gebhart/patrepeval huggingface dataset:
Profiling of D-alanine production by the microbial isolates of rat gut microbiota (2021)

D-alanine (D-Ala) and several other D-amino acids (D-AAs), unusual amino acids present in mammals, act as hormones and neuromodulators in nervous and endocrine systems. Unlike the endogenously synthesized D-serine in animals, D-Ala may be from exogenous sources, e.g., diet and intestinal microorganisms. However, it is unclear if the capability to produce D-Ala and other D-AAs varies among different microbial strains in the gut. We isolated individual microorganisms of rat gut microbiota and profiled their D-AA secretion in vitro, focusing on D-Ala. Serial dilutions of intestinal content from adult male rats were plated on agar to obtain clonal cultures. Using MALDI-TOF MS for rapid strain typing, we identified 38 unique isolates, grouped into 11 species based on 16S rRNA gene sequences. We then used two-tier screening to profile bacterial D-AA secretion, combining a D-amino acid oxidase-based enzymatic assay for rapid assessment of overall D-AA amount, followed by chiral LC-MS/MS to quantify individual D-AAs, revealing 19 out of the 38 isolated strains as D-AA producers. LC-MS/MS analysis of the eight top D-AA producers showed high levels of D-Ala in all strains tested, with substantial inter- and intra-species variations. Though results from enzymatic assay and LC-MS/MS analysis aligned well, LC-MS/MS further revealed the existence of D-glutamate and D-aspartate, which are poor substrates for enzymatic assay. We observed large inter- and intra-species variation of D-AA secretion profiles from rat gut microbiome species, demonstrating the importance of chemical profiling of gut microbiota in addition to sequencing, furthering the idea that microbial metabolites modulate host physiology.
Efficient And Secure Pseudo-Random Number Generation (2005)

Cryptographically secure pseudo-random number generators known so far suffer from the handicap of being inefficient; the most efficient ones can generate only one bit on each modular multiplication (n/sup 2/ steps). Blum, Blum and Shub ask the open problem of outputting even two bits securely. We state a simple condition, the XOR-Condition, and show that any generator satisfying this condition can output logn bits on each multiplication. We also show that the logn least significant bits of RSA, Rabin's Scheme, and the x/sup 2/ mod N generator satisfy boolean predicates of these bits are secure. Furthermore, we strengthen the security of the x/sup 2/ mod N generator, which being a Trapdoor Generator, has several applications, by proving it as hard as Factoring.
Reactions of pentafluorophenyl(ylide)-silver(I) or -gold(I) complexes with chlorobis(pentafluorophenyl)thallium(III) (1988)

Chlorobis(pentafluorophenyl)thallium(III) reacts with silver–ylide complexes [Ag(C6F5)(CH2ER3)](ER3= PPh3, PPh2Me, PPhMe2, or AsPh3) to give AgCl and [Tl(C6F5)3(CH2ER3)], whereas the reactions with gold–ylide complexes, [Au(C6F5)(CH2PR3)], lead to gold(III) complexes of the types trans-[Au(C6F5)2Cl(CH2PR3)] and [Au(CH2PR3)2][Au(C6F5)4] which have been isolated and characterized.
A printed planar helix antenna (2015)

This paper presents design, fabrication and measurement results of a novel broadband, circularly polarized, planar helix antenna operating at X-band that is fabricated using printed circuit techniques. The conventional circular helix antenna is modified into a planar helix antenna, and the effect of various parameters like pitch angle, dimensions, feed and substrate, etc. on the impedance and radiation characteristics is studied. The performance parameters under investigation are S 11 , directivity, side lobe level, and axial ratio. These parameters are obtained using CST Microwave Studio. For a design with 5 turns of the planar helix, the results of the simulations are as follows: over a frequency range of 8.3 – 11.7 GHz, S 11 is less than −10 dB, directivity ranges from 11.7 – 12.6 dBi, and the axial ratio ranges from 0.68 – 3.3 dB. The corresponding design is fabricated using RO4003C dielectric substrates. The measurement results match the simulation results reasonably well.
Involvement of major histocompatibility complex products in tolerance induction in the thymus. (1988)

