gebhart/patrepeval huggingface dataset:
Multiple genes encode the translation elongation factor EF-1λ in<i>Saccharomyces cerevisiae</i> (1994)

A gene encoding a yeast homologue of translation elongation factor 1 gamma (EF-1 gamma), TEF3, was isolated as a gene dosage extragenic suppressor of the cold-sensitive phenotype of the Saccharomyces cerevisiae drs2 mutant. The drs2 mutant is deficient in the assembly of 40S ribosomal subunits. We have identified a second gene, TEF4, that encodes a protein highly related to both the Tef3p protein (Tef3p), and EF-1 gamma isolated from other organisms. In contrast to TEF3, the TEF4 gene contains an intron. Gene disruptions showed that neither gene is required for mitotic growth. Haploid spores containing disruptions of both genes are viable and have no defects in ribosomal subunit composition or polyribosomes. Unlike TEF3, extra copies of TEF4 do not suppress the cold-sensitive 40S ribosomal subunit deficiency of a drs2 strain. Low-stringency genomic Southern hybridization analysis indicates there may be additional yeast genes related to TEF3 and TEF4.
Open Access to Scientific Publications – An Analysis of the Barriers to Change? (2004)

One of the effects of the Internet is that the dissemination of scientific publications in a few years has migrated to electronic formats. The basic business practices between libraries and publishers for selling and buying the content, however, have not changed much. In protest against the high subscription prices of mainstream publishers, scientists have started Open Access (OA) journals and e-print repositories, which distribute scientific information freely. Despite widespread agreement among academics that OA would be the optimal distribution mode for publicly financed research results, such channels still constitute only a marginal phenomenon in the global scholarly communication system. This paper discusses, in view of the experiences of the last ten years, the many barriers hindering a rapid proliferation of Open Access. The discussion is structured according to the main OA channels; peer-reviewed journals for primary publishing, subject- specific and institutional repositories for secondary parallel publishing. It also discusses the types of barriers, which can be classified as consisting of the legal framework, the information technology infrastructure, business models, indexing services and standards, the academic reward system, marketing, and critical mass.
Hardware &#x2014; software hybrid open single phase diagnostic scheme for PMAC machines (2013)

Electric machines being the sole means of converting electrical energy to mechanical energy, advancement of hybrid electric vehicle technology and electric vehicle technology demands sophisticated motor controls. Inherent advantages of permanent magnet AC (PMAC) machines have made it one of the most preferable means of electromechanical energy conversion in a wide range of applications with the transportation industry (ground, sea and air) being a crucial area. Fault detection capabilities in transportation applications are crucial in guaranteeing safe and reliable operation. Increasing regulations require more safety features to be included in HEVs and EVs. Open phase fault diagnostic scheme presented in this paper reduces the burden on the Digital Signal Processor by eliminating RMS calculation of phase current with the means of an RMS generating analog circuit.
Crowd-sourcing based android application for structural health monitoring and data analytics of roads using cloud computing (2017)

In this paper, we propose Crowd-Sourcing based Android Application to detect damaged roads and generate a report which will assist the vehicle driver for safer driving by providing an early warning system to warn the driver of any abrupt discontinuities on the road. We have designed and implemented a model using layered approach that consists of sensor data collected from the users, cloud based data analytics and a response model for the mobile which is integrated with Google Maps. This paper discusses about the review for previous works in the related domain, our proposed architecture, its implementation, obtained results and its detailed inference.
Distributing electronic folders: the digital electoral campaign of 1998 in the Netherlands (1998)

Paper presented at 'Horizon 1999: Conference on Communication', organized by the German Society for Communication Science, the Dutch Society for Communication Studies, the European Communication Association and the Department of Media and Communication of Utrecht University, 12-14 May, Utrecht.
Oh, the Places You’ll Go with Graphene (2013)

