gebhart/patrepeval huggingface dataset:
Development of an insertional expression vector system for Methylobacterium extorquens AM1 and generation of null mutants lacking mtdA and/or fch (2003)

Over the past few years, the genetic 'toolkit' available for use with Methylobacterium extorquens AM1 has expanded significantly. Here a further advance is presented and demonstrated, an insertional expression system that allows expression of genes from a stable, unmarked chromosomal locus. This system has been used to better understand the role of the tetrahydrofolate (H4F) pathway in methylotrophy. Previously, it has not been possible to generate null mutants lacking either mtdA (encoding an NADP-dependent methylene-H4F/methylene-tetrahydromethanopterin dehydrogenase) or fch (encoding methenyl-H4F cyclohydrolase). An unmarked strain was generated that expressed the analogous folD gene (encoding a bifunctional NADP-dependent methylene-H4F dehydrogenase/methenyl-H4F cyclohydrolase) from Methylobacterium chloromethanicum CM4T. In this strain, null mutants could be obtained that grew normally on multicarbon substrates but were defective for growth on C1 substrates. Additionally, null mutants of mtdA and/or fch could also be generated in the wild-type by supplementing the succinate medium with formate. These strains were unable to grow on C1 compounds but were not methanol-sensitive. These approaches have demonstrated that the apparent essentiality of mtdA and fch is due to the need for formyl-H4F for biosynthesis of purines and other compounds, and have provided clear genetic evidence that the H4F pathway is required for methylotrophy.
Geometric Mismatches within the Concentric Layers of Rotavirus Particles: a Potential Regulatory Switch of Viral Particle Transcription Activity (2008)

Rotaviruses are prototypical double-stranded RNA viruses whose triple-layered icosahedral capsid constitutes transcriptional machinery activated by the release of the external layer. To understand the molecular basis of this activation, we studied the structural interplay between the three capsid layers by electron cryo-microscopy and digital image processing. Two viral particles and four virus-like particles containing various combinations of inner (VP2)-, middle (VP6)-, and outer (VP7)-layer proteins were studied. We observed that the absence of the VP2 layer increases the particle diameter and changes the type of quasi-equivalent icosahedral symmetry, as described by the shift in triangulation number (T) of the VP6 layer (from T = 13 to T = 19 or more). By fitting X-ray models of VP6 into each reconstruction, we determined the quasi-atomic structures of the middle layers. These models showed that the VP6 lattices, i.e., curvature and trimer contacts, are characteristic of the particle composition. The different functional states of VP6 thus appear as being characterized by trimers having similar conformations but establishing different intertrimeric contacts. Remarkably, the external protein VP7 reorients the VP6 trimers located around the fivefold axes of the icosahedral capsid, thereby shrinking the channel through which mRNA exits the transcribing rotavirus particle. We conclude that the constraints arising from the different geometries imposed by the external and internal layers of the rotavirus capsid constitute a potential switch regulating the transcription activity of the viral particles.
Novel methodology to obtain salient biomechanical characteristics of insole materials (1997)

Viscoelastic inserts are commonly used as artificial shock absorbers to prevent neuropathic foot ulcerations by decreasing pressure on the sole of the foot. Unfortunately, there is little scientific information available to guide physicians in the selection of appropriate insole materials. Therefore, a novel methodology was developed to form a rational platform for biomechanical characterizations of insole material durability, which consisted of in vivo gait analysis and in vitro bioengineering measurements. Results show significant differences in the compressive stiffness of the tested insoles and the rate of change over time in both compressive stiffness and peak pressures measured. Good correlations were found between pressure-time integral and Young's modulus (r2 = 0.93), and total energy applied and Young's modulus (r2 = 0.87).
Grease Degradation in R0F Bearing Tests (2007)

This paper is the second in a series that examines grease lubrication mechanisms and failure in rolling element bearings. The aim of the work was to understand the grease condition changes during use and the relationship to lubrication performance and failure. R0F bearing tests were carried out with two lithium hydroxystearate greases and the effects of the temperature, the speed, and the additive package on lubrication life was studied. Post-test, one pair of bearings (fail and non-fail) was dismantled and grease distribution and condition assessed. IR spectroscopy was then used to determine the lubricant composition and the oxidation level of the grease remaining on the shields, the inner raceway, and the cage pockets. The additive package increased the grease life by 100-700% depending on the test condition. Most of the grease remaining in the bearing was found on the shields, with only trace amounts in the cage pockets or close to the rolling track. The IR analysis showed that the composition of the shield sample was similar to the fresh grease although the base oil oxidation was evident and this increased with the running time. The cage pocket and inner raceway films contained a number of chemical species; these included the base oil and the thickener and their oxidation products. The study concludes that after an initial running-in period the “active” lubricant is heavily degraded grease, which contains oxidized species from the base oil and the thickener. Different failure mechanisms are identified depending on the test condition. High-speed tests that fail relatively quickly are due to poor boundary lubrication performance or cage failure rather than the lubricant reaching its “oxidation” limit. Long-term tests at slower speeds suffer considerable base oil oxidation. Under these conditions, failure is due to a reduction in the amount and/or mobility of the raceway lubricant.
The single crystal growth and laser rod fabrication of Nd:YVO/sub 4/. Interim report 1 Jul 76--1 Jan 77 (1977)

