gebhart/patrepeval huggingface dataset:
Inhibitory effects of ammonia on methanogen<i>mcrA</i>transcripts in anaerobic digester sludge (2013)

Methanogens in anaerobic ammonia-rich digesters show differential responses to ammonia stress. The mechanism for this is poorly understood. In the present study, we determined the rates of methane production, the composition of methanogen mcrA (the gene coding for the alpha subunit of methyl-coenzyme M reductase) and their transcripts in response to ammonium addition in the anaerobic sludge retrieved from a full-scale digester treating swine manure. The rate of CH4 production substantially reduced with increased addition of ammonium. The analysis of natural (13)C abundances of CH4 and CO2 indicated that the aceticlastic methanogenesis was more sensitive than hydrogenotrophic methanogenesis. Quantitative PCR analysis revealed that mcrA copy number decreased by one order of magnitude in the treatment with a large amount of ammonium (10 g NH4+-N L(-1)) but did not change much with treatments of smaller amounts (3 and 7 g NH4+-N L(-1)) compared with the control. T-RFLP analysis of mcrA compositions showed that the structure of the methanogen community remained highly stable, with Methanosaetaceae dominating the methanogen community in all incubations. The composition of mcrA transcripts, however, showed a substantial response to the addition of ammonium. The relative abundance of Methanosaetaceae transcripts declined with increasing amounts of ammonium, whereas the transcript level of Methanobacteriales mcrA was relatively resistant. The differential responses corresponded to the shift of methanogenic pathway inferred from (13)C isotope fractionation. Our study suggests that methanogens in anaerobic sludge have a strong mcrA transcriptional response to ammonia stress without a change in the community structure.
Relational indexing using a grammarless parser (2002)

The article proposes an alternate view on natural language parsing. Instead of looking for some predefined (phrase) structure it takes inter-word relations as a starting point. The reason for this is twofold: firstly it circumvents traditional parsing and linguistic problems and secondly it offers a possibility to extract information specifically needed by IR applications. The close relationship with index expressions opens the door to feedback mechanisms like 'Query By Navigation' (P.D. Bruza and T.P. van der Weide, 1992) and conceptual knowledge extraction (F. Grootjen, 2000). The presented ideas are accompanied by an implementation and a small scale experiment.
Glycine receptors: recent insights into their structural organization and functional diversity (2006)

Strychnine-sensitive glycine receptors (GlyRs) are known to mediate synaptic inhibition in spinal cord, brainstem and other regions of the CNS. During the past 5 years, considerable progress has been made in delineating structural determinants of ligand binding and channel activation in recombinant GlyRs. Furthermore, immunohistochemical and gene inactivation studies have disclosed distinct distributions and functions of differentially expressed GlyR subtypes in retina, hippocampus and the dorsal horn of the spinal cord. Accordingly, GlyRs regulate not only the excitability of motor and sensory neurones, but are also essential for the processing of photoreceptor signals, neuronal development and inflammatory pain sensitization. Hence, these receptors constitute promising targets for the development of clinically useful compounds.
Demonstration of repeaterless bidirectional transmission of multiple AM-VSB CATV signals over conventional single-mode fiber (2000)

A repeaterless bidirectional wavelength-division-multiplexing (WDM) transmission system for delivery of AM-VSB CATV analog video signals over conventional single-mode fiber (SMF) is demonstrated for the first time. Two kinds of multiplexers, the optical circulator and the WDM multiplexer configurations, for supporting bidirectional operation are used and compared. Satisfied system performance is achieved over a 50-km SMF link. Extending the repeaterless bidirectional transmission distance is also addressed. This technology will play an important role in the shortest fiber link for trunk delivery of any two multiple system operators (MSO's) across another CATV-operator system.
Analysis of worst-case delay bounds for best-effort communication in wormhole networks on chip (2009)

