gebhart/patrepeval huggingface dataset:
Regulation of the ldhA gene, encoding the fermentative lactate dehydrogenase of Escherichia coli (2001)

The fermentative lactate dehydrogenase (LDH) of Escherichia coli is induced by low pH under anaerobic conditions. Both translational and transcriptional gene fusions to ldhA, which encodes the fermentative LDH, have now been made. Both types of ldhA-lacZ fusion were induced by low pH, but only in the absence of air. However, the translational fusions were consistently expressed at a five- to tenfold higher level than the transcriptional fusions, perhaps implying some post-transcriptional effect on ldhA expression. Introduction of arcB::Kan decreased expression of both translational and transcriptional ldhA-lacZ fusions by three- to fivefold. Disruption of mlc, which encodes a repressor of several genes of the phosphotransferase system, almost abolished expression of ldhA. Disruption of csrA caused a moderate drop in expression of both operon and protein ldhA fusions, whereas insertional inactivation of csrB or glgA had the opposite effect. These effects are probably indirect, resulting from alterations in sugar accumulation versus storage. Mutations in ptsG, cra, fnr, narL, rpoS, osmZ, appY, ack/pta, aceEF, pfl and ldhA had no effect on expression of the ldhA fusions. ldhA was not induced by the membrane-permeant weak acid benzoate, implying that it does not respond to the internal pH directly. Little pH induction was seen during growth on glycerol plus fumarate, suggesting that products of sugar fermentation are necessary for acid induction. Addition of succinate, acetate or lactate had no effect on ldhA expression. In contrast, pyruvate caused a two- to fourfold increase in expression of ldhA-lacZ. This accords with the idea that increased sugar metabolism indirectly induces ldhA.
Antioxidants and Zinc to Prevent Progression of Age-Related Macular Degeneration (2001)

BackgroundExperimental and observational data suggest that micronutrients with antioxidant capabilities may retard the development of age-related cataract.ObjectiveTo evaluate the effect of a high-dose antioxidant formulation on the development and progression of age-related lens opacities and visual acuity loss.DesignThe 11-center Age-Related Eye Disease Study (AREDS) was a double-masked clinical trial. Participants were randomly assigned to receive daily oral tablets containing either antioxidants (vitamin C, 500 mg; vitamin E, 400 IU; and beta carotene, 15 mg) or no antioxidants. Participants with more than a few small drusen were also randomly assigned to receive tablets with or without zinc (80 mg of zinc as zinc oxide) and copper (2 mg of copper as cupric oxide) as part of the age-related macular degeneration trial. Baseline and annual (starting at year 2) lens photographs were graded at a reading center for the severity of lens opacities using the AREDS cataract grading scale.Main Outcome MeasuresPrimary outcomes were (1) an increase from baseline in nuclear, cortical, or posterior subcapsular opacity grades or cataract surgery, and (2) at least moderate visual acuity loss from baseline (≥15 letters). Primary analyses used repeated-measures logistic regression with a statistical significance level of P = .01. Serum level measurements, medical histories, and mortality rates were used for safety monitoring.ResultsOf 4757 participants enrolled, 4629 who were aged from 55 to 80 years had at least 1 natural lens present and were followed up for an average of 6.3 years. No statistically significant effect of the antioxidant formulation was seen on the development or progression of age-related lens opacities (odds ratio = 0.97, P= .55). There was also no statistically significant effect of treatment in reducing the risk of progression for any of the 3 lens opacity types or for cataract surgery. For the 1117 participants with no age-related macular degeneration at baseline, no statistically significant difference was noted between treatment groups for at least moderate visual acuity loss. No statistically significant serious adverse effect was associated with treatment.ConclusionUse of a high-dose formulation of vitamin C, vitamin E, and beta carotene in a relatively well-nourished older adult cohort had no apparent effect on the 7-year risk of development or progression of age-related lens opacities or visual acuity loss.
Synthesis and biological activity of certain nucleoside and nucleotide derivatives of pyrazofurin (1986)

