gebhart/patrepeval huggingface dataset:
A Stress Surveillance System Based on Calcium and Nitric Oxide in Marine Diatoms (2006)

Diatoms are an important group of eukaryotic phytoplankton, responsible for about 20% of global primary productivity. Study of the functional role of chemical signaling within phytoplankton assemblages is still in its infancy although recent reports in diatoms suggest the existence of chemical-based defense strategies. Here, we demonstrate how the accurate perception of diatom-derived reactive aldehydes can determine cell fate in diatoms. In particular, the aldehyde (2E,4E/Z)-decadienal (DD) can trigger intracellular calcium transients and the generation of nitric oxide (NO) by a calcium-dependent NO synthase-like activity, which results in cell death. However, pretreatment of cells with sublethal doses of aldehyde can induce resistance to subsequent lethal doses, which is reflected in an altered calcium signature and kinetics of NO production. We also present evidence for a DD-derived NO-based intercellular signaling system for the perception of stressed bystander cells. Based on these findings, we propose the existence of a sophisticated stress surveillance system in diatoms, which has important implications for understanding the cellular mechanisms responsible for acclimation versus death during phytoplankton bloom successions.
Diversity and organization of human T cell receptor delta variable gene segments. (1989)

Previous studies of the human TCR-delta gene identified a single commonly used V delta segment, denoted V delta 1. To better understand the extent of the human TCR-delta V gene repertoire, TCR-delta transcripts and gene rearrangements were examined in a new panel of cloned human TCR-gamma/delta lymphocytes. Through this analysis we identified and determined the structures of two new V delta segments, denoted V delta 2 and V delta 3. These V delta segments are different from previously characterized V alpha segments, supporting the notion that the human V delta and V alpha repertoires are distinct. Examination of V gamma gene segment usage in these cells reveals that the V delta 2 gene segment is used in conjunction with the V gamma 2 gene segment. Blot hybridization indicates that the V delta 2 gene segment lies between V delta 1 and D delta-J delta-C delta, and within 100 kb of the latter. Analysis of genomic clones indicates that the V delta 3 gene segment lies in an inverted orientation, approximately 2 kb 3' of C delta. This implies that rearrangement of V delta 3 to D delta-J delta-C delta occurs by inversion. Together with previous mapping studies, these results indicate that human V delta segments are dispersed, rather than clustered, within the TCR-alpha/delta locus. The analysis of rearrangements in polyclonal thymocyte DNA suggests that there may be a limited number of additional V delta gene segments yet to be characterized.
PFID: Pittsburgh fast-food image dataset (2009)

We introduce the first visual dataset of fast foods with a total of 4,545 still images, 606 stereo pairs, 303 360 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sup> videos for structure from motion, and 27 privacy-preserving videos of eating events of volunteers. This work was motivated by research on fast food recognition for dietary assessment. The data was collected by obtaining three instances of 101 foods from 11 popular fast food chains, and capturing images and videos in both restaurant conditions and a controlled lab setting. We benchmark the dataset using two standard approaches, color histogram and bag of SIFT features in conjunction with a discriminative classifier. Our dataset and the benchmarks are designed to stimulate research in this area and will be released freely to the research community.
Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 A resolution. (1990)

The three-dimensional structure of human erythrocytic purine nucleoside phosphorylase has been determined at 3.2 A resolution using x-ray diffraction data. Intensity data were measured using radiation from the Synchrotron Radiation Source, Daresbury, England, and oscillation film techniques. Phases were determined by using multiple isomorphous replacement methods with four heavy-atom derivatives and were improved using solvent flattening techniques. Purine nucleoside phosphorylase exists in the crystal as a trimer in which subunits are related by a crystallographic 3-fold axis. Each subunit contains an eight-stranded mixed beta-sheet and a five-stranded mixed beta-sheet which join to form a distorted beta-barrel structure. This core beta-structure is flanked by seven alpha-helices in a manner that generates a novel folding pattern. The active site, which was characterized from binding of the substrate analogs 8-iodoguanine and 5'-iodoformycin B, is located near the subunit-subunit boundary within the trimer and involves seven different segments from one subunit and an additional short segment from an adjacent subunit. In the crystal, the phosphate-binding site is probably occupied by a sulfate ion. The specificity of purine nucleoside phosphorylase for guanine, hypoxanthine, and their analogs can be explained on the basis of the arrangement of hydrogen bond donors and acceptors in the active site.
A scanning micromirror with angular comb drive actuation (2003)

