gebhart/patrepeval huggingface dataset:
Site-specific cleavage and joining of single-stranded DNA by VirD2 protein of Agrobacterium tumefaciens Ti plasmids: analogy to bacterial conjugation. (1993)

As an early stage of plant transformation by Agrobacterium tumefaciens, the Ti plasmid is nicked at the border sequences that delimit the T-DNA. Cleavage results in covalent attachment of VirD2 to the 5' terminal of the nicked strand by a process resembling initiation of DNA transfer that occurs in the donor cell during bacterial conjugation. We demonstrate that this cleavage can be reproduced in vitro: VirD2 protein, the border-cleaving enzyme, was overproduced and purified. Cleavage assays were performed with single-stranded oligodeoxyribonucleotides encompassing the Ti plasmid border region or the transfer origin's nick region of the conjugative plasmid RP4. VirD2 of pTiC58 cleaves both border- and nick region-containing oligonucleotides. However, the relaxase TraI of RP4 can cut only the cognate nick regions. The respective proteins remain covalently bound to the 5' end of the cleavage sites, leaving the 3' termini unmodified. VirD2-mediated oligonucleotide cleavage was demonstrated to be an equilibrium reaction that allows specific joining of cleavage products restoring border and nick regions, respectively. The possible role of VirD2 in T-DNA integration into the plant cell's genome is discussed in terms of less stringent target-sequence requirements.
Detection and false alarm probability of PN codeacquisition in DS-CDMA system (1997)

The authors present the performance of double dwell acquisition using a continuous integration detector. One performance measure in an acquisition system is the mean acquisition time, which depends on detection and false alarm probability. The detection and false alarm probability of double dwell acquisition using continuous integration detector is derived.
Role of 5S RNA in assembly and function of the 50S subunit from Escherichia coli. (1976)

Total reconstitution experiments performed under various conditions revealed that 5S RNA plays an important role during the last assembly step in vitro leading to an active 50S particle. For the preceding steps this RNA species is dispensable. However, 50S RNA can be integrated efficiently during any of the assembly steps in vitro. The 47S particle, reconstituted in two steps and lacking 5S RNA, shows low but significant activity in many functional tests. High activity could be obtained by incubating this particle with 5S RNA alone, demonstrating the importance of the 5S RNA in generating an active ribosomal conformation. In particular, the activity of the peptidyltransferase (peptidyl-tRNA:aminoacyl-tRNA N-peptidyltransferase; EC 2.3.2.12) center is drastically influenced by 5S RNA. No significant factor-dependent tRNA binding to the A-site was observed with the 47S particle, in contrast to the corresponding P-site binding. The elongation factor G dependent GTPase activity was not affected by the lack of 5S RNA.
<i>SAMBLASTER</i>: fast duplicate marking and structural variant read extraction (2014)

Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the requirement to read, write, sort and compress large BAM files multiple times. Results: We present SAMBLASTER, a tool that reduces the number of times such costly operations are performed. SAMBLASTER is designed to mark duplicates in read-sorted SAM files as a piped post-pass on DNA aligner output before it is compressed to BAM. In addition, it can simultaneously output into separate files the discordant read-pairs and/or split-read mappings used for structural variant calling. As an alignment post-pass, its own runtime overhead is negligible, while dramatically reducing overall pipeline complexity and runtime. As a stand-alone duplicate marking tool, it performs significantly better than PICARD or SAMBAMBA in terms of both speed and memory usage, while achieving nearly identical results. Availability and implementation: SAMBLASTER is open-source C++ code and freely available for download from https://github.com/GregoryFaust/samblaster. Contact: imh4y@virginia.edu
Photoresist outgassing in high energy and high current ion implantation (2003)

Photoresist (PR) outgassing during ion implantation can alter the real-time measurements of implanted dose, limit the maximum allowed dose rate, and introduce unwanted changes to as-implanted depth profiles. Equipment manufacturers assume that the instantaneous gas load resulting from PR outgassing is almost exclusively hydrogen, However, we show that this is not the case during a significant portion of many production implant processes. In particular, we show that high energy implants are typically characterized by constant gas loads in which up to 50% of the evolved gas consists of species other than hydrogen, while in high current implants, the peak pressure excursions often occur during the first few per cent of the implant, when the effluents are largely carbon monoxide (CO) and hydrocarbons (HC). These differences are shown to be quantitatively related to both the instantaneous dose rate, and to the proximity of the dose endpoint to the critical dose. For example, we show how the gas composition from a 150 kV P source/drain implant begins to abruptly change from approximately 40% H/sub 2/, 60% (CO+CO/sub 2/+HC) at a critical dose of 4.5E14, to saturate at 95% H/sub 2/ at a dose of 1E15. We believe this transition to be a consequence of PR amorphization, since the critical dose is in good agreement with the PR outgassing model of T.C. Smith.
Characteristic functions and quantum measurements of optical observables (1989)

