gebhart/patrepeval huggingface dataset:
APAC: Augmented PAttern Classification with Neural Networks (2015)

Deep neural networks have been exhibiting splendid accuracies in many of visual pattern classification problems. Many of the state-of-the-art methods employ a technique known as data augmentation at the training stage. This paper addresses an issue of decision rule for classifiers trained with augmented data. Our method is named as APAC: the Augmented PAttern Classification, which is a way of classification using the optimal decision rule for augmented data learning. Discussion of methods of data augmentation is not our primary focus. We show clear evidences that APAC gives far better generalization performance than the traditional way of class prediction in several experiments. Our convolutional neural network model with APAC achieved a state-of-the-art accuracy on the MNIST dataset among non-ensemble classifiers. Even our multilayer perceptron model beats some of the convolutional models with recently invented stochastic regularization techniques on the CIFAR-10 dataset.
Identification, Recombinant Expression, Immunolocalization in Macrophages, and T-Cell Responsiveness of the Major Extracellular Proteins of Francisella tularensis (2006)

A safer and more effective vaccine than the previously developed live attenuated vaccine is needed for combating Francisella tularensis, a highly infectious bacterial pathogen. To search for potential candidates for inclusion in a new vaccine, we characterized the proteins present in the culture filtrates of a virulent recent clinical isolate and the attenuated live vaccine strain of F. tularensis using a proteomic approach. We identified a total of 12 proteins; among these, catalase-peroxidase was much more abundant in the culture filtrate of the virulent clinical isolate, whereas bacterioferritin was more abundant in the culture filtrate of the live vaccine strain. Streptolysin O treatment of infected human macrophages indicated that catalase-peroxidase and the heat shock protein GroEL are released intracellularly by actively growing F. tularensis. Mice immunized with F. tularensis developed significant cell-mediated immune responses to catalase-peroxidase, the heat shock protein GroEL, and bacterioferritin as measured by splenic lymphocyte proliferation and gamma interferon production. Finally, we expressed the major culture filtrate proteins that are promising vaccine candidates in Escherichia coli at high levels in soluble form to facilitate study of their immunobiology and potential role in vaccines.
ChemInform Abstract: Intra vs. Intermolecular Amidoalkylation of Aromatics. (1987)

Abstract Various types of intramolecular amidoalkylation reactions of aromatics are studied and their mechanistic implications are discussed in detail.
Spot cooling using thermoelectric microcoolers (2003)

In this paper, we investigate the possibility of creating spot cooling using thermoelectric microcoolers. An analytical model and a numerical scheme are developed to investigate the steady-state cooling surrounding microcoolers. The effects considered include the thermal and the electrical contact resistances and the spreading heat resistance. Parametric studies are carried out on the influences of the geometry and materials properties on the device performance. Simulation results show that local deep cooling can be reached if heat spreading materials are properly chosen.
The Squarate Ester−Polyquinane Connection. An Analysis of the Capacity of Achiral Divinyl Adducts To Rearrange Spontaneously to Polycyclic Networks Housing Multiple Stereogenic Centers (1997)

The condensation of diisopropyl squarate and related cyclobutene-1,2-diones with 2 equiv of the same alkenyl anion or 1 equiv each of two different alkenyl anions can be a very effective method for the highly stereocontrolled synthesis of di-, tri-, and tetraquinanes. Two reaction cascades have been identified. The most prevalent and often exclusive reaction course is triggered by trans 1,2-addition of the two nucleophiles. Two consecutive conrotatory processes subsequently arise to deliver a doubly charged eight-membered ring intermediate, protonation of which leads to transannular adolization. The second option begins with cis 1,2-addition, this event triggering structural reorganization via a dianionic oxy-Cope rearrangement. When the alkenyl anions are sufficiently substituted, the two pathways are distinguishable on stereochemical grounds. A minor pathway consisting of trans 1,4-addition is seen to operate in certain contexts, especially when the alkenyllithium is “soft”. Acetylide anions can also be utilized successfully; in such cases, the benefit of regiocontrolled protonation surfaces and gives rise to a single product. Other aspects of these complex tandem reactions have been investigated and are discussed.
Safety of Local Delivery of Low- and Intermediate-Dose Adenovirus Gene Transfer Vectors to Individuals with a Spectrum of Morbid Conditions (2002)

