gebhart/patrepeval huggingface dataset:
Susceptibility of <i>Candida</i> Species to Photodynamic Effects of Photofrin (2004)

The in vitro susceptibility of pathogenic Candida species to the photodynamic effects of the clinically approved photosensitizing agent Photofrin was examined. Internalization of Photofrin by Candida was confirmed by confocal fluorescence microscopy, and the degree of uptake was dependent on incubation concentration. Uptake of Photofrin by Candida and subsequent sensitivity to irradiation was influenced by culture conditions. Photofrin uptake was poor in C. albicans blastoconidia grown in nutrient broth. However, conversion of blastoconidia to filamentous forms by incubation in defined tissue culture medium resulted in substantial Photofrin uptake. Under conditions where Photofrin was effectively taken up by Candida, irradiated organisms were damaged in a drug dose- and light-dependent manner. Uptake of Photofrin was not inhibited by azide, indicating that the mechanism of uptake was not dependent on energy provided via electron transport. Fungal damage induced by Photofrin-mediated photodynamic therapy (PDT) was determined by evaluation of metabolic activity after irradiation. A strain of C. glabrata took up Photofrin poorly and was resistant to killing after irradiation. In contrast, two different strains of C. albicans displayed comparable levels of sensitivity to PDT. Furthermore, a reference strain of C. krusei that is relatively resistant to fluconazole compared to C. albicans was equally sensitive to C. albicans at Photofrin concentrations of >/=3 microg/ml. The results indicate that photodynamic therapy may be a useful adjunct or alternative to current anti-Candida therapeutic modalities, particularly for superficial infections on surfaces amenable to illumination.
Efficient Action Localization with Approximately Normalized Fisher Vectors (2014)

The Fisher vector (FV) representation is a high-dimensional extension of the popular bag-of-word representation. Transformation of the FV by power and ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> normalizations has shown to significantly improve its performance, and led to state-of-the-art results for a range of image and video classification and retrieval tasks. These normalizations, however, render the representation non-additive over local descriptors. Combined with its high dimensionality, this makes the FV computationally expensive for the purpose of localization tasks. In this paper we present approximations to both these normalizations, which yield significant improvements in the memory and computational costs of the FV when used for localization. Second, we show how these approximations can be used to define upper-bounds on the score function that can be efficiently evaluated, which enables the use of branch-and-bound search as an alternative to exhaustive sliding window search. We present experimental evaluation results on classification and temporal localization of actions in videos. These show that the our approximations lead to a speedup of at least one order of magnitude, while maintaining state-of-the-art action recognition and localization performance.
Antimicrobial Activity of Newly Synthesized Thiadiazoles, 5-benzyl-2Htetrazole and Their Nucleosides (2012)

A number of new substituted tetrazole and their hydrazide derivatives as well as the corresponding sugar hydrazone derivatives were synthesized and tested for their antimicrobial activity against Bacillus subtilis (Gram-positive), Pseudomonas aeruginosa (Gram-negative), and Streptomyces species (Actinomycetes) and antifungal activity against four fungal strains namely, Aspergillus flavus, Aspergillus fumigates, Penicillium marneffei and Trichophyton mentagrophytes. The synthesized compounds displayed different degrees of antimicrobial activity.
A survey on congestion control for mobile ad hoc networks (2007)

Abstract Congestion control is a key problem in mobile ad hoc networks. The standard congestion control mechanism of the Transmission Control Protocol (TCP) is not able to handle the special properties of a shared wireless multi‐hop channel well. In particular, the frequent changes of the network topology and the shared nature of the wireless channel pose significant challenges. Many approaches have been proposed to overcome these difficulties. In this paper, we give an overview over existing proposals, explain their key ideas and show their interrelations. Copyright © 2007 John Wiley & Sons, Ltd.
Sensitive HPLC-Fluorescence Method for Irinotecan and Four Major Metabolites in Human Plasma and Saliva: Application to Pharmacokinetic Studies (2003)

