gebhart/patrepeval huggingface dataset:
Conversion of arachidonic acid to prostaglandins in homogenates of human skeletal muscle and kidney (1979)

The capacity of human skeletal muscle and kidney homogenates to synthetize prostaglandins (PGs) from exogenous precursor was investigated. Low-speed supernatants of muscle as well as renal medullary and cortical homogenates were incubated with 14C-labelled arachidonic acid (14C-AA) prepared as a sodium salt. 14C-PGs in the incubates were extracted, separated with thin-layer chromatography (TLC) and quantified by radioscanning. In the skeletal muscle incubates 14C-AA was converted into 14C-PGs with a time-dependent yield, most effectively after 10--15 min incubation. Well-defined radiopeaks parallel to unlabelled standards of PGD2, PGE2, PGF2 alpha and 6-keto-PGF1 alpha were obtained in the chromatograms. PGE2 was the main PG formed, constituting over 50% of 14C-activity, whereas 6-keto-PGF1 alpha, PGD2 and PGF2 alpha were found in considerably lower proportions. In the renal medullary incubates, PGE2 likewise accounted for the largest part of 14C-PGs formed, but significant relative amounts of PGF2 alpha and PGD2 were also found. A minor peak, corresponding to 6-keto-PGF1 alpha and thus indicating formation of PGI2, was also obtained. In contrast to the medulla, no 14C-PGs could be found in the renal cortical incubates. The results demonstrate the existence of a considerable tissue specificity in the quantitative and qualitative expression of PG biosynthesis in man.
Consistently faster and smaller compressed bitmaps with Roaring (2016)

Summary Compressed bitmap indexes are used in databases and search engines. Many bitmap compression techniques have been proposed, almost all relying primarily on run‐length encoding (RLE). However, on unsorted data, we can get superior performance with a hybrid compression technique that uses both uncompressed bitmaps and packed arrays inside a two‐level tree. An instance of this technique, Roaring, has recently been proposed. Due to its good performance, it has been adopted by several production platforms (e.g., Apache Lucene, Apache Spark, Apache Kylin, and Druid). Yet there are cases where run‐length‐encoded bitmaps are smaller than the original Roaring bitmaps—typically when the data are sorted so that the bitmaps contain long compressible runs. To better handle these cases, we build a new Roaring hybrid that combines uncompressed bitmaps, packed arrays, and RLE‐compressed segments. The result is a new Roaring format that compresses better. Overall, our new implementation of Roaring can be several times faster (up to two orders of magnitude) than the implementations of traditional RLE‐based alternatives (WAH, Concise, and EWAH) while compressing better. We review the design choices and optimizations that make these good results possible. Copyright © 2016 John Wiley & Sons, Ltd.
Efficient induction of functional neurons from adult human fibroblasts (2011)

Cellular reprogramming is a rapidly developing technology by which somatic cells are turned into pluripotent stem cells or other somatic cell types through expression of specific combinations of genes. This allows for the generation of patient-specific cell lines that can serve as tools for understanding disease pathogenesis, for drug screens and, potentially, for cell replacement therapies. Several cellular models of neurological disorders based on induced pluripotent cells (iPS cells) have been developed, and iPS-derived neurons are being explored as candidates for transplantation. Recent findings show that neurons can also be induced directly from embryonic and postnatal somatic cells by expression of defined combinations of genes. This conversion does not occur through a pluripotent stem cell stage, which eliminates the risk for tumor formation. Here, we demonstrate for the first time that functional neurons can be generated via direct conversion of fibroblasts also from adult individuals. Thus, this technology is an attractive alternative to iPS cells for generating patient- and disease-specific neurons suitable for disease modeling and autologous transplantation.
A logarithmic poisson execution time model for software reliability measurement (1984)

A new software reliability model is developed that predicts expected failures (and hence related reliability quantities) as well or better than existing software reliability models, and is simpler than any of the models that approach it in predictive validity. The model incorporates both execution time and calendar time components, each of which is derived. The model is evaluated, using actual data, and compared with other models.
Evaluation of an E1E4-Deleted Adenovirus Expressing the Herpes Simplex Thymidine Kinase Suicide Gene in Cancer Gene Therapy (1999)

