gebhart/patrepeval huggingface dataset:
Endogenous cleavage of the Arg-379-Ala-380 bond in vitronectin results in a distinct conformational change which ‘buries’ Ser-378, its site of phosphorylation by protein kinase A (1991)

Activation of blood platelets by thrombin was previously shown to specifically release protein kinase A, which in human plasma singles out and phosphorylates one protein, identified as vitronectin. This protein is known to be involved in processes that follow platelet stimulation, specifically, in the binding of heparin (interfering with the heparin-mediated inhibition of thrombin and Factor Xa by antithrombin III), in the growth of endothelial cells and in fibrinolysis. This paper shows that phosphorylation of vitronectin by protein kinase A is stoichiometric (approx. 1 mol/mol), that it is targeted to one site (Ser-378) at the C-terminal edge of the heparin-binding domain, and that it distinguishes between the two physiologically occurring forms of vitronectin: the one-chain (75 kDa) form, and the nicked two-chain (65 + 10 kDa) form, held together by an interchain disulphide bridge. Protein kinase A phosphorylates the one-chain form but not the two-chain form, although Ser-378 and the complete recognition sequence of the kinase are still present in the clipped 65 kDa chain. Cleavage of the Arg-379-Ala-380 bond results therefore in a conformationally distinct form of vitronectin in which Ser-378 is 'buried'. This is demonstrated by our finding that Ser-378 is present in the 65 kDa chain of clipped vitronectin but inaccessible to phosphorylation at physiological pH. Upon binding heparin, the phosphorylation site becomes exposed and able to undergo a stoichiometric phosphorylation at physiological pH.
A RAKE Combining Scheme for an Energy Detection Based Noncoherent OOK Receiver in UWB Impulse Radio Systems (2006)

Ultra-wideband (UWB) impulse radio systems based on non-coherent on-off keying (OOK) energy detection are relatively simpler to implement than their coherent counterparts, because the strict synchronization requirements are relaxed. However, the design challenge is to set a hard decision threshold value after energy detection because the detected energy may vary due to multipath fading and inter-pulse interference (IPI). Moreover, to find and track the starting point of the integration for energy detection, a timing recovery block is needed. This block requires a fairly accurate phase-locked loop (PLL) circuit, the cost of which is prohibitive for a low cost and low power UWB device. In this paper, we propose an orthogonal code sequence with RAKE combining for an energy detection based noncoherent OOK receiver. It uses a RAKE combiner with soft despreading to combat the severe IPI. With this structure, threshold setting for conventional energy detector can be avoided and a larger integration timing offset can be tolerated. Simulation results show that the energy detection based OOK receiver using the proposed orthogonal code sequence and the RAKE combining scheme can improve packet error rate performance significantly in a dense multipath fading channel
Overexpression of human calnexin in yeast improves measles surface glycoprotein solubility (2011)

The limitations of high-level expression of virus surface proteins in yeast are not well understood. The inefficiency of yeast to produce active human virus surface glycoproteins, as well as other mammalian glycoproteins, is usually explained by the inefficient folding of the glycoprotein into its characteristic and functional three-dimensional structure from a random coil. The endoplasmic reticulum (ER) is a highly versatile protein factory that is equipped with chaperones and folding enzymes essential for protein folding. To improve folding and solubility of viral surface glycoprotein, the genes encoding human ER resident chaperones calnexin, calreticulin, immunoglobin binding protein (BiP), protein disulfide isomerase (PDI) and foldase (ERp57) were coexpressed together with hemagglutinin gene from measles virus in the yeast Saccharomyces cerevisiae. The effect of coexpressing chaperones on the total yield of measles virus hemagglutinin (MeH) as well as the intracellular fate of the glycoprotein was determined. Our results demonstrated that coexpression of human calnexin noticeably enhanced the quantity of the soluble glycosylated form of MeH in yeast. The coexpression of human calreticulin-, PDI-, ERp57- and BiP-encoding genes did not improve the quality of recombinant MeH.
Engineered Dengue Virus Domain III Proteins Elicit Cross-Neutralizing Antibody Responses in Mice (2018)

