gebhart/patrepeval huggingface dataset:
Polymer principles and protein folding (1999)

This paper surveys the emerging role of statistical mechanics and polymer theory in protein folding. In the polymer perspective, the folding code is more a solvation code than a code of local phipsi propensities. The polymer perspective resolves two classic puzzles: (1) the Blind Watchmaker's Paradox that biological proteins could not have originated from random sequences, and (2) Levinthal's Paradox that the folded state of a protein cannot be found by random search. Both paradoxes are traditionally framed in terms of random unguided searches through vast spaces, and vastness is equated with impossibility. But both processes are partly guided. The searches are more akin to balls rolling down funnels than balls rolling aimlessly on flat surfaces. In both cases, the vastness of the search is largely irrelevant to the search time and success. These ideas are captured by energy and fitness landscapes. Energy landscapes give a language for bridging between microscopics and macroscopics, for relating folding kinetics to equilibrium fluctuations, and for developing new and faster computational search strategies.
Electroplated Metal Microstructures Embedded in Fusion-Bonded Silicon: Conductors and Magnetic Materials (2004)

Fabrication methods for integrating thick (tens or hundreds of micrometers) electroplated metallic microstructures inside fusion-bonded silicon wafers are proposed and validated. Cu and Ni/sub 80/Fe/sub 20/ (permalloy) test structures were embedded inside of cavities in silicon wafers, which were fusion-bonded at 500/spl deg/C for 4h with nearly 100% yield. Resistance tests validated the electrical integrity of the metals after annealing, and magnetic measurements indicated the Ni-Fe maintained its magnetic performance after annealing. Additional mechanical tests verified a strong, uniform bond, and that the presence of the metals does not degrade the bond strength. These results demonstrate the ability to integrate conductive and magnetic materials in wafer-bonded silicon, a method useful for a variety of multiwafer, MEMS devices.
A Chloroquine-like Molecule Designed to Reverse Resistance in <i>Plasmodium falciparum</i> (2006)

A class of hybrid molecules which we term 'reversed chloroquines' (RCQs) was designed, and a prototype molecule, N'-(7-chloroquinolin-4-yl)-N-[3-(10,11-dihydrodibenzo[b,f]azepin-5-yl)propyl]-N-methylpropane-1,3-diamine (1), was synthesized and tested against both chloroquine-sensitive and chloroquine-resistant strains of Plasmodium falciparum. An in vitro assay against the two strains indicated that 1 was effective at low-nM concentrations against both strains. A preliminary study in mice demonstrated oral efficacy against P. chabaudi and the absence of obvious toxicity. The RCQ approach therefore appears to be feasible.
The Valsalva maneuver: mechanisms and clinical implications. (1984)

The previous discussion has focused on the mechanisms, both respiratory and circulatory, that occur during the Valsalva maneuver. The increase in intrathoracic pressure that occurs during the Valsalva maneuver incites a sequence of rapid changes in preload and afterload stress. During the strain, venous return to the heart is decreased and peripheral venous pressures become increased. Within the next few beats, systolic and pulse pressures begin to fall while mean arterial pressure remains near (or is elevated above) control levels owing to the transmission of airway pressure. Thus it would appear that the benefits to cardiac contractility derived from a decrease in systolic and pulse pressure are counterbalanced by an increase in mean arterial pressure. Increases in total peripheral resistance that begin after about 7 seconds of strain produce further increases in afterload. Recruitment of autonomically mediated increases in heart rate and cardiac contractility assists the heart to maintain its cardiac output in the presence of diminished venous return. With the increased venous return that accompanies termination of Valsalva strain, there is an increase in diastolic filling and stroke volume output by means of the Frank-Starling mechanism. Heart rate and total peripheral resistance continue to be increased during the immediate poststrain period, and the ejection of an increased stroke volume into a constricted arterial system produces a rapid and marked increase in arterial pressure--the phase IV overshoot with its subsequent slowing of heart rate.
VISCOSITY STUDIES OF SYSTEM CaO–MgO–Al <sub>2</sub> O <sub>3</sub> –SiO <sub>2:</sub> 1, 40% SiO <sub>2</sub> * (1945)

