gebhart/patrepeval huggingface dataset:
A Gene Expression Screen in Zebrafish Embryogenesis (2001)

A screen for developmentally regulated genes was conducted in the zebrafish, a system offering substantial advantages for the study of the molecular genetics of vertebrate embryogenesis. Clones from a normalized cDNA library from early somitogenesis stages were picked randomly and tested by high-throughput in situ hybridization for restricted expression in at least one of four stages of development. Among 2765 clones that were screened, a total of 347 genes with patterns judged to be restricted were selected. These clones were subjected to partial sequence analysis, allowing recognition of functional motifs in 163 among them. In addition, a portion of the clones were mapped with the aid of the LN54 radiation hybrid panel. The usefulness of the in situ hybridization screening approach is illustrated by describing several new markers for the characteristic structure in the fish embryo named the yolk syncytial layer, and for different regions of the developing brain.
Rigorous field theory design of millimeter-wave E-plane integrated circuit multiplexers (1989)

The overall field theory designs of two types of quasi-planar millimeter-wave multiplexers utilizing low-cost, low-insertion-loss printed metallic E-plane filters are described. Very compact components are achieved by using E-plane filters printed on a common metal sheet which is directly integrated in the septate sections of an E-plane n-furcated split-block waveguide housing. The second configuration proposed extends the useful principle of waveguide H-plane slit-coupled manifold multiplexers to the case of millimeter-wave printed metallic E-plane filters. Based on the model scattering matrix description of suitable key building blocks, the rigorous simulation technique used comprises the complete multiplexer structure including the E-plane transformer or iris elements, the waveguide E- or H-plane junctions, and the filter sections.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Segregation of Proteinase-negative Mutants from Heterozygous Candida albicans (1987)

The extracellular acidic proteinase (EC 3.4.23.6) produced by Candida albicans has been reported to be a virulence factor. In studying the role of this proteinase in human disease, we determined the optimum conditions for stimulating proteinase production in order to isolate proteinase-negative (Prt-) mutants. We found that in liquid medium containing bovine serum albumin (BSA) as the sole nitrogen source, at pH 4 and 27 degrees C, the sensitivity of proteinase detection was considerably greater than when assayed on BSA agar at 37 degrees C. This observation is due, in part, to temperature sensitivity of proteinase induction. Nitrogen starvation did not induce proteinase. Proteinase production on agar was increased by adding 0.01% yeast extract (YE) to BSA medium. Using BSA + YE agar to isolate mutants, it was discovered that C. albicans ATCC 28366 was heterozygous for a Prt- mutation. Spontaneous Prt- mutants occurred at a frequency of 2 x 10(-3). Ultraviolet light increased the mitotic segregation of Prt- cells to a frequency of 1 x 10(-2). The Prt- phenotype showed a large inoculum effect, Prt- segregants reverted with a high frequency, and the revertants were unstable.
Cocrystal Formation between Chiral Compounds: How Cocrystals Differ from Salts (2014)

A cocrystal screening on a series of chiral target compounds was performed in order to investigate the propensity for two optically active compounds to cocrystallize in an enantiospecific manner. 13 novel cocrystal systems were identified, out of which 11 are enantiospecific and two present a diastereomeric cocrystal pair, yielding a total of 15 novel cocrystals. 6 out of these are structurally characterized in this study. A meticulous search in the Cambridge Structural Database (CSD) has allowed expanding this study. The results lead us to the conclusion that enantiospecific cocrystallization seems to be the common rule of thumb, as over 85% of cocrystal systems behave enantiospecifically. Directionality of the hydrogen bonding motifs is likely responsible for cocrystals predilection towards enantiospecificity, while salts are mainly stabilized by less directional electrostatic interactions, leading to the formation of diastereomeric pairs.
A symmetric CMOS NOR gate for high-speed applications (1988)

A novel CMOS n-input NOR gate is proposed, having n parallel NMOS pull-downs to V/sub ss/ and n parallel PMOS pull-ups to V/sub cc/. The structure, which consumes DC power, is approximately twice as fast as a conventional full-CMOS NOR gate, and is slightly faster than a CMOS inverter. For gates with small fan-in (n<or=3), the proposed circuit is also faster than the grounded-PMOS NOR gate when operated at equal DC power levels.<<ETX>>
Arabidopsis Rho-Related GTPases: Differential Gene Expression in Pollen and Polar Localization in Fission Yeast (1998)