Describes a single crystal silicon, 1/spl times/1 mm/sup 2/, scanning micromirror, which incorporates a novel angular vertical comb drive actuator. Results from our model for the angular vertical comb show that a 50% higher scan angle can be achieved when compared to a staggered vertical comb of equivalent dimensions. The simplified, cost effective, silicon on insulator micro-electromechanical systems, (SOI MEMS), process features self-alignment of the fixed and moving teeth and is fabricated on a single SOI wafer. Static deflection for our fabricated device fits well with the model and a resonant mode optical scan angle of /spl plusmn/18/spl deg/ at 1.4 kHz has been measured.
Angiogenic properties of normal and psoriatic skin associate with epidermis, not dermis. (1989)

Psoriasis is a chronic inflammatory and proliferative epidermal skin disease associated with prominent new vessels in the dermis. Heretofore, unresolved was the question which skin element causes stimulation of vessel formation in this lesion: the epidermis, the dermis, vessels themselves, inflammatory cells, and so forth. It has been argued that the dermis by means of its vessels is responsible for the rapid and prominent epidermal growth and that psoriasis is simply a dermal-induced epidermal disease. Recognizing that vascular proliferations do not occur in the absence of an angiogenic stimulus we asked where in psoriatic skin is that angiogenic element found. By using the rabbit cornea angiogenic assay, the vessel-stimulating properties of epidermis and dermis (separated after cold trypsinization overnight), collected from psoriatic-plaque skin and normal skin both nonpsoriatic and psoriatic patients, were measured. The corneas were examined on days 2, 4, 8, 10, and 12 and graded from 1 to 5+ for vessel growth. Psoriatic plaque epidermis revealed a 4 to 5+ stimulus (8 of 12 corneas). Epidermis from normal subjects or from nonlesional psoriatic patient skin also revealed a 4 to 5+ stimulus (3 of 5 and 5 of 8, respectively). In no case was the dermal implant from normal (7 implants) or psoriatic patients (3 implants of lesional skin) angiogenic. The angiogenic activity of epidermis is stable to freezing and boiling. This study indicates that the vessel-stimulating properties of psoriatic and nonpsoriatic skin are associated with the epidermis and that the developing psoriatic lesion may involve complex epidermal to dermal as well as dermal to epidermal signals.
ChemInform Abstract: Synthesis, Structure, and Photophysical Properties of Polyarylated Imidazoles [cf. (I), 23 examples] and Oxazoles [cf. (II), 11 examples]. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Molecular cloning and expression of the human interleukin 5 receptor. (1992)

Human interleukin 5 (IL-5) plays an important role in proliferation and differentiation of human eosinophils. We report the isolation of cDNA clones from cDNA libraries of human eosinophils by using murine IL-5 receptor alpha chain cDNA as a probe. Analysis of the predicted amino acid sequence indicated that the human IL-5 receptor has approximately 70% amino acid sequence homology with the murine IL-5 receptor and retains features common to the cytokine receptor superfamily. One cDNA clone encodes a glycoprotein of 420 amino acids (Mr 47,670) with an NH2-terminal hydrophobic region (20 amino acids), a glycosylated extracellular domain (324 amino acids), a transmembrane domain (21 amino acids), and a cytoplasmic domain (55 amino acids). Another cDNA encodes only the extracellular domain of this receptor molecule. Other cDNA clones encode molecules having diversified cytoplasmic domains. COS7 cells transfected with the cDNA expressed a approximately 60-kD protein and bound IL-5 with a single class of affinity (Kd = 250-590 pM). The Kd values were similar to that observed in normal human eosinophils. In contrast to the murine 60-kD alpha chain, which binds IL-5 with low affinity (Kd = approximately 10 nM), the human alpha chain homologue can bind IL-5 with much higher affinity by itself. RNA blot analysis of human cells demonstrated two transcripts (approximately 5.3 and 1.4 kb). Both of them were expressed in normal human eosinophils and in erythroleukemic cell line TF-1, which responds to IL-5. The human IL-5 receptor characterized in this paper is essential for signal transduction, because expression of this molecule in murine IL-3-dependent cell line FDC-P1 allowed these cells to proliferate in response to IL-5.
Role of alendronate in therapy for posttraumatic complex regional pain syndrome type I of the lower extremity (2004)