Studies with first-generation adenoviral vectors have uncovered limitations that include finite transgene persistence, potential hepatotoxicity, and contamination with replication-competent adenovirus (RCA). To address these limitations within the context of cancer suicide gene therapy, a new adenoviral vector was developed containing the herpes simplex virus type 1 thymidine kinase (HSV tk) gene inserted in the E1 region of a recombinant vector containing deletions in the E1 and E4 regions of the Ad5 genome. The HSV tk minigene was placed under transcriptional control of a Rous sarcoma virus (RSV) promoter. This new E1E4-deleted vector was compared with the first-generation E1E3-deleted Ad.RSVtk vector. Generation of replication-competent adenovirus during production was eliminated. Using semiquantitative immunoblotting, the two vectors produced equivalent amounts of the expected 44-kDa tk-encoded protein in three different cell lines tested. The ability of the E1E4-deleted vector to sensitize tumor cells to ganciclovir (GCV) using in vitro assays and mixing studies was comparable to that of the E1E3-deleted vector. In vivo bystander effects were investigated using mixing studies in a syngeneic flank tumor model and demonstrated no difference between vectors in either immunocompetent or immunodeficient mice. To test the efficiency of these vectors in treating tumors in clinically relevant models, virus was injected intraperitoneally into tumor-bearing SCID mice and intrapleurally in a syngeneic rat mesothelioma model. After treatment of animals with ganciclovir, both vectors were roughly equivalent in their ability to increase mean survival (from approximately 40 to approximately 70 days) and markedly reduce tumor burden. Finally, formal toxicology studies were performed and showed similar amounts of local inflammation without systemic toxicity. In summary, this series of in vitro and in vivo experiments indicates that the performance of the recombinant E1E4-deleted adenoviral vector was virtually identical to that of the E1E3-deleted vector. Since the E1E4 vector has a much lower rate of recombination during production and has been shown to be less hepatotoxic in animal models, this new vector should prove superior to the first-generation Ad.HSVtk vectors in clinical cancer gene therapy trials.
Artesunate Induces ROS-Mediated Apoptosis in Doxorubicin-Resistant T Leukemia Cells (2007)

Our studies raise the possibility to develop ART in combination with other established anticancer drugs which induce apoptosis through the pathways or mechanisms different from ART.
The GALILEO Frequency Structure and Signal Design (2001)

This paper outlines the tentative Galileo frequency
structure and signal design being developed by the
European Commission’s Galileo Signal Task Force
(Signal Task Force of the European Commission). The
Signal Task Force is a working group supporting the
design of the Galileo frequency and signal plan.
After discussing the various frequency and signal
requirements the present tentative Galileo frequency and
signal plan is outlined. Detailed comments explain the
motivation for the choice of signal in the lower, middle
and upper L-band. GPS/Galileo interference analysis
shows that the degradation on GPS signals in L1 is below
the ITU permissible interference.
The presented tentative Galileo frequency and signal plan
has the potential of a performance superior to GPSIIF/III.
By using the same center frequencies than GPS on E5a
(L5) and E2-L1-E1 (L1) a maximum interoperability is
provided for the future user of an integrated GNSS
consisting of GPS and Galileo. Further studies within the
presently running Development and Validation Phase B2
should consolidate the whole frequency and signal
structure, and complete the evaluation of the several
frequency scenarios under analyses.
Segmentation of periodically moving objects (2008)

We present a new approach for the identification and segmentation of objects undergoing periodic motion. Our method uses a combination of maximum likelihood estimation of the period, and segments moving objects using correlation of image segments over an estimated period of interest. Correlation provides the best locations of the moving objects in each frame. Segmentation tree provides the image segments at multiple resolutions. We ensure that children regions and their parent regions have the same period estimates. We show results of testing our method on real videos.
Design, Synthesis, Biological Activity, and ADME Properties of Pyrazolo[3,4-<i>d</i>]pyrimidines Active in Hypoxic Human Leukemia Cells: A Lead Optimization Study (2011)

