gebhart/patrepeval huggingface dataset:
A partial loss of function allele of Methyl-CpG-binding protein 2 predicts a human neurodevelopmental syndrome (2008)

Rett Syndrome, an X-linked dominant neurodevelopmental disorder characterized by regression of language and hand use, is primarily caused by mutations in methyl-CpG-binding protein 2 (MECP2). Loss of function mutations in MECP2 are also found in other neurodevelopmental disorders such as autism, Angelman-like syndrome and non-specific mental retardation. Furthermore, duplication of the MECP2 genomic region results in mental retardation with speech and social problems. The common features of human neurodevelopmental disorders caused by the loss or increase of MeCP2 function suggest that even modest alterations of MeCP2 protein levels result in neurodevelopmental problems. To determine whether a small reduction in MeCP2 level has phenotypic consequences, we characterized a conditional mouse allele of Mecp2 that expresses 50% of the wild-type level of MeCP2. Upon careful behavioral analysis, mice that harbor this allele display a spectrum of abnormalities such as learning and motor deficits, decreased anxiety, altered social behavior and nest building, decreased pain recognition and disrupted breathing patterns. These results indicate that precise control of MeCP2 is critical for normal behavior and predict that human neurodevelopmental disorders will result from a subtle reduction in MeCP2 expression.
The Local Path Constraint for the Recognition of Speech (1989)

In this paper, an local path constraint Is proposed in order to increase the speech recognition rate. An input speech signal is analyzed by autocorrelation and LPC coefficient as parameters. The local path constraint of the proposed type was compared with the conventional five types. The speechs used in this search are the subway stops, and the 130 words pronounced 10 times for the different 13 words consisting of 11 characters of syllable by 2 male and 1 female are tested. As a result, we proved that this proposed type is the most optimal type and the recognition rate of is obtained .
Thermoelectric Transport in Silicon Germanium Nanocomposite (2008)

Direct energy conversion between heat and electrical energy based on thermoelectric effects is attractive for potential applications in waste heat recovery and environmentally-friendly refrigeration. The energy conversion efficiency depends on the dimensionless figure of merit of thermoelectric materials, ZT, which is proportional to the electrical conductivity, the square of the Seebeck coefficient, and the inverse of the thermal conductivity. Currently, the low ZT values of available materials restrict the applications of this technology. However, significant enhancements in ZT were recently reported in nanostructured materials such as superlattices mainly due to their low thermal conductivities. According to recent studies, the reduced thermal conductivity of nanostructures is attributed to the large number of interfaces at which phonons are scattered. Based on this idea, nanocomposites are expected to have a lower thermal conductivity than their bulk counterparts with low fabrication cost just by mixing nano sized particles. In this work, we will discuss mechanisms of thermoelectric transport via modeling and provide experimental evidence on the enhancement of thermoelectric figure of merit in SiGe-based nanocomposites.
The prognostic value of preoperative serum levels of CEA, CA19-9 and CA72-4 in patients with colorectal cancer (2001)

Subject headings tumor markers/biological; colorectal neoplasms/
Synthesis and Evaluation of New Alkylamides Derived from α-Hydroxysanshool, the Pungent Molecule in Szechuan Pepper (2009)

Szechuan pepper is widely used in Asia as a spice for its pleasant pungent and tingling sensations, produced by natural alkylamides called sanshools. alpha-Hydroxysanshool, the main alkylamide found in the pericarp of the fruit, stimulates sensory neurons innervating the mouth by targeting two chemosensitive members of the transient receptor potential (TRP) channels, TRPV1 and TRPA1. As it was previously found that configuration of the unsaturations in the alpha-hydroxysanshool alkyl chain is required for TRPA1 but not TRPV1 selectivity, this study aimed at obtaining more potent and selective TRPA1 agonists using alpha-hydroxysanshool as a starting material. This paper reports the preparation of new alkylamides derived from sanshool and their efficacy in stimulating TRPA1 and TRPV1 receptors. The data provide knowledge of the main sanshool chemical functionalities required for TRP channel activation, but they also evidence new selective and potent TRPA1 agonists based on alpha-hydroxysanshool.
Genetic Reactivation of Cone Photoreceptors Restores Visual Responses in Retinitis Pigmentosa (2010)

