gebhart/patrepeval huggingface dataset:
Binding properties and evolution of homodimers in protein-protein interaction networks (2005)

We demonstrate that protein-protein interaction networks in several eukaryotic organisms contain significantly more self-interacting proteins than expected if such homodimers randomly appeared in the course of the evolution. We also show that on average homodimers have twice as many interaction partners than non-self-interacting proteins. More specifically, the likelihood of a protein to physically interact with itself was found to be proportional to the total number of its binding partners. These properties of dimers are in agreement with a phenomenological model, in which individual proteins differ from each other by the degree of their 'stickiness' or general propensity toward interaction with other proteins including oneself. A duplication of self-interacting proteins creates a pair of paralogous proteins interacting with each other. We show that such pairs occur more frequently than could be explained by pure chance alone. Similar to homodimers, proteins involved in heterodimers with their paralogs on average have twice as many interacting partners than the rest of the network. The likelihood of a pair of paralogous proteins to interact with each other was also shown to decrease with their sequence similarity. This points to the conclusion that most of interactions between paralogs are inherited from ancestral homodimeric proteins, rather than established de novo after duplication. We finally discuss possible implications of our empirical observations from functional and evolutionary standpoints.
EXAMPLES OF EVALUATION METHODS OF ENERGY-ABSORBING PROPERTIES FOR UPPER INTERIOR HEAD PROTECTION (1996)

Various types of samples, including plastic foams, elastomers, and hollow-shaped plastics, are evaluated by both high-speed impact tests and the static compression tests. It was found that the high-speed impact tests together with proper data analyses are very effective in evaluating Energy-Absorbing (E/A) properties of various materials. Analyses from the data obtained from those tests, estimation of E/A properties for different types of samples from the compression data should be avoided and the compression data are effective only among the same type of samples. With the high-speed impact tests, plastic foams and hollow-shaped plastics showed excellent head protection properties. Foamed plastics, which can be easily applied to interior trim parts, are focused on and some typical plastic foams are additionally tested under various conditions. Comparison of those test results to actual vehicle tests, design guidelines in applying plastic foams to head protection trims are introduced as final conclusion. [A] For the covering abstract, see IRRD 896528.
Expression of a type II collagen-specific TCR transgene accelerates the onset of arthritis in mice (1998)

Animal models of autoimmune diseases have been instrumental in advancing our understanding of autoimmunity in humans. Collagen-induced arthritis in mice is an autoimmune disease model of rheumatoid arthritis, which is MHC class II restricted and CD4 T cell dependent. To better understand the fundamental role of T cells in arthritis, we have generated a transgenic mouse carrying the rearranged Valpha11.1 and Vbeta8.2 TCR chain genes isolated from a type II collagen (CII)-specific T cell hybridoma. Cell surface analysis indicated that Vbeta8.2 chain was expressed on the surface of nearly all peripheral T cells. Analysis of T cell subsets in transgenic mice revealed a profound skewing in peripheral T cells towards the CD4 population. Although peripheral T cells were not tolerant to CII and responded to CII stimulation in vitro, transgenic mice did not develop spontaneous arthritis. However, a rapid onset of arthritis with severe clinical signs was detected in transgenic mice after immunization with CII in complete Freund's adjuvant. Histological analysis of inflamed joints showed a great resemblance to arthritic joints in man. This unique transgenic mouse model provides valuable insights into the mechanism of arthritis and into potential specific immune interventions.
Reduction of leptin gene expression by dietary polyunsaturated fatty acids. (2001)

