gebhart/patrepeval huggingface dataset:
Determination of Affinities for <i>lck </i>SH2 Binding Peptides Using a Sensitive Fluorescence Assay:  Comparison between the pYEEIP and pYQPQP Consensus Sequences Reveals Context-Dependent Binding Specificity (1996)

The development of a sensitive fluorescence binding assay for evaluating the binding of phosphotyrosyl (pY) peptides to the recombinant SH2 domain of lck in solution is described. Several fluorescent peptides containing the consensus sequence of the viral hamster polyoma middle T antigen (pYEEI) were characterized. The peptides contained either the acetamido-anilino-naphthyl sulfonic acid (AANS), acrylodan, or dansyl groups as fluorophores. The spectral features of these probes were characterized in the presence and absence of the lck SH2 domain. The binding affinities (Kd) for the fluorescent peptides studied ranged from 40 to 500 nM. The fluorescent peptide containing the sequence FTATEC(AANS)QpYEEIP exhibited the highest binding affinity (Kd = 3.98 x 10(-8) M) and largest change in emission intensity (approximately 8.7-fold) upon binding the SH2 domain. This probe was subsequently used in competitive binding assays to study the interaction of the lck SH2 domain with a series of phosphopeptides related to the pYEEIP and pYQPQP (the pY505 C-terminal) consensus sequences. The effects of peptide length and substitutions of residues within the pYEEIP sequence are discussed in terms of binding affinities. Comparison between the two peptide series revealed that the contributions of individual substitutions to binding affinity are context-dependent. The data also led to the conclusion that the presence of P at +2 results in a functional "truncation" of the binding sequence; i.e., residues at positions higher than +2 do not participate significantly in binding. This implicit truncation may actually be a desired property for the autoregulatory nature of the pYQPQP sequence, since it retains specificity for the SH2 domain while adjusting the Kd to a value appropriate for maintaining the delicate balance of receptor-ligand interactions that are involved in signal transduction events.
Brief Report: The Dopamine-3-Receptor Gene (DRD3) is Associated with Specific Repetitive Behavior in Autism Spectrum Disorder (ASD) (2011)

Recently the DRD3 gene has been associated with ASD in two independent samples. Follow up analysis of the risk allele of the SNP rs167771 in 91 subjects revealed a significant association with a specific type of repetitive behavior: the factor "insistence on sameness" (IS) derived from the Autism Diagnostic Interview. This risk allele was associated with a decreased risk for IS, but not with any other symptomatology. Further study and replication of this finding is necessary, bearing in mind that these results would not be statistically significant if corrected for multiple testing.
MRI-based computational hemodynamics in patients with aortic coarctation using the lattice Boltzmann methods: Clinical validation study (2016)

3 J. Magn. Reson. Imaging 2017;45:139-146.
Scatter restoration in PET imaging (2004)

Positron emission tomography (PET) is a quantitative tool having the capability of estimating physiological parameters in vivo. However, in order for these parameters to be accurate, PET data need to be corrected for image degrading effects such as scatter. The amount of scatter and its axial and transaxial distributions in the images depend on the position of the emitting sites, on the scattering object and on the collimators. Generally scatter functions are determined from point sources, or by extrapolation or the radioactivity distribution from out of the object in the image, or by analytical estimation of single scatter based on emission, transmission and photon detection. In this work, scatter fraction is determined by Monte Carlo calculations based on PET images in humans and in rats measured with the Philips Allegro scanner and the Sherbrooke small animal scanner, respectively. Assuming the image slice is made of tissue only, the scatter fraction estimated as a function of the number of Compton interactions in human (rat): no scatter: 9.75% (66.16%), single scatter: 21.92% (26.96%), double scatter (both photons scatter once): 12.42% (2.71%), multiple scatter: 55.89% (4.18%). Moreover, the distribution of each of these types of scatter has its characteristics, generally having its maximum corresponding to source location. In conclusion, scatter functions need to be determined as a function of the type of scatter in order to process an accurate scatter correction.
Text mining for security threat detection discovering hidden information in unstructured log messages (2016)

