nils-herrmann/clean_scirepeval huggingface dataset:
Phenylalanine ammonia lyase (PAL) From discovery to enzyme substitution therapy for phenylketonuria.
Venue: Molecular genetics and metabolism
Year: 2018

Phenylketonuria (PKU) is a genetic inborn error in metabolism that impacts many people globally, with profound individual and societal consequences when left untreated. The journey of phenylalanine ammonia lyase (PAL) from plant enzyme to enzyme substitution therapy for PKU is a fascinating story that illustrates the importance of collaboration between basic scientists and industry in the drug development process. The story begins with the curiosity of plant physiologists about the origin of lignin, a polymer involved in maintaining the rigidity of plants. They learned that the critical element in this synthesis was an intermediary enzyme that deaminates phenylalanine to cinnamic acid and ammonia (later called phenylalanine ammonia lyase or PAL) Recognition of this ability to metabolize phenylalanine led to subsequent consideration of PAL as a treatment for PKU. This was initially attempted as enteral therapy with extracted enzyme, but that showed only minimal efficacy. Crucially, further development of PAL as a therapy for PKU required quantities of enzyme that could only be obtained after successfully cloning the gene, expressing the enzyme in vitro and modifying the protein via PEGylation to enable parenteral administration of this non mammalian enzyme. Ultimately, PEGylated PAL was developed as an enzyme substitution therapy for PKU now approved under the name "Palynziq." The multidisciplinary academic industrial partnership engaged throughout this process has been key to the successful pursuit of this therapeutic possibility and serves as a model for the development of future innovative therapies.
T matrix method and its applications to electromagnetic scattering by particles: A current perspective
Year: 2010

This note serves as a short introduction to the reprint of our article 'T matrix computations of light scattering by nonspherical particles: a review' (JQSRT 1996; 55:535 75) We first discuss the motivation for writing that article and explain its historical context. This is followed by a short overview of more recent developments.
Influence of lncRNA MALAT1 on septic lung injury in mice through p38 MAPK/p65 NF kB pathway.
Venue: European review for medical and pharmacological sciences
Year: 2019

To investigate the influence of long non coding ribonucleic acid (lncRNA) metastasis associated lung adenocarcinoma transcript 1 (MALAT1) on septic lung injury in mice and its mechanism, so as to provide references for the clinical prevention and treatment of septic lung injury in the future.  A total of 60 male C57 mice were randomly divided into Control group (n=20) lipopolysaccharide (LPS) group (n=20) and LPS+MALAT1 siRNA group (n=20) using a random number table. The mouse model of septic lung injury was established via intraperitoneal injection of LPS (10 mg/kg) and the MALAT1 knockdown model was established via tail intravenous injection of MALAT1 siRNA. After 12 h, the lung was taken to measure the wet weight/dry weight ratio. Also, the activity of myeloperoxidase (MPO) in lung tissues was detected. The number of neutrophils and macrophages in bronchoalveolar lavage fluid (BALF) was detected via bronchoalveolar lavage. Moreover, the messenger RNA (mRNA) expression levels of inflammatory cytokines, including tumor necrosis factor a (TNF a) interleukin 1 (IL 1) and IL 6, in lung tissues were detected via Reverse Transcription Polymerase Chain Reaction (RT PCR) Finally, the expression level of p38 in lung tissues was detected via immunohistochemical staining, and the expressions of p38 mitogen activated protein kinase (MAPK)/p65 nuclear factor kB (NF kB) signaling pathway related proteins in lung tissues of mice were detected via Western blotting.  The expression of lncRNA MALAT1 in lung tissues of mice with septic lung injury was significantly increased (p<0.05) After knockdown of lncRNA MALAT1, the LPS induced pathological injury of lungs could be improved, and the wet weight/dry weight ratio of lungs could be reduced (p<0.05) Compared with those in LPS group, the total number of inflammatory cells and the number of neutrophils and macrophages in BALF were significantly decreased in LPS+MALAT1 siRNA group (p<0.05) and the levels of inflammatory cytokines were also significantly inhibited (p<0.05) The immunohistochemical results manifested that the knockdown of lncRNA MALAT1 could inhibit the LPS induced up regulation of p38 in lung tissues in mice. According to the results of Western blotting, the p38 MAPK/p65 NF kB signaling pathway was significantly activated in lung tissues in LPS group (p<0.05) while it was significantly suppressed after inhibition on lncRNA MALAT1 (p<0.05)  The knockdown of lncRNA MALAT1 can significantly improve the septic lung injury in mice, whose mechanism may be related to its inhibition on the p38 MAPK/p65 NF kB signaling pathway.
Frequency of dyslipidemia in patients with psoriasis
Year: 2016