Retinitis pigmentosa refers to a diverse group of hereditary diseases that lead to incurable blindness, affecting two million people worldwide. As a common pathology, rod photoreceptors die early, whereas light-insensitive, morphologically altered cone photoreceptors persist longer. It is unknown if these cones are accessible for therapeutic intervention. Here, we show that expression of archaebacterial halorhodopsin in light-insensitive cones can substitute for the native phototransduction cascade and restore light sensitivity in mouse models of retinitis pigmentosa. Resensitized photoreceptors activate all retinal cone pathways, drive sophisticated retinal circuit functions (including directional selectivity), activate cortical circuits, and mediate visually guided behaviors. Using human ex vivo retinas, we show that halorhodopsin can reactivate light-insensitive human photoreceptors. Finally, we identified blind patients with persisting, light-insensitive cones for potential halorhodopsin-based therapy.
Antibodies in HIV-1 Vaccine Development and Therapy (2013)

Despite 30 years of study, there is no HIV-1 vaccine and, until recently, there was little hope for a protective immunization. Renewed optimism in this area of research comes in part from the results of a recent vaccine trial and the use of single-cell antibody-cloning techniques that uncovered naturally arising, broad and potent HIV-1-neutralizing antibodies (bNAbs). These antibodies can protect against infection and suppress established HIV-1 infection in animal models. The finding that these antibodies develop in a fraction of infected individuals supports the idea that new approaches to vaccination might be developed by adapting the natural immune strategies or by structure-based immunogen design. Moreover, the success of passive immunotherapy in small-animal models suggests that bNAbs may become a valuable addition to the armamentarium of drugs that work against HIV-1.
<title>Usability engineering: domain analysis activities for augmented-reality systems</title> (2002)

This paper discusses our usability engineering process for the Battlefield Augmented Reality System (BARS). Usability engineering is a structured, iterative, stepwise development process. Like the related disciplines of software and systems engineering, usability engineering is a combination of management principals and techniques, formal and semi- formal evaluation techniques, and computerized tools. BARS is an outdoor augmented reality system that displays heads- up battlefield intelligence information to a dismounted warrior. The paper discusses our general usability engineering process. We originally developed the process in the context of virtual reality applications, but in this work we are adapting the procedures to an augmented reality system. The focus of this paper is our work on domain analysis, the first activity of the usability engineering process. We describe our plans for and our progress to date on our domain analysis for BARS. We give results in terms of a specific urban battlefield use case we have designed.
Human RAS Superfamily Proteins and Related GTPases (2004)

The tumor oncoproteins HRAS, KRAS, and NRAS are the founding members of a larger family of at least 35 related human proteins. Using a somewhat broader definition of sequence similarity reveals a more extended superfamily of more than 170 RAS-related proteins. The RAS superfamily of GTP (guanosine triphosphate) hydrolysis-coupled signal transduction relay proteins can be subclassified into RAS, RHO, RAB, and ARF families, as well as the closely related Galpha family. The members of each family can, in turn, be arranged into evolutionarily conserved branches. These groupings reflect structural, biochemical, and functional conservation. Recent findings have provided insights into the signaling characteristics of representative members of most RAS superfamily branches. The analysis presented here may serve as a guide for predicting the function of numerous uncharacterized superfamily members. Also described are guanosine triphosphatases (GTPases) distinct from members of the RAS superfamily. These related proteins employ GTP binding and GTPase domains in diverse structural contexts, expanding the scope of their function in humans.
Nanoscale Hydrophobic Recovery:  A Chemical Force Microscopy Study of UV/Ozone-Treated Cross-Linked Poly(dimethylsiloxane) (2003)