To help define the safety profile of the use of adenovirus (Ad) gene transfer vectors in humans, this report summarizes our experience since April 1993 of the local administration of E1(-)/E3(-) Ad vectors to humans using low (<10(9) particle units) or intermediate (10(9)-10(11) particle units) doses. Included in the study are 90 individuals and 12 controls, with diverse comorbid conditions, including cystic fibrosis, colon cancer metastatic to liver, severe coronary artery disease, and peripheral vascular disease, as well as normals. These individuals received 140 different administrations of vector, with up to seven administrations to a single individual. The vectors used include three different transgenes (human cystic fibrosis transmembrane conductance regulator cDNA, E. coli cytosine deaminase gene, and the human vascular endothelial growth factor 121 cDNA) administered by six different routes (nasal epithelium, bronchial epithelium, percutaneous to solid tumor, intradermal, epicardial injection of the myocardium, and skeletal muscle). The total population was followed for 130.4 patient-years. The study assesses adverse events, common laboratory tests, and long-term follow-up, including incidence of death or development of malignancy. The total group incidence of major adverse events linked to an Ad vector was 0.7%. There were no deaths attributable to the Ad vectors per se, and the incidence of malignancy was within that expected for the population. Overall, the observations are consistent with the concept that local administration of low and intermediate doses of Ad vectors appears to be well tolerated.
Oxidative Deamination of Amino Acids by Pyridoxal and Metal Salts1 (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxidative Deamination of Amino Acids by Pyridoxal and Metal Salts1Miyoshi Ikawa and Esmond E. SnellCite this: J. Am. Chem. Soc. 1954, 76, 19, 4900–4902Publication Date (Print):October 1, 1954Publication History Published online1 May 2002Published inissue 1 October 1954https://pubs.acs.org/doi/10.1021/ja01648a041https://doi.org/10.1021/ja01648a041research-articleACS PublicationsRequest reuse permissionsArticle Views348Altmetric-Citations27LEARN 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
A new blind receiver for downlink DS-CDMA communications (1999)

A linear receiver is proposed for downlink DS-CDMA communications over unknown frequency-selective fading channels. The new receiver exploits the fact that all synchronized downlink signals go through the same channel and recovers the desired signal with a constrained channel equalizer followed by a despreader. Such a scheme allows the receiver to operate blindly in a time varying environment for both periodic CDMA and aperiodic CDMA systems.
Directed evolution relieves product inhibition and confers in vivo function to a rationally designed tyrosine aminotransferase (2004)

The Escherichia coli aspartate (AATase) and tyrosine (TATase) aminotransferases share 43% sequence identity and 72% similarity, but AATase has only 0.08% and 0.01% of the TATase activities (k(cat)/K(m)) for tyrosine and phenylalanine, respectively. Approximately 5% of TATase activity was introduced into the AATase framework earlier both by rational design (six mutations, termed HEX) and by directed evolution (9-17 mutations). The enzymes realized from the latter procedure complement tyrosine auxotrophy in TATase deficient E. coli. HEX complements even more poorly than does wild-type AATase, even though the (k(cat)/K(m)) value for tyrosine exhibited by HEX is similar to those of the enzymes found from directed evolution. HEX, however, is characterized by very low values of K(m) and K(D) for dicarboxylic ligands, and by a particularly slow release for oxaloacetate, the product of the reaction with aspartate and a TCA cycle intermediate. These observations suggest that HEX exists largely as an enzyme-product complex in vivo. HEX was therefore subjected to a single round of directed evolution with selection for complementation of tyrosine auxotrophy. A variant with a single amino acid substitution, A293D, exhibited substantially improved TATase function in vivo. The A293D mutation alleviates the tight binding to dicarboxylic ligands as K(m)s for aspartate and alpha-ketoglutarate are >20-fold higher in the HEX + A293D construct compared to HEX. This mutation also increased k(cat)/K(m)(Tyr) threefold. A second mutation, I73V, elicited smaller but similar effects. Both residues are in close proximity to Arg292 and the mutations may function to modulate the arginine switch mechanism responsible for dual substrate recognition in TATases and HEX.
Significance of chick quality score in broiler production (2012)

