gebhart/patrepeval huggingface dataset:
Energy detection using very large antenna array receivers (2014)

We propose the use of energy detection for single stream transmission and reception by a very large number of antennas, with primary application to millimeter wave communications. The reason for applying energy detection is low complexity, cost and power efficiency. While both energy detection and millimeter wave communications are limited to short ranges due respectively to noise sensitivity and propagation attenuation, processing by a large number of receive antennas overcomes those shortcomings to provide significant reach extension. This processing is solely based on long-term statistics of the channel and noise, making it robust to user mobility and imperfect channel knowledge.
Nucleic Acid-Triggered Fluorescent Probe Activation by the Staudinger Reaction (2004)

Highly sequence specific and sensitive detection systems for DNA or RNA in vivo would be of great use in biology and medicine for monitoring gene expression and diagnosing diseased cells. Herein we describe a new nucleic acid-triggered fluorescent probe system that is activated by a biocompatible and chemoselective Staudinger reaction.
Differential Inhibition of Staphylococcus aureus PBP2 by Glycopeptide Antibiotics (2005)

The glycopeptide antibiotics prevent maturation of the bacterial cell wall by binding to the terminal d-alanyl-d-alanine moiety of peptidoglycan precursors, thereby inhibiting the enzymes involved in the final stages of peptidoglycan synthesis. However, there are significant differences in the biological activity of particular glycopeptide derivatives that are not related to their affinity for d-Ala-d-Ala. We compare the ability of vancomycin and a set of clinically relevant glycopeptides to inhibit Staphylococcus aureus PBP2 (penicillin binding protein), the major transglycosylase in a clinically relevant pathogen, S. aureus. We report experiments suggesting that activity differences between glycopeptides against this organism reflect a combination of substrate binding and secondary interactions with key enzymes involved in peptidoglycan synthesis.
Clonal Characterization of Sporadic Cribriform-Morular Variant of Papillary Thyroid Carcinoma by Laser Microdissection–BasedAPCMutation Analysis (2007)

Cribriform-morular variant (C-MV) of papillary thyroid carcinoma (PTC) is a rare and unusual neoplasm composed of multiple histologic components, including cribriform, papillary, solid, tall columnar, and morular patterns. Analyses of gross C-MV of PTC lesions has linked adenomatous polyposis coli (APC) mutations to its pathogenesis; however, the extent of involvement of mutations in the development of individual components is unclear. We report on bidirectional sequencing of the mutation cluster region (codons 1032-1565) of the APC gene in individually laser-microdissected components of a previously unreported C-MV of PTC. A silent Thr1493Thr gene variant was found in all tumoral components, whereas a 5-base-pair frameshift deletion at codon 1309 was identified only in the morules. Neither variant was observed in matched normal thyroid tissue. These results show the histologic components of C-MV of PTC to have some common mutational background, although additional somatic mutations may be involved in the development of morular structures.
Differential Privacy as a Mutual Information Constraint (2016)

Differential privacy is a precise mathematical constraint meant to ensure privacy of individual pieces of information in a database even while queries are being answered about the aggregate. Intuitively, one must come to terms with what differential privacy does and does not guarantee. For example, the definition prevents a strong adversary who knows all but one entry in the database from further inferring about the last one. This strong adversary assumption can be overlooked, resulting in misinterpretation of the privacy guarantee of differential privacy. Herein we give an equivalent definition of privacy using mutual information that makes plain some of the subtleties of differential privacy. The mutual-information differential privacy is in fact sandwiched between ε-differential privacy and (ε,δ)-differential privacy in terms of its strength. In contrast to previous works using unconditional mutual information, differential privacy is fundamentally related to conditional mutual information, accompanied by a maximization over the database distribution. The conceptual advantage of using mutual information, aside from yielding a simpler and more intuitive definition of differential privacy, is that its properties are well understood. Several properties of differential privacy are easily verified for the mutual information alternative, such as composition theorems.
Purification, characterization and specificity of chondroitin lyases and glycuronidase from Flavobacterium heparinum (1995)

