gebhart/patrepeval huggingface dataset:
Hsp90 dictates viral sequence space by balancing the evolutionary tradeoffs between protein stability, aggregation and translation rate (2017)

Abstract Acquisition of mutations is central to evolution but the detrimental effects of most mutations on protein folding and stability limit protein evolvability. Molecular chaperones, which suppress aggregation and facilitate polypeptide folding, are proposed to promote sequence diversification by buffering destabilizing mutations. However, whether and how chaperones directly control protein evolution remains poorly understood. Here, we examine the effect of reducing the activity of the key eukaryotic chaperone Hsp90 on poliovirus evolution. Contrary to predictions of a buffering model, inhibiting Hsp90 increases population sequence diversity and promotes accumulation of mutations reducing protein stability. Explaining this counterintuitive observation, we find that Hsp90 offsets the evolutionary tradeoff between protein stability and aggregation. Lower chaperone levels favor sequence variants of reduced hydrophobicity, thus decreasing protein aggregation propensity but at a cost to protein stability. Notably, reducing Hsp90 activity also promotes clusters of codon-deoptimized synonymous mutations at inter-domain boundaries, likely to promote local ribosomal slowdown to facilitate cotranslational domain folding. Our results reveal how a chaperone can shape the sequence landscape at both the protein and RNA levels to harmonize the competing constraints posed by protein stability, aggregation propensity and translation rate on successful protein biogenesis.
Hybrid Rop-pIII proteins for the display of constrained peptides on filamentous phage capsids. (1993)

In order to increase the versatility of phage display technology, it is desirable to be able to impose some structural constraints on the peptides that are presented by the phage particles. This is currently not feasible since the conformation of the capsid proteins, used to link the foreign peptide to the phage, are either unknown (pIII) or too simple (pVIII) to permit the engineering of peptide inserts into a constrained context. To reach this scope we have modified the amino-terminus of gene III by appending a well-characterized protein motif, the four-helix bundle of the bacterial protein Rop. Phage particles displaying Rop can be separated from wild-type (wt) particles by affinity purification with an antibody. Rop can be extensively modified by substituting its solvent-exposed residues and/or by inserting peptides either into the carboxy-terminal tail or into the bend region that connects the two alpha-helices of the monomer. These results open the possibility to construct peptide libraries where the peptides are constrained either into an omega-loop type conformation or an alpha-helix. Libraries formed by peptides inserted into the carboxy-terminus can also be constructed. Furthermore, the system that we have developed permits to produce large quantities of the elements of the libraries in the cytoplasm or to display them on the capsid of filamentous phages.
Electromagnetic matched field processing for source localization (2002)

Matched field processing (MFP) refers to signal and array processing techniques in which, rather than a planewave arrival model, complex-valued (amplitude and phase) field predictions for propagating signals are used. Matched field processing has been successfully applied in ocean acoustics. In this paper the extension of MFP to the electromagnetic domain, i.e., electromagnetic (EM) MFP (EM-MFP) is described. Simulations of EM-MFP in the tropospheric setting suggest that, under suitable conditions, EM-MFP methods can enable EM sources to be both detected/localized and used as sources of opportunity for estimating the environmental parameters that determine EM propagation.
A Feature-Based Bayesian Method for Content Popularity Prediction in Edge-Caching Networks (2019)

peer reviewed
High Speed Red Point Source LED for POF Communication. (2002)

A high speed red point source LED (Red-PSL) for POF communication has been successfully developed. It has AlGaInP MQW and DBR structures grown by MOCVD. A current confinement structure is made by H+ implantation and the diameter of emitting window is 150Ém. Excellent performances were achieved with output power of 0.7 mW at 20 mA and cut-off frequency of 30 MHz at 20 mA +10 mAp-p. 125 Mbps data communication was realized by using the Red-PSL
A multidatabase transaction model for InterBase (1990)