The exponential growth of unstructured messages generated by the computer systems and applications in modern computing environment poses a significant challenge in managing and using the information contained in the messages. Although these data contain a wealth of information that is useful for advanced threat detection, the sheer volume, variety, and complexity of data make it difficult to analyze them even by well-trained security analysts. While conventional Security Information and Event Management (SIEM) systems provide some capability to collect, correlate, and detect certain events from structured messages, their rule-based correlation and detection algorithms fall short in utilizing the information within the unstructured messages. Our study explores the possibility of utilizing the techniques for data mining, text classification, natural language processing, and machine learning to detect security threats by extracting relevant information from various unstructured log messages collected from distributed non-homogeneous systems. The extracted features are used to run a number of experiments on the Packet Clearing House SKAION 2006 IARPA Dataset, and their prediction capability is evaluated. In comparison with the base case without feature extraction, an average of 16.73% performance gain and 84% time reduction was achieved using extracted features only, and a 23.48% performance gain was attained using both unstructured free-text messages and extracted features. The results also show a strong potential for further increase in performance by increasing size of training datasets and extracting more features from the unstructured log messages.
A Comparison of Lithium and T <sub>3</sub> Augmentation Following Two Failed Medication Treatments for Depression: A STAR*D Report (2006)

Remission rates with lithium and T(3) augmentation for participants who experienced unsatisfactory results with two prior medication treatments were modest and did not differ significantly. The lower side effect burden and ease of use of T(3) augmentation suggest that it has slight advantages over lithium augmentation for depressed patients who have experienced several failed medication trials.
Nuclear—organelle interactions: the <i>immutans</i> variegation mutant of <i>Arabidopsis</i> is plastid autonomous and impaired in carotenoid biosynthesis (1994)

The immutans (im) variegation mutant of Arabidopsis thaliana contains green- and white-sectored leaves due to the action of a nuclear recessive gene. The mutation is somatically unstable, and the degree of sectoring is influenced by light and temperature. Whereas the cells in the green sectors contain normal chloroplasts, the cells in the white sectors are heteroplastidic and contain non-pigmented plastids that lack organized lamellar structures, as well as small pigmented plastids and/or rare normal chloroplasts. This indicates that the plastids in im white cells are not affected equally by the nuclear mutation and that the expression of immutans is 'plastid autonomous'. In contrast to other variegation mutants with heteroplastidic cells, the defect in im is not maternally inherited. immutans thus represents a novel type of nuclear gene-induced variegation mutant. It has also been found that the white tissues of immutans accumulate phytoene, a non-colored C40 carotenoid intermediate. This suggests that immutans controls, either directly or indirectly, the activity of phytoene desaturase (PDS), the enzyme that converts phytoene to zeta-carotene in higher plants. However, im is not the structural gene for PDS. A secondary effect of carotenoid deficiency, both in immutans and in wild-type plants treated with a herbicide that blocks carotenoid synthesis, is an increase in acid ribonuclease activity in white tissue. It is concluded that the novel variegation generated by the immutans mutation should offer great insight into the complex circuitry that regulates nuclear-organelle interactions.
Terrain following/terrain avoidance path optimization using the method of steepest descent (2003)

A path-optimization algorithm for terrain following/terrain avoidance and threat avoidance is presented. The algorithm uses the gradient method for generating the optimal ground track that minimizes a quadratic cost function of the aircraft's altitude above sea level to maximize terrain masking while penalizing large deviations from a prescribed initial ground track. The vertical flight path for each ground track is obtained by using parabolic flight segments that satisfy vertical path constraints. Confining the optimization process to the horizontal plane improves the convergence properties of the algorithm, reduces the storage requirements, and allows the algorithm to be used on fine-grain terrain data. Simulation results are presented which validate the algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Impact and Prevention of Ultra-Low Contamination of Platinum Group Metals on SCR Catalysts Due to DOC Design (2009)