Three characteristic functions are reviewed along with the quantum theory of linear systems and used to derive the P-representation, Wigner distribution and quasi-probability density of coherent states and squeezed states. The quasiprobability density is interpreted as the outcome of measurements utilising a beamsplitter with homodyne detection. The quasiprobability density concept is generalised and its interpretation in terms of a measurement is presented. The measurement utilises a beam splitter with one of its inputs in a squeezed state followed by two homodyne detectors.
DCE-MRI Segmentation and Motion Correction Based on Active Contour Model and Forward Mapping (2006)

This paper presents an automatic method to segment and correct motion artifact on dynamic contrast enhanced magnetic resonance imaging (DCE-MRI). The breast region is segmented from DCE-MRI using mathematical morphology, region growing, and active contour models. The motion artifact presented in the image is then corrected by applying B-spline curve fitting, active contour model and forward mapping algorithm. Our segmentation method has been tested on 72 DCR-MRI studies from 33 patients. The average segmentation accuracy was 96.76%, and the confidence interval was [95.55%, 97.97%] with p<0.05. Simulation and validation experiments for motion correction are working in progress. The detail experimental results were presented at the conference. The paper represents work-in-progress in our effort to build a CAD system for breast DCE-MRI
Multi-echelon stochastic inventory systems with centralized stock information (1993)

As information technology (e.g., Electronic Data Interchange or EDI) proliferates, more and more companies now possess centralized stock information for their inventory systems. This dissertation examines how the centralized stock information can be used to improve inventory management. We consider several multi-echelon networks with centralized stock information and stochastic demand. These include serial, assembly, and one-warehouse multi-retailer systems. A natural replenishment strategy based on centralized stock information is to replenish each stage of a multi-echelon system according to its echelon stock level. The echelon stock of a stage is the aggregate inventory level of the subsystem consisting of the stage and all its downstream stages. Such replenishment strategies are in a sharp contrast with those based on installation stock information under which each stage replenishes its inventory according to its local stock level. We study a class of control policies--the so-called (R,nQ) policies--that operate according to echelon stock levels. An echelon stock (R,nQ) policy at a stage orders an integer multiple of Q, the base lot-size, once its echelon stock level falls to or below R, the reorder point. Such policies are easy to implement, and are similar to the widely used reorder-point order-quantity policies in practice. Our examination of the cost effectiveness of echelon stock (R,nQ) policies consists of three main steps: (1) performance evaluation of any given policy in the class, (2) optimization within the class, and (3) benchmarking. The first two steps are based on observations of the operation details of echelon stock (R,nQ) policies, and the third step is carried out by comparing the minimum costs of echelon stock (R,nQ) policies with lower bounds on the minimum achievable costs (by any policy) of the systems. Our benchmarking studies for serial and one-warehouse multi-retailer systems suggest that echelon stock (R,nQ) policies are close to optimal. We also compare echelon stock (R,nQ) policies with their installation-stock counterpart.
[The effect of molecular structure of hydroxyethyl starch on the elimination kinetics and fluidity of blood in human volunteers]. (1993)

Influence of the Molecular Structure of Hydroxyethyl Starch on Elimination Kinetics and Blood Fluidity in Voluntary Subjects In a cross-over study 6 volunteers received an infusion of 500 ml hydroxyethyl starch of a batch with a high C2/C6-substitution ratio (10.8), or after a washout period of 3 months they received a batch with a low C2/C6-substitution ratio (5.8). The infusion solution was administered at random. The batches were identical as regards their physicochemical characteristics (HES 200/0.5 10%). The concentration and molecular weight distribution of the intravascular hydroxyethyl starch molecules were determined after infusion up to 24 h, the blood fluidity before and after infusion. The substitution ratio of the C2- or C6-atoms in the glucose ring has an effect on the degradation of the hydroxyethyl starch molecule: the molecules with a high C2/C6-substitution ratio appear to be degraded within the same period of time, the resulting degradation products, however, have a higher molecular weight. This influences the blood fluidity. While the haematocrit decrease occurring 1 h after end of infusion is comparable, it keeps up for a longer time in case of a higher C2/C6-substitution ratio. The increase of plasma viscosity is more pronounced in case of a high C2/C6-substitution ratio. Clinical consequences are discussed.
Properties and modification methods for vegetable fibers for natural fiber composites (1996)

