gebhart/patrepeval huggingface dataset:
A Hidden Markov Model approach to variation among sites in rate of evolution (1996)

The method of Hidden Markov Models is used to allow for unequal and unknown evolutionary rates at different sites in molecular sequences. Rates of evolution at different sites are assumed to be drawn from a set of possible rates, with a finite number of possibilities. The overall likelihood of phylogeny is calculated as a sum of terms, each term being the probability of the data given a particular assignment of rates to sites, times the prior probability of that particular combination of rates. The probabilities of different rate combinations are specified by a stationary Markov chain that assigns rate categories to sites. While there will be a very large number of possible ways of assigning rates to sites, a simple recursive algorithm allows the contributions to the likelihood from all possible combinations of rates to be summed, in a time proportional to the number of different rates at a single site. Thus with three rates, the effort involved is no greater than three times that for a single rate. This "Hidden Markov Model" method allows for rates to differ between sites and for correlations between the rates of neighboring sites. By summing over all possibilities it does not require us to know the rates at individual sites. However, it does not allow for correlation of rates at nonadjacent sites, nor does it allow for a continuous distribution of rates over sites. It is shown how to use the Newton-Raphson method to estimate branch lengths of a phylogeny and to infer from a phylogeny what assignment of rates to sites has the largest posterior probability. An example is given using beta-hemoglobin DNA sequences in eight mammal species; the regions of high and low evolutionary rates are inferred and also the average length of patches of similar rates.
Intravenous regional anaesthesia of the arm (1989)

The effects of different techniques of exsanguination of the upper arm during intravenous regional anaesthesia on prilocaine plasma concentrations, quality of anaesthesia, toxic symptoms after deflation of the tourniquet and injection pressure of the anaesthetic were studied in 10 healthy male volunteers. The nondominant arm was exsanguinated using either Esmarch's bandage or elevation of the arm for 2 minutes plus arterial occlusion by compression of the brachial artery. The injection pressure after the prilocaine dose (3 mg/kg) was significantly higher in the elevation group (maximally 98 mmHg). There were no statistically significant differences in the onset of, or recovery from, anaesthesia between the groups. Various mild toxic symptoms were experienced in the central nervous system after deflation of the tourniquet. However, there was no correlation between the two techniques and the degree of severity of the toxic symptoms. The highest single venous plasma concentration (total) of prilocaine was 2.3 micrograms/ml measured from the contralateral cubital vein (elevation group, 2 minutes). The differences in prilocaine concentrations between the groups were not statistically significant.
Fuel option for gas turbine (2002)

Growth in electricity demand is an average of 10% per year. Energy, emission, and economy are important critical concerns for generating systems. Therefore, combined cycle power plant is prefered for the Electricity Generating Authority of Thailand's (EGAT) new power generating capacity. The various options of available fuel for gas turbines are natural gas, liquid fuel and coal fuel. Particularly with the tremendous price increases in imported and domestic fuel supplies, natural gas is an attractive low cost alternative for power generation. EGAT has studied and researched the use of heavy fuel instead of natural gas since the 1991. The problems of various corrosion characteristics have been found. In addition, fuel treatment for gas turbines are needed, and along with it, the environmental considerations are options that provide the limitation of environmental regulation.
PGASUS: A Framework for C++ Application Development on NUMA Architectures (2016)

For the implementation of data-intensive C++ applications for cache coherent Non-Uniform Memory Access (NUMA) systems, both massive parallelism and data locality have to be considered. While massive parallelism has been largely understood, the shared memory paradigm is still deeply entrenched in the mindset of many C++ software developers. Hence, data locality aspects of NUMA systems have been widely neglected thus far. At first sight, applying shared nothing approaches might seem like a viable workaround to address locality. However, we argue that developers should be enabled to address locality without having to surrender the advantages of the shared address space of cache coherent NUMA systems. Based on an extensive review of parallel programming languages and frameworks, we propose a programming model specialized for NUMA-aware C++ development that incorporates essential mechanisms for parallelism and data locality. We suggest that these mechanisms should be used to implement specialized data structures and algorithm templates which encapsulate locality, data distribution, and implicit data parallelism. We present an implementation of the proposed programming model in the form of a C++ framework. To demonstrate the applicability of our programming model, we implement a prototypical application on top of this framework and evaluate its performance.
Foliar Sprays of Silver Thiosulfate Produce Male Flowers on Female Hemp Plants (2018)