In packet-switched network-on-chip, computing worst-case delay bounds is crucial for designing predictable and cost-effective communication systems but yet an intractable problem due to complicated resource sharing scenarios. For wormhole networks with credit-based flow control, the existence of cyclic dependency between flit delivery and credit generation further complicates the problem. Based on network calculus, we propose a technique for analyzing communication delay bounds for individual flows in wormhole networks. We first propose router service analysis models for flow control, link and buffer sharing. Based on these analysis models, we obtain a buffering-sharing analysis network, which is open-ended and captures both flow control and link sharing. Furthermore, we compute equivalent service curves for individual flows using the network contention tree model in the buffer-sharing analysis network, and then derive their delay bounds. Our experimental results verify that the theoretical bounds are correct and tight.
Synthesis of stereochemically homogeneous oligoribonucleoside all-R<sub>P</sub>-phosphorothioates by combining H-phosphonate chemistry and enzymatic digestion (1994)

H. Almer, J. Stawinski and R. Strömberg, J. Chem. Soc., Chem. Commun., 1994, 1459 DOI: 10.1039/C39940001459
Direct yaw moment control for four wheel independent steering and drive vehicles based on centripetal force detection (2012)

In this paper, a deterministic yaw moment controller for four wheel independent steering and drive vehicles is proposed to enhance driving stability and controllability. Different to conventional methods that track a desired yaw rate, the proposed controller stabilizes a vehicle by additionally tracking the heading angle of a vehicle which is more efficient and robust. The heading angle of a vehicle is obtained by a novel method which is based on centripetal force detection. It eliminates the prerequisite knowledge of the characteristics between wheels and road surface which are time varying and difficult to be measured in real time. The proposed system only requires low cost sensing equipment such as wheel speed sensor and accelerometer that makes the system practical to be utilized. The proposed heading angle detection method can be generally applied to any kind of vehicle. The deterministic yaw moment controller is also applicable to any type of four wheel independent drive vehicles.
Reflection Backdoor: A Natural Backdoor Attack on Deep Neural Networks (2020)

Recent studies have shown that DNNs can be compromised by backdoor attacks crafted at training time. A backdoor attack installs a backdoor into the victim model by injecting a backdoor pattern into a small proportion of the training data. At test time, the victim model behaves normally on clean test data, yet consistently predicts a specific (likely incorrect) target class whenever the backdoor pattern is present in a test example. While existing backdoor attacks are effective, they are not stealthy. The modifications made on training data or labels are often suspicious and can be easily detected by simple data filtering or human inspection. In this paper, we present a new type of backdoor attack inspired by an important natural phenomenon: reflection. Using mathematical modeling of physical reflection models, we propose reflection backdoor (Refool) to plant reflections as backdoor into a victim model. We demonstrate on 3 computer vision tasks and 5 datasets that, Refool can attack state-of-the-art DNNs with high success rate, and is resistant to state-of-the-art backdoor defenses.
The ecdysone inducible gene expression system: unexpected effects of muristerone A and ponasterone A on cytokine signaling in mammalian cells. (2001)

Inducible gene expression systems in mammalian cells have been shown to be valuable processes to study the specific function of a protein in differentiation, proliferation or survival/apoptosis. Usually, these systems use as inducible reagents, compounds that are thought to be neutral and devoid of physiological or biologically undesirable effects in mammalian cells. We recently used the ecdysone inducible gene expression system in hematopoietic cells and found that the two inducer analogs of ecdysone, muristerone A and ponasterone A, altered the signaling pathways induced by IL-3 in the pro-B cell-line, Ba/F3. Indeed, we showed that these two analogs potentiate the IL-3-dependent activation of the PI 3-kinase/Akt pathway, which could ultimately interfere with the growth, and/or survival of these cells.
Oxidation of Microcystin-LR by Ferrate(VI): Kinetics, Degradation Pathways, and Toxicity Assessments (2014)

