gebhart/patrepeval huggingface dataset:
Low-Complexity Regions in Plasmodium falciparum Proteins (2001)

Full-sequence data available for Plasmodium falciparum chromosomes 2 and 3 are exploited to perform a statistical analysis of the long tracts of biased amino acid composition that characterize the vast majority of P. falciparum proteins and to make a comparison with similarly defined tracts from other simple eukaryotes. When the relatively minor subset of prevalently hydrophobic segments is discarded from the set of low-complexity segments identified by current segmentation methods in P. falciparum proteins, a good correspondence is found between prevalently hydrophilic low-complexity segments and the species-specific, rapidly diverging insertions detected by multiple-alignment procedures when sequences of bona fide homologs are available. Amino acid preferences are fairly uniform in the set of hydrophilic low-complexity segments identified in the two P. falciparum chromosomes sequenced, as well as in sequenced genes from Plasmodium berghei, but differ from those observed in Saccharomyces cerevisiae and Dictyostelium discoideum. In the two plasmodial species, amino acid frequencies do not correlate with properties such as hydrophilicity, small volume, or flexibility, which might be expected to characterize residues involved in nonglobular domains but do correlate with A-richness in codons. An effect of phenotypic selection versus neutral drift, however, is suggested by the predominance of asparagine over lysine.
Various members of the Toll‐like receptor family contribute to the innate immune response of human epidermal keratinocytes (2005)

Toll-like receptors (TLRs) are important pattern recognition molecules that activate the nuclear factor (NF)-kappaB pathway leading to the production of antimicrobial immune mediators. As keratinocytes represent the first barrier against exogenous pathogens in human skin, we investigated their complete functional TLR1-10 expression profile. First, reverse transcription-polymerase chain reaction (PCR) analysis revealed a very similar pattern of TLR mRNA expression when comparing freshly isolated human epidermis and cultured primary human keratinocytes. Thus, further experiments were carried out with primary keratinocytes in comparison with the spontaneously immortalized human keratinocyte cell line HaCaT. The quantitative expression of TLR1-10 mRNA in real-time PCR of primary human keratinocytes and HaCaT cells was analysed. Both cell types constitutively expressed TLR2, TLR3, TLR5, and to a lesser extent TLR10. TLR4 was only found in HaCaT cells, TLR1 to a higher degree in primary keratinocytes. In line with this, LPS induced mRNA expression of CD14 and TLR4 only in HaCaT cells. After stimulation with various TLR ligands, the NF-kappaB-activated chemokine interleukin-8 (IL-8) was measured. In primary keratinocytes and HaCaT cells the TLR3 ligand poly (I:C) was the most potent stimulator of IL-8 secretion. The TLR ligands peptidoglycan, Pam3Cys and flagellin which bind to TLR2, TLR1/TLR2 heterodimer, and TLR5, respectively, also induced IL-8 secretion, whereas no IL-8 was induced by LPS, R-848, loxoribine and cytosine guanine dinucleotide-containing oligodeoxynucleotide. A corresponding pattern was found in the RelA NF-kappaB translocation assay after ligand stimulation of primary keratinocytes. These studies provide substantial evidence for a functional TLR expression and signalling profile of normal human keratinocytes contributing to the antimicrobial defence barrier of human skin.
Novel insight into the biological functions of syndecan ectodomain core proteins (2013)

Syndecans are a four member family of multifunctional transmembrane heparan sulphate bearing cell surface receptors. Each family member has common molecular architecture but a distinct expression profile. Numerous molecular interactions between syndecan heparan sulphate chains, growth factors, cytokines, and extracellular matrix molecules have been reported and syndecans are intimately associated with cell adhesion and migration. Here, we describe the important emerging concept that contained within syndecan extracellular core proteins are "adhesion regulatory domains." Cell adhesion is driven by the integrins and syndecan ectodomain adhesion regulatory domains can alter integrin driven cellular responses. Cell adhesion and migration is central to numerous pathologies and an understanding of how syndecan ectodomains influence integrins will lead to novel therapeutic strategies.
Notes - Bromination of α-Methylstyrene with N-Bromosuccinimide (1957)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNotes - Bromination of α-Methylstyrene with N-BromosuccinimideHerman Pines, Husni Alul, and Marjan KolobielskiCite this: J. Org. Chem. 1957, 22, 9, 1113–1114Publication Date (Print):September 1, 1957Publication History Published online23 April 2003Published inissue 1 September 1957https://pubs.acs.org/doi/10.1021/jo01360a608https://doi.org/10.1021/jo01360a608research-articleACS PublicationsRequest reuse permissionsArticle Views500Altmetric-Citations28LEARN 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
Scalable Privacy-Preserving Record Linkage for Multiple Databases (2014)

