gebhart/patrepeval huggingface dataset:
Molecular Studies on Entry Exclusion in Escherichia coli Minicells (1972)

Minicells produced by abnormal cell division in a strain of Escherichia coli (K-12) have been employed here to investigate the phenomenon of "entry exclusion." When purified minicells from strains containing F' or R factors, or both, are mated with radioactive thymidine-labeled Hfr or R(+) donors, the recipient minicells can be conveniently separated from normal-sized donors following mating, and the products of conjugation can be analyzed in the absence of donors and of further growth of the recipients. Transmissible plasmids or episomes are transferred less efficiently to purified minicells derived from strains carrying similar or related elements than to strains without them. Measurement of deoxyribonucleic acid (DNA) degradation and determination of weight-average molecular weights following transfer indicate that degradation of transferred DNA or transfer of smaller pieces cannot account for the comparative reduction in transfer to entry-excluding recipients. Therefore, we conclude that entry exclusion operates to prevent the physical entry of DNA into recipients expressing the exclusion phenotype. The R-produced repressor (product of the drd(+) gene), which represses fertility (i.e., ability to act as donor), reduces exclusion mediated by R or F factor, or both, in matings between strains carrying homologous elements. Furthermore, the data suggest that the presence of the F pilus or F-like R pilus on recipient cells ensures maximum expression of the exclusion phenotype but is not essential for its expression. In contrast to previous suggestions, we found no evidence for a reduction of entry exclusion attributable to the DNA temperature-sensitive chromosomal mutation dnaB(TS).
EVOLUTION OF THE NADR REGULON IN ENTEROBACTERIACEAE (2005)

The NAD biosynthetic pathway and NAD transformations in E. coli and S. typhi are well characterized. Using comparative genomics methods we describe the NadR regulon in other Enterobacteriaceae, identity new candidate regulon members and demonstrate that even a very simple regulon covering an essential methabolic pathway could be different in closely related genomes.
Portable Intelligent Traffic Management System for Work Zones and Incident Management Systems: Best Practice Review (2008)

An intelligent portable traffic management system is an integrated system which consists of portable variable messages signs (PVMSs), vehicle detection systems (such as detectors, cameras and other surveillance equipment), a computer-based control center and communication systems. Based on detected traffic information, the system automatically determines messages to be displayed on the PVMSs and may also disseminate the information through highway advisory radios (HARs) and the Internet. This study involved a comprehensive review of the application of various intelligent portable traffic management systems for use in work zones and incident management and speed management technologies for use in work zones; it also identified innovative technologies that have the potential to improve highway traffic operations. Interviews were conducted with representatives from departments of transportation (DOTs) in various states and private industry regarding their experience with and knowledge of work zone and incident management deployment initiatives and innovative technologies. A summary of various systems, including their features, deployments, and evaluation results, if any, has been included in this paper. Some guidelines are developed in this study for the effective application of automated portable traffic management systems in work zones and incident areas.
Inertial navigation systems for mobile robots (1995)

A low-cost solid-state inertial navigation system (INS) for mobile robotics applications is described. Error models for the inertial sensors are generated and included in an extended Kalman filter (EKF) for estimating the position and orientation of a moving robot vehicle. Two different solid-state gyroscopes have been evaluated for estimating the orientation of the robot. Performance of the gyroscopes with error models is compared to the performance when the error models are excluded from the system. Similar error models have been developed for each axis of a solid-state triaxial accelerometer and for a conducting-bubble tilt sensor which may also be used as a low-cost accelerometer. An integrated inertial platform consisting of three gyroscopes, a triaxial accelerometer and two tilt sensors is described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Development and Evaluation of a Practical ELISA for Human Urinary Lipocalin-Type Prostaglandin D Synthase (2002)

This ELISA system is suitable for measurement of urinary L-PGDS in a routine clinical assay and may be useful to detect less advanced stages of renal diseases.
Canonical Wnt Signaling Regulates Organ-Specific Assembly and Differentiation of CNS Vasculature (2008)

