gebhart/patrepeval huggingface dataset:
Improved serodiagnosis of non-A, non-B hepatitis by an assay detecting antibody to hepatitis C virus core antigen (1992)

We examined sequential serum samples from 12 patients with well-characterized posttransfusion non-A, non-B hepatitis who had an acute, resolving self-limited type of clinical course for the presence of antibody to the hepatitis C virus nucleocapsid (core) protein (p22) expressed by a recombinant baculovirus. These sera were simultaneously examined for antibody to the hepatitis C virus nonstructural protein (C100-3) that is presently used for blood screening worldwide. In three patients, both anti-p22 and anti-C100-3 antibodies were detected, but anti-p22 was detected much earlier. In four patients, only anti-p22 was detected. Two other patients were considered to be hepatitis C virus carriers who had been already infected with hepatitis C virus. In one patient, only anti-C100-3 was detected, and it was transient. In two patients, neither antibody was detected. Anti-p22 was detected in at least one of eight samples of transfused blood. Of the nine samples of donated blood that were positive for anti-p22, only four were positive for anti-C100-3. This new assay detecting the antibody to the p22 protein is thus useful for the serodiagnosis of non-A, non-B hepatitis in the acute phase and for blood screening.
A programmable BIST core for embedded DRAM (1999)

The programmable BIST design presented here supports various test modes using a simple controller. With the March C algorithm, the BIST circuit's overhead is under 1.3% for a 1-Mbit DRAM and under 0.3% for a 16-Mbit DRAM. The BIST design presented for embedded DRAM supports built-in self-diagnosis by feeding error information to the external tester. Moreover, using a specific test sequence, it can test for critical timing faults, reducing tester time for ac parametric test. The design supports wafer test, pre-burn-in test, burn-in, and final test. It is field-programmable; the user can program test algorithms using predetermined test elements (such as march elements, surround test elements, and refresh modes). The user can optimize the hardware for a specific embedded DRAM with a set of predetermined test elements. Our design is different from the microprogram-controlled BIST described by J. Dreibelbis et al. (1998) which has greater flexibility but higher overhead. Because our design begins at the register-transfer language level, test element insertion (for higher test coverage) and deletion (for lower hardware overhead are relatively easy.
A CMOS distributed amplifier with active input balun using GBW and linearity enhancing techniques (2011)

A CMOS highly linear 818 GHz-GBW distributed amplifier (DA) with distributed active input balun is presented. Each g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> cell within the DA employs dual-output 2-stage g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> topology that improves gain and linearity without adversely affecting bandwidth and power. Fabricated in a 65 nm LP CMOS process, the 0.9 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> DA achieves 22 dB of gain and 10 dBm of P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1dB</sub> while consuming 97 mW from a 1.3 V supply. A distributed balun using the same g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> cell achieves >;70 GHz bandwidth and 4 dB gain with 19.5 mW power consumption from 1.3 V supply.
Combined nanomechanical and nanomagnetic analysis of magnetoelectric memories (2012)

Magneto-electro-elastic and multiferroic materials can be combined in appealing nanostructures characterized by the coexistence and coupling of electric, magnetic, and mechanical phases with potential applications in novel multifunctional devices. Here, we derive a theory for nonvolatile room-temperature memory elements composed of magnetostrictive nanoparticles embedded in a piezoelectric matrix: two stable orthogonal magnetization states are obtained by the competition of anisotropy and external magnetic polarization. The innovative nontoggle switching between the states is modeled by a thorough combination of the nanomechanical Eshelby approach with the nanomagnetic Landau-Lifshitz-Gilbert formalism, yielding a robust picture of the dynamical behavior and allowing the improvement of the energetic efficiency.
Persistent Memory Transactions (2018)

