gebhart/patrepeval huggingface dataset:
Protein structure prediction (2003)

The 'Protein Folding Problem' is probably the greatest remaining challenge in structural molecular biology. There are three main categories of protein structure prediction methods: comparative modelling methods, fold recognition methods and ab initio methods. In comparative modelling, the structure of the new protein is predicted by comparing its sequence with the sequences of proteins of known structure. Ab initio methods are so-called because they use only the information in the target sequence itself. There are two branches of ab initio prediction: knowledge-based methods; and simulation methods. The chapter discusses the prediction of protein secondary structure. There are two aspects of protein structure that are exploited in predicting secondary structure from just a single protein sequence: the intrinsic secondary structure propensities of amino acids, and the hydropathic nature of amino acids. The most effective method of secondary structure prediction is neural networks used to analyze substitution patterns in multiple sequence alignments.
The U.S. Food and Drug Administration's Mini‐Sentinel program: status and direction (2012)

The Mini-Sentinel is a pilot program that is developing methods, tools, resources, policies, and procedures to facilitate the use of routinely collected electronic healthcare data to perform active surveillance of the safety of marketed medical products, including drugs, biologics, and medical devices. The U.S. Food and Drug Administration (FDA) initiated the program in 2009 as part of its Sentinel Initiative, in response to a Congressional mandate in the FDA Amendments Act of 2007. After two years, Mini-Sentinel includes 31 academic and private organizations. It has developed policies, procedures, and technical specifications for developing and operating a secure distributed data system comprised of separate data sets that conform to a common data model covering enrollment, demographics, encounters, diagnoses, procedures, and ambulatory dispensing of prescription drugs. The distributed data sets currently include administrative and claims data from 2000 to 2011 for over 300 million person-years, 2.4 billion encounters, 38 million inpatient hospitalizations, and 2.9 billion dispensings. Selected laboratory results and vital signs data recorded after 2005 are also available. There is an active data quality assessment and characterization program, and eligibility for medical care and pharmacy benefits is known. Systematic reviews of the literature have assessed the ability of administrative data to identify health outcomes of interest, and procedures have been developed and tested to obtain, abstract, and adjudicate full-text medical records to validate coded diagnoses. Mini-Sentinel has also created a taxonomy of study designs and analytical approaches for many commonly occurring situations, and it is developing new statistical and epidemiologic methods to address certain gaps in analytic capabilities. Assessments are performed by distributing computer programs that are executed locally by each data partner. The system is in active use by FDA, with the majority of assessments performed using customizable, reusable queries (programs). Prospective and retrospective assessments that use customized protocols are conducted as well. To date, several hundred unique programs have been distributed and executed. Current activities include active surveillance of several drugs and vaccines, expansion of the population, enhancement of the common data model to include additional types of data from electronic health records and registries, development of new methodologic capabilities, and assessment of methods to identify and validate additional health outcomes of interest.
Antioxidative efficacy of parallel and combined supplementation with coenzyme Q10 and d-<i>α</i>-Tocopherol in mildly hypercholesterolemic subjects: a randomized placebo-controlled clinical study (2000)

It has been claimed that coenzyme Q10 (Q10) would be an effective plasma antioxidant since it can regenerate plasma vitamin E. To test separate effects and interaction between Q10 and vitamin E in the change of plasma concentrations and in the antioxidative efficiency, we carried out a double-masked, double-blind clinical trial in 40 subjects with mild hypercholesterolemia undergoing statin treatment. Subjects were randomly allocated to parallel groups to receive either Q10 (200 mg daily), d-alpha-tocopherol (700 mg daily), both antioxidants or placebo for 3 months. In addition we investigated the pharmacokinetics of Q10 in a separate one-week substudy. In the group that received both antioxidants, the increase in plasma Q10 concentration was attenuated. Only vitamin E supplementation increased significantly the oxidation resistance of isolated LDL. Simultaneous Q10 supplementation did not increase this antioxidative effect of vitamin E. Q10 supplementation increased and vitamin E decreased significantly the proportion of ubiquinol of total Q10, an indication of plasma redox status in vivo. The supplementations used did not affect the redox status of plasma ascorbic acid. In conclusion, only vitamin E has antioxidative efficiency at high radical flux ex vivo. Attenuation of the proportion of plasma ubiquinol of total Q10 in the vitamin E group may represent in vivo evidence of the Q10-based regeneration of the tocopheryl radicals. In addition, Q10 might attenuate plasma lipid peroxidation in vivo, since there was an increased proportion of plasma ubiquinol of total Q10.
The problem of frequency synthesis (1961)

