gebhart/patrepeval huggingface dataset:
Recognition Thresholds for Letters with Simulated Dioptric Blur (2000)

We examined the effects of simulated dioptric blur on the degradation of visual acuity using digitally filtered letters. Four types of digital filters were applied to 5 letters (C, D, E, O, and S), constructed to the specifications of Sloan optotypes. These filters were: (1) "normal," designed to simulate the positive and negative lobes of the modulation transfer function (MTF) produced by dioptric blur; (2) "truncated," which passed only those spatial frequencies up to the first zero of the MTF; (3) "phase-rectified," which inverted all of the negative lobes of the MTF to positive; and (4) "truncated-plus-negative," which eliminated all positive lobes above the first zero of the MTF. The letter size required to achieve 60%-correct identification was determined for letters that were filtered to simulate +1, +2, and +4 D of blur. Letters subjected to normal, truncated, and truncated-plus-negative filtering had approximately the same acuity threshold, whereas the threshold size for phase-rectified letters was significantly better. Our interpretation of these results is that dioptric blur hinders letter recognition because useful spatial frequency information is limited to that below the first zero of the MTF, and not because of interference from the phase-reversed spatial frequency information above the first zero. Our letter identification thresholds are consistent with recent evidence that the critical information for letter acuity corresponds to approximately 1.5 cycles/letter.
"Speckle" in Continuous Wave Doppler Ultrasound Spectra: A Simulation Study (1986)

The statistical properties of continuous wave (CW) Doppler ultrasound signals are investigated. First, the analysis of some Doppler data obtained from a human carotiadr tery is reported. Based on the chi-square test, it was found that for each of seven recorded cardiac cycles, the amplitude histogram of a stationary signal segment of a duration of 10 ms around peak systole satisfies the Gaussian hypothesis. Second, it is shown that the Doppler signal, wihs i cehv idently a band-limited Gaussian noise, can be synthesized on a computer using a sinusoidal model. The statistical behavior of the synthesized signals in both the time and the frequency domains, are shown to be in close agreement with the Doppler signals observed over a IO-ms interval around peak systole. This work has led to an understanding of the structure of the conventional grey-scale Doppler spectrogram, particularly its granular structure, which has been likened to the speckle seen in ultrasound B-mode images. Finally, some potential applications of the simulation model are discussed.
Identification of the Putative Staphylococcal AgrB Catalytic Residues Involving the Proteolytic Cleavage of AgrD to Generate Autoinducing Peptide (2005)

The P2 operon of the staphylococcal accessory gene regulator (agr) encodes four genes (agrA, -B, -C, and -D) whose products compose a quorum sensing system: AgrA and AgrC resemble a two-component signal transduction system of which AgrC is a sensor kinase and AgrA is a response regulator; AgrD, a polypeptide that is integrated into the cytoplasmic membrane via an amphipathic alpha-helical motif in its N-terminal region, is the propeptide for an autoinducing peptide that is the ligand for AgrC; and AgrB is a novel membrane protein that involves in the processing of AgrD propeptide and possibly the secretion of the mature autoinducing peptide. In this study, we demonstrated that AgrB had endopeptidase activity, and identified 2 amino acid residues in AgrB (cysteine 84 and histidine 77) that might form a putative cysteine endopeptidase catalytic center in the proteolytic cleavage of AgrD at its C-terminal processing site. Computer analysis revealed that the cysteine and histidine residues were conserved among the potential AgrB homologous proteins, suggesting that the Agr quorum sensing system homologues might also exist in other Gram-positive bacteria.
Integration of in Silico and in Vitro Tools for Scaffold Optimization during Drug Discovery: Predicting P-Glycoprotein Efflux (2013)

