gebhart/patrepeval huggingface dataset:
Computational Tools and Algorithms for Designing Customized Synthetic Genes (2014)

Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein-coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review, we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.
Subunit structure, expression, and function of NAD(H)-specific isocitrate dehydrogenase in Saccharomyces cerevisiae (1990)

Mitochondrial NAD(H)-specific isocitrate dehydrogenase was purified from Saccharomyces cerevisiae for analyses of subunit structure and expression. Two subunits of the enzyme with different molecular weights (39,000 and 40,000) and slightly different isoelectric points were resolved by denaturing electrophoretic techniques. Sequence analysis of the purified subunits showed that the polypeptides have different amino termini. By using an antiserum to the native enzyme prepared in rabbits, subunit-specific immunoglobulin G fractions were obtained by affinity purification, indicating that the subunits are also immunochemically distinct. The levels of NAD(H)-specific isocitrate dehydrogenase activity and immunoreactivity were found to correlate closely with those of a second tricarboxylic acid cycle enzyme, malate dehydrogenase, in yeast cells grown under a variety of conditions. S. cerevisiae mutants with defects in NAD(H)-specific isocitrate dehydrogenase were identified by screening a collection of yeast mutants with acetate-negative growth phenotypes. Immunochemical assays were used to demonstrate that one mutant strain lacks the 40,000-molecular-weight subunit (IDH1) and that a second strain lacks the 39,000-molecular-weight subunit (IDH2). Mitochondria isolated from the IDH1 and IDH2 mutants exhibited a markedly reduced capacity for utilization of either isocitrate or citrate for respiratory O2 consumption. This confirms an essential role for NAD(H)-specific isocitrate dehydrogenase in oxidative functions in the tricarboxylic acid cycle.
Three‐Dimensional Models of Individual Cardiac Histoanatomy: Tools and Challenges (2006)

There is a need for, and utility in, the acquisition of data sets of cardiac histoanatomy, with the vision of reconstructing individual hearts on the basis of noninvasive imaging, such as MRI, enriched by reference to detailed atlases of serial histology obtained from representative samples. These data sets would be useful not only as a repository of knowledge regarding the specifics of cardiac histoanatomy, but could form the basis for generation of individualized high-resolution cardiac structure-function models. The current article presents a step in this general direction: it illustrates how whole-heart noninvasive imaging can be combined with whole-heart histology in an approach to achieve automated construction of histoanatomically detailed models of cardiac 3D structure and function at hitherto unprecedented resolution and accuracy (based on 26.4 x 26.4 x 24.4 microm MRI voxel size, and enriched by histological detail). It provides an overview of the tools used in this quest and outlines challenges posed by the approach in the light of applications that may benefit from the availability of such data and tools.
<i>N</i>-Methyl-d-aspartate receptor antagonism decreases motility and inflammatory activation in the early phase of acute experimental colitis in the rat (2009)

These data demonstrate a potential modulatory mechanism of NMDA-R in altered colonic motility in TNBS colitis. Inhibition of the enteric NMDA-Rs may provide a therapeutic option via which to influence intestinal hypermotility, microcirculatory changes and inflammatory activation simultaneously.
Optimal state filtering and parameter identification for linear systems (2007)

Abstract This paper presents the optimal filtering and parameter identification problem for linear stochastic systems with unknown multiplicative and additive parameters over linear observations, where unknown parameters are considered Wiener processes. The original problem is reduced to the filtering problem for an extended state vector that incorporates parameters as additional states. The obtained optimal filter for the extended state vector also serves as the optimal identifier for the unknown parameters. Performance of the designed optimal state filter and parameter identifier is verified for both stable and unstable linear uncertain systems. Copyright © 2007 John Wiley & Sons, Ltd.
A Technique for Predicting the Solvent-Producing Ability of <i>Clostridium acetobutylicum</i> (1987)