The management of multidatabase transactions presents new and interesting challenges, due mainly to the requirement of the autonomy of local database systems.In this paper, we present an extended transaction model which provides the following features useful in a multidatabase environment:(1) It allows the composition of flexi.bletransactions which can tolerate failures of individual sub transactions by taking advantage of the fact that a given function can frequently be accomplished by more than one database system; (2) It supports the concept of mixed transactions allowing compensatable and non-compensatable subtransactions to coexist within a single global transaction; and (3) It incorporates the concept of time jn both the subtransaction and global transaction processing, thus allowing more flexibility in transaction scheduling.We formally define the extended transaction model and discuss its transaction scheduling mechanism.
The p12f2/TaqI Y-specific polymorphism in three groups of Italians and in a sample of Senegalese. (1987)

The TaqI/p12f2 Y-specific RFLP was studied in 258 Italians (69 from North, 74 from Centre-South and 115 from Southern Sardinia) and in 65 Senegalese. The two allelic fragments of 10 and 8 kb characterizing this polymorphism were both found in the Italians but only the 10 kb band was found among the Senegalese. The observed frequency of the 8 kb allele was 32.4% in Central-Southern Italians, 17.4% in Northern Italians and 13.0% in Southern Sardinians. The last figure is significantly lower than that (34.3%) previously reported for a smaller sample of the same population.
A Practical System For 5-axis VolumetricCompensation (1970)

Compensation is a recognised technique for correcting the systematic errors inherent to machine tool positioning systems. It offers a cost effective and flexible solution to the problem of enhancing machine accuracy. In spite of this controller manufacturers provide limited facilities for applying compensation, and in many cases linear positioning compensation only is available. The main reason for this is the potential complexity of a comprehensive compensation system able to cope with the variety of axis combinations and configurations available in the modern machine tool market. This problem is compounded by the demand from industry for precision 5 axis machining. This paper describes a practical geometric error compensation system that can be applied to any machine tool that has up to 5 axes. The system can correct for the effects of all the geometric errors associated with a machine's linear axes, together with the geometric errors associated with a fork type servo head. The system applies compensation dynamically and in real time as the machine moves throughout its working volume.
Clinical study of Marjolin's ulcer (1990)

Marjolin's ulcer is the malignant lesion which develops in a burn scar or chronic fistula. Due to the low prevalence of this lesion, there has been disagreement regarding its clinical features, methods of treatment, and prognosis. We evaluated 19 cases of patients who had been admitted to Severance Hospital from Jan. 1970 to Dec. 1985. The results were as follows: The previous lesion was a burn scar in 52% of the cases and a fistula of chronic osteomyelitis in 32%. The mean latent period was 31.5 years. The initial symptoms were increased pain (74%), discharge with foul odor (68%) and bleeding (58%). Upon histological examination, all of the cases were squamous cell carcinoma. The rate of metastasis at the time of diagnosis was 32%. Of the 16 patients treated by surgery, local recurrence was noted in 4 cases. Three of these cases were patients who had been treated by excision and split thickness skin graft. The time interval for local recurrence ranged from 6 months to 11 months (average 8.8 months). In conclusion, the squamous cell carcinoma of marjolin's ulcer seems to have a worse prognosis than other squamous cell carcinomas and it requires aggressive treatment. The burn scar or chronic fistula that occurs in elderly patients especially requires more adequate treatment and close observation.
Direct time integration of Maxwell’s equations in nonlinear dispersive media for propagation and scattering of femtosecond electromagnetic solitons (1992)

We report the initial results for femtosecond electromagnetic soliton propagation and collision obtained from first principles, i.e., by a direct time integration of Maxwell’s equations. The time integration efficiently implements linear and nonlinear convolutions for the electric polarization and can take into account such quantum effects as Kerr and Raman interactions. The present approach is robust and should permit the modeling of two- and three-dimensional optical soliton propagation, scattering, and switching from the full-vector Maxwell’s equations.
Erratum: Carrier-Controlled Ferromagnetism in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi>SrTiO</mml:mi><mml:mn>3</mml:mn></mml:msub></mml:math>[Phys. Rev. X<b>2</b>, 021014 (2012)] (2012)