Since the first reported isolation of graphene by peeling graphite with cellophane tape in 2004, there has been a paradigm shift in research. In just nine years, graphene has had a major impact on fields ranging from physics and chemistry to materials science and engineering leading to a host of interdisciplinary advances in nanotechnology. Graphene is attractive because it possesses many extraordinary characteristics that are a direct consequence of its unique atomic structure, as discussed here. For over a decade, our group has been exploring new routes to synthesize graphene so that this potentially important material can be scaled up for use in practical applications. We have made several significant discoveries starting with the synthesis of few-layer graphene from intercalation/exfoliation reactions that upon sonication produce carbon nanoscrolls. Next, we developed high-throughput methods for producing chemically converted graphene from graphene oxide using either aqueous or anhydrous hydrazine. Recently, we introduced an inexpensive process that uses the laser in an optical drive to deoxygenate graphite oxide layers to create laser scribed graphene. The impetus of this Account is to discuss both synthetic routes to graphene and their applications. The first part highlights both our top-down and bottom-up routes to graphene, which includes intercalation/exfoliation, chemical reduction with hydrazine and other organic reagents, chemical vapor deposition, and laser scribed graphene. In the later part, we emphasize the significance of these contributions to the field and how each approach has afforded us unique opportunities to explore graphene's properties. This has resulted in new applications such as practical chemical sensors, flash memory storage devices, transparent conductors, distributed ignition, and supercapacitors.
Non-contact Reflection Photoplethysmography towards Effective Human Physiological Monitoring (2010)

A non-contact reflection photoplethysmography (NRPPG) with its engineering model was created to access human\nphysiological information. The NRPPG engineering setup with a vertical cavity surface emitting laser (VCSEL) as a\nlight source and a high-speed PiN photodiode as a photodetector was configured based upon the principles of\nlight-tissue interaction and Beer-Lambert’s law. In this paper, we present three aspects of the NRPPG performance: (1)\nphotonics engineering work to capture photoplethysmographic signals with a non-contact manner in an optimal setup of\nthe NRPPG; (2) a 5-minute protocol with 22 participants to determine a good agreement between NRPPG and contact\nphotoplethysmography (CPPG) by means of Bland-Altman statistical analysis and Pearson’s correlation coefficient; and\n(3) a physiological experiment designed for cardiac-physiological monitoring utilizing NRPPG. The experimental\nresults suggest that clean PPG signal can be obtained between 30-110 mm. The outcome from agreement study indicates\nthat the performance of NRPPG is compatible with CPPG. The NRPPG technique has great potential in\ncardiac-physiological assessment in a required clinical circumstance.
Structural basis of action for a human ether-a-go-go-related gene 1 potassium channel activator (2007)

Activation of human ether-a-go-go-related gene 1 (hERG1) K(+) channels mediates cardiac action potential repolarization. Drugs that activate hERG1 channels represent a mechanism-based approach for the treatment of long QT syndrome, a disorder of cardiac repolarization associated with ventricular arrhythmia and sudden death. Here, we characterize the mechanisms of action and the molecular determinants for binding of RPR260243 [(3R,4R)-4-[3-(6-methoxy-quinolin-4-yl)-3-oxo-propyl]-1-[3-(2,3,5-trifluoro-phenyl)-prop-2-ynyl]-piperidine-3-carboxylic acid] (RPR), a recently discovered hERG1 channel activator. Channels were heterologously expressed in Xenopus laevis oocytes, and currents were measured by using the two-microelectrode voltage-clamp technique. RPR induced a concentration-dependent slowing in the rate of channel deactivation and enhanced current magnitude by shifting the voltage dependence of inactivation to more positive potentials. This mechanism was confirmed by demonstrating that RPR slowed the rate of deactivation, but did not increase current magnitude of inactivation-deficient mutant channels. The effects of RPR on hERG1 kinetics and magnitude could be simulated by reducing three rate constants in a Markov model of channel gating. Point mutations of specific residues located in the S4-S5 linker or cytoplasmic ends of the S5 and S6 domains greatly attenuated or ablated the effects of 3 microM RPR on deactivation (five residues), inactivation (one residue), or both gating mechanisms (four residues). These findings define a putative binding site for RPR and confirm the importance of an interaction between the S4-S5 linker and the S6 domain in electromechanical coupling of voltage-gated K(+) channels.
Development of Efficient Packaging Method of Oligodeoxynucleotides by a Condensed Nano Particle in Lipid Envelope Structure (2005)