The quality of day old chicks is crucial for profitable broiler production, but a difficult trait to define. In research, both qualitative and quantitative measures are used with variable predictive value for subsequent performance. In hatchery practice, chick quality is judged on a binomial scale, as chicks are divided into first grade (Q1-saleable) and second grade (Q2) chicks right after hatch. Incidences and reasons for classifying chicks as Q2, and potential of these chicks for survival and post-hatch performance have hardly been investigated, but may provide information for flock performance. We conducted an experiment to investigate (1) the quality of a broiler flock and the relation with post-hatch flock performance based on a qualitative score (Pasgar©score) of Q1 chicks and based on the incidence of Q2 chicks and (2) the reasons for classifying chicks as Q2, and the potential of these chicks for survival and post-hatch growth. The performance was followed of Q1 and Q2 chicks obtained from two breeder flocks that hatched in two different hatching systems (a traditional hatcher or a combined hatching and brooding system, named Patio). Eggs were incubated until embryo day 18, when they were transferred to one of the two hatching systems. At embryo day 21/post-hatch day 0, all chicks from the hatcher (including Q2 chicks) were brought to Patio, where the hatchery manager marked the Q2 chicks from both flocks and hatching systems and registered apparent reasons for classifying these chicks as Q2. Chick quality was assessed of 100 Q1 chicks from each flock and hatching system. Weights of all chicks were determined at days 0, 7, 21 and 42. There were no correlations between mean Pasgar©score and post-hatch growth or mortality, and suboptimal navel quality was the only quality trait associated with lower post-hatch growth. Growth was clearly affected by breeder flock and hatching system, which could not be linked to mean Pasgar©score or incidence of Q2 chicks. Q2 chicks showed lower post-hatch growth compared to Q1 chicks but effects on flock performance at slaughter weight were limited because early mortality in Q2 chicks was high (62.50% at 7 days). We concluded that chick qualitative scores and the incidence of Q2 chicks may be informative for the quality of incubation, but are not predictive for post-hatch flock performance. Culling Q2 chicks after hatch is well-founded in terms of both animal welfare and profitability.
Manganese-based Superoxide Dismutase Mimetics Inhibit Neutrophil Infiltration in Vivo (1996)

In a previous study (Hardy et al. (1994) J. Biol. Chem. 269, 18535-18540), we observed that the manganese-based superoxide dismutase mimetic Mn(II)-dichloro(1,4,7,10,13-pentaazacyclopentadecane) (MnPAM) inhibited neutrophil-mediated cell injury in vitro. We have extended these studies with the low molecular weight superoxide dismutase mimic to evaluate the role of superoxide in neutrophil-mediated tissue injury in vivo. In a dose-dependent manner, MnPAM inhibited colonic tissue injury and neutrophil accumulation into the colonic tissue induced by the intracolonic instillation of dilute aqueous acetic acid in mice. Tissue injury was assessed by visual and histological analysis. Neutrophil infiltration was determined by tissue myeloperoxidase activity and confirmed by histological analysis. Two novel Mn(II) dichloro complexes of the carbon-substituted macrocycles 2-methyl-1,4,7,10,13-pentaazacyclopentadecane (MnMAM) and 2-(2-methylpropyl)-1,4,7,10,13-pentaazacyclopentadecane (MnBAM) effectively catalyzed the dismutation of superoxide with catalytic rate constants (kcat) of 3. 31 x 10(7) M-1 s-1 and 1.91 x 10(7) M-1 s-1, respectively, as determined by stopped-flow kinetic analysis at pH 8.1 and 21 degrees C. The superoxide dismutase mimetics MnMAM and MnBAM also attenuated dilute aqueous acetic acid-induced tissue injury and neutrophil infiltration into colonic tissue; however, two Mn(II) complexes that had little or no detectable SOD activity (kcat </= 0.1 x 10(7) M-1 s-1), specifically the Mn(II) dichloro complexes of 1,4,7,10,13-pentaazacyclohexadecane and 1,4,7,11,14-pentaazacycloheptadecane, failed to inhibit the colonic tissue injury or infiltration of neutrophils in mice treated intracolonically with dilute aqueous acetic acid. These results are consistent with a proinflammatory role for superoxide in the mediation of neutrophil infiltration in vivo.
Inhibition of Human Cancer Cell Growth by Inducible Expression of Human Ribonucleotide Reductase Antisense cDNA (2000)