This project was initiated to investigate the single crystal growth and laser rod fabrication of (100) oriented Nd:YVO/sub 4/. The desired size and quality of the crystals were obtained most advantageously by Czochralski growth methods. RF heated iridium crucibles and commercially developed crystal growth equipment were used to evaluate many variables. Two growth stations were used continuously.
Micro-optical elements functioning in non-visible spectral range (2010)

Nowadays novel micro-fabrication and wafer-based manufacturing approach allows realizing micro-optics in a way scientists have dreamt for generations, in particular, utilizing nano-imprint lithography as fabrication tooling enables greatly accelerating the micro-optics technology to its frontier. In this report, we present wafer-scale fabrication of various types of micro-optical elements based on photoresist, benzocyclobutene, photocurable imprint resist, and semiconductor materials by using thermal reflow, reactive ion etching, and imprint techniques. Especially, several concave or convex 3-dimensional micro-optical structures shaped by imprint method are detailed. These micro-optical elements can be monolithically or hybrid integrated onto optoelectronics devices, such as photodetectors and emitters as optical beam focuser, collimator, filter, or anti-reflectance elements. As application examples, polymer microlenses were integrated directly on the top of UV dual functional devices and quantum dot long wavelength infrared photodetectors, respectively.
Radiation of Millimeter Waves from a Leaky Dielectric Waveguide with a Light-Induced Grating Layer (1987)

A theoretical analysis is presented for the radiation characteristics of millimeter waves in a periodic dielectric waveguide having a light-induced grating layer. The waveguide is assumed to be composed of an insulator (sapphire) slab whose one surface is coated with a high-resistivity semiconductor (silicon) film. A boundary-integral-equation formulation is employed to obtain characteristic solutions of the waveguide. Numerical calculations are made at 94 GHz for both TM and TE polarizations. Estimations of the illumination power required to produce the grating are given. The waveguide presented in this paper, in conjunction with a high-power semiconductor diode laser array as a light source, may be developed to operate as an electronically beam-steerable leaky-wave antenna at millimeter-wave frequencies.
Generalized channeled polarimetry (2014)

Channeled polarimeters measure polarization by modulating the measured intensity in order to create polarization-dependent channels that can be demodulated to reveal the desired polarization information. A number of channeled systems have been described in the past, but their proposed designs often unintentionally sacrifice optimality for ease of algebraic reconstruction. To obtain more optimal systems, a generalized treatment of channeled polarimeters is required. This paper describes methods that enable handling of multi-domain modulations and reconstruction of polarization information using linear algebra. We make practical choices regarding use of either Fourier or direct channels to make these methods more immediately useful. Employing the introduced concepts to optimize existing systems often results in superficial system changes, like changing the order, orientation, thickness, or spacing of polarization elements. For the two examples we consider, we were able to reduce noise in the reconstruction to 34.1% and 57.9% of the original design values.
Protection of primary neurons and mouse brain from Alzheimer's pathology by molecular tweezers (2012)

Alzheimer's disease is a devastating cureless neurodegenerative disorder affecting >35 million people worldwide. The disease is caused by toxic oligomers and aggregates of amyloid β protein and the microtubule-associated protein tau. Recently, the Lys-specific molecular tweezer CLR01 has been shown to inhibit aggregation and toxicity of multiple amyloidogenic proteins, including amyloid β protein and tau, by disrupting key interactions involved in the assembly process. Following up on these encouraging findings, here, we asked whether CLR01 could protect primary neurons from Alzheimer's disease-associated synaptotoxicity and reduce Alzheimer's disease-like pathology in vivo. Using cell culture and brain slices, we found that CLR01 effectively inhibited synaptotoxicity induced by the 42-residue isoform of amyloid β protein, including ∼80% inhibition of changes in dendritic spines density and long-term potentiation and complete inhibition of changes in basal synaptic activity. Using a radiolabelled version of the compound, we found that CLR01 crossed the mouse blood-brain barrier at ∼2% of blood levels. Treatment of 15-month-old triple-transgenic mice for 1 month with CLR01 resulted in a decrease in brain amyloid β protein aggregates, hyperphosphorylated tau and microglia load as observed by immunohistochemistry. Importantly, no signs of toxicity were observed in the treated mice, and CLR01 treatment did not affect the amyloidogenic processing of amyloid β protein precursor. Examining induction or inhibition of the cytochrome P450 metabolism system by CLR01 revealed minimal interaction. Together, these data suggest that CLR01 is safe for use at concentrations well above those showing efficacy in mice. The efficacy and toxicity results support a process-specific mechanism of action of molecular tweezers and suggest that these are promising compounds for developing disease-modifying therapy for Alzheimer's disease and related disorders.
Elaboration of Cellulose Nanocrystal/Ge-Imogolite Nanotube Multilayered Thin Films (2018)

