gebhart/patrepeval huggingface dataset:
Fine-mapping of shotgun template-libraries; an efficient strategy for the systematic sequencing of genomic DNA (1995)

To test the effectiveness of ordering shotgun DNA-templates prior to sequence analysis, the 450 kb left arm of yeast chromosome XII was randomly subcloned into a phagemid vector. Clones were ordered by hybridisation to an average map density of one new insert every 125 bp and are currently used for sequencing the chromosomal fragment. An 11.5 kb overlap between the template map and a DNA fragment that had been sequenced earlier allowed an independent evaluation of the strategy's effectiveness. To this end, clones were selected from the map and tag-sequenced from either end, thus comparing the map position with the actual location within the 11.5 kb. Of 65 selected clones, taken mostly at random from a total of 423, 58 mapped on average about a quarter of a clone length around their predicted position, with the other seven being between 0.6 and 1.5 clone length off. 75-86 sequencing reactions on clones selected from the map would have been sufficient for completely sequencing both strands of the 11.5 kb fragment. The results demonstrate the efficacy of such template sorting, considerably assisting sequencing at relatively little cost on the mapping level.
The Rice Bacterial Blight Resistance Gene <i>xa5</i> Encodes a Novel Form of Disease Resistance (2004)

The rice xa5 gene for disease resistance to Xanthomonas oryzae pv. oryzae has been positionally cloned and encodes the gamma subunit of transcription factor IIA (TFIIAgamma). TFIIAgamma is a general eukaryotic transcription factor with no previously known role in disease resistance. xa5 is unusual in that it is recessive and does not conform to one of the typical resistance gene structural classes. Sequencing of TFIIAgamma in resistant and susceptible isolines revealed two nucleotide substitutions resulting in an amino acid change between resistant and susceptible cultivars. This association was conserved across 27 resistant and nine susceptible rice lines in the Aus-Boro group.
Antireflective grating in the resonance domain for displays (2007)

An antireflective periodic structure different from the moth-eye structure is proposed in a resonance domain whose period is greater than the wavelength of incident light. Using rigorous coupled-wave analysis in the TE mode, a reflectivity of less than 0.2% is performed in a period larger than the wavelength, when an aspect ratio is unity. Changes in diffraction efficiency and transmissivity are small at different wavelengths. This is explained by a newly derived equation based on the vector theory.
What is the prevalence of resistant hypertension in the United States? (2012)

In coming years, even if the prevalence of hypertension remains stable, resistant hypertension is likely to increase, especially as the proportion of treated hypertension increases. Because of increased use of healthcare resources, resistant hypertensive patients should be identified early, and greater efforts made to control their blood pressures.
An integrated approach for Arabic-English named entity translation (2005)

Translation of named entities (NEs), such as person names, organization names and location names is crucial for cross lingual information retrieval, machine translation, and many other natural language processing applications. Newly named entities are introduced on daily basis in newswire and this greatly complicates the translation task. Also, while some names can be translated, others must be transliterated, and, still, others are mixed. In this paper we introduce an integrated approach for named entity translation deploying phrase-based translation, word-based translation, and transliteration modules into a single framework. While Arabic based, the approach introduced here is a unified approach that can be applied to NE translation for any language pair.
Oxide based photosensor thin film transistor for interactive display (2013)

Among various semiconductor devices, electronically active oxide thin film transistors (TFTs) have received considerable attention for a wide range of device applications. Double metal-oxide thin film transistor (TFT) shows high photo current as Ilight/Idark >106, a mobility of >10cm2/Vs and high stability under LCD operation condition. In this paper, the possibility of a novel application of an optical touch screen which is entirely based on the metal oxide TFT is proposed.
Effects of feeding<i>Cuphea</i> oil to three generations of CBA/2 and C57B1/6 mice (1993)

Three generations of CBA/2 and C57B1/6 mice were reared on semipurified diets containing either 17.2% beef tallow and 3.5% corn oil or 8.6% beef tallow, 8.6% crude Cuphea oil and 3.5% corn oil. The Cuphea oil contained 76% decanoic acid; therefore, health effects of long‐term feeding of moderate amounts of medium‐chain triacylglycerols were evaluated. The reproductive performance of both strains of mice varied little with diet but, compared with the F1 generation, survival of F2 and F3 pups was diminished. At several time points during 13 wk, Cuphea feeding suppressed body weights and food intakes of males of three generations of both strains. But during long‐term feeding of males (5–12 mon), Cuphea did not suppress body weight or food intake. Mice of both strains developed fatty livers. Mice of the CBA/2 strain had hepatic nodular hyperplasia. Cuphea oil feeding caused no specific pathological changes. Although medium‐chain triacylglycerols have been reported to be hypocholesterolemic, the substitution of Cuphea for half of the dietary beef tallow did not suppress serum cholesterol concentrations in males aged 4–13 mon. The effects of long‐term substitution of medium‐chain triacylglycerols for beef tallow do not differ from feeding the beef tallow diet. Long‐term and multigenerational feeding of crude Cuphea oil does not cause any specific toxic effect in mice.
Predicting tumor failure in prostate carcinoma after definitive radiation therapy: limitations of models based on prostate-specific antigen, clinical stage, and Gleason score. (1999)