Every organ depends on blood vessels for oxygen and nutrients, but the vasculature associated with individual organs can be structurally and molecularly diverse. The central nervous system (CNS) vasculature consists of a tightly sealed endothelium that forms the blood-brain barrier, whereas blood vessels of other organs are more porous. Wnt7a and Wnt7b encode two Wnt ligands produced by the neuroepithelium of the developing CNS coincident with vascular invasion. Using genetic mouse models, we found that these ligands directly target the vascular endothelium and that the CNS uses the canonical Wnt signaling pathway to promote formation and CNS-specific differentiation of the organ's vasculature.
Tandem inverted repeat system for selection of effective transgenic RNAi strains in Chlamydomonas (2004)

RNA interference (RNAi), the double-stranded RNA (dsRNA) triggered post-transcriptional gene silencing, is becoming a powerful tool for reverse genetics studies. Stable RNAi, induced by the expression of inverted repeat (IR) transgenes, has been achieved in protozoa, algae, fungi, plants, and metazoans. However, the level of gene silencing is often quite variable, depending on the type of construct, transgene copy number, site of integration, and target gene. This is a hindrance in functional genomics studies, where it is desirable to suppress target genes reliably to analyze unknown phenotypes. Consequently, we explored strategies for direct selection of effective transgenic RNAi lines in Chlamydomonas reinhardtii. We initially attempted to suppress expression of the Rubisco small subunit multigene family by placing an IR, homologous to the conserved coding sequence, in the 3'UTR of a transgene conferring resistance to bleomycin. However, this approach was fairly inefficient at inducing RNAi as many strains displayed defective transgene integration, resulting in partial or complete deletion of the IR, or low levels of dsRNA expression, presumably due to transcriptional silencing of the integrated IR transgenes. To overcome these problems we designed a system consisting of tandem IR transgenes that consistently triggered co-silencing of a gene with a selectable RNAi-induced phenotype (encoding tryptophan synthase beta subunit) and another gene of interest (encoding either Ku80, an RNA-binding protein, or a thioredoxin isoform). We anticipate that this approach will be useful for generating stable hypomorphic epi-mutants in high-throughput phenotypic screens.
Rat Porphobilinogen Deaminase Gene: A Pseudogene-Free Internal Standard for Laser-Assisted Cell Picking (1999)

Analysis of gene expression and its transcriptional regulation requires a reliable access to target mRNA. However, mRNA extractions from homogenized tissue are limited because only average data are obtained, and cell-specific expression may not be addressed. Here, we describe a new method that combines the microscopic selection of oligocellular clusters or a few isotypic cell profiles from complex tissues by UV-laser-assisted cell picking with a simplified and highly efficient protocol for mRNA amplification. For positive control and quantitation reference, a reliable housekeeping gene is needed. For this purpose, we designed primers of the rat porphobilinogen deaminase (PBGD) gene. In contrast to many commonly used housekeeping primer pairs that co-amplify processed pseudogenes, this sequence allowed detection of a pseudogene-free rat cDNA sequence, thus eliminating the need for a DNase-digestion step. PBGD mRNA was consistently expressed in all complex tissues investigated and in 21 specific cell types harvested by laser-assisted cell picking. PBGD is suggested as a reliable new rat housekeeping gene, particularly suitable for analysis of oligocellular samples such as those obtained by laser-assisted cell picking in complex tissues.
A Better Microstrip Connector (2005)

A microstrip connector has been developed which has a VSWR /spl ap/1.07 up to 18 GHz. Such low reflections allow very precision measurements to be made when characterizing microstrip components and circuit elements. Consequently this improvement in measurement resolution results in better design control and fewer design iterations. This performance has been achieved by incorporating a unique design which matches the electrical field patterns at the interface. Although a 7mm coax to 25 mil substrate design is shown here, the technique is applicable to other configurations and has been so applied.
Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand (2013)

