gebhart/patrepeval huggingface dataset:
Cistrome: an integrative platform for transcriptional regulation studies (2011)

The increasing volume of ChIP-chip and ChIP-seq data being generated creates a challenge for standard, integrative and reproducible bioinformatics data analysis platforms. We developed a web-based application called Cistrome, based on the Galaxy open source framework. In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery. Cistrome is available at http://cistrome.org/ap/.
Optimal Search Engine Marketing Strategy (2005)

Buyers using search engines to look for information tend to trust and follow links displayed in the editorial section of the search-results page. Most on-line sellers, however, do not invest in search engine optimization (SEO) to get higher search-results rankings for their listings, but instead prefer paid placements. They explain that SEO is more expensive than paid placements, produces results that do not justify its cost, and does not consistently lead to high search-results rankings. This implies that sellers would invest in SEO if it were less expensive and its rankings were more consistent. However, even if SEO and paid placement cost the same, and SEO always produced high rankings, paid placement would still be the search engine marketing (SEM) strategy of choice for most on-line sellers. Interestingly, no optimal SEM strategy includes SEO. These findings are especially significant for advertising professionals who have to justify investing in paid placements despite overwhelming evidence that buyers ignore them and follow links in the editorial section of the search-results page.
Plasticity of Adult Human Pancreatic Duct Cells by Neurogenin3-Mediated Reprogramming (2012)

The results provide further insight into the plasticity of adult human duct cells and suggest measurable routes to enhance Ngn3-mediated in vitro reprogramming protocols for regenerative beta cell therapy in diabetes.
Conjugated Linoleic Acid Isomers and Mammary Cancer Prevention (2002)

Abstract There is increasing evidence that individual isomers of conjugated linoleic acid (CLA) may have unique biological or biochemical effects. A primary objective of this study was to determine whether there might be differences in the anticancer activity of 9,11-CLA and 10,12-CLA. This was achieved by evaluating the reduction in premalignant lesions and carcinomas in the mammary gland of rats that had been treated with a single dose of methylnitrosourea and given 0.5% of either highly purified CLA isomer in the diet. Our results showed that the anticancer efficacies of the two isomers were very similar. At 6 wk after carcinogen administration, the total number of premalignant lesions was reduced by 33-36%. At 24 wk, the total number of mammary carcinomas was reduced by 35-40%. The concentration of each CLA isomer and its respective metabolites was analyzed in the mammary fat pad. Tissue level of 10,12-CLA was much lower than that of 9,11-CLA. The pool of metabolites from each isomer was very similar between the two groups and represented only a small fraction of total conjugated diene fatty acids. Feeding of 9,11-CLA resulted in minimal changes in other unsaturated fatty acids. In contrast, feeding of 10,12-CLA produced a wider spectrum of perturbations. Small but significant increases in 16:1 and 16:2 were detected; these were accompanied by decreases in 20:2, 20:3, 20:4, 22:4, and 22:6. The above observation suggests that 10,12-CLA might be more potent than 9,11-CLA in interfering with elongation and desaturation of linoleic and linolenic acids. In summary, our study showed that, at the 0.5% dose level, the anticancer activity of 9,11-CLA and 10,12-CLA was very similar, even though accumulation of 10,12-CLA in the mammary tissue was considerably less than that of 9,11-CLA. These confounding changes of the other unsaturated fatty acids in contributing to the effect of 10,12-CLA need to be clarified.
The low-density parity-check codes based on The n-queen problem (2004)

This paper presents a new family of low-density parity-check (LDPC) code, the sparse parity-check matrix of which is constructed by self-defining non-diagonal identity sub-matrix that is a solution of the "n-queen problem". So this sub-matrix is called the Q-matrix and these LDPC codes are called the Q-matrixes LDPC codes. The Q-matrixes LDPC codes are good or very good codes with iterative decoding and their Tanner graphs are free of 4-lines cycle. Furthermore, they can be created in cycle form. Their encoding can be achieved in linear time. Especially, their code length and code rate can be flexible and quickly adjusted according to the practical situation, and the performance of high rate is also very good. The other unique excellence is that the large sparse parity-check matrixes of long Q-matrixes LDPC codes require very small storage space. The result of this paper is very significant not only for designing low complexity encoder, improving performance and reducing the complexity of the sum-product iterative decoding algorithm, but also for building practice system of encodable and decodable LDPC code.
HPV testing as a screen for cervical cancer (2015)