Ribonucleotide reductase (RR) is a rate-limiting enzyme in DNA synthesis and repair. The enzyme consists of two dissimilar subunits, M1 and M2. It is known that the M2 subunit plays a role in tumorgenicity and metastasis. In this study, we transfected human oropharyngeal KB cancer cells with human RR M1 and M2 antisense cDNA expressed by an inducible vector system. The transfectants were double-selected with hygromycin and G418. The clones, designated KB-M1AS, KB-M2AS and KB-CAT, represented transfectant clones that contained M1 antisense cDNA, M2 antisense cDNA, and a CAT reporter gene, respectively. In a colony-forming assay, colony formation for the KB-M2AS clone decreased approximately 50% when M2 antisense mRNA expression was induced by isopropylthiogalactose (IPTG). However, the KB-M1AS clone revealed no significant inhibition under IPTG induction. RR enzyme activity, as measured by 14CDP reduction assay, revealed a 30% decrease in the IPTG-induced KB-M2AS clone relative to non-IPTG-induced samples at 144 hours. As shown by Northern blot, expression of the M2 antisense mRNA showed peaks at 48 hours and 144 hours after induction by IPTG. M2 antisense mRNA expression induced by IPTG was 33-fold greater than the uninduced control at 144 hours. Western blot analysis showed that the M2 subunit protein level decreased in the KB-M2AS clone beginning at 72 hours after induction and continued to decrease to 50% of the uninduced control at 144 hours, then showed a slight recovery at 168 hours. In conclusion, M2 antisense mRNA expression by an inducible system can effectively decrease RR M2 protein expression, reduce enzyme activity, and inhibit growth. Furthermore, this approach can be employed in future antisense investigations.
Development and Characterization of a Transformed Human Periodontal Ligament Cell Line (1997)

Periodontal ligament (PDL) cells are thought to be important for establishing and maintaining a stable interface between bone and teeth. In addition, PDL cells are thought to play critical roles in both the pathogenesis of periodontal disease and the regeneration of periodontal ligament tissues. The purpose of this study was to develop a continuous or stable human PDL cell line as an in vitro model for the investigation of cellular mechanisms involved in periodontal regeneration and destruction. Human PDL cells, derived from a primary cell culture, were transfected with simian virus 40 (SV40) T antigen-containing virus with a neomycin resistance gene. The transformed cells expressed the SV40 T antigen mRNA as assayed by reverse transcription polymerase chain reaction (RT-PCR). This cell line was also characterized for morphological changes and growth characteristics compared to primary PDL cell cultures. The transformed cells were shown to form a multilayer pattern and distinct colonies on tissue culture surfaces. However, no colony formation was found in soft agar. The transformed PDL cell line was found to have a greater rate of proliferation in 10% fetal bovine serum than primary culture, and continued to proliferate in low serum concentrations capable of producing quiescence in primary cells. Interleukin-1 beta (IL-1 beta) was shown to produce a 7-fold elevation in collagenase (MMP-1) mRNA levels, consistent with primary PDL cells. In addition, IL-1 beta was shown to produce a decrease in alkaline phosphatase activity in a concentration-dependent manner. The transformed cell line has been maintained for over 30 generations of cell culture. In conclusion, a stable human PDL cell line has been established to serve as a model for future in vitro investigations into periodontal pathogenic mechanisms and to evaluate therapies directed at the regeneration of periodontal ligament.
Integrated a hybrid CATV/GPON transport system based on 1.31/1.49/1.55 &#956;m WDM transceiver module (2005)