Selective photocrosslinking reaction between 3-cyanovinylcarbazole nucleoside (CNVK) and 5-methylcytosine (mC), which is known as epigenetic modification in genomic DNA, was developed. The reaction was completely finished within 5 s of 366 nm irradiation, and the rate of this photocrosslinking reaction was ca. 30-fold higher than that in the case of unmodified normal cytosine. There were no significant differences in the thermodynamic parameters and the kinetics of hybrid formation of oligonucleotide (ODN) containing CNVK and its complementary ODN containing C or mC at the photocrosslinking site, and suggesting that the quick and selective photoreaction has potential for the selective detection of mC in the DNA strand via the photocrosslinking reaction.
Three-dimensional subband coding techniques for wireless video communications (2002)

We present a new 3D subband coding framework that achieves a good balance between high compression performance and channel error resilience. Various data transform methods for video decorrelation were examined and compared. The coding stage of the algorithm is based on a generalized adaptive quantization framework which is applied to the 3D transformed coefficients. It features a simple coding structure based on quadtree coding and lattice vector quantization. In typical applications, good performance at high compression ratios is obtained, often without entropy coding. Because temporal decorrelation is absorbed by the transform, traditional motion compensated prediction becomes unnecessary, resulting in a significant computational advantage over standard video coders. Error-resilience is achieved through classifying the compressed data streams into separated sub-streams with different error sensitivity levels. This enables a good adaptation to different channel models according to their noise statistics and error-protection protocols. Experimental results have shown that the subband video coder is able to achieve highly competitive performance relative to MPEG-2 in both noiseless and noisy environments. Lapped transforms are shown experimentally to outperform other transforms in the 3D subband environment. The subband coding framework provides a practical solution for video communications over wireless channels, where efficiency, error resilience and computational simplicity are vital in providing superior quality of service.
Predicting Inter-Thread Cache Contention on a Chip Multi-Processor Architecture (2005)

This paper studies the impact of L2 cache sharing on threads that simultaneously share the cache, on a chip multi-processor (CMP) architecture. Cache sharing impacts threads nonuniformly, where some threads may be slowed down significantly, while others are not. This may cause severe performance problems such as sub-optimal throughput, cache thrashing, and thread starvation for threads that fail to occupy sufficient cache space to make good progress. Unfortunately, there is no existing model that allows extensive investigation of the impact of cache sharing. To allow such a study, we propose three performance models that predict the impact of cache sharing on co-scheduled threads. The input to our models is the isolated L2 cache stack distance or circular sequence profile of each thread, which can be easily obtained on-line or off-line. The output of the models is the number of extra L2 cache misses for each thread due to cache sharing. The models differ by their complexity and prediction accuracy. We validate the models against a cycle-accurate simulation that implements a dual-core CMP architecture, on fourteen pairs of mostly SPEC benchmarks. The most accurate model, the inductive probability model, achieves an average error of only 3.9%. Finally, to demonstrate the usefulness and practicality of the model, a case study that details the relationship between an application's temporal reuse behavior and its cache sharing impact is presented.
Evidence that transgenes encoding components of the Wnt signaling pathway preferentially induce mammary cancers from progenitor cells (2003)