The chondroitin lyases from Flavobacterium heparinum (Cytophaga heparinia) have been widely used in depolymerization of glycosaminoglycan and proteoglycan chondroitin sulphates. Oligosaccharide products derived from chondroitin sulphate can be further degraded by glycuronidases and sulphatases obtained from the same organism. There has been no reported purification of these enzymes to homogeneity nor is there any information on their physical and kinetic characteristics. The absence of pure enzymes has resulted in a lack of understanding of the optimal conditions for their catalytic activity and their substrate specificity. This has limited the use of these enzymes as reagents for preparation of oligosaccharides for structure and activity studies. Reproducible schemes to purify a chondroitin AC lyase, a glycuronidase and chondroitin B lyase from Flavobacterium heparinum to apparent homogeneity are described. Chondroitin AC lyase (chondroitinase AC, EC 4.2.2.5), glycuronidase [chondro-(1-->3)-glycuronidase, no EC number] and chondroitin B lyase (chondroitinase B, no EC number) have M(r) values (assessed by SDS/PAGE) of 74,000, 41,800 and 55,200 respectively, and isoelectric points (determined by isoelectric focusing) of 8.85, 9.28 and 9.05 respectively. Chondroitin lyase AC and B contain pyroglutamic acid at their N-termini precluding their analysis by Edman degradation. Deblocking with pyroglutamate aminopeptidase facilitated the determination of their N-terminal sequences. The kinetic properties of these enzymes have been determined as well as the optimum conditions for their catalytic activity. The specificity of the glycouronidase, determined using 17 different disaccharide substrates, shows that it only acts on unsulphated or 6-O-sulphated 1-->3 linkages. The chondroitin lyases are both endolytic enzymes, and oligosaccharide mapping shows their expected specificity towards the chondroitin and dermatan sulphate polymers.
Transcriptional regulation by MAP kinases (1995)

Tyrosine kinase growth factor receptors activate MAP kinase by a complex mechanism involving the SH2/3 protein Grb2, the exchange protein Sos, and Ras. The GTP-bound Ras protein binds to the Raf kinase and initiates a protein kinase cascade that leads to MAP kinase activation. Three MAP kinase kinase kinases have been described--c-Raf, c-Mos, and Mekk--that phosphorylate and activate Mek, the MAP kinase kinase. Activated Mek phosphorylates and activates MAP kinase. Subsequently, the activated MAP kinase translocates into the nucleus where many of the physiological targets of the MAP kinase signal transduction pathway are located. These substrates include transcription factors that are regulated by MAP kinase phosphorylation (e.g., Elk-1, c-Myc, c-Jun, c-Fos, and C/EBP beta). Thus the MAP kinase pathway represents a significant mechanism of signal transduction by growth factor receptors from the cell surface to the nucleus that results in the regulation of gene expression. Three MAP kinase homologs have been identified in the rat: Erk1, Erk2, and Erk3. Human MAP kinases that are similar to the rat Erk kinases have also been identified by molecular cloning. The human Erk1 protein kinase has been shown to be widely expressed as a 44-kDa protein in many tissues. The human Erk2 protein kinase is a 41-kDa protein that is expressed ubiquitously. In contrast, a human Erk3-related protein kinase has been found to be expressed at a high level only in heart muscle and brain. The loci of these MAP kinase genes are widely distributed within the human genome: erk2 at 22q11.2; erk1 at 16p11.2; and ek3-related at 18q12-21. In the yeast Saccharomyces cerevisiae, five MAP kinase gene homologs have been described: smkl, mpk1, hog1, fus3, and kss1. Together, these kinases are a more diverse group than the human erks that have been identified. Thus the erks are likely to represent only one subgroup of a larger human MAP kinase gene family. A candidate for this extended family of MAP kinases is the c-Jun NH2-terminal kinase (Jnk), which binds to and phosphorylates the transcription factor c-Jun at the activating sites Ser-63 and Ser-73. Evidence is presented here to demonstrate that Jnk is a distant relative of the MAP kinase group that is activated by dual phosphorylation at Tyr and Thr.
A 350&#x03BC;W CMOS MSK transmitter and 400&#x03BC;W OOK super-regenerative receiver for Medical Implant Communications (2008)