The presence of the potent cyanotoxin, microcystin-LR (MC-LR), in drinking water sources poses a serious risk to public health. The kinetics of the reactivity of ferrate(VI) (Fe(VI)O4(2-), Fe(VI)) with MC-LR and model compounds (sorbic acid, sorbic alcohol, and glycine anhydride) are reported over a range of solution pH. The degradation of MC-LR followed second-order kinetics with the bimolecular rate constant (kMCLR+Fe(VI)) decreasing from 1.3 ± 0.1 × 10(2) M(-1) s(-1) at pH 7.5 to 8.1 ± 0.08 M(-1) s(-1) at pH 10.0. The specific rate constants for the individual ferrate species were determined and compared with a number of common chemical oxidants employed for water treatment. Detailed product studies using liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) indicated the oxidized products (OPs) were primarily the result of hydroxylation of the aromatic ring, double bond of the methyldehydroalanine (Mdha) amino acid residue, and diene functionality. Products studies also indicate fragmentation of the cyclic MC-LR structure occurs under the reaction conditions. The analysis of protein phosphatase (PP1) activity suggested that the degradation byproducts of MC-LR did not possess significant biological toxicity. Fe(VI) was effective for the degradation MC-LR in water containing carbonate ions and fulvic acid (FA) and in lake water samples, but higher Fe(VI) dosages would be needed to completely remove MC-LR in lake water compared to deionized water.
Isolation and identification of dendritic cells from human peripheral blood (2007)

AIM: To isolate, culture and identify in vitro of dendritic cells (DCs) from human peripheral blood, and observe the function of antigen presentation. METHODS: The experiment was done from May 2005 to November 2006 in Biotherapy Laboratory Tumor Center, Nanfang Hospital, Southern Medical University. Peripheral blood monocytes were isolated from the healthy volunteers (who had known the facts), and then cultured for 5 hours. The adherent cells were washed and then cultured with RPMI1640 medium containing 10% AB serum, granulocyte-macrophage colony stimulating factor (GM-CSF) and interleukin-4 (IL-4). The cellular morphous and phenotypes were examined, respectively at days 1, 3 and 6, and the cellular purity and yield were also detected. Peripheral blood was obtained from different healthy volunteers (who had known the facts). The blood was isolated with lymphocyte separating-medium, and non-adherent cell were cultured with 1640 medium containing 10% AB serum and interleukin-2 (IL-2). At the sixth day, the allogeneic T lymphocytes were harvested. The DCs were divided into two groups: one group was cultured with regular process for 6 days; another group was cultured with Melanoma Associated Antigen Gene A3 (MAGE-A3) peptide on the 5th day. After another 24 hours, 1×104,5×103,2×103,1×103 /per well of DCs were added in ultraviolet-treated 96-well plate. The auto-lymphocytes were used as control, and there were 3 sub-wells in each well, and 1×105 lymphocytes were added in each well to evaluate the ability of DCs stimulating lymphocytes proliferation. RESULTS: ①A large number of DCs with high purity (90.81%) were generated culturing for six days in vitro. DCs expressed highly 21.8%CD1a, 99.0%HLA-DR, 63.4%CD80, 18.9%CD83 and 80.6%CD86. ②Lymphocyte proliferation was induced by mixing allogeneic lymphocytes with variant proportional DCs cultured for 6 days. The ability of stimulating lymphocyte proliferation was significantly strengthened by various proportional DCs with MAGE-A3 peptide than corresponding proportional DCs without MAGE-A3 peptide. The most powerful effectiveness was developed with higher density of DCs, which could intensively stimulating allogeneic lymphocyte proliferation in mixed lymphocyte reaction. CONCLUSION: A group of dendritic cells, which highly express CD83, CD86 and HLA-DR molecules, and stimulate strongly allogeneic T lymphocyte proliferation in vitro, are obtained.
Selective Detection of Iron(III) by Rhodamine‐Modified Fe<sub>3</sub>O<sub>4</sub> Nanoparticles (2010)