Breast cancer is a genetically and clinically heterogeneous disease, and the contributions of different target cells and different oncogenic mutations to this heterogeneity are not well understood. Here we report that mammary tumors induced by components of the Wnt signaling pathway contain heterogeneous cell types and express early developmental markers, in contrast to tumors induced by other signaling elements. Expression of the Wnt-1 protooncogene in mammary glands of transgenic mice expands a population of epithelial cells expressing progenitor cell markers, keratin 6 and Sca-1; subsequent tumors express these markers and contain luminal epithelial and myoepithelial tumor cells that share a secondary mutation, loss of Pten, implying that they arose from a common progenitor. Mammary tumors arising in transgenic mice expressing beta-catenin and c-Myc, downstream components of the canonical Wnt signaling pathway, also contain a significant proportion of myoepithelial cells and cells expressing keratin 6. Progenitor cell markers and myoepithelial cells, however, are lacking in mammary tumors from transgenic mice expressing Neu, H-Ras, or polyoma middle T antigen. These results suggest that mammary stem cells and/or progenitors to mammary luminal epithelial and myoepithelial cells may be the targets for oncogenesis by Wnt-1 signaling elements. Thus, the developmental heterogeneity of different breast cancers is in part a consequence of differential effects of oncogenes on distinct cell types in the breast.
Presystemic Extraction: Mechanisms and Consequences (1993)

Many drugs have incomplete systemic availability after oral dosage. This can be attributed to incomplete absorption from the gastrointestinal tract, or to presystemic extraction, in which a fraction of an orally administered dose is biotransformed before reaching the systemic circulation. Presystemic extraction can occur either via biotransformation by gastrointestinal mucosa or enteric flora, or via metabolism during the "first-pass" through the liver. For drugs with low oral bioavailability due to high presystemic extraction, impaired clearance leads to increased peak plasma levels and greater area under the concentration-time curve, but minimal change in elimination half-life.
Classical Quantum Mechanics (2003)

Despite its successes, quantum mechanics (QM) has remained mysterious to all who have encountered it. Starting with Bohr and progressing into the present, the departure from intuitive, physical reality has widened. The connection between QM and reality is more than just a “philosophical” issue. It reveals that QM is not a correct or complete theory of the physical world and that inescapable internal inconsistencies and incongruities arise when attempts are made to treat it as physical as opposed to a purely mathematical “tool.” Some of these issues are discussed in a review by F. Laloe [Am. J. Phys. 69, 655 (2001)]. In an attempt to provide some physical insight into atomic problems and starting with the same essential physics as Bohr of e moving in the Coulombic field of the proton and the wave equation as modified by Schrodinger, a classical approach is explored that yields a remarkably accurate model and provides insight into physics on the atomic level. The proverbial view, deeply seated in the wave-particle duality notion, that there is no large-scale physical counterpart to the nature of the electron may not be correct. Physical laws and intuition may be restored when dealing with the wave equation and quantummechanical problems. Specifically, a theory of classical quantum mechanics (CQM) is derived from first principles that successfully applies physical laws on all scales. Rather than using the postulated Schrodinger boundary condition “Ψ → 0 as r → ∞,” which leads to a purely mathematical model of the electron, the constraint is based on experimental observation. Using Maxwell’s equations, the classical wave equation is solved with the constraint that the bound (n = 1)state electron cannot radiate energy. By further application of Maxwell’s equations to electromagnetic and gravitational fields at particle production, the Schwarzschild metric is derived from the classical wave equation, which modifies general relativity to include conservation of spacetime in addition to momentum and matter/energy. The result gives a natural relationship among Maxwell’s equations, special relativity, and general relativity. CQM holds over a scale of spacetime of 85 orders of magnitude — it correctly predicts the nature of the universe from the scale of the quarks to that of the cosmos. A review is given by G. Landvogt [Internat. J. Hydrogen Energy 28, 1155 (2003)].
The antibody paradigm: present and future development as a scaffold for biopharmaceutical drugs (2009)

Early studies of the humoral immune response revealed an apparent paradox: an infinite diversity of antibody specificities encoded within a finite genome. In consequence antibodies became a focus of interest for biochemists and geneticists. It resulted in the elucidation of the basic structural unit, the immunoglobulin (Ig) domain, comprised of ~ 100 amino acid residues that generate the characteristic "immunoglobulin (Ig) fold". The Ig fold has an anti-parallel ß-pleated sheet (barrel) structure that affords structural stability whilst the ß-bends allow for essentially infinite structural variation and functional diversity. This versatility is reflected in the Ig domain being the most widely utilised structural unit within the proteome. Human antibodies are comprised of multiple Ig domains and their structural diversity may be enhanced through the attachment of oligosaccharides. This review summarizes our current understanding of the immunoglobulin structure/function relationships and the application of protein and oligosaccharide engineering to further develop the Ig domain as a scaffold for the generation of new and novel antibody based therapeutics.
The conformational quality of insoluble recombinant proteins is enhanced at low growth temperatures (2006)