The developed assay can be used to determine pharmacokinetic parameters for CPT-11, SN-38, SN-38 G, APC, and NPC in plasma and saliva from patients with metastatic colorectal cancer.
Real-Time Lane Region Detection Using a Combination of Geometrical and Image Features (2016)

Over the past few decades, pavement markings have played a key role in intelligent vehicle applications such as guidance, navigation, and control. However, there are still serious issues facing the problem of lane marking detection. For example, problems include excessive processing time and false detection due to similarities in color and edges between traffic signs (channeling lines, stop lines, crosswalk, arrows, etc.). This paper proposes a strategy to extract the lane marking information taking into consideration its features such as color, edge, and width, as well as the vehicle speed. Firstly, defining the region of interest is a critical task to achieve real-time performance. In this sense, the region of interest is dependent on vehicle speed. Secondly, the lane markings are detected by using a hybrid color-edge feature method along with a probabilistic method, based on distance-color dependence and a hierarchical fitting model. Thirdly, the following lane marking information is extracted: the number of lane markings to both sides of the vehicle, the respective fitting model, and the centroid information of the lane. Using these parameters, the region is computed by using a road geometric model. To evaluate the proposed method, a set of consecutive frames was used in order to validate the performance.
Major cold shock protein of Escherichia coli. (1990)

When exponentially growing Escherichia coli cell cultures were transferred from 37 degrees C to 10 degrees C or 15 degrees C, the production of a 7.4-kDa cytoplasmic protein (CS7.4) was prominently induced. The rate of CS7.4 production reached 13% of total protein synthesis within 1-1.5 hr after a shift to 10 degrees C and subsequently dropped to a lower basal level. Regulation of CS7.4 expression was very strict, such that synthesis of the protein was undetectable at 37 degrees C. We have cloned the gene encoding this protein and have completed the nucleotide sequence analysis, which revealed that the gene encodes a hydrophilic protein of 70 amino acid residues.
New Method for Constructing Wavefunctions for Bound States and Scattering (1969)

A new method is developed for integrating coupled differential equations arising in bound state and scattering problems in quantum mechanics. The wavefunctions are easily constructed in piecewise analytic form, to any prescribed accuracy.
Wavelength demultiplexer consisting of Photonic crystal superprism and superlens (2005)

We propose a novel compact wavelength demultiplexer, for which two functions arising from the anomalous dispersion characteristics of photonic crystals are combined. One is the superprism that exhibits large angular dispersion and expansion of light beam. The other is the superlens used for the focusing of the expanded light beam. Theoretically, a high resolution of 0.4 nm will be realized in the 1.55 ?m wavelength range with device areas of 0.2 and 2.0 mm2, respectively, for available bandwidths of 3 and 35 nm. Also, a low insertion loss of less than 1 dB is expected by the optimization of input and output ends of the photonic crystals. The demultiplexing function is clearly demonstrated in finite-difference timedomain simulation.
Short-Term Lamivudine Therapy in Patients with Chronic Hepatitis B (2003)