The Rho small GTP-binding proteins are versatile, conserved molecular switches in eukaryotic signal transduction. Plants contain a unique subfamily of Rho-GTPases called Rop (Rho-related GTPases from plants). Our previous studies involving injection of antibodies indicated that the pea Rop GTPase Rop1Ps is critical for pollen tube growth. In this study we show that overexpression of an apparent Arabidopsis ortholog of Rop1Ps, Rop1At, induces isotropic cell growth in fission yeast (Schizosaccharomyces pombe) and that green fluorescence protein-tagged Rop1At displays polar localization to the site of growth in yeast. We found that Rop1At and two other Arabidopsis Rops, Rop3At and Rop5At, are all expressed in mature pollen. All three pollen Rops fall into the same subgroup as Rop1Ps and diverge from those Rops that are not expressed in mature pollen, suggesting a coupling of the structural conservation of Rop GTPases to their gene expression in pollen. However, pollen-specific transcript accumulation for Rop1At is much higher than that for Rop3At and Rop5At. Furthermore, Rop1At is specifically expressed in anthers, whereas Rop3At and Rop5At are also expressed in vegetative tissues. In transgenic plants containing the Rop1At promoter:GUS fusion gene, GUS is specifically expressed in mature pollen and pollen tubes. We propose that Rop1At may play a predominant role in the regulation of polarized cell growth in pollen, whereas its close relatives Rop3At and Rop5At may be functionally redundant to Rop1At in pollen.
Interference suppression in FMICW radar with staggered pulse repetition interval (2007)

Abstract FMCW (frequency‐modulated continuous wave) radar is a radar system which can achieve high resolution by relatively low signal processing load. The authors have reported on clutter suppression by FMICW (FM interrupted CW) radar, where the transmission/reception of FMCW radar in pulse waveform is switched in order to assure transmission/reception isolation and to suppress undesired waves from short distances. This paper proposes the FM staggered PRI system, in which the pulse repetition interval (PRI) is randomized for each pulse in order to suppress the interference when FMICW radars are congested within the search distance. The target‐signal in the FM staggered PRI system is formulated. Conditions such as the average PRI and the possible range of staggering are derived from requirements such as the maximum search distance. The output S/I is statistically evaluated by computer simulation, with the average PRI, the pulse width, the number of interference waves, and the input S/I (signal‐to‐interference ratio) as variables. The effectiveness of the FM staggered PRI system is demonstrated. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 90(12): 86–100, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/ecja.20326
High-resolution Mass Spectrometry and Accurate Mass Measurements with Emphasis on the Characterization of Peptides and Proteins by Matrix-assisted Laser Desorption/Ionization Time-of-flight Mass Spectrometry (1997)

Fundamental concepts of high-resolution mass spectrometry as it relates to the issue of accurate mass measurements are presented. Important issues specific to magnetic sector instruments, Fourier transform ion cyclotron resonance and time-of-flight (TOF) methods are discussed. Recent high-resolution TOF measurements on peptides and proteins, ionized by matrix-assisted laser desorption/ionization (MALDI), are presented and discussed in terms of basic concepts important to accurate mass measurements. © 1997 by John Wiley & Sons, Ltd.
Genetic Diversity of Three Aristichthys nobilis Populations and One Inbreeding Stock (2002)

threeAristichthys nobilis 人口和一使随机的放大多态的 DNA (RAPD ) 方法近交存货的基因差异用被学习。自然人口的材料从 Guangxi 省， Hengxian (NH ) 和 Shanglin (NS ) 和湖北省的一个城市的二个县被收集，武汉城市。(NW ) 。Shanglin 和 Hengxian 分别地是河系统属于 Qianjiang 和 Yujiang 河，到 Xunjiang 河， Xijiang 河的主要支流，它是 Zhujiang 河系统的最大的支流，和武汉的二支流 confluencing 是水系统属于扬子江河系统。使近交的股票(RS ) 是由交配其父母从 Shanglin 镇定的系统的兄弟姐妹的超过 10 产生后代。结果证明 RS 的个人的基因变化是很低的(0.105 4 ) 而自然人口的相对高，它从对高低是 0.158 1 (NW ) ， 0.132 0 (NH ) 并且 0.110 5 (NS ) 。作为为基因距离的一个索引对明智的人口，在人口之间的基因变化被学习，它描绘了在人口之间的基因距离。而 NH 和 NS， NS 和 RS， NH 和 RS 的是低的， NW 和 NH， NW 和 NS， NW 和 RS 的基因距离分别地高。Chi-test (2 ) 和对明智的人口作为有效被拿的基因变化的分析为学习人口差别来临。
Threats, vulnerabilities, prevention, detection, and management (2006)