Interest in hemp ( Cannabis sativa ) for its medicinal compounds, cannabidiol (CBD), and Δ-9-tetrahydrocannabidiol (THC), continues to increase. Maximizing yield of CBD and/or THC requires female plants because female inflorescences accumulate significantly greater concentrations of these compounds than male inflorescences. Production of all female seed requires induction of female plants to develop male flowers that produce genetically female pollen. Growers would like access to feminized seed to produce all-female crops. We evaluated the efficacy of 0, 0.3, and 3 m m silver thiosulfate (STS) applied as a foliar spray (on three occasions 7 days apart) to produce male flowers on four strains of female hemp (having a THC concentration of ≤0.3%), designated CBD hemp A, CBD hemp B, CBD hemp C, and industrial hemp. Silver thiosulfate at 3 m m was the most efficacious treatment for all strains. The majority of inflorescences had 100% male flowers at 3 m m STS, and terminal inflorescences had ≥95% conversion to male flowers. Silver thiosulfate at 0.3 m m produced partial conversion to male flowers, whereas most inflorescences had around 50% male flowers, except for CBD hemp A, which demonstrated greater levels of masculinization. At 0.3 m m STS, terminal inflorescences of CBD hemp A had 91% conversion to male flowers. This study demonstrates that male flowers can be produced easily and consistently on female plants through application of foliar sprays of STS under short-day conditions.
A simple method for detecting HIV antibodies hidden in circulating immune complexes. (1987)

A method previously used for studying the specificity of antibody components of circulating immune complexes in different diseases has been applied to analyse circulating immune complexes in HIV-infected patients. Antibodies against HIV antigens hidden in circulating immune complexes were studied in 14 sera from 13 patients with asymptomatic HIV infection (group 1) and in 11 sera from seven patients with HIV symptoms (group 2). HIV antigen-coated wells from the Vironostika kit as well as core and envelope antigen-coated beads from the Abbott confirmatory kit were used as solid-phase antigen. Using the Vironostika plates, HIV antibodies were demonstrated in circulating immune complexes in three and five sera in groups 1 and 2, respectively. Anti-core antibodies hidden in circulating immune complexes were present in three out of eight and two out of nine sera, respectively, in groups 1 and 2, whereas anti-envelope antibodies were present in circulating immune complexes in one out of eight and six out of nine sera in the same groups. These findings demonstrate that not only core-anti-core but also envelope-anti-envelope immune complexes are present in the sera of HIV infected patients.
Suppression of Cytokines and Nitric Oxide Production, and Protection Against Lethal Endotoxemia and Viral Myocarditis by a New NF-κB Inhibitor (2003)

These findings suggest that the activation of NF-kappaB plays an important role in the pathogenesis of endotoxemia and viral myocarditis, and that the NF-kappaB inhibitor, SUN C8079, may be therapeutic in these disorders.
Stoma care nursing management: cost implications in community care (2009)

Successfully rehabilitating the stoma patient in the community means continuing the care provided by the hospital and preparing the patient for this new phase of life. It is well documented that this transition from hospital to home can often be a difficult time for the stoma patient and that home visits and ongoing support from the district nursing team are needed for many patients in the long term. This article aims to help community nurses understand the needs of the stoma patient in their homes and looks at the current situation, including costs, of supplying stoma appliances in the community.
Effects of Divalent Metals on Nanoscopic Fiber Formation and Small Molecule Recognition of Helical Proteins (2012)