Dengue virus is the most globally prevalent mosquito-transmitted virus. Primary infection with one of four cocirculating serotypes (DENV-1 to -4) causes a febrile illness, but secondary infection with a heterologous serotype can result in severe disease, due in part to antibody-dependent enhancement of infection (ADE). In ADE, cross-reactive but nonneutralizing antibodies, or subprotective levels of neutralizing antibodies, promote uptake of antibody-opsonized virus in Fc-γ receptor-positive cells. Thus, elicitation of broadly neutralizing antibodies (bNAbs), but not nonneutralizing antibodies, is desirable for dengue vaccine development. Domain III of the envelope glycoprotein (EDIII) is targeted by bNAbs and thus is an attractive immunogen. However, immunization with EDIII results in sera with limited neutralization breadth. We developed "resurfaced" EDIII immunogens (rsDIIIs) in which the A/G strand epitope that is targeted by bNAb 4E11 is maintained but less desirable epitopes are masked. RsDIIIs bound 4E11, but not serotype-specific or nonneutralizing antibodies. One rsDIII and, unexpectedly, wild-type (WT) DENV-2 EDIII elicited cross-neutralizing antibody responses against DENV-1 to -3 in mice. While these sera were cross-neutralizing, they were not sufficiently potent to protect AG129 immunocompromised mice at a dose of 200 μl (50% focus reduction neutralization titer [FRNT<sub>50</sub>], ∼1:60 to 1:130) against mouse-adapted DENV-2. Our results provide insight into immunogen design strategies based on EDIII.<b>IMPORTANCE</b> Dengue virus causes approximately 390 million infections per year. Primary infection by one serotype causes a self-limiting febrile illness, but secondary infection by a heterologous serotype can result in severe dengue syndrome, which is characterized by hemorrhagic fever and shock syndrome. This severe disease is thought to arise because of cross-reactive, non- or poorly neutralizing antibodies from the primary infection that are present in serum at the time of secondary infection. These cross-reactive antibodies enhance the infection rather than controlling it. Therefore, induction of a broadly and potently neutralizing antibody response is desirable for dengue vaccine development. Here, we explore a novel strategy for developing immunogens based on domain III of the E glycoprotein, where undesirable epitopes (nonneutralizing or nonconserved) are masked by mutation. This work provides fundamental insight into the immune response to domain III that can be leveraged for future immunogen design.
Thyroid associated orbitopathy (2012)

Thyroid associated orbitopathy, also known as Graves' orbitopathy, is typically a self-limiting autoimmune process associated with dysthyroid states. The clinical presentation may vary from very mild disease to severe irreversible sight-threatening complications. Despite ongoing basic science and clinical research, the pathogenesis and highly effective therapeutic strategies remain elusive. The present article reviews the pathophysiology, clinical presentation, and management of this common, yet poorly understood disease, which remains a challenge to the ophthalmologist.
Disorders of Phagocyte Function (1987)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
Pilot-assisted estimation of mimo fading channel response and achievable data rates (2003)

We analyze the effects of pilot-assisted channel estimation on achievable data rates (lower bound on information capacity) over a frequency flat time-varying channel. Under a block-fading channel model, the effects of the estimation error are evaluated in the case of the estimates being available at the receiver only (open loop) and in the case when the estimates are fed back to the transmitter allowing water pouring transmitter optimization (closed loop). Using a characterization of the effective noise due to estimation error, we analyze the achievable rates as a function of the power allocated to the pilot, the channel coherence time, the background noise level, as well as the number of transmit and receive antennas. The analysis presented here can be used to optimally allocate pilot power for various system and channel operating conditions, and to also determine the effectiveness of closed loop feedback.
Chemotactic peptides modulate adherence of human polymorphonuclear leukocytes to monolayers of cultured endothelial cells. (1986)