Our findings support the use of oral alendronate in posttraumatic CRPS I. By reducing local acceleration of bone remodeling, alendronate might relieve pain by effects on nociceptive primary afferents in bone, pain-associated changes in the spinal cord, and possibly also through a central mechanism.
Applying wavelet analysis to speech segmentation and classification (1994)

We propose the design of a hearing aid based on the wavelet transform. The fast wavelet transform is used to decompose speech into different frequency components. This paper presents the difficulties in the use of wavelet transforms for speech processing and shows how the careful selection of wavelet coefficients can enable the four major categories of speech - voiced speech, plosives, fricatives, and silence - to be identified. With knowledge of these four categories, it is shown how speech can be easily and effectively segmented.
Inorganic Phosphorus Homeostasis during the First Hour of Dialysis (2011)

Unchanged P(ERY) concentration during the first hour of an HD session does not reject the hypothesis of a simultaneous efflux and influx of phosphorus from/to intracellular compartment.
Optical coherence tomography implemented by photonic crystal fiber (2005)

We report a fabricated photonic crystal fiber (PCF) coupler, which has a rather flat coupling ratio over a 400 nm spectral range and enabled a 3-/spl mu/m resolution. It might enable a white-light as the source for biological samples.
Modular Assembly of Glycoproteins: Towards the Synthesis of GlyCAM‐1 by Using Expressed Protein Ligation (2004)

Put the two together: Physiologically relevant glycoproteins containing saccharides at predetermined sites, such as GlyCAM-1, can be generated from small synthetic and bacterially derived fragments by using the expressed protein ligation methodology. This technique was used for the synthesis of three semisynthetic GlyCAM-1 variants 1–3 (see scheme). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z52673_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Association of the phosphatase and tensin homolog gene (PTEN) with smoking initiation and nicotine dependence (2005)

Since PTEN (phosphatase and tensin homolog) has elevated expression in rat brain (amygdala) after chronic administration of nicotine and the PTEN gene is located in the vicinity of the chromosome 10q23 linkage peak in a genome-scan study of nicotine dependence, PTEN seems a plausible candidate gene for smoking behavior. To test this hypothesis, we use a three-group case-control design and genotype five SNPs in the PTEN gene. We compare allele and genotype frequencies between the smokers and nonsmokers and between the low nicotine dependent and high nicotine dependent subjects. Three SNPs in the PTEN gene are significantly associated with smoking initiation (rs1234221, P = 0.0311; rs1234213, P = 0.0002; and rs2735343, P = 0.0028). Rs1234213 also shows association with nicotine dependence (P = 0.0278). Haplotype analyses indicate that a major haplotype, 1-1-2-2-1 for rs1234221-rs2299939-rs1234213-rs2735343-rs70184, is associated with smoking initiation. A minor haplotype (about 3%), 1-2-2-2-1 for the same five SNPs, is observed only in the high nicotine dependence group. These results suggest that the PTEN gene may be involved in the etiology of both smoking initiation and nicotine dependence.
Development and current status of the CHARMM force field for nucleic acids (2000)

The CHARMM27 all-atom force field for nucleic acids represents a highly optimized model for investigations of nucleic acids via empirical force field calculations. The force field satisfactorily treats the A, B, and Z forms of DNA as well as RNA, and it also useful for nucleosides and nucleotides. In addition, it is compatible with the CHARMM force fields for proteins and lipids, allowing for simulation studies of heterogeneous systems.
Rapid plasmid library screening using RecA-coated biotinylated probes. (1986)

