gebhart/patrepeval huggingface dataset:
Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics (2019)

We present an improved version of the ABSINTH implicit solvation model and force field paradigm (termed ABSINTH-C) by incorporating a grid-based term that bootstraps against experimentally derived and computationally optimized conformational statistics for blocked amino acids. These statistics provide high-resolution descriptions of the intrinsic backbone dihedral angle preferences for all 20 amino acids. The original ABSINTH model generates Ramachandran plots that are too shallow in terms of the basin structures and too permissive in terms of dihedral angle preferences. We bootstrap against the reference optimized landscapes and incorporate CMAP-like residue-specific terms that help us reproduce the intrinsic dihedral angle preferences of individual amino acids. These corrections that lead to ABSINTH-C are achieved by balancing the incorporation of the new residue-specific terms with the accuracies inherent to the original ABSINTH model. We demonstrate the robustness of ABSINTH-C through a series of examples to highlight the preservation of accuracies as well as examples that demonstrate the improvements. Our efforts show how the recent experimentally derived and computationally optimized coil-library landscapes can be used as a touchstone for quantifying errors and making improvements to molecular mechanics force fields.
Subword-level Composition Functions for Learning Word Embeddings (2018)

Subword-level information is crucial for capturing the meaning and morphology of words, especially for out-of-vocabulary entries. We propose CNN-and RNN-based subword-level composition functions for learning word embeddings, and systematically compare them with popular word-level and subword-level models (Skip-Gram and FastText). Additionally, we propose a hybrid training scheme in which a pure subword-level model is trained jointly with a conventional word-level embedding model based on lookup-tables. This increases the fitness of all types of subwordlevel word embeddings; the word-level embeddings can be discarded after training, leaving only compact subword-level representation with much smaller data volume. We evaluate these embeddings on a set of intrinsic and extrinsic tasks, showing that subwordlevel models have advantage on tasks related to morphology and datasets with high OOV rate, and can be combined with other types of embeddings.
The Hunt for New Tuberculosis Vaccines: Anti-TB Immunity and Rational Design of Vaccines (2001)

Tuberculosis (TB) remains to be a leading infectious cause of death worldwide. Apparently, the current BCG vaccine that has been used for 80 years, has failed to control the TB epidemic. Hunting for improved TB vaccine formulations represents a daunting task to TB research community. Anti-TB host defense requires T cell-mediated immunity and we are in desperate need of enhanced understanding of how to develop a new generation of TB vaccines that are able to provoke potent and long-lasting protective cell-mediated immunity, different from almost all of the vaccines currently in use. It is of importance to successful TB vaccine development to identify the key cellular and molecular events governing the generation of anti-TB immunity, but unfortunately little has been understood as to why 90% of infected humans never develop active TB. However, waiting would not help us to win the battle and an ever-intensifying effort is being made to develop various new formulations according to the immunology that we have been learning, in large part, from experimental models. This review article attempts to unite the current understanding of anti-TB immunity with the rational design of anti-TB vaccines. It examines what may have confounded the immunogenicity of current BCG vaccine and the major obstacles to successful development of TB vaccines. It also discusses about antigen presentation, activation of Th1 and Tc1 cells, anti-TB immune effectors and the generation of memory T cells. The vaccine section describes four types of major TB vaccines under development: mycobacterial-, subunit-, plasmid DNA- and viral-based vaccines. A special section is dedicated to the rationale and current design of cytokine-based adjuvant formulations for TB vaccines. We also take this opportunity to introduce our recent development in cytokine transgene adjuvanted BCG vaccination and recombinant adenoviral-based TB vaccines.
Continuous synthesis of two protein-kinase-C-related proteins after down-regulation by phorbol esters. (1988)

