gebhart/patrepeval huggingface dataset:
Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide (2020)

The COVID-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), was declared on March 11, 2020 by the World Health Organization. As of the 31st of May, 2020, there have been more than 6 million COVID-19 cases diagnosed worldwide and over 370,000 deaths, according to Johns Hopkins. Thousands of SARS-CoV-2 strains have been sequenced to date, providing a valuable opportunity to investigate the evolution of the virus on a global scale. We performed a phylogenetic analysis of over 1,225 SARS-CoV-2 genomes spanning from late December 2019 to mid-March 2020. We identified a missense mutation, D614G, in the spike protein of SARS-CoV-2, which has emerged as a predominant clade in Europe (954 of 1,449 (66%) sequences) and is spreading worldwide (1,237 of 2,795 (44%) sequences). Molecular dating analysis estimated the emergence of this clade around mid-to-late January (10-25 January) 2020. We also applied structural bioinformatics to assess the potential impact of D614G on the virulence and epidemiology of SARS-CoV-2. In silico analyses on the spike protein structure suggests that the mutation is most likely neutral to protein function as it relates to its interaction with the human ACE2 receptor. The lack of clinical metadata available prevented our investigation of association between viral clade and disease severity phenotype. Future work that can leverage clinical outcome data with both viral and human genomic diversity is needed to monitor the pandemic.
[2+2+2] Cycloaddition Reactions Catalyzed by Transition Metal Complexes (2006)

Abstract Recent progress in the synthesis of benzene and 1,3‐cyclohexadiene derivatives, and heterocyclic compounds such as pyridines, pyridones, pyrans, pyrimidine diones, etc, has been reviewed. The general mechanistic aspects of the [2+2+2] cycloaddition reaction are discussed. The asymmetric variants of these reactions are also discussed along with the proposed models of asymmetric induction.
The elasticity of synthetic phospholipid vesicles obtained by photon correlation spectroscopy (1991)

Osmotic-swelling experiments were conducted on a variety of preparations of "uniform" unilamellar vesicle systems. The synthetic lipid preparations included both vesicles produced by extrusion through polycarbonate ultrafiltration membranes and vesicles produced by the pH-adjustment method. The vesicles were monitored by photon correlation spectroscopy during swelling as the osmolarity of the external solution was decreased. Contrary to our previously reported results [Aurora, T. S., Li, W., Cummins, H. Z., & Haines, T. H. (1985) Biochim. Biophys. Acta 820, 250-258; Li, W., & Haines, T. H. (1986) Biochemistry 25, 7477-7483; Li, W., Aurora, T. S., Haines, T. H., & Cummins, H. Z. (1986) Biochemistry 25, 8220-8229; Haines, T. H., Li, W., Green, M., & Cummins, H. Z. (1987) Biochemistry 26, 5439-5447] large unilamellar vesicles produced from acidic lipids by the pH-adjustment technique were highly polydisperse and did not swell in a manner that permitted the computation of a Young's modulus, presumably due to the polydispersity. Also contrary to our previous reports, membranes derived from bovine submitochondrial particles did not produce evidence of swelling when subjected to similar protocols. Analysis of osmotic swelling of extruded unilamellar vesicles has allowed us to assign Young's moduli for bilayers of dioleoylphosphatidylcholine and dioleoylphosphatidylglycerol, in the range (5-8) x 10(8) and (3-6) x 10(8) dyn/cm2, respectively. The diameters and polydispersites obtained with electron microscopy and photon correlation spectroscopy were compared directly and with computer-modeling techniques. While excellent agreement was obtained for distributions with low polydispersity (approximately greater than 0.1), serious disagreement was found when the polydispersity exceeded approximately 0.2.
Socio-technical transitions from coal and gas: an unfinished story (2021)

