gebhart/patrepeval huggingface dataset:
Enhancing Multistep DNA Processing by Solid-Phase Enzyme Catalysis on Polyethylene Glycol Coated Beads (2018)

Covalent immobilization of enzymes on solid supports provides an alternative approach to homogeneous biocatalysis by adding the benefits of simple enzyme removal, improved stability, and adaptability to automation and high-throughput applications. Nevertheless, immobilized (IM) enzymes generally suffer from reduced activity compared to their soluble counterparts. The nature and hydrophobicity of the supporting material surface can introduce enzyme conformational change, spatial confinement, and limited substrate accessibility, all of which will result in loss of the immobilized enzyme activity. In this work, we demonstrate through kinetic studies that flexible polyethylene glycol (PEG) moieties modifying the surface of magnetic beads improve the activity of covalently immobilized DNA replication enzymes. PEG-modified immobilized enzymes were utilized in library construction for Illumina next-generation sequencing (NGS) increasing the read coverage across AT-rich regions.
Growth of <i>Saccharomyces cerevisiae</i> is controlled by its limited respiratory capacity: Formulation and verification of a hypothesis (1986)

A novel mechanistic model for the growth of baker's yeast on glucoseis presented. It is based on the fact that glucose degradation proceeds via two pathways under conditions of aerobic ethanol formation. Part is metabolized oxidatively and part reductively, with ethanol being the end product of reductive energy metabolism. The corresponding metabolic state is designated oxidoreductive. Ethanol can be used oxidatively only. Maximum rates of oxidative glucose and ethanol degradation are governed by the respiratory capacity of the cells. The model is formulated by using the stoichiometric growth equations for pure oxidative and reductive (fermentative) glucose and ethanol metabolism. Together with the experimentally determinable yield coefficients (Y(X/S)) for the respective metabolic pathways, the resulting equation system is sufficiently determined. The superiority of the presented model over hitherto published ones is based on two essential novelities. (1) The model was developed on experimentally easily accessible parameters only. (2) For the modeling of aerobic ethanol formation, the substrate flow was split into two simultaneously operating (i.e., in parallel) metabolic pathways that exhibit different but constant energy-generating efficiencies (respiration and fermentation) and consequently different and constant biomass yields (Y(X/S)). The model allows the prediction of experimental data without parameter adaption in a biologically dubious manner.
Conciencia, cerebro y neurociencia: Parte II: La relación qualia, conciencia fenoménica, cerebro (2006)

Tal vez ningún aspecto de la mente es tan familiar y enigmático para nosotros como la conciencia fenoménica, nuestra capacidad para tener experiencias conscientes: deseamos entender qué es la experiencia consciente y cómo se relaciona con los demás aspectos del mundo. La argumentación que a continuación se desarrollará sobre la conciencia fenoménica se enfocará en la noción de qualia; en la primera sección se trata de precisar una noción de qualia, en la segunda se examina el argumento anti-fisicalista de los zombis. Asimismo, se exploran las posiciones según las cuales los qualia son entidades epifenoménicas, no-físicas o irreductibles a la actividad del cerebro. Luego, se explora la idea según la cual los qualia surgen de cierto tipo de actividad cerebral en ciertas áreas cerebrales, y se concluye considerando una manera en que los qualia podrían ser propiedades cerebrales.
Surface Functionality and Carbon Structures in Lignocellulosic-Derived Biochars Produced by Fast Pyrolysis (2011)