Human papillomavirus (HPV) has been identified as a necessary factor in the development of pre-invasive and invasive cancers of the lower genital tract, of which cervical cancer is the most prevalent. A molecular understanding of malignant transformation and epidemiologic information has led to the development of many strategies for detection and early intervention. Newer tests for oncogenic subtypes of HPV have made it possible to predict the risk of future development of cervical cancer. This review summarizes the current understanding of HPV related disease and examines the role of HPV testing as a screening tool for cervical cancer. It summarizes the data from prospective and randomized controlled trials on HPV screening from Europe and North America and includes smaller studies from low and middle income countries where cervical cancer is the most common cancer in women.
On Scaling Up Balanced Clustering Algorithms (2002)

1 Introduction The past few years have witnessed a growing interest in clustering algorithms that are suitable for data-mining problems [15, 14, 9]. Clustering algorithms for data-mining problems must be extremely scalable. In addition, several data mining applications demand that the clusters obtained be balanced, i.e., be of approximately the same size or importance. There are several notable approaches that address the scalability issue. Some approaches try to build the clusters dynamically by maintaining sufficient statistics and other summarized information in main memory while minimizing the number of database scans involved. For example, Bradley et al. [4, 5] propose out-of-core methods that scan the database once to form a summarized model (for instance, the size, sum and sum-squared values of potential cluster, and well as a small number of unallocated data-points) in main memory. Subsequent refinement based on this summarized information is then restricted to main memory operations without resorting to further disk scans. Another method with a similar flavor [24] compresses the data objects into many small subclusters using modified index trees and performs clustering with these subclusters. A different approach is to subsample the original data before applying the actual clustering algorithms [6, 12]. Ways of effectively sampling large datasets have also been proposed [20]. A recent work [8] suggests using less number of points in each step of an iterative relocation optimization algorithm like k-means as long as the model produced does not differ significantly from the one that would be obtained with full data.
Adaptive Statistical Iterative Reconstruction Technique for Radiation Dose Reduction in Chest CT: A Pilot Study (2011)

http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.11101450/-/DC1.
Improving the operation of distribution substations (2002)

This paper presents examples of a completely integrated control and protection system used to implement and improve process automation, maintenance automation, information management, and information distribution. Specific examples explored include improving transformer operations by pre-cooling for capacity improvement, time-to-trip on overload, and delta-VAr control for parallel banks between local and remote buses; automatic SAIDI/SAIFI reporting; integrating fault reports; and dynamic settings group/protection scheme changes.
Suppressive Effect of Saturated Acyl <scp>l</scp>-Ascorbate on the Oxidation of Linoleic Acid Encapsulated with Maltodextrin or Gum Arabic by Spray-Drying (2002)

6-O-Palmitoyl L-ascorbate was added to linoleic acid at various molar ratios of the ascorbate to the acid, the mixtures were emulsified with a maltodextrin or gum arabic solution, and the emulsions were spray-dried to produce microcapsules. At higher molar ratios, the oil droplets in the emulsions were smaller, and the oxidative stabilities of the encapsulated linoleic acid were higher for both the maltodextrin- and gum arabic-based microcapsules. 6-O-Capryloyl, caproyl, and lauroyl L-ascorbates, which were synthesized through lipase-catalyzed condensation in acetone, were also used for the microencapsulation of linoleic acid. Except for capryloyl L-ascorbate, the addition of a saturated acyl ascorbate, especially caproyl ascorbate, to linoleic acid was effective for preparing oil droplets of small particle diameter and for suppressing the oxidation of the encapsulated linoleic acid.
The Linux As The Operating System For Computational Node Of Custom Computing Machine Class System (2006)