KJ23a+ T cell clones, which bear the determinant encoded by the V beta 17a T cell receptor gene segment, frequently recognize IE molecules of various murine H-2 haplotypes. In the presence of IE molecules, thymic maturation of KJ23a+ clones is infrequent. We investigated the basis of this phenomenon by blocking expression of IE molecules with monoclonal anti-IE antibodies in organ cultures of fetal thymus and in neonates from the C57BR/cdJ strain (H-2k, V beta 17a homozygous). Our data support the contention that this process results from deletion of clones with anti-IE reactivity, as functional blocking of the IE molecule results in maturation of IE-reactive clones and increased numbers of KJ23a+ mature cells. In addition, we noted that blocking of functional IE expression in this haplotype permitted development of both CD4+/KJ23a+ and CD8+/KJ23a+ T cells. The CD4+ clones isolated from anti-IE-treated animals were frequently reactive against IEk; we could demonstrate no alloreactivity against B cell or B lymphoma stimulators in the CD4- clones. We conclude that clonal deletion events during thymic development may be initiated by T cell precursor interactions with MHC molecules against which the mature clones display no measurable reactivity. Specifically, clones destined to be MHC Class I-reactive may be deleted during development by interactions with MHC Class II molecules.
Hybrid Structured Illumination Expansion Microscopy Reveals Microbial Cytoskeleton Organization (2017)

Recently developed tissue-hydrogel methods for specimen expansion now enable researchers to perform super-resolution microscopy with ∼65 nm lateral resolution using ordinary microscopes, standard fluorescent probes, and inexpensive reagents. Here we use the combination of specimen expansion and the optical super-resolution microscopy technique structured illumination microscopy (SIM) to extend the spatial resolution to ∼30 nm. We apply this hybrid method, which we call ExSIM, to study the cytoskeleton of the important human pathogen Giardia lamblia including the adhesive disc and flagellar axonemes. We determined the localization of two recently identified disc-associated proteins, including DAP86676 , which localizes to disc microribbons, and the functionally unknown DAP16263 , which primarily localizes to dorsal microtubules of the disc overlap zone and the paraflagellar rod of ventral axonemes. Based on its strong performance in revealing known and unknown details of the ultrastructure of Giardia, we find that ExSIM is a simple, rapid, and powerful super-resolution method for the study of fixed specimens, and it should be broadly applicable to other biological systems of interest.
Analysis of quantum error-correcting codes: symplectic lattice codes and toric codes (2004)

Quantum information theory is concerned with identifying how quantum mechanical resources, such as entangled quantum states, can be utilized for a number of information processing tasks, including data storage, computation, communication, and cryptography. Efficient quantum algorithms and protocols have been developed for performing some tasks (e.g., factoring large numbers, securely communicating over a public channel, and simulating quantum mechanical systems) that appear to be very difficult with just classical resources. In addition to identifying the separation between classical and quantum computational power, much of the theoretical focus in this field over the last decade has been concerned with finding novel ways of encoding quantum information that are robust against errors, which is an important step toward building practical quantum information processing devices.

In this thesis I present some results on the quantum error-correcting properties of oscillator codes (also described as symplectic lattice codes) and toric codes. Any harmonic oscillator system, such as a mode of light, can be encoded with quantum information via symplectic lattice codes that are robust against shifts in the system's continuous quantum variables. I show the existence of lattice codes whose achievable rates match the one-shot coherent information over the Gaussian quantum channel. Also, I construct a family of symplectic self-dual lattices and search for optimal encodings of quantum information distributed between several oscillators.