Frequency synthesis employs precise frequency standards to obtain by means of a frequency conversion process many output frequencies from the one accurate source, each of which can be individually selected. The output frequencies are multiples of harmonic fractions of the frequency standard.The paper reviews the basic techniques of addition or subtraction and division employed and analyses some of the present frequency synthesizer designs.
기획 특집 : 문화산업/이미지/예술 ; 예술과 문화 -칸트, Fr. 슐레겔, 키에르케고어, 니체를 돌이켜보며 (2010)

예술은 문화와 구체적으로 어떻게 연관된 것인가? 예술과 미적 경험은 지배적인 문화가 암암리에 억압하고 있는 ``자연``과 ``감성``이 표출되고 실험되는 장소인가? 분명한 것은 예술과 문화의 의미, 예술과 문화의 관계가 결코 일상적인 의식이 쉽게 전제하듯이 명확하고 단순한 문제가 아니라는 점이다. 본고는 이러한 문제의식에서 서구 근현대 미학사상의 흐름 가운데 몇 몇 중요한 사상가들의 이론을 토론해 보고자 한다. 이들은 칸트, Fr. 슐레겔, 키에르케고어, 니체 등이다. 본고는 예술과 문화라는 주제와 관련하여 이들이 성찰이 아직도 유효한지, 유효하다면 어떤 맥락에서, 또 어떤 철학적 문제들과 관련하여 유효한 것인지를 염두에 두고 논의를 전개한다. 이들 모두 예술과 문화에 대해 심층적인 이론적 논의를 전개했지만, 이들이 예술과 미적 경험에 대해 철학적-인간학적 의미를 부여하는 방식과 내용은 분명한 차이점을 보여준다. 또한 이들은 예술과 미적 경험이 전체 문화 속에서 어떤 위상을 갖고 있으며, 어떤 역할을 할 수 있는가에 대해서도 각기 고유한 방식으로 고민했다. 각각의 방식은 이들이 직면하고 있던 사회정치적 상황과 기대고 있던 사상적 전통, 특히 이들이 실천했던 독특한 철학함의 방식만큼이나 서로 달랐다. 하지만 그럼에도 이들을 공통적으로 아우르는, 근원적인 사유의 태도 내지 사유의 방향성을 지적할 수는 있다. 이들은 모두 문화를 어떤 주어진 체계나 완결된 구조로 보지 않았다. 반대로 이들은 문화를 근본적으로 변화하는 ``과정``으로서, 혁신해야 할 ``과제``로서 파악했다. 또한 이들은 - 키에르케고어의 경우 근본적인 지향점이 다르긴 하지만 - 공통적으로 이 도전적 실천 과정에서 예술과 미적 경험이 의미심장한 역할을 할 수 있으며 또 해야 한다고 역설하였다. 바로 이러한 측면에서만 보더라도, 이들의 성찰은 지나간 과거가 아니라 살아 있는 현재라 할 수 있다. 좀 더 정확히 말해, 이들의 성찰은 한편으로 예술과 문화에 대한 현대적 자기이해의 한 부분을 이루고 있으며, 다른 한편으로 오늘날 미학적 반성이 늘 고민해야 할 과제로 남아있는 것이다.
Single step, complementary doping of graphene (2010)

A single-step doping method capable of high resolution n- and p-type doping of large area graphene is presented. Thin films of hydrogen silsesquoxane on exfoliated graphene are used to demonstrate both electron and hole doping through control of the polymer cross-linking process. This dual-doping is attributed to the mismatch in bond strength of the Si–H and Si–O bonds in the film as well as out-gassing of hydrogen with increasing cross-linking. A high-resolution graphene p-n junction is demonstrated using this method.
Preparation of a differentially expressed, full-length cDNA expression library by RecA-mediated triple-strand formation with subtractively enriched cDNA fragments (1996)

We have developed a fast and general method to obtain an enriched, full-length cDNA expression library with subtractively enriched cDNA fragments. The procedure relies on RecA-mediated triple-helix formation of single-stranded cDNA fragments with a double-stranded cDNA plasmid library. The complexes were then captured from the solutions using the digoxigenin-antidigoxigenin paramagnetic beads followed by recovery of the enriched double-stranded cDNA expression library. We have observed a linear relation between the capture of full-length cDNAs in the library and the fold enrichment in the subtracted cDNA population.
Peroxisome Proliferator-Activated Receptors Protect against Apoptosis via 14-3-3 (2010)