This chapter addresses the technological and socioeconomic processes and pressures that led countries and people to embrace oil, gas and their associated technologies, uses and cultures. It outlines how, why, when and where socio-technical transitions to oil and gas unfolded, and how social science and history help understand them. It explores transitions from coal to oil, refined oil products and natural gas that unfolded at a global scale, and in the UK, Europe, North America and Latin America. The countries discussed embrace diverse political systems, societies, economies, cultures, geographies and energy resource availabilities, factors that have affected the nature, pace and duration of their transitions. This chapter shows that focusing simply on technology’s role fails to reveal how and why energy transitions unfold. We need to understand how energy is used, what different actors want from it, and how we can use it in ways that fit into our lives and enable us to coexist with nature.
Recommending Teammates with Deep Neural Networks (2018)

The effects of team collaboration on performance have been explored in a variety of settings. Online games enable people with significantly different skills to cooperate and compete within a shared context. Players can affect teammates' performance either via direct communication or by influencing teammates' actions. Understanding such effects can help us provide insights into human behavior as well as make team recommendations. In this work, we aim at recommending teammates to each individual player for maximal skill growth. We study the effect of collaboration in online games using a large dataset from Dota 2, a popular Multiplayer Online Battle Arena game. To this aim, we construct an online coplay teammate network of players, whose links are weighted based on the gain in skill achieved due to team collaboration. We then use the performance network to devise a recommendation system based on a modified deep neural network autoencoder method.
A multiversion concurrency control algorithm for concurrent execution of partial update and bulk retrieval transactions (2002)

A novel multiversion concurrency control algorithm is presented which substantially improves concurrency between batch and online transactions. A bulk retrieval transaction which reads all data objects and partial update transactions which read and write a few data objects are studied as batch and online transactions, respectively. The algorithm is based on a mixture of multiversion time-stamp ordering and modified two-version two-phase locking. It can remove the interference between the retrieval and the update transactions, and reduce the interference between the update transactions themselves. Results of a simulation study show that the completion ratio of those transactions with this algorithm is much better than that with existing algorithms, when the number of transactions is large and the data contention between those transactions is high.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Experimental Comparison of Different BER Estimation Methods for Coherent Optical QPSK Transmission Systems (2011)

We experimentally compare several bit-error-rate (BER) estimation approaches in a 10-Gbaud coherent optical nonreturn-to-zero quadrature-phase-shift-keying (NRZ-QPSK) system. The probability density function (pdf) fitting via the generalized exponential function offers the most reliable estimation of the system performance, which agrees well with the error counting measurement. We also propose a novel definition of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> -factor applicable to QPSK constellations, which is more credible compared to the error vector magnitude (EVM).
New Proteins for a New Perspective on Syphilis Diagnosis (2012)

Syphilis is a sexually transmitted disease caused by Treponema pallidum subsp. pallidum; it can be effectively treated with penicillin yet remains prevalent worldwide, due in part to the shortcomings of current diagnostic tests. Here we report the production of soluble recombinant versions of three novel diagnostic candidate proteins, Tp0326, Tp0453, and a Tp0453-Tp0326 chimera. The sensitivities of these recombinant proteins were assessed by screening characterized serum samples from primary, secondary, and latent stages of infection (n = 169). The specificities were assessed by screening false positives identified with the standard diagnostic testing algorithm (n = 21), samples from patients with potentially cross-reactive infections (Leptospira spp., Borrelia burgdorferi, Helicobacter pylori, Epstein-Barr virus, hepatitis B virus, hepatitis C virus, or cytomegalovirus) (n = 38), and samples from uninfected individuals (n = 11). The sensitivities of Tp0326, Tp0453, and the Tp0453-Tp0326 chimera were found to be 86%, 98%, and 98%, respectively, and the specificities were 99%, 100%, and 99%. In a direct comparison, the Captia syphilis (T. pallidum)-G enzyme immunoassay (Trinity Biotech) was used to screen the same serum samples and was found to have a sensitivity of 98% and a specificity of 90%. In particular, Tp0453 and the chimera exhibited superior accuracy in classifying analytical false-positive samples (100%, compared to 43% for the Captia assay). These findings identify Tp0453 and the Tp0453-Tp0326 chimera as novel syphilis-specific diagnostic candidates that surpass the performance of a currently available diagnostic enzyme immunoassay test for syphilis and that allow accurate detection of all stages of infection.
Vortioxetine in the treatment of adult patients with major depressive disorder: a meta-analysis of randomized double-blind controlled trials (2014)