Toric codes provide encodings of quantum information into two-dimensional spin lattices that are robust against local clusters of errors and which require only local quantum operations for error correction. Numerical simulations of this system under realistic error models provide a calculation of the accuracy threshold for quantum memory using toric codes, which can be related to phase transitions in particular condensed matter models. I also present a local classical processing scheme for correcting errors on toric codes, which demonstrates that quantum information can be maintained in two dimensions by purely local quantum and classical resources.
Proceedings of the 12th National Symposium of Organic Chemistry (XII SINAQO), Los Cocos, Cordoba, Argentina, 14-17 November 1999 (2000)

This Paper is downloadable at http://www.mdpi.org/molecules/papers/50300252.pdf
Involvement of adipose tissues in the early hypolipidemic action of PPARγ agonism in the rat (2006)

Agonists of the peroxisome proliferator-activated receptor gamma (PPARgamma) are insulin sensitizers that potently improve lipemia in rodents. This study aimed to determine the contribution of lipid secretion vs. clearance and the involvement of white adipose tissue (WAT) and brown adipose tissue (BAT) in the rapid hypolipidemic action of PPARgamma agonism. Male rats were treated with rosiglitazone (RSG; 15 mg x kg(-1) x day(-1)) for 1 to 4 days, and determinants of lipid metabolism were assessed postprandially. Serum triglycerides (TG) were lowered (-54%) after 3 days of RSG treatment, due to accelerated clearance from blood without contribution of changes in secretion rates. Both BAT and WAT were the major sites of RSG action on TG clearance, the increase in TG-derived fatty acid (FA) uptake reaching threefold in BAT and 60-90% in WAT depots. Accelerated TG clearance was associated with increased lipoprotein lipase (LPL) activity mostly in BAT. Serum nonesterified FA were lowered (-20%) by a single dose of RSG, an effect associated with increased expression levels of FA binding/transport (fatty acid binding protein-4), esterification (diacylglycerol acyltransferase-1), and recycling glycerol kinase and phosphoenolpyruvate carboxykinase enzymes in BAT and WAT, suggesting FA trapping. After 4 days of RSG treatment, nonesterified fatty acid (NEFA) uptake was also stimulated in both BAT (2.5-fold) and WAT (40%). These findings demonstrate the causal involvement of increased efficiency of LPL-mediated TG clearance and reveal the important contribution of TG-derived and albumin-bound FA uptake by BAT in the rapid hypolipidemic action of PPARgamma agonism in the rat.
ANTI-THROMBOTIC EFFECT IN CANINE CORONARY ARTERIES OF A COMBINED TXA2 synthetase/TXA2-prostaglandin ENDOPEROXIDE RECEPTOR INHIBITOR (R 68070) (1987)

The effects of R 68070 an oxime-alkane carboxylic acid derivative combining specific thromboxane A2 (TXA2) synthetase inhibition with TXA2/prostaglandin endoperoxide receptor blockade in one molecule, on thrombus formation in a coronary artery following electrically-induced endothelial injury and on its myocardial repercussions were examined in dogs. In an open-chest model in anaesthetized dogs, a stainless steel electrode was inserted into the left anterior descending coronary artery (LAD) distally (+ 1 cm) from an electromagnetic flow probe. ECG and heart rate were derived from limb leads. Serum TXB2 levels were measured by RIA on venous spontaneously coagulated blood (1 h, 37°C). Endothelial cell injury in the LAD coronary artery was induced by the application of an anodal current of 300 μA during 30 min; after an additional 60 min observation period, the thrombus wet weight was determined. In comparison with solvent treatment (n = 8), R 68070 (1.25 mg/kg I.V. 10 min before electrical stimulation, n = 7), significantly reduced the thrombus mass (solvent : 43 mg; R 68070 : 18 mg median value, p &lt; 0.05), the incidence of ECG changes indicative for myocardial ischemia (fibrillation : solvent 1/8; R 68070 0/7; arrhythmias : solvent 3/8; R 68070 2/7; ST changes : solvent 7/8; R 68070 1/7, p &lt; 0.05) and the decrease in coronary blood flow after electrical stimulation (solvent : from 13 to 6.5 ml/min; R 68070 : from 13 to 11 ml/min median values, p &lt; 0.05). Serum TXB2 levels were reduced by 92 % at 100 min after the injection of the active compound (median value, n = 7). Heart rate and coronary blood flow measured before the induction of the endothelial injury were not modified by R 68070. The present study thus demostrates that R 68070 exerts a potent anti-thrombotic effect in canine coronary arteries. The relative contributions to this effect of TXA2 synthetase inhibition and of TXA2/prostaglandin endoperoxide receptor blockade exerted by the compound are being investigated.
Beyond ribosome rescue: tmRNA and co‐translational processes (2009)