Studies on structure and properties of natural vegetable fibers (NVF) show that composites made of NVF combine good mechanical properties with a low specific mass. The high level of moisture absorption by the fiber, its poor wettability, as well as the insufficient adhesion between untreated fibers and the polymer matrix lead to debonding with age. To build composites with high mechanical properties, therefore, a surface modification of the fibers is necessary. The existing physical and chemical NVF modification methods—e.g., plasma treatment or graft copolymerization—which are used for the development of NVF–polymer composite properties is discussed. It is shown that modified cellulose fiber–polymer interaction mechanisms are complex and specific to every definite system. By using an coupling agent, like silanes or stearin acid, the Young's modulus and the tensile strength increases, dependent on the resin, until 50%. Simultaneously, the moisture absorption of the composites decreases for about 60%. With other surface modifications, similar results are obtained. © 1996 John Wiley & Sons, Inc.
ILT3.Fc–CD166 Interaction Induces Inactivation of p70 S6 Kinase and Inhibits Tumor Cell Growth (2017)

The blockade of immune checkpoints by anti-receptor and/or anti-ligand mAb is one of the most promising approaches to cancer immunotherapy. The interaction between Ig-like transcript 3 (ILT3), a marker of tolerogenic dendritic cells, also known as LILRB4/LIR5/CD85k, and its still unidentified ligand on the surface of activated human T cells is potentially important for immune checkpoint blockade. To identify the ILT3 ligand, we generated mAb by immunizing mice with Jurkat acute T cell leukemia, which binds ILT3.Fc to its membrane. Flow cytometry, mass spectrometry, and Biacore studies demonstrated that the ILT3 ligand is a CD166/activated leukocyte cell adhesion molecule. Knockdown of CD166 in primary human T cells by nucleofection abolished the capacity of ILT3.Fc to inhibit CD4<sup>+</sup> T<sub>h</sub> cell proliferation and to induce the generation of CD8<sup>+</sup>CD28<sup>-</sup> T suppressor cells. CD166 displays strong heterophilic interaction with CD6 and weaker homophilic CD166-CD166 cell adhesion interaction. ILT3.Fc inhibited the growth of CD166<sup>+</sup> tumor cell lines (TCL) derived from lymphoid malignancies in vitro and in vivo. CRISPR-Cas9-based knockout of CD166 from TCL abrogated ILT3.Fc binding and its tumor-inhibitory effect. The mechanism underlying the effect of ILT3.Fc on tumor cell growth involves inhibition of the p70S6K signaling pathway. Blockade of CD166 by ILT3.Fc inhibited progression of human TCL in NOD.Cg-Prkdc Il-2rg/SzJ mice, suggesting its potential immunotherapeutic value.
RF-system-on-package (SOP) for wireless communications (2002)

Anew industrial revolution, often called the “third wave” or information technology (IT), is in the making. The products of this revolution will require entirely different systems hardware technologies: those with multifunctions, such as digital, analog, RF, and optical circuitries. RF and microwave design and packaging have been established as key technologies of this revolution. The demand for increasingly higher rates of data, voice, and video drives RF technology to ever higher frequencies where bandwidth for channel capacity is easy to find. Such emerging high-performance applications as personal communication networks, wireless local-area networks (WLAN), and RF-optical networks have defined a trend toward more flexible and reconfigurable systems. They impose very stringent specifications never before reached in term of low noise, high linearity, low power consumption, small size and weight, and low cost. The RF front-end module is the foundation of these systems, and its integration poses a great challenge. Microelectronics technology, since the invention of the transistor, has revolutionized many aspects of electronic products. This integration and cost path has led the microelectronics industry to believe that this kind of progress can go on forever, leading to so-called “system-on-chip” (SOC) for all applications. But it is becoming clear that the production of a complete solution for the new wireless communication front-end is still a dream. When you consider the characteristics of an RF front-end module  high performance up to 100-GHz operating frequency  a large number of high-performance discrete passive components  design flexibility
A New Via Hole Structure of MLB (Multi-Layered Printed Circuit Board) for RF and High Speed Systems (2005)