To determine the frequency of dyslipidaemia in psoriatic patients.  A cross sectional study was carried out in the Department of Dermatology, Jinnah hospital, Lahore for the duration of six months. A total of 120 patients suffering from psoriasis, of any severity, belonging to either sex and with age between 15 70 years were included in the study. All patients in the study were investigated for total cholesterol, triglycerides, low density lipoproteins and high density lipoproteins after 12 14 hours of overnight fasting.  The mean age of the patients was 38.59 13.86 years. There were 78 (65% male and 42 (35% female patients. The mean duration of psoriasis was 5.46 4.49 years. The mean PASI score was 14.98 8.95. There were 67 (55.8% patients having dyslipidaemia and 53 (44.2% patients had normal lipid levels. 34 (28.3% patients had raised total cholesterol >200mg/dl) 32 (26.7% raised low density lipoprotein cholesterol >130 mg/dl) 44 (36.7% hypertriglyceridemia >150mg/dl) and 35 (29.2% patients had reduced high density lipoprotein cholesterol levels <40mg/dl)  It is concluded from this study that patients of psoriasis have a high incidence of dyslipidaemia, as it was found in 55.8% of psoriatic patients.
Cavity ring down Doppler broadening primary thermometry
Year: 2018

A step forward in Doppler broadening thermometry is demonstrated using a comb assisted cavity ring down spectroscopic approach applied to an isolated near infrared line of carbon dioxide at thermodynamic equilibrium. Specifically, the line shape of the {P}_{\mathrm{e}(12) line of the (30012)\ensuremath{\leftarrow}(00001) band of \mathrm{C}\mathrm{O}}_{2} at 1.578 \textmu{}m is accurately measured and its Doppler width extracted from a refined multispectrum fitting procedure accounting for the speed dependence of the relaxation rates, which were found to play a role even at the very low pressures explored, from 1 to 7 Pa. The thermodynamic gas temperature is retrieved with relative uncertainties of $8\ifmmode\times\else\texttimes\fi{{10}\ensuremath{ }6} (type A) and $11\ifmmode\times\else\texttimes\fi{{10}\ensuremath{ }6} (type B) which ranks the system at the first place among optical methods. Thanks to a measurement time of only \ensuremath{\approx}5\phantom{\rule{0.16em}{0ex}\mathrm{h} the technique represents a promising pathway toward the optical determination of the thermodynamic temperature with a global uncertainty at the {10}\ensuremath{ }6} level.
Sketch Based Shape Retrieval via Multi view Attention and Generalized Similarity
Venue: 2018 7th International Conference on Digital Home (ICDH)
Year: 2018

Sketch based shape retrieval has received increasing attention in computer vision and computer graphics. It suffers from the challenge gap between 2D sketches and 3D shapes. In this paper, we propose a generalized similarity matching framework based on a multi view attention network (MVAN) which can retrieve 3D shape that is most similar to the query sketch. In proposed approach, firstly we compute 2D projections of 3D shapes from multiple viewpoints and utilize a convolutional neural network to extract low level feature maps of these 2D projections. Secondly a multi view attention network is designed to fuse the feature maps and forms a more accurate 3D shape representation. Meanwhile we use a CNN to extract the feature of sketches. Thirdly the similarity between sketches and 3D shapes is estimated via a generalized similarity model, which fuses some traditional similarity model into a generalized form and optimizes its parameters using a data driven method. Finally we combine the MVAN and generalized similarity model into a unified network and train the model in an end to end manner. The experimental results on SHREC'13 and SHREC'14 sketch track benchmark datasets demonstrate that the proposed method can outperform state of the art methods.
Detection of chlorobenzene in water using a wettability controlled three dimensional graphene selective filter
Year: 2017