Supplementation with n-3 polyunsaturated fatty acids (PUFA) for 6 weeks did not alter plasma leptin concentrations in male smokers. Changes in dietary intake of saturated fatty acids (FA) correlated positively, whereas changes in the intake of PUFA correlated negatively to changes in plasma leptin levels. A 3-week n-3 PUFA-enriched diet, as compared with a 3-week lard-enriched diet, induced lower plasma leptin concentration and reduced leptin mRNA expression in rat epididymal adipose tissue. In the human trophoblast cell line (BeWo), n-3 PUFA had a dose- and time-dependent effect on leptin expression. One mM of eicosapentaenoic acid or docosahexaenoic acid (DHA) reduced leptin expression by 71% and 78%, respectively, as compared with control, after 72 h. There was no effect on expression of the signal transducing form of the leptin receptor. In BeWo cells transfected with the human leptin promoter, we found that n-3 PUFA reduced leptin promoter activity; in contrast saturated and monounsaturated FA had no effect on leptin promoter activity. The transcription factors peroxysomal proliferator activated receptor gamma and sterol regulatory element binding protein-1 mRNAs were reduced after incubation with n-3 PUFA, whereas the expression of CCAAT/enhancer binding protein alpha was unchanged. DHA-reduced leptin expression was abolished in BeWo cells grown in cholesterol-free medium. In conclusion, n-3 FA decreased leptin gene expression both in vivo and in vitro. The direct effects of PUFA on leptin promoter activity indicate a specific regulatory action of FA on leptin expression.
Airborne Concentrations and Particle Size Distribution of Allergen Derived from Domestic Cats ( <i>Felis domesticus</i> ): Measurements Using Cascade Impactor, Liquid Impinger, and a Two-site Monoclonal Antibody Assay for <i>Fel d</i> I (1990)

The recent development of a sensitive two-site monoclonal antibody immunoassay for the major cat allergen (Fel d I) has made it possible to make accurate measurements of airborne cat allergen using low volume samplers that do not disturb the room. Houses with cats had from 2 to 20 ng Fel d I/m3 air compared with less than 0.2 ng/m3 in houses without cats. Using a cascade impactor and a multistage liquid impinger, the particle size distribution of airborne Fel d I in nine houses was 75% on particle greater than or equal to 5 microns in diameter and 25% (range, 10 to 62%) on particles less than or equal to 2.5 microns. In a cat vivarium with 12 cats, the air contained 40 ng Fel d I/m3, but less than 2% was detected on particles less than or equal to 2.5 microns. The air exchange rate in the vivarium (approximately 15 changes/h) appears to be the major difference from domestic houses (less than 0.5 changes/h). Repeated studies in one house confirmed a very high proportion (approximately 60%) of Fel d I on small particles. During domestic cleaning, the levels of small particle allergen in this house approached those produced by a nebulizer for bronchial provocation, i.e., 40 ng/m3. These results show unequivocally that significant airborne Fel d I is associated with small particles, which remain airborne for long periods. These findings are strikingly different from previous results obtained with airborne dust mite allergen. The results provide an explanation for the distinctive rapid onset of asthma or rhinitis in patients allergic to cats and a basis for designing a policy to reduce airborne allergen in houses with cats.
Evaluation of zero-velocity detectors for foot-mounted inertial navigation systems (2010)

A study of the performance of four zero-velocity detectors for a foot-mounted inertial sensor based pedestrian navigation system is presented. The four detectors are the acceleration moving variance detector, the acceleration magnitude detector, the angular rate energy detector, and a novel generalized likelihood ratio test detector, refereed to as the SHOE. The performance of each detector is assessed by the accuracy of the position solution provided by the navigation system employing the detector to perform zero-velocity updates. The results show that for leveled ground forward gait at a speed of 5 km/h, the angular rate energy detector and the SHOE give the highest performance, with a position accuracy of 0.14% of the travelled distance. The results also indicate that during leveled ground forward gait, the gyroscope signals hold the most reliable information for zero-velocity detection.
Cardiac autoimmunity in HIV related heart muscle disease (1998)

There is an increased frequency of circulating cardiac specific autoantibodies in HIV positive individuals, particularly those with heart muscle disease. The data support a role for cardiac autoimmunity in the pathogenesis of HIV related heart muscle disease, and suggest that cardiac autoantibodies may be markers of the development of left ventricular dysfunction in HIV positive patients with normal hearts.
Predicting the Morphology and Viscosity of Microemulsions Using the HLD-NAC Model (2010)

