gebhart/patrepeval huggingface dataset:
S-Phase Population Analysis Does Not Correlate with the Cytotoxicity of Camptothecin and 10,11-Methylenedioxycamptothecin in Human Colon Carcinoma HT-29 Cells (1991)

Previous studies in rapidly proliferating rodent cells have suggested that the lethal effect of the DNA topoisomerase I inhibitor, camptothecin (CPT) is dependent upon the active participation of DNA replication (Holm et al. Cancer Res. 49:6365-6368; 1989). The purpose of the current study was to determine if this relationship applies to more slowly growing human cells. In our present study, we employed the human colon carcinoma cell line, HT-29 (45 hr doubling time). Flow cytometric determination of S-phase cells either by S-phase fit model or rectangle fit model analysis predicted that 21% of exponentially growing HT-29 cells were undergoing DNA replication. These findings were confirmed by immunofluorescence microscopy of bromodeoxyuridine labeled cells. Based on these findings, we would have expected only 20-30% of the cells to be susceptible to brief treatment (30 min) with CPT. Instead, 90-95% of HT-29 cells were killed. This apparent disparity was not due to prolonged cellular retention of drug after treatment because protein-linked DNA strand breaks reversed within 15 min of drug removal. Moreover, the DNA replication inhibitor, aphidicolin, fully protected HT-29 cells against CPT-induced killing but did not affect the production of CPT-induced protein-linked DNA strand breaks. Similar results were also obtained using the CPT-analog, 10,11-methylenedioxy-camptothecin, which was 5- to 10-fold more potent than camptothecin (O'Connor et al. Cancer Commun. 2:395-400; 1990).(ABSTRACT TRUNCATED AT 250 WORDS)
Kinetic resolution of α-methylbenzylamine with ο-transaminase screened from soil microorganisms: Application of a biphasic system to overcome product inhibition (1997)

Two microorganisms showing high omicron-transaminase activity (Klebsiella pneumoniae JS2F and Bacillus thuringiensis JS64) were screened by the enrichment method using (S)-alpha-methylbenzylamine (alpha-MBA) as a sole nitrogen source. Optimal carbon and nitrogen sources for enzyme induction and the properties of omicron-transaminases were investigated. omicron-Transaminase from B. thuringiensis JS64 was highly enantioselective (E = 75.3) for (S)-enantiomer of alpha-MBA and showed remarkable stability. However, omicron-transaminase showed severe product inhibition by acetophenone. An aqueous/organic two-phase system was introduced to overcome this problem. Through solvent screening, cyclohexanone and ethyl acetate were selected as the best organic phases. The acetophenone-extracting capacity of the solvent and the biocompatibility of the solvent to the cell were important determinants in the reaction rate at high concentrations of alpha-MBA. The reaction rate of omicron-transamination was strongly influenced by the volume ratio of organic phase to aqueous phase as well as agitation speed in the biphasic mixture. Using the optimal volume ratio (Vorg:Vaq = 1:4) in the biphasic system with cyclohexanone, the reaction rate of omicron-transaminase under vigorous mixing conditions increased ninefold compared with that in the monophasic aqueous system. At the same optimal conditions, using whole cells, 500 mM alpha-MBA could be resolved successfully to above 95% enantiomeric excess of (R)-alpha-MBA with ca. 51% conversion. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 348-358, 1997.
Direction of coupling from phases of interacting oscillators: An information-theoretic approach (2003)

A directionality index based on conditional mutual information is proposed for application to the instantaneous phases of weakly coupled oscillators. Its abilities to distinguish unidirectional from bidirectional coupling, as well as to reveal and quantify asymmetry in bidirectional coupling, are demonstrated using numerical examples of quasiperiodic, chaotic, and noisy oscillators, as well as real human cardiorespiratory data.
Transcriptome Analysis Reveals Candidate Genes Related to Color Fading of ‘Red Bartlett’ (Pyrus communis L.) (2017)