A number of nucleoside and nucleotide derivatives of 4-hydroxy-3-beta-D-ribofuranosylpyrazole-5-carboxamide (pyrazofurin, 1) were prepared and tested for their antiviral and cytostatic activity in cell culture. Treatment of 1 with benzyl bromide gave 4-O-benzylpyrazofurin (4). Methylation of 4 with CH2N2 and subsequent removal of the benzyl group by catalytic hydrogenation provided 1-methylpyrazofurin (8). Direct methylation of 1 with CH3I furnished 4-O-methylpyrazofurin (6). Dehydration of the pentaacetylpyrazofurin (9) with phosgene furnished 4-acetoxy-3-(2,3,5-tri-O-acetyl-beta-D-ribofuranosyl)-1-acetylpyrazol e-5-carbonitrile (10). A similar dehydration of the precursor tetraacetyl derivative of 4 gave the corresponding carbonitrile, which on deprotection and subsequent treatment with hydroxylamine furnished 4- (benzyloxy)-3-beta-D-ribofuranosylpyrazole-5-carboxamidoxime (13). Treatment of the tetraacetyl derivative of 4 with Lawesson's reagent and subsequent deacetylation furnished a mixture of 4- (benzyloxy)-3-beta-D-ribofuranosylpyrazole-5-thiocarboxamide (15) and the corresponding nitrile derivative (16). Phosphorylation of unprotected 4 with POCl3 and subsequent debenzylation of the intermediate 17 gave pyrazofurin 5'-phosphate (18), which provided the first chemical synthesis of 18. Similar phosphorylation of 4 with POCl3 and quenching the reaction mixture with either EtOH or MeOH, followed by debenzylation, furnished the 5'-O-(ethyl phosphate) (19b) and 5'-O-(dimethyl phosphate) (20b) derivatives of pyrazofurin. DCC-mediated cyclization of 17, followed by debenzylation, gave pyrazofurin 3',5'-(cyclic)phosphate (21b). The NAD analogue 23b was also prepared by the treatment of 17 with an activated form of AMP in the presence of AgNO3. The structural assignment of 7,8, and 20a were made by single-crystal X-ray analysis, and along with pyrazofurin, their intramolecular hydrogen bond characteristics have been studied. All of these compounds were tested in Vero cell cultures against a spectrum of viruses. Compounds 18 and 23b were active at concentrations very similar to pyrazofurin but are less toxic to the cells than pyrazofurin. Compounds 19b, 20b, and the 3',5'-(cyclic)phosphate 21b are less active than 1. Compounds 18, 19b, 20b, and 23b also exhibited significant inhibitory effects on the growth of L1210 and P388 leukemias and Lewis lung carcinoma cells in vitro, whereas B16 melanoma cells were less sensitive to growth inhibition by these compounds. Pyrazofurin derivatives modified at the 1-, 4-, or 5-position showed neither antiviral nor cytostatic activity in cell culture.
High-speed and drop-on-demand printing with a pulsed electrohydrodynamic jet (2010)

We present a pulsed dc voltage printing regime for high-speed, high-resolution and high-precision electrohydrodynamic jet (E-jet) printing. The voltage pulse peak induces a very fast E-jetting mode from the nozzle for a short duration, while a baseline dc voltage is picked to ensure that the meniscus is always deformed to nearly a conical shape but not in a jetting mode. The duration of the pulse determines the volume of the droplet and therefore the feature size on the substrate. The droplet deposition rate is controlled by the time interval between two successive pulses. Through a suitable choice of the pulse width and frequency, a jet-printing regime with a specified droplet size and droplet spacing can be created. Further, by properly coordinating the pulsing with positioning commands, high spatial resolution can also be achieved. We demonstrate high-speed printing capabilities at 1 kHz with drop-on-demand and registration capabilities with 3–5 µm droplet size for an aqueous ink and 1–2 µm for a photocurable polymer ink.
KIZUKI Processing for Visual Inspection: A Smart Pattern Pop-Out Algorithm Based on Human Visual Architecture (2014)