Multilayered thin films combining two oppositely charged nanoparticles (NPs), i.e., cellulose nanocrystals (CNCs) and Ge-imogolites, have been successfully obtained by the layer-by-layer method. CNC/Ge-imogolite (NP/NP) film growth patterns were studied by comparing growth mode of all of the nanoparticles thin films to that of films composed of CNC or Ge-imogolites combined with polyelectrolytes (PEs), i.e., cationic poly(allylamine hydrochloride) and anionic poly-4-styrene sulfonate (NP/PE films). NP/NP and NP/PE films growth patterns were found to be different. To get a deeper understanding of the growth mode of NP/NP, impact of different parameters, such as imogolites aspect ratio, adsorption time, ionic strength, and repeated immersion/drying, was evaluated and influence of the drying step is emphasized. The aspect ratio of imogolites was identified as an important feature for the film's architecture. The short Ge-imogolites form denser films because the surface packing was more efficient.
A Monte Carlo pencil beam scanning model for proton treatment plan simulation using GATE/GEANT4 (2011)

This work proposes a generic method for modeling scanned ion beam delivery systems, without simulation of the treatment nozzle and based exclusively on beam data library (BDL) measurements required for treatment planning systems (TPS). To this aim, new tools dedicated to treatment plan simulation were implemented in the Gate Monte Carlo platform. The method was applied to a dedicated nozzle from IBA for proton pencil beam scanning delivery. Optical and energy parameters of the system were modeled using a set of proton depth-dose profiles and spot sizes measured at 27 therapeutic energies. For further validation of the beam model, specific 2D and 3D plans were produced and then measured with appropriate dosimetric tools. Dose contributions from secondary particles produced by nuclear interactions were also investigated using field size factor experiments. Pristine Bragg peaks were reproduced with 0.7 mm range and 0.2 mm spot size accuracy. A 32 cm range spread-out Bragg peak with 10 cm modulation was reproduced with 0.8 mm range accuracy and a maximum point-to-point dose difference of less than 2%. A 2D test pattern consisting of a combination of homogeneous and high-gradient dose regions passed a 2%/2 mm gamma index comparison for 97% of the points. In conclusion, the generic modeling method proposed for scanned ion beam delivery systems was applicable to an IBA proton therapy system. The key advantage of the method is that it only requires BDL measurements of the system. The validation tests performed so far demonstrated that the beam model achieves clinical performance, paving the way for further studies toward TPS benchmarking. The method involves new sources that are available in the new Gate release V6.1 and could be further applied to other particle therapy systems delivering protons or other types of ions like carbon.
Characterization of the novel HLA‐DQA1*01:64:02 allele by sequencing‐based typing (2023)

HLA-DQA1*01:64:02 differs from HLA-DQA1*01:64:01 by one nucleotide substitution in codon 123 in exon 3.
Syntheses of Rare Earth Dioxymonocyanamides (Ln2O2CN2, Ln = La, Ce, Pr, Nd, Sm, Eu, Gd) (1994)

Abstract A series of new compounds were prepared by heating Ln2O3 (Ln = La, Nd, Sm, Eu, Gd), Pr6O11, or Ce2(CO3)3·8H2O in the presence of carbon under an ammonia atmosphere. Thermogravimetric and CHN analyses revealed that these compounds are of rare earth dioxymonocyanamides (Ln2O2CN2). They are classified into two structure types depending on Ln3+ ionic radii, viz., type I (tetragonal) for Ln = La, Ce and type II (trigonal) for Ln = Ce, Pr, Nd, Sm, Eu, Gd. Ce2O2CN2 takes both structure types depending upon preparative temperature.
Casual versus Constitutive Explanations (or, on the Difficulty of Being so Positive...) (2017)