The red color of fruit is an attractive plant trait for consumers. Plants with color-faded fruit have a lower commercial value, such as 'Red Bartlett' pears (<i>Pyrus communis</i> L.) that have dark-red fruit in the early stages of fruit development that subsequently fade to red-green at maturity. To identify the reason for color fading, we first analyzed the anthocyanin content of peel from 'Red Bartlett,' which displays the color fading phenomenon, and 'Starkrimson,' which has no color fading. Results showed that the anthocyanin content of 'Red Bartlett' peel decreased significantly late in fruit development, while in 'Starkrimson' there was no significant decrease. Next, RNA-Sequencing was used to identify 947 differentially expressed genes (DEGs) between 'Red Bartlett' and 'Starkrimson.' Among them, 471 genes were upregulated and 476 genes were downregulated in 'Red Bartlett' at the late development stage relative to 'Starkrimson.' During 'Red Bartlett' color fading, the structural gene <i>LDOX</i> and six GST family genes were downregulated, while FLS, LAC, POD, and five light-responding genes were significantly upregulated. Additionally, 45 genes encoding transcription factors MYB, bHLH, WRKY, NAC, ERF, and zinc finger were identified among 947 DEGs. Changes in the expression of these genes may be responsible for the decrease in anthocyanin accumulation in 'Red Bartlett' fruit. Taken together, this study demonstrated that color fading of 'Red Bartlett' was closely linked to reduced anthocyanin biosynthesis, increased anthocyanin degradation and suppression of anthocyanin transport. It also provided novel evidence for the involvement of light signals in the color fading of red-skinned pears.
SETGAN: Scale and Energy Trade-off GANs for Image Applications on Mobile Platforms (2021)

We consider the task of photo-realistic unconditional image generation (generate high quality, diverse samples that carry the same visual content as the image) on mobile platforms using Generative Adversarial Networks (GANs). In this paper, we propose a novel approach to trade-off image generation accuracy of a GAN for the energy consumed (compute) at run-time called Scale-Energy Tradeoff GAN (SETGAN). GANs usually take a long time to train and consume a huge memory hence making it difficult to run on edge devices. The key idea behind SETGAN for an image generation task is for a given input image, we train a GAN on a remote server and use the trained model on edge devices. We use SinGAN, a single image unconditional generative model, that contains a pyramid of fully convolutional GANs, each responsible for learning the patch distribution at a different scale of the image. During the training process, we determine the optimal number of scales for a given input image and the energy constraint from the target edge device. Results show that with SETGAN's unique client-server-based architecture, we were able to achieve a 56% gain in energy for a loss of 3% to 12% SSIM accuracy. Also, with the parallel multi-scale training, we obtain around 4x gain in training time on the server.
The Natural History of Nitrogen Fixation (2004)

In recent years, our understanding of biological nitrogen fixation has been bolstered by a diverse array of scientific techniques. Still, the origin and extant distribution of nitrogen fixation has been perplexing from a phylogenetic perspective, largely because of factors that confound molecular phylogeny such as sequence divergence, paralogy, and horizontal gene transfer. Here, we make use of 110 publicly available complete genome sequences to understand how the core components of nitrogenase, including NifH, NifD, NifK, NifE, and NifN proteins, have evolved. These genes are universal in nitrogen fixing organisms-typically found within highly conserved operons-and, overall, have remarkably congruent phylogenetic histories. Additional clues to the early origins of this system are available from two distinct clades of nitrogenase paralogs: a group composed of genes essential to photosynthetic pigment biosynthesis and a group of uncharacterized genes present in methanogens and in some photosynthetic bacteria. We explore the complex genetic history of the nitrogenase family, which is replete with gene duplication, recruitment, fusion, and horizontal gene transfer and discuss these events in light of the hypothesized presence of nitrogenase in the last common ancestor of modern organisms, as well as the additional possibility that nitrogen fixation might have evolved later, perhaps in methanogenic archaea, and was subsequently transferred into the bacterial domain.
Preparing an annotated gold standard corpus to share with extramural investigators for de-identification research (2014)

We successfully modified a de-identification dataset for external sharing while preserving the de-identification research value of the modified gold standard corpus with limited drop in machine learning de-identification performance.
Molecular Epidemiology of Coagulase-Negative Staphylococcus Blood Isolates from Neonates with Persistent Bacteremia and Children with Central Venous Catheter Infections (1994)

