gebhart/patrepeval huggingface dataset:
Internal dynamics of semiflexible polymers with active noise (2017)

The intramolecular dynamics of flexible and semiflexible polymers in response to active noise is studied theoretically. The active noise may either originate from interactions of a passive polymer with a bath of active Brownian particles or the polymer itself is comprised of active Brownian particles. We describe the polymer by the continuous Gaussian semiflexible-polymer model, taking into account the finite polymer extensibility. Our analytical calculations predict a strong dependence of the polymer dynamics on the activity. In particular, active semiflexible polymers exhibit a crossover from a bending elasticity-dominated dynamics at weak activity to that of flexible polymers at strong activity. The end-to-end vector correlation function decays exponentially for times longer than the longest polymer relaxation time. Thereby, the polymer relaxation determines the decay of the correlation function for long and flexible polymers. For shorter and stiffer polymers, the relaxation behavior of individual active Brownian particles dominates the decay above a certain activity. The diffusive dynamics of a polymer is substantially enhanced by the activity. Three regimes can be identified in the mean square displacement for sufficiently strong activities: an activity-induced ballistic regime at short times, followed by a Rouse-type polymer-specific regime for any polymer stiffness, and free diffusion at long times, again determined by the activity.
Dynamic optimistic interprocedural analysis (2001)

In this paper, we address the problem of dynamic optimistic interprocedural analysis. Our goal is to build on past work on static interprocedural analysis and dynamic optimization by combining their advantages. We present a framework for performing dynamic optimistic interprocedural analysis. the framework is designed to be used in the context of dynamic class loading and dynamic compilation, and includes mechanisms for event notification (on class loading and method compilation) and dependence tracking (to enable invalidation of optimistic assumptions). We illustrate the functionality of the framework by using it to be used in the context of dynamic class loading and dynamic compilation, and includes mechanisms for event notification (on class loading and method compilaton) and dependence tracking (to enable invalidation of optimistic assumptions). We illustrate the functionality of the framework by using it to implement a dynamic optimistic interprocedural type (DOIT) analysis algorithm. The DOIT algorithm uses a new global data structure called the Value Graph. The framework and DOIT analysis of the IBM Jalapeño Java virtual machine. Our experimental results for the SPECjvm benchmarks and two larger programs show promising benefits due to dynamic optimistic analysis. Compared to pessimistic analysis, the reduction in number of methods and fields analyzed was in the 2.7x-4.6x and 1.6-2.4x ranges respectively. The average fraction of polymorphic virtual calls decreased from 39.5% to 24.4% due to optimistic analysis, with a best-case decrease from 47.0% to 8.1%. The average fraction of polymorphic interface calls decreased from 96.4% to 36.2% due to optimistic analysis, with a best-case decrease from 100.0% to 0.0%. These benefits were obtained with a low dynamic analysis overhead in the range of 570-930 bytecode bytes/millisecond (about 2.5x-5.4x faster than the Jalapeño baseline compiler)
Construction of subtractive cDNA library using magnetic beads and PCR. (1995)

References http://genome.cshlp.org/content/4/4/S168.refs.html This article cites 11 articles, 4 of which can be accessed free at: License Commons Creative . http://creativecommons.org/licenses/by-nc/3.0/ described at as a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), ). After six months, it is available under http://genome.cshlp.org/site/misc/terms.xhtml for the first six months after the full-issue publication date (see This article is distributed exclusively by Cold Spring Harbor Laboratory Press
Anti-Unification and Natural Language Processing (2018)

Anti-unification is a well-known method to compute generalizations in logic. Given two objects, the goal of anti-unification is to reflect commonalities between these objects in the computed generalizations, and highlight differences between them. Anti-unification appears to be useful for various tasks in natural language processing. Semantic classification of sentences based on their syntactic parse trees, grounded language learning, semantic text similarity, insight grammar learning, metaphor modeling: This is an incomplete list of topics where generalization computation has been used in one form or another. The major anti-unification technique in these applications is the original method for first-order terms over fixed arity alphabets, introduced by Plotkin and Reynolds in 1970s, and some of its adaptations. The goal of this paper is to give a brief overview about existing linguistic applications of anti-unification, discuss a couple of powerful and flexible generalization computation algorithms developed recently, and argue about their potential use in natural language processing tasks.
Different levels of circulating Th22 cell and its related molecules in Graves' disease and Hashimoto's thyroiditis. (2014)