Switchgrass- and pine wood-derived biochars produced by fast pyrolysis were characterized to estimate the degree of thermochemical transformation and to assess their potential use as a soil amendment and to sequester carbon. The feedstocks were pyrolyzed to biochars in an auger reactor at 450, 600, and 800 °C with a residence time of 30 s. Ash contents of switchgrass and pine wood biochars varied from 13 to 22% and from 1.3 to 5.2%, respectively. Nutrients, such as N, P, K, S, Mg, and Ca, in switchgrass biochars ranged from 0.16 to 1.77%. Under combustion conditions, switchgrass chars were decomposed at lower temperatures than pine wood biochars because of the structural differences between the two feedstocks. Principal component analysis of the Fourier transform infrared (FTIR) spectra allowed for the discrimination of all biochars by significant contributions of cellulose-derived functionality at low pyrolysis temperatures, while the same analysis of the Raman spectra presented apparent separation of all biochars by two broad bands at 1587 and 1350 cm–1. These two broad peaks were deconvoluted into pseudo-subpeaks, which revealed that the number of aromatic rings linearly increased with the pyrolysis temperature. Cross-linkages between aromatic rings were also found to increase with thermal treatment, and switchgrass biochars contained a higher number of aromatic rings and cross-linkages than pine wood biochars, which was consistent with turbostratic carbon crystallites in the X-ray diffraction (XRD) pattern.
<title>Submicrometer Pattern Correction For Optical Lithography</title> (1988)

To realize higher CD controls of submicrometer devices, the submicrometer pattern corrections were investigated in optical reduction steppers considering the primary residual aberrations. The optical pattern fidelities on the reduction pattern transfer were estimated at first using the three-dimensional photoresist image simulator RESPROT (Resist Process Three-Dimensional Simulator), which is examined the Seidel's primary aberrations, i.e. spherical aberration, astigmatism, field curvature, distortion and coma. From RESPROT calculations it was known that astigmatism affects pattern shape depending on image height, coma and distortion make position shifts in exposure field, and image contrast is influenced by field curvature. These results were reflected to device design rules, process latitude enhancements and lens manufacturings. To use premature high NA g-line lenses and minimize the diffraction limit for submicrometer area, reticle pattern corrections are very useful for sub-space patterns writing in contact holes, "tailoring" of W/L for MOS-gate patterns, and sub-field position control for distortion correction on ER writing. For almost of this investigation, 5-10nm order corrections were required from original design on wafer. In order to make good use of higher NA lenses, focus latitude enhancement are required because field curvature control is very severe. For these demand, multi-step superpositions of focus and exposure, FLEX -method, is useful to enhance the depth of focus effectively. These simulated and examined results are covenient to realize submicrometer devices on advantageous optical lithography using more shorter wavelength, i.e. i-line or excirner laser steppers.
Effect of Fasting, Refeeding, and Dietary Fat Restriction on Plasma Leptin Levels (1997)

The factors responsible for the variability in plasma leptin levels\n observed among individuals with similar body compositions remain unclear.\n To examine the impact of dietary variables, we compared the changes in\n leptin levels induced by fasting and dietary fat restriction with the\n expected decrease following a significant loss in adipose mass. A 21.4 +/-\n 3.7% weight loss led to a 76.3 +/- 8.1% decrease in mean plasma leptin\n level (25.2 +/- 9.3 to 6.1 +/- 3.4 ng/mL, P = 0.0001) in a group of 9\n obese males. Despite a weight loss of only 2.6 +/- 0.8%, mean plasma\n leptin levels fell by 61.9 +/- 25.2% (8.5 +/- 4.5 to 2.4 +/- 0.5 ng/mL, P\n < 0.01) in 7 nonobese females subjected to 3 days of fasting. Leptin\n levels in fasted subjects returned to baseline within 12 h of refeeding.\n Individual high- and low-fat meals given to 19 subjects after an overnight\n fast had no effect on plasma leptin levels. Reduction in dietary fat\n content from 37-10% of total calories for 7 weeks was also without effect\n on plasma leptin levels in these subjects. We conclude that plasma leptin\n levels primarily reflect total adipose mass, rather than meal consumption\n or dietary energy source, but that the reduction in leptin levels with\n ongoing fasting is disproportionate to the reduction in adipose mass. The\n ability of fasting to deactivate this presumed physiological satiety\n system may have been advantageous in environments characterized by rapid\n changes in food availability.
Overview of recent work on geometry images (2004)

