gebhart/patrepeval huggingface dataset:
Plasmid-mediated bacteriocin production by Shigella flexneri isolated from dysenteric diarrhoea and their transformation into Escherichia coli (2006)

A 3-kb plasmid that harboured information for the production of bacteriocin by Sh. flexneri strains was described. The production of this bacteriocin may be related to dysenteric diarrhoea produced by these bacterial strains.
Privacy-aware Publishing of Decentralized Access-Controlled Content (2013)

LSIR
A survey of methods for encrypted traffic classification and analysis (2015)

Summary With the widespread use of encrypted data transport, network traffic encryption is becoming a standard nowadays. This presents a challenge for traffic measurement, especially for analysis and anomaly detection methods, which are dependent on the type of network traffic. In this paper, we survey existing approaches for classification and analysis of encrypted traffic. First, we describe the most widespread encryption protocols used throughout the Internet. We show that the initiation of an encrypted connection and the protocol structure give away much information for encrypted traffic classification and analysis. Then, we survey payload and feature‐based classification methods for encrypted traffic and categorize them using an established taxonomy. The advantage of some of described classification methods is the ability to recognize the encrypted application protocol in addition to the encryption protocol. Finally, we make a comprehensive comparison of the surveyed feature‐based classification methods and present their weaknesses and strengths. Copyright © 2015 John Wiley & Sons, Ltd.
Effects of retinal pigment epithelial cell-secreted factors on neonatal rat retinal explant progenitor cells (1996)

This study demonstrates the effects of conditioned media from transformed neonatal rat retinal pigment epithelial cells (tnrRPE-CM) in a culture system consisting of neonatal rat retinal explants. For this study, retinal explants from postnatal day 2 (PN2) normal rats were cultured for over 3 weeks on a poly-D-L-ornithine-coated surface in RPE-CM only, 10% serum, or a serum-free defined media, and then examined by phase-contrast and scanning electron microscopy and immunocytochemistry. After 2 days in vitro, long ganglion cell-like neurites projected from retinal explants grown in tnrRPE-CM. These neurites increased in number and length with prolonged time in culture. In addition, by 5 days, round cells were observed adjacent to neonatal explants grown in tnrRPE-CM. By day 10, these round cells had increased in number and were seen along the neurites, in massive clusters immediately adjacent to these explants and dispersed throughout the culture-plate surface. Media conditioned by primary cultures of normal neonatal rat RPE cells caused a similar, but less robust, cellular response in retinal explants when compared to tnrRPE-CM. At 10 days, retinal explants grown in 10% serum showed only a few short processes, but no round cells, while those explants grown in defined media appeared to be degenerating. The round migrating cells are classified as retinal progenitor cells since they immunostained for opsin and interphotoreceptor retinoid-binding protein (IRBP), two photoreceptor cell markers, and a few for cellular retinaldehyde binding protein (CRALBP), a Muller cell marker. Neurite outgrowth and retinal progenitor cell production from explants were eliminated when the tnrRPE-CM was subjected to trypsin or heat treatment, indicating that the factor(s) responsible for promoting these cellular events was most likely proteinaceous. Growth factors, including basic fibroblast growth factor, were unable to generate long neurite outgrowth or progenitor cell production as observed in RPE-CM-supplemented explant cultures. We report that CM from cultures of primary and transformed neonatal rat RPE cells promoted ganglion cell-like neurites and the production of migrating retinal progenitor cells that primarily expressed photoreceptor-specific markers, from neonatal rat retinal explants. This evidence further confirms the important role of RPE in retinal development. The production of large numbers of progenitor cells by an RPE-secreted factor(s) may have important implications for possible therapeutic approaches to help correct retinal disease states by replacing lost cells through transplantation technology.
An Overview of Custom Array Sequencing (2009)