Rh-odin's masterpiece: Coupling N-(rhodamine-6G)lactam-ethylenediamine to Fe3O4 nanoparticles through a polyethylene glycol chain renders the rhodamine unit more water soluble and useful for sensitive and selective detection of FeIII at the 2 ppb level in water. This sensitivity is also demonstrated in HeLa cells, thus indicating potential applications of this detection method in biological systems. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Type A Viral Hepatitis (1985)

IN recent years, our understanding of the nature and diversity of viruses causing hepatitis in human beings has been sharply increased.1 Those agents now include the viruses of hepatitis A (classic short-incubation infectious hepatitis) and hepatitis B (long-incubation serum hepatitis), one or more still-undefined viruses responsible for "non-A,non-B hepatitis," and the recently recognized delta virus. Among these types of hepatitis, each of which occurs commonly within the United States, hepatitis A is uniquely and primarily transmitted by the fecal—oral route and thus possesses an unequaled potential for epidemic spread. Although it is relatively benign and never eventuates in chronic hepatitis, . . .
Aggregation-induced heterogeneities in the emission of upconverting nanoparticles at the submicron scale unfolded by hyperspectral microscopy (2019)

Transparent upconverting hybrid nanocomposites are exciting materials for advanced applications such as 3D displays, nanosensors, solar energy converters, and fluorescence biomarkers. This work presents a simple strategy to disperse upconverting β-NaYF<sub>4</sub>:Yb<sup>3+</sup>/Er<sup>3+</sup> or Tm<sup>3+</sup> nanoparticles into low cost, widely used and easy-to-process polydimethylsiloxane (PDMS)-based organic-inorganic hybrids. The upconverting hybrids were shaped as monoliths, films or powders displaying in the whole volume Tm<sup>3+</sup> or Er<sup>3+</sup> emissions (in the violet/blue and green/red spectral regions, respectively). For the first time, hyperspectral microscopy allows the identification at the submicron scale of differences in the hybrids' emission colour, due to variations in the relative intensity of the distinct components of the upconversion spectrum. The effect is attributed to the size distribution of the agglomerates of nanoparticles, highlighting the importance of studying the emission at submicron scales, since this effect is not observable in measurements recorded in larger areas.
Identification and Relative Quantitation of Protein Mixtures by Enzymatic Digestion Followed by Capillary Reversed-Phase Liquid Chromatography−Tandem Mass Spectrometry (2002)

In this report, we describe an approach for identification and relative quantitation of individual proteins within mixtures using LC/MS/MS analysis of protein digests. First, the proteins are automatically identified by correlating the tandem mass spectra with peptide sequences from a database. Then, peak areas of identified peptides from one protein are added together to define the total reconstructed peak area of the protein digest. The total reconstructed peak area is further normalized to the peak area of an internal standard protein digest present in the mixture at a constant level. The method was illustrated using digested mixtures of five standard proteins as follows. One protein was gradually diluted while the other four components were present in the mixtures at constant level. This study revealed that relative peak area of the variable protein increased linearly (trend line R2 = 0.9978) with increasing amount from 10 to 1000 fmol, while relative peak areas of four constant proteins remained approximately the same (within 20% relative standard deviation). To further evaluate the applicability of this method for the quantitation of proteins from complex mixtures, human plasma protein digest was spiked with 200 and 400 fmol of myoglobin digest. Total peak area of myoglobin peptides was normalized to the total peak area of apolipoprotein A-I peptides from human plasma, which played the role of an internal standard. The myoglobin/apolipoprotein A-I peak area ratio was 2 times larger for the human plasma digest spiked with a double amount of myoglobin. After several repetitions, the error of the relative peak area measurements remained below 11%, suggesting that the method described here can be used for relative concentration measurements of proteins in the complex biological mixtures. In the presented method, chemical derivatization steps are not needed to create an internal standard, as in isotope-coded affinity tag or similar methods.
Neutrino interactions in a dense plasma (1991)