<div class="htmlview paragraph">Diesel aftertreatment systems configured with a diesel oxidation catalyst (DOC) upstream of an urea selective catalytic reduction (SCR) catalyst run the risk of precious metal contamination. During active diesel particulate filter (DPF) regeneration events, the DOC bed temperature can reach up to 850°C. Under these conditions, precious metal (especially Pt) can be volatized and then deposited on a downstream SCR catalyst. In this paper, the impact of ultra-low contamination of platinum group metals (PGM) on the SCR catalyst was studied. A method based on precious metal volatilization of a Pt-rich DOC at 850°C and under lean gas conditions was employed to contaminate downstream FeSCR and CuSCR formulations. The contamination resulted in poor NOx conversion (via NOx remake) and excessive N<sub>2</sub>O formation. The precious metal volatilization method was employed to screen various Pt/Pd based DOCs to avoid contamination of the downstream FeSCR. A correlation was developed that showed a reduction in SCR catalyst contamination as the Pt/Pd ratio decreased. The Pd-only DOC showed no impact to NOx conversion and no increase in N<sub>2</sub>O formation. The Pt-rich DOC showed the most impact. DOC formulations with higher Pd content demonstrated enhanced CO and HC light-off stability. The higher Pd content served to stabilize Pt in the DOC formulations. The higher Pd content resulted in less Pt vaporization. This, in turn, reduced the subsequent contamination risk on the downstream SCR. The vaporization of Pd from the DOC formulations was determined to be very low. However, an incipient wetness technique was used to purposely dope Pd on the FeSCR formulation and Pt on the CuSCR formulation. Contamination up to 0.004wt% Pd was required to alter the NOx performance by 5–10% on the FeSCR formulation. However, contamination up to 0.008wt% Pt was required to alter the NOx conversion 5–10% on the CuSCR formulation. A second ethylene hydrogenation method was used on the contaminated SCR catalysts to determine presence of precious metals.</div>
Secondary prevention of coronary heart disease in South Wales: a survey following myocardial infarction: Table 1 (2004)

Coronary heart disease (CHD) remains a major cause of morbidity and mortality in the UK. Following a myocardial infarction (MI) the risk of disease progression is high. Modification of vascular risk factors in such patients—secondary prevention—is particularly effective with evidence supporting use of antiplatelet agents, oral anticoagulants, β blockers, angiotensin converting enzyme (ACE) inhibitors, statins, and smoking cessation. Good diabetic control and provision of cardiac rehabilitation are also important.

The aim of this study was to assess the level of secondary prevention for CHD. We based the current survey on the experience we had with a previous smaller audit conducted between 1998–99.1

The audit departments from the University Hospital of Wales in Cardiff, Llandough Hospital, Cardiff, Royal Gwent Hospital, Newport, and Prince Charles Hospital Merthyr Tydfil, assisted in our survey; each generated a list of patients discharged between 1 January and 31 December 1999 following a new MI ( International classification of diseases , 10th revision (ICD-10) codes 121.0–121.4, 121.9, 122.0, 122.1, 122.8, 122.9). One hundred patients were randomly selected from each hospital. Pro-formas modified from our previous audit were completed to assess CHD secondary prevention. Each set of medical and nursing records was assessed independently by two specialist registrars. Pro-formas were then compared, differences discussed and, with further reference to the case notes, resolved.