Summary form only given. Surfaces in computer graphics are commonly represented using irregular meshes. While such meshes can approximate a given shape using few vertices, their irregularity comes at a price, since most mesh operations require random memory accesses through vertex indices and texture coordinates. Also, filter kernels must handle arbitrary mesh neighborhoods, and techniques like morphing, level-of-detail (LOD) control, and compression are complicated. As an alternative, we have introduced the geometry image representation, which captures shape using a completely regular sampling, i.e. a 2D grid of (x, y, z) values (Guet et al., 2002). The benefits of uniform grids are often taken for granted. Grids allow efficient traversal, random access, convolution, composition, down-sampling, and compression. We briefly review our recent work on constructing geometry images from given input models, and highlight some benefits of this new regular shape representation.
In vivo bioluminescence imaging for integrated studies of infection (2004)

Understanding biological processes in the context of intact organ systems with fine temporal resolution has required the development of imaging strategies that reveal cellular and molecular changes in the living body. Reporter genes that confer optical signatures on a given biological process have been used widely in cell biology and have been used more recently to interrogate biological processes in living animal models of human biology and disease. The use of internal biological sources of light, luciferases, to tag cells, pathogens, and genes has proved to be a versatile tool to provide in vivo indicators that can be detected externally. The application of this technology to the study of animal models of infectious disease has not only provided insights into disease processes, but has also revealed new mechanisms by which pathogens may avoid host defences during infection.
Comment: Trait EI Moderates the Relationship Between Ability EI and Emotion Regulation (2016)

Mestre, MacCann, Guil, and Roberts (2016) propose a model that suggests emotion regulation provides the mechanism through which ability emotional intelligence influences important outcomes. We argue that important nuance in our understanding of people’s choice of emotion regulation strategy can be gained by incorporating personality constructs such as trait emotional intelligence within this model.
Lie-group methods (2000)

Many differential equations of practical interest evolve on Lie groups or on manifolds acted upon by Lie groups. The retention of Lie-group structure under discretization is often vital in the recovery of qualitatively correct geometry and dynamics and in the minimization of numerical error. Having introduced requisite elements of differential geometry, this paper surveys the novel theory of numerical integrators that respect Lie-group structure, highlighting theory, algorithmic issues and a number of applications.
Investigating the relationship between word segmentation performance and retrieval performance in Chinese IR (2002)

It is commonly believed that word segmentation accuracy is monotonically related to retrieval performance in Chinese information retrieval. In this paper we show that, for Chinese, the relationship between segmentation and retrieval performance is in fact nonmonotonic; that is, at around 70% word segmentation accuracy an over-segmentation phenomenon begins to occur which leads to a reduction in information retrieval performance. We demonstrate this effect by presenting an empirical investigation of information retrieval on Chinese TREC data, using a wide variety of word segmentation algorithms with word segmentation accuracies ranging from 44% to 95%. It appears that the main reason for the drop in retrieval performance is that correct compounds and collocations are preserved by accurate segmenters, while they are broken up by less accurate (but reasonable) segmenters, to a surprising advantage. This suggests that words themselves might be too broad a notion to conveniently capture the general semantic meaning of Chinese text.
Bioavailability of new synthesised glucooligosaccharides in the intestinal tract of gnotobiotic rats (1993)

Abstract Using germ‐free rats and previously germ‐free rats inoculated with a complex human flora (heteroxenic rats), the digestibility of new glucooligosaccharides (GOS) and the effect of the digestive flora on their fermentation were studied. The GOS were synthesized using a glucosyltransferase reaction and were composed of a mixture of mono‐ to heptasaccharides (degree of polymerisation (DP) from 1 to 7), with α‐1,6 and α‐1,2 linkages. In germ‐free rats, two diets containing GOS (20 g kg −1 diet and 40 g kg −1 diet) were compared to a control diet containing sucrose. The extent of GOS digestion was about 20% and the major component, DP 5, was almost fully resistant to the action of endogenous enzymes. In heteroxenic rats, only GOS (20 g kg −1 diet) was compared to the control diet. Gaseous H 2 and CH 4 excretions measured in a respiratory chamber significantly increased by GOS fermentation (1.8 and 2.9 times, respectively, P < 0.001). As compared to the control group, there were no modifications of the pH, short‐chain fatty acids (SCFA), and lactic acid concentrations in the caecum of rats fed with the GOS diet, but there were changes of the SCFA profile, ie butyric, isobutyric and isovaleric acid proportions significantly decreased ( P < 0.01), whereas the caproic acid proportion increased ( P < 0.05). GOS appeared to be completely fermented. Changes in the gaseous excretion and in the SCFA profile suggest that the intake of a low amount of this new synthetised GOS led to some decrease in the proteolytic activity and in an enhancement of the glycolytic fermentation.
Two hundred years ago, 1739 (1939)

