nils-herrmann/clean_scirepeval huggingface dataset:
Comparison of automated SARS CoV 2 antigen test for COVID 19 infection with quantitative RT PCR using 313 nasopharyngeal swabs, including from seven serially followed patients
Venue: International Journal of Infectious Diseases
Year: 2020

Severe acute respiratory syndrome coronavirus 2 (SARS CoV 2) infection is determined by reverse transcription PCR (RT PCR) in routine clinical practice. In the current pandemic situation, a more rapid and high throughput method is in growing demand. Here, we validated the performance of a new antigen test (LUMIPULSE) based on the chemiluminescence enzyme immunoassay. A total of 313 nasopharyngeal swabs (82 serial samples from 7 infected patients, 231 individual samples from 4 infected patients and 215 non infected individuals) were analyzed for SARS CoV 2 by quantitative RT PCR (RT qPCR) and then subjected to LUMIPULSE. We determined the cutoff value for antigen detection using receiver operating characteristic curve analysis and compared the antigen test performance with that of RT qPCR. Further, we compared the viral loads and antigen levels in serial samples from seven infected patients. When using RT qPCR as the reference, the antigen test exhibited 55.2% sensitivity and 99.6% specificity with a 91.4% overall agreement rate (286/313) In specimens with 100 viral copies and between 10 and 100 copies, the antigen test showed 100% and 85% concordance with RT qPCR, respectively. This concordance declined with lower viral loads. In the serially followed patients, the antigen levels showed a steady decline along with viral clearance. This gradual decline was in contrast with the abrupt "positive to negative" and "negative to positive" status changes observed with RT qPCR, particularly in the late phase of infection. In summary, the LUMIPULSE antigen test can rapidly identify SARS CoV 2 infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients.
Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes
Venue: Nature
Year: 2007

A decisive step in the biosynthesis of many proteins is their partial or complete translocation across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. Most of these proteins are translocated through a protein conducting channel that is formed by a conserved, heterotrimeric membrane protein complex, the Sec61 or SecY complex. Depending on channel binding partners, polypeptides are moved by different mechanisms: the polypeptide chain is transferred directly into the channel by the translating ribosome, a ratcheting mechanism is used by the endoplasmic reticulum chaperone BiP, and a pushing mechanism is used by the bacterial ATPase SecA. Structural, genetic and biochemical data show how the channel opens across the membrane, releases hydrophobic segments of membrane proteins laterally into lipid, and maintains the membrane barrier for small molecules.
Management accounting change: critical review and a new contextual framework
Year: 2015

This paper aims to introduce and discuss a new contextual framework to explain the processes of management accounting change in various organizations.  Having an institutional perspective, the paper develops a "conceptual contextual framework" of management accounting change. The methodology to accomplish this theory building consists of an integration of a number of different works summarizing the common elements, contrasting the differences and extending the work in some fashion. Particularly, it draws on theoretical triangulation by adopting three approaches: old institutional economics for internal processes and factors (Burns and Scapens, 2000) new institutional sociology for external processes and pressures (Dillard et al. 2004) and power and politics mobilization (Hardy, 1996)  The proposed framework provides an understanding of the complex "mixture" of interrelated factors that may influence management accounting change at multi institutional le.
Multimedia Security and Privacy on Real Time Behavioral Monitoring in Machine Learning IoT Application Using Big Data Analytics
Year: 2020

The Internet of Things (IoT) is an advancing idea where physical articles are associated with one another and customer through the Internet so as to share information among contraptions and structures. Under IoT, splendid contraptions are transmitted to screen, follow, and dissect business, individual and social activities. The IoT's unavoidable idea will conceivably be fruitful; however, it additionally uncovers a risk from malware, developer obstruction, diseases, etc. The subsequent security and insurance issues can cause physical mischief and even compromise human lives. This paper targets two zones; from the start, the paper gives an examination of the IoT layered engineering to set up an IoT space with the security challenges/attack. From that point on, the paper proposes a response that can protect the security of mixed media information within an IoMT state (Internet of Multimedia Things) at its observation layer. The proposed security structure would improve the mixed media to operate adequately while at the same time safeguarding the privacy of the transmitted data and protecting people.
Development of Acquired Immunity following Repeated Respiratory Syncytial Virus Infections in Cotton Rats
Venue: PloS one
Year: 2016

