nils-herrmann/clean_scirepeval huggingface dataset:
Sequence Analysis and Structure Prediction of SARS CoV 2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus
Venue: BioMed research international
Year: 2020

Severe acute respiratory syndrome coronavirus 2 (SARS CoV 2) has a single stranded RNA genome that encodes 14 open reading frames (ORFs) eight of which encode accessory proteins that allow the virus to infect the host and promote virulence. The genome expresses around 29 structural and nonstructural protein products. The accessory proteins of SARS CoV 2 are not essential for virus replication but do affect viral release, stability, and pathogenesis and finally contribute to virulence. This paper has attempted the structure prediction and functional analysis of two such accessory proteins, 9b and ORF14, in the absence of experimental structures. Sequence analysis, structure prediction, functional characterization, and evolutionary analysis based on the UniProtKB reviewed the amino acid sequences of SARS CoV 2 9b (P0DTD2) and ORF14 (P0DTD3) proteins. Modeling has been presented with the introduction of hybrid comparative and ab initio modeling. QMEANDisCo 4.0.0 and ProQ3 for global and local (per residue) quality estimates verified the structures as high quality, which may be attributed to structure based drug design targets. Tunnel analysis revealed the presence of 1 2 highly active tunneling sites, perhaps which will able to provide certain inputs for advanced structure based drug design or to formulate potential vaccines in the absence of a complete experimental structure. The evolutionary analysis of both proteins of human SARS CoV 2 indicates close relatedness to the bat coronavirus. The whole genome phylogeny indicates that only the new bat coronavirus followed by pangolin coronaviruses has a close evolutionary relationship with the novel SARS CoV 2.
Cultural e Learning Through Erasmus Experience Management
Year: 2018

The practice of cultural orientation through e learning is one of the achieved success of our technology use, as culture is said to be a form or stage of civilization of a certain nation or period, this might imply that we are the culture and learning the culture is learning ourselves. This paper is trying to bring close to our vision the need for the cultural experience management system, through which people that have the knowledge of another culture can share and document their experiences of that culture. A cultural knowledge system can build a vocal community with human understanding that will help in, use of cultural signs, selection of words for communication, and guide us in our physical appearance to a certain community, with respect and preservation of human integrity from each society. The system will assist in bringing up a civilized young generation that will be good ambassadors in any geographic location they found themselves. Based on this, we may say, a student that goes to Erasmus program can have a lot to share regarding to a culture in a different perspective that is likely not to be the same with a person who learn about the culture through papers or by attending classes. Culture is taught and learned and shared, these can be better accomplished through the management of such experience.
Impact of Famotidine Use on Clinical Outcomes of Hospitalized Patients With COVID 19
Venue: The American journal of gastroenterology
Year: 2020

To compare outcomes in patients hospitalized with coronavirus (COVID 19) receiving famotidine therapy with those not receiving famotidine.  Retrospective, propensity matched observational study of consecutive COVID 19 positive patients between February 24, 2020, and May 13, 2020.  Of 878 patients in the analysis, 83 (9.5% received famotidine. In comparison to patients not treated with famotidine, patients treated with famotidine were younger (63.5 15.0 vs 67.5 15.8 years, P 0.021) but did not differ with respect to baseline demographics or preexisting comorbidities. Use of famotidine was associated with a decreased risk of in hospital mortality (odds ratio 0.37, 95% confidence interval 0.16 0.86, P 0.021) and combined death or intubation (odds ratio 0.47, 95% confidence interval 0.23 0.96, P 0.040) Propensity score matching to adjust for age difference between groups did not alter the effect on either outcome. In addition, patients receiving famotidine displayed lower levels of serum markers for severe disease including lower median peak C reactive protein levels (9.4 vs 12.7 mg/dL, P 0.002) lower median procalcitonin levels (0.16 vs 0.30 ng/mL, P 0.004) and a nonsignificant trend to lower median mean ferritin levels (797.5 vs 964.0 ng/mL, P 0.076) Logistic regression analysis demonstrated that famotidine was an independent predictor of both lower mortality and combined death/intubation, whereas older age, body mass index >30 kg/m2, chronic kidney disease, National Early Warning Score, and higher neutrophil lymphocyte ratio were all predictors of both adverse outcomes.  Famotidine use in hospitalized patients with COVID 19 is associated with a lower risk of mortality, lower risk of combined outcome of mortality and intubation, and lower levels of serum markers for severe disease in hospitalized patients with COVID 19.
Modelling green multimodal transport route performance with witness simulation software
Year: 2020

