gebhart/patrepeval huggingface dataset:
Mid-ultraviolet light-emitting diode detects dipicolinic acid. (2005)

Dipicolinic acid (DPA, 2,6-pyridinedicarboxylic acid) is a substance uniquely present in bacterial spores such as that from anthrax (B. anthracis). It is known that DPA can be detected by the long-lived fluorescence of its terbium chelate; the best limit of detection (LOD) reported thus far using a large benchtop gated fluorescence instrument using a pulsed Xe lamp is 2 nM. We use a novel AlGaN light-emitting diode (LED) fabricated on a sapphire substrate that has peak emission at 291 nm. Although the overlap of the emission band of this LED with the absorption band of Tb-DPA ({lambda}{sub max} doublet: 273, 279 nm) is not ideal, we demonstrate that a compact detector based on this LED and an off-the-shelf gated photodetection module can provide an LOD of 0.4 nM, thus providing a basis for convenient early warning detectors.
<i>Eimeria</i> species: studies using rRNA and rDNA probes (1990)

rRNA and a heterologous cloned rDNA probe have been used to detect the rRNA genes of Eimeria species which infect the chicken, and has allowed the isolation and preliminary characterization of cloned rDNA sequences from a genomic DNA library of Eimeria tenella. It is demonstrated that rRNA and rDNA probes can be used to identify individual Eimeria species by the restriction fragment patterns detected after Southern hybridization. In addition, studies have shown that the large and small subunit rRNAs are expressed throughout sporulation.
Protocol stack mapping of software defined protocol for next generation mobile networks (2016)

Virtualization of network functions and centralized management are anticipated to provide 5G mobile networks with flexibility, lower end-to-end latency and reduced cost. Based on the concept of emerging Software Defined Network (SDN) and Network Function Virtualization (NFV) techniques, we propose Software Defined Protocol (SDP) technique to facilitate a flexible service-oriented protocol stack deployment under centralized network control. The design objective of SDP is to provide high-throughput, low-latency and elastic mobile services by making data-plane protocol programmable. In this paper, we first elaborate the SDP mechanisms and then address one of the most important issues in SDP, namely protocol stack mapping (PSM). We formulate the PSM problem as a 0-1 quadratic programming for selecting the optimal SDP servers to balance network load. We employ the legacy LTE data-plane processing as a benchmark for validating the effectiveness of the SDP and PSM algorithm. Numerical results show that SDP is effective to provide elastic low-latency mobile services and the proposed PSM algorithm significantly outperforms the benchmark in stack processing delay, mapping cost and resource utilization.
Ether lipids and platelet-activating factor: evolution and cellular function. (1997)

This review considers the relation between the evolution of ether lipids and platelet-activating factor (PAF) in living organisms for the first time. Ether lipids are shown to be the main structural lipid components in the cells of the most primitive organisms on the Earth; during evolution they were gradually substituted for lipids with ester and vinyl bonds. Synthesis of PAF has been found in some bacteria, protozoans, yeasts, plants, marine invertebrates, lower vertebrates, and mammals. The regulatory role of PAF is suggested to already appear in protozoans and later be maintained during the subsequent evolution of living organisms. During evolution, functions of PAF in the cell have been changing and enlarging, while ether lipids have been gradually losing their role as the main structural lipid component of the cells of living organisms.
Discovery of a Novel Potent and Selective HSD17B13 Inhibitor, BI-3231, a Well-Characterized Chemical Probe Available for Open Science (2023)

Genome-wide association studies in patients revealed HSD17B13 as a potential new target for the treatment of nonalcoholic steatohepatitis (NASH) and other liver diseases. However, the physiological function and the disease-relevant substrate of HSD17B13 remain unknown. In addition, no suitable chemical probe for HSD17B13 has been published yet. Herein, we report the identification of the novel potent and selective HSD17B13 inhibitor <b>BI-3231</b>. Through high-throughput screening (HTS), using estradiol as substrate, compound <b>1</b> was identified and selected for subsequent optimization resulting in compound <b>45 (BI-3231)</b>. In addition to the characterization of compound <b>45</b> for its functional, physicochemical, and drug metabolism and pharmacokinetic (DMPK) properties, NAD<sup>+</sup> dependency was investigated. To support Open Science, the chemical HSD17B13 probe <b>BI-3231</b> will be available to the scientific community for free via the opnMe platform, and thus can help to elucidate the pharmacology of HSD17B13.
1,3-Cyclohexadiene Polymers. 2. Near-Monodisperse Star and Star-Block Polymers Based on Poly(1,3-cyclohexadiene) (2001)