There are many cases in which it is difficult to detect defects by visual inspection. These defects, such as very small cracks and thin stains, etc., are slight difference and hide in background texture. Even if a skilled inspector can detect these defects, they are undetectable by basic image processing algorithms. This special ability of the inspectors is called "KIZUKI" in Japanese. This paper describes how to develop irregular region extraction programs based on human visual architectures. Two theories have been used to model the "defects pop-out = KIZUKI" process of visual inspection: the peripheral vision and the involuntary eye micro-vibration theories in the field of psychology of vision. We have implemented this model experimentally. It consists of two steps: forming low resolution images by variable re-sampling, and then detecting relatively salience regions at each low resolution image and integrating these regions. Experiment results indicate that our approach have been reasonable. Since our programs have been very simple and effective, it might be incorporable into different visual examination systems widely.
siRNA directed against TrkA sensitizes human pancreatic cancer cells to apoptosis induced by gemcitabine through an inactivation of PI3K/Akt-dependent pathway (2007)

Previously, we have documented that the aggressive and highly metastatic behavior of pancreatic cancer may be due to the aberrant expression of nerve growth factor (NGF) and its high-affinity receptor, proto-oncogene TrkA. In this study, we sought to determine the effect of suppressing TrkA expression on pancreatic cancer chemosensitivity to gemcitabine. Human pancreatic cancer cell lines PANC-1, MIA-PaCa-2 and ASPC-1 were studied. The expression and kinase activity of TrkA were determined by Western blot analysis and in vitro kinase assay respectively. RNA interference was used to suppress TrkA expression. Gemcitabine-induced cytotoxicity was determined by tetrazolium reduction assay and caspase profiling was performed. The effect of TrkA-specific siRNA on PI3K/Akt activity was also quantified. TrkA expression and kinase activity in cell lines were directly correlated with gemcitabine chemoresistance. TrkA-specific siRNA suppressed TrkA expression and kinase activity, and furthermore increased gemcitabine-induced, caspase-mediated apoptosis. PI3K/Akt activity was decreased by suppression of TrkA expression. Taken together, these data demonstrated that TrkA is a determinant of pancreatic adenocarcinoma chemoresistance and PI3K/Akt is a key signaling component by which NGF activation of the TrkA signal transduction pathway protects pancreatic cancer cells from chemotherapy-induced cell death.
Applying One-Comparator Counter-Based Sampling to Current Sharing Control of Multichannel LED Strings (2011)

In this paper, a fully digitalized current sharing strategy without any analog-to-digital converter (ADC) is presented and applied to light-emitting diode (LED) lighting. By doing so, the cost for digital control is reduced significantly due to no ADC used. Aside from this, LED dimming is easy to realize. Above all, the proposed current sharing method has the capability of resisting variations in input voltage and component parameter. Such a control topology is demonstrated by some experiments and hence is very suitable for LED street lighting.
CMOS contact imager for monitoring cultured cells (2005)

There is a growing interest in developing low cost, low power, highly integrated biosensor systems to characterize individual cells for applications such as cell analysis, drug development, environmental monitoring, and medicine. In such micro-systems, it is desirable to track individual cells in real time in order to steer cells using on-chip micro-actuators or monitor the movement of motile cells. To address this requirement, we are developing an embedded optical image sensor, called a contact imager, for imaging of a biological specimen directly coupled to the chip surface. The designed CMOS image sensor comprises an array of active pixel sensors (APS), logic and control signal generation, and readout circuits. The pixel layout has a pitch of 8.4 /spl mu/m (24 /spl lambda/). The design was fabricated in a commercially available 0.5 /spl mu/m CMOS technology. The imager was first characterized on the bench as a normal CMOS image sensor, and then as a contact imager with microbeads (16 /spl mu/m) placed directly on the chip surface. After further packaging with bio-compatible material, the chip was tested with cells cultured directly on the chip surface. Test results confirm successful detection of both beads and cells.
Harnessing Context Sensing to Develop a Mobile Intervention for Depression (2011)

Clinicaltrials.gov NCT01107041; http://clinicaltrials.gov/ct2/show/NCT01107041 (Archived by WebCite at http://www.webcitation.org/60CVjPH0n).
Phase retrieval from one single phase contrast x-ray image (2009)