An efficient delivery system is required if antisense oligodeoxynucleotides (ODN) are to be utilized for gene therapy. We report herein on the development of a novel ODN delivery system, ODN-encapsulated nano particles (ODN-ENP) using an efficient and simple packaging method. The ODN-ENP consists of a condensed ODN particle and a lipid envelope, which can be equipped with various functional devices for the efficient delivery of ODN with a small diameter (150 nm). The encapsulation efficiency and ODN recovery of ODN-ENP were significantly higher than those of other packaging methods, such as a stabilized antisense-lipid particles method or a freeze-thaw method. Furthermore, the time required for the preparation of the ODN-ENP was shorter than the other methods. The method developed in this study is a simple and efficient packaging method for ODN with a condensed nano particle in lipid-envelope structure.
The role of Neuropilin-1 in COVID-19 (2021)

Neuropilin-1 (NRP-1), a member of a family of signaling proteins, was shown to serve as an entry factor and potentiate SARS Coronavirus 2 (SARS-CoV-2) infectivity in vitro. This cell surface receptor with its disseminated expression is important in angiogenesis, tumor progression, viral entry, axonal guidance, and immune function. NRP-1 is implicated in several aspects of a SARS-CoV-2 infection including possible spread through the olfactory bulb and into the central nervous system and increased NRP-1 RNA expression in lungs of severe Coronavirus Disease 2019 (COVID-19). Up-regulation of NRP-1 protein in diabetic kidney cells hint at its importance in a population at risk of severe COVID-19. Involvement of NRP-1 in immune function is compelling, given the role of an exaggerated immune response in disease severity and deaths due to COVID-19. NRP-1 has been suggested to be an immune checkpoint of T cell memory. It is unknown whether involvement and up-regulation of NRP-1 in COVID-19 may translate into disease outcome and long-term consequences, including possible immune dysfunction. It is prudent to further research NRP-1 and its possibility of serving as a therapeutic target in SARS-CoV-2 infections. We anticipate that widespread expression, abundance in the respiratory and olfactory epithelium, and the functionalities of NRP-1 factor into the multiple systemic effects of COVID-19 and challenges we face in management of disease and potential long-term sequelae.
Growth Differentiation Factor 15 (GDF-15) Plasma Levels Increase during Bleomycin- and Cisplatin-Based Treatment of Testicular Cancer Patients and Relate to Endothelial Damage (2015)

An unbiased approach in a preclinical model revealed genes related to chemotherapy-induced endothelial damage, like GDF-15. The increases in plasma GDF-15 levels in testicular cancer patients during chemotherapy and its association with vWF and hsCRP suggest that GDF-15 is a potentially useful biomarker related to endothelial damage.
Investigation of accurate detection of large-scale objects under a wide field of view (2020)

A new method is proposed to achieve large-scale cigarette filters detection under a wide field of view. It is expected to obtain accurate detection under the situation of overlapping, sheltering, distortion and low contrast. Firstly, by adding the spatially aware based the self-attention argument module and a Focal Loss function, an improved U-net model named as SAAU-net is proposed, which can achieve highly accurate semantic segmentation. After receiving a correct segmentation mask, the circle center of the cigarette filters is determined by object detection. Based on the circle theorem, the structural element matching is used to detect the circle centers. Hidden Markov model(HMM) is employed for direction searching. Experiments performed in simulation and industry application environments(with 5000 boxes) verify that the accuracy of the proposed approach can achieve 99.95%. Results also show that the proposed method has strong robustness to adapt different challenging environments.
Identification of novel transcriptional regulators involved in macrophage differentiation and activation in U937 cells (2009)

Up regulation of MEF2 family, HDACs, and H2AV during cell differentiation and inflammation sheds new lights onto regulation events on transcriptional and epigenetic level controlling these processes. Data generated will serve as a source for further investigation of macrophages differentiation pathways and related biological responses.
Evaluating the evaluation of cancer driver genes (2016)