The paper presents the application of the modified real-time Linux kernel as the operating system for the computational node of CCM (custom computing machine) class parallel system designed to aid the simulations of three-dimensional electromagnetic field. The computational node is the application-specific design optimized for the implementation in the FPGA. It is based on Xilnx VirtexIIPro FPGA equipped with two embedded cores of the PowerPC processors. The presented real-time kernel is designed to run on one of the cores. The paper details the procedure needed to create the kernel customized for the specific architecture of the system. The software packages and tools utilized in the kernel development process are also presented
Quantitative chemical topography of polycrystalline Si anisotropically etched in Cl2/O2 high density plasmas (1995)

The spatially resolved surface chemical composition or ‘‘chemical topography’’ of submicron features [polycrystalline silicon (poly-Si) masked with photoresist (PR) lines] etched in high density, low pressure helical resonator Cl2/O2 plasmas has been quantitatively determined using angle resolved x-ray photoelectron spectroscopy (XPS). The chemical topography of plasma etched microelectronic materials is important in understanding how impinging ions and neutrals interact with surfaces to influence etched profiles. The spatial origin of XPS signals was determined from a combination of geometric shadowing of photoelectrons by adjacent features, electrostatic charging of insulating surfaces, XPS signal calibration versus take-off angle, x-ray attenuation, and geometric modeling. Equal line and space width (0.75–2.0 μm) features, unmasked poly-Si, and unpatterned PR surfaces were examined following plasma etching and vacuum sample transfer. For pure Cl2 plasmas, Cl surface concentration was found to be similar for horizontal and vertical surfaces of the poly-Si and PR. Only a small amount of Si was found on the PR sidewall, and similarly, little C or O was observed on the side of the poly-Si features, indicating that sidewall passivation is not occurring. O coverage on all surfaces increased with O2 addition to the plasma. For Cl2/5% O2 plasmas, a small amount of O was found on the poly-Si trench bottom, and more (but still submonolayer) on the poly-Si sidewall. Also, more Cl, O, and Si were found on the PR sidewall with 5% O2. For Cl2/10% O2 plasmas, rough surfaces were observed by scanning electron microscopy (SEM). On poly-Si trench bottoms, O coverage is comparable to Cl at roughly a monolayer. On poly-Si sidewalls, O and Cl coverages are again comparable, but the O coverage is about double that found on the trench bottoms. The most dramatic effect by far at 10% added O2 is the formation of a thick SiOx Cly layer (where x≊y≊1) on the side of the PR, detected by both XPS and SEM. The quantitative analysis method developed in this study is readily applicable to other etching gases and materials.
Effect of microaggregate blood filtration on granulocyte concentrates in vitro (1983)

To determine the effect of transfusing granulocyte concentrates through microaggregate blood filters, granulocytes prepared with a cell processor were passed through screen and depth microaggregate filters. Pre- and postfiltration evaluations were made of total granulocyte count, levels of muramidase, granulocyte viability, motility, phagocytosis, bactericidal activity, and hydrogen peroxide-forming capacity. Compared to prefiltration levels, a significant (p less than 0.05) decrease in postfiltration granulocyte counts was seen for all the depth filters studied but not for the standard 170 microns (control) or the 40 microns screen filter. For the various tests of granulocyte function evaluated prefiltration, no significant postfiltration differences (p greater than 0.05) were seen for any of the filters studied. Screen microaggregate filters retained only 1 to 3 percent of granulocytes contained in the concentrates, and thus appear satisfactory for use in clinical transfusions. The large percentage of neutrophils retained by the depth filters (20-62%), however, precludes their use for transfusion of granulocyte concentrates.
THERMODYNAMICS OF PORPHYRIN BINDING TO SERUM ALBUMIN: EFFECTS OF TEMPERATURE, OF PORPHYRIN SPECIES and OF ALBUMIN‐CARRIED FATTY ACIDS (1987)