Chemical force microscopy (CFM) in water was used to map the surface hydrophobicity of UV/ozone-treated poly(dimethylsiloxane) (PDMS; Sylgard 184) as a function of the storage/recovery time. In addition to CFM pull-off force mapping, we applied indentation mapping to probe the changes in the normalized modulus. These experiments were complemented by results on surface properties assessed on the micrometer scale by X-ray photoelectron spectroscopy and water contact-angle measurements. Exposure times of < or = 30 min resulted in laterally homogeneously oxidized surfaces, which are characterized by an increased modulus and a high segmental mobility of PDMS. As detected on a sub-50-nm level, the subsequent "hydrophobic recovery" was characterized by a gradual increase in the pull-off forces and a decrease in the normalized modulus, approaching the values of unexposed PDMS after 8-50 days. Lateral imaging on briefly exposed PDMS showed the appearance of liquid PDMS in the form of droplets with an increasing recovery time. Longer exposure times (60 min) led to the formation of a hydrophilic silica-like surface layer. Under these conditions, a gradual surface reconstruction within the silica-like layer occurred with time after exposure, where a hydrophilic SiOx-enriched phase formed < 100-nm-sized domains, surrounded by a more hydrophobic matrix with lower normalized modulus. These results provide new insights into the lateral homogeneity of oxidized PDMS with a resolution in the sub-50-nm range.
Complementary DNA Sequencing: Expressed Sequence Tags and Human Genome Project (1991)

Automated partial DNA sequencing was conducted on more than 600 randomly selected human brain complementary DNA (cDNA) clones to generate expressed sequence tags (ESTs). ESTs have applications in the discovery of new human genes, mapping of the human genome, and identification of coding regions in genomic sequences. Of the sequences generated, 337 represent new genes, including 48 with significant similarity to genes from other organisms, such as a yeast RNA polymerase II subunit; Drosophila kinesin, Notch, and Enhancer of split; and a murine tyrosine kinase receptor. Forty-six ESTs were mapped to chromosomes after amplification by the polymerase chain reaction. This fast approach to cDNA characterization will facilitate the tagging of most human genes in a few years at a fraction of the cost of complete genomic sequencing, provide new genetic markers, and serve as a resource in diverse biological research fields.
A Simple and Robust Method for Preparation of cDNA Nylon Microarrays (2004)

DNA array technology has made remarkable progress in recent years and has become an indispensable tool in molecular biology research. However, preparing high-quality custom-made DNA arrays at a reasonable cost is still an important concern because we cannot abandon the use of DNA array systems designed for specific purposes. To address these problems, we here report the use of rolling circle amplification products of cDNA plasmids dissolved in 80% formamide as DNA probes immobilized on a nylon membrane. First, because formamide is practically non-volatile under ambient conditions and nucleic acids are easily dissolved in it, the use of formamide as a DNA solvent ensures that the DNA concentration of the solution will not change during arraying, which often takes several hours to a day depending on the number of DNA spots and arrays to produce. Secondly, the use of rolling circle amplification technology greatly reduced the labor needed to prepare the spotted DNA. The results in this study demonstrate that the introduction of these two modifications in preparation of nylon DNA array greatly improved its quality.
A Small-molecule Inhibitor Directed against the Chemokine Receptor CXCR4 Prevents its Use as an HIV-1 Coreceptor (1997)

The chemokine receptor CXCR4 is the major coreceptor used for cellular entry by T cell- tropic human immunodeficiency virus (HIV)-1 strains, whereas CCR5 is used by macrophage (M)-tropic strains. Here we show that a small-molecule inhibitor, ALX40-4C, inhibits HIV-1 envelope (Env)-mediated membrane fusion and viral entry directly at the level of coreceptor use. ALX40-4C inhibited HIV-1 use of the coreceptor CXCR4 by T- and dual-tropic HIV-1 strains, whereas use of CCR5 by M- and dual-tropic strains was not inhibited. Dual-tropic viruses capable of using both CXCR4 and CCR5 were inhibited by ALX40-4C only when cells expressed CXCR4 alone. ALX40-4C blocked stromal-derived factor (SDF)-1alpha-mediated activation of CXCR4 and binding of the monoclonal antibody 12G5 to cells expressing CXCR4. Overlap of the ALX40-4C binding site with that of 12G5 and SDF implicates direct blocking of Env interactions, rather than downregulation of receptor, as the mechanism of inhibition. Thus, ALX40-4C represents a small-molecule inhibitor of HIV-1 infection that acts directly against a chemokine receptor at the level of Env-mediated membrane fusion.
Temperature‐gradient gel electrophoresis for the detection of polymorphic DNA and for quantitative polymerase chain reaction (1992)

