gebhart/patrepeval huggingface dataset:
Automated Design of Programmable Enzyme-Driven DNA Circuits (2014)

Molecular programming allows for the bottom-up engineering of biochemical reaction networks in a controlled in vitro setting. These engineered biochemical reaction networks yield important insight in the design principles of biological systems and can potentially enrich molecular diagnostic systems. The DNA polymerase-nickase-exonuclease (PEN) toolbox has recently been used to program oscillatory and bistable biochemical networks using a minimal number of components. Previous work has reported the automatic construction of in silico descriptions of biochemical networks derived from the PEN toolbox, paving the way for generating networks of arbitrary size and complexity in vitro. Here, we report an automated approach that further bridges the gap between an in silico description and in vitro realization. A biochemical network of arbitrary complexity can be globally screened for parameter values that display the desired function and combining this approach with robustness analysis further increases the chance of successful in vitro implementation. Moreover, we present an automated design procedure for generating optimal DNA sequences, exhibiting key characteristics deduced from the in silico analysis. Our in silico method has been tested on a previously reported network, the Oligator, and has also been applied to the design of a reaction network capable of displaying adaptation in one of its components. Finally, we experimentally characterize unproductive sequestration of the exonuclease to phosphorothioate protected ssDNA strands. The strong nonlinearities in the degradation of active components caused by this unintended cross-coupling are shown computationally to have a positive effect on adaptation quality.
The effects of BCNU (1,3-bis(2-chloroethyl)-1-nitrosourea) and CCNU (1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea) on glutathione reductase and other enzymes in mouse tissue. (1983)

BCNU has been reported to cause a rapid, irreversible inhibition of human erythrocyte glutathione reductase (GR) at chemotherapeutic dosage, without affecting metabolic enzymes. This inhibition may mediate some of the therapeutic and toxic effects of BCNU. Thiol containing agents such as reduced glutathione can protect cells against BCNU and a change in glutathione concentrations could modify BCNU effectiveness. At doses of 50 mg/kg (LD-50) and 100 mg/kg, i.p., BCNU decreased the activity of GR in mouse kidney, liver, brain, and heart with a greater loss in those animals which died from drug administration. GR activity tended to recover but still remained below control at 96 hours. Erythrocyte GR activity was reduced only at the higher BCNU dose. CCNU (100 mg/kg, i.p.) did not affect GR activity. BCNU also decreased creatine kinase, malate dehydrogenase, and lactate dehydrogenase activities. The inhibition of GR in vitro occurred only after biochemical reduction of the enzyme with NADPH. The oxidation state of GR may determine its sensitivity to BCNU in the human erythrocyte but we were unable to demonstrate an unusually high sensitivity or a specific effect of BCNU on GR in mouse tissues.
Self-Assembly of Fluid-Filled KHCO<sub>3</sub> Microfibers (2003)

Self-assembly of KHCO(3) fibers is observed when glassy oligomerized films of poly[(aminopropyl)siloxane] containing K(+) ions, denoted K(+)/poly-APS, are exposed to CO(2) and H(2)O. The fibers are crystalline, narrow (0.4-3 microm diam), high aspect ratio (up to at least 300), and, on the basis of Raman spectroscopy, dominated by KHCO(3). The fibers contain fluid that is dominated by aqueous potassium formate (KOOCH). A multistep phenomenological model is proposed to account for the self-assembly.
Exercise Physiology (2013)

This chapter provides a broad overview of the primary physiological responses involved in maintaining homeostasis during exercise and when exposed to environmental stressors. It covers cardiorespiratory function, neuromuscular function, thermoregulatory function, fatigue, and principles of training. Within each of these topics, implications for sports nutrition are identified. The study of exercise physiology centers around the contraction of skeletal muscle, the fundamental requirement for all human movement. Exercise physiology and sports nutrition are closely connected. There is little doubt that proper nutrition plays an indispensable role in helping athletes maintain, recover from, and adapt to rigorous training and competition. For example, it has long been recognized that minimizing dehydration during exercise helps protect health and performance by minimizing negative perturbations in cardiovascular and thermoregulatory function.
Two-dimensional thin-layer chromatography of polar lipids from milk and mammary tissue (1967)

A two-dimensional thin-layer chromatographic system that separates all of the known polar lipids of milk and mammary tissue is described. The compositions of phospholipids of milk and of the mammary tissue from which the milk was derived are presented.
Bifunctional Cyclopentadienyl Ligands in Organotransition Metal Chemistry (1994)