We have used a new centrifugation assay to examine the effects of highly purified human C5a and C5a des Arg, as well as effects of N-formyl-methionyl-leucyl-phenylalanine (FMLP), on both the extent and strength of human polymorphonuclear leukocyte (PMN) adherence to monolayers of cultured human umbilical vein endothelial cells. At concentrations that were chemotactic for PMN, C5a (0.1 nM), C5a des Arg (5.0 nM), and FMLP (1.0 nM) significantly reduced the percentage of PMN that adhered to endothelial monolayers. Adherence also was reduced by C5a des Arg that was generated by incubating (37 degrees C, 30 min) fresh human serum with either zymosan or purified C5a. High concentrations of C5a (greater than 1.0 nM) and FMLP (greater than 50 nM) that diminished PMN chemotaxis significantly enhanced the percentage of PMN that adhered tightly to endothelial cells (adherent cells resisted a dislodgment force of 1200 X G). Tight adherence of PMN to endothelial cells also was increased by high concentrations of C5a that were added to human serum in which carboxypeptidase N activity was destroyed by heating (56 degrees C, 30 min), and by C5a that was generated by incubating (37 degrees C, 30 min) fresh human serum with zymosan in the presence of the carboxypeptidase N inhibitor, epsilon-aminocaproic acid. High concentrations of C5a des Arg (up to 80 nM) neither enhanced adherence of PMN to endothelial cells nor decreased PMN migration. Thus, a reciprocal relation exists between PMN migration and PMN adherence to endothelial cells in response to chemotactic factors. At concentrations that are chemotactic for human PMN, C5-derived peptides and FMLP reduce the adherence of PMN to endothelial monolayers. Only at concentrations that decrease PMN migration do C5a and FMLP augment PMN adherence.
Key-Exposure Free Chameleon Hashing and Signatures Based on Discrete Logarithm Systems. (2009)

Chameleon signatures simultaneously provide the properties of nonrepudiation and non-transferability for the signed message. However, the initial constructions of chameleon signatures suffer from the problem of key exposure. This creates a strong disincentive for the recipient to forge signatures, partially undermining the concept of non-transferability. Recently, some specific constructions of discrete logarithm based chameleon hashing and signatures without key exposure are presented, while in the setting of gap Diffile-Hellman groups with pairings. In this paper, we propose the first key-exposure free chameleon hash and signature scheme based on discrete logarithm systems, without using the gap DiffileHellman groups. This provides more flexible constructions of efficient key-exposure free chameleon hash and signature schemes. Moreover, one distinguishing advantage of the resulting chameleon signature scheme is that the property of “message hiding” or “message recovery” can be achieved freely by the signer, i.e., the signer can efficiently prove which message was the original one if he desires.
Effect of side‐chain structure on inhibition of yeast fatty‐acid synthase by cerulenin analogues (1993)

Yeast fatty-acid synthase (FAS) inhibition by cerulenin analogs with varying side-chain lengths was compared with that of cerulenin, tetrahydrocerulenin and iodoacetamide. Although inhibition by cerulenin was the highest, the analogs having (E,E)-delta 7,10 double bonds showed high inhibition. This strongly suggests that the (E,E)-delta 7,10 double bonds play an important role in the interaction of the inhibitors with the enzyme. It was suggested that the size of the hydrophobic cavity in the condensing enzyme terminates fatty-acid chain elongation by decreasing inhibition by the C18 analog. Like cerulenin itself, the shortest analog (C6) did not induce malonyl-CoA decarboxylase activity.
Natural Language Processing in the FAQ Finder System: Results and Prospects (1997)

This paper describes some recent results regarding the employment of natural language processing techniques in the FAQ Finder system. FAQ Finder is a natural language question-answering system that uses files of frequently-asked questions as its knowledge base. Unlike AI questionanswering systems that focus on the generation of new answers, FAQ Finder retrieves existing ones found in frequently-asked question files. FAQ Finder uses a combination of statistical and natural language techniques to match user questions against known question/answer pairs from FAQ files. We strove in our experiments to identify the contribution of these techniques to the overall success of the system. One unexpected result was that our parsing technique was not contributing as much to the system&apos;s performance as we expected. We discuss some of the reasons why this may have been the case, and describe further natural language processing research designed to address the system&apos;s current needs. Introduction ...
Influence of Controlled Fluid Shear on Nucleation Rates in Glycine Aqueous Solutions (2014)