Respiratory syncytial virus (RSV) infections occur every year worldwide. Most infants are infected with RSV by one year of age and are reinfected because immune responses after the first infection are too weak to protect against subsequent infections. In the present study, immune responses against RSV were investigated in order to obtain a better understanding of repetitive RSV infections in cotton rats. No detectable neutralizing antibody (NT) was developed after the first infection, and the second infection was not prevented. The results of histological examinations revealed severe inflammation, viral antigens were detected around bronchial epithelial cells, and infectious viruses were recovered from lung homogenates. Following the second infection neutralizing antibodies were significantly elevated, and CD8+ cells were activated in response to RSV F253 265. No viral antigens was detected thereafter in lung tissues and infectious viruses were not recovered. Similar results were obtained in the present study using the subgroups A and B. These results support the induction of humoral and cellular immune responses following repetitive infections with RSV; however, these responses were insufficient to eliminate viruses in the first and second infections.
Functional reconstitution of TatB into the thylakoidal Tat translocase.
Venue: Biochimica et biophysica acta. Molecular cell research
Year: 2019

We have established an experimental system for the functional analysis of thylakoidal TatB, a component of the membrane integral TatBC receptor complex of the thylakoidal Twin arginine protein transport (Tat) machinery. For this purpose, the intrinsic TatB activity of isolated pea thylakoids was inhibited by affinity purified antibodies and substituted by supplementing the assays with TatB protein either obtained by in vitro translation or purified after heterologous expression in E. coli. Tat transport activity of such reconstituted thylakoids, which was analysed with the authentic Tat substrate pOEC16, reached routinely 20 25% of the activity of mock treated thylakoid vesicles analysed in parallel. In contrast, supplementation of the assays with the purified antigen comprising all but the N terminal transmembrane helix of thylakoidal TatB did not result in Tat transport reconstitution which confirms that transport relies strictly on the activity of the TatB protein added and is not due to restoration of the intrinsic TatB activity by antibody release. Unexpectedly, even a mutated TatB protein (TatB,E10C) assumed to be incapable of assembling into the TatBC receptor complex showed low but considerable transport reconstitution underlining the sensitivity of the approach and its suitability for further functional analyses of protein variants. Finally, quantification of TatB demand suggests that TatA and TatB are required in approximately equimolar amounts to achieve Tat dependent thylakoid transport.
Literary Criticism from Plato to the Present: An Introduction
Year: 2011

Acknowledgments.  Part I Classical Literary Criticism and Rhetoric. 1 Classical Literary Criticism.  Plato (428 ca. 347 BC) Aristotle (384 322 BC) 2 The Traditions of Rhetoric. Greek Rhetoric. Roman Rhetoric. The Subsequent History of Rhetoric: An Overview. The Legacy of Rhetoric. 3 Greek and Latin Criticism During the Roman Empire. Horace (65 8 BC) Longinus (First Century AD) Neo Platonism. Part II The Medieval Era. 4 The Early Middle Ages.  Intellectual and Theological Currents. 5 The Later Middle Ages.  Intellectual Currents of the Later Middle Ages. The Traditions of Medieval Criticism.  Medieval Humanism. Part III The Early Modern Period to the Enlightenment. 6 The Early Modern Period.  Confronting the Classical Heritage. Defending the Vernacular. Poetics and the Defense of Poetry.  The Aesthetics of Kant and Hegel. Immanuel Kant (1724 1804) Hegel (1770 1831) Part IV Romanticism and the Later Nineteenth Century. 10 Romanticism. Germany. France. England. America. 11 Realism, Naturalism, Symbolism, and Aestheticism.  The Later Nineteenth Century. Realism and Naturalism. Symbolism and Aestheticism. 12 The Heterological Thinkers. Arthur Schopenhauer (1788 1860) Friedrich Nietzsche (1844 1900) Henri Bergson (1859 1941) Matthew Arnold (1822 1888) Part V The Twentieth Century: A Brief Introduction.  From Liberal Humanism to Formalism. The Background of Modernism. The Poetics of Modernism: W. B. Yeats, Ezra Pound, and T. S. Eliot.  The New Criticism. 14 Socially Conscious Criticism of the Earlier Twentieth Century. F. R. Leavis. Marxist and Left Wing Criticism. The Fundamental Principles of Marxism. Marxist Literary  A Historical Overview. Early Feminist Criticism: Simone de Beauvoir and Virginia Woolf. 15 Phenomenology, Existentialism, Structuralism. Phenomenology. Existentialism. Heterology. Structuralism. 16 The Era of Poststructuralism (I) Later Marxism, Psychoanalysis, Deconstruction. Later Marxist Criticism.   The Era of Poststructuralism (II) Postmodernism, Modern Feminism, Gender Studies. Jurgen Habermas (b. 1929) Jean Baudrillard (1929 2007) Jean Fran,cois Lyotard (1924 1998) bell hooks (Gloria Jean Watkins b. 1952) Modern Feminism. Gender Studies. 18 The Later Twentieth Century: New Historicism, Reader Response Theory, Postcolonial Criticism, Cultural Studies. The New Historicism. Reader Response and Reception Theory. Postcolonial Criticism. Cultural Studies. Epilogue New Directions: Looking Back, Looking Forward. Index.
L G 2 J ul 2 01 9 Voting Based Multi Agent Reinforcement Learning
Year: 2019