A bstract The measurement of glass viscosities at elevated temperatures with an oscillating cylinder‐type viscometer is described. Viscosity data are presented covering those compositions in the CaO–MgO–Al 2 O 3 –SiO 2 system which contain 40% SiO 2 and which are liquid at 1500°C. The pattern of the system of isokoms presented indicates that viscosity is closely related to the ratio of basic to acidic components. Theoretical aspects of the variation of viscosity with composition in silicate‐aluminate systems are discussed in terms of silica‐alumina polymers.
Mass spectrometry of cytokinin metabolites. Per(trimethylsilyl) and permethyl derivatives of glucosides of zeatin and 6-benzylaminopurine (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMass spectrometry of cytokinin metabolites. Per(trimethylsilyl) and permethyl derivatives of glucosides of zeatin and 6-benzylaminopurineJohn K. MacLeod, Roger E. Summons, and David S. LethamCite this: J. Org. Chem. 1976, 41, 25, 3959–3967Publication Date (Print):December 1, 1976Publication History Published online1 May 2002Published inissue 1 December 1976https://pubs.acs.org/doi/10.1021/jo00887a006https://doi.org/10.1021/jo00887a006research-articleACS PublicationsRequest reuse permissionsArticle Views130Altmetric-Citations41LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Selective Induction of Tumor Necrosis Receptor Factor 6/Decoy Receptor 3 Release by Bacterial Antigens in Human Monocytes and Myeloid Dendritic Cells (2003)

Tumor necrosis factor (TNF) receptor 6/decoy receptor 3 (TR6/DcR3) is an antiapoptosis soluble receptor of the TNF family produced by tumor cells. In this study, TR6 expression in human immune cells was investigated. TR6 mRNA and protein were detectable in selected antigen-presenting cells. Monocytes and myeloid-derived dendritic cells (MDC) released the protein exclusively following stimulation of Toll-like receptor 2 (TLR2) and TLR4 by gram-positive and gram-negative bacterial antigens. Plasmacytoid dendritic cells, activated by bacterial antigens via TLR9 or by viral infection, did not produce the protein. Similarly, activated T cells did not release TR6. The release of TR6 by MDC was dependent on the activation of p42/p44 mitogen-activated protein kinases, Src-like protein tyrosine kinases, and phosphatidylinositol 3-kinase, signaling pathways important for MDC maturation and survival. In agreement with the in vitro data, TR6 levels in serum were significantly elevated in patients with bacterial infections. Overall, these data suggest a novel role for TR6 in immune responses to bacteria.
Application of Hydrodynamic Cavitation to Wastewater Treatment (2016)

Abstract Hydrodynamic cavitation is a promising application in wastewater treatment due to its simple reactor design and capacity in large‐scale operation. Theoretical studies including the basic mechanism of pollutant degradation, modeling of pressure distribution in the cavitation reactor, and bubble dynamics models coupled with chemical reactions are evaluated. Experimental setups with different cavitation reactors and operation parameters are compared for degrading specific kinds of pollutants. The effort directions for both theoretical and experimental investigations are suggested on the basis of the reviewed contents. Easy large‐scale operation, effective combination with intensified strategies, and capability to deal with biorefractory or toxic compounds contribute to the great potential of hydrodynamic cavitation.
An E-Health Solution for Automatic Sleep Classification according to Rechtschaffen and Kales: Validation Study of the Somnolyzer 24 × 7 Utilizing the Siesta Database (2005)