We propose a new via hole structure that reduces the amount of reflection noise of RF and high speed digital signals in multilayered PCB (printed circuit boards) and compare the electrical characteristics of the proposed via hole with them of conventional vias such as stacked, staggered and through via types. To verify the performance, after extracting RLC (resistance-inductance-capacitance) parameter from the actual structure, II-type equivalent lumped-circuit model including interaction between power and ground planes is established and the deviation of transmission properties for each type is analyzed through S-parameter and eye-diagram. At 5GHz, the reflection noise of the proposed via structure can be 2.3-3.8 times smaller than that of conventional ones. ISI (intersymbol interference) is reduced less than 5ps and TOF (time of flight) is 77ps shorter than any other types. It improves the output voltage efficiency 15-30% and extends the bandwidth 1.5-2 times. The effective density to layout the trace around it can be increased because of shielding signal via holes
Near-Field Scanning Optical Microscopy of Single Fluorescent Dendritic Molecules (1999)

Individual dendritic molecules adsorbed on glass containing a single fluorescent rhodamine B core have been observed with near-field scanning optical microscopy (NSOM); height and fluorescence images were obtained simultaneously. The dendritic assemblies can be discriminated from free fluorescent cores on the basis of accurate simultaneous localization of both the fluorescent core and the surrounding dendritic shell. There are no significant differences between the photophysical properties of the free and dendritic fluorophores. The full three-dimensional orientation of each individual fluorescent core can be resolved and millisecond time resolution accuracy has been achieved. Most dendritic structures exhibited rotational motion of the fluorescent core on a millisecond−second time scale, revealing intramolecular conformational dynamics.
Motility of Catalytic Nanoparticles Through Self‐Generated Forces (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Rapid, Modified Kirby-Bauer Susceptibility Test with Single, High-Concentration Antimicrobial Disks (1973)

A rapid (6-7 hr), modified Kirby-Bauer disk-susceptibility method, by which derivatives of tetrazolium dyes are used to enhance delineation between areas of growth and zones of inhibition, has been developed. Inoculated petri plates, prepared by the Kirby-Bauer method, were sprayed, after 6 to 7 hr of incubation (37 C), with aqueous solutions of MTT-tetrazolium or INT-tetrazolium resulting in readily detectable zones of inhibition. Excellent correlation was obtained between the modified test and the standard Kirby-Bauer test when challenged with a variety of gram-negative bacteria and Staphylococcus aureus strains. Additionally, the modified test has demonstrated reproducibility comparable to the standard Kirby-Bauer test. It is demonstrated that the modified test is applicable to susceptibility determinations with representative, commercially available antimicrobial disks. This applicability indicates that the modified method could provide rapid in vitro guidelines for in vivo therapy.
동아시아 문명권의 공자 형상과 인식 (2013)