Th22 cells may participate in the pathogenesis of AITDs as a proinflammatory factor, especially in GD, through expressing and secreting IL-22.
Integrating constraints and metric learning in semi-supervised clustering (2004)

Semi-supervised clustering employs a small amount of labeled data to aid unsupervised learning. Previous work in the area has utilized supervised data in one of two approaches: 1) constraint-based methods that guide the clustering algorithm towards a better grouping of the data, and 2) distance-function learning methods that adapt the underlying similarity metric used by the clustering algorithm. This paper provides new methods for the two approaches as well as presents a new semi-supervised clustering algorithm that integrates both of these techniques in a uniform, principled framework. Experimental results demonstrate that the unified approach produces better clusters than both individual approaches as well as previously proposed semi-supervised clustering algorithms.
Brain Connectivity Dissociates Responsiveness from Drug Exposure during Propofol-Induced Transitions of Consciousness (2016)

Accurately measuring the neural correlates of consciousness is a grand challenge for neuroscience. Despite theoretical advances, developing reliable brain measures to track the loss of reportable consciousness during sedation is hampered by significant individual variability in susceptibility to anaesthetics. We addressed this challenge using high-density electroencephalography to characterise changes in brain networks during propofol sedation. Assessments of spectral connectivity networks before, during and after sedation were combined with measurements of behavioural responsiveness and drug concentrations in blood. Strikingly, we found that participants who had weaker alpha band networks at baseline were more likely to become unresponsive during sedation, despite registering similar levels of drug in blood. In contrast, phase-amplitude coupling between slow and alpha oscillations correlated with drug concentrations in blood. Our findings highlight novel markers that prognosticate individual differences in susceptibility to propofol and track drug exposure. These advances could inform accurate drug titration and brain state monitoring during anaesthesia.
Terminator Oligo Blocking Efficiently Eliminates rRNA from <i>Drosophila</i> Small RNA Sequencing Libraries (2013)

A large number of methods are available to deplete ribosomal RNA reads from high-throughput RNA sequencing experiments. Such methods are critical for sequencing Drosophila small RNAs between 20 and 30 nucleotides because size selection is not typically sufficient to exclude the highly abundant class of 30 nucleotide 2S rRNA. Here we demonstrate that pre-annealing terminator oligos complimentary to Drosophila 2S rRNA prior to 5' adapter ligation and reverse transcription efficiently depletes 2S rRNA sequences from the sequencing reaction in a simple and inexpensive way. This depletion is highly specific and is achieved with minimal perturbation of miRNA and piRNA profiles.
Recognition hysteresis of the acetylcholine receptor of torpedo Californica (1988)

Abstract The nicotinic acetylcholine receptor (nAcChR) of the electric organ of Torpedo californica fish exhibits a pronounced hysteresis loop in the high affinity binding of the neurotransmitter acetylcholine (AcCh). When increasing amounts of AcCh are added (pulse mode) an extremely long‐lived, metastable conformer distribution is obtained (lower hysteresis branch) between low affinity AcCh binding states (R l ) and high (R h ) and very high (R vh ) affinity states. Dialysis conditions always lead to the equilibrium binding curve (upper hysteresis branch; K̄ A = 5 × 10 −9 M, 4°C; one A bound to the R‐monomer of M r ≈ 290 000). Cyclic, pulse mode addition and dilution of AcCh results in scanning loops within the main hysteresis. The kinetic analysis of the changes in free and bound AcCh during the open‐system conditions of dialysis, that releases the metastability, shows that the AcCh (A) binding proceeds along an induced‐fit pathway according to A+R h ⇋ AR n ⇋ AR vh . The rate constant of the step AR h → AR vh is k 2 = 6 × 10 −3 s −1 and that of the reverse step is k −2 = 3 × 10 −4 s −1 . Direct binding of A to free R vh can be excluded. Therefore, the state R vh does not preexist, it is induced and only stable, as AR vh , by bound AcCh. The metastability can be described in terms of long‐lived AR vh ·R 1 hybrid dimers. Physiologically, the metastable hybrid may be viewed as a saving device: the functionally important, channel‐active R 1 conformer is, at low AcCh‐concentrations [A] < 1μM, prevented to convert to the desensitized states R h and AR vh . Furtheron, AcCh enhances the phosphorylation of phosphatidyl inositol and the auto‐phosphorylation of the receptor. If the AcCh binding hysteresis causes a phosphorylation hysteresis the desensitized nAcChR may serve as a memory molecule of the transsynaptic information signalling of the neurotransmission.
Fibroblast-adapted human CMV vaccines elicit predominantly conventional CD8 T cell responses in humans (2017)