This unit provides an overview of oligo hybridization-based resequencing and a wide range of considerations for implementing the technology and analyzing the resulting data. The specific technology discussed is the Affymetrix GeneChip CustomSeq Resequencing Array platform. Concepts related to array design, experimental protocols, and base-calling using existing algorithms are presented. Details that should be evaluated during development of sequence tiling, target amplification, and PCR protocols are addressed. An overview of the Affymetrix GeneChip Sequence Analysis Software (GSEQ) is provided, along with factors that influence base-calling coverage and accuracy. Also outlined are performance measures that can be used to characterize base-calling with resequencing arrays, as well as factors known to affect their performance. Limitations associated with detection of insertions and deletions (indels) are discussed, with empirical data from our experiments used to outline possible approaches to indel detection. Critical topics in the design, implementation, and analysis of targeted sequencing arrays not previously discussed in detail are highlighted.
Studies on Seven-membered Ring Compounds. XIII. Reaction of 2-Bromo-7-methoxytropone with Active Methylene Compounds (1965)

Reaction of 2-bromo-7-methoxytropone (III) with active methylene compounds was carried out. III reacted with malononitrile to afford heptafulvene derivative, whereas III reacted with cyanoacetamid, diethyl malonate and ethyl p-nitrophenylacetate to yield rearrangement products, coumarin derivatives. III didn't react with ethyl carbamoylacetate, 2-cyanoacetophenone and cyanoacetone, which easily reacted with 2-chlorotropone.
Convenient Synthesis <sup>1</sup>H, <sup>13</sup>C NMR Study and X-Ray Crystal Structure Determination of Some New Disubstituted Thiophenes (1999)

Abstract 2,5-, 3,4- and 2,3-Thienylenediacrylic (1, 4 and 7 respectively) were synthesized in one step reaction by catalytic vinylation of the corresponding dibromothiophenes in the presence of cyclohexylamine salt of acrylic acid. 2,4-Thienylenediacrylic acid 10 was prepared by catalytic vinylation of 3-(4-bromo-2-thienyl)acryilic acid.
Characterization and measurement of time and frequency stability (1979)

The roles which spectral density of fractional frequency fluctuations, two‐sample variance, and power spectra play in different parts of the electromagnetic spectrum are introduced. Their relationship is discussed. Data acquisition in the frequency and the time domain is considered, and examples are given throughout the spectrum. Recently proposed methods for the characterization of a single high‐quality frequency source are briefly described. Possible difficulties and limitations in the interpretation of measurement results are specified, mostly in the presence of a dead time between measurements. The link between past developments in the field, such as two‐sample variance and spectral analysis from time domain measurement, and recently introduced structure functions is emphasized.
On the efficiency of coupling light from stripe-geometry GaAs lasers into multimode optical fibers (1974)

The coupling between GaAs injection lasers and multimode optical fibers using spherical ends on the optical fibers is examined. In particular, the results previously published by Kato are shown to be overly optimistic, although considerable improvement over using a flat-ended fiber is still predicted. Neglecting reflection losses, we predict maximum coupling efficiencies of the order of 60–70% for our typical double-heterostructure laser diodes and have experimentally measured 62% in a case for which 60% is expected from the theory.
Noninvasive Creation of an Atrial Septal Defect by Histotripsy in a Canine Model (2010)

Under real-time ultrasound guidance, atrial septal defects were successfully created with extracardiac histotripsy in a live canine model. Although further studies in an intact animal model are needed, these results provide promise of histotripsy becoming a valuable clinical tool.
506. The structure of pyoluteorin (1964)

A. J. Birch, P. Hodge, R. W. Rickards, R. Takeda and T. R. Watson, J. Chem. Soc., 1964, 2641 DOI: 10.1039/JR9640002641
Preclinical Diagnosis of Magnetic Resonance (MR) Brain Images via Discrete Wavelet Packet Transform with Tsallis Entropy and Generalized Eigenvalue Proximal Support Vector Machine (GEPSVM) (2015)

