gebhart/patrepeval huggingface dataset:
Anti‐adhesive property of P‐selectin glycoprotein ligand‐1 (PSGL‐1) due to steric hindrance effect (2012)

P-selectin glycoprotein ligand-1 (PSGL-1) is an adhesive molecule that is known to be a ligand for P-selectin. An anti-adhesive property of PSGL-1 has not been previously reported. In this study, we show that PSGL-1 expression is anti-adhesive for adherent cells and we have elucidated the underlying mechanism. Overexpression of PSGL-1 induced cell rounding and floating in HEK293T cells. Similar phenomena were demonstrated in other adherent cell lines with overexpression of PSGL-1. PSGL-1 overexpression inhibits access of antibodies to cell surface molecules such as integrins, HLA and CD25. Cells transfected with PSGL-1 deletion mutants that lack a large part of the extracellular domain and chimeric construct expressing extracellular CD86 and intracellular PSGL-1 only showed rounded morphology, but there are no floating cells. These results indicated that PSGL-1 causes steric hindrance due to the extended structure of its extracellular domain that is highly O-glycosylated, but intracellular domain also has some effect on cell rounding. This study implies that PSGL-1 has Janus-faced functions, being both adhesive and anti-adhesive.
Temporal Modulation of the Response of Sensory Fibers to Paired-Pulse Stimulation (2019)

Multi-channel nerve cuff electrode arrays can provide sensory feedback to prosthesis users. To develop efficacious stimulation protocols, an understanding of the impact that spatio-temporal patterned stimulation can have on the response of sensory fibers is crucial. We used experimental and modelling methods to investigate the response of nerve fibers to paired-pulse stimulation. Nerve cuff electrode arrays were implanted for stimulation of the sciatic nerves of rats and the sensory compound action potentials were recorded from the L<sub>4</sub> dorsal root. A model of the nerve cuff electrode array and sciatic nerve was also developed. The experimental and modelling results were compared. Experiments showed that it took 8 ms for the sensory fibers to completely recover from a conditioning stimulus, regardless of the relative position of the electrodes used for stimulation. The results demonstrate that the electrodes on the cuff cannot be considered independent. Additionally, at 120% of the threshold, there is a large overlap in the fibers that were activated by the different electrodes. If a stimulus paradigm considered the electrodes as independent, stimuli from the different electrodes would need to be interleaved, and the intervals between the stimuli should be greater than 8 ms.
Molecular diversity of marine glues: polyphenolic proteins from five mussel species. (1991)

Adhesive polyphenolic proteins have been purified and characterized from the feet of five marine mussels (Brachidontes exustus, Modiolus modiolus squamosus, Mytella guyanensis, Septifer bifurcatus, and Trichomya hirsuta). All five proteins contain high levels of 3,4-dihydroxyphenylalanine (DOPA), lysine, glycine, and serine or threonine. All but B. exustus also contain high levels (> or = 10%) of proline or 4-hydroxyproline. The polyphenolic proteins of all the mussels have repeated sequences of the motif X1-Y*-X2-Y*-X3-K, where Y* denotes tyrosine or DOPA. In two species (S. bifurcatus and B. exustus), X2 represents 3 amino acids (frequently glycine) and X3 is absent. M. guyanensis is similar except that X2 is reduced to 2 amino acids. In T. hirsuta and M. m. squamosus, however, X2 is absent and X3 occurs as alanine or hydroxyproline. All proteins share approximately equimolar proportions of tyrosyl- and lysyl-derived residues. Although all of the mussels examined thus far are adhesively opportunistic with respect to substratum type, a rigidly invariant sequence does not appear to be necessary for achieving this.
Mode of Delivery Shapes Gut Colonization Pattern and Modulates Regulatory Immunity in Mice (2014)

