gebhart/patrepeval huggingface dataset:
Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast (2010)

The packaging of eukaryotic DNA into chromatin has profound consequences for gene regulation, as well as for other DNA transactions such as recombination, replication and repair. Understanding how this packaging is determined is consequently a pressing problem in molecular genetics. DNA sequence, chromatin remodelers and transcription factors affect chromatin structure, but the scope of these influences on genome-wide nucleosome occupancy patterns remains uncertain. Here, we use high resolution tiling arrays to examine the contributions of two general regulatory factors, Abf1 and Rap1, to nucleosome occupancy in Saccharomyces cerevisiae. These factors have each been shown to bind to a few hundred promoters, but we find here that thousands of loci show localized regions of altered nucleosome occupancy within 1 h of loss of Abf1 or Rap1 binding, and that altered chromatin structure can occur via binding sites having a wide range of affinities. These results indicate that DNA-binding transcription factors affect chromatin structure, and probably dynamics, throughout the genome to a much greater extent than previously appreciated.
Dual APD array readout of LSO crystals: optimization of crystal surface treatment (2002)

Summary form only received as follows: The authors are developing a compact PET detector module by coupling an LSO scintillator array with two APD arrays to achieve high sensitivity, and high and uniform spatial resolution. They report studies on improving the depth-of-interaction (DOI) resolution by optimizing the crystal surface treatment, and on the effect of crystal geometry on DOI resolution. Three 2/spl times/2/spl times/20 mm LSO crystals were treated with different surface finishes along their length: raw saw cut, polished with 12 mm grade AlO2 paper, and fine mirror polish. The 2/spl times/2 mm ends were fine mirror polished. The ratio of the signals from the APD arrays was used to measure DOI, and the sum of the signals to measure the total light output. Crystals finished with the 12 mm grade paper gave the best overall detector performance, with DOI resolutions ranging from 3.1 to 3.9 mm for all interactions with energy above /spl sim/150 keV threshold, and uniform light output for different DOI positions. The energy resolution averaged /spl sim/17%. A 1/spl times/1/spl times/20 mm and a 2/spl times/2/spl times/30 mm LSO crystals finished with saw-cut and 12 /spl mu/m grade paper were also measured, and gave DOI resolutions in the range of 2.7 to 4.4 mm, and 4.7 to 6.6 mm, respectively.
Optimizing the data cache performance of a software MPEG-2 video decoder (1997)

Multimedia functionality has become an established component of core computer worHoads. MPEG-2 video decoding represents a particularly important and computationally demanding application example. Instruction set extensions like Intel's MMX significantly reduce the computational challenges of this and other multimedia algorithms. However, memory subsystem deficiencies have now become the major barrier to increased performance, partly as a consequence of this improved CPU performance.
Cells depleted of mitochondrial DNA (p<sup>0</sup>) yield insight into physiological mechanisms (1999)

A resurgence of interest in mitochondrial physiology has recently developed as a result of new experimental data demonstrating that mitochondria function as important participants in a diverse collection of novel intracellular signaling pathways. Cells depleted of mitochondrial DNA, or rho0 cells, lack critical respiratory chain catalytic subunits that are encoded in the mitochondrial genome. Although rho0 cells contain petit mitochondria, they cannot support normal oxidative phosphorylation and must survive and replicate using ATP derived solely from glycolysis. Without a functional electron transport chain, rho0 cells cannot normally regulate redox potential and their mitochondria appear to be incapable of generating reactive oxygen species. Emerging evidence suggests that these signals are important components in a number of mitochondria-initiated signaling pathways. The present article focuses on how rho0 cells have contributed to an understanding of the role that mitochondria play in distinct physiological pathways involved with apoptosis, glucose-induced insulin secretion, and oxygen sensing.
Addiction and the brain: the role of neurotransmitters in the cause and treatment of drug dependence. (2001)

Recent scientific advances have led to a greater understanding of the neurobiological processes that underlie drug abuse and addiction. These suggest that multiple neurotransmitter systems may play a key role in the development and expression of drug dependence. These advances in our knowledge promise not only to help us identify the underlying cause of drug abuse and dependence, but also to aid the development of effective treatment strategies.
Synthesis of Pyrrolopyrimidines and Thienopyrimidines (1972)