Abstract The coordination chemistry of cyclopentadienyl ligands that contain an additional coordination site appended to the ring-periphery by a covalent bridge Z, C5R4−Z-X or C5R4−Z-L, is outlined. When transition metals are coordinated both to the cyclopentadienyl group C5R4 and the pendent donor site X or L (X = CH2 NR′, O; L = HC[dbnd]CH2 NR2′, PR2′, OR′, SR′), the resulting complexes possess distinct properties due to the chelate effect. In such complexes the coordination sphere is defined by the nature of the bridge Z and the coordinating groups X and L and a series of metallacyclic complexes becomes available of which the chemistry is different from that of their non-bridged analogs.
S3-Leitlinie Reizdarmsyndrom: Definition, Pathophysiologie, Diagnostik und Therapie. Gemeinsame Leitlinie der Deutschen Gesellschaft für Verdauungs- und Stoffwechselkrankheiten (DGVS) und der Deutschen Gesellschaft für Neurogastroenterologie und Motilität (DGNM) (2011)

Kapitel 1 Definition und Epidemiologie 242 1 -1 Definition und Epidemiologie des RDS bei Erwachsenen (AG 1) 242 1 -2 Definition und Epidemiologie des RDS bei Kindern (AG 9) 245 Kapitel 2 Pathophysiologie 247 2 -1 Pathophysiologie des RDS bei Erwachsenen (AGs 2, 11, 12) 247 2 -1 Pathophysiologie des RDS bei Kindern (AG 9) 251 Teil III Diagnosesicherung 252 Kapitel 3 Diagnostisches Vorgehen bei V. a. RDS 252 3 -1 Diagnostisches Vorgehen bei V. a. RDS bei Erwachsenen (AG 3) 252 3 -2 Diagnostisches Vorgehen bei V. a. RDS bei Kindern (AG 9)
Switching in polystyrene films: Transition from on to off state (1976)

Experiments on polystyrene films formed by a glow-discharge technique shows a reproducible bistable switching. Various interpretations are briefly reviewed. It is shown that the resistance of the on state is strictly related to the energy needed by the on-off transition. From the value of this energy it is concluded that the most probable explanation is that the on current takes place along a filamentary path constituted by carbon atoms. A quantitative analysis is made on the basis of the heat balance equation. Formation of carbonated chains is confirmed by a chromatography analysis in vapor phase which shows an hydrogen release.
The First Chapter in Caribbean History (1955)

(1955). The First Chapter in Caribbean History. Caribbean Quarterly: Vol. 4, No. 1, pp. 68-74.
Friction and contact resistance during sliding in vacuum of some-low-resistivity metals lubricated with sputtered molybdenum disulfide films (1969)

Friction and contact resistance during sliding in vacuum of low resistivity metals lubricated with sputtered molybdenum disulfide
Wintering, grazing and fattening heifers (1954)

Thirty good quality Hereford heifer calves, 10 head to a lot, were\nused in the study They cost 20 cents a pound delivered to Manhattan,\nKansas, September 15, 1952. They originated in the Sterling City,\nTexas, area. From delivery date until November 15, 1952, they were\nfed prairie hay and 1 pound of soybean oilmeal pellets per head daily.\nThe system of management for each lot follows:\nLot 1-wintered on dry bluestem pasture supplemented with 1 ½ \nto 2 pounds of concentrate feed per head daily, grazed on bluestem\npasture May 1 to July 15, full fed in drylot 100 days.\nLot 2-wintered on Atlas sorgo silage, prairie hay, 1 pound of soybean pellets, and 2 pounds of corn per head daily; grazed on bluestem pasture\n May 1 to July 15; full fed in drylot 100 days.\nLot 3-wintered on brome pasture until January 1 then moved to\ndrylot. In drylot they were fed sorghum silage, prairie hay, and\n1 pound of soybean pellets per head daily. From April 9, 1953, to\nJuly 14. 1953, they were grazed on brome pasture' starting July 14\nthey were full fed grain 100 days in drylot.
Perceptually Optimizing Deep Image Compression (2020)

Mean squared error (MSE) and $\ell_p$ norms have largely dominated the measurement of loss in neural networks due to their simplicity and analytical properties. However, when used to assess visual information loss, these simple norms are not highly consistent with human perception. Here, we propose a different proxy approach to optimize image analysis networks against quantitative perceptual models. Specifically, we construct a proxy network, which mimics the perceptual model while serving as a loss layer of the network.We experimentally demonstrate how this optimization framework can be applied to train an end-to-end optimized image compression network. By building on top of a modern deep image compression models, we are able to demonstrate an averaged bitrate reduction of $28.7\%$ over MSE optimization, given a specified perceptual quality (VMAF) level.
A multilayered architecture for hiding executable files in 3D images (2010)