This work focuses on extending the HLD-NAC model to help predict the shape and viscosity of SDHS−toluene−water microemulsions from readily available formulation parameters. To do so, a new shape-based NAC model was introduced which relates the net and average curvatures to the length and radius of microemulsion droplets possessing a hypothesized cylindrical core with hemispherical end caps. Knowing the shape of these droplets, theoretical scattering profiles and maximum hydrodynamic radii were predicted. Furthermore, considering the predicted volume fraction of the dispersed droplets alongside the shape allows for the accurate prediction of the microemulsion viscosity. It was found that treating the microemulsion phase as a dilute suspension of rigid rods yielded predicted viscosities close to the experimental values near the bicontinuous phase transition limits. These correlations were further extended to published experimental data with regard to the viscosities of nonionic surfactant systems. The predicted microemulsion morphology and viscosity may be useful in the design of formulations for nanoparticle synthesis, enhanced oil recovery, and various environmental remediation technologies.
A new interleaver design and its application to turbo codes (2003)

We present a general interleaver structure that can be systematically derived from any existing block interleaver. When used in a turbo code with proper encoding and decoding procedures, the proposed interleaver is capable of providing unbounded interleaving depth with bounded decoding delay. Given a fixed decoding delay, the new interleaver results in superior bit error rate (BER) performance. The algebraic properties of the associated turbo codes are examined to provide guidelines in design the permutation rule.
Variability and determinants of total homocysteine concentrations in plasma in an elderly population (1998)

The variability of plasma total homocysteine (tHcy) was examined in 96 individuals over a 1-yr period. Blood tHcy concentrations varied from 7.1 micromol/L in the bottom quintile to 14.5 micromol/L in the top quintile. The mean tHcy was 10.4 micromol/L, the between-person SD was 2.5 micromol/L, and the within-person SD was 0.93 micromol/L. There was little seasonal variation, and the reliability coefficient was 0.88. Mean tHcy concentrations were inversely related to mean plasma folate (r = -0.36) and vitamin B12 (r = -0.35) concentrations. Median tHcy concentrations were approximately 1 micromol/L higher in men than in women and in older (70 to 74 years) than in younger (65 to 69 years) individuals and higher in those with the TT and CT genotypes for the methylenetetrahydrofolate reductase polymorphism than in those with the CC genotype (10.7 and 10.6 vs 9.6 micromol/L). Epidemiological studies based on single tHcy measurements may underestimate the magnitude of any risk associations with disease by 10-15%.
Determinants of 14-3-3σ Protein Dimerization and Function in Drug and Radiation Resistance (2013)

Many proteins exist and function as homodimers. Understanding the detailed mechanism driving the homodimerization is important and will impact future studies targeting the "undruggable" oncogenic protein dimers. In this study, we used 14-3-3σ as a model homodimeric protein and performed a systematic investigation of the potential roles of amino acid residues in the interface for homodimerization. Unlike other members of the conserved 14-3-3 protein family, 14-3-3σ prefers to form a homodimer with two subareas in the dimeric interface that has 180° symmetry. We found that both subareas of the dimeric interface are required to maintain full dimerization activity. Although the interfacial hydrophobic core residues Leu(12) and Tyr(84) play important roles in 14-3-3σ dimerization, the non-core residue Phe(25) appears to be more important in controlling 14-3-3σ dimerization activity. Interestingly, a similar non-core residue (Val(81)) is less important than Phe(25) in contributing to 14-3-3σ dimerization. Furthermore, dissociating dimeric 14-3-3σ into monomers by mutating the Leu(12), Phe(25), or Tyr(84) dimerization residue individually diminished the function of 14-3-3σ in resisting drug-induced apoptosis and in arresting cells at G2/M phase in response to DNA-damaging treatment. Thus, dimerization appears to be required for the function of 14-3-3σ.
Brain Peptides: What, Where, And Why? (1983)

Within the past decade, a large number of peptides have been described within the vertebrate central nervous system. Some of these peptides were previously known to be present in nonneural vertebrate tissues, as well as in lower species, in which they may serve as primitive elements of intercellular communication prior to the development of neuronal or endocrine systems. In vertebrates, these peptides are thought to have neurotransmitter or neuromodulatory roles and appear to be involved in the regulation of a number of homeostatic systems, although the mechanisms of their actions are still unclear.
Fluorescent Antibody Techniques (1961)