7-Substituted 1, 3-dimethyl-7H-2, 4, 6-(5H, 6H) pyrrolo [2, 3-d] pyrimidinetriones (IIIa, b, c) were prepared from 6-amino-1, 3-dimethyluracil (I) and ethyl α-bromoacetate. Reactionof I and α-bromo-ketones afforded 6, 7-disubstituted 1, 3-dimethyl-7H-2, 4-pyrrolo-[2, 3-d] pyrimidinediones (IV, V, VI). On the other hand, reaction of 6-mercapto-1, 3-dimethyluracil (VIII) and cc-bromocarbonyl compound afforded thieno [2, 3-d] pyrimidines (X, XI).
Oxidative Damage of Cardiomyocytes Is Limited by Extracellular Regulated Kinases 1/2-mediated Induction of Cyclooxygenase-2 (1999)

Oxidative stress causes cardiac damage following ischemia/reperfusion and in response to anthracyclines. Extracellular signal-regulated kinases (ERK) 1/2 are activated by oxidative stress in cardiac myocytes and protect cardiac myocytes from apoptosis. Prostaglandins (PG) also protect cells from injury in a number of tissues, including the cardiomyocyte. Cyclooxygenase (COX) the rate-limiting enzyme in PG biosynthesis has two isoforms, the constitutive COX-1 and an inducible COX-2. Here, we examined the effects of two oxidative stresses, hydrogen peroxide (H2O2) and the anthracycline doxorubicin on the activity of ERK1/2 and the expression of COX isoforms and PG formation in neonatal rat primary cardiomyocytes. These cells expressed COX-1 at rest and both COX isoforms on treatment with phorbol 12-myristate 13-acetate. Exposure to 50 microM H2O2 for 10 min or doxorubicin at 10 and 100 micrograms/ml caused expression of COX-2 that was prevented by free radical scavengers. COX-2 induction was associated with activation of ERK1/2 and the specific ERK-inhibitor PD098059 abolished COX-2 expression. Treatment of cells with decoy oligonucleotides corresponding to COX-2 promoter elements implicated the AP-1 and NF-kappaB-2 but not the NF-kappaB-1 in the transcription of COX-2. Induction of COX-2 mRNA and protein was accompanied by increased prostacyclin formation, which was abolished by the selective COX-2 inhibitor, NS-398, and PD098059. H2O2 and doxorubicin enhanced the release of lactate dehydrogenase and free radical scavengers prevented this. NS-398 enhanced the release of lactate dehydrogenase in response to H2O2 and doxorubicin, whereas the injury was prevented by iloprost, a stable prostacyclin analogue. In cardiomyocytes cell injury by H2O2 and doxorubicin is limited by an increase in prostacyclin formation that reflects induction of COX-2 mediated by ERK1/2 activation.
In vivo repair of methylation damage in Aag 3-methyladenine DNA glycosylase null mouse cells (2000)

3-Methyladenine (3MeA) DNA glycosylases initiate base excision repair by removing 3MeA. These glycosylases also remove a broad spectrum of spontaneous and environmentally induced base lesions in vitro. Mouse cells lacking the Aag 3MeA DNA glycosylase (also known as the Mpg, APNG or ANPG DNA glycosylase) are susceptible to 3MeA-induced S phase arrest, chromosome aberrations and apoptosis, but it is not known if Aag is solely responsible for repair of 3MeA in vivo. Here we show that in AAG:(-/-) cells, 3MeA lesions disappear from the genome slightly faster than would be expected by spontaneous depurination alone, suggesting that there may be residual repair of 3MeA. However, repair of 3MeA is at least 10 times slower in AAG:(-/-) cells than in AAG:(+/+) cells. Consequently, 24 h after exposure to [(3)H]MNU, 30% of the original 3MeA burden is intact in AAG:(-/-) cells, while 3MeA is undetectable in AAG:(+/+) cells. Thus, Aag is the major DNA glycosylase for 3MeA repair. We also investigated the in vivo repair kinetics of another Aag substrate, 7-methylguanine. Surprisingly, 7-methylguanine is removed equally efficiently in AAG:(+/+) and AAG:(-/-) cells, suggesting that another DNA glycosylase acts on lesions previously thought to be repaired by Aag.
Radiofrequency ablation of bone metastases induces long-lasting palliation in patients with untreatable cancer. (2008)

