli]. (2002)

Our results confirm that it is feasible to design a hybrid multifunctional protein that targets various components of the haemostatic process.
FORMATION AND STRUCTURE OF THE SPORE OF <i>BACILLUS COAGULANS </i> (1962)

Spore formation in Bacillus coagulans has been studied by electron microscopy using an epoxy resin (Araldite) embedding technique. The developmental stages from the origin of the initial spore septum to the mature spore were investigated. The two forespore membranes developed from the double layer of cytoplasmic membrane. The cortex was progressively deposited between these two membranes. The inner membrane finally became the spore protoplasmic membrane, and the outer membrane part of the inner spore coat or the outer spore coat itself. In the mature spore the completed integuments around the spore protoplasm consisted of the cortex, a laminated inner coat, and a dense outer coat. No exosporium was observed. The method of formation of the cortex and the spore coats is discussed.
EXPERIMENTAL STUDY OF BIAS TEMPERATURE INSTABILITY AND PROGRESSIVE BREAKDOWN OF ADVANCED GATE DIELECTRICS (2005)

With shrinking gate dielectrics, the reliability requirements of semiconductor gate dielectrics become more and more difficult to maintain. New physical mechanisms and phenomena are discovered and new challenges arise. At the same time, some issues, which have been minor in the past, begin to show bigger impact, such as the Negative Bias Temperature Instability issue. The dynamic NBTI phenomenon was studied with ultrathin SiO2 and HfO2 devices. With a dynamic stress condition, the device lifetime can be largely extended due to the reduced NBTI degradation. This reduction is contributed to the annealing of fixed oxide charges during the stress off period. A mathematical model is also established to explain this phenomenon. With alternative gate dielectrics' introduction, new issues associated with these materials and device structures are also raised. Those issues need to be studied in detail before fully incorporation of new materials. Compared with SiO2 devices, the NBTI degradation of HfO2 has a similar trend. However, it is found that they have different frequency response than the SiO2 devices. This difference is later found due to the traps inside the gate dielectrics. Detailed studies show that NBTI degradations at dc stress and dynamic stress conditions have different temperature acceleration factors due to the bulk traps. The disappearance of this difference by insetting a detrapping period further proves this observation. As we enter the ultrathin gate dielectrics regime, the electron tunneling mechanisms behind the gate dielectrics breakdown shift. Consequently, gate dielectrics breakdown mode also shifts from the clear-detected hard breakdown to the noisy soft breakdown. Thus new lifetime extrapolation models are needed. The progressive breakdown of ultrathin SiO2 is studied by a two-step test methodology. By monitoring the degradation of the progressive breakdown path in terms of the activation energy, the voltage acceleration factor, two kinds of breakdown filaments, the stable one and the unstable one, were studied. The stable filament is found to be a breakdown filament independent of the original breakdown filament, and the unstable filament is the continuing degradation of the original filament.
Toward automatic task design (2010)

A central challenge in human computation is in understanding how to design task environments that effectively attract participants and coordinate the problem solving process. In this paper, we consider a common problem that requesters face on Amazon Mechanical Turk: how should a task be designed so as to induce good output from workers? In posting a task, a requester decides how to break down the task into unit tasks, how much to pay for each unit task, and how many workers to assign to a unit task. These design decisions affect the rate at which workers complete unit tasks, as well as the quality of the work that results. Using image labeling as an example task, we consider the problem of designing the task to maximize the number of quality tags received within given time and budget constraints. We consider two different measures of work quality, and construct models for predicting the rate and quality of work based on observations of output to various designs. Preliminary results show that simple models can accurately predict the quality of output per unit task, but are less accurate in predicting the rate at which unit tasks complete. At a fixed rate of pay, our models generate different designs depending on the quality metric, and optimized designs obtain significantly more quality tags than baseline comparisons.
Detecting Botnets in Computer Networks Using Multi-agent Technology (2009)

The paper presents a hybrid model of the bots detector which is a combination of host intrusion detection system and the operating system event log analyzer. Bot can be defined as a computer that have been attacked by a hacker or infected with malicious software and is used for illegal activities. Collections of infected computers form a botnet. The proposed system is used to detect bots based on the evaluation of events occurring in the operating system and network environment. Detection algorithms based on the signatures derived from the analysis of the various types of malicious software that creates bots. The model has been implemented using multi-agent technology.
Differentially Private Data Releasing for Smooth Queries with Synthetic Database Output (2014)