Lamivudine is a nucleoside analogue with potent inhibitory effects on hepatitis B virus (HBV) polymerase/reverse transcriptase activity. The rate of hepatitis B e antigen (HBeAg) seroconversion in a large series of Asian patients treated with lamivudine 100 mg daily for 1 year was only 16% and the incidence of YMDD mutants was 14%. Further analysis of this Asian trial has shown that patients with a pretreatment alanine aminotransferase (ALT) level higher than 5-fold the upper limit of normal (ULN) have a much higher HBeAg seroconversion rate as compared with patients with a pretreatment ALT level <2 x upper limit of normal (64 vs. 5%; p < 0.001). In order to avoid the development of YMDD mutants, we selected 186 patients with acute exacerbation for treatment with lamivudine during 9 months, if possible, and not more than 15 months. They were all seropositive for both hepatitis B surface antigen and HBeAg for more than 6 months and also had serum HBV DNA; 138 (74%) of them were male. HBV genotypes were A in 2 (1%), B in 115 (62%), C in 65 (35%), D in 2 (1%) and F in the remaining 2 (1%). Four patients (2%) had liver cirrhosis. They had mean pretreatment levels of ALT at 608 IU/l (range: 184-2,400 IU/l), total bilirubin at 1.5 mg/dl (0.3-14.8 mg/dl), and HBV DNA at 2,246 pg/ml (0.5-25,903 pg/ml). After a median of 8.2 months (3-15 months) on lamivudine, 96 patients (51%) achieved HBeAg seroconversion, while the other 90 (48%) patients did not. Genotype B was detected comparably frequently in seroconverters and nonconverters (63 vs. 61%). During 1-year follow-up after withdrawal of lamivudine, 56 (58%) of the 96 seroconverters experienced flare-ups with ALT levels elevated higher than 5 x ULN in 50 (89%). Of 90 patients who remained HBeAg-positive, in contrast, 80 (86%) experienced ALT flares (with ALT >5 x ULN in 84%) within 1 year. YMDD mutants did not develop in any of these 186 patients during the course of lamivudine therapy. In conclusion, short-term lamivudine therapy in patients with chronic active hepatitis B can reduce the incidence of YMDD mutants and achieve an acceptable HBeAg seroconversion rate. However, the relapse rate was high (60% during 1-year follow-up). Further study is needed to establish how to improve a sustained HBeAg response.
Development trends in pressure-sensitive adhesive systems (2005)

Pressure-sensitive adhesives (PSA) present an interesting class of products that offers a potential to produce a novel generation of self-adhesives with a great number at excellent properties. The term pres-sure-sensitive describes adhesives that are aggressively and permanently tacky in the dry form at room temperature and firmly adhere to a variety of dissimilar surfaces upon mere contact, without the need of more than finger or hand pressure. Acrylic self-adhesive polymers are nowadays synthesized from a wide selection of acrylic ester monomers, often with low levels of monomers having pendant functional groups. The three basic types of acrylic common today are solvent-borne, water-borne, and solvent-free acrylic PSAs. They can be used in the production of single- and double-sided self-adhesive tapes, foil labels, carrier-free tapes, self-adhesive bioelectrodes, and decorative PVC signs and marking films. A pressure-sensitive adhesive requires a balance of cohesive strength and viscoelastic properties. These characteristics are based on three parameters: tack, adhesion, and cohesion.
UNAL-NLP: Combining Soft Cardinality Features for Semantic Textual Similarity, Relatedness and Entailment (2014)

This paper describes our participation in the SemEval-2014 tasks 1, 3 and 10. We used an uniform approach for addressing all the tasks using the soft cardinality for extracting features from text pairs, and machine learning for predicting the gold standards. Our submitted systems ranked among the top systems in all the task and sub-tasks in which we participated. These results confirm the results obtained in previous SemEval campaigns suggesting that the soft cardinality is a simple and useful tool for addressing a wide range of natural language processing problems.
Engineering Lactococcus lactis for the scaffold protein-mediated surface display of recombinant enzymes (2012)