The synthesis of well-defined, near-monodisperse, three-arm star and star-block copolymers based on poly(1,3-cyclohexadiene) (PCHD) is described. The stars were prepared by the reaction of living anionic chain ends of PCHD, poly(styrene−1,3-cyclohexadiene) (PS-PCHD), and poly(1,3-cyclohexadiene−styrene) (PCHD-PS) with CH3SiCl3 in benzene. 1,4-Diazabicyclo[2.2.2]octane (DABCO) was used to control the anionic polymerization of 1,3-CHD; it also acted as a promoter during the linking reaction. The star polymers were fractionated to remove excess arm material and thoroughly characterized by size exclusion chromatography, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, and light scattering.
Effect of extraction time and acid concentration on the separation of proglycogen and macroglycogen in horse muscle samples. (2002)

The objective of this study was to determine whether the concentrations of proglycogen (PG) and macroglycogen (MG) in biopsy samples of horse muscle are influenced by extraction time or perchloric acid (PCA) concentration. In study 1, individual muscle-biopsy samples from 10 horses were divided into 4 parts each and then randomly subjected to 4 periods of extraction (10, 20, 60, or 120 min) with 1.5 M PCA. In study 2, individual muscle-biopsy samples from 6 horses were divided into 24 pieces each and then randomly subjected to 12 combinations of extraction time (10, 20, 30, or 40 min) and PCA concentration (0.5, 1.5, or 3.0 M). The results from study 1 indicated that PG and MG concentrations are affected only after extraction for 120 min; the PG concentration decreased significantly (P < 0.05), and the MG concentration increased (not significantly). In study 2, extraction in 3.0 M PCA yielded significantly lower PG and higher MG concentrations (P < 0.05) than extraction in 0.5 or 1.5 M PCA with each of the extraction times. The results of this study further support the existence of 2 glycogen pools and demonstrate that they are not an extraction artifact. The study also suggests that the 2 pools are stable during extraction over a range of extraction times and acid concentrations. However, if the exposure to acid is very long and, or, the acid concentration is high, some of the insoluble PG appears to be hydrolyzed and to enter the MG pool.
Convenient Synthesis of <sup>68</sup>Ga‐Labeled Gadolinium(III) Complexes: Towards Bimodal Responsive Probes for Functional Imaging with PET/MRI (2013)

A killer application? Recently, fully integrated full-body positron-emission tomography (PET) and magnetic-resonance imaging (MRI) scanners were brought to market, allowing simultaneous recording of complementary 3D data sets. By using bimodal PET/MRI probes (see figure), in vivo 3D mapping of various parameters with medical relevance could become feasible.
Cluster Formation in Aqueous Electrolyte Solutions Observed by Dynamic Light Scattering (2000)

Using dynamic light scattering we show that aqueous super- to undersaturated solutions of NaCl, (NH4)2SO4, and Na-citrate contain submicrometer size clusters at room temperature. The particle size distributions deduced by Laplace inversion of the spectra contain two predominant components. The smaller components with radii below 1 nm are attributed to mixtures of solvated ions and the larger with radii between 50−500 nm to ion clusters. Knowledge of the mesoscale structure of concentrated electrolyte solutions may be necessary to describe effective protein−protein interactions which are of importance in biochemical applications such as protein crystallization.
The <i>galE</i> Gene of <i>Campylobacter jejuni</i> Is Involved in Lipopolysaccharide Synthesis and Virulence (2000)