This paper presents a comprehensive analysis of performance trade offs between implementation choices for transaction runtime systems on persistent memory. We compare three implementations of transaction runtimes: undo logging, redo logging, and copy-on-write. We also present a memory allocator that plugs into these runtimes. Our microbenchmark based evaluation focuses on understanding the interplay between various factors that contribute to performance differences between the three runtimes -- read/write access patterns of workloads, size of the persistence domain (portion of the memory hierarchy where the data is effectively persistent), cache locality, and transaction runtime bookkeeping overheads. No single runtime emerges as a clear winner. We confirm our analysis in more realistic settings of three "real world" applications we developed with our transactional API: (i) a key-value store we implemented from scratch, (ii) a SQLite port, and (iii) a persistified version of memcached, a popular key-value store. These findings are not only consistent with our microbenchmark analysis, but also provide additional interesting insights into other factors (e.g. effects of multithreading and synchronization) that affect application performance.
Mutation of the important Tyr-33 residue of chicken avidin: functional and structural consequences (2003)

The strong interaction between avidin and biotin is so tight (dissociation constant 10(-15) M) that conditions usually sufficient for protein denaturing fail to dislodge biotin from the avidin-biotin complex. This kind of irreversible binding hinders the use of avidin in applications such as affinity purification or protein immobilization. To address this concern, we have constructed a series of mutants of the strategically positioned Tyr-33 in order to study the role of this residue in biotin binding, and to create avidin variants with more reversible ligand-binding properties. Unexpectedly, an avidin mutant in which Tyr-33 was replaced with phenylalanine (Avm-Y33F) displayed similar biotin-binding characteristics to the native avidin, indicating that the hydrogen bond formed between the hydroxy group of Tyr-33 and the carbonyl oxygen of biotin is not as important for the tight binding of biotin as previously suggested. In terms of the reversibility of biotin binding, Avm-Y33H was the most successful substitution constructed in this study. Interestingly, the binding of this mutant exhibited clear pH-dependence, since at neutral pH it bound to the biotin surface in an irreversible fashion, whereas, at pH 9, 50% of the bound protein could be released with free biotin. Furthermore, although Tyr-33 is located relatively distant from the monomer-monomer interfaces, the mutagenesis of this residue also weakened the quaternary structure of avidin, indicating that the high ligand binding and the high stability of avidin have evolved together and it is difficult to modify one without affecting the other.
N‐terminal characterization of the <i>Bordetella pertussis</i> filamentous haemagglutinin (1998)

The major adhesin of Bordetella pertussis, filamentous haemagglutinin (FHA), is produced and secreted at high levels by the bacterium. Mature FHA derives from a large precursor, FhaB, that undergoes several post-translational maturations. In this work, we demonstrate by site-directed mutagenesis that the N-terminal signal peptide of FHA is composed of 71 amino acids, including a 22-residue-long 'N-terminal extension' sequence. This sequence, although highly conserved in various other secretory proteins, does not appear to play an essential part in FHA secretion, as shown by deletion mutagenesis. The entire N-terminal signal region of FhaB is removed in the course of secretion by proteolytic cleavage at a site that corresponds to a Lep signal peptidase recognition sequence. After this maturation, the N-terminal glutamine residue is modified to a pyroglutamate residue. This modification is not crucial for heparin binding, haemagglutination or secretion. Interestingly, however, the modification is absent from Escherichia coli secreted FHA derivatives. In addition, it is dependent in B. pertussis on the presence of all three cysteines contained in the signal peptide of FhaB. These observations suggest that it does not occur spontaneously but perhaps requires a specific enzymatic machinery.
FRUDP: A Reliable Data Transport Protocol for Aeronautical Ad Hoc Networks (2018)