Therapy with vortioxetine was significantly associated with reduction in depression symptoms from baseline compared to placebo. Nevertheless, a significant number of patients who were on vortioxetine therapy have reported more adverse events.
Power Source Electronic Ballast for Electrodeless Fluorescent Lamps (2019)

This paper presents the design, control strategy and experimental results of a two-step, power factor correction stage (PFC) and resonant inverter (RI), electronic ballast proposal to supply 150 W electrodeless fluorescent lamps (EFL). The PFC acts as a controlled power source and provides mid and long-term stability to the system, while the stability of the current through the lamp is achieved with the RI. In addition, the power-mode control requires limitation of the output voltage. The dual operation mode of the PFC (voltage source mode and power source mode) enables an efficient soft resonant ignition and the implementation of simple dimming regulation.
Devulcanization of Whole Passenger Care Tire Material (2013)

Ground tire rubber (GTR) from whole passenger car tires is devulcanized using the conditions which are the best compromise for tire rubbers. The elaboration of the optimal devulcanization process for GTR is performed in order to obtain a homogeneous and high degree of devulcanization. Swelling of GTR in a mixture of an oil and a devulcanization aid before devulcanization was studied as a way to achieve a more homogenous breakdown of the crosslink network. Further optimization of the parameters in terms of devulcanization oil loading and process time were elaborated. By using these optimized devulcanization conditions, a significant reduction of crosslink density can be achieved for GTR
Plasma torch with meltable electrodes: From research to novel technologies (2009)

A plasma reactor based on a plasma generator with meltable electrodes is described. The specific features of the plasma generator, which are the absence of electrode erosion and the possibility of using steam as a plasma gas, extend the range of potential practical application of thermal plasma. The results of study of the arc properties are presented, and examples of industrial implementation of processes run in the plasma reactor based on the meltable-electrode plasma torch are given.
Improving practice with a nurse nutrition team (2001)

This article describes how the introduction of a nurse nutrition team has led to improved staff morale and communication, as well as increasing the number of appropriate referrals to the dietician.
Inside Cover: Small 1/2009 (2009)

The inside cover image shows lizards (10-µm line thickness) etched into a potassium haxacyanoferrate crystal (red) using a reaction-diffusion process initiated from a hydrogel stamp. The technique allows for direct printing of complex microarchitectures into a variety of materials with submicrometer resolution. These images are inspired by M. C. Escher's famous drawings and lithographs. For more information, please read the Concept by K. J. M. Bishop and B. A. Grzybowski, beginning on page 22.
Prevalence and specificity of immunoglobulin G and immunoglobulin A non‐complement‐binding anti‐HLA alloantibodies in retransplant candidates (2008)

The role of complement-binding donor-directed anti-human leukocyte antigen (HLA) antibodies in graft rejection is well established, whereas the prevalence and relevance of non-complement-binding (NCB) anti-HLA antibodies are less well defined. The aim of our study was to establish a sensitive and reliable test system for the detection and the specification of these NCB anti-HLA antibodies. Sera from 60 patients awaiting retransplantation were analysed for the presence of anti-HLA class I alloantibodies with complement-dependent cytotoxicity (CDC) tests. Immunoglobulin (Ig)G(all) anti-HLA class I and class II alloantibodies were differentiated on generic level by plate-based solid phase enzyme-linked immunosorbent assay. Subsequently, a modified bead-based (Luminex) assay was applied, allowing the investigation of IgG(2/4) NCB isotypes as well as IgA(1/2). The anti-HLA specificities of the NCB alloantibodies were determined and compared with known mismatches from previous transplants. Seventeen of the 60 sera (28%) were positive in the CDC increasing to 26 of 60 (43%) in the class I and 33 of 60 (55%) in the class II plate-based assay. Using the modified bead-based system 24 of 60 sera (40%) contained NCB IgG(2/4), which were mostly donor specific. In addition, a high prevalence of NCB IgA antibodies was detected (26 of 60 sera), which occurred independently of IgG(2/4) NCB, and half of which were donor specific. NCB anti-HLA alloantibodies, including the IgA isotype, can reliably be detected using the modified bead-based test system. These NCB alloantibodies had a high prevalence in retransplant candidates and were mostly donor specific.
Anti-Helicobacter pylori therapy followed by celecoxib on progression of gastric precancerous lesions (2009)

