gebhart/patrepeval huggingface dataset:
Three-dimensional ultrastructural analysis of the Saccharomyces cerevisiae mitotic spindle. (1995)

The three dimensional organization of microtubules in mitotic spindles of the yeast Saccharomyces cerevisiae has been determined by computer-aided reconstruction from electron micrographs of serially cross-sectioned spindles. Fifteen spindles ranging in length from 0.6-9.4 microns have been analyzed. Ordered microtubule packing is absent in spindles up to 0.8 micron, but the total number of microtubules is sufficient to allow one microtubule per kinetochore with a few additional microtubules that may form an interpolar spindle. An obvious bundle of about eight interpolar microtubules was found in spindles 1.3-1.6 microns long, and we suggest that the approximately 32 remaining microtubules act as kinetochore fibers. The relative lengths of the microtubules in these spindles suggest that they may be in an early stage of anaphase, even though these spindles are all situated in the mother cell, not in the isthmus between mother and bud. None of the reconstructed spindles exhibited the uniform populations of kinetochore microtubules characteristic of metaphase. Long spindles (2.7-9.4 microns), presumably in anaphase B, contained short remnants of a few presumed kinetochore microtubules clustered near the poles and a few long microtubules extending from each pole toward the spindle midplane, where they interdigitated with their counterparts from the other pole. Interpretation of these reconstructed spindles offers some insights into the mechanisms of mitosis in this yeast.
A nonsecreted variant of interleukin-4 is associated with apoptosis: implication for the T helper–2 polarization in HIV infection (2003)

We report the detection of an interleukin-4 (IL-4) variant whose expression is tightly associated with deprivation apoptosis. It is detected with the 8D4 anti-IL-4 monoclonal antibody (mAb) not only in T helper-2 (Th2) but also in Th1 clones, and primary T cells, and it is a nonsecreted molecule. It is not expressed during primary necrosis. Our data suggest that de novo IL-4 transcription of an alternative IL-4 mRNA (IL-4 delta(13)) is induced during deprivation apoptosis. In HIV-infected patients, increased expression of IL-4 in T cells is highly correlated to increased apoptosis, restricted to 8D4 reactivity (r(2) = 0.84 between % 8D4-8(+) and % 7- amino-actinomycin D-positive [7-AAD(+)] peripheral T cells, P <.0001), and associated with disease progression. The particular reactivity of apoptotic T cells to 8D4 mAb may explain some discordances among studies analyzing the Th1/Th2 balance in HIV infection and questions the function of this intracellular type 2 signal.
Ambipolar Carrier Injections Governed by Electrochemical Potentials of Ionic Liquids in Electric-Double-Layer Thin-Film Transistors of Lead- and Titanyl-Phthalocyanine (2013)

Electric-double-layer thin-film transistors of lead- and titanyl-phthalocyanine with ionic-liquid gate dielectrics exhibit ambipolar behavior with low threshold voltages less than ±2 V. Their threshold gate voltages are found to depend significantly on the ionic liquids, being proportional to the electrochemical potential of the ionic liquids. This dependence can be understood by an energy diagram of the frontier orbitals of PbPc and TiOPc, and the electrochemical potentials of the ionic liquids.
Distinct gene expression profiles of acute myeloid/T-lymphoid leukemia with silenced CEBPA and mutations in NOTCH1 (2007)

Gene expression profiling of acute myeloid leukemia (AML) allows the discovery of previously unrecognized molecular entities. Here, we identified a specific subgroup of AML, defined by an expression profile resembling that of AMLs with mutations in the myeloid transcription factor CCAAT/enhancer-binding protein alpha (C/EBPalpha), while lacking such mutations. We found that in these leukemias, the CEBPA gene was silenced, which was associated with frequent promoter hypermethylation. The leukemias phenotypically showed aberrant expression of T-cell genes, of which CD7 was most consistent. We identified 2 mechanisms that may contribute to this phenotype. First, absence of Cebpa led to up-regulation of specific T-cell transcripts (ie, Cd7 and Lck) in hematopoietic stem cells isolated from conditional Cebpa knockout mice. Second, the enhanced expression of TRIB2, which we identify here as a direct target of the T-cell commitment factor NOTCH1, suggested aberrantly activated Notch signaling. Putatively activating NOTCH1 mutations were found in several specimens of the newly identified subgroup, while a large set of control AMLs was mutation negative. A gene expression prediction signature allowed the detection of similar cases of leukemia in independent series of AML.
Alterations in Gene Expression and DNA Methylation during Murine and Human Lung Alveolar Septation (2014)