Peroxisome proliferator-activated receptors (PPARs) were reported to prevent cells from stress-induced apoptosis and protect tissues against ischemia-reperfusion injury. The underlying transcriptional mechanism is unclear. Recent reports indicate that the antiapoptotic actions of ligand-activated PPARδ and PPARγ are mediated through enhanced binding of PPAR to the promoter of 14-3-3ε and upregulation of 14-3-3ε expression. We propose that ligand-activated PPARα exerts its anti-apoptotic actions via the identical pathway. The PPAR to 14-3-3 transcriptional axis plays an important role in protection of cell and tissue integrity and is a target for drug discovery.
Equivalent source distribution for efficient 3-D acoustic wave equation modelling in the Laplace domain (2011)

Since the recent introduction of the Laplace-domain full waveform inversion, an efficient and accurate modelling technique for the 3-D Laplace-domain wave equation has been sought. The efficiency and accuracy of the 3-D acoustic wave equation modelling in the Laplace domain strongly depends on how to accurately account for free surface conditions and the actual source and receiver locations. In terms of efficiency, fortunately, the Laplace-domain wave equation can be solved on a coarse grid because the field is not propagating as if it were a potential field. However, it is not possible to accurately compute the Laplace-domain response by assuming that the source and the receivers are located at the grid nodes when we use a coarse grid. To resolve this problem, we propose an equivalent source distribution algorithm that allows us to simulate the free surface condition accurately using a coarse-grid finite-element or finite-difference method. It is shown that the equivalent source vector obtained from a homogeneous half-space model can be used for arbitrarily complex models. The extension of the equivalent source to complex heterogeneous media is explained by the approximation of the Dirac delta function. Numerical tests show that our algorithm is better than the Kaiser windowed sinc function method in the Laplace domain. Our technique for solving the 3-D Laplace-domain wave equation can significantly reduce the computational time required for the 3-D Laplace-domain acoustic full waveform inversion because we can use the coarse grid to accurately simulate conventional marine seismic exploration.
Untersuchungen über die Topographie des latenten Innen‐ und Außenbildes (1963)

Abstract Durch ein gesteuertes Fällungsverfahren lassen sich photographische Silberhalogenidkristalle regelmäßiger, kubischer Kristalltracht und enger Korngrößenverteilung herstellen, die an definierter Lage im Korninnern und bzw. oder an der Kornoberfläche latente Bildkeime oder Reifkeime enthalten. Versuche mit photographischen Schichten aus Emulsionen mit einem in verschiedener Tiefe befindlichen latenten Bild geben Auskunft über die Tiefenwirkung photographischer Entwickler und von Silberoxydationsmitteln. Aus dem sensitometrischen Verhalten derartiger Emulsionen kann auf eine Fallenwirkung des latenten Bildes gegenüber Photoelektronen geschlossen werden. Auf einer Konkurrenz zwischen Kornoberfläche und Korninnerem auf Grund dieser Fallenwirkung beruhen verschiedene photographische Erscheinungen wie die Solarisation, der Clayden‐Effekt und der Intensitäts‐Umkehreffekt.
The effects of taurochenodeoxycholic acid in preventing pulmonary fibrosis in mice. (2013)

The present study prepared the pulmonary fibrosis model in mice by using Bleomycin and carry out the investigations on the effects of taurochenodeoxycholic acid (TCDCA) in preventing pulmonary fibrosis in mice. Expression profiles of the bile acid receptors in the lung of mice FXRα and TGR5 were examined, and pulmonary coefficient, pathohistology as well as expression of TNF-α, MMP-2, MMP-9 and TIMP-2 in pulmonary fibrosis mice. The results showed that FXRα and TGR5 simultaneously expressed in the lung of the mice; TCDCA in dosages of 0.05 and 0.1g/kg can extremely significantly decrease the pulmonary coefficient in the model mice (P>0.01), TCDCA in a dosage of 0.2g/kg significantly decreased the pulmonary coefficient in the model mice (P<0.05); TCDCA in dosages of 0.05 and 0.1g/kg significantly reduce the pathological damages on their lungs; TCDCA can extremely significantly decrease the expression levels of TNF-α and TIMP-2 in pulmonary tissues in the pulmonary fibrosis mice (P>0.01), the expression level of MMP-9 extremely significantly increased (P>0.01), while it has no significant effects on MMP2. The results as mentioned above indicated that TCDCA had antagonistic actions on pulmonary fibrosis in mice.
Geographically-aware information retrieval for collections of digitized historical maps (2007)