Changes in colony morphology were associated with the degeneration of solvent-producing strains of Clostridium acetobutylicum. The most efficient solvent-producing strains gave rise exclusively to colonies with dense centers containing large numbers of spores. Many outgrowths of various morphologies developed from the perimeter of such colonies after several days of incubation. The most degenerate cultures did not produce solvents and gave rise to large diffuse colonies that did not contain spores. These diffuse colonies did not produce outgrowths. Intermediate colony types were also observed. These could be derived from liquid cultures that were relatively poor solvent producers or from the outgrowths of colonies of efficient solvent-producing strains. Some of these intermediate types produced spores but did so less frequently than the high-solvent-producing strains. The spores of the intermediate types could not be distinguished from those of the most efficient solvent producers on the basis of heat sensitivity. The relationship observed between colony morphology and solvent production provides a method for predicting the solvent-producing potential of C. acetobutylicum cultures.
Generating multiple images for integrated circuits by Fourier-transform holograms (1968)

A new technique of generating multiple images for integrated circuits is described in detail. The technique is based on the Fourier-transform property of lenses. A Fourier-transform hologram of an array of point sources forms the basis for generating multiple images and determines the array of images to be formed.
Evaluation of the circulatory dynamics via observation of the inferior vena cava using ultrasonography (2013)

救急室や集中治療室で超音波検査（ultrasonography: US）は手軽に利用できるようになり，循環動態の評価のため焦点を絞ったUSによる下大静脈（inferior vena cava: IVC）の観察が広く行われるようになってきた。USによるIVC径（IVC diameter: IVCD）の計測では，IVCDに影響を及ぼす因子を事前に理解しておくことが大切である。患者の状態が安定していれば，体位は通常仰臥位にするが，症例により左側臥位による再評価が推奨される。呼吸はsniff（鼻をすする動作）が適切である。計測部位は一般に肝下面で右房入口部から0.5-3cm程度の位置とする。IVCの縦断像でIVCDを計測するが，事前に横断像で形態を確認しておくことは有用である。表示としてBモードもしくはMモードを選択するが，それぞれのモードの特性を考慮して利用する。IVCDの実測の代用として目測による評価も有用で，素早く施行可能なことからとくに重症患者において利用価値が高い。これまで日常臨床ではIVCDとその呼吸性変動の組み合せで右房圧の推定が行われてきたが，近年欧米ではその推定規準が見直された。またIVCDやその呼吸性変動を指標にすれば，非代償性心不全の診断や水分管理，初期蘇生における循環血液量減少の評価，人工呼吸中の輸液反応性の評価にも有用であるという報告がなされている。急性期診療において焦点を絞ったUSによるIVCの観察を加えることで，より非侵襲的で正確な輸液管理が可能になるかもしれないが，その確証を得るには今後標準化された計測方法と評価基準を用いた臨床研究が必要となる。
A 480-MHz to 1-GHz sub-picosecond clock generator with a fast and accurate automatic frequency calibration in 0.13-µm CMOS (2007)

In this paper, an ultra-low jitter clock generator that employs a novel automatic frequency calibration (AFC) technique is presented. To achieve low jitter, the clock generator uses an LC-VCO with 5-bit switched tuning scheme. The clock output is taken from the output of a multi-modulus divider, which increases the output frequency range with small variation in the loop bandwidth. The capacitor array of the the VCO is controlled by a novel AFC technique that performs binary search for fast calibration and fine search to select an optimum tuning curve. A prototype chip implemented in 0.13-µm CMOS process achieves 480 MHz to 1 GHz of output frequency while consuming 22 mW from a 1.2 V supply. The measured rms jitter and calibration time of the proposed clock generator are 940 fs at 600 MHz and 350 ns, respectively. These numbers are the fastest calibration time and one of the lowest jitter that have been reported in a clock generator.
Multiple components in an epidermal growth factor-stimulated protein kinase cascade (1991)