Sequencing has identified millions of somatic mutations in human cancers, but distinguishing cancer driver genes remains a major challenge. Numerous methods have been developed to identify driver genes, but evaluation of the performance of these methods is hindered by the lack of a gold standard, that is, bona fide driver gene mutations. Here, we establish an evaluation framework that can be applied to driver gene prediction methods. We used this framework to compare the performance of eight such methods. One of these methods, described here, incorporated a machine-learning-based ratiometric approach. We show that the driver genes predicted by each of the eight methods vary widely. Moreover, the P values reported by several of the methods were inconsistent with the uniform values expected, thus calling into question the assumptions that were used to generate them. Finally, we evaluated the potential effects of unexplained variability in mutation rates on false-positive driver gene predictions. Our analysis points to the strengths and weaknesses of each of the currently available methods and offers guidance for improving them in the future.
Antimicrobial peptide LL-37 on surfaces presenting carboxylate anions (2015)

Antimicrobial peptides (AMPs) are part of the immune system in a wide range of organisms. They generally carry positive charges under physiological conditions, allowing them to accumulate on the negatively charged bacterial membrane as the first step of bactericidal action. The concentration range of AMPs necessary for rapid killing of bacteria tested in vitro is much higher than levels found at epithelial surfaces and body fluids in vivo, and close to the a level that is toxic to the host cells. It is likely that AMPs in vivo are localized and act cooperatively to enhance antimicrobial activity, while the global concentration is low thus demonstrating low toxicity to host cells. Herein we employed well-defined mixed self-assembled monolayers (SAMs) to localize LL-37, one of the most studied AMPs, via electrostatic interactions. We systematically varied the surface density of LL-37, and found that the immobilized AMPs not only attracted bacteria Pseudomonas aeruginosa to the surface, but also killed nearly all bacteria when above a threshold density. More significantly, the AMPs displayed low toxicity to human corneal epithelial cells. The results indicated that localization of AMPs on suitable polyanion substrates facilitated the bactericidal activity while minimizing the cytotoxicity of AMPs.
Fiber Bragg grating cryogenic temperature sensors (1996)

Temperature sensing to as low as 80 K was demonstrated with 1.55-μm fiber Bragg gratings. The gratings were bonded on substrates to increase sensitivity, and a shift of the reflection wavelength was measured. The temperature sensitivity was 0.02 nm/K at 100 K when an aluminum substrate was used and 0.04 nm/K at 100 K when a poly(methyl methacrylate) substrate was used. These values are smaller than those at room temperature because of the nonlinearity of both the thermal expansion and the thermo-optic effect. Extension to the liquid helium temperature is also discussed.
Pattern of metastases in renal cell carcinoma: A single institution study (2005)

Background: Increasing numbers of patients with renal cell carcinoma\n(RCC) are incidentally detected and can be potentially cured by surgery\nalone. In treating metastatic RCC, worthwhile survival rates are\nachieved in cases of low burden recurrences. This necessitates a\nrational follow up protocol, which picks up early recurrences and\navoids costly surveillance for those with a favorable prognosis. Aims:\nWe studied the patterns of metastases occurring in patients operated\nfor localized or locally advanced renal cell carcinoma in the Indian\nsetting and try to evolve a suitable follow up protocol. Setting and\nDesign: Institution based, retrospective data.\tMethod and Materials:\nRecords of patients from January 1988 to December 2003, operated for\ninitially localized RCC were reviewed. Follow up was performed using an\nestablished protocol. Occurrence of metastases and their patterns were\nstudied. Statistical analysis used: Comparison of the different\nsurvival times was performed using the one-way analysis method.\nMultiple comparisons (post hoc test) were performed using the\nBonferroni method. Result: Follow up was available on 209 patients.\nMean survival was 43.75 months (SD ± 28.72). Thirty-nine patients\ndeveloped 59 metastases. Lungs were the commonest site of metastases\n(37%), followed by bone (22%), liver (19%) and brain (8%). Relapse and\nsurvival showed significant correlation with pathological stage (p <\n0.001), with higher stage being associated with greater relapses and\nlesser survival. There was no correlation between site of recurrence\nand stage of disease. Conclusions: Occurrence of metastases correlate\nwith the pathological stage of the disease at primary presentation.\nTailored, stage-based follow up protocols allow adequate surveillance\nfor disease activity and progression without escalating the overall\ncosts.
LiMn<sub>2</sub>O<sub>4</sub> microspheres as high-performance cathode materials for Li-ion batteries (2018)