A method for the rapid physical isolation of recombinant plasmids of interest from a mixture of plasmids such as a plasmid cDNA library is presented. This method utilizes the ability of RecA protein to form stable complexes between linear single-stranded and circular double-stranded DNA molecules sharing sequence homology, and procedures allowing isolation of biotinylated nucleic acid. Biotinylated linear DNA probes coated with RecA have been used to screen reconstituted plasmid libraries consisting of two plasmid species, one homologous and the other heterologous to the probe. When the link between biotin and the nucleotide base could be cleaved by reducing agents, the complex was purified by streptavidin-agarose chromatography and the recovered plasmid was propagated in Escherichia coli. When the link was not cleavable the complex was bound to avidin in solution and purified by cupric iminodiacetic acid-agarose chromatography. The complex was then dissociated and the plasmids were propagated in E. coli. With either protocol, homologous plasmid recovery was between 10% and 20%, and enrichment was between 10(4)- and 10(5)-fold. Potential applications and extensions of this method, such as plasmid, cosmid, and phage library screening and facilitation of physical mapping of macroregions of mammalian genomes are presented and discussed.
Birthplace and Classic Kaposi's Sarcoma in Italy (1995)

Journal Article Birthplace and Classic Kaposi's Sarcoma in Italy Get access Marco Geddes, Marco Geddes 1Servizio di Epidemiologia Descrittiva Valutativa e di Cancerogenesi Ambientale, Sezione Dell'ISTFirenze, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar Silvia Franceschi, Silvia Franceschi 2Servizio di Epidemiologia, Centro di Riferimento OncologicoAviano, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar Daniela Balzi, Daniela Balzi 3Unità Operativa di Epidemiologia, Servizio Multizonale di Prevenzione OncologicaFirenze Search for other works by this author on: Oxford Academic PubMed Google Scholar Stefania Arniani, Stefania Arniani 1Servizio di Epidemiologia Descrittiva Valutativa e di Cancerogenesi Ambientale, Sezione Dell'ISTFirenze, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar LOrenzo Gafà, LOrenzo Gafà 4Registro Tmori RagusaItaly Search for other works by this author on: Oxford Academic PubMed Google Scholar Roberto Zanetti Roberto Zanetti * 5Registro Tumori per il Piemonte e la Valle d' Aosta, Ospedale S. Giovanni Antica SedeTorino, Italy * Correspondence to: Silvia Franceschi, M.D., Servizio di Epidemiologia, Centro di Riferimento Oncologico, Via Pedemontana Occ., 33081 Aviano(PN), Italy. Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 87, Issue 13, 5 July 1995, Pages 1015–1017, https://doi.org/10.1093/jnci/87.13.1015 Published: 05 July 1995
Cloning of MITF, the human homolog of the mouse microphthalmia gene and assignment to chromosome 3p14. 1-p12.3 (1994)

The mouse microphthalmia (mi) gene encodes a basic-helix-loop-helix-zipper protein whose mutations may lead to loss of pigmentation in the eye, inner ear and skin, and to reduced eye size and early onset deafness. Mice with mutations at mi serve as models for human pigment disturbances in skin and eye that may be combined with sensorineural deafness. We have now obtained cDNA and genomic clones of the human homolog of mouse mi, identified a restriction fragment length polymorphism in the gene, and mapped the gene by somatic cell hybrid and fluorescence in situ hybridization techniques to a region of human chromosome 3 that shows a disrupted syntenic conservation with the region on mouse chromosome 6 to which mi maps. These studies will help to verify if any of the hereditary pigment disturbances in humans are due to mutations in this gene.
Disruptive Technology and Common Law Lawmaking: A Brief Analysis of A&M Records, Inc. v. Napster, Inc. (2002)

This symposium Article analyzes the Ninth Circuit's decision in AM (2) the court's treatment of vicarious liablility for copyright infringement is doctrinally incoherent because it suggests that liability depends on whether a third party has turn[ed] a blind eye toward infringement or has exercised its supervisory power over the infringer to the fullest extent; and (3) the court's choice to sidestep analysis of the service provider safe harbors in Section 512 of the Copyright Act should have been better explained but was understandable given the state of the record.
Biosynthesis and Assembly of Capsular Polysaccharides in Escherichia coli (2006)