In this report, we use new patient data to test three popular models developed to predict the outcome of definitive radiation therapy. The data come from 240 men with localized prostate cancer and who were treated with definitive radiation therapy at a community hospital. All three models tested were based on the three commonly available variables of pretreatment prostate-specific antigen (PSA), Gleason score, and tumor stage, and we used the Cox proportional hazards model and the logistic regression model to relate these variables to outcome. We discovered that in our data, the optimal way to use pretreatment PSA was as natural log(PSA), the optimal way to use T stage was in three categories: T1 and T2, T3, and T4, and that the optimal use of Gleason score was as <7 versus > or =7. Nevertheless, models confined to the optimal use of these three variables leave much uncertainty about important outcomes, such as the probability of relapse within 5 years.
Performance Evaluation of a System for Estimating Relative Positions of Vehicles During GPS Outages (2006)

Active safety applications for vehicles have been at the forefront of the automotive safety community for a number of years. Cooperative collision warning based on vehicle-to-vehicle radio communications and GPS systems is one such promising active safety application that has evoked considerable interest among automobile manufacturers and research communities worldwide. In this paper, we address one of the key functional components of the cooperative collision warning application, which is, accurate estimation of relative positions of all the neighboring vehicles based on real-time exchange of their individual GPS position coordinates, and then we propose a novel system solution for achieving the same (relative positioning functionality) during persistent GPS outages. Our proposed system solution essentially involves integration of the most suitable set of vehicle clustering, radio based ranging, and relative position coordinate establishment techniques, and based on the results of a comprehensive literature survey, we reason that the two-way reciprocal time of arrival based ranging, and the distributed beacon-less relative positioning techniques may constitute the most viable set for our proposed system solution. Having developed a system simulator to accurately model the functionality of our proposed system solution, we then quantify the impact of various levels of ranging error on the overall performance of the system and thereby assess the functional viability of our proposed system solution. The simulation results look quite promising and support the fact that our proposed system solution can enable relative positioning of vehicles without any GPS information within acceptable levels of positioning accuracy, as required for the 360-degrees cooperative collision warning application
Assessing the Risks of Manufactured Nanomaterials (2006)

ADVERTISEMENT RETURN TO ISSUEPREVFEATURENEXTAssessing the Risks of Manufactured NanomaterialsMark R. Wiesner, Greg V. Lowry, Pedro Alvarez, Dianysios Dionysiou, and Pratim BiswasCite this: Environ. Sci. Technol. 2006, 40, 14, 4336–4345Publication Date (Web):July 15, 2006Publication History Published online15 July 2006Published inissue 1 July 2006https://pubs.acs.org/doi/10.1021/es062726mhttps://doi.org/10.1021/es062726mnewsACS Publications. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views12724Altmetric-Citations954LEARN 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 PDF (1 MB) Get e-Alertsclose SUBJECTS:Manufacturing,Nanomaterials Get e-Alerts
No longer lost in translation: study protocol for preventing delirium post hip fracture (2019)

Introduction: Hip fractures are serious injuries commonly experienced by older adults. Delirium has been identified as the most frequent post-operative complication among hospitalized older people, following hip fracture. A quality assurance audit within our hospital demonstrated that delirium screening, prevention and management were not performed routinely or systematically. This study protocol describes an implementation research project which aims to implement and evaluate the effect of an intervention bundle to prevent delirium in patients with hip fracture admitted to an acute orthopaedic ward. Methods: This implementation research project seeks to assess whether the intervention bundle reduces the incidence of delirium in patients with hip fracture patients identified via the use of a validated tool in screening delirium. We will also examine the length of hospital stay, duration of delirium episode and the prevalence of the use of a validated tool to screen delirium. Intervention: Specific intervention strategies, informed by contemporary Behaviour Change Wheel Framework have been selected to address the identified barriers. The final components of the intervention are care pathway, education, audit and feedback, change champions, adaptation of forms and documentation and infographics. Conclusion: This study describes an implementation project which evaluates the effect of a delirium prevention bundle on incidence of delirium in patients with hip fractures. The clinical goal of the delirium prevention care bundle is to bridge the gap between the current and best practice in delirium recognition, prevention and management.
Identification of major proteins associated with <i>Dictyostelium discoideum</i> endocytic vesicles (1995)