To date, the only standard for the classification of sleep-EEG recordings that has found worldwide acceptance are the rules published in 1968 by Rechtschaffen and Kales. Even though several attempts have been made to automate the classification process, so far no method has been published that has proven its validity in a study including a sufficiently large number of controls and patients of all adult age ranges. The present paper describes the development and optimization of an automatic classification system that is based on one central EEG channel, two EOG channels and one chin EMG channel. It adheres to the decision rules for visual scoring as closely as possible and includes a structured quality control procedure by a human expert. The final system (Somnolyzer 24 x 7) consists of a raw data quality check, a feature extraction algorithm (density and intensity of sleep/wake-related patterns such as sleep spindles, delta waves, SEMs and REMs), a feature matrix plausibility check, a classifier designed as an expert system, a rule-based smoothing procedure for the start and the end of stages REM, and finally a statistical comparison to age- and sex-matched normal healthy controls (Siesta Spot Report). The expert system considers different prior probabilities of stage changes depending on the preceding sleep stage, the occurrence of a movement arousal and the position of the epoch within the NREM/REM sleep cycles. Moreover, results obtained with and without using the chin EMG signal are combined. The Siesta polysomnographic database (590 recordings in both normal healthy subjects aged 20-95 years and patients suffering from organic or nonorganic sleep disorders) was split into two halves, which were randomly assigned to a training and a validation set, respectively. The final validation revealed an overall epoch-by-epoch agreement of 80% (Cohen's kappa: 0.72) between the Somnolyzer 24 x 7 and the human expert scoring, as compared with an inter-rater reliability of 77% (Cohen's kappa: 0.68) between two human experts scoring the same dataset. Two Somnolyzer 24 x 7 analyses (including a structured quality control by two human experts) revealed an inter-rater reliability close to 1 (Cohen's kappa: 0.991), which confirmed that the variability induced by the quality control procedure, whereby approximately 1% of the epochs (in 9.5% of the recordings) are changed, can definitely be neglected. Thus, the validation study proved the high reliability and validity of the Somnolyzer 24 x 7 and demonstrated its applicability in clinical routine and sleep studies.
Fast Anion-Exchange in Highly Luminescent Nanocrystals of Cesium Lead Halide Perovskites (CsPbX<sub>3</sub>, X = Cl, Br, I) (2015)

Postsynthetic chemical transformations of colloidal nanocrystals, such as ion-exchange reactions, provide an avenue to compositional fine-tuning or to otherwise inaccessible materials and morphologies. While cation-exchange is facile and commonplace, anion-exchange reactions have not received substantial deployment. Here we report fast, low-temperature, deliberately partial, or complete anion-exchange in highly luminescent semiconductor nanocrystals of cesium lead halide perovskites (CsPbX3, X = Cl, Br, I). By adjusting the halide ratios in the colloidal nanocrystal solution, the bright photoluminescence can be tuned over the entire visible spectral region (410-700 nm) while maintaining high quantum yields of 20-80% and narrow emission line widths of 10-40 nm (from blue to red). Furthermore, fast internanocrystal anion-exchange is demonstrated, leading to uniform CsPb(Cl/Br)3 or CsPb(Br/I)3 compositions simply by mixing CsPbCl3, CsPbBr3, and CsPbI3 nanocrystals in appropriate ratios.
The global north (2014)

The epidemiology of HIV in high-income countries in 2013 depicts both the successes and challenges of HIV prevention. The stable to decreasing death rates and stable or declining trends in heterosexual populations are likely attributable, at least in part, to the broader availability of effective treatments for HIV and relatively broad availability of antiretroviral treatment in these countries. However, late diagnoses undermine the individual and public health value of antiretroviral treatment, and epidemics of HIV among MSM remain largely uncontrolled despite broad availability and coverage of treatment.
A Practical Synthesis of α,β-Unsaturated Imides, Useful Substrates For Asymmetric Conjugate Addition Reactions (2002)

We report an improved synthesis of α,β-unsaturated imides, a class of compounds that has been identified as broadly useful in (salen)aluminum-catalyzed asymmetric conjugate addition reactions. An efficient, scaleable procedure for the synthesis of phosphonate imide reagent 4 is described, as well as a DBU-mediated Horner WadsworthEmmons reaction that affords the target compounds in high yield and (E)-selectivity and with good functional group tolerance.
Visibly “white” light generation in uniform photonic crystal fiber using a microchip laser (2008)