A family of dual Src/Abl inhibitors characterized by a substituted pyrazolo[3,4-d]pyrimidine scaffold was previously reported by us and proved to be active against several tumor cell lines. Among these compounds, a promising antileukemia lead (1) has been recently identified, but, unfortunately, it suffers from substandard pharmaceutical properties. Accordingly, an approach for the optimization of the lead 1 is described in the present work. A series of more soluble pyrazolo[3,4-d]pyrimidine derivatives were rationally designed and proved to maintain the dual Src/Abl activity of the lead. Selected compounds showed an interesting activity profile against three different leukemic cells also in hypoxic conditions, which are usually characterized by imatinib-resistance. Finally, in vitro ADME properties (PAMPA permeation, water solubility, microsomal stability) for the most promising inhibitors were also evaluated, thus allowing the identification of a few optimized analogues of lead 1 as promising antileukemia agents.
Synthesis and Antiviral Evaluation of 6-(Alkyl-heteroaryl)furo[2,3-<i>d</i>]pyrimidin-2(3<i>H</i>)-one Nucleosides and Analogues with Ethynyl, Ethenyl, and Ethyl Spacers at C6 of the Furopyrimidine Core (2007)

Sonogashira coupling strategies were employed to synthesize new furo[2,3-d]pyrimidin-2(3H)-one (FuPyrm) 2'-deoxynucleoside analogues. Partial or complete reduction of ethyne-linked compounds afforded ethenyl- and ethyl-linked derivatives. Levels of inhibition of varicella-zoster virus (VZV), human cytomegalovirus (HCMV), a broad range of other DNA and RNA viruses, and several cancer cell lines were evaluated in cell cultures. The anti-VZV potency decreased with increasing rigidity of the side chain at C6 of the FuPyrm ring in the order dec-1-yn-1-yl < dec-1-en-1-yl < decan-1-yl. In contrast, compounds with a rigid ethynyl spacer between C6 of the FuPyrm ring and a 4-alkylphenyl moiety were more potent inhibitors of VZV than the corresponding derivatives with an ethyl spacer. Replacement of the phenyl moiety in 6-(4-alkylphenyl) derivatives with a pyridine ring (in either regioisomeric orientation) gave analogues with increased solubility in methanol but reduced anti-VZV potency, and replacement with a pyrimidine ring reduced the anti-VZV activity even further. The pyridine-ring-containing analogues were approximately 20-fold more potent inhibitors of VZV than acyclovir but were approximately 6-fold less potent than BVDU and approximately 60-fold weaker than the most active 6-(4-pentylphenyl)-substituted prototype.
Fabrication, characterization, and stability of supported single-atom catalysts (2017)

Strong metal–support interactions are key requirements for development of stable single-atom catalysts with pronounced catalytic activity.
Nucleotide sequence of a human cytomegalovirus DNA fragment encoding a 67-kilodalton phosphorylated viral protein (1985)

Previously, we demonstrated that a DNA fragment from the L-unique region at 0.37 to 0.39 map units of human cytomegalovirus DNA codes for a 67-kilodalton phosphorylated tegument protein. (Davis et al., J. Virol. 52:129-135, 1984). We have determined the nucleotide sequence of this DNA, transcription initiation and termination, and putative promoter region. We also compared the properties of the protein product predicted from the DNA sequence with the properties of the protein isolated by immunoabsorbent column chromatography. This viral structural protein may have important functions, such as protein kinase activity, DNA binding, and possible transcriptional activation of immediate-early genes.
The factor IX gene as a model for analysis of human germline mutations: an update (1996)

The variation generated by germline mutation is essential for evolution, but individuals pay a steep price in the form of Mendelian disease and genetic predisposition to complex disease. Indeed, the health of a species is determined ultimately by the rate of germline mutation. Analysis of the factor IX gene in patients with hemophilia B has provided insights into the human germline mutational process. Herein, seven topics will be reviewed with emphasis on recent advances: (i) proposed mechanisms of deletions, inversions, and insertions; (ii) discordant sex ratios of mutation and associated age effects; (iii) somatic mosaicism; (iv) founder effects; (v) mutation rates; (vi) the factor IX gene as a germline mutagen test; and (vii) cancer as a possible mechanism for maintaining a constant rate of germline mutation.
Hydrogen exchange in native and denatured states of hen egg‐white lysozyme (1992)