In our preliminary experience, RFA showed good and long-lasting efficacy for pain control in bone metastases. A possible role of RFA as a coadjuvant palliative treatment in these cases is suggested.
Mobile Broadcast Business Dynamics (2006)

Mobile broadcast technology has matured to a point where commercial launches are either taking place or being delayed by issues related to regulation, content IPR or business models and revenue sharing. There are several competing radio technologies, mobile broadcast service platforms and numerous handset vendors are producing—or ready to start producing—mobile television capable terminals. In this situation we need to clarify the service concepts and operator roles so that both the academic and industry participants can formulate their views on a common ground, which is namely the purpose of this paper. In addition, the aim is to point out the features rising from the technologies used and the existing business environment, that have most significant consequences to the mobile broadcast value chain and revenue sharing.
Impact of long-period line-edge roughness (LER) on accuracy in CD measurement (2005)

The influence of long-period line-edge roughness (LER) on measured critical-dimension (CD) values is identified, and a guideline for LER-impact-free CD measurement is introduced. There are two kinds of meanings of CD, one is the average pattern-size calculated in a limited area (i.e., local CD), and the other is the representative pattern-size (average CD). The width of a line pattern measured by CD-SEM is a local CD, which deviates from the average CD because of long-period LER. This LER impact on the CD measurement is investigated in two typical measurements of CD-SEM, evaluation of across-wafer CD-variation and dynamic repeatability of the equipment. It is shown that both results strongly depend upon the height of the inspection area along the line-edge (L) because of long-period LER. It is found that a large L can reduce the LER-impact, and a 2-μm inspection-area or more is recommended for CD measurements. Furthermore, the validity and limitation of the patchwork method, in which several inspection areas are connected to obtain one large area, is examined.
Locus of Failure and Its Implications for Adhesion Measurements (1978)

The extreme importance of correctly establishing the locus of separation in an adhering system, such as a film on a solid, is pointed out. Two theories as to the level of possibility that true interfacial separation will occur are described and both are criticized. A logically rigorous formulation which draws upon both these theories is given.
ELECTRICAL RESISTANCE TOMOGRAPHIC SENSING SYSTEMS FOR INDUSTRIAL APPLICATIONS (1999)

Abstract The effects of electrode configuration and design are investigated using a grouped node finite element method (FEM). An estimated expression for an appropriate experimental/actual electrode-angle β is given for an electrode system modelled with grouped-node FEM or single-node FEM. Analyses and methods for reducing sensor noise are discussed in practical terms. Examples of ERT sensors for different applications are given, which comprise from one to eight sensing planes sized from 6 to 1500 mm in diameter. A novel image reconstruction method based on the sensitivity theorem is presented. The capabilities of ERT and its data interpretation and image processing are discussed for pipelines, hydrocyclones and mixing vessels.
Silatranes and Their Tricyclic Analogs (1998)

This chapter contains sections titled: General Introduction Silatranes Methods of Synthesis Introduction Formation from Organyltrialkoxysilanes Formation from Organyltriacetoxysilanes Formation from Organylhalosilanes Formation from Organyltris(dialkylamino)silanes Formation from Organylsilanes Miscellaneous Preparations Structure and Physical Properties Molecular Structure Bonding Model Quantum Mechanical Studies Thermochemical Data Dipole Moments Photoelectron Spectra Ultraviolet Spectra Vibrational Spectra NMR Spectra 1H NMR Spectra 13C NMR Spectra 29Si NMR Spectra 15N NMR Spectra Other NMR Studies Electronic Effects of the Silatranyl Group Electrochemical Studies Mass Spectra Chemical Properties Introduction Hydrolysis 1-hydrosilatranes 1-halosilatranes 1-hydroxysilatrane 1-alkoxysilatranes 1-alkyl-, 1-aralkyl- and 1-arylsilatranes 1-alkenylsilatranes Carbofunctional Silatranes Silatranyl Arene and Cyclohexadiene Complexes Silatrane Analogs 3-homosilatranes Silatranones Carbasilatranes Benzosilatranes Triazasilatranes Miscellaneous Acknowledgments References
Universal platform for quantitative analysis of DNA transposition (2010)