Abstract Porphyrin binding to serum albumin was studied at the molecular level probing the effects of: porphyrin self‐aggregation, porphyrin species, temperature and protein‐bound fatty acids. Human serum albumin was found to have a single high‐affinity site for porphyrin monomers, with binding constants of 2 x 10 6 , 5 x 10 7 and 3 x 10 8 (37 o C, neutral pH, M −1 ), for hemato‐, deutero‐ and protoporphyrins, respectively. Three equilibria models for the dimer binding were developed and tested. The data were found to fit best with a model proposing a single high‐affinity binding site for the dimer, independent of and different than the monomer site. The binding constants of the hematoporphyrin and deuteroporphyrin dimers to human serum albumin (37 o C, neutral pH, M −l ) being 4 x 10* and 5 x 10 8 respectively. The temperature dependence (Dp and HSA, 22‐37 o C) of the monomer binding showed the process to be entropy‐driven (δG o = ‐45 kJ mol −1 ; δS o =+146 kJ mol −1 ; δH o = 0 kJ mol −1 ). For the dimer binding, the enthalpy change was found to be highly temperature‐dependent implying continuous changes in the heat capacity of the system over the entire temperature range, the trend at the 37 o C region fitting an entropy‐driven process. The monomer vs dimer differences in temperature dependence strongly support separate and independent binding sites for these species. Similar thermodynamics were determined for fatty‐acid carrying as well as for fatty‐acid free HSA, with mild quantitative (but not qualitative) shifts.
The importance of information on relatives for the prediction of genomic breeding values and the implications for the makeup of reference data sets in livestock breeding schemes (2012)

An animal's relationship to the reference data set is an important factor for the accuracy of genomic predictions. Animals that share a close relationship to the reference data set had the highest accuracy from genomic predictions. However a baseline accuracy that is driven by the reference data set size and the overall population effective population size enables gBLUP to estimate a breeding value for unrelated animals within a population (breed), using information previously ignored by pedigree based BLUP methods.
Display of Expression Products of cDNA Libraries on Phage Surfaces (1994)

Techniques for cloning cDNAs from bacteriophage libraries immobilised on solid supports are well established. However, these techniques do not allow selective enrichment of clones expressing proteins of interest. Screening of cDNA libraries would be simplified if the proteins encoded by cDNAs could be expressed on the surface of phage. Phage carrying genes encoding proteins for which a ligand is available can be selected directly by affinity interaction [Crameri, R. & Suter, M. (1993) Gene (Amst.) 137 , 69–75]. The expression products from a cDNA library from Aspergillus fumigatus have been displayed on the surface of the filamentous phage M13 and screened for gene products binding to human serum IgE. The physical linkage of cDNA‐encoded proteins to the genetic information required for their production, achieved by exploiting the high‐affinity interaction of the Jun and Fos leucine zippers, allows screening of up to 1 × 10 10 independent clones in 50‐μl aliquots applied to a well of a microtiter plate coated with the ligand. Phage displaying IgE‐binding proteins were selectively enriched 10 5 –10 6 ‐fold over non‐specific phage after six rounds of growth and selection. The apparent molecular mass of the proteins selected from the cDNA library was in the range 20–40 kDa. Restriction enzyme analysis and preliminary sequence determination of 12 selected inserts revealed different sequences. The ability of the proteins to bind to human serum IgE was corroborated by enzyme‐linked immunosorbent assay and by Western‐blot analysis. The developed cloning strategy allows isolation of cDNAs encoding proteins for which a ligand is available and circumvents immobilisation of the libraries on solid‐phase supports which hamper selective enrichment of clones expressing the desired protein.
Light scatter and total protein signal distribution of platelets by flow cytometry as parameters of size. (1988)

