gebhart/patrepeval huggingface dataset:
Determinants of Gliadin-Specific T Cell Selection in Celiac Disease (2015)

In HLA-DQ8-associated celiac disease (CD), the pathogenic T cell response is directed toward an immunodominant α-gliadin-derived peptide (DQ8-glia-α1). However, our knowledge of TCR gene usage within the primary intestinal tissue of HLA-DQ8 (+) CD patients is limited. We identified two populations of HLA-DQ8-glia-α1 tetramer(+) CD4(+) T cells that were essentially undetectable in biopsy samples from patients on a gluten-free diet but expanded rapidly and specifically after antigenic stimulation. Distinguished by expression of TRBV9, both T cell populations displayed biased clonotypic repertoires and reacted similarly against HLA-DQ8-glia-α1. In particular, TRBV9 paired most often with TRAV26-2, whereas the majority of TRBV9(-) TCRs used TRBV6-1 with no clear TRAV gene preference. Strikingly, both tetramer(+)/TRBV9(+) and tetramer(+)/TRBV9(-) T cells possessed a non-germline-encoded arginine residue in their CDR3α and CDR3β loops, respectively. Comparison of the crystal structures of three TRBV9(+) TCRs and a TRBV9(-) TCR revealed that, as a result of distinct TCR docking modes, the HLA-DQ8-glia-α1 contacts mediated by the CDR3-encoded arginine were almost identical between TRBV9(+) and TRBV9(-) TCRs. In all cases, this interaction centered on two hydrogen bonds with a specific serine residue in the bound peptide. Replacement of serine with alanine at this position abrogated TRBV9(+) and TRBV9(-) clonal T cell proliferation in response to HLA-DQ8-glia-α1. Gluten-specific memory CD4(+) T cells with structurally and functionally conserved TCRs therefore predominate in the disease-affected tissue of patients with HLA-DQ8-mediated CD.
Sequence analysis of a cDNA clone encoding the liver cell adhesion molecule, L-CAM. (1987)

The liver cell adhesion molecule (L-CAM) appears on non-neural epithelial tissues and mediates calcium-dependent adhesion in these tissues both in the embryo and in the adult. It appears on cell surfaces as a glycoprotein of Mr 124,000 but is synthesized as a precursor of Mr 135,000. We have isolated and determined the nucleic acid sequence of a cDNA clone (lambda L320) encoding chicken L-CAM. The 5' end of this clone has an open reading frame extending for 2520 base pairs, followed by an 850-base-pair untranslated region terminating with a polyadenylylation site at its 3' end. Protein sequence analysis of intact L-CAM and of cyanogen bromide fragments of the protein confirmed the reading frame and indicated that lambda L320 encodes the complete sequence of L-CAM as it is expressed on the cell surface as well as the bulk of the precursor. The sequence includes a hydrophobic segment of 31 amino acids, supporting our earlier conclusion that L-CAM is an intrinsic membrane protein. There are five potential asparagine glycosylation sites on the extracellular part of the molecule and an intracellular domain that is phosphorylated in vivo. The mature L-CAM polypeptide consists of 727 amino acids, with a calculated Mr of 79,900 for the carbohydrate-free protein. The L-CAM sequence is not homologous to other known protein sequences, including those of the neural cell adhesion molecule (N-CAM) and other members of the immunoglobulin superfamily, but the L-CAM molecule does contain three contiguous segments (113 amino acids each) that are homologous to each other. The similarities among these segments suggest that at least part of the L-CAM molecule arose by gene duplication.
Soil type affects accuracy of dielectric moisture sensors (2000)

Several types of dielectric soil moisture sensors were evaluated at various locations in California. The TRASE and ThetaProbe devices were reasonably accurate over a range of soil textures. In silt loam and silty clay soil types, the Enviroscan readings were inaccurate. The Aquaterr meter, which provides a qualitative measurement of soil moisture content, responded to changes in soil moisture content for several different soils, but little response occurred in one sandy soil.
Virtual machine migration planning in software-defined networks (2015)