We consider accurately answering smooth queries while preserving differential privacy. A query is said to be $K$-smooth if it is specified by a function defined on $[-1,1]^d$ whose partial derivatives up to order $K$ are all bounded. We develop an $ε$-differentially private mechanism for the class of $K$-smooth queries. The major advantage of the algorithm is that it outputs a synthetic database. In real applications, a synthetic database output is appealing. Our mechanism achieves an accuracy of $O (n^{-\frac{K}{2d+K}}/ε)$, and runs in polynomial time. We also generalize the mechanism to preserve $(ε, δ)$-differential privacy with slightly improved accuracy. Extensive experiments on benchmark datasets demonstrate that the mechanisms have good accuracy and are efficient.
AverageExplorer (2014)

This paper proposes an interactive framework that allows a user to rapidly explore and visualize a large image collection using the medium of average images . Average images have been gaining popularity as means of artistic expression and data visualization, but the creation of compelling examples is a surprisingly laborious and manual process. Our interactive, real-time system provides a way to summarize large amounts of visual data by weighted average(s) of an image collection, with the weights reflecting user-indicated importance. The aim is to capture not just the mean of the distribution, but a set of modes discovered via interactive exploration. We pose this exploration in terms of a user interactively "editing" the average image using various types of strokes, brushes and warps, similar to a normal image editor, with each user interaction providing a new constraint to update the average. New weighted averages can be spawned and edited either individually or jointly. Together, these tools allow the user to simultaneously perform two fundamental operations on visual data: user-guided clustering and user-guided alignment, within the same framework. We show that our system is useful for various computer vision and graphics applications.
Obligatory intracellular parasitism by<i>Ehrlichia chaffeensis</i>and<i>Anaplasma phagocytophilum</i>involves caveolae and glycosylphosphatidylinositol-anchored proteins (2003)

Obligatory intracellular, human ehrlichiosis agents Ehrlichia chaffeensis and Anaplasma phagocytophilum create unique replicative compartments devoid of lysosomal markers in monocytes/macrophages and granulocytes respectively. The entry of these bacteria requires host phospholipase C (PLC)-gamma2 and protein tyrosine kinases, but their entry route is still unclear. Here, using specific inhibitors, double immunofluorescence labelling and the fractionation of lipid rafts, we demonstrate that bacterial entry and intracellular infection involve cholesterol-rich lipid rafts or caveolae and glycosylphosphatidylinositol (GPI)-anchored proteins. By fluorescence microscopy, caveolar marker protein caveolin-1 was co-localized with both early and replicative bacterial inclusions. Additionally, tyrosine-phosphorylated proteins and PLC-gamma2 were found in bacterial early inclusions. In contrast, clathrin was not found in any inclusions from either bacterium. An early endosomal marker, transferrin receptor, was not present in the early inclusions of E. chaffeensis, but was found in replicative inclusions of E. chaffeensis. Furthermore, several bacterial proteins from E. chaffeensis and A. phagocytophilum were co-fractionated with Triton X-100-insoluble raft fractions. The formation of bacteria-encapsulating caveolae, which assemble and retain signalling molecules essential for bacterial entry and interact with the recycling endosome pathway, may ensure the survival of these obligatory intracellular bacteria in primary host defensive cells.
The Emergence of Spectral Universality in Deep Networks (2018)

Recent work has shown that tight concentration of the entire spectrum of singular values of a deep network's input-output Jacobian around one at initialization can speed up learning by orders of magnitude. Therefore, to guide important design choices, it is important to build a full theoretical understanding of the spectra of Jacobians at initialization. To this end, we leverage powerful tools from free probability theory to provide a detailed analytic understanding of how a deep network's Jacobian spectrum depends on various hyperparameters including the nonlinearity, the weight and bias distributions, and the depth. For a variety of nonlinearities, our work reveals the emergence of new universal limiting spectral distributions that remain concentrated around one even as the depth goes to infinity.
The <i>ob</i> Gene and Insulin: A Relationship Leading to Clues to the Understanding of Obesity (1995)