A 350 muW MSK direct modulation transmitter and a 400 muW OOK super-regenerative receiver (SRR) are implemented in 90 nm CMOS technology. The transceiver tunes 24 MHz in frequency steps smaller than 2 kHz and is designed to meet the specifications of the Medical Implant Communications Service (MICS) standard in the 402-405 MHz band. The transmitter meets MICS mask specifications with data rates up to 120 kbps, and the receiver has a sensitivity better than -99 dBm with a data rate of 40 kbps or -93 dBm with a data rate of 120 kbps.
Beta conformation of polyglutamine track revealed by a crystal structure of Huntingtin N-terminal region with insertion of three histidine residues (2013)

Huntington disease is an autosomal-dominant neurodegenerative disorder caused by a polyglutamine (polyQ) expansion (> 35Q) in the first exon (EX1) of huntingtin protein (Htt). mHtt protein is thought to adopt one or more toxic conformation(s) that are involved in pathogenic interactions in cells . However, the structure of mHtt is not known. Here, we present a near atomic resolution structure of mHtt36Q-EX1. To facilitate crystallization, three histidine residues (3H) were introduced within the Htt36Q stretch resulting in the sequence of Q 7HQHQHQ 27. The Htt36Q3H region adopts α-helix, loop, β-hairpin conformations. Furthermore, we observed interactions between the backbone of the Htt36Q3H β-strand with the aromatic residues mimicking putative-toxic interactions with other proteins. Our findings support previous predictions that the expanded mHtt-polyQ region adopts a β-sheet structure. Detailed structural information about mHtt improves our understanding of the pathogenic mechanisms in HD and other polyQ expansion disorders and may form the basis for rational design of small molecules that target toxic conformations of disease-causing proteins.
Fairness and load balancing in wireless LANs using association control (2004)

Recent studies on operational wireless LANs (WLANs) have shown that user load is often unevenly distributed among wireless access points (APs). This unbalanced load results in unfair bandwidth allocation among users. We observe that the unbalanced load and unfair bandwidth allocation can be greatly alleviated by intelligently associating users to APs, termed association control, rather than having users greedily associate APs of best received signal strength.In this study, we present an efficient algorithmic solution to determine the user-AP associations that ensure max-min fair bandwidth allocation. We provide a rigorous formulation of the association control problem that considers bandwidth constraints of both the wireless and backhaul links. Our formulation indicates the strong correlation between fairness and load balancing, which enables us to use load balancing techniques for obtaining near optimal max-min fair bandwidth allocation. Since this problem is NP-hard, we present algorithms that achieve a constant-factor approximate max-min fair bandwidth allocation. First, we calculate a fractional load balancing solution, where users can be associated with multiple APs simultaneously. This solution guarantees the fairest bandwidth allocation in terms of max-min fairness. Then, by utilizing a rounding method we obtain an efficient integral association. In particular, we provide a 2-approximation algorithm for unweighted greedy users and a 3-approximation algorithm for weighted and bounded-demand users. In addition to bandwidth fairness, we also consider time fairness and we show it can be solved optimally. We further extend our schemes for the on-line case where users may join and leave. Our simulations demonstrate that the proposed algorithms achieve close to optimal load balancing and max-min fairness and they outperform commonly used heuristic approaches.
Evidence that a Chloroplast Surface Protein Is Associated with a Specific Binding Site for the Precursor to the Small Subunit of Ribulose-1,5-Bisphosphate Carboxylase (1987)

Most chloroplast proteins are encoded by nuclear genes and synthesized in the cytoplasm as higher molecular weight precursors. These precursors are imported posttranslationally into the chloroplasts, where they are proteolytically processed, and sorted to their proper locations. The first step of this import process is thought to be the binding of precursors to putative receptors on the outer envelope membrane of chloroplasts. We have investigated the interaction of the precursor to the small subunit of ribulose-1,5-bisphosphate carboxylase with its putative receptor by using a heterobifunctional, photoactivatable cross-linker. The resulting cross-linked conjugate has a molecular weight of 86,000, and is present on the surface of chloroplasts as determined by its sensitivity to digestion with protease. Control experiments demonstrated that the label in the conjugate is derived from small subunit precursor and that the conjugate is formed only when modified precursor is reacted in the presence of chloroplasts. Based on these results, we postulate that a protein on the surface of chloroplasts is part of the receptor which interacts with the small subunit precursor.
A framework for separating server scalability and availability from internet application functionality (1998)