Phase retrieval is required for achieving artifact-free x-ray phase-sensitive 3D imaging. A phase-retrieval approach based on the phase-attenuation duality with high energy x-rays can greatly facilitate for phase sensitive imaging by allowing phase retrieval from only one single projection image. The previously derived phase retrieval formula is valid only for small Fresnel propagator phases corresponding to common clinical imaging tasks. In this work we presented a new duality-based phase retrieval formula that can be applied for cases with large Fresnel propagator phases corresponding to high spatial resolution imaging. The computer simulation demonstrated superiority of this new formula over the previous phase retrieval formula in reconstructing the high frequency components of imaged objects. A modified Tikhonov regularization technique has been devised for phase retrieval in cases of very high resolution and large object-detector distance such that some Fresnel propagator phases may be close or greater than pi. This new phase retrieval formula lays the foundation for implementing high-resolution phase-sensitive 3D imaging of soft tissue objects.
The Opportunistic Human Pathogen<i>Acinetobacter baumannii</i>Senses and Responds to Light (2010)

Light is a ubiquitous environmental signal that many organisms sense and respond to by modulating their physiological responses accordingly. While this is an expected response among phototrophic microorganisms, the ability of chemotrophic prokaryotes to sense and react to light has become a puzzling and novel issue in bacterial physiology, particularly among bacterial pathogens. In this work, we show that the opportunistic pathogen Acinetobacter baumannii senses and responds to blue light. Motility and formation of biofilms and pellicles were observed only when bacterial cells were incubated in darkness. In contrast, the killing of Candida albicans filaments was enhanced when they were cocultured with bacteria under light. These bacterial responses depend on the expression of the A. baumannii ATCC 17978 A1S_2225 gene, which codes for an 18.6-kDa protein that contains an N-terminal blue-light-sensing-using flavin (BLUF) domain and lacks a detectable output domain(s). Spectral analyses of the purified recombinant protein showed its ability to sense light by a red shift upon illumination. Therefore, the A1S_2225 gene, which is present in several members of the Acinetobacter genus, was named blue-light-sensing A (blsA). Interestingly, temperature plays a role in the ability of A. baumannii to sense and respond to light via the BlsA photoreceptor protein.
Inhibition of endotoxin effects on cultured human middle ear epithelium by bactericidal permeability-increasing protein. (2000)

rBPI21 can inhibit morphologic changes in the middle ear epithelium due to endotoxin. Hence, the authors believe that rBPI21 can be a new therapeutic agent in the treatment of OME.
SURVEY AND SUMMARY: Antizyme expression: a subversion of triplet decoding, which is remarkably conserved by evolution, is a sensor for an autoregulatory circuit (2000)

The efficiency of programmed ribosomal frameshifting in decoding antizyme mRNA is the sensor for an autoregulatory circuit that controls cellular polyamine levels in organisms ranging from the yeast Schizosaccharomyces pombe to Drosophila to mammals. Comparison of the frameshift sites and flanking stimulatory signals in many organisms now permits a reconstruction of the likely evolutionary path of the remarkably conserved mRNA sequences involved in the frameshifting.
Dendritic Spines (2016)

Abstract Dendritic spines are small protrusions from dendrites that host the majority of excitatory synapses in the central nervous system. Structurally, excitatory synapses located on dendritic spines are asymmetric, with a presynaptic bouton that contains round clear vesicles apposed to a postsynaptic density where glutamate receptors are anchored. Spines form biochemical compartments that can isolate activated signalling pathways that occur at one synapse from those at other synapses, thereby providing a way to enhance the specificity of connections between neurons in the brain. Structural changes of dendritic spines in response to stimulation facilitate changes in synaptic strength, and these changes are likely to underlie important higher brain functions such as learning and memory. Dysregulation of spine morphology is seen in several neurological disorders such as Alzheimer's disease and fragile X syndrome. Key Concepts Spines are the primary site of excitatory synapses. Smooth endoplasmic reticulum can form complex structures localized to large spines. The cytoskeleton of spines is mostly composed of actin. Trans‐synaptic adhesion molecules as well as proteins secreted from astroglia help stabilise synapses. Spines can act as small biochemical compartments. Spine structure is responsive to activity.
Single-cell paired-end genome sequencing reveals structural variation per cell cycle (2013)