The phorbol 12-myristate 13-acetate (PMA)-dependent down-regulation of immunoprecipitable protein kinase C was studied in human breast cancer cell lines that display different growth inhibitions toward the tumor promoter. PMA induces translocation of [35S]methionine-prelabeled cytosolic protein kinase C to membranes, followed by complete degradation of the enzyme (t1/2, 2 hr). PMA does not affect the protein kinase C synthesis; 20-80% of total protein kinase C of control cells was still immunoprecipitable as membrane-bound 74- and 80-kDa protein kinase C-related polypeptides if cells were allowed to incorporate [35S]methionine during PMA exposure for greater than 6 hr. These two proteins lack protein kinase activity and phorbol ester binding but reveal V8 peptide patterns identical to the active forms of protein kinase C (77/80 kDa) of PMA-untreated cells. The amounts of the immunoprecipitable membrane-bound 80-kDa protein kinase C-related polypeptide synthesized during the prolonged PMA treatment appear to inversely correlate with the extent of PMA-mediated growth inhibition of the respective human breast cancer cell line. These data suggest that after homologous down-regulation, functional protein kinase C (77/80 kDa) is replaced by a population of membrane-associated but enzymatically inactive protein kinase C-related polypeptides (74/80 kDa).
Requirements for NADPH oxidase and myeloperoxidase in neutrophil extracellular trap formation differ depending on the stimulus (2012)

Release of NETs by neutrophils is linked with immune protection and host damage. A variety of stimuli promotes NET formation. However, findings from different laboratories often vary, and it is possible that more than one mechanism of NET formation exists. NET formation induced by PMA has been shown to require NADPH oxidase activity, and there is evidence that the granule enzyme MPO is also involved. However, requirements for NADPH oxidase or MPO with other stimuli are less well established. We investigated the role of oxidants in NET formation by human neutrophils induced with PMA, several bacterial genera, and the calcium ionophore ionomycin. With the use of inhibitors of the NADPH oxidase and MPO, oxidant scavengers, and cells from a MPO-deficient individual, we observed that requirements for oxidant generation depend on the stimulus. NADPH oxidase activity was required with PMA and bacterial stimulation but not with ionomycin. Whereas MPO was required for efficient NET formation with PMA, incubation with bacteria induced NETs independently of MPO activity. Although the specific mechanisms whereby oxidants participate in NET formation remain to be clarified, it is possible that other stimuli that mobilize calcium act like ionomycin via an oxidant-independent mechanism, and it cannot be inferred from results with PMA that MPO is required with more physiological stimuli.
A self-timed method to minimize spurious transitions in low power CMOS circuits (2002)

Spurious transitions and associated power are inherent disadvantages of a static logic design. Though pre-charged dynamic logic has the advantage of one valid transition per clock cycle, it has a considerable power overhead . In this paper, a low power self-timed double pass-gate logic (DPL) circuit combining the merits of dynamic and static logic families is proposed to minimize power in a 32-bit carry look-ahead static adder. This technique can be applied to any static circuit implementation, at any level of design hierarchy where power and performance are important. For a 100 MHz, 32-bit adder implementation in a 0.6 /spl mu/m CMOS technology results on output spurious transition density, total power dissipation and energy efficiency for different loads are presented.
<title>Optical waveguides from low-melting-temperature glasses with organic dyes</title> (1993)

Polymers and, more recently, sol-gel glasses are generally regarded as the better hosts for optical devices which rely on organic dye molecules as the active component. Most traditional low melting temperature glasses are too easily attacked by water to be a serious alternative; however, a novel composition family based on SnF<SUB>2</SUB> eliminates many of the shortcomings of other glasses with similar viscosity properties and they seem to have an affinity for dissolving many organic dye molecules. The properties of these glasses and the ongoing efforts to demonstrate the feasibility of fabricating guided wave structures are described.
Assessing the Nitrogen and Carbon Nucleophilicities of 2-Aminothiazoles through Coupling with Superelectrophilic 4,6-Dinitrobenzofuroxan (2006)