Multilocus enzyme electrophoresis was used to genetically characterize sequential isolates of coagulase-negative staphylococci (CONS) from 3 neonates with persistent bacteremia and organisms cultured from several sites in 23 children with presumed catheter-related sepsis (CRS). For 2 of 3 neonates and 21 (91%) of 23 of the patients with presumed CRS, the same CONS clone was isolated from multiple consecutive blood cultures (mean, 7.3 isolates; range, 3-19). For the 23 children with presumed CRS, 7 (30%) had catheter hub (CH) and 7 (30%) had catheter exist site (CES) cultures positive for CONS; cultures from 3 of these patients (from both CH and CES) grew CONS. Genetic analysis of isolates recovered from the CH and peripheral and central venous catheter blood cultures of all 7 patients revealed clonal identity of the strain grown from all sites. In contrast, only 4 (57%) of 7 of the CONS isolates from the CES were the same clone as that isolated from the blood. These data suggest that repetitive isolation of CONS during the course of CRS is due to ongoing bacteremia, not culture contamination with distinct CONS isolates. The results also are consistent with the hypothesis that the CH is a more likely site of initial colonization by CONS than the exist site in patients with CRS.
Association of Sepsis with an Immunosuppressive Polypeptide in the Serum of Burn Patients (1978)

One hundred ninety serum samples from 51 burned patients were tested for immunosuppressive activity which might explain decreased host immune competence following thermal injury. The serum from a variable but significant percentage of these patients suppressed the response of normal human peripheral blood lymphocytes to phytohemagglutinin. The occurrence of immunosuppressive activity paralleled the severity of the injury. Ten of ten severely burned patients (severity index greater than 40), but only 20 of 30 patients with index 10--39.9, and three of 11 patients with Index 0--9.9 developed suppressive serum. Differences between these groups were significant (p less than .05). In all 19 patients who became septic, immunosuppressive serum activity immediately preceded or coincided with the septic episode. In contrast to the effect on lymphocytes, burn sera stimulated fibroblast proliferation. Immunosuppressive activity did not correlate with serum cortisol levels, blood transfusion, protein-calorie malnutrition, or anesthesia. Suppressive sera were not cytotoxic. A majority of the active serum factor(s) was contained in a low molecular weight (less than 10,000 daltons) polypeptide subfraction.
Adaptive control of input field to achieve desired output intensity profile in multimode fiber with random mode coupling (2012)

We develop a method for synthesis of a desired intensity profile at the output of a multimode fiber (MMF) with random mode coupling by controlling the input field distribution using a spatial light modulator (SLM) whose complex reflectance is piecewise constant over a set of disjoint blocks. Depending on the application, the desired intensity profile may be known or unknown a priori. We pose the problem as optimization of an objective function quantifying, and derive a theoretical lower bound on the achievable objective function. We present an adaptive sequential coordinate ascent (SCA) algorithm for controlling the SLM, which does not require characterizing the full transfer characteristic of the MMF, and which converges to near the lower bound after one pass over the SLM blocks. This algorithm is faster than optimizations based on genetic algorithms or random assignment of SLM phases. We present simulated and experimental results applying the algorithm to forming spots of light at a MMF output, and describe how the algorithm can be applied to imaging.
Featureless Domain-Specific Term Extraction with Minimal Labelled Data (2016)

Supervised domain-specific term extraction often suffers from two common problems, namely labourious manual feature selection, and the lack of labelled data. In this paper, we introduce a weakly supervised bootstrapping approach using two deep learning classifiers. Each classifier learns the representations of terms separately by taking word embedding vectors as inputs, thus no manually selected feature is required. The two classifiers are firstly trained on a small set of labelled data, then independently make predictions on a subset of the unlabeled data. The most confident predictions are subsequently added to the training set to retrain the classifiers. This co-training process minimises the reliance on labelled data. Evaluations on two datasets demonstrate that the proposed co-training approach achieves a competitive performance with limited training data as compared to standard supervised learning baseline.
Carbon black–filled immiscible blends of poly(vinylidene fluoride) and high density polyethylene: The relationship between morphology and positive and negative temperature coefficient effects (1999)