VOLUME I: KEY CONCEPTS, INFRASTRUCTURE, STANDARDS, AND PROTOCOLS. Part 1: Key Concepts and Applications related to Information Security. Part 2: Infrastructure for the Internet, Computer Networks, and Secure Information Transfer. Part 3: Standards and Protocols for Secure Information Transfer. VOLUME II: INFORMATION WARFARE SOCIAL, LEGAL, AND INTERNATIONAL ISSUES AND SECURITY FOUNDATIONS. Part 1: Information Warfare. Part 2: Social and Legal Issues. Part 3: Foundations of Information, Computer and Network Security. VOLUME III: THREATS, VULNERABILITIES, PREVENTION, DETECTION, AND MANAGEMENT. Part 1: Threats, Vulnerabilities, Prevention, Detection, and Management. Part 2: Prevention: Keeping the Hackers and Crackers at Bay. Part 3: Detection, Recovery, Management, and Policy Considerations.
Repeat Injection Studies of Technetium-99M-Labeled Peg-Liposomes in the Same Animal (1998)

This study was designed to determine if repeat injections of polyethylene glycol (PEG) coated liposomes in the same animal lead to a change in biodistribution due to a biological response. To evaluate the long-term storage of PEG-liposomes for imaging applications and to remove any concerns of batch variability, one large batch of PEG-liposomes containing glutathione and sucrose was prepared and used for the entire study. On each day that an imaging study was performed, an aliquot of PEG-liposomes were labeled with techne-tium-99m (99mTc) using hexamethylpropyleneamine oxime. Rabbits (n = 4) were injected with 99mTc-PEG-liposomes (2 ml; 13 mg phospholipid/kg body wt; 2 mCi 99mTc-activity) at 8 days after manufacture and imaged under a gamma camera. Heart-to-lung ratios, heart-to-liver ratios and organ activities were determined by region of interest analysis. Blood samples were collected to generate blood clearance curves. Six weeks later the same rabbits were given a second dose of 99mTc-PEG-liposomes at 50 days after manufacture and imaged as before. A set of new rabbits (n = 3) were also imaged at six weeks using 99mTc-PEG-liposomes in order to differentiate any differences in organ distribution due to storage vs. reinjection. Images acquired for each set of rabbits at 30 minutes demonstrated little change in organ distribution following reinjection. Heart-to-lung ratios decreased from 2.25 ± 0.06 at baseline to 2.05 0.05 on reinjection and 2.10 ± 0.01 upon storage. Heart-to-liver ratios were 1.46 ± 0.06 on reinjection, significantly lower than the ratio of 1.72 ± 0.10 at baseline or 1.68 ± 0.09 upon storage. Circulation half-life of 29 hours did not change within the three groups. Although a slight change in organ biodistribution occurred with storage and reinjection, these effects were minimal and are not likely to affect drug targeting or diagnostic imaging on repeat injection.
Synthesis and applications of cyano‐vinylene‐based polymers containing cyclopentadithiophene and dithienosilole units for photovoltaic cells (2011)

Abstract Two β‐cyano‐thiophenevinylene‐based polymers containing cyclopentadithiophene ( CPDT‐CN ) and dithienosilole ( DTS‐CN ) units were synthesized via Stille coupling reaction with Pd(PPh 3 ) 4 as a catalyst. The effects of the bridged atoms (C and Si) and cyano‐vinylene groups on their thermal, optical, electrochemical, charge transporting, and photovoltaic properties were investigated. Both polymers possessed the highest occupied molecular orbital (HOMO) levels of about −5.30 eV and the lowest unoccupied molecular orbital (LUMO) levels of about −3.60 eV, and covered broad absorption ranges with narrow optical band gaps (ca. 1.6 eV). The bulk heterojunction polymer solar cell (PSC) devices containing an active layer of electron‐donor polymers ( CPDT‐CN and DTS‐CN ) blended with an electron‐acceptor, that is, [6,6]‐phenyl‐C 61 ‐butyric acid methyl ester (PC 61 BM) or [6,6]‐phenyl‐C 71 ‐butyric acid methyl ester (PC 71 BM), in different weight ratios were explored under 100 mW/cm 2 of AM 1.5 white‐light illumination. The PSC device based on DTS‐CN: PC 71 BM (1:2 w/w) exhibited a best power conversion efficiency (PCE) value of 2.25% with V o c = 0.74 V, J sc = 8.39 mA/cm 2 , and FF = 0.36. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011.
Correlation of lithium ion distribution and X-ray absorption near-edge structure in O3- and O2-lithium cobalt oxides from first-principle calculation (2012)