Multi-enzyme complexes are responsible for the synthesis of a number of biochemical compounds and the degradation of complex polymers. An example of the latter is the degradation of cellulose by enzyme complexes termed “cellulosomes” which are produced by several bacteria of the class Clostridia. The basic structure of a cellulosome comprises a central scaffold protein, which associates with a multitude of cellulases via cohesin-dockerin interactions. The advent of cellulose utilization as feedstock for producing biofuels has garnered much interest towards designing custom-tailored recombinant cellulosomes and expressing them in microbes of interest. The metabolic diversity among bacteria also make this approach an appealing strategy for bestowing cellulolytic capabilities upon organisms which produce non-biofuel commodity chemicals such as lactic acid, succinic acid, acetone, amino acids, food additives and carotenoids. In addition, the display of recombinant multi-enzyme complexes in bacteria can yield novel insights into the mechanisms and parameters affecting their secretion, assembly and function. The industrially relevant lactic acid bacterium, Lactococcus lactis, is a model organism for the secretion and display of recombinant proteins, and the numerous biological techniques available for its manipulation make this organism particularly appealing for such a task. In this thesis, I present my work describing the incremental steps taken towards the surface display of custom-tailored multi-enzyme complexes on the surface of L. lactis. Chapter 1 describes the proof of concept for this project, including the choice of promoters, secretion signal peptide, and reporter enzymes. It also discusses the major bottlenecks observed based on the organism’s physiology. Chapter 2 describes the engineering of scaffold chimeras with cohesins of different specificity and the display of two enzymes on such scaffolds. I also investigated the catalytic profiles of the resulting complexes when enzymes were simultaneously or sequentially bound to the displayed scaffold. Finally, chapter 3 describes the optimization of the type 2 dockerin-cohesin interaction by the inclusion of the CipA “X” module, as well as the engineering of enzyme complexes with novel architectures by use of secondary “adapter” scaffolds and the subsequent assembly of multi-scaffold complexes. Also investigated is the potential of using a dual-plasmid system for the full in vivo assembly of such complexes without the exogenous addition of components.
Malaria Vaccine-Related Benefits of a Single Protein Comprising<i>Plasmodium falciparum</i>Apical Membrane Antigen 1 Domains I and II Fused to a Modified Form of the 19-Kilodalton C-Terminal Fragment of Merozoite Surface Protein 1 (2007)

We show that the smallest module of Plasmodium falciparum AMA1 (PfAMA1) that can be expressed in the yeast Pichia pastoris while retaining the capacity to induce high levels of parasite-inhibitory antibodies comprises domains I and II. Based on this, two fusion proteins, differing in the order of the modules, were developed. Each comprised one module of PfAMA1 (FVO strain, amino acids [aa] 97 to 442) (module A) and one module of PfMSP1(19) (Wellcome strain, aa 1526 to 1621) (module Mm) in which a cystine had been removed to improve immune responses. Both fusion proteins retained the antigenicity of each component and yielded over 30 mg/liter purified protein under fed-batch fermentation. Rabbits immunized with purified fusion proteins MmA and AMm had up to eightfold-higher immune responses to MSP1(19) than those of rabbits immunized with module Mm alone or Mm mixed with module A. In terms of parasite growth inhibition, fusion did not diminish the induction of inhibitory antibodies compared with immunization with module A alone or module A mixed with module Mm, and fusion outperformed antibodies induced by immunization with module M or Mm alone. When tested against parasites expressing AMA1 heterologous to the immunogen, antibodies to the fusion proteins inhibited parasite growth to a greater extent than did antibodies either to the individual antigens or to the mixture. These results suggest that compared with the individual modules delivered separately or as a mixture, fusion proteins containing these two modules offer the potential for significant vaccine-related advantages in terms of ease of production, immunogenicity, and functionality.
Advances in Biometric Encryption: Taking Privacy by Design from Academic Research to Deployment (2012)

Abstract An organization should address ethical issues including privacy before deploying biometric systems. Threats to informational privacy rights related to potential data misuse, function creep, and the data linkage of personal information contained in diverse databases makes possible such unintended consequences as surveillance, profiling, and discrimination. Unlike passwords, biometric data are unique, irrevocable, and variable. Biometric encryption (BE) is highlighted as a prominent example of Privacy by Design, where privacy is embedded as a core functionality in the biometric system. BE binds a digital key to (or extracts the key from) the biometrics. Earlier technical challenges to this new technology, as well as recent advances, are presented. Lastly, an overview is provided of an application using facial recognition (FR) in a watch list scenario, known to be the first and largest successful deployment of BE using FR, in a casino context.
Structural and Thermodynamic Characterization of a Bioactive Peptide Model of Apolipoprotein E: Side-Chain Lactam Bridges To Constrain the Conformation (1994)