In this paper, we cope with the reliable and efficient data transfer problem in aeronautical ad hoc networks (AANETs). AANETs are different from terrestrial ad hoc networks and these distinctions feature AANETs with large propagation delay, highly dynamic network topology, and high error probability, which pose many new challenges for data transfer in such environments. In this paper, we propose a protocol, called FRUDP, which combines reliable UDP and fountain code to achieve reliable and efficient data transfer in AANETs. It employs Raptor codes to recover from data losses to mitigate retransmission caused by high channel losses in AANETs. A code rate determining algorithm is developed to estimate the redundancy on the fly by taking into full consideration the time-varying aeronautical network conditions. Moreover, the improved selective negative acknowledgment scheme is utilized to solve the bandwidth asymmetry problem in AANETs and a congestion control scheme is deployed to decouple congestion decisions from packet losses in order to avoid the erroneous congestion decisions due to frequent link handoffs. The proposed FRUDP is fully implemented directly on top of UDP in Linux and examined over a variety of emulation network environments. The experimental results show that FRUDP is suitable for reliable and efficient data transfer service in AANETs.
Miniature atomic clock for space applications (2015)

This paper presents a novel architecture for a high performance atomic clock based on the use of miniature optical whispering gallery mode (WGM) resonators. Following the approach of stabilizing a laser local oscillator to an optical transition in an atom or ion, as used in advanced atomic clock, a semiconductor laser is used for stabilization to the D<sub>1</sub> line of Rb atoms, held in a small vapor cell. The laser is self-injection locked to a WGM resonator to reduce its linewidth. To produce the RF output of the clock, a second WGM resonator excited with a second cw semiconductor laser produces an optical frequency comb that is demodulated on a fast photodiode. Locking the resonator that generates the frequency comb to the laser stabilized to the Rb transition transfers the stability of the atomic transition to the RF output of the clock. In this way, a miniature all-optical atomic clock is realized. Details of the operation of the clock and application of the architecture to other atomic systems, such as a ytterbium ion, will be described.
Tumor-Targeting with Novel Non-Benzoyl 6-Substituted Straight Chain Pyrrolo[2,3-<i>d</i>]pyrimidine Antifolates via Cellular Uptake by Folate Receptor α and Inhibition of de Novo Purine Nucleotide Biosynthesis (2013)

A new series of 6-substituted straight side chain pyrrolo[2,3-d]pyrimidines 3a-d with varying chain lengths (n = 5-8) was designed and synthesized as part of our program to provide targeted antitumor agents with folate receptor (FR) cellular uptake specificity and glycinamide ribonucleotide formyltransferase (GARFTase) inhibition. Carboxylic acids 4a-d were converted to the acid chlorides and reacted with diazomethane, followed by 48% HBr to generate the α-bromomethylketones 5a-d. Condensation of 2,4-diamino-6-hydroxypyrimidine 6 with 5a-d afforded the 6-substituted pyrrolo[2,3-d]pyrimidines 7a-d. Hydrolysis and subsequent coupling with diethyl l-glutamate and saponification afforded target compounds 3a-d. Compounds 3b-d showed selective cellular uptake via FRα and -β, associated with high affinity binding and inhibition of de novo purine nucleotide biosynthesis via GARFTase, resulting in potent inhibition against FR-expressing Chinese hamster cells and human KB tumor cells in culture. Our studies establish, for the first time, that a side chain benzoyl group is not essential for tumor-selective drug uptake by FRα.
A study of radial error propagation and self-servowriting in disk drives (2002)

In this paper, the present state of the art in self servowriting of disk drives is discussed. Servowriting is a process whereby the position burst information of the track is written onto the disk by means of a apparatus known as a servowriter. Since servowriters are expensive machinery, it is desired to maximize throughput on the factory floor by minimizing the time needed for servowriting the drive. Self servowriting is a process whereby this is accomplished without a servowriter by using the servo information from a previously written track as a reference (seed) for writing the burst information on the remaining tracks. An obstacle to this process is radial error propagation, whereby the tracking errors buildup causing distortion from circularity and variable track spacing. The problem and potential solutions in this process are discussed and verified by means of simulation.
Silicon Nitride Thin Films for Nanofluidic Device Fabrication (2016)