Questionnaires (maximum of two) were then sent to surviving patients requesting a current medication …
Design of 200-nm, 170-nm, and 140-nm DUV contact sweeper high-transmission attenuating phase-shift mask through simulation I (1998)

Simulations for 140 nm, 170 nm, and 200 nm contacts were optimized on an 18% transmitting phase shift mask. A transmission of 18% is shown to have the most linear aerial image behavior through focus. The simulations were run using a primitive positive photoresist model in order to predict trends in resolution and to predict when side lobes begin printing. The contact hole design was optimized such that the process windows for various pitches overlap and the sidelobes are suppressed. By adding both opaque and clear sub-resolution assist features, the simulations show contacts as small as 140 nm resolve with 0.83 micrometer focus latitude and 2.00 mJ/cm<SUP>2</SUP> exposure latitude for a pitch of 0.98 micrometer, and with 0.36 micrometer focus latitude and 0.50 mJ/cm<SUP>2</SUP> exposure latitude for a pitch of 0.44 micrometer. Simulation shows that the serifs which create an effective contact bias also suppress side lobe printing. Vector simulation shows that the coupling between the electric and magnetic fields reduces the peak intensity and side lobe intensity.
Defect-oriented testing and defective-part-level prediction (2001)

After an integrated circuit (IC) design is complete, but before first silicon arrives from the manufacturing facility, the design team prepares a set of test patterns to isolate defective parts. Applying this test pattern set to every manufactured part reduces the fraction of defective parts erroneously sold to customers as defect-free parts. This fraction is referred to as the defect level (DL). However, many IC manufacturers quote defective part level, which is obtained by multiplying the defect level by one million to give the number of defective parts per million. Ideally, we could accurately estimate the defective part level by analyzing the circuit structure, the applied test-pattern set, and the manufacturing yield. If the expected defective part level exceeded some specified value, then either the test pattern set or (in extreme cases) the design could be modified to achieve adequate quality. Although the IC industry widely accepts stuck-at fault detection as a key test-quality figure of merit, it is nevertheless necessary to detect other defect types seen in real manufacturing environments. A defective-part-level model combined with a method for choosing test patterns that use site observation can predict defect levels in submicron ICs more accurately than simple stuck-at fault analysis.
Synthesis of monodispersed bimetallic palladium-copper nanoscale colloids (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of monodispersed bimetallic palladium-copper nanoscale colloidsJohn S. Bradley, Ernestine W. Hill, Carl Klein, Bruno Chaudret, and Anne DuteilCite this: Chem. Mater. 1993, 5, 3, 254–256Publication Date (Print):March 1, 1993Publication History Published online1 May 2002Published inissue 1 March 1993https://pubs.acs.org/doi/10.1021/cm00027a005https://doi.org/10.1021/cm00027a005research-articleACS PublicationsRequest reuse permissionsArticle Views1020Altmetric-Citations133LEARN 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
Multimodality Imaging of Chronic Ischemia (2010)

Although ischemic cardiomyopathy is commonly caused by chronic obstructive coronary disease, the mechanism of the cause is still under investigation. We present echocardiographic strain, magnetic resonance, and histology findings in a chronic ischemia model in preclinical study. This case illustrates the features of multimodality imaging in chronic obstructive coronary disease and gives us great insight into understanding the mechanism of ischemic cardiomyopathy.
Was wissen wir über das Symptom Rückenschmerz? (2005)

Back pain belongs to the major individual and societal health problems in Germany. While extensive epidemiological evidence exists for the prevalence of back pain, its severity, course and associated risk factors, little systematic knowledge is available about the medical treatment of back pain.
Development and evaluation of transdermal formulations containing metronidazole and norfloxacin for the treatment of burn wound. (1999)

In an attempt for better treatment of partial thickness burn wounds topical ointments containing metronidazole and norfloxacin in different bases were prepared and in vitro release was conducted in phosphate buffer pH 6. It was found that, diffusion of the metronidazole and norfloxacin from the lanolin petrolatum base with 0.25% w/w dimethyl sulfoxide was maximum through hairless rat abdominal skin. Antimicrobial activity of different prepared formulations was found to be more effective both against aerobic and anaerobic bacteria than marketed formulation (1% silver sulfadiazine cream USP). Formulations were significantly effective as compared to that of marketed formulation in wound contraction of the partial thickness burn wound. Histopathological reports supported effectiveness of formulations. It was found that 1% metronidazole and 1% norfloxacin ointments are suitable for treating the partial thickness burn wound.
Tyrosine-containing activation motif-dependent phagocytosis in mast cells. (1994)