DNA methylation, a major epigenetic mechanism, may regulate coordinated expression of multiple genes at specific time points during alveolar septation in lung development. The objective of this study was to identify genes regulated by methylation during normal septation in mice and during disordered septation in bronchopulmonary dysplasia. In mice, newborn lungs (preseptation) and adult lungs (postseptation) were evaluated by microarray analysis of gene expression and immunoprecipitation of methylated DNA followed by sequencing (MeDIP-Seq). In humans, microarray gene expression data were integrated with genome-wide DNA methylation data from bronchopulmonary dysplasia versus preterm and term lung. Genes with reciprocal changes in expression and methylation, suggesting regulation by DNA methylation, were identified. In mice, 95 genes with inverse correlation between expression and methylation during normal septation were identified. In addition to genes known to be important in lung development (Wnt signaling, Angpt2, Sox9, etc.) and its extracellular matrix (Tnc, Eln, etc.), genes involved with immune and antioxidant defense (Stat4, Sod3, Prdx6, etc.) were also observed. In humans, 23 genes were differentially methylated with reciprocal changes in expression in bronchopulmonary dysplasia compared with preterm or term lung. Genes of interest included those involved with detoxifying enzymes (Gstm3) and transforming growth factor-β signaling (bone morphogenetic protein 7 [Bmp7]). In terms of overlap, 20 genes and three pathways methylated during mouse lung development also demonstrated changes in methylation between preterm and term human lung. Changes in methylation correspond to altered expression of a number of genes associated with lung development, suggesting that DNA methylation of these genes may regulate normal and abnormal alveolar septation.
Assessment of accommodative facility using MEM retinoscopy. (1990)

Subjective testing of accommodative facility can be difficult with young or nonverbal children, and children with learning problems. A new technique to objectively assess accommodative facility using monocular estimation method (MEM) retinoscopy is described. The objective technique was compared to a subjective assessment of accommodative facility, and the techniques were in agreement 86% of the time. Possible clinical usefulness of the objective procedure is discussed.
<title>High-pressure pulsed COIL assisted with an instantaneous production of atomic iodine II</title> (2003)

Pulsed oscillation of chemical oxygen-iodine laser, which is comprised of a pulsed singlet oxygen generator (SOG) and a photolytic iodine laser, is studied. This scheme allows one to produce a large aperture and high-pressure laser medium while maintaining a minimum degradation of stored energy by water vapor. The experimental apparatus consists of a porous pipe SOG, an iodine donor (CH<sub>3</sub>I) injector, a flash lamp and an optical resonator. Laser oscillation experiments are conducted and the operational characteristics of the apparatus are investigated. Pulse duration is inversely proportional to the iodine donor concentration as expected. The oscillation capability for different iodine donors is studied and it is concluded that the iodine donors containing fluorine are not suitable for the proposed scheme. Unfavorable chemical dissociation of iodate, which was observed in the previous study, is avoided by the optimization of the iodine donor injection and flash exposure timings. Maximum output energy of 730mJ with pulse duration of 65μm is obtained.
Gluco‐oligosaccharide synthesis by free and immobilized β‐glucosidase (1993)

Gluco-oligosaccharides were synthesized through the enzymatic condensation of D-glucose at high concentration using a commercial almond beta-glucosidase. The synthesis reactions were carried out with both free and immobilized enzyme, with or without sorbitol, an efficient depressor of water activity (a(w)) in the presence of different glucose concentrations. The yield and the composition of the gluco-oligosaccharides produced changed with the reaction mixture and the form of the enzyme used (free or immobilized). The use of 5 M glucose solution permitted only disaccharides to be obtained, whereas with a glucose concentration of 7.5 M glucose, di-, tri-, and tetrasaccharides were produced. A 7.5 M glucose solution used with 4.4 M sorbitol gave three times more disaccharides than the same solution without sorbitol. Moreover, the immobilized enzyme was much more active in synthesis. The synthesis yield (oligomers mg/mL . mg of enzyme) after immobilization was 573% compared to that of the free enzyme, when a 7.5 M glucose solution was tested. The effects of substrate concentration, sorbitol addition and enzyme immobilization were investigated.
Deposition of Ru Adatoms on Pt Using Organometallic Chemistry: Electro‐oxidation of Methanol, Ethanol, 1,2‐Ethanediol, and D‐Glucose over a Surface Optimized for Oxidation of Methanol (1998)