We report on visibly white supercontinuum generation in photonic crystal fibers using a sub ns pump source at 1064 nm. The spectra extend from below 400 nm to 2450 nm, some 50 nm further into the blue than previously reported spectra. The extra bandwidth which is achieved by a simple modification to the fiber structure gives a higher apparent color temperature and a truly "white" visual appearance. The mechanism for the generation of the deeper blue to ultraviolet frequencies is outlined and our modified fiber is compared with fibers which have been conventionally used for supercontinuum generation.
Milk Protein Polymorphisms in California Dairy Cattle (1991)

Abstract Milk samples from 1454 first lactation heifers were collected from five breeds of cattle in a representative sampling of the California dairy cattle population. Samples were phenotyped for α s1 -casein, β-casein, κ-casein, and β-lactoglobulin using PAGE. Lactation yields for milk, fat, and protein were available on 1166 heifers. Genetic linkage of the casein loci and the relationship between milk protein genotypes and production parameters (milk, fat and protein yield, fat and protein percentage) was investigated. Gene frequencies were similar to those found in other studies of the American dairy cattle population. Linkage was found between β-casein and κ-casein in four of the five breeds and between β-casein and α s1 -casein in the Jersey breed. Casein haplotypes BBB and CA 3 A (α s1 -, β-, κ-casein respectively) occurred in the Holstein population more often than would be expected from a random combination of the alleles. Least squares analysis of the production data indicated that the only significant effect was that of κ-casein genotype on protein yield; the highest yields were obtained for the BB genotype.
A Synthetic Dolastatin 10 Analogue Suppresses Microtubule Dynamics, Inhibits Cell Proliferation, and Induces Apoptotic Cell Death (2013)

We have synthesized eight analogues (D1-D8) of dolastatin 10 containing several unique amino acid subunits. Of these agents, D5 was found to be most effective in inhibiting both HeLa cell proliferation and microtubule assembly in vitro. At low nanomolar concentrations, D5 inhibited the proliferation of several types of cancer cells in culture. D5 bound to tubulin with a dissociation constant of 29.4 ± 6 μM. D5 depolymerized microtubules in cultured cells and produced mulitpolar spindles. At its half-maximal inhibitory concentration (15 nM), D5 strongly suppressed the dynamics of individual microtubules in live MCF-7 cells. D5 increased the accumulation of checkpoint proteins BubR1 and Mad2 at the kinetochoric region and caused G2/M block in these cells. The blocked cells underwent apoptosis with the activation of Jun N-terminal kinase. The results suggested that D5 exerts its antiproliferative action by dampening microtubule dynamics.
Text-to-speech algorithms based on FFT synthesis (2003)

The authors present FFT synthesis algorithms for a French text-to-speech system based on diphone concatenation. FFT synthesis techniques are capable of producing high quality prosodic modifications of natural speech. Several approaches are presented to reduce the distortions due to diphone concatenation. They are based on appropriate manipulations of the phase spectrum, either by phase equalization across all the diphones, or by phase smoothing between successive diphones. The resulting speech is significantly better quality than with conventional LPC synthesis. An experiment to reduce the computational cost by performing all the FFTs off-line is described. The resulting speech is slightly degraded with respect to 'full' FFT synthesized speech, but it remains more natural in comparison with the LPC speech.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Validation of functional diffusion maps (fDMs) as a biomarker for human glioma cellularity (2010)

This study suggests fDMs are valid biomarkers for brain tumor cellularity.
The Civil War in History and Memory (2006)

It has been a difficult time for the Civil War Book Review and the rest of the Louisiana community the past several months. In the aftermath of Katrina, Frank Hardie, both my successor and predecessor as editor of the Review, was forced through difficult circumstances to leave Louisiana and ....
Poly(sulfobetaine)s and corresponding cationic polymers. VIII. Synthesis and aqueous solution properties of a cationic poly(methyl iodide quaternized styrene–<i>n</i>,<i>n</i>‐dimethylaminopropyl maleamidic acid) copolymer (2001)