Delivery mode has been associated with long-term changes in gut microbiota composition and more recently also with changes in the immune system. This has further been suggested to link Cesarean section (C-section) with an increased risk for development of immune-mediated diseases such as type 1 diabetes. In this study, we demonstrate that both C-section and cross-fostering with a genetically distinct strain influence the gut microbiota composition and immune key markers in mice. Gut microbiota profiling by denaturing gradient gel electrophoresis and 454/FLX-based 16S rRNA gene amplicon sequencing revealed that mice born by C-section had a distinct bacterial profile at weaning characterized by higher abundance of Bacteroides and Lachnospiraceae, and less Rikenellaceae and Ruminococcus. No clustering according to delivery method as determined by principal component analysis of denaturing gradient gel electrophoresis profiles was evident in adult mice. However, the adult C-section-born mice had lower proportions of Foxp3(+) regulatory T cells, tolerogenic CD103(+) dendritic cells, and less Il10 gene expression in mesenteric lymph nodes and spleens. This demonstrates long-term systemic effect on the regulatory immune system that was also evident in NOD mice, a model of type 1 diabetes, born by C-section. However, no effect of delivery mode was seen on diabetes incidence or insulitis development. In conclusion, the first exposure to microorganisms seems to be crucial for the early life gut microbiota and priming of regulatory immune system in mice, and mode of delivery strongly influences this.
The impact of dietary fat withdrawal on carcass iodine value, belly characteristics, and changes in body fat over time1 (2015)

The inclusion of unsaturated fats in pig diets has raised issues related to pork carcass fat quality. The objective of this experiment was to understand how withdrawal from the diet of unsaturated dietary fat before slaughter impacts the composition of jowl fat during the growth cycle and at market. Fifty individually housed pigs (PIC 337 × C22/29; initial BW = 59.3 ± 0.55 kg) were allotted based on sex and initial BW to 10 treatments for an 82-d experiment as follows: 3 dietary fat withdrawal times before slaughter (21, 42, or 63 d) by 3 dietary fat unsaturation loads (DFUL), which includea high intake of unsaturated fatty acids supplied through an inclusion of 5% corn oil (HIGH), a high intake of a mixture of saturated and unsaturated fatty acids supplied through an inclusion of 5% animal-vegetable blend (MED), and a moderate intake of unsaturated fatty acids supplied through an inclusion of 2.5% corn oil (LOW). Pigs were weighed and jowl adipose samples were collected on d 0, 21, 42, and 63 and at harvest on d 82. Data were analyzed using PROC MIXED with treatment and sex as fixed effects. At market (d 82), increasing the withdrawal of dietary fat further away from market increased 18:1 (P = 0.045) and tended to increase 14:0 concentrations (P = 0.054). It also significantly decreased 18:2 (P < 0.001) and tended to decrease 18:3 concentrations (P = 0.081). A HIGH DFUL resulted in the greatest 18:2 concentrations in jowl fat followed by LOW; MED resulted in the lowest 18:2 levels (P < 0.001). Dietary fat withdrawal before market significantly reduced carcass iodine value (IV) measured at d 82 (P = 0.006). In conclusion, elevated 18:2 intake makes lowering carcass IV in the depot fat very difficult and may take as long as 61 d. The withdrawal of unsaturated dietary fat apparently altered the fat depot to be more reflective of fat synthesized de novo, resulting in a more saturated depot fat. Importantly, this alteration of deposited fat composition did not translate into improved belly firmness, depth, weight, or fat color.
Highly Scalable OXC-based Contentionless ROADM Architecture with Reduced Network Implementation Costs (2012)

We present a novel OXC-based colorless/directionless/contentionless ROADM architecture that resolves many of the issues of previous OXC-based solutions. We show cost savings of up to 52% over typical WSS-based architectures in a reference BT network.
Human and feline adipose-derived mesenchymal stem cells have comparable phenotype, immunomodulatory functions, and transcriptome (2017)

Findings suggest that feline ASCs modulate lymphocyte proliferation using soluble mediators that mirror the human ASC secretion pattern. Uninduced feline ASCs have similar gene expression profiles to uninduced human ASCs, as revealed by transcriptome analysis. These data will help inform clinical trials using cats with naturally occurring diseases as surrogate models for human clinical trials in the regenerative medicine arena.
Centralized cooperative spectrum sensing with multiple antennas over imperfect feedback channels (2014)