Cytomegalovirus (CMV)-based vaccines have shown remarkable efficacy in the rhesus macaque model of acquired immune deficiency syndrome, enabling 50% of vaccinated monkeys to clear a subsequent virulent simian immunodeficiency virus challenge. The protective vaccine elicited unconventional CD8 T cell responses that were entirely restricted by MHC II or the nonclassical MHC I molecule, MHC-E. These unconventional responses were only elicited by a fibroblast-adapted rhesus CMV vector with limited tissue tropism; a repaired vector with normal tropism elicited conventional responses. Testing whether these unusual protective CD8 T responses could be elicited in humans requires vaccinating human subjects with a fibroblast-adapted mutant of human CMV (HCMV). In this study, we describe the CD8 T cell responses of human subjects vaccinated with two fibroblast-adapted HCMV vaccines. Most responses were identified as conventional classically MHC I restricted, and we found no evidence for MHC II or HLA-E restriction. These results indicate that fibroblast adaptation alone is unlikely to explain the unconventional responses observed in macaques.
Distributed sensor processing over an ad hoc wireless network: simulation framework and performance criteria (2002)

The evaluation of existing and future distributed sensor processing system concepts can be done well using simulation, provided that the simulation is faithful in representing both the medium in which the sensors interface with the phenomena that they measure or detect and the medium in which the sensors interface with each other to achieve a distributed mode of operation. Performance criteria for distributed sensor processing over ad hoc wireless networks are stated and an architecture for analysis and simulation of this kind of system is described.
Myrtaceae Plant Essential Oils and their β-Triketone Components as Insecticides against Drosophila suzukii (2017)

Spotted wing drosophila (SWD, Drosophila suzukii (Matsumura), Diptera: Drosophilidae) is recognized as an economically important pest in North America and Europe as well as in Asia. Assessments were made for fumigant and contact toxicities of six Myrtaceae plant essential oils (EOs) and their components to find new alternative types of insecticides active against SWD. Among the EOs tested, Leptospermum citratum EO, consisting mainly of geranial and neral, exhibited effective fumigant activity. Median lethal dose (LD<sub>50</sub>; mg/L) values of L. citratum were 2.39 and 3.24 for males and females, respectively. All tested EOs except Kunzea ambigua EO exhibited effective contact toxicity. LD<sub>50</sub> (µg/fly) values for contact toxicity of manuka and kanuka were 0.60 and 0.71, respectively, for males and 1.10 and 1.23, respectively, for females. The LD<sub>50</sub> values of the other 3 EOs-L. citratum, allspice and clove bud were 2.11-3.31 and 3.53-5.22 for males and females, respectively. The non-polar fraction of manuka and kanuka did not show significant contact toxicity, whereas the polar and triketone fractions, composed of flavesone, isoleptospermone and leptospermone, exhibited efficient activity with the LD<sub>50</sub> values of 0.13-0.37 and 0.22-0.57 µg/fly for males and females, respectively. Our results indicate that Myrtaceae plant EOs and their triketone components can be used as alternatives to conventional insecticides.
Identification and Characterization of ADAMTS-20 Defines a Novel Subfamily of Metalloproteinases-Disintegrins with Multiple Thrombospondin-1 Repeats and a Unique GON Domain (2003)

