gebhart/patrepeval huggingface dataset:
Immunization of Cats against Fel d 1 Results in Reduced Allergic Symptoms of Owners (2020)

An innovative approach was tested to treat cat allergy in humans by vaccinating cats with Fel-CuMV (HypoCat<sup>TM</sup>), a vaccine against the major cat allergen Fel d 1 based on virus-like particles derived from cucumber mosaic virus (CuMV-VLPs). Upon vaccination, cats develop neutralizing antibodies against the allergen Fel d 1, which reduces the level of reactive allergen, thus lowering the symptoms or even preventing allergic reactions in humans. The combined methodological field study included ten cat-allergic participants who lived together with their cats (<i>n</i> = 13), that were immunized with Fel-CuMV. The aim was to determine methods for measuring a change in allergic symptoms. A home-based provocation test (petting time and organ specific symptom score (OSSS)) and a general weekly (or monthly) symptom score (G(W)SS) were used to assess changes in allergic symptoms. The petting time until a pre-defined level of allergic symptoms was reached increased already early after vaccination of the cats and was apparent over the course of the study. In addition, the OSSS after provocation and G(W)SS recorded a persistent reduction in symptoms over the study period and could serve for long-term assessment. Hence, the immunization of cats with HypoCat<sup>TM</sup> (Fel-CuMV) may have a positive impact on the cat allergy of the owner, and changes could be assessed by the provocation test as well as G(W)SS.
Dictionaries for Sparse Representation Modeling (2010)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Sparse and redundant representation modeling of data assumes an ability to describe signals as linear combinations of a few atoms from a pre-specified dictionary. As such, the choice of the dictionary that sparsifies the signals is crucial for the success of this model. In general, the choice of a proper dictionary can be done using one of two ways: i) building a sparsifying dictionary based on a mathematical model of the data, or ii) learning a dictionary to perform best on a training set. In this paper we describe the evolution of these two paradigms. As manifestations of the first approach, we cover topics such as wavelets, wavelet packets, contourlets, and curvelets, all aiming to exploit 1-D and 2-D mathematical models for constructing effective dictionaries for signals and images. Dictionary learning takes a different route, attaching the dictionary to a set of examples it is supposed to serve. From the seminal work of Field and Olshausen, through the MOD, the K-SVD, the Generalized PCA and others, this paper surveys the various options such training has to offer, up to the most recent contributions and structures. </para>
Are Ruminal Bacteria Armed with Bacteriocins? (1996)

The production of toxic compounds or antibiotics is a common component of intermicrobial competitive interactions, and many of these toxins have been adopted and adapted for the control of microbial populations. One class of these toxins, the bacteriocins, is a heterogeneous group of proteinaceous antibiotics that often display a high degree of target specificity, although many have a very wide spectrum of activity. To date, only limited information is available concerning the occurrence of bacteriocins among ruminal isolates or the sensitivity of ruminal microorganisms to exogenous bacteriocins. A survey of 50 strains of Butyrivibrio spp. isolated from a variety of sources (sheep, deer, and cattle) for bacteriocin production indicated a high incidence of bacteriocin-like activity (50%). Many of these inhibitory compounds appear to have a broad spectrum of activity, which suggests that bacteriocins may have a significant impact on both the competitive fitness of individual microbial strains within the rumen and on the overall structure of the microbial population within the rumen. Selected bacteriocins from lactic acid bacteria also were shown to have activity against Butyrivibrio spp. and may have application in ruminant systems. Bacteriocins may provide an alternative group of antibiotics for the manipulation of ruminal microbial populations. Bacteriocins have significant advantages over other antibiotics in target specificity, susceptibility to proteolytic digestion, possibility of genetic transfer and manipulation, and, in the case of some bacteriocins derived from lactic acid bacteria, a long history of safe use.
Reduction of Liver Fibrosis by CCR2 Antagonist CCX872 in Murine Models of NASH (2016)