Privacy-preserving record linkage (PPRL) is the process of identifying records that correspond to the same real-world entities across several databases without revealing any sensitive information about these entities. Various techniques have been developed to tackle the problem of PPRL, with the majority of them only considering linking two databases. However, in many real-world applications data from more than two sources need to be linked. In this paper we consider the problem of linking data from three or more sources in an efficient and secure way. We propose a protocol that combines the use of Bloom filters, secure summation, and Dice coefficient similarity calculation with the aim to identify all records held by the different data sources that have a similarity above a certain threshold. Our protocol is secure in that no party learns any sensitive information about the other parties' data, but all parties learn which of their records have a high similarity with records held by the other parties. We evaluate our protocol on a large dataset showing the scalability, linkage quality, and privacy of our protocol.
<title>Hollow metallic micromachined needles with multiple output ports</title> (1999)

In this paper, hollow metallic micromachined needles with multiple output ports are designed, fabricated, characterized, and packaged. The hollow metallic needles include design features such as tapered needle tips and multiple output ports on the bottom and top of each needle. The needle tip and shaft are formed by microelectroformed metal. The flow characteristics of the needles are currently being experimentally investigated and modeled using a finite element numerical model. The experimental results and theoretical models will be presented as part of this paper. The micromachined needles can be fabricated on a variety of substrates and can use micro-electroformed palladium as the structural material. The use of palladium as a structural material provides high mechanical strength and durability, as well as, biocompatibility for use in biomedical applications. The cross-sectional dimensions of individual needle tips begin at less than 10 micrometers in width and 15 micrometers in height and then taper to 200 micrometers in width and 60 micrometers in height. The significance of this work includes the development of hollow metallic micromachined needles for biomedical applications, as well as, a discussion of structural, fluidic, and packaging design considerations.
Ultrasonic tissue characterization using a generalized Nakagami model (2001)

The statistics of the backscattered ultrasonic echo from tissue have been described using Rayleigh, K, and Nakagami distributions. The Nakagami and K distributions, each with two parameters, can model the envelope reasonably well. However, a three-parameter distribution is likely to match the envelope of the backscattered echo much better than these two-parameter distributions. Starting with the Nakagami distribution and including an additional parameter to account for the tails of the density function, a generalized Nakagami distribution has been derived. Computer simulation of A-scans and analysis of data collected from tissue-mimicking phantoms show that the generalized Nakagami distribution fits the statistics of the echo of the envelope better than the Nakagami distribution. The parameters of the generalized Nakagami distribution appear to be far more sensitive to the scattering conditions than the parameters of the Nakagami distribution.
Changes observed in slow-growing melanomas during long-term dermoscopic monitoring (2012)

While their diameter changed minimally over time, most SGM became more disorganized, revealed loss of network in favour of structureless areas, and developed new colours.
Selective catalytic reaction of hydrogen with nitric oxide in the presence of oxygen (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelective catalytic reaction of hydrogen with nitric oxide in the presence of oxygenMordecai Shelef, James H. Jones, Joseph T. Kummer, Klaus Otto, and E. Eugene WeaverCite this: Environ. Sci. Technol. 1971, 5, 9, 790–798Publication Date (Print):September 1, 1971Publication History Published online1 May 2002Published inissue 1 September 1971https://pubs.acs.org/doi/10.1021/es60056a003https://doi.org/10.1021/es60056a003research-articleACS PublicationsRequest reuse permissionsArticle Views318Altmetric-Citations81LEARN 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
Incorporation of nitric oxide‐releasing crosslinked polyethyleneimine microspheres into vascular grafts (1997)

Over the years, many attempts have been made to increase the patency of small- to medium-sized prosthetic vascular grafts. However, none of them has greatly affected long-term rates. Recently, nitric oxide (NO) has been shown to inhibit thrombus formation in such grafts, suggesting that local delivery of NO may help to increase graft patency. This study describes the site-specific delivery of NO by entrapping NO-releasing microspheres in the pores of a vascular graft. NO-releasing polyethyleneimine microspheres (PEIX) were developed using a novel water-in-oil emulsion technique involving chemical crosslinking with a bis-epoxide. The PEIX microspheres were then derivatized with NO forming the [N(O)NO]− moiety of the diazeniumdiolates formerly known as NONOates. These polymeric NO-releasing particles were found to spontaneously release 194 nmol NO/mg with a half-life of over 66 h under physiologic conditions. Fluorescein isothiocyanate-labeled microspheres were then embedded into the pores of a 60-μm nonreinforced Gore-tex vascular graft using a simple evacuation technique and evaluated for microsphere placement and NO release. Scanning electron microscopic analysis showed the microspheres entrapped in the pores of the vascular graft releasing 10 nmol NO/mg with a half-life of 51 h. The microspheres remained entrapped in the graft even after immersion and NO release, as confirmed by fluorescence of the medium. These results suggest that NO-releasing particles can be incorporated into the pores of a vascular graft to deliver therapeutic amounts of NO for the prevention of thrombosis in small-diameter prosthetic grafts. © 1997 John Wiley & Sons, Inc. J Biomed Mater Res, 37, 182–189, 1997.
The value and limitation of dual-energy X-ray absorptiometry. (1995)