The reactions of 2-aminothiazole (1a), 4-methyl-2-aminothiazole (1b), and 4,5-dimethyl-2-aminothiazole (1c) with superelectrophilic 4,6-dinitrobenzofuroxan (DNBF) have been studied in acetonitrile and a 70/30 (v/v) H2O/Me2SO mixture. While exhibiting a somewhat higher nitrogen basicity than that of anilines, 1a and 1b do not react as nitrogen nucleophiles, affording exclusively anionic C-bonded sigma-adducts (C-1a and C-1b) through electrophilic S(E)Ar substitution of the thiazole ring by DNBF. Only in the case of the 4,5-dimethyl derivative 1c a N-adduct, N-1c, was obtained. On the basis of 1H-15N correlations, it is demonstrated that this adduct, N-1c;1c,H+, is derived from DNBF addition at the exocyclic amino group and not at the endocyclic nitrogen center of 1c. Rate constants have been determined in the two solvents for the formation of the adducts, revealing a reactivity sequence which accounts well for the finding that 1a and 1b behave preferentially as carbon rather than nitrogen nucleophiles. The enaminic character of these thiazoles is assessed through an estimation of the pKa values for their C-protonation in aqueous solution as well as through a positioning of their reactivity on the nucleophilicity scale recently developed by Mayr et al. (Acc. Chem. Res. 2003, 36, 66). With N values of the order of 6.80 and 5.56, 1b and 1a have a carbon nucleophilicity comparable to that of N-methylindole and indole, respectively.
A High Performance Co-design of 26 nm 64 Gb MLC NAND Flash Memory using the Dedicated NAND Flash Controller (2011)

It is progressing as new advents and remarkable developments of mobile device every year. On the upper line reason, NAND FLASH large density memory demands which can be stored into portable devices have been dramatically increasing. Therefore, the cell size of the NAND Flash memory has been scaled down by merely 50% and has been doubling density each per year. [1] However, side effects have arisen the cell distribution and reliability characteristics related to coupling interference, channel disturbance, floating gate electron retention, write-erase cycling owing to shrinking around 20㎚ technology. Also, FLASH controller to manage shrink effect leads to speed and current issues. In this paper, It will be introduced to solve cycling, retention and fail bit problems of sub-deep micron shrink such as Virtual negative read used in moving read, randomization. The characteristics of retention, cycling and program performance have 3 K per 1 year and 12.7 MB/s respectively. And device size is 179.32 ㎟ (16.79 ㎜ × 10.68 ㎜) in 3 metal 26 ㎚ CMOS.
New Pain Guideline for Older Patients (2009)

PHYSICIANS TREATING PATIENTS aged 75 years or older for chronic pain should avoid using nonsteroidal anti-inflammatory drugs (NSAIDs), according to an updated guideline issued by the American Geriatrics Society (AGS) in May. NSAIDsshouldbe“consideredrarely, and with extreme caution, in highly selected individuals,” the new guideline states, contradicting the AGS’s 2002 guideline.Thenewrecommendationreflects evidence about serious cardiovascular and gastrointestinal tract risks associated with this class of drugs that has emerged since 2002, said Bruce Ferrell, MD, chair of the panel that created new guideline and professor of medicine and geriatrics at the University of California, LosAngeles.Thesedrugsalsomaycomplicate the treatment of common conditions in this population, such as hypertension and congestive heart failure. Acetaminophen remains the initial therapy of choice, though the guideline cautions against using it in patients with liver conditions. But it encourages physicians to consider opioids for elderly patients with persistent pain. Persistent pain is a common and often undertreated problem in older adults, according to the AGS. Such pain is particularly common among those with degenerative spine conditions, arthritis, nightly leg pain, or those with cancer. But selecting an appropriate analgesic for older patients who may have multiple conditions and who may take several medications requires careful thought. Ferrell notes that nondrug therapies also may be appropriate and have been addressed in previous versions of the guideline. Despiteanimprovedunderstandingof the risks that NSAIDs pose to older patients, including that of gastrointestinal bleeding, these drugs have remained a
Detection of <i>Vibrio cholerae</i> by Real-Time Nucleic Acid Sequence-Based Amplification (2007)