Magnetic isolation of endocytic vesicles from Dictyostelium discoideum was accomplished after feeding the amoebae with iron oxide particles. Proteins associated with the endocytic vesicles were resolved by SDS-PAGE and digested 'in-gel' with endoproteinase Lys-C or Asp-N to generate peptides for amino acid sequencing. This strategy allowed the identification of the major protein constituents of the vesicles: namely, the A, B, D, E and 110 kDa subunits of a vacuolar type H(+)-ATPase, actin, a Rab 7-like GTPase, a p34 protein corresponding to a new cysteine proteinase and the 25 kDa product of a recently sequenced D. discoideum open reading frame.
Effect of implementation of the accrual-based financial system on transparency and accountability in Qazvin University of Medical Sciences (2014)

Background: Public managers are always looking to achieve clear and accurate information about the financial performance of the organization to have better accountability in this area in addition to efficient management and improvement of indices. Objective: The aim of this study was to evaluate the effect of implementing the accrual-based financial system on transparency and accountability. Methods: This survey was conducted in Qazvin University of Medical Sciences, 2013. The study population consisted of 70 financial managers, auditors of Supreme Audit Court, heads of accounting units, financial and budget staff, middle and high rank managers, auditors of Board of Trustees of Qazvin University of Medical Sciences that were selected by random sampling method. The measurement tool was a two-part questionnaire consisted of 15 questions for financial transparency, 11 questions for financial accountability in three dimensions and 6 questions for operational accountability in three dimensions. Data were analyzed using one-sample T-test. Findings: There were statistically significant relationship between the implementation of the accrual-based financial system and the followings: increased financial transparency and the possibility for assessment of the approved budget control, the application of the financial regulations, the financial reporting to increase financial accountability and the possibility for assessment of efficiency and economic profit to increase operational accountability. The association of the accrual-based financial system and the possibility for assessment of effectiveness to increase operational accountability was not statistically significant. Conclusion: With regards to the results, the implementation of the accrual-based financial system led to increased financial transparency and financial and operational accountability in Qazvin University of Medical Sciences.
Toward a common classification approach for biorefinery systems (2009)

Abstract This paper deals with a biorefinery classification approach developed within International Energy Agency (IEA) Bioenergy Task 42. Since production of transportation biofuels is seen as the driving force for future biorefinery developments, a selection of the most interesting transportation biofuels until 2020 is based on their characteristics to be mixed with gasoline, diesel and natural gas, reflecting the main advantage of using the already‐existing infrastructure for easier market introduction. This classification approach relies on four main features: (1) platforms; (2) products; (3) feedstock; and (4) processes. The platforms are the most important feature in this classification approach: they are key intermediates between raw materials and final products, and can be used to link different biorefinery concepts. The adequate combination of these four features represents each individual biorefinery system. The combination of individual biorefinery systems, linked through their platforms, products or feedstocks, provides an overview of the most promising biorefinery systems in a classification network. According to the proposed approach, a biorefinery is described by a standard format as ‘platform(s) – products – and feedstock(s)’. Processes can be added to the description, if further specification is required. Selected examples of biorefinery classification are provided; for example, (1) one platform (C6 sugars) biorefinery for bioethanol and animal feed from starch crops (corn); and (2) four platforms (lignin/syngas, C5/C6 sugars) biorefinery for synthetic liquid biofuels (Fischer‐Tropsch diesel), bioethanol and animal feed from lignocellulosic crops (switchgrass). This classification approach is flexible as new subgroups can be added according to future developments in the biorefinery area. © 2009 Society of Chemical Industry and John Wiley & Sons, Ltd
Machine learning in dental, oral and craniofacial imaging: a review of recent progress (2021)

Artificial intelligence has been emerging as an increasingly important aspect of our daily lives and is widely applied in medical science. One major application of artificial intelligence in medical science is medical imaging. As a major component of artificial intelligence, many machine learning models are applied in medical diagnosis and treatment with the advancement of technology and medical imaging facilities. The popularity of convolutional neural network in dental, oral and craniofacial imaging is heightening, as it has been continually applied to a broader spectrum of scientific studies. Our manuscript reviews the fundamental principles and rationales behind machine learning, and summarizes its research progress and its recent applications specifically in dental, oral and craniofacial imaging. It also reviews the problems that remain to be resolved and evaluates the prospect of the future development of this field of scientific study.
Long-term use of progestogens: Colon adenoma and colon carcinoma (2007)