In silico tools are regularly utilized for designing and prioritizing compounds to address challenges related to drug metabolism and pharmacokinetics (DMPK) during the process of drug discovery. P-Glycoprotein (P-gp) is a member of the ATP-binding cassette (ABC) transporters with broad substrate specificity that plays a significant role in absorption and distribution of drugs that are P-gp substrates. As a result, screening for P-gp transport has now become routine in the drug discovery process. Typically, bidirectional permeability assays are employed to assess in vitro P-gp efflux. In this article, we use P-gp as an example to illustrate a well-validated methodology to effectively integrate in silico and in vitro tools to identify and resolve key barriers during the early stages of drug discovery. A detailed account of development and application of in silico tools such as simple guidelines based on physicochemical properties and more complex quantitative structure-activity relationship (QSAR) models is provided. The tools were developed based on structurally diverse data for more than 2000 compounds generated using a robust P-gp substrate assay over the past several years. Analysis of physicochemical properties revealed a significantly lower proportion (<10%) of P-gp substrates among the compounds with topological polar surface area (TPSA) <60 Å(2) and the most basic cpKa <8. In contrast, this proportion of substrates was greater than 75% for compounds with TPSA >60 Å(2) and the most basic cpKa >8. Among the various QSAR models evaluated to predict P-gp efflux, the Bagging model provided optimum prediction performance for prospective validation based on chronological test sets. Four sequential versions of the model were built with increasing numbers of compounds to train the models as new data became available. Except for the first version with the smallest training set, the QSAR models exhibited robust prediction profiles with positive prediction values (PPV) and negative prediction values (NPV) exceeding 80%. The QSAR model demonstrated better concordance with the manual P-gp substrate assay than an automated P-gp substrate screen. The in silico and the in vitro tools have been effectively integrated during early stages of drug discovery to resolve P-gp-related challenges exemplified by several case studies. Key learning based on our experience with P-gp can be widely applicable across other DMPK-related challenges.
Quantitative measurement of ethylene incorporation into propylene copolymers by carbon-13 nuclear magnetic resonance and infrared spectrometry (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuantitative measurement of ethylene incorporation into propylene copolymers by carbon-13 nuclear magnetic resonance and infrared spectrometryJohn R. Paxson and James C. RandallCite this: Anal. Chem. 1978, 50, 13, 1777–1780Publication Date (Print):November 1, 1978Publication History Published online1 May 2002Published inissue 1 November 1978https://pubs.acs.org/doi/10.1021/ac50035a016https://doi.org/10.1021/ac50035a016research-articleACS PublicationsRequest reuse permissionsArticle Views186Altmetric-Citations21LEARN 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
Update on antiphospholipid syndrome. (2008)

This review addresses new clinical issues (revealed at the 2006 Sydney update of the 1999 Sapporo Classification criteria; cardiac, renal, and multiple sclerosis-like disease; catastrophic syndrome), mechanisms of action of antiphospholipid antibody (very likely complement mediated), current therapies (moderate dose warfarin recommended for prophylaxis, aspirin not recommended for primary prophylaxis), and potential new therapies.
Participation of Amadori rearrangement products and carbonyl compounds in oxygen-dependent browning of soy sauce (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTParticipation of Amadori rearrangement products and carbonyl compounds in oxygen-dependent browning of soy sauceHironaga HashibaCite this: J. Agric. Food Chem. 1976, 24, 1, 70–73Publication Date (Print):January 1, 1976Publication History Published online1 May 2002Published inissue 1 January 1976https://pubs.acs.org/doi/10.1021/jf60203a042https://doi.org/10.1021/jf60203a042research-articleACS PublicationsRequest reuse permissionsArticle Views305Altmetric-Citations43LEARN 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
Electrochemical Identification of Metallic and Semiconducting Single-Walled Carbon Nanotubes (2008)

Single-walled carbon nanotubes (SWNTs) are promising building blocks for nanoelectronics. However, because of the mixture of metallic and semiconducting single-walled carbon nanotubes (m-SWNTs and s-SWNTs), it is necessary to identify them for nanodevice integerations. In this work, we have observed obvious electrodeposition differences of ultralong m-SWNTs and s-SWNTs. Using high-resolution atomic force microscopy (AFM) and field emission scanning electron microscopy (FE-SEM), particle densities along different carbon nanotubes were examined. Interestingly, m-SWNTs and s-SWNTs showed obviously different deposition behaviors, i.e., exponential decay of particle densities with different decay coefficients. This electrochemical approach can be used for a simple identification of m-SWNTs and s-SWNTs.
Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins (2015)

RNA binding proteins of the conserved CUGBP1, Elav-like factor (CELF) family contribute to heart and skeletal muscle development and are implicated in myotonic dystrophy (DM). To understand their genome-wide functions, we analyzed the transcriptome dynamics following induction of CELF1 or CELF2 in adult mouse heart and of CELF1 in muscle by RNA-seq, complemented by crosslinking/immunoprecipitation-sequencing (CLIP-seq) analysis of mouse cells and tissues to distinguish direct from indirect regulatory targets. We identified hundreds of mRNAs bound in their 3' UTRs by both CELF1 and the developmentally induced MBNL1 protein, a threefold greater overlap in target messages than expected, including messages involved in development and cell differentiation. The extent of 3' UTR binding by CELF1 and MBNL1 predicted the degree of mRNA repression or stabilization, respectively, following CELF1 induction. However, CELF1's RNA binding specificity in vitro was not detectably altered by coincubation with recombinant MBNL1. These findings support a model in which CELF and MBNL proteins bind independently to mRNAs but functionally compete to specify down-regulation or localization/stabilization, respectively, of hundreds of mRNA targets. Expression of many alternative 3' UTR isoforms was altered following CELF1 induction, with 3' UTR binding associated with down-regulation of isoforms and genes. The splicing of hundreds of alternative exons was oppositely regulated by these proteins, confirming an additional layer of regulatory antagonism previously observed in a handful of cases. The regulatory relationships between CELFs and MBNLs in control of both mRNA abundance and splicing appear to have evolved to enhance developmental transitions in major classes of heart and muscle genes.
Low power VLSI architectures for variable-length encoding and decoding (2005)