In population studies, in which patients and controls are of comparable size, bone mineral area density (BMD) gives reliable results for mean bone mass data although, with sequential data, BMD may under-estimate the degree of change in bone mass. In children BMD data should be reliable, provided that patients and controls, matched for age and sex, are also of the same size. With disease children may be small for their age so that low bone mass by BMD may be due to small body size and not necessarily to osteopoenia. In these situations the bone mineral content (BMC) index may be more reliable than BMD. To assess bone mass status in individuals, BMC index, as well as BMD, should be used, particularly with adults at the extremes of body size (the very small or very tall).
Prologue. Remarques (2012)

Lorsque, il y a quelques mois, Véronique Montémont et Christelle Reggiani m’ont parlé pour la première fois de leur projet intitulé Georges Perec artisan de la langue, je me suis exclamée : « Quelle bonne idée ! » En effet, si l’œuvre de Georges Perec a suscité un grand nombre d’études (je ne prétends pas les connaître toutes), celles portant sur la langue sont plutôt rares. On a parlé, certes, de l’homme de lettres ou des lettres, les vingt-six de l’alphabet, dont Georges Perec affirmait qu’...
DNRA in intertidal sediments of the Yangtze Estuary (2017)

Abstract Dissimilatory nitrate reduction to ammonium (DNRA) plays an important role in regulating the fate of reactive nitrogen in estuarine and coastal ecosystems. In this work, intertidal sediments of the Yangtze Estuary were collected in January and August 2015. Potential rates of DNRA and associated functional gene were investigated with nitrogen isotope‐tracing and molecular techniques. The measured DNRA rates ranged from 0.14 to 5.57 μmol 15 N kg −1 h −1 in the intertidal sediments. DNRA rates were tightly related to abundance of nrfA gene ( p < 0.001), demonstrating that fermentation reaction may be the dominant pathway of DNRA in the study area. Redundancy analysis (RDA) showed a relationship between DNRA and organic matter and NO 2 − , suggesting that these substrates stimulated the metabolism of DNRA microorganisms. On the other hand, the correlation between abundances of nrfA gene and Fe 2+ and sulfide in the RDA analysis implied that oxidation of both Fe 2+ and sulfide can enhance fermentative DNRA by providing extra free energy. DNRA converted approximately 2.29 × 10 5 t of nitrate to ammonia annually in the sampling area of the Yangtze Estuary, and most of the converted ammonium was retained in the estuarine ecosystem. DNRA may further contribute to eutrophication in the Yangtze Estuary and also in the other hypereutrophic estuaries.
A 3d facial expression database for facial behavior research (2006)

Traditionally, human facial expressions have been studied using either 2D static images or 2D video sequences. The 2D-based analysis is incapable of handing large pose variations. Although 3D modeling techniques have been extensively used for 3D face recognition and 3D face animation, barely any research on 3D facial expression recognition using 3D range data has been reported. A primary factor for preventing such research is the lack of a publicly available 3D facial expression database. In this paper, we present a newly developed 3D facial expression database, which includes both prototypical 3D facial expression shapes and 2D facial textures of 2,500 models from 100 subjects. This is the first attempt at making a 3D facial expression database available for the research community, with the ultimate goal of fostering the research on affective computing and increasing the general understanding of facial behavior and the fine 3D structure inherent in human facial expressions. The new database can be a valuable resource for algorithm assessment, comparison and evaluation. 1.
Thermal Analysis of Lithium‐Boron Alloys (1979)

Lithium‐boron alloys have been studied by differential scanning calorimetry (DSC), x‐ray diffraction, and metallography over the composition range of 50–90 atomic percent (a/o) lithium. The results indicate that the alloy apparently is a two‐phase material consisting of the metallide, , and excess lithium. The alloy, utilizing the electrochemical superiority of lithium, is being developed as an anode material for molten salt batteries.
Studies on &alpha;-Lipoic Acid and its Related Compounds. II (1956)

Synthesis of DL-dimethyl-, DL-dibenzyl-, DL-S8-methyl-S6-benzyl-, and DL-S8-benzyl-S6-methyl-dihydro-α-lipoic acids was carried out and they were all obtained as an oil, except the S-dibenzyl compound. In order to obtain crystalline derivatives, formation of various salts were attempted. Although S-benzyl- and S-(p-nitrobenzyl)-thiuronium salts of the four compounds crystallized, they showed no depression of the melting point when fused with each other. Their benzhydryl-amine salts, however, showed about 10° depression of the melting point on admixture with each other and were found to have good properties as salts for their identification.
Seeing 3D objects in a single 2D image (2009)