The diagnosis of early, mild, or atypical whooping cough is dependent upon identification of the etiologic agent. Although procedures for the isolation of Bordetella pertussis<sup>1</sup>have been available for many years and are of proven diagnostic aid, they have not gained the wide usage they seem to deserve. A recognized limitation is the time needed: 3, more often 4, and occasionally more, days are required for a positive report. The possibility of using fluorescent antibody methods for rapid identification of B. pertussis in nasopharyngeal specimens is suggested by the promising results reported in recent studies of a number of bacterial infections. For example, Group A streptococci,<sup>2,3</sup>enteropathogenic Escherichia coli,<sup>4</sup>Haemophilus influenzae, Type B,<sup>5</sup>Neisseria gonorrhoeae,<sup>6</sup>Vibrio comma,<sup>7</sup>Leptospira,<sup>8</sup>and certain other bacterial agents have been demonstrated by means of this technique in specimens taken directly from the patient. The work of de Repentigny
Identification of malicious web pages for crawling based on network-related attributes of web server (2010)

In this paper, we propose an identification algorithm of malicious Web pages for crawlers, which collect Web pages for the later task to detect malicious Web pages based on the content. Recently, some organization would have to automatically crawl the Web pages with the crawlers for later checking by humans. However, since manually checking Web pages is an expensive task, the total cost would be enormous if the crawlers collected Web pages indiscriminately. Some automatically checking systems can make the human task more efficient, however, they cannot be used to increase the number of malicious Web pages. To solve these problems, we propose an efficient algorithm to determine whether the sites include malicious or dangerous content for crawling Web pages. The feature of the algorithm is that it can determine the probability of a site being malicious or harmless as calculated from the network-related attributes of the Web server derived from the URL string. The attributes refer to the domain name, directory name, and the IP (Internet Protocol) address of the nearest router from the Web server. To confirm the effectiveness of the proposed algorithm, we conducted an evaluation experiment in a simulated environment. We compared the number of the collected malicious Web pages by the proposed algorithm with that of a random sampling algorithm in the experiment. The advantage is +82.8% high in maximum on a stable condition. We also showed an example of crawling trajectories using the proposed algorithm and conventional crawling algorithms. The example showed that the proposed algorithm is able to collect more malicious Web pages than the conventional algorithms.
Scattering delay and renormalization of the wave-diffusion constant (1992)

Recent work by van Albada, van Tiggelen, Lagendijk, and Tip reveals the existence of a significant correction to the wave-diffusion constant. We give a simple physical picture for this, along with a derivation for the case of scalar wave and weak disorder. The result of van Albada et al. is largely confirmed and its inevitability established using the notion of Wigner scattering time.
A double-blind, randomized, placebo-controlled clinical trial to evaluate the safety and efficacy of mupirocin calcium ointment for eliminating nasal carriage of <i>Staphylococcus aureus</i> among hospital personnel (1995)

Sixty-eight health care workers were enrolled in a double-blind clinical trial and randomized to receive either mupirocin calcium ointment or placebo, intranasally bid for 5 days. Nasal cultures were taken immediately before starting treatment, 1 and 2 during treatment, at the end of treatment, 3 days later, weekly for 1-5 weeks and then monthly for 2-6 months after treatment. Mupirocin eliminated nasal carriage with Staphylococcus aureus in 58% of subjects within two days and 86.7% subjects by the end of therapy compared to 9.4% subjects at the end of treatment with placebo (P < 0.001). Post-treatment colonization rates of 43%, 56% and 67% were attained after 1 month, 2-4 and 6 months treatment with mupirocin respectively and recolonisation with the same strain of S. aureus that had been isolated before treatment was noted in 32%, 40% and 48%. No resistance to mupirocin developed and the drug was well tolerated. Mupirocin is safe and effective in suppressing nasal carriage of S. aureus.
Mueller matrix optical imaging with application to tissue diagnostics (2003)

In this paper we present experimental results demonstrating processing techniques developed in our laboratory that can be utilized to decode or extract useful information from two-dimensional Mueller matrices of turbid media. Through the use of these methods, involving the partial least squares technique, it is shown how scattering coefficient contributions as a function of particle size can be estimated for a given sample. Furthermore, we demonstrate how a spatial selection algorithm known as "chain select" can be used to help facilitate the interpretation of the measured Mueller matrix images. The samples utilized in this investigation were comprised of polystyrene spheres with diameters ranging from 200 nm to 2000 nm and analyzed with 514 nm light. At this wavelength, both Rayleigh and Mie-types of scattering are observed.
Intestinal intraepithelial lymphocytes bind to colon cancer cells by HML-1 and CD11a. (1993)