New low power VLSI architectures are presented for variable-length encoding and decoding. Look-up table partitioning by symbol probability is shown to reduce the total power consumption; the variable-length decoder and encoder are reduced by as much as 66% and 75%, respectively. Design examples for a subband image CODEC are presented with measurements from extracted VLSI layouts.
A Novel Group-Aware Pruning Method for Few-shot Learning (2019)

Few-shot learning, which focuses on solving machine learning problems in the setting of scarce data, has become a hot spot in the field of neural network and machine learning recently. Inspired by BlockDrop that performs pruning compression on the network using reinforcement learning, in this paper, we present a Group-Aware Pruning (GAP) method with new unifying pruning strategies and different training/testing ways to fit few-shot learning. The proposed GAP consists of three modules, that is, a pruning module, a strategy consensus module (SCM), and a classification module. The whole support set is first fed into the pruning module to get a pruning strategy for each image. Next, the strategies are fed into SCM to fuse into a group strategy for further pruning. When the classification module makes a prediction for a query image, it no longer needs re-output the pruning strategy for the query image since pruning strategies have been unified. Note that in SCM, strategy unification is proposed to achieve the group-aware strategy, which assures an existing deep network that has been pruned by the group-aware strategy work well for few-shot learning problems. Additionally, the testing will be speeded up due to the fact that only one classification model is required in the proposed GAP. Experiments on two benchmark datasets, namely, Omingnet and miniImageNet, and comparisons with the existing state-of-the-art methods show that the accuracy of the proposed GAP is 4.94% higher than the state-of-the-art methods on the 5-way 5-shot task, which shows the effectiveness of the proposed method.
A Comparison between Chinese and Western Theories and Methods on Painting (2001)

There is much difference between Chinese and Western theories and methods on painting,because they come from different philosophy and aesthetics systems.The Chinese traditional philosophy that“humanity is harmonious with nature” fosters the fashion that elegancy is favored in Chinese painting,that the subjective spirit and ideal of the artist are emphasized,that Chinese traditional poetry and calligraphy are regarded as the essential parts of the art creation,and that the harmony between emptiness and tangibility on the canvass,and the vividness of the art,are pursued.It is decided by western traditional philosophy that “humanity conflicts with nature” that western painting upholds magnificence.The appearance of object is emphasized.Focus perspective is adopted for a stereophonic description in an effort to truly represent the objective world.The comparison of the two painting styles aims to help the artists and appreciators to appreciate painting arts of different races with the respective art conceptions and in respective approaches.It also helps us to start from the traditions to create our new art with reference to any positive foreign arts.
[Two cases of encephalo-myelo-radiculoneuropathy, triggered by herpes simplex virus type-1 infection]. (1997)

We report two cases of encephalo-myelo-radiculoneuropathy, triggered by herpes simplex virus type-1 (HSV-1) infection. Patient 1 (a 25-year-old man) and patient 2 (a 52-year-old man) were admitted to the hospital because of fever, headache, abnormal behavior, and loss of consciousness. In each case, cerebrospinal fluid (CSF) showed lymphocytic pleocytosis with protein elevation, and serum and CSF IgG antibody titers to HSV-1 were elevated markedly. Although patient 1 was treated with aciclovir in the early phase of encephalitis, he developed severe quadriparesis as a sequela. Patient 2 was treated with a combination of aciclovir and corticosteroids, and he recovered completely about 4 months after the onset of the disease. There have been only a few reports of encephalo-myelo-radiculoneuropathy triggered by HSV-1 infection. Early corticosteroid therapy was effective in our patients with post-HSV-1 infectious encephalo-myelo-radiculoneuropathy. These two patients were studied with flow cytometry for peripheral blood lymphocyte subsets during the disease course. In the active stage of the disease, the helper-inducer (CD4 + CD29+), activated T cell (CD4 + CD25+), and cytotoxic/NK (CD8 Dull + CD11b Bright+) subsets were increased compared with subsets in controls. An interesting finding was mismatched responses with an increased suppressor-inducer (CD4 + Leu8+) subset and a decreased suppressor-effecter (CD8 Bright+ CD11b Dull+) subset, indicating a possible autoimmune character of encephalo-myelo-radiculoneuropathy triggered by viral infection.
Automating and streamlining inference of function of plant ESTs within a data analysis system (1994)