Obesity and non-insulin-dependent diabetes are estimated to affect millions of people in the world. This pathology is multifactorial, comprising complex interactions of genetic and environmental factors and lacking a specific therapy. Great interest arose from the recent discovery of the ob gene expressed only in adipose tissue and coding for a protein that appears to regulate adiposity, potentially by acting as a satiety factor. We report here that in normal rats, ob mRNA is respectively up- or downregulated by a rise in insulinemia (induced by 2-day insulin infusion while maintaining euglycemia) or a decrease in insulinemia (induced by a 3-day fast). Our results also show that in genetically obese fa/fa rats studied longitudinally, white adipose tissue ob mRNA levels increase in parallel with early occurringand steadily increasing hyperinsulinemia. This results in adult obese animals having markedly higher ob mRNA levels than age-matched normoinsulinemic lean rats. Furthermore, in adult obese rats, ob mRNA escapes down-regulation as normalization of hyperinsulinemia due to fasting fails to reduce the high ob mRNA levels.
Index compression using fixed binary codewords (2004)

quantities of text. The static costs associated with storing the index can be traded against dynamic costs associated with using it during query evaluation. Typically, index representations that are effective and obtain good compression tend not to be efficient, in that they require more operations during query processing. In this paper we describe a scheme for compressing lists of integers as sequences of fixed binary codewords that has the twin benefits of being both effective and efficient. Experimental results are given on several large text collections to validate these claims.
Design and analysis of IC power delivery with on-chip voltage regulation (2012)

Distributed on-chip voltage regulation offers an appealing solution to many power delivery challenges in modern chip designs. In-depth understanding of such power delivery networks (PDNs) that encompass large on-chip passive power grids and active on-chip and/or off-chip voltage regulators is hampered by high network complexity and the intricate interactions between a multitude of active regulators and the large passive network. In this paper, we discuss some of the key challenges and opportunities in designing power delivery networks with on-chip voltage regulation. We discuss important network simulation and design issues and present illustrative results to demonstrate the potential benefits resulted from holistic optimization of the power delivery network.
A safe, low current, high gradient, superconducting quadrupole magnet for high energy physics beam transport (1983)

A superconducting quadrupole magnet has been fabricated and tested that generates a gradient of 60 T/m at a peak operating current of 1100 amperes. The cold bore of the magnet is 12.7 cm in diameter and 2.8 m long, and the unwanted field multipoles sum to 4 parts per thousand of the quadrupole field at a bore radius of 5.0 cm. The magnet operates safely without quench protection and peak coil temperatures following quenches deliberately induced at full field do not exceed 50 K. Testing at the design gradient of 50 T/m indicates a beam energy deposition quench threshold of approximately 5 mJ/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> .
Progress with the PRINTS protein fingerprint database (1996)

PRINTS is a compendium of protein motif 'fingerprints' derived from the OWL composite sequence database. Fingerprints are groups of motifs within sequence alignments whose conserved nature allows them to be used as signatures of family membership. To date, 400 fingerprints have been constructed and stored in Prints, the size of which has doubled in the last year. The current version, 9.0, encodes approximately 2000 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. Fingerprints inherently offer improved diagnostic reliability over single motif methods by virtue of the mutual context provided by motif neighbours. PRINTS thus provides a useful adjunct to the widely used PROSITE dictionary of patterns. The database is now accessible via the Database Browser on the UCL Bioinformatics server at http://www.biochem.ucl.ac.uk/bsm/dbbrowser .
Proton conducting membranes based on sulfonated poly(ether ether ketone)/TiO<sub>2</sub> nanocomposites for a direct methanol fuel cell (2006)

Abstract This paper presents an evaluation of the effects of titanium dioxide nanoparticles in sulfonated poly(ether ether ketone) (SPEEK) with a sulfonation degree of 57%. A series of inorganic/organic hybrid membranes was prepared with a systematic variation of titanium dioxide nanoparticle content. Their water uptake, methanol permeability and proton conductivity as a function of temperature were investigated. The results obtained show that the inorganic oxide network decreases the proton conductivity and water swelling. It is also found that increasing the inorganic oxide content leads to a decrease of methanol permeability. In terms of morphology, the membranes are homogeneous and exhibit good adhesion between inorganic domains and the polymer matrix. The proton conductivity and fuel cell performances of the nanocomposite membranes showed very good prospective in direct methanol fuel cell usages. The properties of the composite membranes are compared with those of standard Nafion membranes. Copyright © 2006 Society of Chemical Industry
Post-Implementation Usability of Erp Training Manuals: The User's Perspective (2005)