Abstract Metal dependent protein‐based assemblies derived from the cartilage oligomeric matrix protein (C) coiled‐coil domain (His 6 ‐C) and two variants with mutation at position 40 (His 6 ‐T40A) and 44 (His 6 ‐L44A) are explored. All proteins have an N‐terminal hexahistidine tag (His 6 ) that interacts with divalent metal ions Zn(II) and Ni(II). Binding to Zn(II) confers enhanced helical structure and stability, while Ni(II) promotes aggregation. Surprisingly, His 6 ‐L44A undergoes a conformational switch from unstructured to α‐helix in the presence of Zn(II). Both His 6 ‐C and His 6 ‐T40A further assemble into discrete nanofibers that appear to be stabilized by Zn(II) in which the fiber formation is dictated by the α‐helical content. Because Ni(II) promotes aggregation, the proteins visibly cluster, forming large fiber mats in the case of His 6 ‐C and His 6 ‐T40A or aggregated structures as observed for His 6 ‐L44A. Due to the unique pentameric assembly of the proteins, recognition of a small molecule within the pore is assessed using curcumin as the guest molecule. In the presence of Zn(II), there is enhanced binding to curcumin, while the addition of Ni(II) causes a loss in binding. It is shown that metal binding serves as a trigger to control the conformation of the proteins, affecting the nanoscopic fibrous assemblies and small molecule recognition abilities.
Automotive Software Development for a Multi-Core System-on-a-Chip (2007)

There are many economic and technical arguments for the reduction of the number of Electronic Control Units (EC Us) aboard a car. One of the key obstacles to achieve this goal is the limited composability, fault isolation and error containment of today's single- processor architectures. However, significant changes in the chip architecture are taking place in order to manage the synchronization, energy dissipation, and fault-handling requirements of emerging billion transistor SoCs (systems-on-a-chip). The single processor architecture is replaced by multi-core SoCs that communicate via networks-on-chip (NoC). These emerging multi-core SoCs provide an ideal execution environment for the integration of multiple automotive ECUs into a single SoC This paper presents a model-based software development method for designing applications using these multi-core SoCs.
Detection of retinal changes from illumination normalized fundus images using convolutional neural networks (2017)

Automated detection and quantification of spatio-temporal retinal changes is an important step to objectively assess disease progression and treatment effects for dynamic retinal diseases such as diabetic retinopathy (DR). However, detecting retinal changes caused by early DR lesions such as microaneurysms and dot hemorrhages from longitudinal pairs of fundus images is challenging due to intra and inter-image illumination variation between fundus images. This paper explores a method for automated detection of retinal changes from illumination normalized fundus images using a deep convolutional neural network (CNN), and compares its performance with two other CNNs trained separately on color and green channel fundus images. Illumination variation was addressed by correcting for the variability in the luminosity and contrast estimated from a large scale retinal regions. The CNN models were trained and evaluated on image patches extracted from a registered fundus image set collected from 51 diabetic eyes that were screened at two different time-points. The results show that using normalized images yield better performance than color and green channel images, suggesting that illumination normalization greatly facilitates CNNs to quickly and correctly learn distinctive local image features of DR related retinal changes.
First report of autochthonous transmission of Zika virus in Brazil (2015)

In the early 2015, several cases of patients presenting symptoms of mild fever, rash, conjunctivitis and arthralgia were reported in the northeastern Brazil. Although all patients lived in a dengue endemic area, molecular and serological diagnosis for dengue resulted negative. Chikungunya virus infection was also discarded. Subsequently, Zika virus (ZIKV) was detected by reverse transcription-polymerase chain reaction from the sera of eight patients and the result was confirmed by DNA sequencing. Phylogenetic analysis suggests that the ZIKV identified belongs to the Asian clade. This is the first report of ZIKV infection in Brazil.
Monolithic low-power 16 b 1 MSample/s self-calibrating pipeline ADC (2002)