In this paper, we study the performance of a cooperative spectrum sensing (CSS) scheme over imperfect feedback channels, where N secondary users (SUs) collaborate in order to enhance the detection probability of a primary user (PU). The sensing process is divided into two phases: In the first phase each SU, which is equipped with multiple antennas, independently detect the PU signal. In the second phase, the SUs' local decisions are sent via erroneous and orthogonal feedback channels to a fusion center (FC), where a final decision is made. We utilize Bayesian criterion which accounts for the costs of misdetection and false alarm. Quasi-Newton method is employed to obtain the optimal number of antennas for a given SNR and vice versa. Our simulation results concur the mathematical derivations and validate the optimality of quasi-Newton method. We further show that the derived optimal fusion rule outperforms the OR rule, AND rule and MAJORITY rule.
The gamma 2 chain of kalinin/laminin 5 is preferentially expressed in invading malignant cells in human cancers. (1994)

All known laminin isoforms are cross-shaped heterotrimeric molecules, consisting of one heavy alpha chain and two light beta and gamma chains. Recently, a cDNA encoding a new gamma chain from laminin 5 (also known as kalinin) was sequenced. This chain, named gamma 2, showed extended homology to the classical gamma 1 chain but differed from this by lacking the terminal globular domain. Recent data, indicating an important role of the gamma 2 chain gene in establishing adhesion contacts between epithelial cells and basement membranes, prompted us to investigate whether the gamma 2 chain gene is aberrantly expressed in cancer tissue, and if so whether its localization could provide clues to its possible role in cancer dissemination. Routinely processed tissue specimens from 36 cases of human cancer were investigated, including 16 cases of colon adenocarcinoma, 7 ductal mammary carcinomas, 4 squamous cell carcinomas, 3 malignant melanomas and 6 sarcomas. In situ hybridization for the detection of mRNAs for the gamma 2 chain and for the classical laminin chains alpha 1, beta 1, and gamma 1 was performed using S-35 labeled antisense RNA probes. As positive control of the specificity of the gamma 2 chain mRNA detection, two different anti-sense probes derived from two nonoverlapping cDNA clones were used. Malignant cells were found to express the gamma 2 chain in 29 of the 30 carcinomas studied and the expression was particularly high in cancer cells located at the invasion front. In contrast, mesenchymally derived cancer cells in three different types of sarcomas did not express the gamma 2 chain. In colon cancer there was a clear histological correlation between the expression of gamma 2 chain by cancer cells and their engagement in tumor budding processes. Laminin chains alpha 1, beta 1, and gamma 1 were weakly expressed throughout cancerous areas with no apparent correlation to sites of invasion. The aberrant expression of the gamma 2 chain gene seen in invasively growing cancer cells point to a role of this molecule in establishing focal adhesions of cancer cells to the extracellular matrix during their migration through surrounding normal tissue.
INTER:D: a drum sound equalizer for controlling volume and timbre of drums (2005)

A drum sound equalizer, called INTER:D, is described that enables a listener to control the volume and timbre of bass and snare drum sounds in commercial compact-disc recordings. Although the characteristics of the drum sounds are often closely related to the impression made by a musical piece, conventional graphic equalizers cannot adjust their characteristics because they have volume sliders only for the frequency bands. INTER:D provides drum-specific volume sliders that directly control the frequency components of drum sounds, enabling a listener to intuitively cut or boost the volume of each drum. In addition, INTER:D enables a listener to replace the original timbre of each drum with another timbre selected from a drop-down list. These interactive functions are achieved using an automatic music content analysis system based on low-level audio signal processing. This system can estimate the power spectrogram of each drum sound and detect the onset times in a musical piece. Subjective experiments showed that INTER:D can add a new dimension to the way users experience music.
A fast simultaneous input vector generation and gate replacement algorithm for leakage power reduction (2006)

Input vector control (IVC) technique is based on the observation that the leakage current in a CMOS logic gate depends on the gate input state, and a good input vector is able to minimize the leakage when the circuit is in the sleep mode. The gate replacement technique is a very effective method to further reduce the leakage current. In this paper, we propose a fast algorithm to find a low leakage input vector with simultaneous gate replacement. Results on MCNC91 benchmark circuits show that our algorithm produces $14 %$ better leakage current reduction with several orders of magnitude speedup in runtime for large circuits compared to the previous state-of-the-art algorithm. In particular, the average runtime for the ten largest combinational circuits has been dramatically reduced from 1879 seconds to 0.34 seconds.
Production of interleukin-1 but not tumor necrosis factor by human monocytes stimulated with pneumococcal cell surface components (1989)