A surface with 10% Ru adatoms was prepared by hydrogenating (1, COD is 1,5‐cyclooctadiene) over Pt. The onsets of stabilized potentiodynamic oxidation for several fuels ([fuel] = = 0.5 M, sweep range 0.025 to 0.60 V (vs. SHE), 22°C) were ethanol (∼0.2 V), methanol (∼0.3 V), and 1,2‐ethanediol (∼0.45 V). The activity of D‐glucose was low under these conditions. The ratio of specific current densities for potentiostatic oxidation (30 min, [fuel] = = 0.5 M, E = 0.4 V, 22°C) over and over Pt were methanol (42) 1,2‐ethanediol (4.0), ethanol (2.3), and D‐glucose (1.8).
Ion-exclusion chromatography of silicate ion in sea and river water samples by an ion-exchange enhancement of conductivity detection (2004)

イオン交換樹脂カラムと水溶離液を用いる導電率検出イオン排除型イオンクロマトグラフィー（IC）による高精度なケイ酸イオンの分離計測法が開発された．本法では，導電率検出のイオン排除分離において，ケイ酸イオンと溶存する炭酸水素イオンが同じ保持容量であったことから，酸性条件下において窒素封入 し，炭酸水素イオンを除去した試料を用いた．水素型弱酸性陽イオン交換樹脂カラムに導入されたケイ酸イオンは，イオン排除作用によってケイ酸として分離された後，2本のイオン交換樹脂カラム（カリウム型強酸性陽イオン交換樹脂及び水酸化物型強塩基性陰イオン交換樹脂）によるイオン交換作用によって，高い極限当量イオン導電率を有する強塩基の水酸化カリウムに変換され，劇的な検出応答の増大が認められた．これにより，良好な検量線の直線性（0.05～50 ppm）と検出限界（S/N＝3: 0.02 ppm H3SiO4－）が得られた．本法は，環境水中のケイ酸イオンのモニタリングに応用され，10倍及び20倍に希釈された河川水及び海水中のケイ酸イオンの分離定量に適用することができた．
Charge Separation in Triplet C60/TMPD Exciplexes (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCharge Separation in Triplet C60/TMPD ExciplexesKaryn N. Grzeskowiak, Sergei N. Smirnov, and Charles L. BraunCite this: J. Phys. Chem. 1994, 98, 22, 5661–5664Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://doi.org/10.1021/j100073a015RIGHTS & PERMISSIONSArticle Views101Altmetric-Citations14LEARN 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 InReddit PDF (415 KB) Get e-Alerts
A Method of Calculation for Simulation of Action Potentials (1986)

A new method is presented of calculating digital computer simulations of propagating nerve or cardiac action potentials. The calculation is of the implicit type and is done with the "cable model" approach utilizing either well-known nerve or cardiac membrane physiological models. It does not require large computing resources for long fibers because it utilizes a "retarded potential" approach so that large matrix inversions are avoided and voltage profiles can be calculated with only eight spacesteps at one time.
[Heart transplantation--postoperative management]. (1987)

Heart transplantation represents a widely accepted therapeutic modality for patients with end-stage myocardial failure. With increasing experience, 1-year survival rates of over 75% and 5-year survival rates of over 60% have been achieved, mainly due to patient selection, standardized surgical techniques as well as improved postoperative management. During early follow-up, particular attention should focus on diagnosis and treatment of graft rejection and infection, which require individualized immunosuppression, while in the later postoperative course coronary atherosclerosis, hypertension, chronic renal insufficiency and malignancy become more important as potential complications. The general principles in the management of these patients are discussed.
- Library Design, Chemical Space, and Drug Likeness (2015)