A general framework simultaneously addressing pose estimation, 2D segmentation, object recognition, and 3D reconstruction from a single image is introduced in this paper. The proposed approach partitions 3D space into voxels and estimates the voxel states that maximize a likelihood integrating two components: the object fidelity, that is, the probability that an object occupies the given voxels, here encoded as a 3D shape prior learned from 3D samples of objects in a class; and the image fidelity, meaning the probability that the given voxels would produce the input image when properly projected to the image plane. We derive a loop-less graphical model for this likelihood and propose a computationally efficient optimization algorithm that is guaranteed to produce the global likelihood maximum. Furthermore, we derive a multi-resolution implementation of this algorithm that permits to trade reconstruction and estimation accuracy for computation. The presentation of the proposed framework is complemented with experiments on real data demonstrating the accuracy of the proposed approach.
Order Optimal Coded Delivery and Caching: Multiple Groupcast Index Coding. (2014)

The capacity of caching networks has received considerable attention in the past few years. A particularly studied setting is the case of a single server (e.g., a base station) and multiple users, each of which caches segments of files in a finite library. Each user requests one (whole) file in the library and the server sends a common coded multicast message to satisfy all users at once. The problem consists of finding the smallest possible codeword length to satisfy such requests. In this paper we consider the generalization to the case where each user places L ≥ 1 requests. The obvious naive scheme consists of applying L times the order-optimal scheme for a single request, obtaining a linear in L scaling of the multicast codeword length. We propose a new achievable scheme based on multiple groupcast index coding that achieves a significant gain over the naive scheme. Furthermore, through an information theoretic converse we find that the proposed scheme is approximately optimal within a constant factor of (at most) 18.
Energy Efficient Recycling Of In-Plant Fines (2014)

Numerous amounts of metallurgical dusts and sludge containing iron as well as some other valuable elements such as Zn, Pb and C are annually produced in the steelmaking industry. These alternative iron ore resources (fines) with unsatisfying physical and metallurgical properties are difficult to recycle. However, agglomerating these fines to be further used as a feed stock for existing iron and steelmaking processes is practiced successfully at several plants but for limited extent. In the present study, briquettes of integrated steelmaking industry waste materials (namely, BF-dust and sludge, BOF-dust and sludge) were used as feed stock to produce direct reduced iron (DRI). Physical and metallurgical properties of produced briquettes were investigated by means of TGA/DTA/QMS in combination with XRD. Swelling, softening and melting behavior were also studied using heating microscope.
Cyclin E amplification/overexpression is a mechanism of trastuzumab resistance in HER2 <sup>+</sup> breast cancer patients (2011)

Clinical benefits from trastuzumab and other anti-HER2 therapies in patients with HER2 amplified breast cancer remain limited by primary or acquired resistance. To identify potential mechanisms of resistance, we established trastuzumab-resistant HER2 amplified breast cancer cells by chronic exposure to trastuzumab treatment. Genomewide copy-number variation analyses of the resistant cells compared with parental cells revealed a focal amplification of genomic DNA containing the cyclin E gene. In a cohort of 34 HER2(+) patients treated with trastuzumab-based therapy, we found that cyclin E amplification/overexpression was associated with a worse clinical benefit (33.3% compared with 87.5%, P < 0.02) and a lower progression-free survival (6 mo vs. 14 mo, P < 0.002) compared with nonoverexpressing cyclin E tumors. To dissect the potential role of cyclin E in trastuzumab resistance, we studied the effects of cyclin E overexpression and cyclin E suppression. Cyclin E overexpression resulted in resistance to trastuzumab both in vitro and in vivo. Inhibition of cyclin E activity in cyclin E-amplified trastuzumab resistant clones, either by knockdown of cyclin E expression or treatment with cyclin-dependent kinase 2 (CDK2) inhibitors, led to a dramatic decrease in proliferation and enhanced apoptosis. In vivo, CDK2 inhibition significantly reduced tumor growth of trastuzumab-resistant xenografts. Our findings point to a causative role for cyclin E overexpression and the consequent increase in CDK2 activity in trastuzumab resistance and suggest that treatment with CDK2 inhibitors may be a valid strategy in patients with breast tumors with HER2 and cyclin E coamplification/overexpression.
Continuously variable duration Hidden Markov Models for ECG segmentation (1992)

Classical Hidden Markov Models (HMMs) can be extended by explicit modelling of state occupancy and leads to the Continuously Variable Duration HMMs (CVDHMMs). This property is of particular interest when dealing with sequences composed of variable duration electrophysiological events. This paper describes some experiments of CVDHMMs.