While there is considerable evidence that both interleukin-1 (IL-1) and tumor necrosis factor (TNF) are central mediators of inflammation caused by gram-negative bacteria and endotoxin, the roles of these two mediators in gram-positive infection are unknown. Pneumococcal infections are characterized by an intense inflammatory reaction in infected tissues. Current evidence suggests that the component of the pneumococcus which causes this inflammation in many body sites is the cell wall. We determined the ability of native pneumococcal cell wall, lipoteichoic acid, and cell wall subcomponents to stimulate secretion of IL-1 and TNF from human monocytes. Each pneumococcal cell surface component was found to have a different specific activity for induction of IL-1. Teichoication was an important determinant of this activity: teichoicated species were at least 10,000-fold more potent than endotoxin and 100-fold more potent than teichoic acid-free peptidoglycan. IL-1-inducing activity was greatly reduced by chemical alteration of the teichoic acid. In contrast to endotoxin, cell wall did not induce production of TNF. This dissociation of the production of IL-1 and TNF during the response of the human monocyte to pneumococcal surface components suggests that, in at least some circumstances, the mechanisms for generation of an inflammatory response to infection may be fundamentally different between gram-positive and gram-negative disease.
Characteristics of the Membrane Emulsification Method Combined with Preliminary Emulsification for Preparing Corn Oil-in-Water Emulsions. (1996)

A novel membrane emulsification method was used to prepare corn oil/water (O/W) emulsions (25 wt% oil phase) with sharp particle diameter distribution. When pre-emulsified O/W emulsions were used as dispersing fluids instead of the oil phase (corn oil+emulsifier), the membrane emulsification was carried out easily with a high emulsifying rate up to 3.5 m3/(h·m2-membrane). Mean particle diameters of the emulsions were about twofold those of the mean pore sizes of the porous glass membranes used. The particle diameter of the emulsions decreased with increasing applied pressure or flux of the pre-emulsified emulsion through the membrane. Because of the high stability of the membrane emulsified emulsion particles, little change in particle diameter distribution occurred over several weeks. The kind of emulsifying agent influenced the particle diameter distribution and the creaming rate.
Nucleosomal instability and induction of new upstream protein-DNA associations accompany activation of four small heat shock protein genes in Drosophila melanogaster. (1986)

We investigated in detail the structural changes that occur in nuclear chromatin upon activation of the four small heat shock protein genes in D. melanogaster. Both the chemical cleavage reagent methidiumpropyl-EDTA X iron(II) [MPE X Fe(II)] and the nuclease DNase I revealed a complex pattern of four or five hypersensitive sites upstream of each gene before activation. In addition, MPE X Fe(II) detected a short positioned array of nucleosomes located on each coding region. Upon heat shock activation a number of changes in the patterns occurred. For each gene, at least one of the upstream hypersensitive regions was eliminated or substantially shifted in position. Regions were established which became highly refractile to digestion by either MPE X Fe(II) or DNase I and, as such, appeared as small "footprints" in the pattern. The location of these refractile regions relative to the cap site varied for each gene examined. The coding regions themselves became highly accessible to DNase I. The nucleosomal arrays detected by MPE X Fe(II) were characterized by a considerable loss of detail and significantly enhanced accessibility, the extent of which probably reflected the relative transcription rate of each gene. Careful mapping of the location and extent of each upstream footprint and comparison with the DNA sequence revealed the presence at each location of two (or more) contiguous or overlapping segments that bear high homology to the heat shock consensus sequence C-T-N-G-A-A-N-N-T-T-C-N-A-G. A specific protein factor (or factors) is most likely bound at or near these sequence in heat-shocked Drosophila cells.
Complete Nucleotide Sequence of the Bovine ß-casein Gene (1988)