A multitarget molecular beacon-based real-time nucleic acid sequence-based amplification (NASBA) assay for the specific detection of Vibrio cholerae has been developed. The genes encoding the cholera toxin (ctxA), the toxin-coregulated pilus (tcpA; colonization factor), the ctxA toxin regulator (toxR), hemolysin (hlyA), and the 60-kDa chaperonin product (groEL) were selected as target sequences for detection. The beacons for the five different genetic targets were evaluated by serial dilution of RNA from V. cholerae cells. RNase treatment of the nucleic acids eliminated all NASBA, whereas DNase treatment had no effect, showing that RNA and not DNA was amplified. The specificity of the assay was investigated by testing several isolates of V. cholerae, other Vibrio species, and Bacillus cereus, Salmonella enterica, and Escherichia coli strains. The toxR, groEL, and hlyA beacons identified all V. cholerae isolates, whereas the ctxA and tcpA beacons identified the O1 toxigenic clinical isolates. The NASBA assay detected V. cholerae at 50 CFU/ml by using the general marker groEL and tcpA that specifically indicates toxigenic strains. A correlation between cell viability and NASBA was demonstrated for the ctxA, toxR, and hlyA targets. RNA isolated from different environmental water samples spiked with V. cholerae was specifically detected by NASBA. These results indicate that NASBA can be used in the rapid detection of V. cholerae from various environmental water samples. This method has a strong potential for detecting toxigenic strains by using the tcpA and ctxA markers. The entire assay including RNA extraction and NASBA was completed within 3 h.
Terpolymer of maleic anhydride and cycloolefin derivatives as an ArF photoresist (1997)

A number of single layer ArF resist systems based on acrylic polymer have been reported. However, the resist systems generally have poor dry etch durability and unusual developing condition. To overcome these problems, in this work, we have developed a novel alkaline soluble polymer through deprotection. The polymer was prepared by free radical polymerization of maleic anhydride, norbornene, and t-butyl 3- bicyclo-(2,2,1)-hept-5-en-2-yl 3-hydroxypropionate. Since our polymer system contains large amount of alicyclic carbon and hydroxy group in the polymer chain, the system shows good adhesion, thermal stability, and high transmittance at 193 nm. The resist based on the polymer shows positive tone image of 0.17 micrometer L/S in the presence of photoacid generators such as onium salts. We describe this resist system together with the synthese of monomer and polymer, their characterizations and some of results of lithographic performance.
Transmission Properties of Conjugate-Root Pulses (2004)

A family of pulses has recently been reported by Xia that are intersymbol interference-free with and without matched filtering. Reportedly, such pulses are important for systems where both matched filter and unmatched receivers are used. The transmission characteristics of these pulses are compared to the more commonly used raised-cosine pulse for three different receiver scenarios.
Mm-Wave Beam Steering Antenna With Reduced Hardware Complexity Using Lens Antenna Subarrays (2018)

A millimeter (mm)-wave beam steering antenna consisting of L lens antenna subarrays (LASs) is introduced. Each LAS hosts an M-element feed antenna array at its focal plane. The desired feed antenna of each LAS is excited through a single-pole multiple-throw (SPMT) switching network. The pole of each SPMT is connected to a mm-wave phase shifter (PS). The SPMT and PS states can be utilized jointly to steer the radiation pattern. For a given aperture size, the LAS size (i.e., L) can be adjusted to make a tradeoff between the total number of PSs (L) and switch throws (M). This can reduce the PS-related hardware complexities. The concept is demonstrated through a 38 GHz antenna consisting of L = 4 LAS. Each LAS is capable of hosting an M = 5 element aperture-coupled patch antenna array. The antenna prototype uses a single-patch antenna per LAS with mechanical movement to demonstrate the concept without the SP5T networks. The antenna performs with 8.5% |S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> | <; -10 dB bandwidth, 15.7 dBi gain, 5.2° H-plane half-power beamwidth, and 75° field of view.
Assessment of the hardness of different orthodontic wires and brackets produced by metal injection molding and conventional methods (2017)

MIM orthodontic brackets exhibited hardness values much lower than those of SS orthodontic archwires and were more compatible with NiTi and beta-titanium archwires. A wide range of microhardness values has been reported for conventional orthodontic brackets and it should be considered that the manufacturing method might be only one of the factors affecting the mechanical properties of orthodontic brackets including hardness.
Single Image Super-Resolution Based on the Feature Sign Method (2015)

Recently, the super-resolution methods based on sparse representation has became a research hotpot in signal processing. How to calculate the sparse coefficients fast and accurately is the key of sparse representation algorithm. In this paper, we propose a feature sign method to compute the sparse coefficients in the search step. Inspired by the compressed sensing theory, two dictionaries are jointly learnt to conduct super-resolution in this method. The feature sign algorithm changes the non-convex problem to a convex one by guessing the sign of the sparse coefficient at each iteration. It improves the accuracy of the obtained sparse coefficients and speeds the algorithm. Simulation results show that the proposed scheme outperforms the interpolation methods and classic sparse representation algorithms in both subjective inspects and quantitative evaluations.
A Case of Spinocerebellar Ataxia Type 7 with Torticollis (2003)