The recent success of single agent reinforcement learning (RL) encourages the exploration of multi agent reinforcement learning (MARL) which is more challenging due to the interactions among different agents. In this paper, we consider a voting based MARL problem, in which the agents vote to make group decisions and the goal is to maximize the globally averaged returns. To this end, we formulate the MARL problem based on the linear programming form of the policy optimization problem and propose a distributed primal dual algorithm to obtain the optimal solution. We also propose a voting mechanism through which the distributed learning achieves the same sub linear convergence rate as centralized learning. In other words, the distributed decision making does not slow down the global consensus to optimal. We also verify the convergence of our proposed algorithm with numerical simulations and conduct case studies in practical multi agent systems.
Copula Based Analysis of Physical Layer Security Performances Over Correlated Rayleigh Fading Channels
Venue: IEEE Transactions on Information Forensics and Security
Year: 2021

This paper studies performance analysis of physical layer security in a Rayleigh fading wiretap channel, where, the main (transmitter to legitimate receiver) and eavesdropper (transmitter to eavesdropper) channel coefficients are correlated. By exploiting the novel approach called Copula theory, we derive closed form expressions for average secrecy capacity (ASC) secrecy outage probability (SOP) and secrecy coverage region (SCR) Moreover, to more evaluate the impact of channel correlation, the asymptotic behavior of SOP in high signal to noise ratio (SNR) regime and other scenarios is studied, and finally, the analytical results are illustrated numerically under the positive dependence, independence, and negative dependence structures. Based on the insights from this analysis, we found that the effect of correlated fading on the performance of physical layer security can be helpful or harmful in different scenarios, depending on the structure of dependency between the main and eavesdropper channels.
The Description Experience Gap in Risky and Ambiguous Gambles
Year: 2013

Recent research in decision making reported a descriptionexperience (DE) gap: opposite risky choices when decisions are made from descriptions (gambles in which probability distributions and outcomes are explicitly stated) and when decisions are made from experience (the knowledge of the gambles is obtained by sampling outcomes from unknown probability distributions before making a choice) The DE gap has been reported in gambles commonly involving a risky option (outcomes drawn from a fixed probability distribution) and a safe option (probability of the outcome is 1) or in gambles involving two risky options. Here, we extend the study of the DE gap to gambles in which people choose between a risky option and an ambiguous option (with two nested probability distributions, where the event generation mechanism is more opaque than that in the risky option) We report empirical evidence and show a DE gap in gambles involving risky and ambiguous options. Participants' choices are influenced by the information format and by the ambiguous option: participants are ambiguity seeking in experience and ambiguity averse in description in problems involving both gains and losses. In order to find reasons for our results, we investigate participants' sampling behavior, and this analysis indicates choices according to a cognitive model of experiential decisions (instance based learning) In experience, participants have small sample sizes, and participants choose options where high outcomes are experienced more frequently than expected. We discuss the implications of our results for the psychology of decision making in complex environments
Segram a program visualizing stages of grammatical competence
Year: 2009

This paper will report on four machine translation projects dealing with restricted domains and controlled or semi controlled language. The computer program Seatra translates marine forecasts between Swedish and English. It is in daily use by the Swedish meteorological agency (SMHI) and generally needs no postediting. The same basic program but with different lexicons is used in the program Maltra which can translate official Malaysian marine forecasts into English and Chinese. The program Reptra dealing with quarterly company reports and Receptra dealing with recipes use the same platform. All these programs (which can be used bidirectionally) will be presented and commented on, above all from a linguistic point of view. It is suggested that no more than 3 mistakes per 100 words be accepted if the postediting should not be too heavy, and this quality can be obtained in restricted domain systems. 1 Seatra The Canadian program METRO (Kitti edge et al. 1973; Goldberg, Kittredge Polguere 1988) is well known and the task to translate marine forecasts from Swedish into English suggested by the Swedish meteorological agency SMHI didn't seem too hard. Early work is described in Sigurd, Lastow Vavargard 1996. The program Seatra was developed in Prolog (LPAProlog http:/www.lpa.co.uk) using a technique which is based on lexicons containing single words, multi word phrases, discontinuous phrases and some grammatical phrases such as noun phrases, prepositional phrases and adverbial phrases. The program is designed to produce simple and fast translation in a restricted domain without offering deep syntactic and
A Comparison of National and Local Airport Management
Year: 2017