Abstract The Journal Books and the Council Minutes of the Society as well as the manuscript records that are preserved in our Library contain a rich collection of material illustrating the opinions, ideals and achievements of the small body of men who in the seventeenth century were drawn together by a common desire to advance Natural Knowledge. With its aid we may follow the history of science through nearly three centuries which have passed since Charles II gave to the Society its Charter of Incorporation in 1662. Under this it has grown from small beginnings until it has become an institution of high standing in international science.
TREATMENT OF PEYRONIE'S DISEASE WITH INTRALESIONAL VERAPAMIL INJECTION (1997)

Verapamil injection therapy resulted in a reduction of pain in 97% of the patients, an improvement in sexual function in 72%, a reduction of deformity in 86%, an improvement in distal rigidity in 93% and an objective reduction of curvature in 54%. Further studies are required to determine the effectiveness of this nontoxic, inexpensive, nonsurgical approach to Peyronie's disease.
Different transmission rates of herpesvirus thymidine kinase reporter transgenes from founder male parents and male parents of subsequent generations (1995)

Previously we demonstrated that lines of transgenic mice carrying the herpes simplex type 1 virus thymidine kinase (HSV1-tk) reporter gene are male-sterile. Ectopic transcription of the HSV1-tk reporter in the testis was initiated downstream of the normal translation initiation codon and truncated proteins consistent with translational initiation at the second and third ATG codons were synthesized. Here we describe the effects on fertility 1) of converting the second and third ATG codons of the HSV1-tk reporter to CTG codons and 2) of utilizing the HSV type 2 thymidine kinase (HSV2-tk) reporter gene, in which the second ATG codon is located downstream of the ATP-binding pocket of the enzyme. Both reporters were coupled to the bovine thyroglobulin promoter (bTG-tk1 alpha and bTG-tk2 transgenes). The level of ectopic expression of these transgenes in the testis, relative to expression in the thyroid, was one to two orders of magnitude less than that of bTG-tk1. Sixty percent of male founders carrying the bTG-tk1 alpha and bTG-tk2 transgenes were fertile but did not transmit the transgene. In contrast, most males from subsequent generations were fertile and transmitted the transgenes at the expected frequency. This difference between founder males and male descendants is also observed with certain constructs in which the HSV1-tk reporter is coupled to other promoters. We attribute the effect to mosaicism among male founders, leading to competition between transgenic and nontransgenic spermatozoa and/or spermatogenic precursor cells and resulting in a lack of fertilization by transgenic sperm that would successfully fertilize eggs in the absence of competition.
Large-Area Epitaxial Monolayer MoS<sub>2</sub> (2015)