Silicon nitride is a ubiquitous and well-established nanofabrication material with a host of favourable properties for creating nanofluidic devices with a range of compelling designs that offer extraordinary discovery potential. Nanochannels formed between two thin silicon nitride windows can open up vistas for exploration by freeing transmission electron microscopy to interrogate static structures and structural dynamics in liquid-based samples. Nanopores present a strikingly different architecture—nanofluidic channels through a silicon nitride membrane—and are one of the most promising tools to emerge in biophysics and bioanalysis, offering outstanding capabilities for single molecule sensing. The constrained environments in such nanofluidic devices make surface chemistry a vital design and performance consideration. Silicon nitride has a rich and complex surface chemistry that, while too often formidable, can be tamed with new, robust surface functionalization approaches. We will explore how a simple structural element—a ∼100 nm-thick silicon nitride window—can be used to fabricate devices to wrest unprecedented insights from the nanoscale world. We will detail the intricacies of native silicon nitride surface chemistry, present surface chemical modification routes that leverage the richness of available surface moieties, and examine the effect of engineered chemical surface functionality on nanofluidic device character and performance.
A seminaphthofluorescein-based fluorescent chemodosimeter for the highly selective detection of cysteine (2012)

A fluorescent chemodosimeter for cysteine detection was developed based on a tandem conjugate addition and intramolecular cyclization reaction. The method exhibited an excellent selectivity for cysteine over other biothiols such as homocysteine and glutathione.
Controlling Electron Trap Depth To Enhance Optical Properties of Persistent Luminescence Nanoparticles for In Vivo Imaging (2011)

Focusing on the use of nanophosphors for in vivo imaging and diagnosis applications, we used thermally stimulated luminescence (TSL) measurements to study the influence of trivalent lanthanide Ln(3+) (Ln = Dy, Pr, Ce, Nd) electron traps on the optical properties of Mn(2+)-doped diopside-based persistent luminescence nanoparticles. This work reveals that Pr(3+) is the most suitable Ln(3+) electron trap in the diopside lattice, providing optimal trap depth for room temperature afterglow and resulting in the most intense luminescence decay curve after X-ray irradiation. This luminescence dependency toward the electron trap is maintained through additional doping with Eu(2+), allowing UV-light excitation, critical for bioimaging applications in living animals. We finally identify a novel composition (CaMgSi(2)O(6):Eu(2+),Mn(2+),Pr(3+)) for in vivo imaging, displaying a strong near-infrared afterglow centered on 685 nm, and present evidence that intravenous injection of such persistent luminescence nanoparticles in mice allows not only improved but highly sensitive detection through living tissues.
ChemInform Abstract: A Facile Preparation of Imidazolinium Chlorides. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
New developments in flavivirus vaccines with special attention to yellow fever (2005)

Traditional approaches to flavivirus vaccines are still employed, while recent advancements in biotechnology produced new approaches to vaccine design, such as recombinant live virus, subunit and DNA vaccines. Live chimeric vaccines against dengue, Japanese encephalitis and West Nile based on yellow fever 17D virus (ChimeriVax) are in phase I/II trials, with encouraging results. Other chimeric dengue, tick-borne encephalitis and West Nile virus candidates were developed based on attenuated dengue backbones. To further reduce the impact of flavivirus diseases, vaccination policies and vector control programs in affected countries require revision.
Nyquist-exceeding high voxel rate acquisition in mesoscopic multiphoton microscopy for full-field submicron resolution resolvability (2021)