Pipelined architectures enable the implementation of high-speed, high-resolution, low-power analog-to-digital converters (ADCs). Concurrent processing of analog signals results in power and/or speed advantages over flash and multistep ADC architectures. While self-calibration techniques reduce the effects of component mismatches, the digital crosstalk due to correction circuitry can degrade the noise and linearity performance of the overall converter. Previous pipeline ADCs achieve high speed and high resolution, but with the digital circuitry off chip. This 16 b 1 MSample/s pipeline ADC with on-chip digital correction circuitry operates on a single SV analog supply. Problems due to digital crosstalk and solutions reducing its effects are presented. Reduction of integral non-linearity (INL) errors due to capacitor voltage coefficient are discussed.
Aluminum Toxicity and Albumin (1989)

During a study of priming solutions for extracorporeal membrane oxygenation (ECMO) in the intensive care nursery, it was discovered that those solutions using certain brands of 25% albumin contained aluminum levels within the toxic range. When the brand was changed to a brand known to have a lower aluminum (Al) content, a marked drop in priming solution Al levels was measured. The heat exchanger was examined as a possible source of soluble Al. No evidence of elevated Al levels was found in fluids perfusing this heat exchanger when compared with a stainless steel heat exchanger. The Al content of various blood products was evaluated along with various brands of 5% albumin and 25% albumin.
Amphiphilic membranes crosslinked and reinforced by POSS (2004)

Abstract This article concerns the synthesis and characterization of novel tricomponent amphiphilic membranes consisting of hydrophilic poly(ethylene glycol) (PEG) and hydrophobic polydimethylsiloxane (PDMS) segments cocrosslinked and reinforced by octasilane polyhedral oligomeric silsesquioxane (octasilane‐POSS) cages. Rapid and efficient network synthesis was effected by cocrosslinking diallyl‐telechelic PEG (A‐PEG‐A) and divinyl‐telechelic PDMS (V‐PDMS‐V) with pentamethylpentacyclosiloxane (D 5 H), using Karstedt's catalyst in conjunction with Et 3 N cocatalyst and water. Films were prepared by pouring charges in molds and crosslinking by heating at 60 °C for several hours. The films were characterized by sol fractions and equilibrium swelling both in hexane and water, extent of crosslinking, contact angle hysteresis, oxygen permeability, thermogravimetric analysis, and mechanical properties. The crosslinking of octasilane‐POSS achieved by the same catalyst system was studied in separate experiments. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 4337–4352, 2004
Making planar antennas out of solar cells (2002)

A presentation is made of the possibility of replacing metallic patches by solar cells in planar antennas. To demonstrate the concept, a slot-fed microstrip antenna using solar cells instead of a copper patch has been realised and measured. The results show that the ‘solar cell patches’ have characteristics equivalent to copper patches.
The Relationship Of In Vivo 31P Mr Spectroscopy to Histology in Chronic Hepatitis C (2003)

Liver biopsy remains the gold standard for characterizing diffuse liver disease and is associated with significant morbidity and, rarely, mortality. Our aim was to investigate whether a noninvasive technique, in vivo phosphorus 31 ((31)P)-magnetic resonance spectroscopy (MRS), could be used to assess the severity of hepatitis C virus (HCV)-related liver disease. Fifteen healthy controls and 48 patients with biopsy-proven HCV-related liver disease were studied prospectively. Based on their histologic fibrosis (F) and necroinflammatory (NI) scores, patients were divided into mild hepatitis (F <or= 2/6, NI <or= 3/18), moderate/severe hepatitis (3 <or= F < 6 or NI >or= 4/18), and cirrhosis (F = 6/6). Hepatic (31)P MR spectra were obtained using a 1.5-T spectroscopy system. Quantitation of the (31)P signals was performed in the time domain using the Advanced MAgnetic RESonance algorithm. There was a monotonic increase in the mean +/- 1 standard error phosphomonoester (PME) to phosphodiester (PDE) ratios for the control, mild disease, moderate disease, and cirrhosis groups: 0.15 +/- 0.01, 0.18 +/- 0.02, 0.25 +/- 0.02, 0.38 +/- 0.04, respectively (ANOVA, P <.001). An 80% sensitivity and specificity was achieved when using a PME/PDE ratio less than or equal to 0.2 to denote mild hepatitis and a corresponding ratio greater than or equal to 0.3 to denote cirrhosis. No other significant spectral changes were observed. In conclusion, (31)P MRS can separate mild from moderate disease and these 2 groups from cirrhosis. The ability to differentiate these populations of patients has therapeutic implications and (31)P MRS, in some situations, would not only complement a liver biopsy but could replace it and be of particular value in assessing disease progression.
Nucleotide chemistry. XIV. Protecting groups for nucleosides used in synthesizing oligonucleotides (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleotide chemistry. XIV. Protecting groups for nucleosides used in synthesizing oligonucleotidesRobert L. Letsinger and Paul S. MillerCite this: J. Am. Chem. Soc. 1969, 91, 12, 3356–3359Publication Date (Print):June 1, 1969Publication History Published online1 May 2002Published inissue 1 June 1969https://pubs.acs.org/doi/10.1021/ja01040a043https://doi.org/10.1021/ja01040a043research-articleACS PublicationsRequest reuse permissionsArticle Views585Altmetric-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-Alertsclose Get e-Alerts
Flexible and tunable silicon photonic circuits on plastic substrates (2012)