동아시아의 중세는 공자를 선성 혹은 선사로 추숭하고 학문과 가치관의 정점으로 삼은 시기이다. 이는 서구 근대의 문물제도가 정착되기 이전까지 근본적으로 바뀌지 않았다. 공자에 대한 인식은 그의 전기물에 가장 잘 드러났는데, 학문 영역의 수장, 개혁적 정치가, 조롱 받는 사상가, 도통과 학통을 마련한 문화적 영 웅 등의 다양한 형상으로 나타났다. 또한 동아시아는 공자의 사원과 학교를 廟學 제도로 발전시키고, 관료 선거법 인 科擧制까지 결합시켜 중세적 통치의 정당성과 권위를 높였다. 이를 통해 동아 시아는 종교-학문-선발의 제도가 연동하는 높은 문명성을 유지하였다. 중국은 역 대로 공자의 지위를 先師와 先聖 사이에서 조정하면서 공자의 형상을 통해 학문 과 통치의 표준을 제시하였다. 한국은 경향 각지에 여러 종류의 공자 사원과 학 교를 두고 자국 출신의 유학자를 함께 제향 함으로써 학문의 권위를 높이고 가치 관의 통일을 꾀하였다. 베트남은 동일 공간의 공자 사원과 국학에 역대 과거급제 자의 비석을 조성 전시하여 통치의 정당성을 확보하였다. 일본은 동아시아에서 가장 늦게 묘학제를 받아들였고 묘-학-선의 연동성이 제일 느슨했지만, 그 반대급 부로 학교의 기능이 두드러졌으며 공자는 학문 혹은 공부의 신으로 좌정하였다. 위와 같은 공자의 다양한 형상은 역대 도상물에서 유형적으로 검토할 수 있다. 본고에서는 이를 네 분면의 좌표 개념으로 분석했다. 즉 공자에 관한 도상은 그 의 일생과 관련하여 司寇像과 行敎像이, 그에 대한 평가와 관련하여 天子像과 隱者問答像이 두드러진다. 또한 사구상과 행교상은 공자의 정체성 인식을, 천자상과 은자문답상은 공자에 대한 비평 인식을 나타내는 범주로 연결되며, 전자는 공자 의 역할과 관련되는 좌우축으로서, 후자는 공자의 지위와 관련되는 상하 축으로 서 좌표 개념을 구성한다. 이는 공자와 관련된 수많은 형상물을 분석하는 데 유 효한 기준이 되며, 본고에서는 몇 작품을 시론적으로 분석하여 좌표의 유용성을 점검하는 동시에 좌표적 의미를 심화시켰다.
Reseña: “Entre la Economía Social y el Mercado. Reflexiones para un debate abierto en el agro latinoamericano” (2016)

El presente texto es una resena del libro “Entre la Economia Social y el Mercado. Reflexiones para un debate abierto en el agro latinoamericano”
Patient Risk Stratiï¬cation with Time-Varying Parameters: A Multitask Learning Approach (2016)

The proliferation of electronic health records (EHRs) frames opportunities for using machine learning to build models that help healthcare providers improve patient outcomes. However, building useful risk stratiﬁcation models presents many technical challenges including the large number of factors (both intrinsic and extrinsic) inﬂuencing a patient’s risk of an adverse outcome and the inherent evolution of that risk over time. We address these challenges in the context of learning a risk stratiﬁcation model for predicting which patients are at risk of acquiring a Clostridium diﬃcile infection (CDI). We take a novel data-centric approach, leveraging the contents of EHRs from nearly 50,000 hospital admissions. We show how, by adapting techniques from multitask learning, we can learn models for patient risk stratiﬁcation with unprecedented classiﬁcation performance. Our model, based on thousands of variables, both time-varying and time-invariant, changes over the course of a patient admission. Applied to a held out set of approximately 25,000 patient admissions, we achieve an area under the receiver operating characteristic curve of 0.81 (95% CI 0.78-0.84). The model has been integrated into the health record system at a large hospital in the US, and can be used to produce daily risk estimates for each inpatient. While more complex than traditional risk stratiﬁcation methods, the widespread development and use of such data-driven models could ultimately enable cost-eﬀective, targeted prevention strategies that lead to better patient outcomes.
International Image of "Made in China" in Media Discourse (2015)

This study aims at analyzing language forms,
discursive strategies and discourse themes,
focusing on the changes of international image
of “Made in China” in the news reports of “New
York Time” in the past 25 years. The result shows
that the image of “Made in China” is constructed
through methods of lexical choice, discursive
stylistics, and rhetorical strategies, which is
modeled under of framework of social cognition
and interact with social and economic practices
in daily life. The image was reflected in
analyzing the theme of the relevant discourse,
which covers “product symbol, copyright,
product price and quality, working environment
and salary of Chinese workers, and Chinese
environment” and etc. These reports reconstruct
the public’s social cognition towards “Made in
China” by using language forms and discourse
strategies contain derogatory terms, reporting
verbs, and metaphors. These themes correlate
with the export good quality of “Made in China”
Comparison of Image Quality Assessment: PSNR, HVS, SSIM, UIQI (2012)

HE quality of the image degrades from the minute it is captured to the time it is displayed to the human observer. The image is subject to many kinds of distortions during the stages that it might pass through such as storing, processing, compressing, and transmitting, etc... In evaluating image quality there are two followed methods, the subjective and the objective method. The subjective method evaluation is considered costly, expensive, and time consuming; since we have to select a number of observers, show then a number of images and ask them to score images quality depending on their own opinion. The objective evaluation uses automatic algorithms to assess the quality of the image without human interfere.