An oxide nanowire transistor covered with a wettability controlled three dimensional (3D) graphene filter was fabricated to detect chlorobenzene in water. The 3D porous graphene filter allowed chlorobenzene to pass through while blocking water because of its wettability. The chlorobenzene concentration in water could be monitored by observing the threshold voltage shift, which moved to the negative direction with increasing chlorobenzene concentration in water. The advantage of the fabricated device is that it can be used to easily estimate the chlorobenzene concentration in water by consistently monitoring current.
Traits based approaches in bioassessment and ecological risk assessment: strengths, weaknesses, opportunities and threats.
Venue: Integrated environmental assessment and management
Year: 2011

We discuss the application of traits based bioassessment approaches in retrospective bioassessment as well as in prospective ecological risk assessments in regulatory frameworks. Both approaches address the interaction between species and stressors and their consequences at different levels of biological organization, but the fact that a specific species may be less abundant in a potentially impacted site compared with a reference site is, regrettably, insufficient to provide diagnostic information. Species traits may, however, overcome the problems associated with taxonomy based bioassessment. Trait based approaches could provide signals regarding what environmental factors may be responsible for the impairment and, thereby, provide causal insight into the interaction between species and stressors. For development of traits based (TBA) traits should correspond to specific types of stressors or suites of stressors. In this paper, a strengths, weaknesses, opportunities, and threats (SWOT) analysis of TBA in both applications was used to identify challenges and potentials. This paper is part of a series describing the output of the TERA (Traits based ecological risk assessment: Realising the potential of ecoinformatics approaches in ecotoxicology) Workshop held between 7 and 11 September, 2009, in Burlington, Ontario, Canada. The recognized strengths were that traits are transferrable across geographies, add mechanistic and diagnostic knowledge, require no new sampling methodology, have an old tradition, and can supplement taxonomic analysis. Weaknesses include autocorrelation, redundancy, and inability to protect biodiversity directly. Automated image analysis, combined with genetic and biotechnology tools and improved data analysis to solve autocorrelation problems were identified as opportunities, whereas low availability of trait data, their transferability, their quantitative interpretation, the risk of developing nonrelevant traits, low quality of historic databases, and their standardization were listed as threats.
A Companion to the Global Renaissance: English Literature and Culture in the Era of Expansion
Year: 2009

The Global Renaissance: Jyotsna Singh (Michigan StateUniversity) Part I: Mapping the Global: 1. The New Globalism: Transcultural Commerce, Global Systems Theory, and Spenser's Mammon: Daniel Vitkus (Florida State University) 2. "Travailing" Theory: Global Flows of Labor and the Enclosure of the Subject: Crystal Bartolovich (Syracuse University) 3. Islam and Tamburlaine 's World picture: John Michael Archer (New York University) 4.  Global Utopias in the Early Modern Period: Chloe Houston (University of Reading) Part II: "Contact Zones" 5. The Benefits of a Warm Study: The Resistance to Travel before Empire: Andrew Hadfield (University of Sussex) 6. "Apes of Imitation" Imitation and Identity in Sir Thomas Roe's Embassy to India: Nandini Das (University of Liverpool) 7. A Multinational Corporation: Foreign Labor in the London East India Company: Richmond Barbour (Oregon State University) 8. Where was Iceland in 1600? Mary C. Fuller (MIT) 9. East by North east: The English among the Russians, 1553 1603: Gerald MacLean (University of Exeter) 10. The Politics of Identity: William Adams, John Saris, and the English East India Company's Failure in Japan Catherine Ryu (Michigan State University) 11. The  Ian Smith (University of Reading) Part III: Networks of Exchange: Traveling Objects: 12. Guns and Gawds: Elizabethan England's Infidel Trade: Matthew Dimmock (University of Sussex) 13. Cassio, Cash, and the "Infidel 0" Arithmetic, Double entry Book keeping, and Othello' s Unfaithful Accounts: Patricia Parker (Stanford University) 14. Seeds of Sacrifice: Amaranth, the Gardens of Tenochtitlan and Spenser's Faerie Queene: Edward M. Test (Boise State University) 15. "So Pale, So Lame, So Lean, So Ruinous" The Circulation of Foreign Coins in Early Modern England: Stephen Deng (Michigan State University) 16. Canary, Bristoles, Londres, Ingleses: English Traders in the Canaries in the Sixteenth and Seventeenth Centuries: Barbara Sebek (Colorado State University) 17. "The Whole Globe of the Earth" Almanacs and Their Readers: Adam Smyth (University of Reading) 18. Cesare Vecellio, Venetian Writer and Art book Cosmopolitan: Ann Rosalind Jones (Smith College) Part IV: The Globe Staged: 19. Bettrice's Monkey: Staging Exotica in Early Modern London Comedy: Jean E. Howard (Columbia University) 20. The Maltese Factor: The Poetics of Place in The Jew of Malta and The Knight of Malta: Virginia Mason Vaughan (Clark University) 21. Local/Global Pericles International Storytelling, Domestic Social Relations, Capitalism: David Morrow (College of St. Rose)
Combinaison du lavage par biosurfactant et de la biodegradation dynamisee, pour la depollution des eaux souterraines de sites contamines par des HAP
Year: 2020