DIGMAP is a project focused on historical digitized maps. The project will develop a set of services, to be available in the Internet, based on reusable open-source software solutions. The main service will provide discovery and access to resources related to historical cartography, based on metadata from European national libraries and other relevant third part providers. These resources will comprise both physical and digitized objects. In the case of digitized maps, available metadata will be enriched by automatic and semi-automatic processes that will try to extract relevant indexing information from the images of the digitized maps, as also from any kind of associated text. This paper presents an early overview on the project, particularly focusing on the aspects related to geographical information retrieval.
A high-efficiency 1.5 kW, 390-50 V half-bridge converter operated at 100% duty-ratio (2003)

A half-bridge isolated step-down converter operated at nearly unity duty-ratio for very high efficiency is discussed. It is meant to interface the 390 V regulated output of a 1.5 kW power factor correction unit to a 50 V distribution bus. It is based on the zero-voltage switching (ZVS) scheme of the phase-shifted pulse width modulation (PWM) approach, but since the duty ratio does not vary from near unity, the output inductor is omitted. The ring of the output rectifier capacitance with the transformer leakage inductance is therefore clamped by the output capacitor, which permits the oscillation energy to be recovered. This, together with ZVS of the MOSFETs, gives the converter an efficiency greater than 95% at full load.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Design, analogy, and creativity (1997)

Analogical reasoning appears to play a key role in creative design. In briefly reviewing recent research on analogy-based creative design, this article first examines characterizations of creative design and then analyzes theories of analogical design in terms of four questions: why, what, how and when? After briefly describing recent AI theories of analogy-based creative design, the article focuses on three theories instantiated in operational computer programs: Syn, DSSUA (Design Support System Using Analogy) and Ideal. From this emerges a related set of research issues in analogy-based creative design. The main goal is to sketch the core issues, themes and directions in building such theories.
Low-grade-heat energy harvesting using superlattice thermoelectrics for applications in implantable medical devices and sensors (2005)

All implantable medical devices (IMDs), including pacemakers, defibrillators, drug infusion pumps, and pain management technology require electrical power. One limitation of implantable biomedical devices is the longevity of the battery source. Currently, the longevity of pacemakers and defibrillators ranges from 5 to 10 years depending on the model and pacing requirements. After 5-10 years, the patient has to undergo surgery for the pacemaker to be removed and the battery replaced. A solution to this problem would be to use temperature differences, typically as low as 0.3 to 1.5/spl deg/C that can exist between the inner surface of the skin and the core body temperature to create electrical energy. A thermoelectric module generating 70 /spl mu/W or more from such temperature gradients can be useful in such applications. The module can be useful to supplement the battery power. Beyond the medical devices market, these thermal batteries could also be used to power wireless sensors. In order to truly achieve "wireless" and untethered/unattended operation, it would be desirable to have self sustaining power or energy harvesting.
Protein Conformational Switches: From Nature to Design (2012)

Protein conformational switches alter their shape upon receiving an input signal, such as ligand binding, chemical modification, or change in environment. The apparent simplicity of this transformation--which can be carried out by a molecule as small as a thousand atoms or so--belies its critical importance to the life of the cell as well as its capacity for engineering by humans. In the realm of molecular switches, proteins are unique because they are capable of performing a variety of biological functions. Switchable proteins are therefore of high interest to the fields of biology, biotechnology, and medicine. These molecules are beginning to be exploited as the core machinery behind a new generation of biosensors, functionally regulated enzymes, and "smart" biomaterials that react to their surroundings. As inspirations for these designs, researchers continue to analyze existing examples of allosteric proteins. Recent years have also witnessed the development of new methodologies for introducing conformational change into proteins that previously had none. Herein we review examples of both natural and engineered protein switches in the context of four basic modes of conformational change: rigid-body domain movement, limited structural rearrangement, global fold switching, and folding-unfolding. Our purpose is to highlight examples that can potentially serve as platforms for the design of custom switches. Accordingly, we focus on inducible conformational changes that are substantial enough to produce a functional response (e.g., in a second protein to which it is fused), yet are relatively simple, structurally well-characterized, and amenable to protein engineering efforts.
Reduced expression of Wnt-1 and E-cadherin, and diminished β-catenin stability in MCF-7 breast cancer cells that overexpress protein kinase C-α (2001)