First-principle calculation was employed to simulate X-ray absorption near-edge structure (XANES) spectroscopy of two typical types of lithium cobalt oxides to clarify the electronic and local structural changes during lithium-ion de-intercalation. The simulated Co K-edge XANES spectra agreed well with the observed spectra. The differences in the shape of the XANES spectra with structural symmetry and/or lithium contents in lithium cobalt oxides were analyzed based on the partial density of state (PDOS) of the excited energy level. First-principle calculation simulations revealed that the cobalt PDOS overlapped with nearby lithium PDOS via oxygen PDOS, and the overlap difference among various Li1−xCoO2 could be detected using both the experimental and theoretical Co K-edge XANES spectra.
Single-Phase Heat Transfer Enhancement Techniques in Microchannel and Minichannel Flows (2004)

The single-phase heat transfer enhancement techniques are well established for conventional channels and compact heat exchangers. The major techniques include flow transition, breakup of boundary layer, entrance region, vibration, electric fields, swirl flow, secondary flow and mixers. In the present paper, the applicability of these techniques for single-phase flows in microchannels and minichannels is evaluated. The microchannel and minichannel single-phase heat transfer enhancement devices will extend the applicability of single-phase cooling for critical applications, such as chip cooling, before more aggressive cooling techniques, such as flow boiling, are considered.
Caffeic Acid Phenethyl Ester Suppresses the Production of Pro-inflammatory Cytokines in Hypertrophic Adipocytes through Lipopolysaccharide-Stimulated Macrophages (2012)

Obesity is a condition in which excess body fat accumulates due to lipids producing adipocytes and an increased number of differentiated mature cells. Recently, new findings have shown that macrophages infiltrate into adipose tissues and produce various pro-inflammatory cytokines in obese subjects. The inflammatory changes induced by the cross-talk between adipocytes and macrophages are critical for the pathophysiology of obesity and thus of metabolic syndrome. Caffeic acid phenethyl ester (CAPE) is known to have many functions, including antibacterial, anticancer and anti-inflammatory properties, but there is no evidence of its effect on the inflammatory responses in hypertrophic adipocytes through stimulation by macrophages. We investigated the effect of CAPE on macrophages and hypertrophic adipocytes in this study. CAPE significantly suppressed the levels of lipopolysaccharide (LPS)-induced interleukin (IL)-1-beta, tumor necrosis factor (TNF)-alpha and monocyte chemoattractant protein (MCP)-1 from a macrophage cell line, RAW264.7. Supernatants of stimulated RAW264.7 macrophages drastically increased mRNA levels of pro-inflammatory cytokines such as IL-6, MCP-1 and TNF-alpha in 3T3-L1 hypertrophic adipocytes. CAPE also significantly and dose-dependently reduced the gene expression of these cytokines. Our findings indicate that CAPE has inhibitory effects on the production of pro-inflammatory cytokines from LPS-stimulated RAW264.7 macrophages. In addition, CAPE suppressed gene expressions of cytokines under inflammatory conditions of hypertrophic adipocytes, suggesting that it may have the potential to suppress inflammation by macrophage infiltration into adipose tissue in obese patients.
Esterification of Acetic Acid with Butanol in the Presence of Ion-Exchange Resins as Catalysts (2003)

The esterification of acetic acid with n-butanol was studied in the presence of ion-exchange resin catalysts such as Amberlyst-15 to determine the intrinsic reaction kinetics. The effect of various parameters such as temperature, mole ratio, catalyst loading, and particle size was studied. Kinetic modeling was performed to obtain the parameters related to intrinsic kinetics. Pseudohomogeneous, Eley−Rideal, Langmuir−Hinshelwood−Hougen−Watson (LHHW), and modified LHHW models were developed. The kinetics for the side-reaction etherification was also investigated. The rate expressions would be useful in the simulation studies for reactive distillation. The experimental data generated for the reaction under total reflux were validated successfully using the developed rate equation and estimated values of kinetic parameters.
Relationship between cell size and nuclear volume in nucleated red blood cells of developmentally matched diploid and tetraploid mouse embryos (1992)