La presente these, adossee au projet BIOXYVAL, vise a mettre au point une combinaison de traitements gradues efficaces, pour la depollution des eaux souterraines, notamment par les HAPs et HAPPs. Plus particulierement, la these vise a ameliorer l'efficacite des traitements biologiques, sur les polluants en faibles concentrations (en limite des saturations residuelles et du panache de pollution) par deux actions complementaires menees de front l'utilisation de (bio)surfactants et la bioaugmentation dynamisee. Ces deux actions complementaires serviront a rendre les polluants disponibles pour une meilleure biodegradation. Les essais seront realises a differentes echelles du laboratoire au terrain. La production des biosurfactants en quantite suffisante ex situ par la mise en oeuvre des bioreacteurs ou in situ (dans le sol pollue) constituant le verrou principal de cette these. Il s'agira donc d'explorer les modes operatoires permettant de maximiser cette production tout en s'assurant de son impact significatif sur les rendements epuratoires et des concentrations residuelles en HAPs et HAPPs, par rapport a un processus d'attenuation naturelle. Les biosurfactants, qui sont des molecules bio sourcees (biodegradables) et biocompatibles (non toxiques) doivent permettre de developper des techniques de traitement plus respectueuses de l'environnement par rapport aux molecules tensioactives d'origine chimique. Si en plus de l'efficacite en rendement epuratoires ces techniques de bio traitement s'averaient economiques, alors la plus value technico economique et environnementale serait reelle. L'amelioration de la biodegradation des HAP par ajout de surfactants et/ou production de biosurfactants sera conduite tout au long de la these. Par ailleurs, la technique de traitement envisagee entend aussi ameliorer les rendements epuratoires in situ freines par i) la difficulte d'assurer un contact efficace entre les reactifs injectes et les polluants et ii) la difficulte a garantir l'atteinte des objectifs de rehabilitation liee notamment aux problemes d'anisotropie (Hyman et Dupont. 2001 GTGLC, 2006 Colombano et al. 2010) Aussi, une attention particuliere sera apportee a la mise au point de la technique d'injection de bio(surfactants) et de nutriments (pulsee, continue) Il est en effet envisage de realiser un pompage aval et une reinjection amont avec un passage des eaux pompees dans un bioreacteur on site. Ceci permettra de travailler en procede de traitement de type pseudo boues activees ce qui offre une complementarite de traitement on site/in situ ainsi qu'une meilleure maitrise du process (meilleur controle des conditions operatoires et temps de sejour plus consequent) In fine, le process pourra etre considere comme presentant deux zones reactives (in situ et on site)
Monitoring Financial Stability Based on Prediction of Cryptocurrencies Price Using Intelligent Algorithm
Venue: 2020 International Conference on Data Science and Its Applications (ICoDSA)
Year: 2020

Financial stability is the problem that correlated with many aspects. In this digital era, virtual currency has emerged as one of financial assets. Fluctuation from cryptocurrencies price made an impact into financial stability indirectly. It has been proved by the market capitalization of publicly traded cryptocurrencies in 2019 reach USD 240 billion. The percentages reach 66% for the market capitalization. Three highest cryptocurrencies uphold are Bitcoin, Ethereum and XRP. This condition made these three cryptocurrencies become the important investment products. However, cryptocurrency is the product with high volatility. Because of that, this study aims to monitor financial stability from cryptocurrencies prediction using artificial intelligent algorithm. This research copes the problem by predicting bitcoin, Ethereum and XRP using three different intelligent algorithms, which are K Nearest Neighbours (KNN) Support Vector Machine (SVM) and Long Short Term Memory (LSTM) By this prediction had been figured out about up and down value of cryptocurrencies using Root Mean Square Error (RMSE) to evaluate stabilization of finance. Accuration system with LSTM shown that the price of cryptocurrency will fit with the data actual using LSTM, in which the accuracy around 80% This condition meant that LSTM had been succeeded to proposed as algorithm that could fit the cryptocurrencies value. It could strengthen usability to indicate financial stability refer into cryptocurrencies price.
Mixed Flavonoid Supplementation Attenuates Postexercise Plasma Levels of 4 Hydroxynonenal and Protein Carbonyls in Endurance Athletes.
Venue: International journal of sport nutrition and exercise metabolism
Year: 2019