To meet the service demands created by the Internet&amp;apos;s exponential growth, operators are scrambling to deploy application-level services, including Web caches, commerce servers, and intelligent transformation proxies for mobile &amp;quot;thin clients.&amp;quot; On the one hand, the Internet&amp;apos;s growth rate places unprecedented scalability and robustness demands on these services; on the other hand, that same growth rate demands that new services be developed, deployed, and evolved at a pace that is precipitous even by the standards of today&amp;apos;s desktop software development cycles. We demonstrate that for a certain class of applications, these apparently conflicting goals can be reconciled by completely separating the application logic from the runtime support for scalability and high ...
Kinematics and Force Characterisation of a Knifefish-Inspired Mechanical Propulsor (2008)

The knifefish is a weakly electric eel that propels itself by passing waves along a median fin extending ventrally from jaw to tail. To study the forces generated by this fin, we built an undulating propulsion mechanism that mimics the waves passed along the biological fin using several crank-actuated fin rays. In this paper we explore the forces created by the fin and its performance as a propulsor when mounted on a floating pontoon. Thrust in the fish seems to be improved by increasing the amplitude of the wave as it travels along the body. Using our mechanism we look at the limit of thrust production. We proceed by iterative prototying to optimise the magnitude and along-axis directionality of the mechanism's thrust production.
Compensation in pre‐synaptic dopaminergic function following nigrostriatal damage in primates (2006)

Clinical symptoms of Parkinson's disease only become evident after 70-80% reductions in striatal dopamine. To investigate the importance of pre-synaptic dopaminergic mechanisms in this compensation, we determined the effect of nigrostriatal damage on dopaminergic markers and function in primates. MPTP treatment resulted in a graded dopamine loss with moderate to severe declines in ventromedial striatum (approximately 60-95%) and the greatest reductions (approximately 95-99%) in dorsolateral striatum. A somewhat less severe pattern of loss was observed for striatal nicotinic receptor, tyrosine hydroxylase and vesicular monoamine transporter expression. Declines in striatal dopamine uptake and transporter sites were also less severe than the reduction in dopamine levels, with enhanced dopamine turnover in the dorsolateral striatum after lesioning. The greatest degree of adaptation occurred for nicotine-evoked [(3)H]dopamine release from striatal synaptosomes, which was relatively intact in ventromedial striatum after lesioning, despite > 50% declines in dopamine. This maintenance of evoked release was not due to compensatory alterations in nicotinic receptor characteristics. Rather, there appeared to be a generalized preservation of release processes in ventromedial striatum, with K(+)-evoked release also near control levels after lesioning. These combined compensatory mechanisms help explain the finding that Parkinson's disease symptomatology develops only with major losses of striatal dopamine.
Cannabidiol – Recent Advances (2007)

The aim of this review is to present some of the recent publications on cannabidiol (CBD; 2), a major non-psychoactive constituent of Cannabis, and to give a general overview. Special emphasis is laid on biochemical and pharmacological advances, and on novel mechanisms recently put forward, to shed light on some of the pharmacological effects that can possibly be rationalized through these mechanisms. The plethora of positive pharmacological effects observed with CBD make this compound a highly attractive therapeutic entity.
Caco-2 cell permeability vs human gastro-intestinal absorption: QSPR analysis (2000)