The established universal papillation assay platform should be widely applicable to a variety of mobile elements. It can be used for mechanistic studies to dissect transposition and provides a means to screen or scrutinise transposase mutants and genes encoding host factors. In succession, improved versions of transposition systems should yield better tools for molecular biology and offer versatile genome modification vehicles for many types of studies, including gene therapy and stem cell research.
Cytogenetic study of spontaneous abortions using semi‐direct analysis of chorionic villi samples detects the broadest spectrum of chromosome abnormalities (2007)

Conventional tissue culturing and karyotyping of spontaneous abortions has limitations such as culture failure, external contamination and selective growth of maternal cells. Molecular cytogenetic techniques such as FISH, QF-PCR, and CGH allow diagnosis on uncultured cells but are also limited as to the spectrum of cytogenetic abnormalities detected. We describe the cytogenetic findings in a series of 116 first trimester arrested pregnancies, obtained through chorionic villi sampling (CVS) and semi-direct analysis that avoids some of the long-culture pitfalls such as maternal contamination, and compare our results with those that would have been obtained theoretically using molecular cytogenetic techniques. Samples were obtained by transcervical CVS from women with a diagnosis of missed abortion, most of them referred for cytogenetic prenatal diagnosis. Cytogenetic analysis was performed using semi-direct technique. A karyotype was obtained in 103 cases. Eighty-two abnormal karyotypes were found (80%), including 12 triploidies, 10 monosomies, 61 trisomies, and 9 structural abnormalities; a double abnormality being present in 10 cases. Between 10% and 50% of our abnormal results would have been missed using the most common molecular cytogenetic techniques. Semi-direct analysis of CVS may still be considered as a comprehensive, reasonably rapid, cost-effective and reliable method for detecting the broadest spectrum of chromosome abnormalities in missed abortions.
A simple sample container for NMR pressure and temperature studies on liquids (1973)

A simple, yet effective sample cell for NMR pressure and temperature studies on liquids is described. The cell is of all glass construction with a moving mercury seal. It has performed reliably up to pressures of 2 kbar and at temperatures from -15 degrees C to 250 degrees C.
Superfine IC geometries: Gas-plasma etching may supplant chemical etching in manufacturing high-performance integrated circuits (1985)

The advantages that dry etching offers over conventional chemical etching of integrated circuits are discussed. The underlying principle of dry etching is explained, and the various dry etching techniques in current use are described. The way in which voltage is created between plasma and wafer is explained, together with the mechanisms that produce directional etching. Attenuation is then given to the ability to operate over a wide pressure range and to monitoring based on light emission and DC bias. The dangers posed by overetching and energetic ions are discussed. Finally, the prospect of using expert systems in dry etching is assessed.
A Design Space of Visualization Tasks (2013)

Knowledge about visualization tasks plays an important role in choosing or building suitable visual representations to pursue them. Yet, tasks are a multi-faceted concept and it is thus not surprising that the many existing task taxonomies and models all describe different aspects of tasks, depending on what these task descriptions aim to capture. This results in a clear need to bring these different aspects together under the common hood of a general design space of visualization tasks, which we propose in this paper. Our design space consists of five design dimensions that characterize the main aspects of tasks and that have so far been distributed across different task descriptions. We exemplify its concrete use by applying our design space in the domain of climate impact research. To this end, we propose interfaces to our design space for different user roles (developers, authors, and end users) that allow users of different levels of expertise to work with it.
Expression and activation of pro-MMP-2 and pro-MMP-9 during rat liver regeneration (2000)