The beta-casein gene is a member of a small gene family encoding the calcium-sensitive caseins, which are specifically synthesized and secreted by the mammary gland during lactation in response to both peptide and steroid hormones. The caseins are involved in the transport of calcium phosphate in milk, which is important for bone development in the infant mammal. We report here the organization and complete DNA sequence of the 8.5 kb long bovine beta-casein gene. Comparison with the rat beta-casein gene reveals that the exons of both genes correspond exactly. The 5' flanking sequences of all Ca-sensitive casein genes are conserved within the proximal 200 bp and contain several elements that probably function as cis-acting regulatory elements, including an octamer-like motif, and SV40-type core enhancer and a sequence that appears to be common to all lactoprotein genes. The latter sequence is flanked on either side by 12 bp direct repeats. These direct repeats are themselves each part of sequences that display two-fold symmetry. The first 30 nucleotides of the 3' flanking regions in the bovine and rat beta-caseins are well conserved, indicating that they are likely to be involved in the mechanism of 3' end processing of the primary transcript.
Boosting support vector machines for text classification through parameter-free threshold relaxation (2003)

Support vector machine (SVM) learning algorithms focus on finding the hyperplane that maximizes the margin (the distance from the separating hyperplane to the nearest examples) since this criterion provides a good upper bound of the generalization error. When applied to text classification, these learning algorithms lead to SVMs with excellent precision but poor recall. Various relaxation approaches have been proposed to counter this problem including: asymmetric SVM learning algorithms (soft SVMs with asymmetric misclassification costs); uneven margin based learning; and thresholding. A review of these approaches is presented here. In addition, in this paper, we describe a new threshold relaxation algorithm. This approach builds on previous thresholding work based upon the beta-gamma algorithm. The proposed thresholding strategy is parameter free, relying on a process of retrofitting and cross validation to set algorithm parameters empirically, whereas our previous approach required the specification of two parameters (beta and gamma). The proposed approach is more efficient, does not require the specification of any parameters, and similarly to the parameter-based approach, boosts the performance of baseline SVMs by at least 20% for standard information retrieval measures.
Deobfuscation, unpacking, and decoding of obfuscated malicious JavaScript for machine learning models detection performance improvement (2020)

Obfuscation is rampant in both benign and malicious JavaScript (JS) codes. It generates an obscure and undetectable code that hinders comprehension and analysis. Therefore, accurate detection of JS codes that masquerade as innocuous scripts is vital. The existing deobfuscation methods assume that a specific tool can recover an original JS code entirely. For a multi‐layer obfuscation, general tools realize a formatted JS code, but some sections remain encoded. For the detection of such codes, this study performs Deobfuscation, Unpacking, and Decoding (DUD‐preprocessing) by function redefinition using a Virtual Machine (VM), a JS code editor, and a python int_to_str() function to facilitate feature learning by the FastText model. The learned feature vectors are passed to a classifier model that judges the maliciousness of a JS code. In performance evaluation, the authors use the Hynek Petrak's dataset for obfuscated malicious JS codes and the SRILAB dataset and the Majestic Million service top 10,000 websites for obfuscated benign JS codes. They then compare the performance to other models on the detection of DUD‐preprocessed obfuscated malicious JS codes. Their experimental results show that the proposed approach enhances feature learning and provides improved accuracy in the detection of obfuscated malicious JS codes.
Hypervolume visualization: a challenge in simplicity (2002)

Hypervolume visualization is designed to provide simple and fully explanatory images that give comprehensive in-sights into the global structure of scalar fields of any dimension. The basic idea is to have a dimension independent viewing system that scales nicely with the geometric dimension of the dataset and that can be combined with classical approaches like isocontouring and animation of slices of nD data. One completely abandons (for core simplicity) rendering techniques, such as hidden surface removal or lighting or radiosity, that enhance three dimensional realism and concentrate on the real-time display of images that highlight structural (topological) features of the no dataset (holes, tunnels, cavities, depressions, extrema, etc.). Hypervolume visualization on the one hand is a generalization of direct parallel projection methods in volume rendering. To achieve efficiency (and real-time performance on a graphics workstation) the authors combine the advantages of (i) a hierarchical representations of the hypervolume data for multiresolution display and (ii) generalized object space splatting combined with texture-mapped graphics hardware acceleration. The main results of the paper are thus both a multiresolution direct rendering algorithm and scalable graphical user interface that provides global views of scalar fields in any dimension, while maintaining the fundamental characteristics of ease of use, and quick exploratory user interaction.