FcR capable of triggering cell activation share with BCR and TCR a conserved intracytoplasmic tyrosine-containing activation motif (TAM). Besides cell activation, these receptors trigger other biologic responses, such as endocytosis of soluble ligands. Murine mast cells express two types of FcR that, when aggregated by antibodies and multivalent Ag, trigger the release of inflammatory mediators and cytokines. These are high affinity receptors for IgE (Fc epsilon RI) and low affinity receptors for IgG (Fc gamma RIII). They comprise each an IgE- or IgG-binding alpha-subunit and two TAM-containing subunits that associate with both receptors: a beta-subunit and a homodimeric gamma-subunit that can associate also with the other subunits of the TCR. Herein, we focused on biologic activities triggered in mast cells via the TAM of the gamma-subunits. Using rat basophilic leukemia (RBL) cells stably transfected with cDNA-encoding murine Fc gamma RIII alpha, we found that murine Fc gamma RIII trigger the phagocytosis of antibody-coated erythrocytes. Using RBL transfectants expressing Fc gamma RIII with a deletion of the intracytoplasmic domain of Fc gamma RIII alpha or chimeric receptors having the extracellular and transmembrane domains of Fc gamma RII and the intracytoplasmic domain of Fc gamma RIII alpha, we showed that intracytoplasmic sequences of Fc gamma RIII alpha are neither necessary nor sufficient for Fc gamma RIII to trigger phagocytosis. Using RBL transfectants expressing chimeric receptors having the extracellular and transmembrane domains of Fc gamma RII and the TAM-containing intracytoplasmic domain of murine Fc gamma RIII gamma, we demonstrated that intracytoplasmic sequences of Fc gamma RIII gamma are sufficient to trigger phagocytosis. Using RBL transfectants expressing the same Fc gamma RII-III gamma chimeras, in the TAM of which one, the other, or both tyrosine residues were mutated, we established that tyrosines in the TAM sequence are required for phagocytosis. Our results endow TAM gamma with previously unknown triggering capacities and Fc gamma RIII with new biologic properties.
Urban/Indoor Navigation Using Network Assisted GPS (2006)

Abstract : GPS information is an essential element of network centric warfare providing key positioning and timing information in support of communication, positioning and navigation functions. For these networked GPS applications, it is also possible to improve the ability of GPS to operate in challenged environments, such as inside buildings, by using GPS Network Assistance. This paper describes the Network Assisted (NETASSIST) system architecture and a Software GPS Receiver (SGR) Test Bed that has been developed by NAVSYS Corporation under contract to CERDEC. The SGR is designed to use the positioning, timing and navigation data-aiding from a NETASSIST base station across a secure wireless network. This allows the receiver to apply advanced signal processing algorithms to speed direct P(Y) code acquisition and also allow the receiver to track GPS signals down to significantly lower C/N0 thresholds which enhances the receiver's ability to operate inside buildings. Test results collected using the NETASSIST SGR Test Bed are also presented in this paper to demonstrate the advantages of this approach for urban operations.
Spelling Correction for Dialectal Arabic Dictionary Lookup (2011)

The “Did You Mean...?” system, described in this article, is a spelling corrector for Arabic that is designed specifically for L2 learners of dialectal Arabic in the context of dictionary lookup. The authors use an orthographic density metric to motivate the need for a finer-grained ranking method for candidate words than unweighted Levenshtein edit distance. The Did You Mean...? architecture is described, and the authors show that mean reciprocal rank can be improved by tuning operation weights according to sound confusions, and by anticipating likely spelling variants.