gebhart/patrepeval huggingface dataset:
Identification of amino acids in lac repressor protein cross-linked to operator DNA specifically substituted with bromodeoxyuridine. (1991)

Amino acids in lac repressor protein which form cross-links to lac operator DNA specifically substituted with bromodeoxyuridine (BrdU) have been identified. Five sites of cross-linking in BrdU-substituted operator DNA were found at positions +3, +4, +14, +18, and +19 relative to the initiation site for transcription (Wick, K.L., and Matthews, K.S. (1991) J. Biol. Chem. 266, 6106-6112). Irradiation of complexes of repressor and each of these five singly substituted operator DNAs was executed under large scale conditions to generate sufficient complex for proteolysis, separation of the peptide-DNA, and peptide sequencing. The DNAs substituted with BrdU for thymidine at positions +3, +18, and +19 yielded cross-links to the peptide spanning residues 23-33, with the cross-link identified at His-29. Substitution at position +14 resulted in a cross-link to Tyr-17 within the peptide containing amino acids 13-22. These results are consistent with the structure determined by NMR and molecular dynamics calculations of the NH2-terminal headpiece-symmetric operator complex (Lamerichs, R.M.J.N., Boelens, R., van der Marel, G.A., van Boom, J.H., Kaptein, R., Buck, F., Fera, B., and Rüterjans, H. (1989) Biochemistry 28, 2895-2991; de Vlieg, J., Berendsen, H.J.C., and van Gunsteren, W.F. (1989) Proteins 6, 104-127). This structure indicates proximity of His-29 in the major groove to thymidines at positions +3 and +4. Since base pairs at positions +18 and +19 occupy symmetrical positions to +3 and +4 in the promoter distal region of the operator, it would be anticipated that cross-links similar to the +3 and +4 positions would form at these sites; this prediction is not borne out by the behavior at +4/+18, as no peptide could be identified cross-linked to DNA substituted at +4. Molecular dynamics simulations and the NMR data indicate that Tyr-17 interacts with the thymine at position +8, which is symmetrically related to position +14. Although BrdU-associated strand scission at +8 is protected, this site does not cross-link with bound lac repressor; inversely, DNA substituted with BrdU at +14 cross-links to repressor, but is not protected from strand scission by the presence of the protein. These differences at symmetrically related nucleotide positions (+4 versus +18, +8 versus +14) reflect the inherent asymmetry in the interaction. The identification of amino acids in proximity to specifically substituted sites confirms that positions of several amino acids in the intact protein-operator complex correspond to those in the structure of the NH2-terminal headpiece-operator DNA complex.
A microfluidic renal proximal tubule with active reabsorptive function (2017)

In the kidney, the renal proximal tubule (PT) reabsorbs solutes into the peritubular capillaries through active transport. Here, we replicate this reabsorptive function in vitro by engineering a microfluidic PT. The microfluidic PT architecture comprises a porous membrane with user-defined submicron surface topography separating two microchannels representing a PT filtrate lumen and a peritubular capillary lumen. Human PT epithelial cells and microvascular endothelial cells in respective microchannels created a PT-like reabsorptive barrier. Co-culturing epithelial and endothelial cells in the microfluidic architecture enhanced viability, metabolic activity, and compactness of the epithelial layer. The resulting tissue expressed tight junctions, kidney-specific morphology, and polarized expression of kidney markers. The microfluidic PT actively performed sodium-coupled glucose transport, which could be modulated by administration of a sodium-transport inhibiting drug. The microfluidic PT reproduces human physiology at the cellular and tissue levels, and measurable tissue function which can quantify kidney pharmaceutical efficacy and toxicity.
Genomewide comparative analysis of alternative splicing in plants (2006)

Alternative splicing (AS) has been extensively studied in mammalian systems but much less in plants. Here we report AS events deduced from EST/cDNA analysis in two model plants: Arabidopsis and rice. In Arabidopsis, 4,707 (21.8%) of the genes with EST/cDNA evidence show 8,264 AS events. Approximately 56% of these events are intron retention (IntronR), and only 8% are exon skipping. In rice, 6,568 (21.2%) of the expressed genes display 14,542 AS events, of which 53.5% are IntronR and 13.8% are exon skipping. The consistent high frequency of IntronR suggests prevalence of splice site recognition by intron definition in plants. Different AS events within a given gene occur, for the most part, independently. In total, 36-43% of the AS events produce transcripts that would be targets of the non-sense-mediated decay pathway, if that pathway were to operate in plants as in humans. Forty percent of Arabidopsis AS genes are alternatively spliced also in rice, with some examples strongly suggesting a role of the AS event as an evolutionary conserved mechanism of posttranscriptional regulation. We created a comprehensive web-interfaced database to compile and visualize the evidence for alternative splicing in plants (Alternative Splicing in Plants, available at www.plantgdb.org/ASIP).
Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci (2017)