The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although single-cell genome analyses could resolve these problems, such analyses are error-prone because of whole-genome amplification (WGA) artefacts and are limited in the types of DNA mutation that can be discerned. We developed methods for paired-end sequence analysis of single-cell WGA products that enable (i) detecting multiple classes of DNA mutation, (ii) distinguishing DNA copy number changes from allelic WGA-amplification artefacts by the discovery of matching aberrantly mapping read pairs among the surfeit of paired-end WGA and mapping artefacts and (iii) delineating the break points and architecture of structural variants. By applying the methods, we capture DNA copy number changes acquired over one cell cycle in breast cancer cells and in blastomeres derived from a human zygote after in vitro fertilization. Furthermore, we were able to discover and fine-map a heritable inter-chromosomal rearrangement t(1;16)(p36;p12) by sequencing a single blastomere. The methods will expedite applications in basic genome research and provide a stepping stone to novel approaches for clinical genetic diagnosis.
3-D real-time gesture recognition using proximity spaces (2002)

A 3D segment tracking approach to recognition of human pose and gestures is presented. The author has previously developed and refined a stereo based method, called the proximity space method, for acquiring and maintaining the track of object surfaces in 3-space. This method uses LoG filtered images and relies solely on stereo measurement to spatially distinguish between objects in 3D. The objective of the work is to obtain useful state information about the shape, size, and pose of natural (unadorned) objects in their naturally cluttered environments. Thus, the system does not require or benefit from special markers, colors, or other tailored artifacts. Recently he has extended this method in order to track multiple regions and segments of complex objects. The paper describes techniques for applying the proximity space method to a particularly interesting system: the human. Specifically, he discusses the use of simple models for constraining proximity space behavior in order to track gestures as a person moves through a cluttered environment. It is demonstrated that by observing the behavior of the model, used to tract the human's pose through time, different gestures can be easily recognized. The approach is illustrated through a discussion of gestures used to provide logical and spatial commands to a mobile robot.
An invariant V alpha 24-J alpha Q/V beta 11 T cell receptor is expressed in all individuals by clonally expanded CD4-8- T cells. (1994)

The T cell receptor (TCR)-alpha/beta CD4-8- (double negative, DN) T cell subset is characterized by an oligoclonal repertoire and a restricted V gene usage. By immunizing mice with a DN T cell clone we generated two monoclonal antibodies (mAbs) against V alpha 24 and V beta 11, which have been reported to be preferentially expressed in DN T cells. Using these antibodies, we could investigate the expression and pairing of these V alpha and V beta gene products among different T cell subsets. V alpha 24 is rarely expressed among CD4+ and especially CD8+ T cells. In these cases it is rearranged to different J alpha segments, carries N nucleotides, and pairs with different V beta. Remarkably, V alpha 24 is frequently expressed among DN T cells and is always present as an invariant rearrangement with J alpha Q, without N region diversity. This invariant V alpha 24 chain is always paired to V beta 11. This unique V alpha 24-J alpha Q/V beta 11 TCR was found in expanded DN clones from all the individuals tested. These findings suggest that the frequent occurrence of cells carrying this invariant TCR is due to peripheral expansion of rare clones after recognition of a nonpolymorphic ligand.
Getting Smart (2010)

We live in a very critical and exciting time in the evolution of the electric power industry. Society in general and the power industry in particular are faced with the challenges and opportunities of transforming the power grid ushered in by Nicola Tesla some 120 years ago into a smart grid. A smart grid will help the world manage demand growth, conserve energy, maximize asset utilization, improve grid security and reliability, and reduce its carbon footprint. Smart grid technology is not a single silver bullet but a collection of existing and emerging standards-based, interoperable technologies working together. Controllable technologies for supply, demand, power flow, and storage provide the means to implement decisions made by smart control algorithms and thus create value. ABB already provides its customers with many of the smart grid technologies described here and continues to research and develop power control technologies as well as smart grid applications.