Live migration is a key technique for virtual machine (VM) management in data center networks, which enables flexibility in resource optimization, fault tolerance, and load balancing. Despite its usefulness, the live migration still introduces performance degradations during the migration process. Thus, there has been continuous efforts in reducing the migration time in order to minimize the impact. From the network's perspective, the migration time is determined by the amount of data to be migrated and the available bandwidth used for such transfer. In this paper, we examine the problem of how to schedule the migrations and how to allocate network resources for migration when multiple VMs need to be migrated at the same time. We consider the problem in the Software-defined Network (SDN) context since it provides flexible control on routing. More specifically, we propose a method that computes the optimal migration sequence and network bandwidth used for each migration. We formulate this problem as a mixed integer programming, which is NP-hard. To make it computationally feasible for large scale data centers, we propose an approximation scheme via linear approximation plus fully polynomial time approximation, and obtain its theoretical performance bound. Through extensive simulations, we demonstrate that our fully polynomial time approximation (FPTA) algorithm has a good performance compared with the optimal solution and two state-of-the-art algorithms. That is, our proposed FPTA algorithm approaches to the optimal solution with less than 10% variation and much less computation time. Meanwhile, it reduces the total migration time and the service downtime by up to 40% and 20% compared with the state-of-the-art algorithms, respectively.
INTRINSIC REGISTRATION TECHNIQUES FOR MEDICAL IMAGES: A STATE-OF-THE-ART REVIEW (2016)

Medical image registration is the process of mapping two or more medical images into a single more informative image for the purpose of receiving precise and complementary information. The precise mapping of medical images obtained in different time- frames and by the same or different modalities is now possible due to the availability of large number of registration techniques. The purpose of this paper is to present and analyse intrinsic registration techniques for medical imaging in a comprehensive manner. Our approach of analysis is unique from already published work because we have performed detailed investigation on each registration techniques, and analyse similarity measures and assessments according to various parameters. The knowledge on the work that has been developed in the area is presented in a compact form. This work is expected to provide a useful platform for the researchers in the field of medical image registration in general and in intrinsic registration in particular.
Scalability issues for mass multimedia storage systems (1996)

The storage and bandwidth requirements of digital video and audio exceed those that can be supported by conventional file servers. Despite the emergence of new compression algorithms capable of providing extremely high compression ratios, there is still a challenge to provide optimised storage services capable of storing 1000s of hours of multimedia data and providing simultaneous access to hundreds and potentially thousands of clients. A number of prototype multimedia storage devices have been designed and built to address the real-time demands of digital video and audio1,9. These systems use RAID (Redundant Arrays of Inexpensive Disks) technology to increase the bandwidth and storage capacities of single disks. Unfortunately, RAID is non-scalable10 (i.e. disks cannot be incrementally added to provide higher bandwidth and storage facilities) and can prove to be a bottleneck in the system. This server bottleneck only becomes significant when the aggregate disk bandwidth of RAID increases beyond either the network interface or the server CPU / bus speed. Once this occurs the available storage and bandwidth can only be increased by introducing more RAID servers and introducing a load balancing policy where client requests can be shared across multiple server instances. This paper describes a Scalable Multimedia Storage Architecture (SMSA) that supports wide area storage, storage server scalability allowing the addition of extra storage nodes, and maximised available data streams through the use of the load balancing techniques of network striping / file replication. It also allows for the storage of multi-resolution data produced by scalable compression techniques to match the Quality of Service requirements of heterogeneous clients.
The <i>Saccharomyces cerevisiae</i> Ku Autoantigen Homologue Affects Radiosensitivity Only in the Absence of Homologous Recombination (1996)

In mammalian cells, all subunits of the DNA-dependent protein kinase (DNA-PK) have been implicated in the repair of DNA double-strand breaks and in V(D)J recombination. In the yeast Saccharomyces cerevisiae, we have examined the phenotype conferred by a deletion of HDF1, the putative homologue of the 70-kD subunit of the DNA-end binding Ku complex of DNA-PK. The yeast gene does not play a role in radiation-induced cell cycle checkpoint arrest in G1 and G2 or in hydroxyurea-induced checkpoint arrest in S. In cells competent for homologous recombination, we could not detect any sensitivity to ionizing radiation or to methyl methanesulfonate (MMS) conferred by a hdf1 deletion and indeed, the repair of DNA double-strand breaks was not impaired. However, if homologous recombination was disabled (rad52 mutant background), inactivation of HDF1 results in additional sensitization toward ionizing radiation and MMS. These results give further support to the notion that, in contrast to higher eukaryotic cells, homologous recombination is the favored pathway of double-strand break repair in yeast whereas other competing mechanisms such as the suggested pathway of DNA-PK-dependent direct break rejoining are only of minor importance.
Integral ratio: a new class of global thresholding techniques for handwriting images (1999)