We have cloned a mouse brain cDNA encoding a new protein of the ADAMTS family (a disintegrin and metalloproteinase domain, with thrombospondin type-1 repeats), which has been called ADAMTS-20. This protein shows a domain organization similar to that described for other ADAMTSs including signal sequence, propeptide, metalloproteinase domain, disintegrin domain, central TS-1 motif, cysteine-rich region, and C-terminal TS module. However, this last module is more complex than that of other ADAMTSs, being composed of a total of 14 repeats. The structural complexity of ADAMTS-20 is further increased by the presence of an additional domain 200 residues long and located immediately adjacent to the TS module. This domain has been tentatively called GON domain and can also be recognized in some ADAMTSs such as gon-1 from Caenorhabditis elegans and human and mouse ADAMTS-9. The presence of this domain is a hallmark of a novel subfamily of structurally and evolutionarily related ADAMTSs, called GON-ADAMTSs. Expression analysis demonstrated that ADAMTS-20 transcripts can be detected at low levels in several human and mouse tissues, especially in testis. This gene is also overexpressed in some human malignant tumors, including brain, colon, and breast carcinomas. Western blot analysis using polyclonal antibodies raised against recombinant ADAMTS-20 produced in Escherichia coli showed the presence of a 70-kDa band in mouse brain and testis extracts. This recombinant ADAMTS-20 hydrolyzed a synthetic peptide used for assaying matrix metalloproteinases. These data suggest that this novel enzyme may play a role in the tissue remodeling process occurring in both normal and pathological conditions.
Subjective social status moderates back pain and mental health in older men (2021)

Where one ranks oneself within their nation or community matters for the back pain and mental health relationship. Higher SSS may be a psychosocial resource that buffers the negative associations of severe and frequent back pain on mental health in older men.
Mud Volcanoes revealed and sampled on the Western Moroccan Continental Margin (2001)

We surveyed and sampled two active and 3 inactive mud volcanoes on the Atlantic continental margin of Morocco. The active mud volcanoes (named Yuma and Ginsburg) are each about 4 km in diameter, rise between 150–250 meters above the seafloor and are the first active methane‐related mud volcanoes to be identified in this region. The inactive volcanoes range in diameter from 1–3 km, with relief between 50 and 80 meters. Gravity cores from the crest of the active mud volcanoes yielded methane hydrates and mud breccia deposits. Chemosynthetic communities of Pogonophora worms and the bivalve Solemya were found on the surface of the active mud volcanoes. Sediment cores from the inactive volcanoes contained hemipelagic sediments, rich in foraminifera and ahermatypic coral debris, overlying mud breccia
Combining Acoustic Echo Cancellation and Suppression (2003)

The acoustic echo problem arises whenever there is acoustic coupling between a loudspeaker and a microphone, such as in a teleconference system. This problem is traditionally solved by using an acoustic echo canceler (AEC), which models the echo path with adaptive filters. Long adaptive filters are necessary for satisfactory echo cancellation, which makes AEC highly computationally complex. Recently, a low-complexity echo suppression scheme was presented, the perceptual acoustic echo suppressor (PAES). Spectral modification is used to suppress the echoes, and the complexity is reduced by incorporating perceptual theories. However, under ideal conditions AEC performs better than PAES. This thesis considers a hybrid system, which combines AEC and PAES. AEC is used to cancel low-frequency echo components, while PAES suppresses high-frequency echo components. The hybrid system is simulated and assessed, both through subjective listening tests and objective evaluations. The hybrid scheme is shown to have virtually the same perceived quality as a full-band AEC, while having a significantly lower complexity and a higher degree of robustness.
Experimental Investigation of a Reed Valve on the Performance of a Pulse Detonation Engine (2013)

Valve system is an important part of pulse detonation engine (PDE). The purpose of this research was to demonstrate the feasibility of utilizing a reed valve to inject fuel/air mixture into the combustion chamber of a Pulsed Detonation Engine (PDE). Using air as oxidizer and liquid C8H18 as fuel, a series of multi-cycle detonation experiments were investigated. The experimental results indicated that the reed valve was able to realize supply control of single-tube PDE effectively, and achieved stable operation about 3 minutes at 12.5 Hz for 0.15 mm valve sheet and 30° limit baffle plate. The response time and total pressure recovery coefficient of the reed valve were influenced by valve sheet thickness and air mass flow rate. For 0.1 mm valve sheet and 45° limit baffle plate, the service life of valve sheet strikingly shortened. Some factors such as the valve sheet thickness, air mass flow rate and the limit baffle plate's angle, should be comprehensively considered to design a reed valve.
Reactivity of [{Y(C<sub>5</sub>Me<sub>5</sub>)(OC<sub>6</sub>H<sub>3</sub>Bu<sup>t</sup><sub>2</sub>)(µ-H)}<sub>2</sub>] with terminal alkene and alkynes: a model for the first insertion step in alkene polymerization (1992)