Steganography is a technique to hide secret messages in a host media called cover media. The advantage of steganography over cryptography is that messages do not attract attention to attackers and even receivers. Steganography and cryptography are often used together to ensure security of the secret messages. This paper introduces steganography work on 3D models. In this paper, we will exploit the geometric characteristics of 3D models to provide high-capacity data hiding. Capacity and invisibility are more important than robustness in the steganography system. Therefore, we aim at maximizing data hiding capacity while limiting distortion of cover models in a lower bounded value. A novel multilayered embedding scheme is proposed for enlarging the hiding capacity. In the extraction procedure, the embedding order can also be obtained using the secret key in the spatial analysis step. The payload can then be correctly extracted in this embedding order.
Key considerations for measuring allelic expression on a genomic scale using high‐throughput sequencing (2010)

Differences in gene expression are thought to be an important source of phenotypic diversity, so dissecting the genetic components of natural variation in gene expression is important for understanding the evolutionary mechanisms that lead to adaptation. Gene expression is a complex trait that, in diploid organisms, results from transcription of both maternal and paternal alleles. Directly measuring allelic expression rather than total gene expression offers greater insight into regulatory variation. The recent emergence of high-throughput sequencing offers an unprecedented opportunity to study allelic transcription at a genomic scale for virtually any species. By sequencing transcript pools derived from heterozygous individuals, estimates of allelic expression can be directly obtained. The statistical power of this approach is influenced by the number of transcripts sequenced and the ability to unambiguously assign individual sequence fragments to specific alleles on the basis of transcribed nucleotide polymorphisms. Here, using mathematical modelling and computer simulations, we determine the minimum sequencing depth required to accurately measure relative allelic expression and detect allelic imbalance via high-throughput sequencing under a variety of conditions. We conclude that, within a species, a minimum of 500-1000 sequencing reads per gene are needed to test for allelic imbalance, and consequently, at least five to 10 millions reads are required for studying a genome expressing 10 000 genes. Finally, using 454 sequencing, we illustrate an application of allelic expression by testing for cis-regulatory divergence between closely related Drosophila species.
Lab on a Chip: United States of America (2012)

A graphical abstract is available for this content
Stochastic printing failures in extreme ultraviolet lithography (2018)

Stochastic effects in lithography are known to be the cause of critical dimension (CD) variability, quantified, e.g., by linewidth roughness or local CD uniformity, but—when the CDs are small—they can also lead to printing failures, and hence have a significant impact on yield. We will focus on these printing failures and review three important topics in this relatively new field. First, we will look at how these failures can be detected and show how either CD-SEM, e-beam inspection, and optical defect inspection can play a useful role. Next, we consider the important question of how the stochastic failure probability (which we quantify by a metric we call "Not OK," abbreviated NOK) depends on the lithography- and process-settings, a question that is of obvious importance when looking for conditions that will minimize the failure probability and hence maximize the yield. Finally, we will discuss to what extent we can fit experimentally observed failure probabilities, to empirical models. Such models can play a vital role in future OPC-verification flows, where screening full mask layouts for "stochastic hot spots" is expected to become a mandatory step.
The Baculovirus Anti-apoptotic p35 Protein Promotes Transformation of Mouse Embryo Fibroblasts (1998)

The baculovirus p35 protein is a potent inhibitor of programmed cell death induced by a variety of stimuli in insects, nematodes, and mammalian cell lines. The broad ability of p35 in preventing apoptosis has led us to investigate its effect on mouse embryo fibroblasts in vitro and in vivo. For this purpose, we have used R- cells (3T3-like fibroblasts derived from mouse embryos with a targeted disruption of the insulin-like growth factor I receptor (IGF-IR) genes) and R508 cells (derived from R- and with 15 x 10(3) IGF-IRs per cell). Both cell lines grow normally in monolayer, but they do not form colonies in soft agar, and they are non-tumorigenic in nude mice. We show here that, in addition to its anti-apoptotic effect, p35 causes transformation of R508 cells, as evidenced by the following: 1) decreased growth factor requirements, 2) ability to form foci in monolayer and colonies in soft agar, and 3) ability to form tumors in nude mice. Since R- cells stably transfected with p35 do not transform, our observations suggest that in addition to its effect as an inhibitor of apoptosis, the baculovirus p35 protein has transforming potential that requires the presence of the IGF-IR. The possibility that these two properties could be separated was confirmed by demonstrating that R508 cells expressing another anti-apoptotic protein, Bcl-2, could not form tumors in nude mice.
Angiopoietin-2 may contribute to multiple organ dysfunction and death in sepsis* (2012)

: We conclude that angiopoietin-2 induction precedes and contributes to the adverse outcomes in sepsis, opening a new avenue for therapeutic investigation.
Curcumin potentiates the apoptotic effects of chemotherapeutic agents and cytokines through down-regulation of nuclear factor-κB and nuclear factor-κB–regulated gene products in IFN-α–sensitive and IFN-α–resistant human bladder cancer cells (2007)