Flexible microelectronics has shown tremendous promise in a broad spectrum of applications, especially those that cannot be addressed by conventional microelectronics in rigid materials and constructions. These unconventional yet important applications range from flexible consumer electronics to conformal sensor arrays and biomedical devices. A recent paradigm shift in implementing flexible electronics is to physically transfer highly integrated devices made in high-quality, crystalline semiconductors on to plastic substrates. Here we demonstrate a flexible form of silicon photonics using the transfer-and-bond fabrication method. Photonic circuits including interferometers and resonators have been transferred onto flexible plastic substrates with preserved functionalities and performance. By mechanically deforming, the optical characteristics of the devices can be tuned reversibly over a remarkably large range. The demonstration of the new flexible photonic systems based on the silicon-on-plastic (SOP) platform could open the door to many future applications, including tunable photonics, optomechanical sensors and biomechanical and bio-photonic probes.
Acute-phase response of human hepatocytes: Regulation of acute-phase protein synthesis by interleukin-6 (1990)

Human hepatocytes in primary culture were used as a model system to investigate the mechanism(s) involved in the induction of the acute-phase response in human liver. Hepatocytes were incubated with increasing amounts of recombinant human interleukin-1 beta, recombinant interleukin-6 and tumor necrosis factor-alpha. Synthesis of C-reactive protein was studied at the mRNA and protein levels. Only recombinant interleukin-6 was capable of inducing C-reactive protein-mRNA and C-reactive protein-protein synthesis. Also, fibrinogen and alpha-1-antitrypsin synthesis measured by immunoprecipitation with specific antisera increased in a dose-dependent, time-dependent manner, whereas albumin synthesis decreased to about 50% of controls. Maximal effects were observed at 100 to 300 units of recombinant interleukin-6/ml culture medium after 20 hr of incubation. Although the synthetic glucocorticoid dexamethasone slightly modulated the effect of recombinant interleukin-6, it was not an absolute requirement for the induction of acute-phase protein synthesis in human hepatocytes. In pulse-chase experiments it was shown that the time course of the disappearance of the acute-phase proteins from the cells and their appearance in the medium is not influenced by recombinant interleukin-6. This finding suggests that recombinant interleukin-6 exerts its regulatory effect on acute-phase protein synthesis at the pretranslational level.
Magnetic exchange interaction induced by a Josephson current (2002)

We show that a Josephson current flowing through a ferromagnet--normal-metal--ferromagnet trilayer connected to two superconducting electrodes induces an equilibrium exchange interaction between the magnetic moments of the ferromagnetic layers. The sign and magnitude of the interaction can be controlled by the phase difference between the order parameters of the two superconductors. We present a general framework to calculate the Josephson current induced magnetic exchange interaction in terms of the scattering matrices of the different layers. The effect should be observable as the periodic switching of the relative orientation of the magnetic moments of the ferromagnetic layers in the ac Josephson effect.