We propose a class of histogram based global thresholding techniques called integral ratio. They are designed to threshold gray-scale handwriting images and separate the handwriting from the background. The following tight requirements must be met: 1) all the details of the handwriting are to be retained, 2) the writing paper used may contain strong colored and/or patterned background which must be removed, and 3) the handwriting may be written using a wide variety of pens such as a fountain pen, ballpoint pen, or pencil. A specific application area which requires these tight requirements is forensic document examination, where a handwritten document is often considered as legal evidence and the handwriting must not be tampered with or modified in any way. The proposed class of techniques is based on a two stage thresholding approach requiring each pixel of a handwritten image to be placed into one of three classes: foreground, background, and a fuzzy area between them where it is hard to determine whether a pixel belongs to the foreground or the background. Two techniques, native integral ratio (NIR) and quadratic integral ratio (QIR), were created based on this class and tested against two well-known thresholding techniques: Otsu's (1979) technique and the entropy thresholding technique. We found that QIR has superior performance compared to all the other techniques tested.
Experimental Caries in Man (1970)

The purpose of the present study was to develop a method for short-term caries trials in man, using an experimental model already employed in periodontal research. Twelve students were given prophylaxis and instruction to practice meticulous oral hygiene until Plaque Index and Gingival Index approached zero. The carious state of the bucco-gingival enamel areas, excluding molars, was evaluated using a dissection microscope. The cleaned and dried tooth surfaces were scored according to the Caries Index system. During a period of 23 days without oral hygiene 6 participants performed 9 daily mouthrinses with 10 ml of a 50% sucrose solution. At the termination of this period the sucrose group demonstrated a higher mean Caries Index and a greater number of new early lesions than the six control subjects. The mean Plaque Index scores were higher in the sucrose group, whereas the Gingival Index scores were similar for both groups. Smears of plaque showed no significant differences in the percentage distribution of various types of microorganisms. After 30 days of oral hygiene and daily mouthrinses with 0.2 % NaF, fair agreement was found between the Caries Index scores of the two groups. Similar observations were made after a second hygiene and fluoride period. The results demonstrate that it is possible to produce detectable carious alterations within 23 days by abolishment of oral hygiene and frequent sucrose additions and that these alterations are reversible.
Amended Nomenclature for Strains Related to Mycoplasma laidlawii (1970)

SUMMARY: In an earlier paper it was proposed that a second family be re-established within the Mycoplasmatales for those strains not requiring sterol, and the nomenclature of Sabin, who first made this proposal, was followed in the belief that although unsuitable it was valid. It has now been learnt that the generic name Sapromyces is illegitimate, as it is the name of a genus of fungi. It is therefore proposed that the genus be named Acholeplasma in the family Acholeplasmataceae.
Graphene-nickel cobaltite nanocomposite asymmetrical supercapacitor with commercial level mass loading (2012)

A high performance asymmetric electrochemical supercapacitor with a mass loading of 10 mg·cm−2 on each planar electrode has been fabricated by using a graphene-nickel cobaltite nanocomposite (GNCC) as a positive electrode and commercial activated carbon (AC) as a negative electrode. Due to the rich number of faradaic reactions on the nickel cobaltite, the GNCC positive electrode shows significantly higher capacitance (618 F·g−1) than graphene-Co3O4 (340 F·g−1) and graphene-NiO (375 F·g−1) nanocomposites synthesized under identical conditions. More importantly, graphene greatly enhances the conductivity of nickel cobaltite and allows the positive electrode to charge/discharge at scan rates similar to commercial AC negative electrodes. This improves both the energy density and power density of the asymmetric cell. The asymmetric cell composed of 10 mg GNCC and 30 mg AC displayed an energy density in the range of 19.5 Wh·kg−1 with an operational voltage of 1.4 V. At high sweep rate, the system is capable of delivering an energy density of 7.6 Wh·kg−1 at a power density of about 5600 W·kg−1. Cycling results demonstrate that the capacitance of the cell increases to 116% of the original value after the first 1600 cycles due to a progressive activation of the electrode, and maintains 102% of the initial value after 10000 cycles.
Interfacial Tension of Methylbenzene–Water in the Presence of Hydrophilic and Hydrophobic Alumina Nanoparticles at Different Temperatures (2013)