In order to detect mutations in a gene, either known mutations from human diseases or artificial ones in transgenic animals, or to screen for not yet identified mutations in patients, a method is required which guarantees detection of mutations which might occur in every single position of the whole open reading frame (ORF). It will be shown that a combination of polymerase chain reaction (PCR) and temperature gradient gel electrophoresis (TOGE) fulfills these requirements. By thermodynamic calculations the shift in the gel electrophoresis due to a mutation can be calculated in dependence on the position of the mutation. The theoretical results were tested with the mutations known so far. The quantitative determination of the copy number of a specific DNA or RNA sequence in a biological specimen (quantitative PCR) can be performed precisely and easily by combining PCR and TGGE. The system uses a quantification strategy of a new type of internal standardization. TGGE is applied to separate homo- and heteroduplexes which correspond respectively to standard and template sequences. The accuracy of this quantification strategy is very high, with a variability of < 15%. In addition to quantification, PCR/TGGE detects PCR artifacts and template mutants.
Generating Sensor Diversity through Combinatorial Polymer Synthesis (1997)

A new approach for rapid, simple generation of uniquely responding sensors for use in polymer-based sensor arrays has been developed. Polymerization reactions between different combinations of two starting materials have been found to lead to many new, unique sensors with responses not simply related to the proportion of the starting materials. This approach is demonstrated in two ways: (a) the use of discrete polymer sensing cones each comprised of a specific monomer combination and (b) the fabrication of a gradient sensor, containing all combinations between the starting and ending monomer concentrations. Gradient sensors were fabricated using two different binary monomer systems, with both systems showing regions of broadly diverse fluorescence responses to organic vapor pulses.
Cell size distribution as a parameter for the predetermination of exponential growth during repeated batch cultivation of CHO cells (1997)

The routine measurement of the cell size distribution of a Chinese hamster ovary (CHO) cell population during a repeated batch process enables the predetermination of exponential growth even 24 h before the population enters the log phase, due to a short but significantly increased cell size during the lag phase. A prolongation of the stationary phase causes to progressive limitation in asparagine, serine, and ethanolamine. Such extended limitation influences the duration of the following lag phase and obviously induces a synchronization of the cell population that can be monitored easily by a fast cell size analyzing technique. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 793-797, 1997.
Power Scaling for Cognitive Radio (2005)

In this paper we explore the idea of using cognitive radios to reuse locally unused spectrum for their own transmissions. We impose the constraint that they cannot general e unacceptable levels of interference to licensed systems on the same frequency. Using received SNR as a proxy for distance, we prove that a cognitive radio can vary its transmit power while maintaining a guarantee of service to primary users. We consider the aggregate interference caused by multiple cognitive radios and show that aggregation causes a change in the effective decay rate of the interference. We examine the effects of heterogeneous propagation path loss functions and justify the feasibility of multiple secondary users with dynamic transmit powers. Finally, we prove the fundamental constraint on a cognitive radio's transmit power is the minimum SNR it can detect and explore the effect of this power cap.
Interleukin-6 protects liver against warm ischemia/reperfusion injury and promotes hepatocyte proliferation in the rodent (1997)