Partial hepatectomy triggers a variety of biological phenomena, which culminate in regeneration of the liver mass. Hepatocyte proliferation is a major feature of the regenerating liver after partial hepatectomy. Previous studies in our laboratory suggested that hepatic matrix remodeling might be a prerequisite process for hepatocyte proliferation in the regenerating liver. In the present study we use immunohistochemical staining, Western blot analysis, and gelatin zymography to show that the inactive matrix metalloproteinases (MMPs), pro-MMP-2 and pro-MMP-9, are elevated at 30 minutes and activated at 6 to 12 hours and at 3 to 6 hours, respectively, after hepatectomy. Sham-operated livers did not show an increase in inactive pro-MMP-2 and pro-MMP-9 and did not contain active MMP-2 or MMP-9. To examine whether tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) is changed to regulate the activities of MMPs after partial hepatectomy, the level of TIMP-1 protein was analyzed by both immunohistochemistry and Western blot analysis. The level of TIMP-1 protein appears to increase by 6 to 18 hours, implying that an increase in TIMP-1 regulates activities of active MMP-2 and MMP-9. Taken together, these results suggest that hepatic matrix remodeling is mediated by activated MMPs, which contribute to modulation of the environment surrounding hepatocytes during rat liver regeneration.
Efficient evaluation of the valid-time natural join (2002)

Joins are arguably the most important relational operators. Poor implementations are tantamount to computing the Cartesian product of the input relations. In a temporal database, the problem is more acute for two reasons. First, conventional techniques are designed for the optimization of joins with equality predicates, rather than the inequality predicates prevalent in valid-time queries. Second, the presence of temporally-varying data dramatically increases the size of the database. These factors require new techniques to efficiently evaluate valid-time joins. The authors address this need for efficient join evaluation in databases supporting valid-time. A new temporal-join algorithm based on tuple partitioning is introduced. This algorithm avoids the quadratic cost of nested-loop evaluation methods; it also avoids sorting. Performance comparisons between the partition-based algorithm and other evaluation methods are provided. While the paper focuses on the important valid-time natural join, the techniques presented are also applicable to other valid-time joins.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Signal processing and implementation of motion detection neurons in optical pathways (2002)

The signal processing and the communication paths of the visual neural network are reviewed. The organization and communication of neurons in the visual system and artificial directional retina neurons are described. An electronic circuit behaving like the directional neurons of the retina provides directional information about and the speed of motion of a moving object. The obtained information is then processed by higher-level artificial neurons in the optical pathway.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Speaker verification using minimum verification error training (2002)

We propose a minimum verification error (MVE) training scenario to design and adapt an HMM-based speaker verification system. By using the discriminative training paradigm, we show that customer and background models can be jointly estimated so that the expected number of verification errors (false accept and false reject) on the training corpus are minimized. An experimental evaluation of a fixed password speaker verification task over the telephone network was carried out. The evaluation shows that MVE training/adaptation performs as well as MLE training and MAP adaptation when the performance is measured by the average individual equal error rate (based on a posteriori threshold assignment). After model adaptation, both approaches lead to an individual equal error-rate close to 0.6%. However, experiments performed with a priori dynamic threshold assignment show that MVE adapted models exhibit false rejection and false acceptance rates 45% lower than the MAP adapted models, and therefore lead to the design of a more robust system for practical applications.
Advantages of HCO3 solution with low sodium concentration over standard lactate solutions for acute peritoneal dialysis. (1997)

The aim of this study was to identify the advantages of a bicarbonate solution with a low sodium concentration. Twelve children (3 days-6 years) with acute renal failure (ARF), positive fluid balance, and lactate acidosis (> 40 mg/dL) were treated by automated peritoneal dialysis (APD) with frequent exchanges of small fill volumes of a hypertonic solution. For Day 1 we used PD1/PD4 Dianeal (3.86%) (Baxter). After 24 hours we switched to a HCO3 solution: 38 mmol/L, Na 128 mmol/L. As the control group, we studied retrospectively the last 12 children of the previous period who were treated with APD. The age distribution was 4 days to 4 years. No significant differences were found between the groups for serum creatinine, blood urea nitrogen, and fluid overload (Day 1 to Day 4). Although the values for lactate and Na were not different before the start of the study (Day 1) and after 24 hours of Dianeal (Day 2), they were significantly lower in the study group on Day 4 [HCO3 53 (23-83), Na 148 (137-136) mEq/L] than in the control group [lactate 148 (137-156), Na 154 (142-165) mEq/L]. A low sodium concentration results in higher sodium extraction, which is important for patients with fluid overload. Low sodium concentrations in APD are needed because the peritoneal membrane "sieves" the sodium during short dwells. HCO3 dialysis is a logical choice for patients with lactate acidosis, resulting in a significant lower serum lactate and increase of BE after 48 hours of treatment.