tmRNA is a unique bi-functional RNA that acts as both a tRNA and an mRNA to enter stalled ribosomes and direct the addition of a peptide tag to the C terminus of nascent polypeptides. Despite a reasonably clear understanding of tmRNA activity, the reason for its absolute conservation throughout the eubacteria is unknown. Although tmRNA plays many physiological roles in different bacterial systems, recent studies suggest a general role for trans-translation in monitoring protein folding and perhaps other co-translational processes. This review will focus on these new hypotheses and the data that support them.
Stochastic Analysis of a Mammalian Circadian Clock Model: Small Protein Number Effects (2017)

The circadian clock, responsible for coordinating organism function with daily and seasonal changes in the day-night cycle, is controlled by a complex protein network that constitutes a robust biochemical oscillator. Deterministic ordinary differential equation models have been used extensively to model the behavior of these central clocks. However, due to the small number of proteins involved in the circadian oscillations, mathematical models that track stochastic variations in the numbers of clock proteins may reveal more complex and biologically relevant behaviors. In this paper, we compare the response of a robust yet detailed deterministic model for the mammalian circadian clock with its corresponding stochastic version that takes into account low protein number noise. We then use signal analysis techniques in order to examine differences in behavior among components of the stochastic system oscillator. This approach reveals differences in the system response between the stochastic and deterministic model and also allows us to extend bifurcation analysis into the stochastic domain. From our analysis of the unfitted stochastic model, we propose novel explanations of some previous experimental results.
Characterization of nickel(II)-nickel(IV) linear chain compounds by nickel and chlorine K-edge EXAFS (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCharacterization of nickel(II)-nickel(IV) linear chain compounds by nickel and chlorine K-edge EXAFSJohn Evans, J. Trevor Gauntlett, and William LevasonCite this: Inorg. Chem. 1988, 27, 25, 4521–4523Publication Date (Print):December 1, 1988Publication History Published online1 May 2002Published inissue 1 December 1988https://pubs.acs.org/doi/10.1021/ic00298a001https://doi.org/10.1021/ic00298a001research-articleACS PublicationsRequest reuse permissionsArticle Views100Altmetric-Citations6LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Berry-Esseen Bounds for Standardized Subordinators via Moduli of Smoothness (2006)

We introduce moduli of smoothness techniques to deal with Berry? Esseen bounds, and illustrate them by considering standardized subordinators with finite variance. Instead of the classical Berry?Esseen smoothing inequality, we give an easy inequality involving the second modulus. Under finite third moment assumptions, such an inequality provides the main term of the approximation with small constants, even asymptotically sharp constants in the lattice case. Under infinite third moment assumptions, we show that the optimal rate of convergence can be simply written in terms of the first modulus of smoothness of an appropriate function, depending on the characteristic random variable of the subordinator. The preceding results are extended to standardized L?evy processes with finite variance.
Gradient Reversal against Discrimination: A Fair Neural Network Learning Approach (2018)