Abstract Analysis of control diploid and polyploid amphibia indicated that cell and nuclear volumes were closely related to their ploidy, so that an increase in ploidy was generally associated with an increase in cell size. This relationship is also believed to occur in mammalian polyploids. However, since the latter are only rarely encountered spontaneously, or only occasionally following experimental manipulation, no detailed morphometric studies have been carried out to date to confirm whether such a relationship exists. In this study, the cellular and nuclear volume of primitive red blood cells was analyzed in carefully developmentally matched control diploid mouse embryos and tetraploid embryos produced by the technique of electrofusion. All of the cells and/or nuclei studied had a characteristic spherical shape which greatly simplified the morphometric analysis. A defined and predictable relationship between ploidy and cellular and/or nuclear volume was observed in the red blood cells between 8.25 and 14.5 days of gestation. During this period the primitive red blood cells are gradually replaced by the definitive erythrocytes. The ratio of control values to tetraploid values was found to be close to the theoretical value of 1:2 when comparable cells and/or their nuclei were analyzed in carefully developmentally matched material. © 1992 Wiley‐Liss, Inc.
Structural Characterization of Vivapain-2 and Vivapain-3, Cysteine Proteases from<i>Plasmodium vivax</i>: Comparative Protein Modeling and Docking Studies (2004)

Malaria remains one of the most important infectious diseases in the world. Plasmodial cysteine proteases are proposed to be promising targets for novel antimalarial drug design. Vivapain-2 and vivapain-3 are cysteine proteases from Plasmodium vivax and apparent orthologs of falcipain-2 and falcipain-3 from Plasmodium falciparum. Model structures of vivapain-2 and vivapain-3 have been derived using the comparative protein modeling approach and validated by various structure/geometry verification tools. Correlation between the interaction energies calculated based on the docking studies of the inhibitors and the corresponding association constants (k(ass)) provide additional validation for the structures. Moreover, some of the biochemical differences observed between the vivapains may be explained by the results of the docking studies. The overall structures of the two vivapains are similar to each other as well as to the falcipains with most of the catalytic residues conserved. At the same time, some important differences are observed between the sizes of the binding pockets as well as some of the residues involved in binding. The study suggests a likelihood of developing common inhibitors for these enzymes provided the interesting differences in the binding pockets of these enzymes are critically considered during such an attempt. The results of the current study can be utilized in de novo drug design for effective treatment of malaria.
Old friends in new guise: repositioning of known drugs with structural bioinformatics (2011)

Developing a drug de novo is a laborious and costly endeavor. Thus, the repositioning of already approved drugs for the treatment of new diseases is promising and valuable. One computational approach to repositioning exploits the structural similarity of binding sites of known and new targets. Here, we review computational methods to represent and align binding sites. We review available tools, present success stories and discuss limits of the approach.
Feedforward Neural Nets as Models for Time Series Forecasting (1993)

We have studied neural networks as models for time series forecasting, and our research compares the Box-Jenkins method against the neural network method for long and short term memory series. Our work was inspired by previously published works that yielded inconsistent results about comparative performance. We have since experimented with 16 time series of differing complexity using neural networks. The performance of the neural networks is compared with that of the Box-Jenkins method. Our experiments indicate that for time series with long memory, both methods produced comparable results. However, for series with short memory, neural networks outperformed the Box-Jenkins model. Because neural networks can be easily built for multiple-step-ahead forecasting, they may present a better long term forecast model than the Box-Jenkins method. We discussed the representation ability, the model building process and the applicability of the neural net approach. Neural networks appear to provide a promising alternative for time series forecasting. INFORMS Journal on Computing, ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
Acetylcysteine: A Drug with an Interesting Past and a Fascinating Future (1986)

N-acetylcysteine (NAC) possesses a free sulfhydryl group that can rupture disulfide bridges. Although it is considered to be a mucolytic, its mucokinetic actions include expectorant, bronchorrheic and mucoregulatory contributions. New uses include the management of acetaminophen poisoning and the scavenging of free radicals liberated by cancer chemotherapy drugs. The antioxidant effects may be of prophylactic value in lungs at risk from smoking, pollution and infection. Other uses proposed for NAC include the therapy of connective tissue diseases and its use as a component in life extension diets.