This double blinded, placebo controlled, randomized crossover trial investigated the influence of 2 week mixed flavonoid versus placebo supplementation on oxinflammation markers after a 75 km cycling time trial in 22 cyclists (42.3 1.7 years) Blood samples were collected before and after the 2 week supplementation, and then 0 hr, 1.5 hr, and 21 hr post 75 km cycling (176 5.4 min, 73.4 2.0% maximal oxygen consumption) The supplement provided 678 mg flavonoids with quercetin (200 mg) green tea catechins (368 mg, 180 mg epigallocatechin gallate) and anthocyanins (128 mg) from bilberry extract, with caffeine, vitamin C, and omega 3 fatty acids added as adjuvants. Blood samples were analyzed for blood leukocyte counts, oxinflammation biomarkers, including 4 hydroxynonenal, protein carbonyls, and peripheral blood mononuclear mRNA expression for cyclooxygenease 2 and glutathione peroxidase. Each of the blood biomarkers was elevated postexercise (time effects, all ps .01) with lower plasma levels for 4 hydroxynonenal (at 21 hr postexercise) in flavonoid versus placebo (interaction effect, p .008) Although elevated postexercise, no trial differences for the neutrophil/lymphocyte ratio (p .539) or peripheral blood mononuclear mRNA expression for cyclooxygenease 2 (p .322) or glutathione peroxidase (p .839) were shown. Flavonoid supplementation prior to intensive exercise decreased plasma peroxidation and oxidative damage, as determined by 4 hydroxynonenal. Postexercise increases were similar between the flavonoid and placebo trials for peripheral blood mononuclear mRNA expression for cyclooxygenease 2 and the nuclear factor erythroid 2 related factor 2 related gene glutathione peroxidase (NFE2L2) The data support the strategy of flavonoid supplementation to mitigate postexercise oxidative stress in endurance athletes.
Institutionalizing Sustainability Mindset amongst Stakeholders: Case of Interface Carpet
Year: 2017

Reframing has been widely seen as a communication, negotiation and decision making tool for leaders and managers but it is seldom seen as a tool for instilling sustainability mindset. By using grounded theory approach, we explored the use of reframing, by its founder, Ray Anderson, in institutionalizing a sustainability mindset among the various stakeholders of the biggest carpet tiles manufacturer in the world, Interface Inc. This case was chosen because Interface is one of the very few successful examples of a traditional energy intensive manufacturing company moving to one with a focus on sustainability. Back in 1994, very few businesses understood the importance of adopting sustainable business practices. Our study discovered that the leader effectively used stakeholder specific reframing based on the role expected from the various stakeholders of his firm to develop a sustainability mindset across the value chain while surpassing all economic downturns and maintaining the position of Interface as a m.
Multi domain Conversation Quality Evaluation via User Satisfaction Estimation
Venue: ArXiv
Year: 2019

An automated metric to evaluate dialogue quality is vital for optimizing data driven dialogue management. The common approach of relying on explicit user feedback during a conversation is intrusive and sparse. Current models to estimate user satisfaction use limited feature sets and employ annotation schemes with limited generalizability to conversations spanning multiple domains. To address these gaps, we created a new Response Quality annotation scheme, introduced five new domain independent feature sets and experimented with six machine learning models to estimate User Satisfaction at both turn and dialogue level. Response Quality ratings achieved significantly high correlation (0.76) with explicit turn level user ratings. Using the new feature sets we introduced, Gradient Boosting Regression model achieved best (rating [1 5] prediction performance on 26 seen (linear correlation ~0.79) and one new multi turn domain (linear correlation 0.67) We observed a 16% relative improvement (68% 79% in binary "satisfactory/dissatisfactory" class prediction accuracy of a domain independent dialogue level satisfaction estimation model after including predicted turn level satisfaction ratings as features.