We briefly demonstrate the three wavelengths WDM transceiver module with a pigtail fiber designed for GPON and CATV specifications. The discussion is addressed on duplex transmission measurement of gigabit-capable data and multi-channel video signal.
Stereochemistry of the Cholesterol Dichlorides1 (1950)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemistry of the Cholesterol Dichlorides1D. H. R. Barton and E. MillerCite this: J. Am. Chem. Soc. 1950, 72, 1, 370–374Publication Date (Print):January 1, 1950Publication History Published online1 May 2002Published inissue 1 January 1950https://pubs.acs.org/doi/10.1021/ja01157a100https://doi.org/10.1021/ja01157a100research-articleACS PublicationsRequest reuse permissionsArticle Views298Altmetric-Citations50LEARN 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
Surface patterning of (bio)molecules onto the inner wall of fused-silica capillary tubes (2008)

An efficient photochemical method for the site-specific immobilization and patterning of (bio)molecules inside glass capillary tubes is reported. The strategy involves the photodeprotection of reactive aminooxy groups on surfaces and subsequent reaction with aldehyde containing (bio)molecules.
Advances in the proteomic investigation of the cell secretome (2012)

Studies of the cell secretome have greatly increased in recent years owing to improvements in proteomic platforms, mass spectrometry instrumentation and to the increased interaction between analytical chemists, biologists and clinicians. Several secretome studies have been implemented in different areas of research, leading to the generation of a valuable secretome catalogs. Secreted proteins continue to be an important source of biomarkers and therapeutic target discovery and are equally valuable in the field of microbiology. Several discoveries have been achieved in vitro using cell culture systems, ex vivo using human tissue specimens and in vivo using animal models. In this review, some of the most recent advances in secretome studies and the fields that have benefited the most from this evolving technology are highlighted.
Mapping genetic modifiers of survival in a mouse model of Dravet syndrome (2013)

Epilepsy is a common neurological disorder affecting approximately 1% of the population. Mutations in voltage-gated sodium channels are responsible for several monogenic epilepsy syndromes. More than 800 mutations in the voltage-gated sodium channel SCN1A have been reported in patients with generalized epilepsy with febrile seizures plus and Dravet syndrome. Heterozygous loss-of-function mutations in SCN1A result in Dravet syndrome, a severe infant-onset epileptic encephalopathy characterized by intractable seizures, developmental delays and increased mortality. A common feature of monogenic epilepsies is variable expressivity among individuals with the same mutation, suggesting that genetic modifiers may influence clinical severity. Mice with heterozygous deletion of Scn1a (Scn1a(+/-) ) model a number of Dravet syndrome features, including spontaneous seizures and premature lethality. Phenotype severity in Scn1a(+/-) mice is strongly dependent on strain background. On the 129S6/SvEvTac strain Scn1a(+/-) mice exhibit no overt phenotype, whereas on the (C57BL/6J × 129S6/SvEvTac)F1 strain Scn1a(+/-) mice exhibit spontaneous seizures and early lethality. To systematically identify loci that influence premature lethality in Scn1a(+/-) mice, we performed genome scans on reciprocal backcrosses. Quantitative trait locus mapping revealed modifier loci on mouse chromosomes 5, 7, 8 and 11. RNA-seq analysis of strain-dependent gene expression, regulation and coding sequence variation provided a list of potential functional candidate genes at each locus. Identification of modifier genes that influence survival in Scn1a(+/-) mice will improve our understanding of the pathophysiology of Dravet syndrome and may suggest novel therapeutic strategies for improved treatment of human patients.