The effect of almost low concentrations of alumina hydrophilic (bare surface) and hydrophobic (modified surface with hexadecanoic acid) nanoparticles on interfacial tension of methylbenzene (toluene)–water was investigated based on experimental results from drop weight tensiometry. Nanoparticles were suspended in either aqueous or organic phases to provide a stable nanofluid and then were contacted with another phase to measure the interfacial tension. A nanoparticle mass fraction range of 1·10–5 to 5·10–4 (± 5·10–6) and a temperature range of [293.2 to 323.2 (± 0.1)] K were used. Interesting trends of interfacial tension variation were revealed with nanoparticles concentration, showing a sharp increase up to 55.7 mN·m–1 (± 0.1 mN·m–1) at 293.2 K, and a decrease to about 14.0 mN·m–1 at 323.2 K with hydrophilic and hydrophobic forms, respectively. The effect of increasing temperature was found to reduce interfacial tension within the used ranges and significantly higher with hydrophilic nanoparticles.
Sol–gel synthesis and electrochemical properties of fluorophosphates Na2Fe1−xMnxPO4F/C (x = 0, 0.1, 0.3, 0.7, 1) composite as cathode materials for lithium ion battery (2011)

Fluorophosphates Na2Fe1−xMnxPO4F/C (x = 0, 0.1, 0.3, 0.7, 1) composite were successfully synthesized via a sol–gel method. The structure, morphology and electrochemical performance of the as prepared materials were studied by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and charge/discharge measurements. XRD results show that, consistent with Na2FePO4F, Na2Fe0.9Mn0.1PO4F (x = 0.1) crystallize in a two-dimensional (2D) layered structure with space groupPbcn. However, increasing the content of Mn to x ≥ 0.3 results in a structure transition of Na2Fe1−xMnxPO4F from the 2D layered structure of Na2FePO4F to the three-dimensional (3D) tunnel structure of Na2MnPO4F. SEM and TEM analysis indicates nanostructured primary particles (about tens of nanometres in diameter) are obtained for all samples due to uniform carbon distribution and low calcining temperature used. Na2FePO4F is able to deliver a reversible capacity of up to 182 mA h g−1 (about 1.46 electrons exchanged per unit formula) with good cycling stability. Compared with Na2FePO4F, partial replacement of Fe by Mn in Na2Fe1−xMnxPO4F increases the discharge voltage plateau. Similar to Na2FePO4F, iron-manganese mixed solid solution Na2Fe1−xMnxPO4F (x = 0.1, 0.3, 0.7) also show good cycling performance. Furthermore, Na2MnPO4F with high electrochemical activity was successfully prepared for the first time, which is able to deliver a discharge capacity of 98 mA h g−1. The good electrochemical performance of Na2Fe1−xMnxPO4F materials can be attributed to the distinctive improvement of ionic/electronic conduction of the materials by formation of nanostructure composite with carbon.
PICmicro Microcontroller Pocket Reference (2000)

From the Publisher:
Designed to complement Programming & Customizing the PICMICRO,this book contains a minimum of verbiage and serves as an immediate device,code and circuit lookup for experienced PICMICRO applications designers. 
Device,code,and circuit data on one of the most popular microcontrollers aroundit's in your pocket with this guide. You'll never again get stuck in the World Wide Wait or shuffle through coffee-stained printouts,looking for the facts you need. Used alone or with Myke Predko's Programming and Customizing the PIC Microcontroller,this data source saves you from searching for:
*Complete pin-out mappings
*Device feature comparisons
*Processor instructions
*Multi-tier data tables
*Frequently used code snippets
*Clock tables
*Power consumption tables
*Debugging hints
*Common external device interfaces with sample code
*Other handy data Short on verbiage,and long on facts,this is the ideal data tool for the experienced applications designer.
The stability of the hydronium tetrafluoroborate dimer determined by theoretical calculations. Implications for water protonation in nonpolar solvents and on solid acids (2000)