Colon cancer is the second most common cancer in women in the Western world and there is a trend towards an increasing risk. Colon adenoma is a potential precursor for colon cancer. Adenoma and carcinoma of the colon seem to be influenced by estrogens and progesterone/progestins. This is related to the presence of estrogen and progesterone receptors, with apparently higher concentrations in colon cancers than in adenomas. Epidemiological data and the finding of a significant reduction in colon cancer risk related to hormone replacement therapy (HRT), and in particular the length of HRT intake, indicate that progesterone/progestins have a preventive effect. This has not been shown with postmenopausal estrogen replacement therapy (ERT) alone. Furthermore, the recurrence rate of adenoma appears to be reduced, and the survival of colon cancer patients improved, with HRT; such effects have not been documented with ERT.
Intraphagosomal Mycobacterium tuberculosis Acquires Iron from Both Extracellular Transferrin and Intracellular Iron Pools (2002)

Mycobacterium tuberculosis multiplies within the macrophage phagosome and requires iron for growth. We examined the route(s) by which intracellular M. tuberculosis acquires iron. During intracellular growth of the virulent Erdman M. tuberculosis strain in human monocyte-derived macrophages (MDM), M. tuberculosis acquisition of (59)Fe from transferrin (TF) provided extracellularly (exogenous source) was compared with acquisition when MDM were loaded with (59)Fe from TF prior to M. tuberculosis infection (endogenous sources). M. tuberculosis (59)Fe acquisition required viable bacteria and was similar from exogenous and endogenous sources at 24 h and greater from exogenous iron at 48 h. Interferon-gamma treatment of MDM reduced (59)Fe uptake from TF 51% and TF receptor expression by 34%. Despite this, intraphagosomal M. tuberculosis iron acquisition in IFN-gamma-treated cells was decreased by only 30%. Macrophages from hereditary hemochromatosis patients have altered iron metabolism. Intracellular M. tuberculosis acquired markedly less iron in MDM from these individuals than in MDM from healthy donors, regardless of the iron source (exogenous and endogenous): 36 +/- 3.8% and 17 +/- 9.6% of control, respectively. Thus, intraphagosomal M. tuberculosis can acquire iron from both extracellular TF and endogenous macrophage sources. Acquisition of iron from macrophage cytoplasmic iron pools may be critical for the intracellular growth of M. tuberculosis. This acquisition is altered by IFN-gamma treatment to a small extent, but is markedly reduced in macrophages from hemochromatosis patients.
Thermal stabilization of poly(3‐hydroxybutyrate) by poly(glycidyl methacrylate) (2002)

Abstract Poly(3‐hydroxybutyrate) (PHB)/poly(glycidyl methacrylate) (PGMA) blends with the PGMA content up to 30 wt % were prepared by a solution‐precipitation procedure. The thermal decomposition of PHB/PGMA blends was studied by thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and differential thermal analysis (DTA). The thermograms of PHB/PGMA blends contained a two‐step degradation process, while that of pure PHB sample exhibited only one‐step degradation process. This degradation behavior of PHB/PGMA blends, which have a higher thermal stability as measured by maximum decomposition temperature or residual weight after isothermal degradation for 1 h, is probably due to crosslinking reactions of the epoxide groups in the PGMA component with the carboxyl chain ends of PHB fragments during the degradation process, and the occurrence of such reactions can be assigned to the exothermic peaks in their DTA thermograms. An isothermal study of these blends at 200–250°C for 1 h indicated that the residual weight was directly correlated with the amount of epoxide groups in the PHB/PGMA blends. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 83: 2945–2952, 2002; DOI 10.1002/app.10318
Bone Differentiation in Porous Hydroxyapatite in Baboons Is Regulated by the Geometry of the Substratum (1994)

Previous studies have shown the morphogenesis of bone in a porous hydroxyapatite substratum when implanted intramuscularly in baboons. This hydroxyapatite-induced osteogenesis model was used to study the effect of geometry and pore size of the substratum on bone differentiation. Two distinct geometric configurations of porous hydroxyapatite of different pore size were obtained after hydrothermal conversion of the calcium carbonate exoskeleton of corals (genera Porites and Goniopora). Substrata were blocks of hydroxyapatite in rod configuration of 200- and 500-microns pore size and granular hydroxyapatite (400 to 620 microns in diameter) of 200- and 500-microns pore size. A total of 64 granular hydroxyapatite implants and 32 hydroxyapatite rods were implanted intramuscularly in 8 subadult male baboons (Papio ursinus). Specimens were harvested on days 60 and 90 and subjected to histologic and histomorphometric analysis. With the exception of an island of bone that formed in two implants of granular hydroxyapatite of 500-microns pore size, bone differentiation occurred only in blocks of hydroxyapatite in rod configuration of either pore size at both observation periods. The lack of bone formation in the granular hydroxyapatite indicates the critical role of geometry of the substratum in bone differentiation. These results in primates may have implications for the appropriate selection of porous bone substitutes for reconstructive craniofacial surgery in humans.