Background: Developing an accurate computer-aided diagnosis (CAD) system of MR brain images is essential for medical interpretation and analysis. In this study, we propose a novel automatic CAD system to distinguish abnormal brains from normal brains in MRI scanning. Methods: The proposed method simplifies the task to a binary classification problem. We used discrete wavelet packet transform (DWPT) to extract wavelet packet coefficients from MR brain images. Next, Shannon entropy (SE) and Tsallis entropy (TE) were harnessed to obtain entropy features from DWPT coefficients. Finally, generalized eigenvalue proximate support vector machine (GEPSVM), and GEPSVM with radial basis function (RBF) kernel, were employed as classifier. We tested the four proposed diagnosis methods (DWPT + SE + GEPSVM, DWPT + TE + GEPSVM, DWPT + SE + GEPSVM + RBF, and DWPT + TE + GEPSVM + RBF) on three benchmark datasets of Dataset-66, Dataset-160, and Dataset-255. Results: The 10 repetition of K-fold stratified cross validation results showed the proposed DWPT + TE + GEPSVM + RBF method excelled not only other three proposed classifiers but also existing state-of-the-art methods in terms of classification accuracy. In addition, the DWPT + TE + GEPSVM + RBF method achieved accuracy of 100%, 100%, and 99.53% on Dataset-66, Dataset-160, and Dataset-255, respectively. For Dataset-255, the offline learning cost 8.4430s and online prediction cost merely 0.1059s. Conclusions: We have proved the effectiveness of the proposed method, which achieved nearly 100% accuracy over three benchmark datasets.
Solutions of two paramagnetic ions for use in nuclear magnetic resonance phantoms (1988)

The introduction of paramagnetic ions to affect relaxation times has been used in a variety of nuclear magnetic resonance (NMR) applications. All such relaxants used in NMR phantoms to date have consisted of a single paramagnetic ion. The disadvantage of this is that only one relaxation time can be adjusted as desired, either T1 or T2. This study demonstrates that, by properly choosing two paramagnetic ions, it is possible to adjust both T1 and T2 independently over a wide range of values. Specifically, solutions of MnCl2 and NiCl2 were prepared that simultaneously matched target T1 and T2 values to within approximately 6%.
A single nucleotide polymorphism of the cholecystokinin-B receptor predicts risk for pancreatic cancer (2012)

There currently are no tests available for early diagnosis or for the identification of patients at risk for development of pancreatic cancer. We report the discovery of single nucleotide polymorphism (SNP) in the cholecystokinin B receptor (CCKBR) gene predicts survival and risk of pancreatic cancer. Growth of human pancreatic cancer is stimulated by gastrin through the CCKBR and an alternatively spliced isoform of the CCKBR gene called CCKCR. One hundred and ten surgically resected benign and malignant pancreatic tissues as well as normal pancreas were prospectively evaluated for CCKBR genotype and protein expression. Analysis demonstrated the expression of the spliced isoform, CCKCR, was associated with a (SNP) (C > A) at position 32 of the intron 4 (IVS 4) of the CCKBR gene. Since the SNP is within an intron, it has not previously been identified in the GWAS studies. Only patients with the A/A or A/C genotypes, exhibited immunoreactivity to a selective CCKCR antibody. Survival among pancreatic cancer patients with the A-SNP was significantly shorter (p = 0.0001, hazard ratio = 3.63) compared with individuals with C/C genotype. Other variables such as surgical margins, lymph node status, histologic grade or adjuvant chemotherapy were not associated with survival. Furthermore, having one or two of the A-alleles was found to increase the risk of pancreatic adenocarcinoma by 174% (p = 0.0192) compared with the C/C wild type. Cancer cells transfected to overexpress the CCKCR demonstrated increased proliferation over controls. Genetic screening for this SNP may aid in early detection of pancreatic cancer in high risk subjects.
Culture-Independent Microbial Community Analysis Reveals that Inulin in the Diet Primarily Affects Previously Unknown Bacteria in the Mouse Cecum (2002)