Epidermal growth factor stimulates the activity of several cytosolic serine/threonine protein kinases in quiescent Swiss 3T3 cells. Two of these, which use myelin basic protein (MBP) as substrate, act as kinase kinases in that they are able to activate a separate peptide kinase activity in vitro by a mechanism involving protein phosphorylation. In this study, we have identified two activities from extracts of epidermal growth factor-treated cells that stimulate an ATP-dependent activation of both of the MBP kinases, derived in their inactive precursor forms from extracts of untreated cells. The resulting MBP kinase activities are stable to further purification and can be inactivated with either tyrosine or serine/threonine protein phosphatases and then reactivated to their original levels of activity. Thus, we propose that the in vitro activation involves protein phosphorylation, stimulated by the action of novel MBP kinase activating factors that represent intermediate components in a growth factor-stimulated kinase cascade.
Acetylcholine Receptor: An Allosteric Protein (1984)

The nicotine receptor for the neurotransmitter acetylcholine is an allosteric protein composed of four different subunits assembled in a transmembrane pentamer α2 βγδ. The protein carries two acetylcholine sites at the level of the α subunits and contains the ion channel. The complete sequence of the four subunits is known. The membrane-bound protein undergoes conformational transitions that regulate the opening of the ion channel and are affected by various categories of pharmacologically active ligands.
A steroid-triggered switch in E74 transcription factor isoforms regulates the timing of secondary-response gene expression (1997)

The steroid hormone 20-hydroxyecdysone (referred to here as ecdysone) directs Drosophila metamorphosis by activating a series of genetic regulatory hierarchies. ETS domain transcription factors encoded by the ecdysone-inducible E74 early gene, E74A and E74B, act at the top of these hierarchies to coordinate the induction of target genes. We have ectopically expressed these E74 isoforms to understand their regulatory functions during the onset of metamorphosis. We show that E74 can regulate its own transcription, most likely through binding sites within its gene. Ectopic expression of E74B can partially repress the E78B and DHR3 orphan receptor genes, suggesting a role for E74 in the appropriate timing of early-late gene expression. Furthermore, E74A is both necessary and sufficient for E78B induction, implicating E74A as a key regulator of E78B expression. We also show, consistent with our studies of E74 loss-of-function mutations, that E74B is a potent repressor of late gene transcription and E74A is sufficient to prematurely induce the L71-1 late gene. However, ectopic expression of both Broad-Complex and E74A activators in an E74B mutant background is not sufficient to prematurely induce all late genes, indicating that other factors contribute to this regulatory circuit. These observations demonstrate that the steroid-triggered switch in E74 transcription factor isoforms plays a central role in the proper timing of secondary-response gene expression.
Carbohydrate composition of meningococcal lipopolysaccharide modulates the interaction of Neisseria meningitidis with human dendritic cells (2005)

Meningococcal lipopolysaccharide (LPS) is of crucial importance for the pathogenesis of invasive infection. We show that sialylation and elongation of the alpha-chain effectively shields viable unencapsulated Neisseria meningitidis from recognition by human dendritic cells (DC). In contrast, beta- and gamma- chain of the LPS carbohydrate moiety play only a minor role in the interaction with DC. The protective function of the LPS for the bacteria can be counteracted in vivo by phase variation of the lgtA gene encoding LPS glycosyltransferase A. Capsule expression protects N. meningitidis efficiently from recognition and phagocytosis by DC independent of the LPS structure. Despite the significant impact of LPS composition on the adhesion and phagocytosis of N. meningitidis no differences were found in terms of cytokine levels secreted by DC for IL1-beta, IL-6, IL-8, TNF-alpha, IFN-gamma and GM-CSF. However, significantly lower levels of the regulatory mediator IL-10 were induced by encapsulated strains in comparison to isogenic unencapsulated derivatives. IL-10 secretion was shown to depend on phagocytosis because poly alpha-2,8 sialic acid did not influence IL-10 secretion. The use of truncated LPS isoforms in vaccine preparations can therefore not only result in attenuation but also in more efficient targeting of DC.
<title>Integration of diffractive lenses with addressable vertical-cavity laser arrays</title> (1995)