High-throughput screening is a well-established method that dominates the discovery of compounds that can become clinical candidates. A critical factor for its success has been the assembly of an adequate chemical collection, geared to produce multiple high-quality hits with efcient use of resources (Bakken et al., 2012). Library design should not be viewed as an entirely creative process. The term design is used to convey the idea of purpose, planning, and intention in assembling a chemical collection for use. The design process will vary with the intended use of the collection, which may include not only commercially available or easy-to-synthesize compounds, but also virtual collections of structures.
Thermoelectric Properties of Conductive Freestanding Films Prepared from PEDOT:PSS Aqueous Dispersion and Ionic Liquids (2022)

In this study, freestanding poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) films modified with an ionic liquid (IL) were synthesized assuming modulization. These films were easily peeled off the glass substrate in water, producing hydrophobic and flexible freestanding films that exhibited extremely high mechanical strengths. The thermoelectric properties of the IL-doped PEDOT:PSS films depended on the amount of IL incorporated. To analyze the mechanism of this dependence in detail, the compositions, higher-order structures, and electronic states of the polymer films were studied by X-ray photoelectron spectroscopy, X-ray diffraction analysis, and electronic absorption spectroscopy. In addition, the carrier density in the polymer film was quantified using electrochemical techniques, and its correlation with the thermoelectric conversion properties was analyzed.
A Precision Recursive Estimate for Ephemeris Refinement (PREFER) (1980)

CRISPR/Cas system is an adaptive immune system that confers resistance to exogenous virus or plasmid in bacteria and archaea. In recent years, the booming CRISPR/Cas9 genome editing technology modified from type2 CRISPR/Cas adaptive immune system has been widely applied to various research fields of life science and led to revolutionary changes. In this review, we summarize the origin and development of CRISPR/Cas9 genome editing technology as well as its applications in life science research. We focus on the latest application of this system in gene therapy of human diseases and the associated side/off-target effects, which may provide references for researchers in related areas.
Determination of ferroelectric compositional phase transition using a novel virtual crystal approach (2000)

We employ a new method for studying compositionally disordered ferroelectric oxides. This method is based on the virtual crystal approximation (VCA), in which two or more component potentials are averaged into a composite atomic potential. In our method, we construct a virtual atom with the correctly averaged atomic size and atomic eigenvalues. We have used our new method to study the composition dependent phase transition in Pb(Zr1−xTix)O3 lying between x=0.5 and x=0.4. We correctly predict the experimentally determined phase transition from the tetragonal phase to a low-temperature rhombohedral phase between these two compositions.
Probabilistic Modeling of DNA Mismatch Repair Effects on Cell Cycle Dynamics and Iododeoxyuridine-DNA Incorporation (2007)

Previous studies in our laboratory have described increased and preferential radiosensitization of mismatch repair-deficient (MMR(-)) HCT116 colon cancer cells with 5-iododeoxyuridine (IUdR). Indeed, our studies showed that MMR is involved in the repair (removal) of IUdR-DNA, principally the G:IU mispair. Consequently, we have shown that MMR(-) cells incorporate 25% to 42% more IUdR than MMR(+) cells, and that IUdR and ionizing radiation (IR) interact to produce up to 3-fold greater cytotoxicity in MMR(-) cells. The present study uses the integration of probabilistic mathematical models and experimental data on MMR(-) versus MMR(+) cells to describe the effects of IUdR incorporation upon the cell cycle for the purpose of increasing IUdR-mediated radiosensitivity in MMR(-) cells. Two computational models have been developed. The first is a stochastic model of the progression of cell cycle states, which is applied to experimental data for two synchronized isogenic MMR(+) and MMR(-) colon cancer cell lines treated with and without IUdR. The second model defines the relation between the percentage of cells in the different cell cycle states and the corresponding IUdR-DNA incorporation at a particular time point. These models can be combined to predict IUdR-DNA incorporation at any time in the cell cycle. These mathematical models will be modified and used to maximize therapeutic gain in MMR(-) tumors versus MMR(+) normal tissues by predicting the optimal dose of IUdR and optimal timing for IR treatment to increase the synergistic action using xenograft models and, later, in clinical trials.
Functional Network Endophenotypes Unravel the Effects of Apolipoprotein E Epsilon 4 in Middle-Aged Adults (2013)