The aim of this study is to elucidate quantitative structure-permeability relationship (QSPR) of various organic molecules through Caco-2 cells, and to ascertain the relationship between gastrointestinal (GI) absorption in humans and Caco-2 cell permeability. Caco-2 cell permeability and human GI absorption data were obtained from the literature. The maximum hydrogen bond-forming capacity corrected for intra-molecular H-bonding (Hbc) and Lien's QSAR model were used in this study. The latest CQSAR software was utilized in calculating the logarithm of partition coefficient in octanol/water (Clog P) and in deriving all regression equations. For 51 compounds, a significant correlation was obtained between Caco-2 cell permeability (log Pcaco-2) and Hbc, octanol/PBS (phosphate buffered saline, pH 7.4) distribution coefficient (log Doct), log MW and an indicator variable (I) for the charge, with a correlation coefficient of 0.797. When these compounds were divided into three subgroups, namely neutral, cationic and anionic compounds, much better correlations (r = 0.968, 0.915 and 0.931, respectively) were obtained using different combinations of various physico-chemical parameters. A plot of human GI absorption vs. Caco-2 cell permeability obtained from different laboratories reveals that Caco-2 cell permeability cannot be used to precisely predict human GI absorption for compounds with Pcaco-2 below 5 x 10(-6) cm/s, due to interlaboratory and experimental variabilities, and the lack of a simple correlation between human GI absorption and Caco-2 cell permeability. Caco-2 cell permeability may be estimated from the structures of drug molecules using the above-mentioned physicochemical parameters. In general, for compounds with Pcaco-2 above 5 x 10(-6) cm/s, human GI absorption ranges from 50 to 100%. This is generally acceptable for development into oral dosage form. For the compounds with Pcaco-2 below 5 x 10(-6) cm/s, careful interpretation of caco-2 cell permeability and use of internal standard for comparison are recommended. Otherwise, good drug candidates may be excluded due to incorrectly predicted poor absorption.
Amperometric Sensors for Simultaneous Superoxide and Hydrogen Peroxide Detection (1997)

A two-channel sensor capable of almost instantaneous simultaneous detection of superoxide radical and hydrogen peroxide in the concentration range 10(-)(7)-10(-)(4) M is very important for understanding of a number of rapid kinetics processes. A glassy carbon working microelectrode covered by an electrodeposited polypyrrole/horseradish peroxidase (PPy/HRP) membrane was employed as a H(2)O(2) sensor. Another glassy carbon microelectrode covered by a composite membrane of an inside layer of PPy/HRP and an outside layer of superoxide dismutase was employed as a working electrode for superoxide detection. These two working electrodes with Pt counter and tungsten oxide (WO(3)) reference electrodes were contained in one 6 mm diameter Teflon cylinder. Simultaneous measurements were performed at a potential of -60 mV (vs WO(3) reference, pH 5.1). Additional sensor characterization was performed for pH 5.1-9.0. Superoxide sensor behavior as a function of membrane deposition conditions and coating time is reported. Sensors' mutual influence, selectivity, response times, linearity, stability, and sensitivity for hydrogen peroxide and superoxide are presented and discussed. A mathematical model of sensors' responses is proposed, with model calculation corresponding to experiment within 10%.
Regulation of Plasmin-dependent Fibrin Clot Lysis by Annexin II Heterotetramer (2001)

In a previous report we showed that plasmin-dependent lysis of a fibrin polymer, produced from purified components, was totally blocked if annexin II heterotetramer (AIIt) was present during fibrin polymer formation. Here, we show that AIIt inhibits fibrin clot lysis by stimulation of plasmin autodegradation, which results in a loss of plasmin activity. Furthermore, the C-terminal lysine residues of its p11 subunit play an essential role in the inhibition of fibrin clot lysis by AIIt. We also found that AIIt binds to fibrin with a K(d) of 436 nm and a stoichiometry of about 0.28 mol of AIIt/mol of fibrin monomer. The binding of AIIt to fibrin was not dependent on the C-terminal lysines of the p11 subunit. Furthermore, in the presence of plasminogen, the binding of AIIt to fibrin was increased to about 1.3 mol of AIIt/mol of fibrin monomer, suggesting that AIIt and plasminogen do not compete for identical sites on fibrin. Immunohistochemical identification of p36 and p11 subunits of AIIt in a pathological clot provides important evidence for its role as a physiological fibrinolytic regulator. These results suggest that AIIt may play a key role in the regulation of plasmin activity on the fibrin clot surface.