The hydrogen exchange kinetics of 68 individual amide protons in the native state of hen lysozyme have been measured at pH 7.5 and 30 degrees C by 2D NMR methods. These constitute the most protected subset of amides, with exchange half lives some 10(5)-10(7) times longer than anticipated from studies of small model peptides. The observed distribution of rates under these conditions can be rationalized to a large extent in terms of the hydrogen bonding of individual amides and their burial from bulk solvent. Exchange rates have also been measured in a reversibly denatured state of lysozyme; this was made possible under very mild conditions, pH 2.0 35 degrees C, by lowering the stability of the native state through selective cleavage of the Cys-6-Cys-127 disulfide cross-link (CM6-127 lysozyme). In this state the exchange rates for the majority of amides approach, within a factor of 5, the values anticipated from small model peptides. For a few amides, however, there is evidence for significant retardation (up to nearly 20-fold) relative to the predicted rates. The pattern of protection observed under these conditions does not reflect the behavior of the protein under strongly native conditions, suggesting that regions of native-like structure do not persist significantly in the denatured state of CM6-127 lysozyme. The pattern of exchange rates from the native protein at high temperature, pH 3.8 69 degrees C, resembles that of the acid-denatured state, suggesting that under these conditions the exchange kinetics are dominated by transient global unfolding. The rates of folding and unfolding under these conditions were determined independently by magnetization transfer NMR methods, enabling the intrinsic exchange rates from the denatured state to be deduced on the basis of this model, under conditions where the predominant equilibrium species is the native state. Again, in the case of most amides these rates showed only limited deviation from those predicted by a simple random coil model. This reinforces the view that these denatured states of lysozyme have little persistent residual order and contrasts with the behavior found for compact partially folded states of proteins, including an intermediate detected transiently during the refolding of hen lysozyme.
Wavelets and multifractal formalism for singular signals: Application to turbulence data (1991)

The wavelet decomposition is used to generalize the multifractal formalism to singular signals. The singularity spectrum is directly determined from the scaling behavior of partition functions that are defined from the wavelet transform modulus maxima. Illustrations on fractal signals with a recursive structure, e.g., devil's staircases, are shown. Applications to fully developed turbulence data and Brownian signals are reported.
The Value of Circulating Nogo-B for Evaluating Hepatic Functional Reserve in Patients with Cirrhosis (2015)

Nogo-B is mainly expressed in hepatic nonparenchymal cells and is present in plasma. Abnormally high plasma levels of Nogo-B are associated with hepatic cirrhosis and Child-Pugh score, but not correlated with the grade of liver inflammation or portal hypertension. Plasma Nogo-B may be a novel surrogate marker to reflect liver function reserve.
Production of anomalous particles in the process of emulsifier‐free emulsion copolymerization of styrene and 2‐hydroxyethyl methacrylate (1986)

Abstract It was found that copolymer particles produced by emulsifier‐free emulsion copolymerization of styrene and 2‐hydroxyethyl methacrylate had an anomalous shape with uneven surface. The formation mechanism is discussed.
Microprocessor testing by instruction sequences derived from random patterns (2003)

A novel technique for testing a microprocessor by instruction sequences generated with an LFSR (linear-feedback shift register) is presented. By translating pseudorandom patterns into the mnemonic code an efficient test pattern generator can be constructed in a straightforward way. It is shown that the resulting instruction sequence is equivalent to a functional test but less expensive. Subsequently, fault simulations at gate level show that pseudorandom instruction sequences are a cost-effective alternative to the functional test.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Self-potential modeling from primary flows (1983)