Human intraepithelial lymphocytes (IEL), predominantly CD8+ T-lymphocytes located between intestinal epithelial cells (EC), may represent the first-line immune defense against colon cancer. The mechanism by which IEL bind to the colon cancer line, DLD-1, was evaluated. A larger fraction of IEL than peripheral blood mononuclear cells bound to DLD-1 monolayers (25 +/- 16 versus 8 +/- 4% binding, P < 0.05). Binding increased when DLD-1 monolayers were incubated with interferon-gamma but not with tumor necrosis factor-alpha. Similar numbers of IEL adhered to EC tumors, HT-29 and 5637, and the non-EC tumor, A375, but fewer bound to nonmalignant smooth muscle (HISM) and fibroblast (KD) lines (P < 0.01). Binding of IEL to DLD-1 was reduced by monoclonal antibodies to HML-1 and CD11a (47 +/- 9 and 26 +/- 13% inhibition, respectively) and was completely eliminated by both combined (93 +/- 4% inhibition). Anti-HML-1 also inhibited the binding of IEL to other EC tumors but did not affect binding to non-EC tumors or fibroblasts. To conclude, the binding of IEL to EC tumors is mediated by HML-1 and CD11a [A. I. Roberts, S. M. O'Connell, and E. C. Ebert. Binding of intraepithelial lymphocytes to colon cancer cells is mediated by HML-1 and LFA-1 (abstract). Gastroenterology, 102: A685, 1992].
Embryo vitrification using a novel semi-automated closed system yields in vitro outcomes equivalent to the manual Cryotop method (2014)

This study was funded by Genea Ltd. S.B., N.M.T., T.T.P., S.J.M., M.C.B. and T.S. are shareholders of Genea Ltd. E.V., C.H., C.L., S.R.L. and S.M.D. are shareholders of Planet Innovation Pty Ltd. The remaining authors are employees of either Genea Ltd. or Planet Innovation Pty Ltd.
Synthetic vs. Natural/Biodegradable Polymers for Delivery of shRNA-Based Cancer Therapies (2008)

DNA vector-based short hairpin RNA (shRNA) as a means of effecting RNA interference (RNAi) is a promising mechanism for the precise disruption of gene expression to achieve a therapeutic effect. The clinical usage of shRNA therapeutics in cancer is limited by obstacles related to effective delivery into the nuclei of target cancer cells. Significant pre-clinical data have been amassed about biodegradable and non-biodegradable polymeric delivery vehicles that are relevant for shRNA delivery into humans. Here, we will review some leading candidates for clinical usage with a focus on studies relating to their potential for usage in cancer shRNA therapeutics and discuss some of the advantages and disadvantages of using biodegradable and non-biodegradable delivery vehicles.
Circularly Permutated Bioluminescent Probes for Illuminating Ligand-Activated Protein Dynamics (2008)

Engineered bioluminescent enzymes provide a creative approach for illuminating the intracellular molecular events. We demonstrate a new strategy for molecular imaging of bioactive small molecules using circularly permutated luciferases (cpLuc), derived from Gaussia princeps (GLuc), Photinus pyralis (FLuc), and Pyrearinus termitilluminans (CBLuc): (i) the luciferases were first dissected into two fragments, (ii) the original N- and C-termini were linked with a GS linker and the new termini were created in an appropriate site, and (iii) the new ends were correspondingly linked with proteins of interest, e.g., a ligand-binding domain (LBD) and an LBD-recognition protein. When the ends of the cpCBLuc were linked with LBD of estrogen receptor (ER) and Src homology 2 domain of Src (SH2 of Src), the estrogen can trigger an intramolecular ER LBD-Src SH2 binding. This assembly subsequently provokes an approximation of the adjacent fragments of cpCBLuc recovering the enzyme activity. These probes were surprisingly stable in the mammalian cells and largely exhibited a decreased background luminescence (e.g., 1000 times in case of cpGLuc) and improved signal-to-noise ratios, compared with the non-CP indicators. This study offers a new strategy for luciferase-aided probing systems. Our study is the first to fabricate circular permutation (CP) in luciferases for tracing the molecular dynamics of proteins.