Capsules are protective structures on the surfaces of many bacteria. The remarkable structural diversity in capsular polysaccharides is illustrated by almost 80 capsular serotypes in Escherichia coli. Despite this variation, the range of strategies used for capsule biosynthesis and assembly is limited, and E. coli isolates provide critical prototypes for other bacterial species. Related pathways are also used for synthesis and export of other bacterial glycoconjugates and some enzymes/processes have counterparts in eukaryotes. In gram-negative bacteria, it is proposed that biosynthesis and translocation of capsular polysaccharides to the cell surface are temporally and spatially coupled by multiprotein complexes that span the cell envelope. These systems have an impact on both a general understanding of membrane trafficking in bacteria and on bacterial pathogenesis.
Electrowetting of liquid marbles (2006)

Electrowetting of water drops on structured superhydrophobic surfaces are known to cause an irreversible change from a slippy (Cassie-Baxter) to sticky (Wenzel) regime. An alternative approach to using a water drop on a super-hydrophobic surface to obtain a non-wetting system is to use a liquid marble on a smooth solid substrate. A liquid marble is a droplet coated in hydrophobic grains, which therefore carries its own solid surface structure as a conformal coating. Such droplets can be considered as perfect non-wetting systems having contact angles to smooth solid substrates of close to 180 o . In this work we report the electrowetting of liquid marbles made of water coated with hydrophobic Lycopodium grains and show that the electrowetting is completely reversible. Marbles are shown to return to their initial contact angle for both ac and dc electrowetting and without requiring a threshold voltage to be exceeded. Furthermore, we provide a proof-of-principle demonstration that controlled motion of marbles on a finger electrode structure is possible.
Genetic analysis of microcin H47 antibiotic system (1993)

The microcin H47 genetic determinants span a DNA region of ca. 10 kb and represent the first description of an enterobacterial antibiotic system located in the chromosome of the producing strain. Transcriptional and translational fusions to lacZ showed a complex transcriptional organization of the microcin H47 system. Complementation tests identified six genes that are necessary for the production of the antibiotic; the products of two of them are involved in the export of microcin to the extracellular medium. The immunity determinant was located in an 0.8-kb DNA fragment. There is a putative "silent region" of ca. 3 kb inside the system that could not be clearly related to any antibiotic function. Protein products were identified and assigned to three production genes and also to a gene from the silent region.
Effects of Gastric Inhibitory Polypeptide on Glucose and Lipid Metabolism of Isolated Rat Adipocytes (1988)

The effects of gastric inhibitory polypeptide (GIP) on glucose and lipid metabolism of isolated rat adipocytes were investigated. In a dose-dependent manner, GIP stimulated 2-deoxy-glucose uptake increasing the glucose transport rate by up to 140% at a concentration of 10(-7) mol/l. GIP also stimulated the conversion of 14C-glucose into extractable lipids by up to 81% at 10(-7) mol/l. Insulin-stimulated 2-deoxy-glucose uptake and lipogenesis were additively enhanced by the presence of GIP. Insulin binding was slightly but not significantly increased by addition of GIP, mainly due to an increase in receptor affinity. GIP had a weak lipolytic activity, but lipolysis elicited by glucagon or isoproterenol was potently reduced. In conclusion, independent of its insulinotropic action, GIP showed a insulin-like activity on glucose metabolism and lipolysis in rat adipose tissue. The possible role of GIP for the development of obesity is discussed.
Optical Bedside Monitoring of Cerebral Blood Flow in Acute Ischemic Stroke Patients During Head-of-Bed Manipulation (2014)

A lower HOB angle results in an increase in cortical CBF without a significant change in arterial flow velocity in AIS, but there is variability across patients in this response. Bedside CBF monitoring with diffuse correlation spectroscopy provides a potential means to individualize interventions designed to optimize CBF in AIS.