An optical interconnection system is being developed to provide vertical, digital data channels for stacked multichip modules. A key component of the system is an array of individually addressable vertical-cavity surface-emitting lasers with diffractive lenses integrated into the substrate to control beam divergence and direction. The lenses were fabricated by direct-write e-beam lithography and reactive ion beam etching into the GaAs substrate. Preliminary device performance data and the design and fabrication issues are discussed.
Partitioning and scheduling for parallel image processing operations (2002)

Many computer vision and image processing (CVIP) operations can be represented as a sequence of tasks with nested loops, specified by the visual programming language Khoros. This paper addresses the automatic partitioning and scheduling of such operations on distributed memory multiprocessors. The major difficulties in determining the optimal image data distribution for each task are that the number of processors available and the size of the input image may vary at the run time, and the cost of some image processing operations may be data-dependent. This paper proposes a compile-time processor assignment and data partitioning scheme that optimizes the average run-time performance of task chains with nested loops by considering the data redistribution overheads and possible run-time parameter variations. This paper presents the theoretical analysis and experimental results on a Meiko CS-2 distributed memory machine.
GIARDIASIS (1980)

GIARDIASIS Get access ERNEST MEYER, ERNEST MEYER 1Department of Microbiology and Immunology, University of Oregon Health Sciences Center3181 S.W. Sam Jackson Park Road, Portland, OR 97201 reprint requests to Dr. Meyer at this address Search for other works by this author on: Oxford Academic PubMed Google Scholar EDWARD L. JARROLL EDWARD L. JARROLL Search for other works by this author on: Oxford Academic PubMed Google Scholar American Journal of Epidemiology, Volume 111, Issue 1, January 1980, Pages 1–12, https://doi.org/10.1093/oxfordjournals.aje.a112860 Published: 01 January 1980
LEF1/β-Catenin Complex Regulates Transcription of the Cav3.1 Calcium Channel Gene (<i>Cacna1g</i>) in Thalamic Neurons of the Adult Brain (2010)

β-Catenin, together with LEF1/TCF transcription factors, activates genes involved in the proliferation and differentiation of neuronal precursor cells. In mature neurons, β-catenin participates in dendritogenesis and synaptic function as a component of the cadherin cell adhesion complex. However, the transcriptional activity of β-catenin in these cells remains elusive. In the present study, we found that in the adult mouse brain, β-catenin and LEF1 accumulate in the nuclei of neurons specifically in the thalamus. The particular electrophysiological properties of thalamic neurons depend on T-type calcium channels. Cav3.1 is the predominant T-type channel subunit in the thalamus, and we hypothesized that the Cacna1g gene encoding Cav3.1 is a target of the LEF1/β-catenin complex. We demonstrated that the expression of Cacna1g is high in the thalamus and is further increased in thalamic neurons treated in vitro with LiCl or WNT3A, activators of β-catenin. Luciferase reporter assays confirmed that the Cacna1G promoter is activated by LEF1 and β-catenin, and footprinting analysis revealed four LEF1 binding sites in the proximal region of this promoter. Chromatin immunoprecipitation demonstrated that the Cacna1g proximal promoter is occupied by β-catenin in vivo in the thalamus, but not in the hippocampus. Moreover, WNT3A stimulation enhanced T-type current in cultured thalamic neurons. Together, our data indicate that the LEF1/β-catenin complex regulates transcription of Cacna1g and uncover a novel function for β-catenin in mature neurons. We propose that β-catenin contributes to neuronal excitability not only by a local action at the synapse but also by activating gene expression in thalamic neurons.
Identification and determination of sulfur trioxide in sulfur dioxide by Raman spectrometry (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIdentification and determination of sulfur trioxide in sulfur dioxide by Raman spectrometryPeggy A. Skotnicki, Alfred G. Hopkins, and Chris W. BrownCite this: Anal. Chem. 1973, 45, 13, 2291–2292Publication Date (Print):November 1, 1973Publication History Published online1 May 2002Published inissue 1 November 1973https://pubs.acs.org/doi/10.1021/ac60335a035https://doi.org/10.1021/ac60335a035research-articleACS PublicationsRequest reuse permissionsArticle Views171Altmetric-Citations1LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Superimposed technique for OFDM/OQAM based digital terrestrial television broadcasting (2008)