Lipopolysaccharide (LPS) is one of the main virulence factors of gram-negative bacteria. The LPS from Campylobacter spp. has endotoxic properties and has been shown to play a role in adhesion. We previously cloned a gene cluster (wla) which is involved in the synthesis of the Campylobacter jejuni 81116 LPS molecule. Sequence alignment of the first gene in this cluster indicated similarity with galE genes. These genes encode a UDP-glucose 4-epimerase, which catalyzes the interconversion of UDP-galactose and UDP-glucose. A Salmonella galE mutant was transformed with the galE gene from C. jejuni. The LPS analysis of wild-type, galE, and complemented galE Salmonella strains showed that the C. jejuni galE gene could restore the smooth wild-type Salmonella LPS. A UDP-glucose 4-epimerase assay was used to demonstrate that the galE gene from C. jejuni encoded this epimerase. We constructed a C. jejuni galE mutant which expressed a lipid A-core molecule of reduced molecular weight that did not react with antiserum raised against the parental strain. These results show an essential role for the galE gene in the synthesis of C. jejuni LPS. The galE mutant also showed a reduction in its ability to adhere to and invade INT407 cells. However, it was still able to colonize chickens to the same level as the wild-type strain. The serum resistance and hemolytic activity of this mutant were not changed compared to the parent strain. The ability of the mutant to take up DNA and integrate it in its genome was reduced 20-fold. These results show that LPS of C. jejuni is an important virulence factor.
Hyporesponsiveness of “naive” (CD45RA<sup>+</sup>) human T cells to multiple receptor‐mediated stimuli but augmentation of responses by co‐stimuli (1990)

Much remains to be clarified the functional capacities of the two major reciprocal subsets of human CD4+ cells which we interpret to be naive and memory cells. CD4+ naive (CD45RA+, LFA-3-) and memory (CD45R0+, LFA-3+) cells were rigorously purified by immunomagnetic negative selection. Their proliferation was measured in response to four protocols of receptor-mediated activation: soluble anti-CD3 mAb, plastic-immobilized anti-CD3 mAb, activating pairs of anti-CD2 mAb, and "superantigens" staphyloccocal enterotoxins A and B (SEA and SEB). Naive cells proliferated much less than memory cells to each of these four regimens although their capacity to respond was demonstrated by strong PHA-induced proliferation. Although three of the regimens depend on autologous monocytes, poorer naive cell responses are also observed to anti-CD3 mAb immobilized on plastic in the absence of monocytes; this implies an intrinsic hyporesponsiveness of naive cells, independent of their potentially weaker interaction with monocytes. Naive cells proliferated less than memory cells to superantigens SEA and SEB over a wide dose range; this assumes particular importance because such superantigens are believed to more closely mimic antigen-specific stimulation than anti-CD3 mAb. The possibility was explored that hyporesponsiveness of naive cells reflects the fact that naive cells require additional co-stimuli to facilitate their activation. In support of this concept, we observed that proliferation of naive cells to anti-CD3 mAb and SEA or SEB (but not to anti-CD2 mAb pairs) was consistently enhanced by pre-activation of monocytes present in the culture. Naive cell proliferative responses were augmented further in cultures supplemented with interleukin (IL) 1 beta and IL 6 or exposed to the co-stimulating mAb anti-CD28 and anti-CD44. The pattern of augmentation was dependent on the specific triggering regimen: anti-CD44 mAb was particularly effective in augmenting the response to superantigens, anti-CD28 mAb for the anti-CD3 response and IL 1 beta/IL 6 for that induced by anti-CD2 mAb pairs. With particular combinations of stimulus/co-stimuli naive cell proliferation was as strong as that of memory cells. We interpret these findings to indicate that naive cells are capable of responding to antigen, but that such responses are critically dependent on the available co-stimuli in vivo.
Nucleation and evolution of ultrasonic cavitation in a rotating exposure chamber (1992)