We investigate many-body corrections to neutrino scattering from electrons and nuclei. The Coulomb correlations of the electrons screen the weak vector neutral current. Electron screening is important only for electron neutrinos (or antineutrinos) and most effective for neutrino energies of several MeV or less. At electron densities relevant for supernovae, the total quasielastic \ensuremath{\nu}-e cross section can be reduced by 50%, and elastic neutrino-nucleus scattering by up to 85%.
Blue Light Regulation of Cell Division in <i>Chlamydomonas reinhardtii</i> (1992)

A delay in cell division was observed when synchronized cultures of the unicellular green alga Chlamydomonas reinhardtii growing under heterotrophic conditions were exposed to white light during the second half of the growth period. This effect was also observed when photosynthesis was blocked by addition of the photosystem II inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea. Light pulses of 10 minutes were sufficient to induce a delay in cell division in the presence or absence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea. A delay in cell division was induced by blue light but not by illumination with red or far-red light. The equal intensity action spectrum revealed two peaks at 400 and 500 nm.
Effect of duration of postherpetic neuralgia on efficacy analyses in a multicenter, randomized, controlled study of NGX-4010, an 8% capsaicin patch evaluated for the treatment of postherpetic neuralgia (2010)

NCT00068081.
Metal-oxide-semiconductor capacitors with ZrO2 dielectrics grown on In0.53Ga0.47As by chemical beam deposition (2009)

Zirconium oxide films were grown by chemical beam deposition with zirconium tert-butoxide as the source on (2×4) reconstructed, n-type In0.53Ga0.47As surfaces obtained after As decapping. Optimized growth conditions yielded ZrO2/In0.53Ga0.47As interfaces that were free of second phases. Capacitance-voltage (CV) measurements with different top electrodes showed a frequency dispersion of less than 2% per decade in accumulation. The accumulation capacitance and horizontal position of the CV curve were independent of temperature, while the inversion capacitance was strongly temperature dependent. Flat band voltages correlated with the work function of the metal electrode.
Thermosphere zonal winds, vertical motions and temperature as measured from Dynamics Explorer (1982)

In situ measurements of the zonal and vertical components of neutral winds and the kinetic temperature being made by the DE‐B Wind and Temperature Spectrometer (WATS) in the upper thermosphere provide the opportunity to gain new knowledge of polar region physics. On the basis of the data we have obtained to date we confirm that the global thermosphere wind distribution is primarily thermally driven over the earth from the mid‐afternoon sector. The velocities range from tens to a few hundred meters per second. However, the polar cap and auroral region wind systems are highly dynamic with velocities as high as 1 km sec −1 . They appear as superimposed on the thermally driven wind system. The polar regions' zonal wind patterns appear to be generally in accord with the solar and anti‐solar ion convection patterns previously observed and described by investigators in many publications. In addition we have observed vertical motions with velocity peaks from 100‐250 m/sec −1 that frequently correlate well with peaks in the zonal component. Simultaneously observed exospheric kinetic temperatures show expected values at sub‐auroral latitudes and variations of hundred of degrees in the polar regions. There are apparent correlations with vertical motions, but less obvious correlations with the winds' zonal components.
Parish pump politics (2007)

An understanding of the politics of the water sector during the first decade of South Africa's democracy requires an engagement with a series of parallel debates. There is a technical debate about the nature of the water supply challenge. There is an institutional politics around budget allocation, between and within spheres or levels of government. There is a tension between a rights-based approach to service provision and the politics of sustainability and conservation. The interplay between these parallel dynamics is about the politics of the South African transition to democracy. But South Africa is not an island. So, finally, there is the global water debate, with its human rights, economic, anti-privatisation/imperialism and environmental dimensions. The focus of this paper is on how these different politics are playing out and how they impact on South Africans, particularly the poor who have perhaps the most to gain or lose.