Orthogonal frequency division multiplexing offset quadrature amplitude modulation (OFDM/OQAM) is a multi carrier modulation using staggered transmission on the I and Q axes. It uses as well an optimized non-rectangular pulse shaping. There are several advantages with respect to the conventional OFDM modulation, while the main drawback is the intrinsic intersymbol interference, hindering e.g. a proper channel estimation. In this paper to overcome the effect of the intrinsic interference we propose to estimate the channel through the superimposed correlation-based method. We propose then to exploit the superimposed sequence to achieve time synchronization as well. In particular, in this paper we show that, under the realistic conditions (e.g regarding the spectrum masks), the proposed techniques work very well and allow to achieve a significant improvement in spectral efficiency.
Metal artifacts reduction in CT images through Euler's elastica and curvature based sinogram inpainting (2006)

Metal artifacts arise in CT images when X-rays traverse the high attenuating objects such as metal bodies. Portions of projection data become unavailable. In this paper, we present an Euler's elastica and curvature based sinogram inpainting (EECSI) algorithm for metal artifacts reduction, where "inpainting" is a synonym for "image interpolation". In EECSI, the unavailable data are regarded as occlusion and can be inpainted inside the inpainting domain based on elastica interpolants. Numerical simulations demonstrate that, compared to conventional interpolation methods, the algorithm proposed connects the unavailable projection region more smoothly and accurately, thus better reduces metal artifacts and more accurately reveals cross section structures, especially in the immediate neighborhood of the metallic objects.
Liquid Cement: Changing the Paradigm (2007)

Abstract The process of oil well cementing has changed little since the introduction of the ground jet-mixer eighty years ago. While time has brought advancements such as; pneumatic transfer of bulk cement, introduction and application of the re-circulating mixer, liquid additives, advanced density control and additive measuring devices, the basic elements of well cementing have remained largely unchanged over time. In an offshore cementing environment the process involves the pneumatic transfer of cement or cement blended with dry products to a supply boat and the pneumatic transfer of this material to the offshore rig's storage tanks. The material is then pneumatically transferred a third time to the cement unit, where water is added and the slurry is homogenized by a large and expensive cement unit, usually coupled to a batch mixer. This tedious process occurs even on small jobs and in remote facilities. To simplify the process, a new concept using a Liquid Cement Premix (LCP) has been developed. As its name implies, LCP is basically pre-mixed storable cement slurry that can be stored for an extended period in a homogenous fluid state and then can be used in any number of down-hole applications just like conventional cement. There are many benefits implicit in the application of this new technology. Among these are reduced environmental impact, improved quality control, reduction (or even elimination) of conventional cementing and associated equipment, elimination of cement blending and enhanced logistics for remote platforms, reduced in required personnel offshore and considerable time savings. Particularly interesting is the use of this concept for work-over and abandonment operations in situations where deployment of conventional cementing equipment would be impractical or expensive. This paper presents the background of LCP and describes a common example of a field implementation.
Bundles of polytwins as meta-elastic domains in the thin polycrystalline simple multi-ferroic system PZT (2010)

We used enhanced piezo-response force microscopy (E-PFM) to investigate both ferroelastic and ferroelectric nanodomains in thin films of the simple multi-ferroic system PbZr(0.3)Ti(0.7)O(3) (PZT). We show how the grains are organized into a new type of elastic domain bundles of the well-known periodic elastic twins. Here we present these bundle domains and discuss their stability and origin. Moreover, we show that they can arrange in such a way as to release strain in a more effective way than simple twinning. Finally, we show that these bundle domains can arrange to form the macroscopic ferroelectric domains that constitute the basis of ferroelectric-based memory devices.