Abstract This paper discusses a new method for the investigation of self potentials (SP) based on induced current sources. The induced current sources are due to divergences of the convection current which is driven, in turn, by a primary flow, either heat or fluid. As a result of using this approach there is a shift in emphasis toward the vector flow field and its interaction with current cross-coupling structure when compared with the total potential approach of Nourbehecht (1963) which emphasized the primary flow potential and the voltage cross-coupling. This shift in emphasis is advantageous because it is analogous to the actual physical processes. For example, fluid flow in the ground gives rise to drag (convection) currents, and the interaction of the convection currents with the electrical structure gives rise to the electrical potentials (SP). This simple physical picture should aid in developing a better intuitive understanding of the generation of SP effects.The convective current approach is easily adapted to numerical modeling techniques, as illustrated by its implementation using a two-dimensional (2-D) transmission surface algorithm. When the primary flow is driven by the gradient of a potential, joint modeling of the primary flow and the resultant SP is possible with this algorithm.Examples of the SP effects generated by point sources of the primary flow in the presence of simple geometrical structures show the diversity of the possible responses. The various responses can be understood in terms of the distributions of the induced current sources caused by the primary flow.The results from field studies at Red Hill Hot Springs, Utah, are used in an example of the joint modeling of thermal and SP data.
Super-stretchy lithium-ion battery based on carbon nanotube fiber (2014)

Super-stretchy, fiber-shaped lithium-ion batteries with a record strain of 600% are developed by winding two highly aligned carbon nanotube composite fibers. The fiber-shaped battery exhibits high specific capacity, energy density and power density that can be well-maintained under stretching.
A Novel Framework for Learning to Detect Malicious Web Pages (2010)

Malicious web pages are a widely-recognized threat to the security of the web. Malicious web pages launch so-called drive-by download attacks that are able to gain complete control of a user's computer for illegitimate purpose. Even a single visit to a malicious web page enables an automatically download and installation of malicious malware executables. In this paper, we propose a novel approach for classifying web pages automatically as either malicious or benign based on a supervised machine learning. Our approach learns to detect malicious web pages exclusively based on HTTP session information (e.g., HTTP session headers, domains of requests and responses). With the corpus of 50,000 benign web pages and 500 malicious web pages, we are capable of successfully detecting 92.2% of the malicious web pages with a low false positive rate 0.1%.
High‐resolution MALDI‐FT‐ICR MS imaging for the analysis of metabolites from formalin‐fixed, paraffin‐embedded clinical tissue samples (2015)

We present the first analytical approach to demonstrate the in situ imaging of metabolites from formalin-fixed, paraffin-embedded (FFPE) human tissue samples. Using high-resolution matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI-FT-ICR MSI), we conducted a proof-of-principle experiment comparing metabolite measurements from FFPE and fresh frozen tissue sections, and found an overlap of 72% amongst 1700 m/z species. In particular, we observed conservation of biomedically relevant information at the metabolite level in FFPE tissues. In biomedical applications, we analysed tissues from 350 different cancer patients and were able to discriminate between normal and tumour tissues, and different tumours from the same organ, and found an independent prognostic factor for patient survival. This study demonstrates the ability to measure metabolites in FFPE tissues using MALDI-FT-ICR MSI, which can then be assigned to histology and clinical parameters. Our approach is a major technical, histochemical, and clinicopathological advance that highlights the potential for investigating diseases in archived FFPE tissues.
The crystal structure of anthranilate synthase from <i>Sulfolobus solfataricus</i> : Functional implications (1999)

Anthranilate synthase catalyzes the synthesis of anthranilate from chorismate and glutamine and is feedback-inhibited by tryptophan. The enzyme of the hyperthermophile Sulfolobus solfataricus has been crystallized in the absence of physiological ligands, and its three-dimensional structure has been determined at 2.5-A resolution with x-ray crystallography. It is a heterotetramer of anthranilate synthase (TrpE) and glutamine amidotransferase (TrpG) subunits, in which two TrpG:TrpE protomers associate mainly via the TrpG subunits. The small TrpG subunit (195 residues) has the known "triad" glutamine amidotransferase fold. The large TrpE subunit (421 residues) has a novel fold. It displays a cleft between two domains, the tips of which contact the TrpG subunit across its active site. Clusters of catalytically essential residues are located inside the cleft, spatially separated from clustered residues involved in feedback inhibition. The structure suggests a model in which chorismate binding triggers a relative movement of the two domain tips of the TrpE subunit, activating the TrpG subunit and creating a channel for passage of ammonia toward the active site of the TrpE subunit. Tryptophan presumably blocks this rearrangement, thus stabilizing the inactive states of both subunits. The structure of the TrpE subunit is a likely prototype for the related enzymes 4-amino 4-deoxychorismate synthase and isochorismate synthase.