Inulin is a well-known fructose-based prebiotic which has been shown to stimulate the growth of bifidobacteria, a bacterial group generally considered beneficial for intestinal health. In the present study, we analyzed inulin-associated shifts in the total bacterial community of wild-type mice and mice carrying a genetically inactivated adenomatous polyposis coli tumor suppressor gene by using DNA-based approaches independent of bacterial culturability. Mice were fed a high-fat, nonfiber diet with or without inulin inclusion at a 10% (wt/wt) concentration. Cecal contents were analyzed after 0, 3, and 9 weeks on the experimental diets. Inulin inclusion significantly affected the total bacterial community structure of the cecum as determined by both a nonselective percent-guanine-plus-cytosine-based profiling analysis and a more specific 16S ribosomal DNA sequence analysis. The shifts included stimulation of bifidobacteria and suppression of clostridia, but sequence comparison revealed that the major shifts were within previously unknown bacterial taxa. Concomitantly, significantly higher bacterial densities, determined by flow cytometry, were observed with the inulin-amended diet, and the metabolism of the cecal bacterial community was altered, as indicated by higher levels of residual short-chain fatty acids, particularly lactic acid. With regard to all of the microbiological parameters measured, the wild-type mice and mice carrying a genetically inactivated adenomatous polyposis coli tumor suppressor gene were essentially identical. Studies of the implications of pre- and probiotics may need to be expanded to include careful analysis of their effects on the entire microbial community, rather than just a few well-known species. Further studies are needed to increase our understanding of the possible roles of currently unknown gastrointestinal bacteria in health and disease.
FRICTION AND WEAR BEHAVIORS OF TOUGHENED POLYOXYMETHYLENE BLEND UNDER WATER LUBRICATION (2000)

Abstract This article describes the results from an experimental investigation on the friction and wear performances of the toughened polyoxymethylene/polyurethane blend (M-POM) under water drops lubrication. The sliding experiments were carried out on a block-on-ring tribometer. The contact configuration used was a stationary polymer block on a rotating AISI 1045 steel or MC nylon ring. The selected test material includes a polyoxymethylene (POM)-based composite that was toughened by polyurethane (PU) and filled by polytetrafluoroethylene (PTFE) and silicone oil. The results show that the M-POM with 10% PU (by weight) has better antifriction and antiwear properties under water drops lubrication, compared with pure POM and the POM/PTFE composite. The M-POM is more suitable to slide against MC nylon than steel under water lubrication. Because of the entrance of water, the hydrogen bond formed between water and polymers at the frictional surfaces during friction improves greatly the water lubrication performance of M-POM, in addition to the water-cooling action. Keywords: PolyoxymethylenePolyurethaneFriction and wearWater lubrication ACKNOWLEDGMENTS The author wishes to express his thank to Mr. M. Tian for his assistance in this work. The financial support from National Natural Science Foundation of China (Grant No. 59305041) is also acknowledged.
Clustering of P<sup>K</sup>-trisaccharides on amphiphilic cyclodextrin reveals unprecedented affinity for the Shiga-like toxin Stx2 (2017)

Using amphiphilic cyclodextrin as a scaffold, the first class of P<sup>K</sup>-glycoconjugates capable of high avidity binding to both Stx1 and Stx2 toxins in solid-phase assay formats is reported. The generated glycomicroarray effectively mimics the plasma membrane surface while discriminating binding of the two Stx toxins, with unprecedented affinity to Stx2.
Parametric polymorphism and semantic subtyping (2011)

We consider a type algebra equipped with recursive, product, function, intersection, union, and complement types together with type variables and implicit universal quantification over them. We consider the subtyping relation recently defined by Castagna and Xu over such type expressions and show how this relation can be decided in EXPTIME, answering an open question. The novelty, originality and strength of our solution reside in introducing a logical modeling for the semantic subtyping framework. We model semantic subtyping in a tree logic and use a satisfiability-testing algorithm in order to decide subtyping. We report on practical experiments made with a full implementation of the system. This provides a powerful polymorphic type system aiming at maintaining full static type-safety of functional programs that manipulate trees, even with higher-order functions, which is particularly useful in the context of XML.
A comparison of the contributions of common-mode and differential-mode currents in radiated emissions (1989)

It is shown that radiated emissions due to common-mode currents on printed circuit board lands can greatly exceed those due to differential-mode currents. It is concluded that predictions of radiated emissions based solely on differential-mode (transmission line) currents can bear little, if any, resemblance to actual measured emissions. Therefore, radiated emission prediction models that use only differential-mode (transmission-line) currents and ignore common-mode (antenna) currents are not adequate for the prediction of radiated emissions from printed circuit boards (as well as cables).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Deeply Supervised Salient Object Detection with Short Connections (2018)