Abstract A cationic poly(methyl iodide quaternized styrene– N , N ‐dimethylaminopropylmaleamidic acid) copolymer was synthesized through amidoacidification reaction of styrene‐maleic anhydride copolymer with N , N ‐dimethylaminopropylamine (ring‐opening reaction). Its properties in various aqueous salt solutions and pH solutions were studied by measurements of reduced viscosity and intrinsic viscosity. The results indicated that the reduced viscosity and intrinsic viscosity of this cationic polyelectrolyte were related to the type and concentration of the added salts and the results also showed a contrary tendency in some salts with monovalent acid groups to polyelectrolyte. At the same time, some salt ions were observed to strongly attract the quaternary ammonium group of the cationic polymeric side chain and resulted in agglomeration of the polymers. © 2001 John Wiley &amp; Sons, Inc. J Appl Polym Sci 80: 1619–1626, 2001
<i>xia2</i>: an expert system for macromolecular crystallography data reduction (2009)

An expert system for macromolecular crystallography data reduction is presented, which builds on existing software to automate the complete data reduction process from images to merged structure factor amplitudes. This can automatically identify multi-wedge, multi-pass and multiwavelength data sets and includes explicit procedures to test for crystallographic special cases. With the push towards high-thoughput crystallography at synchrotron beamlines and automation of structure solution, the ability to reduce data with no user input fills an important gap in the pipeline.
Benefits of Building Information Modeling for Construction Managers and BIM Based Scheduling (2011)

Building Information Modeling“BIM" is becoming a better known established collaboration process in the construction industry. Owners are increasingly requiring BIM services from construction managers, architects and engineering firms. Many construction firms are now investing in“BIM" technologies during bidding, preconstruction, construction and post construction. The goal of this project is to understand the uses and benefits of BIM for construction managers and examine BIM based scheduling. There are two objectives to this project. First is to identify the current uses of BIM in the Architectural / Engineering / Construction / Facility Management industry to better understand how the BIM-based“build to design" and“design to build" concepts can be used by construction managers under the Construction Management at Risk project delivery system. Second, a focus is placed on analyzing 3D and 4D BIM as well as BIM based scheduling. The research was conducted through literature review, case studies, and interviews. First, the research identified the uses of Building Information Modeling for preconstruction, construction and post construction phases. Then, the project examined the uses and benefits of BIM in the construction of a research facility. Subsequently, a prototype 4D Building Information Model was created and studied. Furthermore, the BIM-based schedule was integrated to the 4D model. Finally, the project concluded with an analysis on the use, advantages and setbacks of BIM and its tools.
Computer-Assisted De-Identification of Free-text Nursing Notes (2005)

Medical researchers are legally required to protect patients ’ privacy by removing personally identifiable information from medical records before sharing the data with other researchers. We present an evaluation of methods for computer-assisted removal and replacement of protected health information (PHI) from free-text nursing notes collected in the intensive care unit as part of the MIMIC II project [1]. A semi-automated method was developed to allow clinicians to highlight PHI on the screen of a tablet PC and to compare and combine the selections of different experts reading the same notes. An analysis of the performance of three human expert de-identifiers and of an automated system is presented. Expert adjudication demonstrated that inter-human variability was high, with few false positives and many false negatives. The sensitivity of human experts working alone ranged from 0.63 to 0.93, with an average of 0.81, and the average positive predictive value was 0.98. An algorithm generated few false negatives but many false positives. Its sensitivity was 0.85, but its positive predictive value was only 0.37. Even highly competent and motivated human experts make errors in de-identification, suggesting that multiple independent reviews are necessary to achieve acceptable levels of de-identification. Our preliminary results indicate that at least some automated methods may be as sensitive as human experts, but additional development is needed to reduce their false positive rate. The de-identified database of nursing notes was reidentified with realistic surrogate (but unprotected) dates, serial numbers, names, and phrases to provide a gold standard database of over 2600 notes (approximately 340,000 words) with over 1700 instances of PHI. This reference gold standard database of nursing notes and the Java source code used to evaluate algorithm performance will be made freely available on Physionet [2, 3] in order to facilitate the development and validation of future deidentification algorithms. 1.