Received 7 July 2012DOI:https://doi.org/10.1103/PhysRevX.2.039901This article is available under the terms of the Creative Commons Attribution 3.0 License. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.Published by the American Physical Society
MANEMO Topology and Addressing Architecture (2007)

This document outlines the MANEMO architecture including possible
topology configuration and addressing assignment. The issues of MANEMO
(previously known as nested NEMO) are already summarized in several
documents. However, there are several ways how to comprehend what is
MANEMO. The MANEMO problems are related to several existing working
groups. This document provides the MANEMO architecture model and
differences of existing solutions so that IETF can classify the
problems and start working on the solutions.
Capacity Limit of the Noiseless, Energy-Efficient Optical PPM Channel (1983)

The energy-efficient capacity of the noiseless optical PPM channel is examined. It is shown that, although the capacity per photon can be made to increase without bound, the capacity per channel use (for best energy efficiency) is always less than 2 nats and approaches 2 nats/symbol as the bandwidth expansion factor goes to infinity.
eSAE: A rapid service creation environment for next-generation services (2002)

The telecommunications industry is entering a brave new world of communication where consumers are looking for new ways to stay connected. To keep up with the pace, service providers need a service creation environment (SCE) to rapidly develop, test, simulate, and deploy next-generation services including wireless data, voice, and Internet applications. Next-generation SCEs have to support a wide variety of network interfaces and protocols that allow network operators, application service providers (ASPs), and third-party developers to build, deploy, and manage such services. The Lucent Enhanced Services Authoring Environment (eSAE, pronounced “easy”) has been developed as an enabler of converged services with speed-to-market mindset. Service developers without any specialized skills in proprietary languages can create most of the services quickly by using industry standard languages like Java, <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∗</sup> C++, and XML. This paper will explore in detail how the eSAE architecture promotes reusability using JavaBeans <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∗</sup> component technology and how the visual assembly paradigm eases service composition. Open network application programming interfaces (APIs) (for example, JTAPI, FullCircle™, Parlay) can be incrementally supported for standards compliance. XML technology is leveraged for complete service specification (data modeling for call logic and service provisioning).3
Trimming the threshold dispersion below 10 e-rms in a large area readout IC working in a single photon counting mode (2016)

We present a new method of an in-pixel threshold dispersion correction implemented in a prototype readout integrated circuit (IC) operating in a single photon counting mode. The new threshold correction method was implemented in a readout IC of area 9.6× 14.9 mm2 containing 23552 square pixels with the pitch of 75 μm designed and fabricated in CMOS 130 nm technology. Each pixel of the IC consists of a charge sensitive amplifier, a shaper, two discriminators, two 14-bit counters and a low-area trim DACs for threshold correction. The user can either control the range of the trim DAC globally for all the pixels in the integrated circuit or modify the trim DACs characteristics locally in each pixel independently. Using a simulation tool based on the Monte-Carlo methods, we estimated how much we could improve the offset trimming by increasing the number of bits in the trim DACs or implementing additional bits in a pixel to modify the characteristics of the trim DACs. The measurements of our IC prototype show that it is possible to reduce the effective threshold dispersion in large-area single-photon counting chips below 10 electrons rms.
Characterization of the Performance of Bin Blenders: Part 1 of 3: Methodology (2004)

In this series of articles, bin blender performance is comprehensively reviewed using both free-flowing and cohesive mixtures. In part 1, an introduction to tools and techniques is presented, followed by an examination of parameter effects, mixing mechanisms, and the effects of cohesion on mixing.
The Morphine–Thebaine group of alkaloids. Part III. The structure of the codeimethines, and related topics (1955)