Recent progress on salient object detection is substantial, benefiting mostly from the explosive development of Convolutional Neural Networks (CNNs). Semantic segmentation and salient object detection algorithms developed lately have been mostly based on Fully Convolutional Neural Networks (FCNs). There is still a large room for improvement over the generic FCN models that do not explicitly deal with the scale-space problem. The Holistically-Nested Edge Detector (HED) provides a skip-layer structure with deep supervision for edge and boundary detection, but the performance gain of HED on saliency detection is not obvious. In this paper, we propose a new salient object detection method by introducing short connections to the skip-layer structures within the HED architecture. Our framework takes full advantage of multi-level and multi-scale features extracted from FCNs, providing more advanced representations at each layer, a property that is critically needed to perform segment detection. Our method produces state-of-the-art results on 5 widely tested salient object detection benchmarks, with advantages in terms of efficiency (0.08 seconds per image), effectiveness, and simplicity over the existing algorithms. Beyond that, we conduct an exhaustive analysis of the role of training data on performance. We provide a training set for future research and fair comparisons.
Development of Lean Burn Catalyst (1995)

<div class="htmlview paragraph">A new type of three way catalyst for lean engine was developed in order to reduce hydrocarbon (HC), carbon-monoxide (CO) and nitrogen-oxides (NOx) in lean exhaust gas. This catalyst has a base support material of MFI zeolite loaded with active metals including platinum (Pt), iridium (Ir) and rhodium (Rh). It showed good catalytic activity and thermal durability on a lean engine. This catalyst made it possible to enlarge the lean operating region of the lean burn engine. It showed the NOx reduction of 51% in Japanese 10-15 mode emission test and the emissions were found low enough to satisfy the new Japanese emission standards. Consequently, fuel economy of the lean vehicle with this catalyst has been improved about 16% in comparison with a comparable current stoichiometric combustion vehicle. This catalyst has been mass-produced for Mazda 323 lean burn vehicle (Z-Lean) for the Japanese domestic market.</div>
HSP27 in patients with ovarian carcinoma: still an independent prognostic indicator at 60 months follow-up. (2004)

Cox-regression analysis found HSP27 to be an independent indicator of prognosis and survival in patients with ovarian carcinoma who had longer follow-up. Decreased HSP27 staining was related to decreased survival. This study confirms the authors' earlier report on the importance of HSP27 as a prognostic indicator in ovarian carcinoma.
<i>N</i>‐Acetylaspartylglutamate acts as an agonist upon homomeric NMDA receptor (NMDAR1) expressed in <i>Xenopus</i> oocytes (1992)

The electrophysiological effects of N-acetylaspartylglutamate (NAAG), an endogenous peptide restrictively distributed in the central nervous system, were studied using Xenopus oocytes injected with RNAs transcribed from cloned glutamate receptor cDNAs. NAAG induced an inward current, dose dependently, in oocytes injected with RNA for an N-methyl-D-aspartate receptor subunit (NMDAR1). In contrast, the oocytes injected with RNAs for AMPA-selective glutamate receptors (GluR1, GluR3, GluR1+GluR2 and GluR2+GluR3) scarcely responded to NAAG, and the oocytes injected with RNA for kainate receptor (GluR6) did not respond to NAAG. The half-maximal response (ED50) value of NAAG on expressed NMDAR1 was 185 microM, which shows that NAAG is about 115-times less potent than L-glutamate (Glu), the ED50 of which value was 1.6 microM. The maximal current amplitude induced by NAAG was about 70% of that by Glu. NAAG-induced current in NMDAR1-injected oocytes was potentiated by glycine, dose-dependently antagonized by DL-2-amino-5-phosphonovaleric acid, and blocked by magnesium ions in a voltage-dependent fashion. These results suggest that NAAG is one of the endogenous agonists selective for NMDAR1.