MCF-7 breast cancer cells stably overexpressing protein kinase C-alpha (MCF-7-PKC-alpha cells) exhibit reduced cell-cell adhesion and increased tumorigenicity in nude mice. We investigated the possibility that alterations in E-cadherin and catenins contribute to the unique phenotype of MCF-7-PKC-alpha cells. Northern and Western blotting indicated that MCF-7-PKC-alpha cells express abnormally low amounts of plakoglobin mRNA and protein, and undetectable levels of E-cadherin mRNA and protein. In contrast, even though MCF-7-PKC-alpha cells express low levels of beta-catenin mRNA, they express undetectable levels of beta-catenin protein, suggesting that post-transcriptional events further diminish beta-catenin expression in these cells. Pulse-labeling of the cells with [35S]methionine showed that the half-life of beta-catenin is less than 15 min in MCF-7-PKC-alpha cells, compared to over 2 h in MCF-7-Vector cells [MCF-7 cells transfected with pSV2M(2)6 vector only]. Incubation with LiCl to inactivate glycogen synthase kinase-3 (GSK-3) significantly prolonged the half-life of beta-catenin in MCF-7-PKC-alpha cells, suggesting that the GSK-3-dependent degradation of beta-catenin contributes to beta-catenin instability in these cells. Northern and Western blotting indicated that Wnt-1, which also inhibits GSK-3 activity, is expressed by MCF-7-Vector cells, but not by MCF-7-PKC-alpha cells. Transfection of (S37A)beta-catenin, which is resistant to GSK-3-dependent degradation, stimulated TCF/LEF-dependent luciferase expression from the pTOPFLASH reporter plasmid by 753-fold in MCF-7-PKC-alpha cells, and by 268-fold in MCF-7-Vector cells. Inactivation of GSK-3 by LiCl stimulated luciferase expression from the pTOPFLASH reporter plasmid by 12.4-fold in MCF-7-PKC-alpha cells, and by 4.8-fold in MCF-7-Vector cells. These results suggest that degradation of beta-catenin by GSK-3 contributes to beta-catenin instability in MCF-7-PKC-alpha cells, diminishing the ability of -catenin to act as a transcriptional co-activator. Reduced Wnt-1 expression by MCF-7-PKC-alpha cells may promote beta-catenin degradation by enhancing GSK-3 activity. Loss of beta-catenin-dependent cell-cell adhesion and transcription may contribute to the aggressive phenotype of MCF-7-PKC-alpha cells.
Fabrication and characterization of a new high density Sc/Si multilayer sliced grating (2008)

State of the art soft x-ray spectroscopy techniques like Resonant Inelastic X-ray Scattering (RIXS) require diffraction gratings which can provide extremely high spectral resolution of 10<sup>5</sup>-10<sup>6</sup>. This problem may be addressed with a sliced multilayer grating with an ultra-high groove density (up to 50,000 mm<sup>-1</sup>) proposed in the recent publication [Voronov, D. L., et al., Proc. SPIE 6705, 67050E (2007)]. It has been suggested to fabricate such a grating by deposition of a soft x-ray multilayer on a substrate which is a blazed saw-tooth grating (echellette) with low groove density. Subsequent polishing applied to the coated grating removes part of the coating and forms an oblique-cut multiline structure that is a sliced multilayer grating. The resulting grating has a short-scale periodicity of lines (bilayers), which is defined by the multilayer period and the oblique-cut angle. We fabricated and tested a Sc/Si multilayer sliced grating suitable for EUV applications, which is a first prototype based on the suggested technique. In order to fabricate an echellette substrate, we used anisotropic KOH etching of a Si wafer. The etching regime was optimized to obtain smooth and flat echellette facets. A Sc/Si multilayer was deposited by dc-magnetron sputtering, and after that it was mechanically polished using a number of diamond pastes. The resulting sliced grating prototype with ~270 nm line period has demonstrated a dispersive ability in the 41-49 nm photon wavelength range with a diffraction efficiency of ~7% for the optimized 38th order assigned to the echellette grating of 10 μm period.
Emulating an operating system on top of another (1993)

Abstract In this paper, we present the design of an operating‐system emulator. This software interface provides the services of one operating system (Oberon) on a machine running a different operating system (Macintosh), by mapping the functions of the first onto equivalent calls to the second. The construction of this emulator proceeded in four distinct phases, documented here through examples from each of these phases. We believe that our four‐phase approach can be beneficial whenever a larger software system needs to be adapted from one architecture onto another. In conclusion, we relate some of the lessons learned and propose guidelines for similar engineering projects.