H pylori eradication therapy followed by celecoxib treatment improves gastric precancerous lesions by inhibiting COX-2 activity, inducing apoptosis, and suppressing cell proliferation and angiogenesis.
Pricing Freight Transport to Account for External Costs: Working Paper 2015-03 (2015)

Although freight transport contributes significantly to the productivity of the U.S. economy, it also involves sizable costs to society. Those costs include wear and tear on roads and bridges; delays caused by traffic congestion; injuries, fatalities, and property damage from accidents; and harmful effects from exhaust emissions. No one pays those external costs directly—neither freight haulers, nor shippers, nor consumers. The unpriced external costs of transporting freight by truck (per ton-mile) are around eight times higher than by rail; those costs net of existing
Targeted therapies to improve CFTR function in cystic fibrosis (2015)

Cystic fibrosis is the most common genetically determined, life-limiting disorder in populations of European ancestry. The genetic basis of cystic fibrosis is well established to be mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that codes for an apical membrane chloride channel principally expressed by epithelial cells. Conventional approaches to cystic fibrosis care involve a heavy daily burden of supportive treatments to combat lung infection, help clear airway secretions and maintain nutritional status. In 2012, a new era of precision medicine in cystic fibrosis therapeutics began with the licensing of a small molecule, ivacaftor, which successfully targets the underlying defect and improves CFTR function in a subgroup of patients in a genotype-specific manner. Here, we review the three main targeted approaches that have been adopted to improve CFTR function: potentiators, which recover the function of CFTR at the apical surface of epithelial cells that is disrupted in class III and IV genetic mutations; correctors, which improve intracellular processing of CFTR, increasing surface expression, in class II mutations; and production correctors or read-through agents, which promote transcription of CFTR in class I mutations. The further development of such approaches offers great promise for future therapeutic strategies in cystic fibrosis.
En Route to Stimuli‐Responsive Boron‐, Nitrogen‐, and Sulfur‐Doped Polycyclic Aromatic Hydrocarbons (2016)

Replacing both meso carbon atoms of the polycyclic aromatic hydrocarbon (PAH) bisanthene by boron atoms creates an efficient blue fluorophore with a strong electron-accepting character. The corresponding meso-B,S-doped bisanthene exhibits a solvent-dependent green-to-orange photoluminescence and undergoes a reversible reduction at E1/2 =-2.06 V (vs. FcH/FcH(+) ). After oxidation of the sulfur atom, the resulting sulfoxide emits in the blue range of the spectrum, shows only negligible solvatochromism, and a reversible redox transition at E1/2 =-1.74 V. Several related B, N- and B, S-containing PAHs have been prepared following the same modular synthetic procedure and are also described herein. In order to systematically compare their optoelectronic properties, all products have been investigated by cyclic voltammetry as well as UV/Vis absorption/emission spectroscopy.
A REVIEW ON BIODIESEL FEEDSTOCKS AND PRODUCTION TECHNOLOGIES (2021)

Biodiesel is a long-chain fatty acid ester made from renewed and biological raw materials such as used cooking, animal fat, vegetable oil, and algae. Biodiesel is a renewable and clean fuel as it reduces carbon monoxide, carbon dioxide, hydrocarbons, and particulate matter emissions compared with petroleum-based diesel fuel. Production of biodiesel from renewable resources is done through the transesterification reaction at which the organic group (alkyl) of alcohol is substituted with the organic group of a triglyceride-the main component of the feedstock -producing fatty acid alkyl ester (biodiesel) and crude glycerol. Biodiesel can be used in pure form (B100) or may be blended with petroleum diesel at any concentration if its specifications is identical to the international standard specifications provided by American standard for testing materials (ASTM) or EN14214 in the European Union for alternative fuels. In this paper, the different types of biodiesel feedstocks, feedstocks treatment methods, and biodiesel production technologies are reviewed and discussed.
Detecting inconsistencies in multi-platform mobile apps (2015)