This study proposes an approach for dynamically calculating multimodal transport line parameters based on a "Witness" software simulation. The approach is designed to reduce the carbon emissions of multimodal transport, as green transportation has recently received increased attention. A multi objective multimodal transport efficiency evaluation framework is combined with an order relation analysis and an entropy weight fuzzy analytical hierarchy process method to assess route performance under various multimodal transport schemes. This study validated the proposed approach using the China Europe railway network from Wuhan, China to Berlin, Germany. The results are as follows: (1) the energy conservation and emission reduction values of a multimodal transport scheme fluctuate significantly, and it is scientifically appropriate to increase the energy conservation and emission reduction values as the indexes for scheme planning; (2) a multi objective and multi scenario efficiency evaluation method can provide a solution for green multi modal transport route planning, and can reduce energy usage and emissions by 24% as compared to an optimal routing considering a single objective; and 3) the China Europe railway express has unique advantages in a multi modal transport network, as it can save more than 60% of the transport time and reduce the carbon emissions by 40% as compared with a traditional water transport. This study presents a green multi modal transport organization approach.
Thermally and flow induced crystallization of polymers at low shear rate
Year: 2010

In semi crystalline thermoplastic products, final properties are strongly dependent on the thermo mechanical history experienced by the polymer melt during processing. More precisely, structural heterogeneities such as rigidity gradients and shrinkage anisotropy are directly related to the crystalline microstructure. Therefore, accurate prediction of part properties by a processing computer simulation code requires the implementation of an appropriate crystallization kinetics model, including both the effects of thermally and flow induced structure development. One issue is the necessity to improve the modeling of shear/extensional experimental data by relating the crystallization accelerating factors to an easily accessible material related variable. Several authors modeled the effect of the flow on the crystallization kinetics by using the isokinetic approach of Nakamura. Often, the resulting kinetic equations of these models account only for the evolution of the crystallinity fraction a leaving the influence of crystalline morphology aside. We may quote the work of Guo and Narh  which connects the flow influence on the crystallization rate to the increase in the thermodynamic melting temperature in the Nakamura model. In 2005, R.I. Tanner presented a comparison of some models describing the polymer crystallization at low shear deformation rates under isothermal conditions. Based on Tanner's study, we developed a model of crystallization at low shearing, applied to non isothermal flows, using only macroscopic measurable parameters. The key features of the concentrated suspension theory were used to characterize the effect of crystallization on the viscosity. In addition, we assumed that the flow generates additional crystallization nuclei via a parameter which combines the deformation and the deformation rate. The concept of germination growth is introduced using the fundamentals of the Avrami Kolmogorov theory, coupled with a modified Schneider's approach. The model is applied to a polypropylene, in a cooled Couette flow configuration. The results show the enhancement of the crystallization kinetics due to the shearing. The definition of global parameters simplifies the type and the number of experiments needed for the model parameter identification. The use of Schneider's approach leads to a new way of discriminating the relative roles of the flow and the temperature on the crystallization phenomenon. The competition between the two driving causes is presented and discussed: at low cooling rate or at high temperature, the shearing effect predominates. Other interesting results show the size distribution of the spherulites as well as the volume proportion for each crystalline size in the polymer.
Abductive Equivalence in First order Logic
Venue: Log. J. IGPL
Year: 2006

In Artificial Intelligence, abduction is often formalized in first order logic. In this article, we focus on the problem of identifying equivalence of two abductive theories represented in first order logic. To this end, two definitions of equivalence are given for abduction. Explainable equivalence requires that two abductive theories have the same explainability for any observation. On the other hand, explanatory equivalence guarantees that any observation has exactly the same explanations in each abductive theory. Explanatory equivalence is a stronger notion than explainable equivalence. In first order logic, explainable equivalence can be verified by the notion of extensional equivalence in default theories, while explanatory equivalence reduces to logical equivalence between background theories. We also show the complexity results for abductive equivalence.
High accuracy calibration of low cost camera using image disturbance factor.
Venue: Optics express
Year: 2016

Nonindustrial low cost cameras have the advantages of cheap and simple structure, but have the disadvantages of low resolution and large image noise. When the existing camera calibration methods are used to calibrate nonindustrial low cost cameras, high accuracy calibration cannot be obtained. A high accuracy calibration method using a high accuracy planar target is introduced in this study to solve this problem. First, the initial values and the uncertainties of all image feature points are determined by the multiscale image analysis method. Then, the image disturbance factor is added to each target image feature point. In addition, the image projection error is established as the minimum objective function according to the homography matrix between the target plane and the image plane. Thus, the optimal coordinates of all image feature points are obtained by the nonlinear optimization method. Finally, the calibration of the intrinsic and extrinsic parameters of the camera will be achieved by using Zhang's method according to the image feature points obtained from the previous step. Simulative and real experiments have been conducted to evaluate the performance of the proposed method, and results show that the calibration accuracy of the proposed method is at least three times that of Zhang's method.
Tabu Search
Venue: Handbook of Heuristics
Year: 2018