Abstract Conductive polymer composites were prepared by melt‐mixing of an immiscible blend of poly(vinylidene fluoride) (PVDF), high density polyethylene (HDPE), and carbon black (CB). Three major factors—the carbon black content, the carbon black type, and the composite morphology—were shown to have remarkable effects on the positive temperature coefficient (PTC) and negative temperature coefficient (NTC) effect of the composites. The relationship between the morphology and the PTC and NTC effects of the composites was investigated using optical microscopy (OM) and scanning electron microscopy (SEM). The OM micrographs indicated that CB was selectively located in the HDPE phase and the SEM micrographs showed that there were some gaps between the two phases. The PTC effect of the composites is caused by the thermal expansion as a result of the melting of the HDPE crystallites. The morphology of the composites greatly affects the PTC and NTC behaviors of the composites. When the CB‐filled HDPE formed a continuous phase and the PVDF formed a dispersed phase, the PTC and NTC behaviors of the composites were similar to those of CB‐filled neat HDPE composite without crosslinking. When the composite exhibited an interlocking structure, a normal PTC effect could also be observed, but the NTC effect was delayed to higher temperatures. A mechanism was proposed to explain this new physical phenomenon, and the mechanism was verified by another CB‐filled polymer blend comprising an alternating copolymer of tetrafluoroethylene‐ethylene and HDPE.
Tracking ground targets with road constraints using an IMM estimator (2002)

This paper presents the development of a tracker based on the Interacting Multiple Model (IMM) estimation algorithm for tracking groups of ground targets using Moving Target Indicator (MTI) reports obtained from an airborne sensor. The targets are moving along a constrained path, for example, a highway, with varying obscuration due to changing terrain conditions. In addition, the roads on which the targets travel can branch, merge, or cross. This constrained motion estimation problem is handled using an IMM estimator with varying mode sets depending on the topography. The design and implementation of the topography based Variable Structure IMM (VS-IMM) estimator is described. Simulation results are also presented.
An estimation of minimal genome size required for life (1995)

The number of indispensable chromosomal loci for a bacterium, Bacillus subtilis was estimated. Seventy-nine randomly selected chromosomal loci were investigated by mutagenesis. Mutation at only six loci rendered B. subtilis unable to form colonies. In contrast, mutants for the rest of the 73 loci retained the ability to form colonies. Mutant B. subtilis with multiple-fold mutations of those dispensable loci (7-, 12- or 33-fold) were not impaired in their ability to form colonies on nutritionally adequate medium, indicating that up to 33 dispensable loci were simultaneously abolished. Given the statistical analyses for the frequency of indispensable loci (6 out of 79), total indispensable genetic material would be included within about 562 kbp. The hypothetical minimum genome size lies in the range of those currently determined smallest genomes for bacteria.
Hepatitis E Virus (HEV) ORF2 Antigen Levels Differentiate Between Acute and Chronic HEV Infection (2016)

<b><it>Background.</it></b> Hepatitis E virus (HEV) genotype 3 infections are frequent in Europe and North America, with acute and chronic courses described in the literature. HEV RNA detection by real-time polymerase chain reaction (PCR) is the gold standard for diagnosis. Recently, an anti-HEV antigen (Ag)–specific enzyme-linked immunosorbent assay (ELISA) directed against the HEV capsid became commercially available. The effectiveness of anti-HEV Ag–specific ELISA at detecting HEV genotype 3 infections remains undefined. <b><it>Methods.</it></b> The performance of anti-HEV Ag–ELISA was compared with that of real-time PCR, using sera from a cohort of acutely infected individuals, in addition to a cohort of chronically infected patients undergoing ribavirin therapy. Furthermore, virion properties were evaluated by density fractionation. <b><it>Results.</it></b> Anti-HEV Ag–specific ELISA was less sensitive than real-time PCR at detection of HEV infection. Anti-HEV Ag–specific ELISA revealed significantly higher HEV Ag in chronically infected individuals as compared to acutely infected patients, with high sensitivity and specificity to distinguish acute from chronic HEV infection. Of note, HEV Ag remained detectable for >100 days after HEV RNA clearance in ribavirin-treated patients with chronic HEV. Density gradients revealed the presence of membrane-associated virions in the sera, with a different distribution as compared to HEV RNA. <b><it>Conclusions.</it></b> The anti-HEV Ag–specific ELISA is less sensitive than HEV RNA real-time PCR but represents a useful tool to discriminate chronic from acute infection.
Cobb's syndrome and its treatment with embolization (1990)