Abstract Training users is critical to the success of ERP implementations. An important aspect of training is documentation in the form of training manuals. However, the effectiveness of the training manuals will depend on their perceived usability. in this study, data on users' perceptions of ERP training manuals, more than two years post-implementation, are analyzed for usability dimensions of task support, learnability, navigation, and presentation.
Phosphatidylinositol 3-Kinase Mediates Bronchioalveolar Stem Cell Expansion in Mouse Models of Oncogenic K-ras-Induced Lung Cancer (2008)

We conclude that PI3K is a critical regulator of BASC expansion, supporting treatment strategies to target PI3K in NSCLC patients.
Zur Anwendung der Sondendiagnostik in einem polymerisierenden Plasma (1975)

Abstract On the example of the Ne glow discharge with a benzol admixture the possibility of applicating the probe diagnostic in polymerizing plasmas is investigated. Heating the probe at 900°C stetady values for the floating potential, the probe characteristic and its second derivation are obtained. The variation with time of these quantities without heating the probe yields informations about the rate of polymerization. The effect of a benzol admixture from 1% to 20% on the energy distribution function of electrons and the plasma parameters in the tube axis is pointed out. From the second derivation of the characteristic at emissive probe conditions it is possible to deduce in addition to the space potential the influence of the benzol admixture on the ionization mechanism.
Window-Level Rate Control for Smooth Picture Quality and Smooth Buffer Occupancy (2010)

In rate control, smooth picture quality and smooth buffer occupancy are both important but contrary to each other at a given bit rate. How to get a good tradeoff between them was not devoted much attention previously. To deal with this problem, a theoretical window model is proposed in this paper, in which several adjacent frames grouped as a window are considered together. The smoothness of both picture quality and buffer occupancy can be gracefully achieved by regulating the size of the window. To illustrate the usage of window model, a window-level rate control algorithm cooperated with the traditional ρ-domain rate-distortion model is further introduced. In experiments, we first show how the proposed window model achieves the tradeoff between picture quality smoothness and buffer smoothness, and then demonstrate the significant PSNR improvement, accuracy of bit control and consistency of visual quality of the proposed window-level rate control algorithm.
Analysis of peptide mixtures by capillary high performance liquid chromatography: A practical guide to small‐scale separations (1992)

Capillary HPLC is a very effective means of separating small amounts of peptides and proteins. Capillary columns ranging from 0.01 mm to 0.5 mm in diameter can be constructed using recycled supports and inexpensive fused silica capillary tubing. Commercial pumping systems and UV detectors can be readily converted for operation in the flow rate range of 0.5-50 microL/min. Detailed procedures are given for the construction of columns and UV detector flow cells. A mixture of peptides derived from the endo Lys C digest of horse heart cytochrome c was used to illustrate various aspects of capillary chromatography of peptides and compares the performance of various-sized capillary columns and UV detector flow cell types.
Potential for use of InP solar cells in the space radiation environment (1985)

Indium phosphide solar cells were observed to have significantly higher radiation resistance than either GaAs or Si after exposure to 10 MeV proton irradiation data and previous 1 MeV electron data together with projected efficiencies for InP, it was found that these latter cells produced more output power than either GaAs or Si after specified fluences of 10 MeV protons and 1 MeV electrons. Estimates of expected performance in a proton dominated space orbit yielded much less degradation for InP when compared to the remaining two cell types. It was concluded that, with additional development to increase efficiency, InP solar cells would perform significantly better than either GaAs or Si in the space radiation environment.
An electrostatic microactuator for electro-mechanical relay (2003)

The author describes the design, the fabrication process, and the estimation of the characteristics of an electrostatic miniature relay. Its characteristics (contact force and response time) are estimated by the boundary-element method for the analysis of electrostatic fields. Problems regarding future development of the prototype and the future of microactuator technology and its applications are considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>