Bladder cancer mortality varies between the countries; whereas being highest in Western countries, it is lowest in Eastern countries, such as India. Cigarette smoking is one of the major risk factors for bladder cancer in affluent nations, such as United States. Localized early-stage bladder cancer is treated with resection and intravesical cytokine therapy, whereas metastatic cancer is typically treated with various combinations of systemic chemotherapy. Whether curcumin, a yellow curry pigment commonly consumed in countries, such as India, has any role in prevention or treatment of bladder cancer was investigated. We found that curcumin inhibited the proliferation, induced cell cycle arrest, and DNA fragmentation in both IFN-alpha-sensitive (RT4V6) and IFN-alpha-resistant (KU-7) bladder cancer cells. Curcumin also potentiated the apoptotic effects of the chemotherapeutic agents (gemcitabine and paclitaxel) and of cytokines [tumor necrosis factor (TNF) and TNF-related apoptosis-inducing ligand]. This effect of curcumin was independent of sensitivity and resistance to IFN-alpha, commonly used for treatment of bladder cancer. Whether the effects of curcumin are mediated through modulation of the nuclear factor-kappaB (NF-kappaB) pathway known to mediate antiapoptosis was investigated. Both gemcitabine and TNF activated NF-kappaB in bladder cancer cells and curcumin suppressed this activation. Similarly, cigarette smoke, a major risk factor for bladder cancer, also activated NF-kappaB and curcumin suppressed it. Cigarette smoke-induced expression of the NF-kappaB-regulated gene products cyclooxygenase-2 and vascular endothelial growth factor, linked with proliferation and angiogenesis, respectively, was also down-regulated by curcumin.
Wireless on-chip microparticle manipulation using pulse-driven dielectrophoresis (2012)

A chip with which to manipulate microparticles using wireless power transfer and pulse-driven dielectrophoresis has been designed and fabricated using a 0.18-µm CMOS process. The chip enables microparticle manipulation under a 0.7-V power supply and a 13-MHz clock, which are generated on the chip by means of an on-chip coil, a rectifier, and a Schmitt trigger circuit.
Resting-state Functional Connectivity Predicts Individual Treatment Outcomes of Repetitive Transcranial Magnetic Stimulation for Major Depressive Disorder (2014)

Repetitive transcranial magnetic stimulation (rTMS) is an emerging treatment for treatment-resistant major depressive disorder (MDD). We recently found that treatment response to rTMS of the dorsomedial prefrontal cortex (DMPFC) was bimodal, with individual patients showing either minimal or marked improvement (Downar et al., 2013). Here, we tested whether treatment response could be predicted before initiating treatment. To this end, we trained support vector machine (SVM) classifiers on whole-brain resting-state functional connectivity magnetic resonance imaging (rs-fcMRI) data to learn the treatment outcomes of 41 patients who received rTMS of the DMPFC. The SVMs classified patients with 90% accuracy (p = 0.035, corrected). Classification was based on 9 functional connections, with a pattern of positive and negative functional connectivity in non-responders and responders, respectively. This study represents the first step towards developing a screening tool that can direct treatment decisions.
Laser flash photolysis study of the magnetic field effect on the photodecomposition of (2,4,6-trimethylbenzoyl)diphenylphosphine oxide in micellar solution (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLaser flash photolysis study of the magnetic field effect on the photodecomposition of (2,4,6-trimethylbenzoyl)diphenylphosphine oxide in micellar solutionHisaharu. Hayashi, Yoshio. Sakaguchi, Mikiharu. Kamachi, and Wolfram. SchnabelCite this: J. Phys. Chem. 1987, 91, 15, 3936–3938Publication Date (Print):July 1, 1987Publication History Published online1 May 2002Published inissue 1 July 1987https://pubs.acs.org/doi/10.1021/j100299a004https://doi.org/10.1021/j100299a004research-articleACS PublicationsRequest reuse permissionsArticle Views106Altmetric-Citations33LEARN 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 options Get e-Alerts
Biogenic Amines in Food (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Expression of a lipocalin in <i>Pichia pastoris</i>: secretion, purification and binding activity of a recombinant mouse major urinary protein (1997)

The proteins of the mouse major urinary protein complex (MUP), members of the lipocalin family, bind volatile pheromones and interact with the vomeronasal neuroepithelium of the olfactory system. We report the expression of a MUP protein using its native signal sequence for secretion in the methylotrophic yeast, Pichia pastoris. Mature recombinant MUP (rMUP) is secreted at a concentration of 270 mg/l in minimal medium and it is isolated from the culture supernatant by one step ion-exchange chromatography in a nearly pure form. Binding activity, tested with an odorant molecule which displays high affinity for native MUP, indicates that rMUP has a behavior similar to the native one. This finding suggests that the protein, and in particular its hydrophobic binding pocket, is properly folded.