Introduction: Liver fibrosis in non-alcoholic steatohepatitis (NASH) is caused by chronic inflammation with macrophage infiltration and cytokine production. Inflammatory macrophages express CCR2, which they use to migrate to the liver. We investigated the efficacy of a CCR2 specific inhibitor, CCX872, in two murine models of NASH. Methods: Two models of NASH were used for determining the efficacy of CCX872 in reducing fibrosis. One model used a high-fat diet (HFD) supplemented with 30% fructose in water, for 30 weeks, to induce NASH and liver fibrosis. After 22 weeks on this diet the mice were given CCX872 (30 mg/kg) once daily or vehicle, both administered subcutaneously for 8 weeks. In the second model the mice were fed a methionine-choline diet deficient (MCD) for 8 weeks to induce liver fibrosis. Mice were treated with CCX872 (30 mg/kg) once daily, or vehicle, both administered subcutaneously for 8 weeks. Liver injury was assessed by standard methods. Liver fibrosis was assessed by sirius red staining, and quantified with the computer program “Image J”. Results: In the HFD/fructose model, mice treated with CCX872 showed reduced accumulation of CD11b+ F4/80+ macrophages in the liver, as compared with vehicle treated mice (p=0.03). Mice treated with CCX872 also had improved insulin sensitivity (p < 0.001) and glucose tolerance (p < 0.001) compared with vehicle. Hepatic triglyceride accumulation was significantly lower in CCX872 treated mice (p < 0.01). Treatment with CCX872 significantly reduced both ALT and AST concentrations in HFD diet fed mice (p < 0.0001 for both ALT and AST). Moreover, 8 weeks of treatment with CCX872 significantly reduced collagen content by approximately 50% based on Sirius red staining (p=0.008), as compared with vehicle treated mice. In the MCD model, ALT was also reduced by CCX872 treatment (p=0.03). Administration of CCX872 reduced collagen content by approximately 25% (p=0.035) in MCD diet fed mice. Conclusion: We investigated the efficacy of a clinical-stage small molecule inhibitor of CCR2, CCX872 for the treatment of steatohepatitis in mice. Mice on HFD treated with CCX872 had reduced hepatic inflammation and steatosis as well as improved insulin sensitivity and glucose tolerance, compared to vehicle treated mice. Moreover, treatment with CCX872 had a marked therapeutic effect on improving liver fibrosis in both mice models of NASH. These findings suggest a potential application of CCR2 inhibitor, CCX872, for treatment of patients with NASH.
High-performance green flexible electronics based on biodegradable cellulose nanofibril paper (2015)

Today's consumer electronics, such as cell phones, tablets and other portable electronic devices, are typically made of non-renewable, non-biodegradable, and sometimes potentially toxic (for example, gallium arsenide) materials. These consumer electronics are frequently upgraded or discarded, leading to serious environmental contamination. Thus, electronic systems consisting of renewable and biodegradable materials and minimal amount of potentially toxic materials are desirable. Here we report high-performance flexible microwave and digital electronics that consume the smallest amount of potentially toxic materials on biobased, biodegradable and flexible cellulose nanofibril papers. Furthermore, we demonstrate gallium arsenide microwave devices, the consumer wireless workhorse, in a transferrable thin-film form. Successful fabrication of key electrical components on the flexible cellulose nanofibril paper with comparable performance to their rigid counterparts and clear demonstration of fungal biodegradation of the cellulose-nanofibril-based electronics suggest that it is feasible to fabricate high-performance flexible electronics using ecofriendly materials.
Adhesive-free bond quasi-noncritical phase-matched and quasi-phase-matched optical parametric oscillations (2010)

With adhesive-free bond (AFB) technology, two walk-off compensated (WOC) KTP composites that consist of 16 layers of 2-mm thick single KTP crystals in each have been designed and prepared for 1.064-μm pumped 2-μm OPO's by means of quasi-noncritical phase-matching (QNCPM) and quasi-phase-matching (QPM). Output pulse energies of 49 μJ and 35 μJ have been achieved for QNCPM and OPM OPO's at pump energy of 523 μJ with pulse duration of 15 ns and repetition rate of 1 KHz, respectively. The OPO pump thresholds were measured as low as 254 μJ (44.6 MW/cm<sup>2</sup>) for the both types of OPO's. The wavelength shifts were measured to be around 11 nm for both the signal and idler beams when KTP temperature was raised from room temperature to 220°C.
A systematic construction of irregular low-density parity-check codes from combinatorial designs (2003)