No methods currently exist for inducing fairness in arbitrary neural network architectures. In this work we introduce GRAD, a new and simplified method for producing fair neural networks that can be used for auto-encoding fair representations or directly with predictive networks. It is easy to implement and add to existing architectures, has only one (insensitive) hyper-parameter, and provides improved individual and group fairness. We use the flexibility of GRAD to demonstrate multi-attribute protection.
Ultra-Widefield Indocyanine Green Angiography Reveals Patterns of Choroidal Venous Insufficiency Influencing Pachychoroid Disease (2022)

In eyes with pachychoroid disease, imbalanced choroidal venous drainage with congestion of specific vortex vein systems may contribute to a state of choroidal venous insufficiency characterized by regional choroidal thickening, CVH and remodeling of venous drainage routes.
Organizational ontologies to support semantic business process management (2009)

The Semantic Business Process Management (SBPM) aims at automation of the Business Process Management life cycle with use of semantics and Semantic Web services technology. The key issue to fulfil this aim is to provide an adequate machine-processable representation of processes. In this article we present one of the most important elements of process description, namely organizational ontologies. Moreover, we discuss their role in the early phases of SBPM and illustrate it with a set of application scenarios.
Systematic evaluation of satellite remote sensing for identifying uranium mines and mills. (2006)

In this report, we systematically evaluate the ability of current-generation, satellite-based spectroscopic sensors to distinguish uranium mines and mills from other mineral mining and milling operations. We perform this systematic evaluation by (1) outlining the remote, spectroscopic signal generation process, (2) documenting the capabilities of current commercial satellite systems, (3) systematically comparing the uranium mining and milling process to other mineral mining and milling operations, and (4) identifying the most promising observables associated with uranium mining and milling that can be identified using satellite remote sensing. The Ranger uranium mine and mill in Australia serves as a case study where we apply and test the techniques developed in this systematic analysis. Based on literature research of mineral mining and milling practices, we develop a decision tree which utilizes the information contained in one or more observables to determine whether uranium is possibly being mined and/or milled at a given site. Promising observables associated with uranium mining and milling at the Ranger site included in the decision tree are uranium ore, sulfur, the uranium pregnant leach liquor, ammonia, and uranyl compounds and sulfate ion disposed of in the tailings pond. Based on the size, concentration, and spectral characteristics of these promising observables, we then determine whether these observables can be identified using current commercial satellite systems, namely Hyperion, ASTER, and Quickbird. We conclude that the only promising observables at Ranger that can be uniquely identified using a current commercial satellite system (notably Hyperion) are magnesium chlorite in the open pit mine and the sulfur stockpile. Based on the identified magnesium chlorite and sulfur observables, the decision tree narrows the possible mineral candidates at Ranger to uranium, copper, zinc, manganese, vanadium, the rare earths, and phosphorus, all of which are milled using sulfuric acid leaching.
Mn(III)—porphyrin‐based thiocyanate‐selective membrane electrodes: Characterization and application in flow injection determination of thiocyanate in saliva (1989)

Abstract The response properties of a new thiocyanate‐selective solvent‐polymeric membrane electrode are reported. The membrane contains (5,10,15,20‐tetrakis(2,4,6‐triphenylphenyl)porphyrinato)manganese(III) chloride (Mn[TPPP]CI) in a plasticized polyvinyl chloride matrix. The electrode deviates from the Hofmeister selectivity pattern by responding to thiocyanate preferentially over inorganic anions (perchlorate, chloride, iodide, and bromide) and several organic anions often present in biological samples (ascorbate, citrate, urate, and salicylate). The performance of this electrode as an ion‐selective detector in a low‐dispersion, flow‐injection system is also evaluated. While selectivity in such a nonequilibrium flow arrangement is found to be somewhat different than that observed under equilibrium conditions, the electrode's response and selectivity is still adequate to allow for measurement of thiocyanate in biological samples. This application is demonstrated via the flow‐injection analysis (FIA) detection of thiocyanate in 22 human saliva samples with good correlation to a classical colorimetric method ( r = 0.981).