Automated sequencing of partial cDNA clones as expressed sequence tags (ESTs) and similarity searches of these ESTs against public DNA and protein sequence databanks is becoming a well-accepted method for identifying genes of any given species. The use of local similarity search algorithms against the public databanks has been preferred as a screening mechanism for the short EST sequences, because they determine scores for only those regions which are conserved between sequences. Furthermore, local similarities of translated EST sequences to the public protein databank sequences can often be detected when similarities to the public DNA databanks appear coincidental. Both human brain and Caenorhabditis elegans cDNA EST projects have used similarity searches for positive identification of known genes and determination of putative function of others. Possible novel genes make up those ESTs which did not show significant similarity to the public databases. The authors show that shorter ESTs are sufficient to meet EST project objectives for plant genomes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fermentation, Isolation and Characterization of Isonitrile Antibiotics (1982)

A number of soil isolates belonging to the genus Trichoderma were found to produce isonitrins A, B, C and D and isonitrinic acids E and F, a new class of antibiotics characterized by the presence of isonitrile groups. Taxonomy of the producing organisms, fermentation, isolation and physicochemical and biological properties of isonitrins and isonitrinic acids are reported. Isonitrin A showed the highest in vitro antimicrobial activities against gram-positive and negative bacteria and fungi.
Structural and chemical analysis of annealed plasma-enhanced atomic layer deposition aluminum nitride films (2016)

Plasma-enhanced atomic layer deposition was utilized to grow aluminum nitride (AlN) films on Si from trimethylaluminum and N2:H2 plasma at 200 °C. Thermal treatments were then applied on the films which caused changes in their chemical composition and nanostructure. These changes were observed to manifest in the refractive indices and densities of the films. The AlN films were identified to contain light element impurities, namely, H, C, and excess N due to nonideal precursor reactions. Oxygen contamination was also identified in the films. Many of the embedded impurities became volatile in the elevated annealing temperatures. Most notably, high amounts of H were observed to desorb from the AlN films. Furthermore, dinitrogen triple bonds were identified with infrared spectroscopy in the films. The triple bonds broke after annealing at 1000 °C for 1 h which likely caused enhanced hydrolysis of the films. The nanostructure of the films was identified to be amorphous in the as-deposited state and to become nanocrystalline after 1 h of annealing at 1000 °C.
The crystalline sponge method updated (2016)

Crystalline sponges are porous metal complexes that can absorb and orient common organic molecules in their pores and make them observable by conventional X-ray structure analysis (crystalline sponge method). In this study, all of the steps in the crystalline sponge method, including sponge crystal preparation, pore-solvent exchange, guest soaking, data collection and crystallographic analysis, are carefully examined and thoroughly optimized to provide reliable and meaningful chemical information as chemical crystallography. Major improvements in the method have been made in the guest-soaking and data-collection steps. In the soaking step, obtaining a high site occupancy of the guest is particularly important, and dominant parameters for guest soaking (e.g. temperature, time, concentration, solvents) therefore have to be optimized for every sample compound. When standard conditions do not work, a high-throughput method is useful for efficiently optimizing the soaking conditions. The X-ray experiments are also carefully re-examined. Significant improvement of the guest data quality is achieved by complete data collection at high angle regions. The appropriate disorder treatment of the most flexible ZnI2 portions of the host framework and refinement of the solvents filling the remaining void are also particularly important for obtaining better data quality. A benchmark test for the crystalline sponge method toward an achiral molecule is proposed with a guaiazulene guest, in which the guest structure (with ∼ 100% site occupancy) is refined without applying any restraints or constraints. The obtained data quality with R int = 0.0279 and R 1 = 0.0379 is comparable with that of current conventional crystallographic analysis for small molecules. Another benchmark test for this method toward a chiral molecule is also proposed with a santonin guest. The crystallographic data obtained [R int = 0.0421, R 1 = 0.0312, Flack (Parsons) = -0.0071 (11)] represents the potential ability of this method for reliable absolute structure determination.
Comparison of Tri-gate FET Characteristics for Various Hydrogen Annealing Process Conditions (2006)

Hydrogen anneal improves the multigate on-off characteristics considerably (Choi, 2003), however, a higher anneal temperature also results in silicon loss from the fin, thereby reducing the effective width of the device, which degrades its total drive current. This, in turn, offsets the improved mobility-driven drive current gain. To retain the tri-gate fin height after hydrogen anneal, a hard mask based process was developed