A case of Cobb's syndrome, which is characterized by spinal and vertebral angiomas and a skin nevus at the same metameric level, is reported. The spinal angiomas were treated with liquid embolization using ethylene vinyl alcohol.
On the Relation Between the Overpotentials and Structures of Graphite Fluoride Electrode in Nonaqueous Lithium Cell (1984)

A study was made of the relation between the cathode overpotentials and structures of two kinds of graphite fluorides, and in nonaqueous lithium battery. The oyerpotential of electrode decreased with increasing interlayer spacing and decreasing thickness of the crystallite along the C axis. However, it was found that the overpotential of electrode primarily depended on the amount of the defects which would be present in the form of polynuclear aromatic carbon rings in . The defects in would give the short circuiting paths for the transfer of a lithium ion in diffusion layer. The higher discharge potential of than that of was mainly attributed to the effect of the defects contained in .
Models of Rebound and Capture for Oblique Microparticle Impacts (1998)

ABSTRACT Simple algebraic, rigid body impact models using coefficients of restitution and coefficient of friction have been used extensively in the study of the impact of microparticles with surfaces. Recent work by the authors has shown that rigid body impact theory can be extended to include an adhesion coefficient to model oblique impacts of microparticles with surfaces in the presence of molecular level forces. In this paper, the model is fully described and exploited for engineering applications. The behavior of coefficients is investigated both analytically and experimentally as initial impact velocity and angel of incidence vary. As the initial velocity of microparticles grows smaller and smaller, the significance of adhesion forces increases, eventually reaching a point where no rebound occurs and the particle is captured. Equations for this region of the growth of the influence of adhesion, designed for empirically fitting, are presented. They are capable of representing the behavior of the material restitution coefficient and the adhesion coefficient for a wide variety of materials and conditions. Experimental results of several investigators are examined using these empirical equations. They not only do a remarkable job of representing adhesion in the transition from rebound to capture but are capable of explicitly determing the capture velocity. The paper also contains a study of the sensitivity of the impact coefficients to small changes in the angle of incidence. The dependence of the capture velocity on microsphere radius also is examined.
Relation between carbon ion ranges and x‐ray CT numbers (2001)

Measurements of carbon ion ranges in various phantom materials and real bones are presented. Together with measured Hounsfield values, an empirical relation between ranges and Hounsfield units is derived, which is an important prerequisite for treatment planning in carbon ion therapy.
Insights into the Impact of the Nafion Membrane Pretreatment Process on Vanadium Flow Battery Performance (2016)

Nafion membranes are now the most widely used membranes for long-life vanadium flow batteries (VFBs) because of their extremely high chemical stability. Today, the type of Nafion membrane that should be selected and how to pretreat these Nafion membranes have become critical issues, which directly affects the performance and cost of VFBs. In this work, we chose the Nafion 115 membrane to investigate the effect of the pretreatment process (as received, wet, boiled, and boiled and dried) on the performance of VFBs. The relationship between the nanostructure and transport properties of Nafion 115 membranes is elucidated by wide-angle X-ray diffraction and small-angle X-ray scattering techniques. The self-discharge process, battery efficiencies, electrolyte utilization, and long-term cycling stability of VFBs with differently pretreated Nafion membranes are presented comprehensively. An online monitoring system is used to monitor the electrolyte volume that varies during the long-term charge-discharge test of VFBs. The capacity fading mechanism and electrolyte imbalance of VFBs with these Nafion 115 membranes are also discussed in detail. The optimal pretreatment processes for the benchmark membrane and practical application are synthetically selected.