From the Publisher: This book explores the meta heuristics approach called tabu search, which is dramatically changing our ability to solve a hostof problems that stretch over the realms of resource planning,telecommunications, VLSI design, financial analysis, scheduling, spaceplanning, energy distribution, molecular engineering, logistics,pattern classification, flexible manufacturing, waste management,mineral exploration, biomedical analysis, environmental conservationand scores of other problems. The major ideas of tabu search arepresented with examples that show their relevance to multipleapplications. Numerous illustrations and diagrams are used to clarifyprinciples that deserve emphasis, and that have not always been wellunderstood or applied. The book's goal is to provide 'hands on' knowledge and insight alike, rather than to focus exclusively eitheron computational recipes or on abstract themes. This book is designedto be useful and accessible to researchers and practitioners inmanagement science, industrial engineering, economics, and computerscience. It can appropriately be used as a textbook in a masterscourse or in a doctoral seminar. Because of its emphasis on presentingideas through illustrations and diagrams, and on identifyingassociated practical applications, it can also be used as asupplementary text in upper division undergraduate courses. Finally, there are many more applications of tabu search than canpossibly be covered in a single book, and new ones are emerging everyday. The book's goal is to provide a grounding in the essential ideasof tabu search that will allow readers to create successfulapplications of their own. Along with the essentialideas,understanding of advanced issues is provided, enabling researchers togo beyond today's developments and create the methods of tomorrow.
Observation of Breathing Dark Pulses in Normal Dispersion Optical Microresonators.
Venue: Physical review letters
Year: 2018

Breathers are localized waves in nonlinear systems that undergo a periodic variation in time or space. The concept of breathers is useful for describing many nonlinear physical systems including granular lattices, Bose Einstein condensates, hydrodynamics, plasmas, and optics. In optics, breathers can exist in either the anomalous or the normal dispersion regimes, but they have only been characterized in the former, to our knowledge. Here, externally pumped optical microresonators are used to characterize the breathing dynamics of localized waves in the normal dispersion regime. High Q optical microresonators featuring normal dispersion can yield mode locked Kerr combs whose time domain waveform corresponds to circulating dark pulses in the cavity. We show that with relatively high pump power these Kerr combs can enter a breathing regime, in which the time domain waveform remains a dark pulse but experiences a periodic modulation on a time scale much slower than the microresonator round trip time. The breathing is observed in the optical frequency domain as a significant difference in the phase and amplitude of the modulation experienced by different spectral lines. In the highly pumped regime, a transition to a chaotic breathing state where the waveform remains dark pulse like is also observed, for the first time to our knowledge; such a transition is reversible by reducing the pump power.
Congenital adrenal hyperplasia due to 21 hydroxylase deficiency management in adults Wrodzony przerost nadnerczy z niedoboru 21 hydroksylazy problemy i postepowanie u doroslych
Year: 2010

Congenital adrenal hyperplasia (CAH) due to 21 hydroxylase deficiency is one of the most common autosomal recessive hereditary diseases. The impairment of cortisol synthesis leads to excessive stimulation of the adrenal glands by adrenocorticotropic hormone (ACTH) adrenal hyperplasia, and excessive androgen synthesis. The syndrome is characterised by a considerable correlation between the genotype and the phenotype with the type of CYP21A2 gene mutation affecting the severity of 21 hydroxylase deficiency. The clinical manifestations of CAH in adults result from adrenocortical and adrenomedullary insufficiency, hyperandrogenism, and the adverse effects of glucocorticosteroids used for the treatment of the condition. Non classic CAH may sometimes be asymptomatic. In patients with classic CAH obesity, hyperinsulinaemia, insulin resistance, and hyperleptinaemia are more often seen than in the general population. These abnormalities promote the development of metabolic syndrome and its sequelae, including endothelial dysfunction, and cardiovascular disease. Long term glucocorticosteroid treatment is also a known risk factor for osteoporosis. Patients with CAH require constant monitoring of biochemical parameters (17a hydroxyprogesterone [17 OHP] and androstenedione) clinical parameters (body mass, waist circumference, blood pressure, glucose, and lipids) and bone mineral density by densitometry. The principal goal of treatment in adults with CAH is to improve quality of life, ensure that they remain fertile, reduce the manifestations of hyperandrogenisation in females, and minimise the adverse effects of glucocorticosteroid treatment. Patients with classic CAH require treatment with glucocorticosteroids and, in cases of salt wasting, also with a mineralocorticosteroid. Radical measures, such as bilateral adrenalectomy, are very rarely needed. Asymptomatic patients with non classic CAH require monitoring: treatment is not always necessary. Medical care for patients with CAH should be provided by reference centres, as the management of such patients requires collaboration between an endocrinologist, diabetologist, gynaecologist, andrologist, urologist, and psychologist.
Profile of Weekly Training Load in Elite Male Professional Basketball Players
Venue: Journal of strength and conditioning research
Year: 2010