Spinel LiMn2O4 microspheres were prepared by lithiating MnCO3 solid microspheres and MnO2 hollow microspheres, respectively. Li2CO3 was used as lithium source. The spinel LiMn2O4 microspheres samples annealed at different temperatures were characterized by XRD, SEM, and galvanostatic charge/discharge profile measurement. The LiMn2O4 microspheres show an initial discharge capacity reaches 128 mAh/g at 1 C, more than 120 mAh/g of capacity is retained after 80 cycles and the best cycling stability. These results indicate that the LiMn2O4 microspheres could be a promising cathode material for lithium ion batteries.
Dual-Comb Ranging (2018)

Absolute distance measurement is a fundamental technique in mobile and large-scale dimensional metrology. Dual-comb ranging is emerging as a powerful tool that exploits phase resolution and frequency accuracy for high-precision and fast-rate distance measurement. Using two coherent frequency combs, dual-comb ranging allows time and phase response to be measured rapidly. It breaks through the limitations related to the responsive bandwidth, ambiguity range, and dynamic measurement characteristics of conventional ranging tools. This review introduces dual-comb ranging and summarizes the key techniques for realizing this ranging tool. As optical frequency comb technology progresses, dual-comb ranging shows promise for various professional applications.
A Study of the Resistance Characteristics of Double Keel Yacht (2011)

The resistance performances of a small leisure yacht with two different keels, center and double, respectively, are investigated using a model test at circulating water channel and CFD analysis. Flow patterns around the keels are observed using a tuft test to make clear the relation between the resistance performance and the flow characteristics around the keels. The results show that the keel does not affect free surface flows and that the double keel yacht has better performance compared to a single keel yacht in oblique condition from the resistance point of view.
The Kuwait-Scotland eHealth Innovation Network (KSeHIN): a sustainable approach to quality improvement in healthcare. (2014)

KSeHIN represents a successful collaboration between multiple stakeholders working across traditional boundaries. It is targeting patient outcomes, system performance and professional development to provide a sustainable transformation in the quality of diabetes healthcare for the growing population of Kuwaitis with diabetes in Kuwait.
Improved Large-Scale Synthesis of(<i>R</i>)-Benzyl 4-Hydroxyl-2-pentynoate from (<i>R</i>)-3-Butyn-2-ol (2002)

A reliable one-pot process for the title compound has been developed for large-scale productions. The effect of reaction conditions such as temperature, order of addition, and amount of the lithiation reagent has been extensively investigated, giving rise to an optimal process with highest attainable yield.
Intersection Types for Class-based Object Oriented Programming (2008)

Intersection type systems have been well studied in the context of the Lambda Calculus and functional programming over the last quarter of a century or so. Recently, the principles of intersection types have been successfully applied in an object oriented context [5]. This work was done using theςobject calculus of Abadi and Cardelli [1], however we note that this calculus leans more towards the object-based approach to object orientation, and wish to investigate how intersection types interact with a quintessentially classbased approach. In order to do this, we define a small functional calculus that expresses class-based object oriented features and is modelled on the similar calculi of Featherweight Java [18] and Middleweight Java [8], which are ultimately based upon the Java programming language. We define a predicate system, similar to the one defined by van Bakel and de’Liguoro [5], and show subject reduction and expansion. We discuss the implications that this has for the characterisation of expressions in our calculus, and define a restriction of the predicate system which we informally argue is decidable. Acknowledgements I gratefully acknowledge the help and guidance that I have received throughout the last few months from my supervisor, Dr. Steffen van Bakel, who was responsible for my interest in intersection types in the first