K. W. Bentley and A. F. Thomas, J. Chem. Soc., 1955, 3237 DOI: 10.1039/JR9550003237
ChemInform Abstract: Synthesis and Properties of Photosensitive Polyimides Containing Cyclobutane Ring Structure. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Preparation and Polymerization of Unsaturated Quaternary Ammonium Compounds. III. Vinyloxyethyl Derivatives<sup>1,2</sup> (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and Polymerization of Unsaturated Quaternary Ammonium Compounds. III. Vinyloxyethyl Derivatives1,2George B. Butler and Robert L. GoetteCite this: J. Am. Chem. Soc. 1952, 74, 8, 1939–1941Publication Date (Print):April 1, 1952Publication History Published online1 May 2002Published inissue 1 April 1952https://pubs.acs.org/doi/10.1021/ja01128a020https://doi.org/10.1021/ja01128a020research-articleACS PublicationsRequest reuse permissionsArticle Views127Altmetric-Citations9LEARN 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
Optical injection and coherent control of a ballistic charge current in GaAs/AlGaAs quantum wells (2003)

We report all-optical injection and coherent control of a ballistic charge current in GaAs/AlGaAs quantum wells. This current arises through quantum interference of one- and two-photon absorption of ∼100 fs pulses with parallel linear polarizations, and its magnitude can be controlled by adjusting the relative phase of the incident pulses. By monitoring differential transmission using a spatially resolved optical pump–probe technique, we observe evidence of carrier motion associated with this ballistic current. Results are consistent with a theoretical treatment specific to quantum wells, and are qualitatively similar to previous measurements in bulk GaAs.
Polyfluoroarenes. Part XV. Diazo-oxides and related compounds (1971)

Pentafluoronitrobenzene reacts with potassium hydroxide in t-butyl alcohol to give mainly tetrafluoro-2-and tetra-fluoro-4-nitrophenol, with traces of trifluoro-4-nitroresorcinol. Reduction of each of the major products with tin and hydrochloric acid gives the corresponding aminophenol, which yields 1-diazotetrafluorobenzene 2-oxide or 1-diazotetrafluorobenzene 4-oxide on treatment with sodium nitrite in aqueous 70% sulphuric acid. Photochemical or thermal decomposition of the 1,2-diazo-oxide in benzene gives 2,3,4,5-tetrafluoro-6-hydroxybiphenyl, and thermal decomposition of the 1,2-diazo-oxide in benzonitrile, acetonitrile, or phenyl isothiocyanate yields 4,5,6,7-tetrafluoro-2-phenylbenzoxazole, 4,5,6,7-tetrafluoro-2-methylbenzoxazole, or 4,5,6,7-tetrafluoro-2-phen-ylimino-1,3-benzoxathiole, respectively. The benzoxazoles may also be obtained from 2-aminotetrafluorophenol and benzoyl chloride or acetic anhydride.
A Mouse Model of Bilateral Cervical Contusion-Compression Spinal Cord Injury (2016)