Manzi, V, D'Ottavio, S, Impellizzeri, FM, Chaouachi, A, Chamari, K, and Castagna, C. Profile of weekly training load in elite male professional basketball players.  2010 The aim of this study was to examine the training load (TL) profile of professional elite level basketball players during the crucial parts of the competitive season (pre play off finals) Subjects were 8 full time professional basketball players (age 28 3.6 years, height 199 7.2 cm, body mass 102 11.5 kg, and body fat 10.4 1.5% whose heart rate (HR) was recorded during each training session and their individual response to TL monitored using the session rate of perceived exertion (RPE) method (200 training sessions) The association between the session RPE method and training HR was used to assess the population validity of the session RPE method. Significant relationships were observed between individual session RPE and all individual HR based TL (r values from 0.69 to 0.85; p 0.001) Coaches spontaneously provided a tapering phase during the competitive weeks irrespective of the number of games played during it (i.e. 1 or 2 games) The individual weekly players' TL resulted in being not significantly different from each other (p 0.05) Elite male professional basketball imposes great physiological and psychological stress on players through training sessions and official competitions (1 2 per week) Consequently, the importance of a practical and valid method to assess individual TL is warranted. In this research, we demonstrated that session RPE may be considered as a viable method to asses TL without the use of more sophisticated tools (i.e. HR monitors) The session RPE method enabled the detection of periodization patterns in weekly planning in elite professional basketball during the crucial part of the competitive season (1 vs. 2 weekly fixtures model)
Exploring adult Playfulness: Examining the accuracy of personality judgments at zero acquaintance and an LIWC analysis of textual information
Year: 2018

Playfulness is an individual difference variable that allows people to (re)frame a situation in a way that it is experienced as entertaining, intellectually stimulating, and/or personally interesting. We examined the interpersonal perception of playfulness at zero acquaintance. One hundred forty four participants wrote short self descriptions which were (1) used by unacquainted judges to infer the author's playfulness and (2) linguistically analyzed using the LIWC methodology. Lens model analyses revealed that playfulness finds its expression through language and that observers utilized linguistic cues to accurately judge playfulness in terms of self other agreement (0.21 0.37) and consensus (0.31 0.44) The findings add knowledge regarding the interpersonal perception of playfulness, its linguistic expressions, and the applicability of the LIWC paradigm outside broad personality traits.
BIM based Automated Design Checking for Building Permit in the Light Frame Building Industry
Venue: Proceedings of the 36th International Symposium on Automation and Robotics in Construction (ISARC)
Year: 2019

Automation of the code compliance checking has been explored extensively, particularly in recent years with the emergence of building information modelling (BIM) Still, automated code compliance checking has not yet been fully realized, as there is no standardized method for rule interpretation and building model preparation for code compliance. Manual verification of design code compliance, meanwhile, requires significant effort and time and is error prone, while uncertainty and inconsistency in assessment lead to delays in the construction process. In this paper, the development of a prototype to automate municipal bylaw and wall framing code compliance checking for residential building is presented. The building rules have been classified into three groups based on the complexity involved in translation into computerreadable format and complexity in retrieving the required information, and they are represented based on building objects, which makes the regulations easier to understand and assists in translating the regulations into a computer readable format. By creating a model view based on the required element's parameters extracted from a model for checking purposes, the prototype application offers automated code compliance checking functionality to validate designs based on building code requirements and construction engineering specifications. The implementation of the prototype and its benefits compared to manual checking is demonstrated.
Task Personalization for Inexpertise Workers in Incentive Based Crowdsourcing Platforms
Venue: 2018 International Conference on Advances in Computing, Communications and Informatics (ICACCI)
Year: 2018

Crowdsourcing is an emerging technology which enables human workers to perform the task that cannot be done using automated tools. The crucial constituent of crowdsourcing platform is human workers. Since crowdsourcing platforms are overcrowded, workers find difficulty in selecting a suitable task for them. Employing task recommendation systems could improve this situation. However, task recommendation for new and inexpert workers is not explored well. We address this problem by designing a task recommendation model using skill taxonomy and participation probability of existing expert workers. The proposed model is validated through experimentation with both real and synthetic dataset.