Protein aggregation is a major bottleneck during the bacterial production of recombinant proteins. In general, the induction of gene expression at sub-optimal growth temperatures improves the solubility of aggregation-prone polypeptides and minimizes inclusion body (IB) formation. However, the effect of low temperatures on the quality of the recombinant protein, especially within the insoluble cell fraction, has been hardly ever explored. In this work, we have examined the conformational status of a recombinant GFP protein when produced in Escherichia coli below 37 degrees C. As expected, the fraction of aggregated protein largely decreased at lower temperatures, while the conformational quality of both soluble and aggregated GFP, as reflected by its specific fluorescence emission, progressively improved. This observation indicates that physicochemical conditions governing protein folding affect concurrently the quality of the soluble and the aggregated forms of a misfolding-prone protein, and that protein misfolding and aggregation are clearly not coincident events.
Cerebrospinal fluid in the differential diagnosis of Alzheimer’s disease: clinical utility of an extended panel of biomarkers in a specialist cognitive clinic (2018)

CSF AβX-42/X-40 and T-tau/Aβ1-42 ratios have utility in distinguishing AD from controls, bvFTD, and SD. None of the biomarkers tested had good specificity at distinguishing AD from DLB or PNFA.
계층분석법을 이용한 환경성과정보지표의 개발 (2004)

기존의 환경성과지표는 환경성과와 기업경영성과와의 관계분석의 미흡, 통합 지표 개발로 인한 기업별 차이점의 간과와 기업 외부용 위주의 지표 개발 등 한계를 가지고 있어서 다양한 이해관계자들에게 유용한 정보로서 그 기능을 다하지 못하고 있다. 이러한 문제를 보완하기 위하여 AHP법을 이용하여 환경성과평과의 가중치를 산정하였다. 평가영역별 가중치는 오염물질 배출처리현황 0.38, 환경경영 일반현황 0.23, 환경개선현황 0.22 순으로 높은 수치를 나타냈으며, 환경재무현황과 환경정보 공개는 0.10, 0.08로 낮게 계산되었다. 이는 투자자들의 평가 우선순위에서 볼 때 오염물질 배출처리현황 처리자료, 환경경영 일반현황 자료, 그리고 환경개선현황 자료를 우선적으로 보고 투자 결정을 한다는 점이다. 환경친화기업에 대한 실증분석결과에서도 대중매체를 통한 환경관련 기사 건수나 환경보고서 발간 유무, 환경친화기업 지정과 ISO, 14001 인증기업 등은 환경성과의 평가를 알려주는 지수의 측정에서도 가장 중요한 역할을 하는 것으로 나왔으며 전자나 제지, 자동차 산업을 경영하는 곳에서 환경경영성과가 우수한 것으로 도출되었다.
Compressive Light Field Displays (2012)

Light fields are the multiview extension of stereo image pairs: a collection of images showing a 3D scene from slightly different perspectives. Depicting high-resolution light fields usually requires an excessively large display bandwidth; compressive light field displays are enabled by the codesign of optical elements and computational-processing algorithms. Rather than pursuing a direct "optical" solution (for example, adding one more pixel to support the emission of one additional light ray), compressive displays aim to create flexible optical systems that can synthesize a compressed target light field. In effect, each pixel emits a superposition of light rays. Through compression and tailored optical designs, fewer display pixels are necessary to emit a given light field than a direct optical solution would require.