Cervical spinal cord injury (cSCI) occurs in over half of all cases of traumatic spinal cord injury (SCI), yet we lack therapies that can generate significant functional recovery in these patients. The development of animal models of cSCI will aid in the pre-clinical assessment of therapies and in understanding basic pathophysiological mechanisms. Here, we describe a clinically relevant model of cervical contusion-compression injury in the mouse. Using a modified aneurysm clip, we generated a bilateral, incomplete injury that mimics contusion-compression injuries most commonly observed in humans. We followed the recovery of injured and sham-operated (laminectomy-only) animals for 8 weeks post-surgery. Behavioral tests, including the Basso Mouse Scale (BMS), wire hanging, grip strength, and CatWalk automated gait analysis, showed that while natural recovery is limited, it occurs in a clinically relevant window during the subacute phase of injury (7-14 days post-SCI). BMS scoring demonstrated that, while injured animals are ambulatory, they do not recover normal locomotor ability. CatWalk analysis quantitatively showed a loss of coordination and motor ability, with minimal recovery. The wire hanging and grip strength tests confirmed a significant decrease in forelimb motor strength in injured animals. Histological analysis carried out during the subacute phase (7-day time point) and chronic phase (8-week time point) demonstrated that the lesion epicenter is formed by 7 days post-SCI. Volumetric analysis of protein kinase C gamma (PKCgamma)-stained axons revealed that this injury results in significant damage to the corticospinal tract caudal to the injury site. Finally, we used quantitative real-time polymerase chain reaction to show that genes associated with inflammation and glial scarring are upregulated as a result of injury. This study confirms that we can effectively model bilateral cervical injury in the mouse and provides a framework for future studies using this model to assess therapies.
Poly-A Binding Protein-1 Localization to a Subset of TDP-43 Inclusions in Amyotrophic Lateral Sclerosis Occurs More Frequently in Patients Harboring an Expansion in<i>C9orf72</i> (2014)

Amyotrophic lateral sclerosis (ALS) is an adult-onset motor neuron disease in which the loss of spinal cord motor neurons leads to paralysis and death within a few years of clinical disease onset. In almost all cases of ALS, transactive response DNA binding protein of 43 kDa (TDP-43) forms cytoplasmic neuronal inclusions. A second causative gene for a subset of ALS is fused in sarcoma, an RNA binding protein that also forms cytoplasmic inclusions in spinal cord motor neurons. Poly-A binding protein-1 (PABP-1) is a marker of stress granules (i.e. accumulations of proteins and RNA indicative of translational arrest in cells under stress). We report on the colocalization of PABP-1 to both TDP-43 and fused-in-sarcoma inclusions in 4 patient cohorts: ALS without a mutation, ALS with an intermediate polyglutamine repeat expansion in ATXN2, ALS with a GGGGCC hexanucleotide repeat expansion in C9orf72, and ALS with basophilic inclusion body disease. Notably, PABP-1 colocalization to TDP-43 was twice as frequent in ALS with C9orf72 expansions compared to ALS with no mutation. This study highlights PABP-1 as a protein that is important to the pathology of ALS and indicates that the proteomic profile of TDP-43 inclusions in ALS may differ depending on the causative genetic mutation.
1,4‐Dichloro‐ and 1,4‐Dibromo‐2‐butenes as Substrates for Cu‐Catalyzed Asymmetric Allylic Substitution (2007)

Cu at the AAA meeting: Difunctionalized allylic substrates can undergo Cu-catalyzed asymmetric allylic alkylation (AAA) reactions with high enantioselectivities. The products have a functional group that remains for further transformation through substitution with a nucleophile (Nu) or electrophile (E) with conservation of optical purity (see scheme; TC=thiophene carboxylate).
Finding markets for microstructures (1998)

Silicon became well known as the base material for high performance microstructures on the basis of cost, performance, durability, and excellent mechanical as well as electrical properties. Numerous market surveys and projections have identified a myriad of high volume opportunities over the past two decades. Yet true commercial success has remained in isolated pockets. The appeal of mechanical and electrical on the same miniature device combined with the photogenic resulting structures has resulted in a general hype of the technology. In concept, microstructures in silicon can fill just about any role as a small scale physical to electrical interface. However, the danger lies in assuming that these applications justify the cost. These costs of ownership include infrastructure cost, cost of compensating for performance limits, time to market, and hidden manufacturing costs. Many technically elegant microstructure solutions become solutions looking for problems. This presentation looks first at the opportunity and characteristics of silicon microstructures that make it an enabling technology, followed by examples where the technology has found markets. A summary of the industry characteristics and a comparison and contrast with the traditional electronics industry follows. A profile of successful microstructure applications and future trends leads to insight on how to structure a commercially viable approach. Finally, a summary of the market drivers and requirements and the true cost of ownership provides guidance on markets where a microstructure solution makes sense.