The nucleation of glycine was investigated in supersaturated aqueous solutions exposed to well-controlled fluid shear under isothermal conditions. Shear rates between 25 s–1 and 1000 s–1 were studied using Couette and capillary flow devices. Induction times were obtained from imaging, transmission and scattering measurements, or visual monitoring. Great care was taken to eliminate any seeding in order to avoid secondary nucleation preceding formation of first crystals through primary nucleation. The observed induction times of sheared solutions were considerably lower than those of unsheared solutions. Increasing the average shear rate was found to reduce the mean induction time through a power law relationship. A detailed statistical analysis showed that the number of experimental repetitions used was sufficient to obtain statistically significant trends for the system studied. Induction times appeared to closely follow a probability distribution based on a previously published model of Jiang and ter Horst. Using their model, where the induction time is related to the rate of formation of primary nuclei and the time it takes them to grow to the size where the secondary nucleation becomes significant, it was found that both the primary nucleation rate and the growth time were strongly dependent on the shear rate imposed.
Xanthone 1,4-dihydropyridine derivatives with a potent selective bradycardic effect. (1990)

A series of xanthone 1,4-dihydropyridine derivatives were prepared. The compounds were evaluated for inotropic, chronotropic and calcium antagonistic properties. The tested compounds are weak calcium antagonists but exert potent selective bradycardic effects.
Event Prediction in Big Data Era: A Systematic Survey (2020)

Events are occurrences in specific locations, time, and semantics that nontrivially impact either our society or the nature, such as earthquakes, civil unrest, system failures, pandemics, and crimes. It is highly desirable to be able to anticipate the occurrence of such events in advance in order to reduce the potential social upheaval and damage caused. Event prediction, which has traditionally been prohibitively challenging, is now becoming a viable option in the big data era and is thus experiencing rapid growth, also thanks to advances in high performance computers and new Artificial Intelligence techniques. There is a large amount of existing work that focuses on addressing the challenges involved, including heterogeneous multi-faceted outputs, complex (e.g., spatial, temporal, and semantic) dependencies, and streaming data feeds. Due to the strong interdisciplinary nature of event prediction problems, most existing event prediction methods were initially designed to deal with specific application domains, though the techniques and evaluation procedures utilized are usually generalizable across different domains. However, it is imperative yet difficult to cross-reference the techniques across different domains, given the absence of a comprehensive literature survey for event prediction. This paper aims to provide a systematic and comprehensive survey of the technologies, applications, and evaluations of event prediction in the big data era. First, systematic categorization and summary of existing techniques are presented, which facilitate domain experts’ searches for suitable techniques and help model developers consolidate their research at the frontiers. Then, comprehensive categorization and summary of major application domains are provided to introduce wider applications to model developers to help them expand the impacts of their research. Evaluation metrics and procedures are summarized and standardized to unify the understanding of model performance among stakeholders, model developers, and domain experts in various application domains. Finally, open problems and future directions for this promising and important domain are elucidated and discussed.
On the Energy-Efficiency of Hybrid Analog–Digital Transceivers for Single- and Multi-Carrier Large Antenna Array Systems (2017)

Hybrid analog-digital transceivers are employed with the view to reduce the hardware complexity and the energy consumption in millimeter wave/large antenna array systems by reducing the number of their radio frequency (RF) chains. However, the analog processing network requires power for its operation and it further introduces power losses, dependent on the number of the transceiver antennas and RF chains that have to be compensated. Thus, the reduction in the power consumption is usually much less than it is expected and given that the hybrid solutions present in general inferior spectral efficiency than a fully digital one, it is possible for the former to be less energy efficient than the latter in several cases. Existing approaches propose hybrid solutions that maximize the spectral efficiency of the system without providing any insight on their energy requirements/efficiency. To that end, in this paper, a novel algorithmic framework is developed based on which energy efficient hybrid transceiver designs are derived and their performance is examined with respect to the number of RF chains and antennas. Solutions are proposed for fully and partially connected hybrid architectures and for both single- and multi-carrier systems under the orthogonal frequency division multiplexing modulation. Simulations and theoretical results provide insight on the cases, where a hybrid transceiver is the most energy efficient solution or not.
Phosphine-Catalyzed Regiospecific Allylic Amination and Dynamic Kinetic Resolution of Morita−Baylis−Hillman Acetates (2004)