Dogs are an excellent model for human disease. For example, the treatment of canine lymphoma has been predictive of the human response to that treatment. However, an incomplete picture of canine (Canis lupus familiaris) immunoglobulin (IG) and T cell receptor (TR)-or antigen receptor (AR)-gene loci has restricted their utility. This work advances the annotation of the canine AR loci and looks into breed-specific features of the loci. Bioinformatic analysis of unbiased RNA sequence data was used to complete the annotation of the canine AR genes. This annotation was used to query 107 whole genome sequences from 19 breeds and identified over 5500 alleles across the 550 genes of the seven AR loci: the IG heavy, kappa, and lambda loci; and the TR alpha, beta, gamma, and delta loci. Of note was the discovery that half of the IGK variable (V) genes were located downstream of, and inverted with respect to, the rest of the locus. Analysis of the germline sequences of all the AR V genes identified greater conservation between dog and human than mouse with either. This work brings our understanding of the genetic diversity and expression of AR in dogs to the same completeness as that of mice and men, making it the third species to have all AR loci comprehensively and accurately annotated. The large number of germline sequences serves as a reference for future studies, and has allowed statistically powerful conclusions to be drawn on the pressures that have shaped these loci.
남자 류마티스 관절염 환자의 임상적 특징 (1996)

Objectives: To document the clinical characteristics of Korean male patients with rheumatoid arthritis that are different from those of female counterparts. Methods: Six hundred and seventy-five patients who had met the ACR criteria for rheumatoid arthritis were included in the study. Clinical and laboratory data were retrospectively reviewed and radiologic features of hands and feet were graded by Steinbrocker`s method. Results: The female: male ratio in the total patients studied is 567:108(5.25). The symptom onset age was 39.5±11.8 in woman and 44.0±11.3 in men. The functional class at the time of diagnosis and the incidence of anemia showed little significant difference. Among the extraarticular manifestations, only interstitial lung disease was more common in males. There were significant differences between both sexes on positivity of antiperinuclear factor, C-reactive protein, and titer of rheumatoid factor in the seropositive groups, but not on rheumatoid factor positivity. Radiologically there was no significant difference in the hands and feet joints between males and females. Higher dosage of steroid was initially prescribed for male patients. Conclusions: The males seem to have slightly more active disease and to show significant differences in antiperinuclear factor positivity, the titer of rheumatoid factor and C-reactive protein, and lung involvement. However, we failed to demonstrate that the disease in males was more severe than compared to that of their female counterparts.
The Pharmacologic Treatment of Alzheimer's Disease: A Guide for the General Psychiatrist (1998)

These data indicate that selected medications can be used to treat cognitive deficits, disease progression, agitation, psychosis, and depression in AD. However, there is considerable heterogeneity in patients' responses to these medications. Pharmacotherapy needs to be considered as a component of a package of care that also includes psychosocial and environmental interventions and support of the caregiver.
Reciprocal continuous inhibition in rigidity of Parkinsonism. (1977)

A reciprocal continuous inhibition by flexor on extensor muscles was proved during Parkinsonian rigidity. Extensor motoneurone excitability was tested by Hoffmann's reflex and flexor activity was altered by lidocaine anaesthesia of the peroneal nerve (PN). During PN anaesthetic block, a gradual increase of Hoffmann's reflex was noted. It was statistically significant at the 15th minute after lidocaine injection, and was maximum at the 30th minute. The reciprocal inhibition was considerable in 16 patients with Parkinsonism, as recorded before treatment. In normal subjects, it was small and non-significant. After one month's treatment with L-dopa at the usual therapeutic dose, this reciprocal inhibition greatly decreased in the same patients. The origin of this reciprocal continuous inhibition is discussed.
Color-based hands tracking system for sign language recognition (2002)

The paper describes a real-time system which tracks the uncovered/unmarked hands of a person performing sign language. It extracts the face and hand regions using their skin colors, computes blobs and then tracks the location of each hand using a Kalman filter. The system has been tested for hand tracking using actual sign-language motion by native signers. The experimental results indicate that the system is capable of tracking hands even while they are overlapping the face.
Method to calculate the far field of three-dimensional objects for computer-generated holography (2010)