This chapter begins by contrasting the perspectives on &quot;causal&quot; explanation; and develops the differences at a theoretical level. It illustrates these differences in dealing with specific issues. This is followed by separate but related reflections on matters of theoretical generalization, methodological techniques, and the respective positions regarding how law figures into social change. The chapter addresses a host of specific points in Rosenberg's review and utilizes examples from his own well-known Hollow Hope to illustrate the differences. Social conventions and knowledges are understood as &quot;constitutive&quot;—rather than independent, exogenous, discrete determi-nants—of citizen meaning making activity. Positivist approaches tend to disaggregate complex processes of social change into scores of discrete causal connections between legal decisions and possible behavioral outcomes. Positivist models of causality not only oversimplify relations among thinking humans, as many interpretivists see it, but they thus also tend to overdetermine actions in ways that discount human agency.
Electromagnetic properties in parallel conductors composed of Bi2223 multifilamentary wires for power transformer windings (1997)

The authors study, theoretically, the AC losses in superconducting parallel conductors exposed to a transverse alternating magnetic field in relation with transposition among the strands. They obtained an analytical expression of the additional coupling loss for the deviation of transposition from an optimum condition. The AC losses for the alternating external field were measured in parallel conductors composed of Bi2223 and NbTi multifilamentary wires. The additional losses can be well explained by the theoretical expression in a wide range of the amplitude of external field. They also estimated, experimentally, the current distribution among the strands in solenoidal coil of the parallel conductor and discussed the effect of transposition on the current distribution.
Hybridization of membranes by sonic irradiation (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHybridization of membranes by sonic irradiationNorihiro Tsukagoshi and C. Fred FoxCite this: Biochemistry 1971, 10, 17, 3309–3313Publication Date (Print):August 1, 1971Publication History Published online1 May 2002Published inissue 1 August 1971https://pubs.acs.org/doi/10.1021/bi00793a023https://doi.org/10.1021/bi00793a023research-articleACS PublicationsRequest reuse permissionsArticle Views36Altmetric-Citations48LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Low bitrate audio coding-state-of-the-art, challenges and future directions (2002)

Perceptual encoding of high quality audio has found its way to many applications including digital radio, electronic music distribution (EMD) systems and portable audio devices. An overview on the basics of high quality low bitrate audio coding is followed by a look into currently widely used and newer, state-of-the-art coding systems like MP3 and MPEG-2 Advanced Audio Coding (AAC). The rapid deployment of older (1992) technologies (like MP3) followed by the news of new and improved algorithms (like AAC) raises the question about future improvements. The paper analyses some candidates for such improvements and provide a view of some current research activities.
Dynamically Shaping the Reordering Search Space of Phrase-Based Statistical Machine Translation (2013)

Defining the reordering search space is a crucial issue in phrase-based SMT between distant languages. In fact, the optimal trade-off between accuracy and complexity of decoding is nowadays reached by harshly limiting the input permutation space. We propose a method to dynamically shape such space and, thus, capture long-range word movements without hurting translation quality nor decoding time. The space defined by loose reordering constraints is dynamically pruned through a binary classifier that predicts whether a given input word should be translated right after another. The integration of this model into a phrase-based decoder improves a strong Arabic-English baseline already including state-of-the-art early distortion cost (Moore and Quirk, 2007) and hierarchical phrase orientation models (Galley and Manning, 2008). Significant improvements in the reordering of verbs are achieved by a system that is notably faster than the baseline, while bleu and meteor remain stable, or even increase, at a very high distortion limit.
Quality of Service and Proactive Content Replication in UPnP based A/V Environments. (2005)

etechnik.uni-rostock.de Multimedia Applications e.g. Video/Audio streaming increasingly strive for deployment in distributed and domain spanning networking environments. In order to ensure the service interoperability between content servers and rendering devices across heterogeneous platforms, distributed middleware approaches offer promising concepts (e.g. Service Oriented Architectures). The UPnP forum has developed a platform-neutral architectural framework that specifies a set of well defined service discovery and access routines concealed behind a unified set of protocols and their APIs. While UPnP supports service interoperability additional service extensions are required to satisfy requirements as imposed by many multimedia applications. These requirements cover QoS support from the application source to the sink which entails the encapsulation of signalling services that allow for resource reservation on network and end-devices. Furthermore we introduce a proactive content replication paradigm: According to popularity forecasts it is possible to create replicas of e.g. movie content to avoid hot-spots maintaining very popular content in large scale networks. The contribution of this paper is to identify domain spanning distributed multimedia scenarios and describe the challenges for developing enhancing services to the UPnP framework that help to establish them.
Collision-induced dispersion of agglomerate suspensions in a shear flow (2000)

Agglomerates suspended in a polymer fluid have been known to disperse in a flow through two mechanisms—rupture and erosion. Using silica agglomerates, it is shown here that a third mechanism can occur, i.e., detachment of fragments due to agglomerate collision. This mechanism requires a much lower overall stress than erosion (and rupture, which occurs at even larger stresses than erosion). The fragment concentration produced by collision at a given time is proportional to the square of the applied shear rate. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 78: 1130–1133, 2000