In this paper, we propose an algorithm to design an irregular low-density parity-check (LDPC) code, with a given degree distribution pair, from a combinatorially constructed regular LDPC code. Richardson et al., (2001) showed that long LDPC codes from irregular bipartite graphs with carefully chosen degree distribution pair performed very close to the Shannon capacity limit. It is known that the cyclic or quasicyclic property of regular LDPC codes, constructed from combinatorial designs Colbourn, J et al., (1996), helps to simplify their encoding procedure and also facilitates a memory-efficient storage of the codes. The proposed algorithm involves splitting columns and rows of a regular LDPC code systematically in order to achieve an irregular code with a given distribution pair. Also, this algorithm is a useful alternative to random generation of irregular codes because it enables to exploit the structural properties of the regular code in efficiently storing the resultant irregular code.
Spectral sparsification via random spanners (2012)

In this paper we introduce a new notion of distance between nodes in a graph that we refer to as robust connectivity. Robust connectivity between a pair of nodes u and v is parameterized by a threshold k and intuitively captures the number of paths between u and v of length at most k. Using this new notion of distances, we show that any black box algorithm for constructing a spanner can be used to construct a spectral sparsifier. We show that given an undirected weighted graph G, simply taking the union of spanners of a few (polylogarithmically many) random subgraphs of G obtained by sampling edges at different probabilities, after appropriate weighting, yields a spectral sparsifier of G. We show how this be done in Õ(m) time, producing a sparsifier with Õ(n/ε2) edges. While the cut sparsifiers of Benczur and Karger are based on weighting edges according to (inverse) strong connectivity, and the spectral sparsifiers are based on resistance, our method weights edges using the robust connectivity measure. The main property that we use is that this new measure is always greater than the resistance when scaled by a factor of O(k) (k is chosen to be O(log n)), but, just like resistance and connectivity, has a bounded sum, i.e. Õ(n), over all the edges of the graph.
Photosensitizing Potencies of the Structural Analogues of Benzoporphyrin Derivative in Different Biological Test Systems (1996)

Benzoporphyrin derivative (BPD) is a potent photosensitizer in biological systems. There are four structural analogues of BPD. The analogues share the same chromophor, which results in their having almost identical optical spectra, extinction coefficients, and yields of singlet oxygen. Small structural differences affect their photosensitizing potency in various biological systems, and thus make them an interesting tool to study the structure-activity relationship. The ranking of the photosensitizing potency of the analogues differed depending on the test system. The more efficient photosensitization of tumor cell lines by the highly lipophilic monoacids as compared to that by less lipophilic diacids correlated positively with the partition coefficient, and was related to the rate of diffusion into the cells. However, in the assay systems where PDT targets were located in the membrane (red blood cells hemolysis, enveloped vesicular stomatitis virus, isolated mitochondria) there was very little difference in photosensitizing potency of BPD analogues. The results indicate that the evaluation of photosensitizers is affected by the test system and thus for photosensitizers screening purposes, the choice of the test system should be made based on the intended ultimate use.
Novel method of reactive magnetron sputtering process control (2013)

Novel method of control of reactive magnetron sputtering process is presented. To control reactive magnetron sputtering process the process pressure is regulated by the flow of the reactive gas (nitrogen). Oscillations of the flow of the reactive gas are determined and used as feedback to find the right overall pressure, where stoichiometric coating is deposited. To see typical process behavior, see fig. 1. Proposed method of control was used for deposition of several coatings (TiN, AlTiN, AlCrN, CrTiN, …) on industrial scale central rotating unbalanced magnetron. To achieve superior adhesion of these layers, novel cleaning method called LGD was used. These coatings were used in industrial applications. Applications results in comparison with market standard coatings will be presented along with other measurements of deposited layers (EDX, SIMS, SEM, … ).
An Extremely Low-Profile Ferrite-Loaded Wideband VHF Antenna Design (2012)