Terminal alkenes H2CCHR (R = H, Me, Bun) react with [{Y(C5Me5)(OAr)(µ-H)}2]1 to give the µ-n-alkyl species trans-[{Y(C5Me5)(OAr)}2(µ-H)(µ-CH2 CH2R)](R = H 2, Me 3, Bun4), respectively; HCCSiMe3 reacts to give [{Y(C5Me5)(OAr)}2(µ-H)(µ-CCSiMe3)]5.
Comparative study of rosmarinic acid content in some plants of Labiatae family (2012)

M. spicata can be considered as a new source of rosmarinic acid .
Towards structure determination of neurotoxin II bound to nicotinic acetylcholine receptor: a solid‐state NMR approach (2004)

Solid-state magic-angle spinning nuclear magnetic resonance (NMR) has sufficient resolving power for full assignment of resonances and structure determination of immobilised biological samples as was recently shown for a small microcrystalline protein. In this work, we show that highly resolved spectra may be obtained from a system composed of a receptor-toxin complex. The NMR sample used for our studies consists of a membrane preparation of the nicotinic acetylcholine receptor from the electric organ of Torpedo californica which was incubated with uniformly 13C-,15N-labelled neurotoxin II. Despite the large size of the ligand-receptor complex ( > 290 kDa) and the high lipid content of the sample, we were able to detect and identify residues from the ligand. The comparison with solution NMR data of the free toxin indicates that its overall structure is very similar when bound to the receptor, but significant changes were observed for one isoleucine.
Oxidative Dearomatization of Indoles via Pd-Catalyzed C–H Oxygenation: An Entry to C2-Quaternary Indolin-3-ones (2016)

An oxidative dearomatization chemistry of 2-arylindole via a unique pathway involving Pd-catalyzed C-H peroxygenation is documented. Coupled with cascade transformation, it provides a new route to access indolin-3-ones bearing a C2-quaternary functionality, including a chiral center (indoxyls), a motif prevalent in indole alkaloids but synthetically underexplored. The method is chemo- and regioselective and compatible with versatile substrates. A mechanism has been outlined on the basis of results of control experiments, isolation/use of intermediates, and spectroscopic studies.
A Sequential Claisen/Ring‐Closing Metathesis Approach to the Synthesis of Spirocyclic Cyclopentanes and Cyclohexanes. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Practice Guidelines for Management of the Difficult Airway (2013)

P RACTICE Guidelines are systematically developed recommendations that assist the practitioner and patient in making decisions about health care.These recommendations may be adopted, modified, or rejected according to clinical needs and constraints and are not intended to replace local institutional policies.In addition, Practice Guidelines developed by the American Society of Anesthesiologists (ASA) are not intended as standards or absolute requirements, and their use cannot guarantee any specific outcome.Practice Guidelines are subject to revision as warranted by the evolution of medical knowledge, technology, and practice.They provide basic recommendations that are supported by a synthesis and analysis of the current literature, expert and practitioner opinion, open-forum commentary, and clinical feasibility data.This document updates the "Practice Guidelines for Management of the Difficult Airway: An Updated Report by the Task Force on Difficult Airway Management," adopted by the ASA in 2002 and published in 2003.* Methodology A. Definition of Difficult AirwayA standard definition of the difficult airway cannot be identified in the available literature.For these Practice Guidelines, a difficult airway is defined as the clinical situation in which a conventionally trained anesthesiologist experiences difficulty with facemask ventilation of the upper airway, difficulty with tracheal intubation, or both.The difficult airway represents a complex interaction between patient factors, the clinical setting, and the skills of the practitioner.Analysis of this interaction requires precise collection and communication of data.The Task Force urges clinicians and investigators to use explicit descriptions of the difficult airway.Descriptions that can be categorized or expressed as numerical values are particularly desirable, because this type of information lends itself to aggregate analysis and cross-study comparisons.
Pharmacodynamic evaluation of tigecycline against Acinetobacter baumannii in a murine pneumonia model (2009)

Tigecycline efficacy in this murine ACB pneumonia model was well predicted by fAUC/MIC. Requisite tigecycline exposures for efficacy appear to be higher for ACB pneumonia than for other pathogens reported of non-respiratory infections.