Apolipoprotein E plays a critical role in plasma lipoprotein clearance. A peptide model of a highly conserved domain of this protein has been shown to increase low-density lipoprotein binding to fibroblast cell surface receptors. To distinguish between two potential structures--one essentially alpha-helical and nonamphiphilic, the other an amphiphilic pi-helix--synthetic side-chain lactam constraints have been incorporated into model peptides in order to restrict conformational flexibility favoring either the alpha- or pi-helix. Here we provide CD and 1H NMR data suggesting that the more biologically active, putatively alpha-helical peptide indeed contains two alpha-helical domains separated by a central bend. Whereas previous studies (Osapay & Taylor, 1992; Felix et al., 1988) indicated stabilization of alpha-helices by cross-links between the i and i + 4 residues, the current paper demonstrates that cross-links between the i and i + 3 residues also stabilize the helix. Indeed, the stabilization afforded by these cross-links is approximately 1 kcal/mol, similar to that reported for peptides cross-linked between the i and i + 4 residues, and derives exclusively from a loss of entropy of the unfolded state. The presence of the alpha-helical structure appears to correlate well with biological activity. This study provides initial insight into the bioactive structure of this domain of apo E and suggests strategies as to how peptides can be conformationally constrained to enhance their stability and biological function.
Management and manipulation of text in dynamic mixed reality workspaces (2013)

Viewing and interacting with text based content safely and easily while mobile has been an issue with see-through displays for many years. For example, in order to effectively use optical see through Head Mounted Displays (HMDs) in constantly changing dynamic environments, variables like lighting conditions, human or vehicular obstructions in a user's path, and scene variation must be dealt with effectively. My PhD research focuses on answering the following questions: 1) What are appropriate methods to intelligently move digital content such as e-mail, SMS messeges, and news articles, throughout the real world? 2) Once a user stops moving, in what way should dynamics of the current workspace change when migrated to a new static environment? 3) Lastly, how can users manipulate mobile content using the fewest number of interactions possible? My strategy for developing solutions to these problems primarily involves automatic or semi-automatic movement of digital content throughout the real world using camera tracking. I have already developed an intelligent text management system that actively manages movement of text in a user's field of view while mobile [11]. I am optimizing and expanding on this type of management system, developing appropriate interaction methodology, and conducting experiments to verify effectiveness, usability, and safety when used with an HMD in various environments.
Long-term storage of Campylobacter pylori (1989)

A reproducible method for long-term storage of Campylobacter pylori has been previously described. We cultured 10 strains of C. pylori in brucella broth that was supplemented with 10% fetal bovine serum. After incubation for 24 h, 10% glycerol and an additional 10% fetal bovine serum were added to the cultures, which when then held in storage at -70 degrees C. After 6 months, each of the strains remained viable. This technique, therefore, represents an excellent method for long-term storage of C. pylori isolates.
Mediators of angiogenesis: the biological significance of basic fibroblast growth factor (bFGF)-heparin and heparan sulfate interactions. (1992)

The interactions of basic fibroblast growth factor (bFGF) with heparin-like molecules appear to be biologically significant. Heparin and heparan sulfate protect bFGF from inactivation by heat, extreme pH and protease degradation. At the cellular level, bFGF binds to heparan sulfate on the cell surface. Cell surface heparan sulfate proteoglycans (HSPG) constitute relatively low affinity binding sites for bFGF. Furthermore, binding of bFGF to cell surface HSPG is necessary for its binding to high affinity FGF receptors and for its mitogenic activity. Thus, bFGF activity requires a dual receptor system composed of a classical protein-type tyrosine kinase receptor and a lower affinity glycosaminoglycan-type receptor. In addition, bFGF is bound to HSPG in the extracellular matrix (ECM). It has been suggested that bFGF may be sequestered in ECM as part of a stable insoluble FGF-HSPG complex from which it is released by specific enzymatic mechanisms when needed for mitogenic activity.