Here, a new method for calculating the computer-generated holograms of three-dimensional (3D) objects is presented along with a review of current techniques. The method, the planar layers method (PLM), is established on the idea of representing 3D objects in discrete planar layers perpendicular to the observation plane, then calculating the total far field pattern by summing up the far field patterns of each layer. Simulation results, computational complexity, and error comparisons reveal that this new method can be used to calculate far field patterns--hence, the holograms--of computer-synthesized objects very efficiently.
Clustering signatures classify directed networks (2008)

We use a clustering signature, based on a recently introduced generalization of the clustering coefficient to directed networks, to analyze 16 directed real-world networks of five different types: social networks, genetic transcription networks, word adjacency networks, food webs, and electric circuits. We show that these five classes of networks are cleanly separated in the space of clustering signatures due to the statistical properties of their local neighborhoods, demonstrating the usefulness of clustering signatures as a classifier of directed networks.
Towards Composable Bias Rating of AI Services (2018)

A new wave of decision-support systems are being built today using AI services that draw insights from data (like text and video) and incorporate them in human-in-the-loop assistance. However, just as we expect humans to be ethical, the same expectation needs to be met by automated systems that increasingly get delegated to act on their behalf. A very important aspect of an ethical behavior is to avoid (intended, perceived, or accidental) bias. Bias occurs when the data distribution is not representative enough of the natural phenomenon one wants to model and reason about. The possibly biased behavior of a service is hard to detect and handle if the AI service is merely being used and not developed from scratch, since the training data set is not available. In this situation, we envisage a 3rd party rating agency that is independent of the API producer or consumer and has its own set of biased and unbiased data, with customizable distributions. We propose a 2-step rating approach that generates bias ratings signifying whether the AI service is unbiased compensating, data-sensitive biased, or biased. The approach also works on composite services. We implement it in the context of text translation and report interesting results.
Laser beam deflection sensor as a detector for high-efficiency chromatography (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLaser beam deflection sensor as a detector for high-efficiency chromatographyJanusz. PawliszynCite this: Anal. Chem. 1986, 58, 1, 243–246Publication Date (Print):January 1, 1986Publication History Published online1 May 2002Published inissue 1 January 1986https://pubs.acs.org/doi/10.1021/ac00292a060https://doi.org/10.1021/ac00292a060research-articleACS PublicationsRequest reuse permissionsArticle Views101Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
<title>Integrated Optical Microwave Spectrum Analyser (IOSA) Using Geodesic Lenses</title> (1983)

We report on an IOSA based on a titanium diffused optical waveguide layer in lithium niobate with geodesic lenses. Lenses were designed by the method of Sottini et al but with essential modifications to smooth over regions of extreme curvature. Ray-tracing analysis showed that the deviation from the ideal profile introduced by this smoothing had negligible effect. Several lens fabrication methods were experimentally evaluated -ultrasonic impact grinding, computer-controlled diamond tool grinding and diamond turning, followed by polishing with large area flexible tools, or with small pads under microprocessor time and position control. The most reliable method was diamond turning followed by polishing with a small pad on a specially constructed computer controlled polishing machine. Data is also presented on factors affecting overall spectrum analyser dynamic range such as in-plane scattering and acousto-optic third-order intermodulation.© (1983) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Confocal laser endomicroscopy features of sessile serrated adenomas/polyps (2015)

This is a novel description of characteristic CLE features of SSA/Ps. The four features we identified are easy to detect and may allow for CLE to serve as a diagnostic modality.
Clustering for collaborative filtering applications (1999)

Collaborative filtering systems assist users to identify items of interest by providing predictions based on ratings of other users. The quality of the predictions depends strongly on the amount of available ratings and collaborative filtering algorithms perform poorly when only few ratings are available. In this paper we identify two important situations with sparse ratings: Bootstrapping a collaborative filtering system with few users and providing recommendations for new users, who rated only few items. Further, we presentanovel algorithm for collaborative filtering, based on hierarchical clustering, which tries to balance robustness and accuracy of predictions, and experimentally show that it is especially efficient in dealing with the previous situations.
Finite Element Analysis of Squirrel Cage Ball Bearingsfor Gas Turbine Engines (2007)

Squirrel cage ball bearings are used in recent aero engines to overcome the vibration andstability problems associated with rotor systems supported by conventional bearings. The criticaldesign feature of squirrel cage bearing is to provide flexible support to rotor system. The outerring of the bearing is configured such that it acts as a flexible bearing support, and hence, weightis minimised. The bearing is mounted directly on a rigid intermediate casing of a gas turbineengine. Finite element analysis helps to obtain a suitable geometry at the design stage. A 3-Dmodel of the bearing is created using IDEAS software. Finite element analysis using contactelement has been carried out for finding the deformation and stresses in the webs at variouslocations using ANSYS software. The deformations are compared with those of experimentalvalues for an axial load. The deformation in the webs is used to check the pressure balance inthe compressor and the load acting on the bearing. Finally, a procedure for doing the finiteelement analysis of ball bearings for combined axial and radial load is laid down.
Adaptive Convolutional Filter Generation for Natural Language Understanding. (2017)