Interleukin-6 (IL-6) is an acute reactant cytokine with anti-inflammatory properties, which has been found to prevent injury in a model of acute hepatitis in mice through downregulation of tumor necrosis factor alpha (TNF-alpha); to correlate inversely with markers of hepatocellular injury in patients with liver ischemia; and to initiate liver regeneration in mice. In this study, we investigated the role of IL-6 in rodent models of hepatic warm ischemia/reperfusion (WI/Rp) injury. IL-6-deficient mice (-/-) were subjected to hepatic WI and compared with C57BL/6 mice, as well as IL-6 -/- mice pretreated with recombinant IL-6 (rIL-6). The effects of rIL-6 following various periods of ischemia were further studied in models of hepatic ischemia in rats. IL-6 -/- mice had increased reperfusion injury as assessed by transaminase levels and a tissue necrosis scoring system when compared with controls, an effect prevented by pretreatment with rIL-6. Similarly, rats pretreated with rIL-6 had reduced reperfusion injury and better survival than controls in each respective WI group. Tissue TNF-alpha expression measured by Northern blot analysis and serum C-reactive protein (CRP) levels, a marker of inflammation, were significantly reduced in animals pretreated with rIL-6. Administration of antibodies to TNF-alpha reproduced the beneficial effect of rIL-6. Hepatocyte proliferation, as assessed by a scoring method for mitotic index and proliferating nuclear cell antigen staining, was markedly increased in rIL-6-treated rats when compared with controls. In conclusion, this study suggests that IL-6 could play an important role in limiting hepatic warm ischemia/reperfusion (WI/Rp) injury, probably through its anti-inflammatory properties, modulation of TNF-alpha, and/or promotion of liver regeneration. rIL-6 might become an important cytokine in clinical situations associated with WI/Rp injury.
Effect of Benzalkonium Chloride/EDTA on the Ocular Bioavailability of Ketorolac Tromethamine following Ocular Instillation to Normal and De-epithelialized Corneas of Rabbits (1996)

This study was designed to examine the effect of benzalkonium chloride/ethylenediaminetetraacetic acid (BAK/EDTA) on the ocular bioavailability (Focular) of ketorolac tromethamine after ocular instillation to normal and de-epithelialized corneas of rabbits both in vitro and in vivo. The in vitro Focular of the formulations was measured in flow-through perfusion chambers. For in vivo studies, a 35 microL dose of 0.5% ketorolac tromethamine with or without BAK/EDTA was instilled into rabbit eyes with intact or de-epithelialized corneas. At 0.5, 1, 2, 4, 6, and 8 h postdose, rabbits were euthanized, and the corneas and aqueous humor were collected from both eyes. The ketorolac concentrations from both in vivo and in vitro samples were quantified by reversed-phase high-performance liquid chromatography. The in vitro study results indicated that BAK/EDTA statistically significantly increased the Focular of ketorolac through de-epithelialized corneas but not through intact corneas. The in vivo study results showed that BAK/EDTA had no effect on the Focular of ketorolac in rabbits with intact corneas, based on the values of the area under the aqueous humor concentration versus time curves (AUC0-6h) of ketorolac. As expected, de-epithelialization of the corneas produced a faster and greater ocular absorption of ketorolac as evidenced by the smaller Tmax and larger AUC values compared to those for the intact corneas in vivo. However, BAK/EDTA decreased the ocular absorption of ketorolac in rabbits with de-epithelialized corneas. The half-lives (t 1/2) of ketorolac in corneal tissue and aqueous humor were longer in rabbits with intact corneas than those in rabbits with de-epithelialized corneas. In conclusion, the in vivo Focular of ketorolac was not altered by BAK/EDTA in rabbits with intact corneas, but it was decreased by BAK/EDTA in rabbits with de-epithelialized corneas. Therefore, the formulation with ketorolac alone may be better as a post-operative ocular analgesic.
Clock, Flip-Flop, and Combinatorial Logic Contributions to the SEU Cross Section in 90 nm ASIC Technology (2009)

Utilizing an application specific integrated circuit (ASIC) with 140 different shift chains, and a wide variety of test modes, a design of experiments (DOE) approach was used to characterize a commercial 90 nm CMOS technology for its sensitivity to single event effects (SEE). The variables characterized included: well structure on the wafer, density of well contacts, logic data pattern, angle of indicence, flip-flop redundancy, variation in sensitive node spacing, and the effect of transients as a function of combinatorial logic type. Analysis of the cross section contribution from the clock, flip-flop and SET target circuitry showed that any hardening technique used in a production integrated circuit may be limited in its effectiveness due to other circuits and logic in the integrated circuit.
Techniques for data hiding (1996)

Data hiding, a form of steganography, embeds data into digital media for the purpose of identification, annotation, and copyright. Several constraints affect this process: the quantity of data to be hidden, the need for invariance of these data under conditions where a "host" signal is subject to distortions, e.g., lossy compression, and the degree to which the data must be immune to interception, modification, or removal by a third party. We explore both traditional and novel techniques for addressing the data-hiding process and evaluate these techniques in light of three applications: copyright protection, tamper-proofing, and augmentation data embedding.