Two-dimensional semiconductors such as MoS2 are an emerging material family with wide-ranging potential applications in electronics, optoelectronics, and energy harvesting. Large-area growth methods are needed to open the way to applications. Control over lattice orientation during growth remains a challenge. This is needed to minimize or even avoid the formation of grain boundaries, detrimental to electrical, optical, and mechanical properties of MoS2 and other 2D semiconductors. Here, we report on the growth of high-quality monolayer MoS2 with control over lattice orientation. We show that the monolayer film is composed of coalescing single islands with limited numbers of lattice orientation due to an epitaxial growth mechanism. Optical absorbance spectra acquired over large areas show significant absorbance in the high-energy part of the spectrum, indicating that MoS2 could also be interesting for harvesting this region of the solar spectrum and fabrication of UV-sensitive photodetectors. Even though the interaction between the growth substrate and MoS2 is strong enough to induce lattice alignment via van der Waals interaction, we can easily transfer the grown material and fabricate devices. Local potential mapping along channels in field-effect transistors shows that the single-crystal MoS2 grains in our film are well connected, with interfaces that do not degrade the electrical conductivity. This is also confirmed by the relatively large and length-independent mobility in devices with a channel length reaching 80 μm.
Clinical Impact of Immune Microenvironment in Stage I Lung Adenocarcinoma: Tumor Interleukin-12 Receptor β2 (IL-12Rβ2), IL-7R, and Stromal FoxP3/CD3 Ratio Are Independent Predictors of Recurrence (2012)

Our investigation confirms the biologic and prognostic significance of the tumor immune microenvironment for patients with stage I lung ADC and provides support for its use to stratify clinical outcome and immunotherapeutic interventions.
ASCA X-ray observations of pre-main-sequence stars (1996)

The results of recent Advanced Satellite for Cosmology and Astrophysics (ASCA) X-ray observations of two pre-main sequence stars are presented: the weak emission line T Tauri star HD 142361, and the Herbig Ae star HD 104237. The solid state imaging spectrometer spectra for HD 142361 shows a clear emission line from H-like Mg 7, and spectral fits reveal a multiple temperature plasma with a hot component of at least 16 MK. The spectra of HD 104237 show a complex temperature structure with the hottest plasma at temperatures of greater than 30 MK. It is concluded that mechanisms that predict only soft X-ray emission can be dismissed for Herbig Ae stars.
A fiber-optic current sensor for aerospace applications (1990)

A robust, accurate, broadband, AC sensor using fiber optics that is being developed for space applications at power frequencies as high as 20 kHz is described. It can also be used in low- and high-voltage 60-Hz terrestrial power systems and in 400-Hz aircraft systems. It is intrinsically immune to electromagnetic interference (EMI) and has the added benefit of excellent isolation. The sensor uses the Faraday effect in optical fiber and standard polarimetric measurements to sense electrical current. The primary component of the sensor is a specially treated coil of single-mode optical fiber, through which the current-carrying conductor passes. Improved precision is accomplished by temperature compensation by means of signals from a novel fiber-optic temperature sensor embedded in the sensing head. The technology used in the sensor is discussed, and the results of precision tests conducted at various temperatures within the wide operating range as well as the results of early EMI tests are reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Space suit heat exchanger Patent (1969)

Space suit body heat exchanger design composed of thermal conductance yarn and liquid coolant loops
The 14–Amino Acid CLV3, CLE19, and CLE40 Peptides Trigger Consumption of the Root Meristem in <i>Arabidopsis</i> through a <i>CLAVATA2</i> -Dependent Pathway (2005)

CLAVATA3 (CLV3), CLV3/ESR19 (CLE19), and CLE40 belong to a family of 26 genes in Arabidopsis thaliana that encode putative peptide ligands with unknown identity. It has been shown previously that ectopic expression of any of these three genes leads to a consumption of the root meristem. Here, we show that in vitro application of synthetic 14-amino acid peptides, CLV3p, CLE19p, and CLE40p, corresponding to the conserved CLE motif, mimics the overexpression phenotype. The same result was observed when CLE19 protein was applied externally. Interestingly, clv2 failed to respond to the peptide treatment, suggesting that CLV2 is involved in the CLE peptide signaling. Crossing of the CLE19 overexpression line with clv mutants confirms the involvement of CLV2. Analyses using tissue-specific marker lines revealed that the peptide treatments led to a premature differentiation of the ground tissue daughter cells and misspecification of cell identity in the pericycle and endodermis layers. We propose that these 14-amino acid peptides represent the major active domain of the corresponding CLE proteins, which interact with or saturate an unknown cell identity-maintaining CLV2 receptor complex in roots, leading to consumption of the root meristem.