A novel, very low-profile wideband antenna operating from 30 to 300 MHz is presented. The maximum diameter and height of this antenna is only 60.96 and 5.08 cm, respectively. This design is composed of a fat grounded metallic plate placed 5.08 cm over a ground plane. Several ferrite bars strategically placed between the plate and ground plane play a critical role in improving the low frequencies gain and pattern at high frequencies. Minimal amount of ferrite was used to keep the antenna's weight below 9.07 kg. Several antenna prototypes were fabricated and tested at an outdoor range with their gain and patterns agreeing well with simulation results.
Tracking the Sleep Onset Process: An Empirical Model of Behavioral and Physiological Dynamics (2014)

The sleep onset process (SOP) is a dynamic process correlated with a multitude of behavioral and physiological markers. A principled analysis of the SOP can serve as a foundation for answering questions of fundamental importance in basic neuroscience and sleep medicine. Unfortunately, current methods for analyzing the SOP fail to account for the overwhelming evidence that the wake/sleep transition is governed by continuous, dynamic physiological processes. Instead, current practices coarsely discretize sleep both in terms of state, where it is viewed as a binary (wake or sleep) process, and in time, where it is viewed as a single time point derived from subjectively scored stages in 30-second epochs, effectively eliminating SOP dynamics from the analysis. These methods also fail to integrate information from both behavioral and physiological data. It is thus imperative to resolve the mismatch between the physiological evidence and analysis methodologies. In this paper, we develop a statistically and physiologically principled dynamic framework and empirical SOP model, combining simultaneously-recorded physiological measurements with behavioral data from a novel breathing task requiring no arousing external sensory stimuli. We fit the model using data from healthy subjects, and estimate the instantaneous probability that a subject is awake during the SOP. The model successfully tracked physiological and behavioral dynamics for individual nights, and significantly outperformed the instantaneous transition models implicit in clinical definitions of sleep onset. Our framework also provides a principled means for cross-subject data alignment as a function of wake probability, allowing us to characterize and compare SOP dynamics across different populations. This analysis enabled us to quantitatively compare the EEG of subjects showing reduced alpha power with the remaining subjects at identical response probabilities. Thus, by incorporating both physiological and behavioral dynamics into our model framework, the dynamics of our analyses can finally match those observed during the SOP.
The gene expression signature of genomic instability in breast cancer is an independent predictor of clinical outcome (2008)

Recently, expression profiling of breast carcinomas has revealed gene signatures that predict clinical outcome, and discerned prognostically relevant breast cancer subtypes. Measurement of the degree of genomic instability provides a very similar stratification of prognostic groups. We therefore hypothesized that these features are linked. We used gene expression profiling of 48 breast cancer specimens that profoundly differed in their degree of genomic instability and identified a set of 12 genes that defines the 2 groups. The biological and prognostic significance of this gene set was established through survival prediction in published datasets from patients with breast cancer. Of note, the gene expression signatures that define specific prognostic subtypes in other breast cancer datasets, such as luminal A and B, basal, normal-like, and ERBB2+, and prognostic signatures including MammaPrint and Oncotype DX, predicted genomic instability in our samples. This remarkable congruence suggests a biological interdependence of poor-prognosis gene signatures, breast cancer subtypes, genomic instability, and clinical outcome.
Opioid Antagonists in the Treatment of Impulse-Control Disorders (1998)

Naltrexone may be of use in select impulse-control disorder patients. Other opioid antagonists such as nalmefene also need to be tested. Until controlled study data become available, the present report should be viewed as preliminary.
Discovery, X-ray Crystallography, and Anti-inflammatory Activity of Bromodomain-containing Protein 4 (BRD4) BD1 Inhibitors Targeting a Distinct New Binding Site (2022)