The nucleation and progression of ultrasonic cavitation in a rotating exposure chamber were investigated by observing hemolysis of a 0.5% suspension of erythrocytes. Bursts of 1.6 MHz ultrasound beams of 11 W/cm2 spatial peak intensity were synchronized with the rotation to aim the bursts down the axis of a cylindrical chamber. Cavitational hemolysis always occurred in fresh phosphate buffered saline (PBS) solution, but cavitation incidence declined to 38% in 4 day old PBS. The amount of hemolysis for 11 ms or 44 ms bursts with 60 rpm rotation increased in proportion to the number of bursts. Hemolysis was found above a minimum burst duration of 5.5 to 8.3 ms in the normal 2 cm chamber. This did not appear to change for 1 cm or 4 cm chamber lengths, but it did change to about 2.2 ms and about 44 ms for over- and undersaturated gas conditions, respectively. Off-times associated with rotation speeds of 15 to 30 rpm reduced the effectiveness of the cavitation, and addition of fixed cells at only 0.01% to 0.02% greatly reduced the hemolysis. For this ultrasonic exposure system, several thousand bubbles, possibly generated from as few as one cavitation nucleus, move across the chamber at up to 10 m/s, each lysing a few hundred cells, and then are cycled back to the front of the chamber by the rotation to reinitiate the cavitation on the next burst.
Failed extradural anaesthesia for Caesarean section. Complication of subsequent spinal block (1992)

Two cases of unexpected high spinal anaesthesia following failed extradural anaesthesia for Caesarean section are described. In both cases rapid and unexpected advance of blockade, after the subarachnoid injection of moderate doses of local anaesthetic, required tracheal intubation. In one of the cases 15 ml of 0.9% saline, but no local anaesthetic, had been injected into the extradural space, suggesting that the mechanism involved is the cephalad displacement of the cerebrospinal fluid by extradural fluid, and not leakage of extradural anaesthetic solution into the subarachnoid space.
Cytokine release in patients with CLL treated with obinutuzumab and possible relationship with infusion-related reactions (2015)

International audience
RNA editing enzyme adenosine deaminase is a restriction factor for controlling measles virus replication that also is required for embryogenesis (2010)

Measles virus (MV), a member of the family Paramyxoviridae and an exclusively human pathogen, is among the most infectious viruses. A progressive fatal neurodegenerative complication, subacute sclerosing panencephalitis (SSPE), occurs during persistent MV infection of the CNS and is associated with biased hypermutations of the viral genome. The observed hypermutations of A-to-G are consistent with conversions catalyzed by the adenosine deaminase acting on RNA (ADAR1). To evaluate the role of ADAR1 in MV infection, we selectively disrupted expression of the IFN-inducible p150 ADAR1 isoform and found it caused embryonic lethality at embryo day (E) 11-E12. We therefore generated p150-deficient and WT mouse embryo fibroblast (MEF) cells stably expressing the MV receptor signaling lymphocyte activation molecule (SLAM or CD150). The p150(-/-) but not WT MEF cells displayed extensive syncytium formation and cytopathic effect (CPE) following infection with MV, consistent with an anti-MV role of the p150 isoform of ADAR1. MV titers were 3 to 4 log higher in p150(-/-) cells compared with WT cells at 21 h postinfection, and restoration of ADAR1 in p150(-/-) cells prevented MV cytopathology. In contrast to infection with MV, p150 disruption had no effect on vesicular stomatitis virus, reovirus, or lymphocytic choriomeningitis virus replication but protected against CPE resulting from infection with Newcastle disease virus, Sendai virus, canine distemper virus, and influenza A virus. Thus, ADAR1 is a restriction factor in the replication of paramyxoviruses and orthomyxoviruses.
Phytoplankton Diversity of a Demineralized Urban Wetland of Meghalaya State of Northeast India: The Spatio-temporal Variations and the Role of Abiotic Factors (2022)

The authors analyze phytoplankton diversity of a small urban wetland of Meghalaya to assess biodiversity and limnology interest of small water bodies. This “slightly acidic-circumneutral, demineralized and soft water” subtropical wetland reveals diverse phytoplankton (64 species), indicates high desmid richness and highlights the speciose littoral constellations of up to 55-58 species per sample. Phytoplankton comprises dominant quantitative component of net plankton and registers Charophyta dominance; Chlorophyta > Bacillariophyta > Dinozoa > Chrysophyta > Cyanobacteria depict sub-dominance, and Euglenozoa and Cryptophyta show poor abundance at the littoral and semi-limnetic regions. The richness of phytoplankton and abundance of phytoplankton, Charophyta, Chlorophyta, Dinozoa, Chrysophyta and Cyanobacteria follow bimodal spatio-temporal variations. Closterium, Cosmarium, Staurastrum, Micrasterias, Netrium, Staurodesmus and Scenedesmus are notable genera, and 14 species collectively influence phytoplankton abundance. Phytoplankton registers high species diversity, lower dominance and high evenness. Amongst 15 abiotic factors, only the rainfall and sulphate exert notable influence individually, while the canonical correspondence analysis registers lower cumulative influence of the selected 10 factors on the littoral and semi-limnetic phytoplankton assemblages. This study merits interest for neglected biodiversity and ecology of small aquatic biotopes of India and urban wetlands in particular.
How can recommendations be presented to TV viewers? (2010)