Due to the increasing popularity and diversity of mobile devices, developers write the same mobile app for different platforms. Since each platform requires its own unique environment in terms of programming languages and tools, the teams building these multi-platform mobile apps are usually separate. This in turn can result in inconsistencies in the apps developed. In this paper, we propose an automated technique for detecting inconsistencies in the same native app implemented for iOS and Android platforms. Our technique (1) automatically instruments and traces the app on each platform for given execution scenarios, (2) infers abstract models from each platform execution trace, (3) compares the models using a set of code-based and GUI-based criteria to expose any discrepancies, and finally (4) generates a visualization of the models, highlighting any detected inconsistencies. We have implemented our approach in a tool called CheckCAMP. CheckCAMP can help mobile developers in testing their apps across multiple platforms. An evaluation of our approach with a set of 14 industrial and open-source multi-platform native mobile app-pairs indicates that CheckCAMP can correctly extract and abstract the models of mobile apps from multiple platforms, infer likely mappings between the generated models based on different comparison criteria, and detect inconsistencies at multiple levels of granularity.
Microflora Ecology of the Chicken Intestine Using 16S Ribosomal DNA Primers (2004)

The microflora in the gastrointestinal tract of broiler chickens influences digestion, health, and wellbeing. Analysis of chicken gut microflora has been mainly by culture-based methods. Studies using these techniques have been useful for identification and analysis of specific groups of bacteria, however, the use of enrichment medium precludes even relative quantitation of bacterial species. Recent advances in ribosomal DNA-based molecular techniques make it possible to identify different bacterial populations in environmental samples without cultivation. In this study, the intestinal microflora was examined using 16S ribosomal DNA (rDNA) targeted probes from bacterial DNA isolated from intestinal and cecal contents of chickens at 4, 14, and 25 d of age. The ribosomal gene sequence was amplified using PCR with universal primers to determine total bacterial DNA and specific primers directed at 6 bacterial species: Lactobacillus, Bifidobacterium, Salmonella, Campylobacter, Escherichia coli, and Clostridium. The use of universal primers extends these methods to allow determination of relative proportions of different bacterial species. The results indicated that in young chicks the major species present in the small intestines and ceca was Lactobacilli, with a Bifidobacteria population becoming more dominant in the ceca at older age. Clostridium was detected in some segments of the small intestine in young chicks. In older chickens, Salmonella, Campylobacter, and E. coli species were found in the ceca. This study has demonstrated the use of molecular techniques for determining relative proportions of bacterial species and monitoring pathogens in the chick gastrointestinal tract.
Treating with Spectacle Lenses: A Novel Idea!? (2002)

A design approach to low-vision device development-vision multiplexing-was introduced recently. This approach has been applied successfully to the design of novel electronic and optical low-vision aids. This paper discusses the application of the vision-multiplexing concept to spectacle lens design to address issues of low vision and to resolve problems of color discrimination and glare in driving. Because spectacles are considered a fashion accessory as much as they are a vision aid, cosmetic considerations are critical to the design of such aids. Spectacle-borne devices that are not concealed or attractive are unlikely to be used widely. Efforts to combine the functionality of vision multiplexing with improved appearance are illustrated.
The fifth principle. Family physicians as advocates. (2001)

y 3-year-old granddaughter tells me she wants to be a doctor. What will the medical world be like when she enters it in 2030? Will the excit-ing promises of the present be the reality of the future? Will there even be family physicians as we know them today? Will family physicians be remem-bered nostalgically as health caregivers from a former era? Will they be disparaged as inefficient and ineffective fuzzy thinkers, replaced by health technicians in walk-in clinics or Internet sites that dispense diagnoses and treatment by algorithms?Our historyTo understand who we can be, we must know who we are. Three seminal papers written by giants of our discipline describe the special nature of family medicine. Gayle Stephens published “The Intellectual Basis of Family Practice”