Bromodomain-containing protein 4 (BRD4) is an emerging epigenetic drug target for intractable inflammatory disorders. The lack of highly selective inhibitors among BRD4 family members has stalled the collective understanding of this critical system and the progress toward clinical development of effective therapeutics. Here we report the discovery of a potent BRD4 bromodomain 1 (BD1)-selective inhibitor ZL0590 (<b>52</b>) targeting a unique, previously unreported binding site, while exhibiting significant anti-inflammatory activities <i>in vitro</i> and <i>in vivo</i>. The X-ray crystal structural analysis of ZL0590 in complex with human BRD4 BD1 and the associated mutagenesis study illustrate a first-in-class nonacetylated lysine (KAc) binding site located at the helix αB and αC interface that contains important BRD4 residues (e.g., Glu151) not commonly shared among other family members and is spatially distinct from the classic KAc recognition pocket. This new finding facilitates further elucidation of the complex biology underpinning bromodomain specificity among BRD4 and its protein-protein interaction partners.
Video Captioning with Transferred Semantic Attributes (2016)

Automatically generating natural language descriptions of videos plays a fundamental challenge for computer vision community. Most recent progress in this problem has been achieved through employing 2-D and/or 3-D Convolutional Neural Networks (CNN) to encode video content and Recurrent Neural Networks (RNN) to decode a sentence. In this paper, we present Long Short-Term Memory with Transferred Semantic Attributes (LSTM-TSA)---a novel deep architecture that incorporates the transferred semantic attributes learnt from images and videos into the CNN plus RNN framework, by training them in an end-to-end manner. The design of LSTM-TSA is highly inspired by the facts that 1) semantic attributes play a significant contribution to captioning, and 2) images and videos carry complementary semantics and thus can reinforce each other for captioning. To boost video captioning, we propose a novel transfer unit to model the mutually correlated attributes learnt from images and videos. Extensive experiments are conducted on three public datasets, i.e., MSVD, M-VAD and MPII-MD. Our proposed LSTM-TSA achieves to-date the best published performance in sentence generation on MSVD: 52.8% and 74.0% in terms of BLEU@4 and CIDEr-D. Superior results when compared to state-of-the-art methods are also reported on M-VAD and MPII-MD.
Development of protein crystallization and processing: femtosecond laser, all solid-state 193 nm laser, and solution stirring techniques (2007)

We have developed novel techniques of protein crystallization and processing using femtosecond laser, all solid-state 193 nm laser, and solution stirring. Femtosecond laser technique enables us to extremely increase the crystallization probability, and to trigger the nucleation at low supersaturation of solution where spontaneous nucleation dose not occur. Since the laser-induced nuclei grow slowly in the low-range supersaturated solution, the crystals exhibit high crystallinity. The processing techniques using femtosecond laser and all solid-state 193 nm laser are effective for processing and manipulation of protein crystals without significant damage. Solution stirring technique also contributes the improvement of the crystal quality. We have succeeded in obtaining high-quality crystals of various proteins using the techniques, and revealing the precise structure of the protein molecules from the X-ray analysis. These techniques can accelerate structural biology and subsequent structure-based drug discoveries, resulting in important revelations in these fields.
Automatic gain flattening in optical fiber amplifiers via clamping of inhomogeneous gain (1993)

An Er-doped fiber amplifier with a flattened gain spectrum is obtained by incorporating the amplifier into a ring laser and making use of inhomogeneous broadening at 77 K. The results indicate several potential benefits for doped-fiber material systems that are inhomogeneously broadened at room temperature.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Tuning band pass filters in the time domain (2003)

This new idea in coupled-resonator filter tuning is based on the time domain response of filter return loss. With this method, individual responses of each resonator and coupling coefficient can be distinguished and can be precisely set to a desired filter response; interactions can be immediately determined and accounted for.
Semisupervised Learning for Machine Translation (2008)

This chapter proposes algorithms for semisupervised learning. It translates sentences from the source language and then uses them to retrain the statistical machine translation (SMT) system in the hopes of getting a better translation system. It presents detailed experimental evaluations using French-English and Chinese-English data. The French-English translation task used bilingual data from the Europarl corpus, and monolingual data from the same domain as the test set which is drawn from the Canadian Hansard corpus. The Chinese-English task used bilingual data from the NIST large-data track and monolingual data from the Chinese Gigaword corpus.