The Nyquist-Shannon criterion has never been realized in a laser-scanning mesoscopic multiphoton microscope (MPM) with a large field-of-view (FOV)-resolution ratio, especially when employing a high-frequency resonant-raster-scanning. With a high optical resolution nature, a current mesoscopic-MPM either neglects the criterion and degrades the digital resolution to twice the pixel size, or reduces the FOV and/or the raster-scanning speed to avoid <i>aliasing</i>. We introduce a Nyquist figure-of-merit (NFOM) parameter to characterize a laser-scanning MPM in terms of its optical-resolution retrieving ability. Based on NFOM, we define the maximum aliasing-free FOV, and subsequently, a cross-over excitation wavelength, below which the FOV becomes NFOM-constrained irrespective of an optimized optical design. We validate our idea in a custom-built mesoscopic-MPM with millimeter-scale FOV yielding an ultra-high FOV-resolution ratio of >3,000, while securing up-to a 1.6 mm Nyquist-satisfied aliasing-free FOV, a ∼400 nm lateral resolution, and a 70 M/s effective voxel-sampling rate, all at the same time.
The synthesis and chemical reactivity of 6‐selenoguanosine and certain related derivatives (1971)

Abstract The synthesis of 6‐selenoguanosine ( 2 ) has been accomplished by a nucleophilic displacement of the chloro group from 2‐amino‐6‐chloro‐9‐(β‐ D ‐ribofuranosyl)purine ( 1 ) with either selenourea or sodium hydrogen selenide. Treatment of 2 with Raney nickel has revealed that the seleno group can be removed much easier under these conditions than the corresponding mercapto group. Alkylation of 2 with several alkylating agents occurred at the exocyclic 6‐seleno group to furnish several 6‐alkylseleno‐2‐amino‐9‐(β‐ D ‐ribofuranosyl)purines. Nucleophilic displacement of the 6‐benzylseleno group from 2‐amino‐6‐benzylseleno‐9‐(β‐ D ‐ribofuranosyl)purine ( 3c ) with sodium methoxide has been observed to occur at a faster rate than that observed for the corresponding 6‐benzylmercapto derivative. A study on the relative stability between 2 and 6‐seleno‐9‐(β‐ D ‐ribofuranosyl)purine toward basic conditions has revealed that the amino group at position two imparts an increase in stability.
Apoptotic Induction in Transformed Follicular Lymphoma Cells by Bcl-2 Downregulation (1998)

The roles of Bcl-2 protein and the protein ratio of Bcl-2/Bax in regulating cell growth in various lymphoma cell lines were examined. A dose-dependent decrease in Bcl-2 protein expression was observed in the different lymphomas incubated with lipid-incorporated bcl-2 antisense oligonucleotides (L-bcl-2). Growth inhibition was observed in a transformed follicular lymphoma (FL) cell line, which has the t(14;18) translocation and Bcl-2 protein overexpression. One of the mechanisms by which L-bcl-2 growth inhibition is mediated in these transformed FL cells might be through apoptotic induction, because the treated cells had an increased apoptotic index and showed the typical DNA fragmentation. These studies indicate that Bcl-2 protein is critical in the growth regulation of transformed FL cells. L-bcl-2 did not induce growth inhibition in lymphoma cells not expressing Bcl-2 or Bax protein. Thus, the protein ratio of Bcl-2/Bax may also be important in regulating the growth of these lymphomas.
Anti-cancer activity of anti-GLUT1 antibody-targeted polymeric micelles co-loaded with curcumin and doxorubicin (2013)

We showed a dramatic improvement in efficacy between the non-targeted and GLUT1-targeted formulations both in vitro and in vivo. Hence, we confirmed that GLUT1-CUR + DOX micelles are effective and deserve further investigation.
Effect of Generation and Soft Lithography on Semiconducting Dendrimer Lasers (2007)

Conjugated dendrimers are promising optoelectronic materials as their modular architecture enables independent tuning of the optical, electronic, and processing properties. Dendrimer distributed feedback lasers are demonstrated, and an improvement in slope efficiency from 0.3 % to 1.6 % is seen as the dendrimer generation is increased. Simple fabrication of the lasers by soft lithography is also shown, giving a high slope efficiency of 14 %. The combination of high efficiency dendrimer gain media and soft lithographic fabrication techniques makes conjugated dendrimers attractive materials for organic semiconductor lasers.