The spinocerebellar ataxia type 7 is an autosomal dominant neurodegenerative disorder with expansion of unstable CAG trinucleotide repeats in a gene on chromosome 3p, and is classified as autosomal dominant cerebellar ataxia type II. Extrapyramidal findings are uncommonly recognized in autosomal dominant cerebellar ataxia type II. A 27-year-old woman showed progressive ataxia, visual disturbance and torticollis. We report a case of genetically confirmed spinocerebellar ataxia type 7 with extrapyramidal finding.
Coherent UWB Radar-on-Chip for In-Body Measurement of Cardiovascular Dynamics (2019)

Coherent ultra-wideband (UWB) radar-on-chip technology shows great promise for developing portable and low-cost medical imaging and monitoring devices. Particularly monitoring the mechanical functioning of the cardiovascular system is of interest, due to the ability of radar systems to track sub-mm motion inside the body at a high speed. For imaging applications, UWB radar systems are required, but there are still significant challenges with in-body sensing using low-power microwave equipment and wideband signals. Recently, it was shown for the first time, on a single subject, that the arterial pulse wave can be measured at various locations in the body, using a coherent UWB radar-on-chip technology. This paper provides more substantial evidence, in the form of new measurements and improved methods, to demonstrate that cardiovascular dynamics can be measured using radar-on-chip. Results across four participants were found to be robust and repeatable. Cardiovascular signals were recorded using radar-on-chip systems and electrocardiography (ECG). Through ECG-aligned averaging, the arterial pulse wave could be measured at a number of locations in the body. Pulse arrival time could be determined with high precision, and blood pressure pulse wave propagation through different arteries was demonstrated. In addition, cardiac dynamics were measured from the chest. This paper serves as a first step in developing a portable and low-cost device for long-term monitoring of the cardiovascular system and provides the fundamentals necessary for developing UWB radar-on-chip imaging systems.
Analysis of the Viral Elements Required in the Nuclear Import of HIV-1 DNA (2009)

HIV-1 possesses an exquisite ability to infect cells independently from their cycling status by undergoing an active phase of nuclear import through the nuclear pore. This property has been ascribed to the presence of karyophilic elements present in viral nucleoprotein complexes, such as the matrix protein (MA); Vpr; the integrase (IN); and a cis-acting structure present in the newly synthesized DNA, the DNA flap. However, their role in nuclear import remains controversial at best. In the present study, we carried out a comprehensive analysis of the role of these elements in nuclear import in a comparison between several primary cell types, including stimulated lymphocytes, macrophages, and dendritic cells. We show that despite the fact that none of these elements is absolutely required for nuclear import, disruption of the central polypurine tract-central termination sequence (cPPT-CTS) clearly affects the kinetics of viral DNA entry into the nucleus. This effect is independent of the cell cycle status of the target cells and is observed in cycling as well as in nondividing primary cells, suggesting that nuclear import of viral DNA may occur similarly under both conditions. Nonetheless, this study indicates that other components are utilized along with the cPPT-CTS for an efficient entry of viral DNA into the nucleus.
Different trigemino-vascular responsiveness between adolescent and adult rats in a migraine model (2012)

Age-dependent differences in TGVS responsiveness in the i.c. capsaicin-induced migraine model of rats are reminiscent of less severe migraine in pediatric patients. This finding may provide new insight into the pathophysiology of migraine and guide the development of new anti-migraine drugs for children.
Signaling Virtual Machine Activity to the Network Virtualization Edge (2013)

This document proposes a simplified approach for provisioning network
parameters related to Virtual Machine creation, migration and
termination on servers. The idea is to provision the server, then have
the server signal the requisite parameters to the relevant network
device(s). Such an approach reduces the workload on the provisioning
system and simplifies the data model that the provisioning system
needs to maintain. It is also more resilient to topology changes in
server-network connectivity, for example, reconnecting a server to a
different network port or switch.