Convolutional neural networks (CNNs) have recently emerged as a popular
building block for natural language processing (NLP). Despite their success,
most existing CNN models employed in NLP are not expressive enough, in the
sense that all input sentences share the same learned (and static) set of
filters. Motivated by this problem, we propose an adaptive convolutional filter
generation framework for natural language understanding, by leveraging a meta
network to generate input-aware filters. We further generalize our framework to
model question-answer sentence pairs and propose an adaptive question answering
(AdaQA) model; a novel two-way feature abstraction mechanism is introduced to
encapsulate co-dependent sentence representations. We investigate the
effectiveness of our framework on document categorization and answer
sentence-selection tasks, achieving state-of-the-art performance on several
benchmark datasets.
A Two-Stage Beamforming Approach for Noise Reduction and Dereverberation (2013)

In general, the signal-to-noise ratio as well as the signal-to-reverberation ratio of speech received by a microphone decrease when the distance between the talker and microphone increases. Dereverberation and noise reduction algorithm are essential for many applications such as videoconferencing, hearing aids, and automatic speech recognition to improve the quality and intelligibility of the received desired speech that is corrupted by reverberation and noise. In the last decade, researchers have aimed at estimating the reverberant desired speech signal as received by one of the microphones. Although this approach has let to practical noise reduction algorithms, the spatial diversity of the received desired signal is not exploited to dereverberate the speech signal. In this paper, a two-stage beamforming approach is presented for dereverberation and noise reduction. In the first stage, a signal-independent beamformer is used to generate a reference signal which contains a dereverberated version of the desired speech signal as received at the microphones and residual noise. In the second stage, the filtered microphone signals and the noisy reference signal are used to obtain an estimate of the dereverberated desired speech signal. In this stage, different signal-dependent beamformers can be used depending on the desired operating point in terms of noise reduction and speech distortion. The presented performance evaluation demonstrates the effectiveness of the proposed two-stage approach.
Pure JavaScript (1999)

From the Publisher:

Pure JavaScript, Second Edition is a substantial and focused reference for experienced Web developers. This book begins with an accelerated introduction to the newest features of JavaScript so that experienced Web developers can quickly understand the concepts of JavaScript and begin developing their own JavaScript solutions immediately. 
Pure JavaScript, Second Edition contains concise descriptions of JavaScript forms, cookies, windows, and layers. Beyond the brief descriptions and short syntax snippets found in most references, this book also provides real-life, well-commented JavaScript examples for each documented object, property, method, and event handler. This not only helps the reader's understanding of the syntax, but also provides a contextual aid in determining how and why a specific object or method may be used. It also includes a special reference section dedicated to server-side JavaScript, coverage of JScript and Active Scripting, and a complete reference to browser-supported JavaScript.
Explaining E-participation Diffusion at the National Level : An Examination of External Environmental Influences (2013)

Recently, information and communication technologies (ICTs) have increasingly been utilized by governments to involve citizens, leading to the rise of e-participation. E-participation has varied across units and levels of government and has attracted attention from both scholars and practitioners. While researchers have explored various factors that impact e-participation, few of them have tested the comprehensive influence of the external environment on e-participation at the national level. This article aims at filling a research gap by examining the direct and indirect impacts of environmental factors on e-participation. The results indicate that environmental factors might significantly influence e-participation nationally. This study argues that the diffusion of e-participation could be explained by its external environment variance.
Thermo‐Responsive Hydrogels with Nanodomains: Rapid Shrinking of a Nanogel‐Crosslinking Hydrogel of Poly(<i>N</i>‐isopropyl acrylamide) (2008)

Abstract Rapidly shrinking poly( N ‐isopropyl acrylamide) (PNIPAM) hydrogels are prepared by crosslinking with self‐assembled nanogels that consist of cholesteryl‐ and methacryloyl‐substituted pullulan (CHPMA). The CHPMA nanogel ( R h = 26.4 nm) was used as a crosslinker for a hydrophilic nanodomain. Transmission electron microscopy images of the nanogel‐crosslinked PNIPAM hydrogel reveal a well‐defined nanoporous structure. The nanogel‐crosslinked PNIPAM hydrogel shows rapid shrinking based on its structure. The shrinking half‐time was ≈2 min, which is about 3 400 times faster than that of a PNIPAM hydrogel crosslinked by methylene(bisacrylamide). magnified image