An overload of content choices on the TV and online is a modern phenomenon. Steering viewers towards content they would like is a challenge for any video-on-demand provider - especially for those who derive revenue from downloaded content. Making the user experience in selecting recommendations engaging and easy is also a challenge. This paper covers research into testing the presentation of recommended items to viewers in a variety of ways to establish best and worst features, and to inform user interface design decisions of future IPTV recommendations services.
Sparse Approximation via Penalty Decomposition Methods (2013)

In this paper we consider sparse approximation problems, that is, general $l_0$ minimization problems with the $l_0$-``norm” of a vector being a part of constraints or objective function. In particular, we first study the first-order optimality conditions for these problems. We then propose penalty decomposition (PD) methods for solving them in which a sequence of penalty subproblems are solved by a block coordinate descent (BCD) method. Under some suitable assumptions, we establish that any accumulation point of the sequence generated by the PD methods satisfies the first-order optimality conditions of the problems. Furthermore, for the problems in which the $l_0$ part is the only nonconvex part, we show that such an accumulation point is a local minimizer of the problems. In addition, we show that any accumulation point of the sequence generated by the BCD method is a block coordinate minimizer of the penalty subproblem. Moreover, for the problems in which the $l_0$ part is the only nonconvex part, we establish that such an accumulation point is a local minimizer of the penalty subproblem. Finally, we test the performance of our PD methods by applying them to sparse logistic regression, sparse inverse covariance selection, and compressed sensing problems. The computational results demonstrate that when solutions of same cardinality are sought, our approach applied to the $l_0$-based models generally has better solution quality and/or speed than the existing approaches that are applied to the corresponding $l_1$-based models.
Chemical Weddings (1998)

Scientists often rely on protein engineering techniques to introduce artificial molecules in protein sequences. Indeed, the introduction of these small molecules (artificial amino acids and peptides, fluorescent tags, resonance probes, or cross-linking agents) can be used to study their effects on the structure-function relationships of proteins and to gain biochemical insight into various biological systems. Of the many methods for introducing such molecules into proteins, most have practical, synthetic limitations. One general approach is to link a peptide thioester to a protein containing an NH2- terminal cysteine: the chemical reaction between the two substrates leads to a product with a native peptide bond at the junction between the two moieties. The technical limitations of this approach, though, have commonly prevented the application of this method to proteins that are larger than 15 kD.
Predicting Microseismicity from the Geomechanical Modeling of Multiple Hydraulic Fractures Interacting with Natural Fractures - Application to the Marcellus and Eagle Ford (2014)

International audience
The Biology of Hepadnaviruses (1986)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Automatic Generation of Imaging Sequence for CD‐SEM Using Design Data (2016)

SUMMARY Critical dimension scanning electron microscope (CD‐SEM) is widely used as a measurement tool of semiconductor patterns. It is necessary to set imaging sequence including corrections of imaging position and focusing of electron beam for the reliable measurement. Conventionally, addressing point (AP) and autofocus point (AF) suitable for these processing are selected by the hand and this is a drop factor of SEM operation rates. We propose a technique to generate imaging sequence from design data of the pattern layout. Proposed method calculates selection indices for pattern complexity, uniqueness, and so on from design data and selects AP and AF templates automatically based on these indices. For 901 evaluation points, success rate of SEM imaging by proposed method was 100% and generation time of imaging sequence was 18 minutes. Compared with manual selection (conventionally, it takes 10 several hours by using SEM), large reduction of operation cost can be realized.
Evolution of the wake of three inline square prisms (2019)

An investigation is conducted on the flow around three tandem prisms, shedding light on the evolution of the primary vortices to the secondary. The secondary-vortex-street onset corresponds to the local maximum vorticity amplitude associated with the secondary frequency.