Exposure of Morita-Baylis-Hillman (MBH) acetates to tertiary phosphine catalysts in the presence of 4,5-dichlorophthalimide enables regiospecific allylic substitution through a tandem S(N)2'-S(N)2' mechanism. Through the use of the chiral phosphine catalyst (R)-Cl-MeO-BIPHEP, chiral racemic MBH acetate 4 is converted to the corresponding allylic amination product in 80% yield and 56% enantiomeric excess, thus establishing the feasibility of dynamic kinetic resolution. [reaction: see text]
Ruthenium red inhibits mitochondrial Na+ and K+ uniports induced by magnesium removal. (1990)

Removal of bound magnesium from the outer surface of the inner mitochondrial membrane opens up a Na+ and Li+ selective electrophoretic uniport pathway whereas simultaneous depletion of intramitochondrial magnesium induces an electrogenic K+ flux as well. In order to clarify the nature of these cation movements we tested the effect of ruthenium red, a potent and specific inhibitor of the mitochondrial Ca2+ uniporter on different Na+ and K+ uniport-associated phenomena. Ruthenium red efficiently inhibited mitochondrial swelling and depolarization induced by either EDTA in a NaCl-based medium (Na+ uniport) or by EDTA plus A23187 in a KCl-based medium (K+ uniport). For both cation uniports half-maximal inhibition was attained at a ruthenium red concentration as low as 40 nM. Complete inhibition was found above 200 nM. Neither the Na+/H+ nor the K+/H+ exchange was affected by ruthenium red. In light of these observations the possibility is raised that the electrogenic Na+ and K+ fluxes provoked by magnesium reduction or depletion may be mediated through the Ca2+ uniporter. It is suggested that intactness of the mitochondrial magnesium pools is necessary for maintaining the Ca2+ selectivity of the Ca2+ uniporter, and alterations of the membrane-associated magnesium content would make this transport route available also for monovalent cations.
Antibodies to Capsular Polysaccharides of Group B<i>Streptococcus</i>in Pregnant Canadian Women: Relationship to Colonization Status and Infection in the Neonate (2001)

In a cohort study of 1207 pregnant women in Alberta, Canada, the serotype distributions of vaginal-rectal group B Streptococcus (GBS) isolates were compared with all isolates from neonates with invasive GBS disease identified by population-based surveillance. Serum concentrations of Ia, Ib, II, III, and V capsular polysaccharide (CPS)-specific IgG also were determined, according to serotype of the vaginal-rectal colonizing GBS strain. GBS colonization was detected in 19.5% (235 of 1207) of women. Serotype III accounted for 20.6% (48 of 233) of colonizing strains available for typing but for 37% (27 of 73) of invasive isolates from neonates (P<.01). Maternal colonization with type III was least likely to be associated with moderate concentrations of III CPS-specific IgG. Serotype III GBS is more invasive than other serotypes in this population; this may be due, at least in part, to poor maternal type III CPS-specific antibody response.
Studies on the thermotropic liquid crystalline polycarbonates. III. Synthesis and properties of fully aromatic liquid crystalline polycarbonates (1993)

Abstract Four series of fully aromatic thermotropic liquid crystalline polycarbonates were prepared by melt polycondensation from various novel phenylene diphenyl dicarbonates with monomers, such as hydroquinone, methylhydroquinone, chlorohydroquinone, resorcinol, bisphenol A, 4,4′‐dihydroxydiphenylsulfone, or phenylhydroquinone, respectively. The thermotropic liquid crystalline properties were studied by polarizing microscope with a heating stage, differential scanning calorimeter (DSC), and wide‐angle x‐ray diffraction (WAXD). It was found that the nonlinearity of the carbonate group was compensated by resorcinol (1,3‐phenylene unit), a bent shape unit. Nematic melts were found for the resulting polycarbonates. © 1993 John Wiley & Sons, Inc.