Apolipoprotein E-ε4 (APOE-ε4) accentuates memory decline, structural volume loss and cerebral amyloid deposition in cognitively healthy adults. We investigated whether APOE-ε4 carriers will show disruptions in the intrinsic cognitive networks, including the default mode (DMN), executive control (ECN) and salience (SN) networks, relative to noncarriers in middle-aged healthy adults; and the extent to which episodic-memory performance is related to the altered functional connectivity (Fc) in these networks. Resting-state functional connectivity MRI (R-fMRI) was used to measure the differences in the DMN, ECN and SN Fc between 20 APOE-ε4 carriers and 26 noncarriers. Multiple linear regression analyses were performed to determine the relationship between episodic-memory performance and Fc differences in the three resting-state networks across all subjects. There were no significant differences in the demographic and neuropsychological characteristics and the gray-matter volumes in the carriers and noncarriers. While mostly diminished DMN and ECN functional connectivities were seen, enhanced connections to the DMN structures were found in the SN in ε4 carriers. Altered DMN and ECN were associated with episodic memory performance. Significant Fc differences in the brain networks implicated in cognition were seen in middle-aged individuals with a genetic risk for AD, in the absence of cognitive decline and gray-matter atrophy. Prospective studies are essential to elucidate the potential of R-fMRI technique as a biomarker for predicting conversion from normal to early AD in healthy APOE-ε4 carriers.
Concurrent Product and Process Design in Hot Forging (2001)

The long and costly lead times necessary in developing new forged products motivate the application of concurrent engineer ing principles and knowledge-based computer software systems in hot forging. Design engineers can benefit significantly from such sys- ' tems, particularly if they incorporate both product and manufacturability knowledge. An Automated Concurrent Engineering Software (ACES) for part design and manufacturing has been developed at the Design and Manufacturing Institute (DMI) at Stevens Institute of Technology. This system combines deterministic and empirical knowledge about a variety of aspects of product design and manufactur ing, and thus, it provides potent reasoning and decision-making power that enables the engineer to reduce drastically the time between product conception and final production. This paper reports on the development of the prototype of a knowledge-based module for hot forging processes.
The TIPP opioid peptide family: Development of ? antagonists, ? agonists, and mixed ? agonist/? antagonists (1999)

The discovery of the prototype delta opioid antagonists TIPP (H-Tyr-Tic-Phe-Phe-OH) and TIP (H-Tyr-Tic-Phe-OH) in 1992 was followed by extensive structure-activity relationship studies, leading to the development of analogues that are of interest as pharmacological tools or as potential therapeutic agents. Stable TIPP-derived delta opioid antagonists with subnanomolar delta receptor binding affinity and extraordinary delta receptor selectivity include TIPP[Psi] (H-Tyr-TicPsi[CH(2)NH]Phe-Phe-OH] and TICP[Psi] (H-Tyr-TicPsi[CH(2)NH]Cha-Phe-OH); Cha: cyclohexylalanine), which are widely used in opioid research. Theoretical conformational analyses in conjunction with the pharmacological characterization of conformationally constrained TIPP analogues led to a definitive model of the receptor-bound conformation of H-Tyr-Tic-(Phe-Phe)-OH-related delta opioid antagonists, which is characterized by all-trans peptide bonds. Further structure-activity studies revealed that the delta antagonist vs delta agonist behavior of TIP(P)-derived compounds depended on very subtle structural differences in diverse locations of the molecule and suggested a delta receptor model involving a number of different inactive receptor conformations. A further outcome of these studies was the identification of a new class of potent and very selective dipeptide delta agonists of the general formula H-Tyr-Tic-NH-X (X = arylalkyl), which are of interest for drug development because of their low molecular weight and lipophilic character. Most interestingly, TIPP analogues containing a C-terminal carboxamide group displayed a mixed mu agonist/delta antagonist profile, and thus were expected to be analgesics with a low propensity to produce tolerance and physical dependence. This turned out to be the case with the TIPP-derived mu agonist/delta antagonist DIPP-NH(2)[Psi] (H-Dmt-TicPsi[CH(2)NH]Phe-Phe-NH(2)); Dmt: 2',6'- dimethyltyrosine).