The use of flow cytometry for determination of platelet size was investigated by measurement of forward-angle light-scatter (FALS) signals and the fluorescent right-angle signals from platelets incubated with the fluorescent protein dye fluorescein isothiocyanate (FITC). Both FALS and fluorescence signals displayed a unimodal log normal pattern of distributions that were almost identical to distributions obtained by resistive particle sizing. As measured on 12 platelet samples from normal individuals, FALS, FITC, and resistive particle size data exhibited a high degree of fit to log normal distributions as shown by the coefficients of determination (R2), which were 0.9962 +/- 0.0035, 0.9966 +/- 0.0056, and 0.9987 +/- 0.0012, respectively. The geometric standard deviation (GSD), reflecting the heterogeneity of the FALS, FITC, and resistive particle size signals, was almost identical: 1.69 +/- 0.03, 1.67 +/- 0.04, and 1.69 +/- 0.02, respectively, for spherical platelets from normal individuals. Platelet FALS signal distributions were compared with Coulter resistive particle size distributions by using platelet samples from 12 normal patients and 27 patients with thrombocytopenia. Significant correlation was found between mean FALS and mean resistive particle size (r = 0.83) and between GSD of FALS and GSD of resistive particle size (r = 0.74) with the platelet samples from the 39 subjects studied. These studies, which document the high degree of correspondence among these three independent measurements of platelet size, based on three entirely different principles, strongly suggest that platelet size is log normal distributed and that the GSD value shown above reflects actual heterogeneity in size. The FALS signal distribution was, however, found to be markedly influenced by changes in platelet shape and internal structure.(ABSTRACT TRUNCATED AT 250 WORDS)
mCoupons: An Application for Near Field Communication (NFC) (2007)

Near field communication (NFC) is a short-range wireless communication standard. It is very comfortable for the user as communication starts without any further configuration steps when bringing two devices very close together. This property makes the standard well suitable for the use with mobile coupons (we call it mCoupons). Nowadays, coupons are a very common way for companies to promote their products or services. These coupons are available as paper-based coupons or electronic coupons (which for example are used on the web). We propose a new form of coupons, so called mCoupons, which can be downloaded from a poster or a newspaper equipped with a passive NFC device to a mobile device. With this mobile device the user can then cash in the mCoupon at the cashier. In most of the cases, the value of each coupon is relatively low but misuse in larger scale can result in a major damage for a company. Therefore, mCoupons shall be secured against attackers. In this paper, we propose protocols for a secure mCoupon system using NFC technology. This protocol can be a basis for future micro-payment or ticketing services.
Phenotypic Diversity of Enterotoxigenic <i>Escherichia coli</i> Strains from a Community-Based Study of Pediatric Diarrhea in Periurban Egypt (1999)

No past studies of diarrhea in children of the Middle East have examined in detail the phenotypes of enterotoxigenic Escherichia coli (ETEC) strains, which are important pathogens in this setting. During a prospective study conducted from November 1993 to September 1995 with 242 children under 3 years of age with diarrhea living near Alexandria, Egypt, 125 episodes of diarrhea were positive for ETEC. ETEC strains were available for 98 of these episodes, from which 100 ETEC strains were selected and characterized on the basis of enterotoxins, colonization factors (CFs), and O:H serotypes. Of these representative isolates, 57 produced heat-stable toxin (ST) only, 34 produced heat-labile toxin (LT) only, and 9 produced both LT and ST. Twenty-three ETEC strains expressed a CF, with the specific factors being CF antigen IV (CFA/IV; 10 of 23; 43%), CFA/II (5 of 23; 22%), CFA/I (3 of 23; 13%), PCFO166 (3 of 23; 13%), and CS7 (2 of 23; 9%). No ETEC strains appeared to express CFA/III, CS17, or PCFO159. Among the 100 ETEC strains, 47 O groups and 20 H groups were represented, with 59 O:H serotypes. The most common O serogroups were O159 (13 strains) and O43 (10 strains). O148 and O21 were each detected in five individual strains, O7 and O56 were each detected in four individual strains, O73, O20, O86, and O114 were each detected in three individual strains, and O23, O78, O91, O103, O128, and O132 were each detected in two individual strains. The most common H serogroups were H4 (16 strains), 12 of which were of serogroup O159; H2 (9 strains), all of which were O43; H18 (6 strains); H30 (6 strains); and H28 (5 strains); strains of the last three H serogroups were all O148. Cumulatively, our results suggest a high degree of clonal diversity of disease-associated ETEC strains in this region. As a low percentage of these strains expressed a CF, it remains possible that other adhesins for which we either did not assay or that are as yet undiscovered are prevalent in this region. Our findings point out some potential barriers to effective immunization against ETEC diarrhea in this population and emphasize the need to identify additional protective antigens commonly expressed by ETEC for inclusion in future vaccine candidates.