Upon geometry optimization with no constraints (MP2/6-31G*), hydronium fluoroborate decomposed, but the dimer (H3O+·BF4−)2 was stable. In the dimer, the anions face each other and create a cavity containing the two cations. Density functional theory calculations (B3LYP/6-31G* to /6-31++G**) gave somewhat different arrangements of clusters and ion geometries. The MP2/6-31G* geometry was symmetrical, with a boron to boron distance of 4.650 Å and the closest interionic fluorine to fluorine distance of 2.783 Å. Hydrogen bonds connect ions of opposite sign. Two groups of equivalent hydrogens generate an AX2-type 1H NMR spectrum, as found for a hydronium salt in Freon solution; dimeric clusters should also be present in nonpolar solvents. In concentrated aqueous solution, however, the 17O NMR spectrum indicates the presence of ion pairs. The double cluster is stable at B···B distances of 5.00, 5.50 and 6.00 Å (F···F distances of 3.10, 3.91 and 4.55 Å), but decomposes to a solvated ion pair at B···B of 6.50 Å. Cooperation of acid sites inside porous solids should also facilitate water protonation, to form double anion–hydronium ion clusters. Whether sites of equal strength protonate water at stoichiometric ratio depends upon the channel size and disposition of sites in it. The expectation of narrowly defined spectral properties for protonated water in solid acids is not warranted. The protonating ability is determined by intrinsic strength, distance between, and relative orientation of sites.
Network cycle features: Application to computer-aided Gleason grading of prostate cancer histopathological images (2011)

Features extracted from cell networks have become popular tools in histological image analysis. However, existing features do not take sufficient advantage of the cycle structure present within the cell networks. We introduce a new class of network cycle features that take advantage of such structures. We demonstrate the utility of these features for automated prostate cancer scoring using histological images. Prostate cancer is commonly scored by pathologists using the Gleason grading system and our automated system based upon network cycle features serves an important need in making this process less labor-intensive and more reproducible. Our system first extracts the cells from the histological images, computes networks from the cell locations and then computes features based upon statistics for the different cycles present in these networks. Using an SVM (Support Vector Machine) classifier on these features, we demonstrate the efficacy of our system in distinguishing between grade 3 and grade 4 prostate tumors. We also show the superiority of our approach over previously developed systems for this problem based upon texture features, fractal features and alternative network features.
In situ hybridization for procollagen types I, III and IV mRNA in normal and fibrotic rat liver: Evidence for predominant expression in nonparenchymal liver cells (1989)

The expression of alpha 2(I), alpha 1(III) and alpha 1(IV) procollagen mRNA was analyzed in normal and CCl4-induced fibrotic rat liver by in situ hybridization using RNA probes. In normal liver, moderate amounts of alpha 2(I) and alpha 1(III) procollagen transcripts were found in sinusoidal cells, in stromal cells of the portal tracts and in the vicinity of central veins, whereas a1(IV) procollagen gene expression was below the threshold of detection. After 2 weeks of CCl4 treatment, increased transcription of alpha 2(I) and alpha 1(III) procollagen genes was observed in sinusoidal cells. At this stage, alpha 1(IV) procollagen mRNA was detectable in the same cell types and localization as alpha 2(I) and alpha 1(III) procollagen transcripts, although with a weaker signal. After 4 weeks, newly formed fibrous septa showed many cells intensely labeled by alpha 2(I), alpha 1(III) and alpha 1(IV) procollagen probes. Neither in normal liver nor at any stage of fibrosis was any hybridization signal above background observed in hepatocytes. These patterns suggest that in the liver Type I, Type III and Type IV procollagen expression takes place predominantly in nonparenchymal cells. Therefore, hepatocytes do not appear to be significantly involved in procollagen production in this experimental model of liver fibrosis.