This chapter aims to address the following issues. First, do national or local airports set lower airport fee? Second, which type of airport undertakes more activities to reduce costs? Finally, which management type is socially preferable? In order to address these problems, this chapter assumes two substitute airports. Each airport locates in the city which has different number of passengers. As a result, this chapter demonstrates that depending on the number of passenger in each city, the comparison results change.
Use of Biomarkers to Guide Decisions on Adjuvant Systemic Therapy for Women With Early Stage Invasive Breast Cancer: American Society of Clinical Oncology Clinical Practice Guideline.
Venue: Journal of clinical oncology official journal of the American Society of Clinical Oncology
Year: 2016

To provide recommendations on appropriate use of breast tumor biomarker assay results to guide decisions on adjuvant systemic therapy for women with early stage invasive breast cancer.  A literature search and prospectively defined study selection sought systematic reviews, meta analyses, randomized controlled trials, prospective retrospective studies, and prospective comparative observational studies published from 2006 through 2014. Outcomes of interest included overall survival and disease free or recurrence free survival. Expert panel members used informal consensus to develop evidence based guideline recommendations.  The literature search identified 50 relevant studies. One randomized clinical trial and 18 prospective retrospective studies were found to have evaluated the clinical utility, as defined by the guideline, of specific biomarkers for guiding decisions on the need for adjuvant systemic therapy. No studies that met guideline criteria for clinical utility were found to guide choice of specific treatments or regimens. RECOMMENDATIONS In addition to estrogen and progesterone receptors and human epidermal growth factor receptor 2, the panel found sufficient evidence of clinical utility for the biomarker assays Oncotype DX, EndoPredict, PAM50, Breast Cancer Index, and urokinase plasminogen activator and plasminogen activator inhibitor type 1 in specific subgroups of breast cancer. No biomarker except for estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 was found to guide choices of specific treatment regimens. Treatment decisions should also consider disease stage, comorbidities, and patient preferences.
School personnel and child abuse and neglect reporting behavior: An integrative review
Year: 2020

Although school personnel are in a good position to identify cases of abuse and neglect, they may fail to report these cases. This failure may leave victims to suffer the negative effects of abuse and neglect and deprives them of possible help. Because the evidence for factors associated with this behavior is insufficient, an integrative review was conducted to synthesize the literature related to factors associated with the reporting by school personnel of child abuse (schoolteachers, principals, counselors, early educators, kindergarten teachers, and daycare teachers)  A systematic search was conducted using the PsychINFO, Embase, ERIC, and PubMed electronic databases that was limited to the past ten years and journal articles in the English language. The search terms were "school personnel," "child abuse," "neglect," and "reporting." Studies were included if their focus was on factors associated with child abuse and neglect reporting by school personnel in private schools, public schools, or daycares. Studies were excluded if their focus was not on child abuse and neglect reporting; if they were non research articles, theses/dissertations, or interventional studies; or if the focus was on special education.  Sixteen articles based on 14 studies were reviewed: nine quantitative studies, three qualitative studies, and two mixed methods. All the studies had used different instruments, and only three had a theoretical framework that was different from each other. Three categories of factors associated with the reporting behavior were identified as system, victim, and reporter characteristics. These studies provide a description of these factors; however, the evidence of the degree of association between these factors and the reporting behavior was still at the beginning stage. No common theories or instruments guide the science of child abuse and neglect reporting behavior. Practice implications Further research should investigate the association between school personnel's reporting behavior and influential factors to facilitate effective interventions. Once evidence exists, school nurses, for example, in collaboration with other professionals, can target school personnel with interventions to increase reporting behavior.
A synopsis of Estonian myriapod fauna (Myriapoda: Chilopoda, Diplopoda, Symphyla and Pauropoda)
Venue: ZooKeys
Year: 2018

The data on Estonian Myriapoda are scattered in various publications and there has been no overview of the fauna up to the present. A critical summary of the previous information on Estonian Myriapoda is given, supplemented by new records and distribution maps. Altogether, 5784 specimens from 276 collecting sites were studied. To the hitherto recorded 14 centipede species are added Lithobiusmelanops, L.microps, Geophiluscarpophagus, G.flavus, Strigamiatranssilvanica and Stenotaenialinearis, a probably introduced species. Of the 27 published Estonian millipede species, the data on two species proved erroneous, and two new species were recorded (Craspedosomaraulinsii and Cylindroiulusbritannicus) Two previously recorded millipede species Brachyiuluspusillus and Mastigophorophyllonsaxonicum were not found in the recent samples, the latter may have become more rare or extinct. Pauropoda and Symphyla lack previous reliable records. Combined with published data, the number of myriapod species known from Estonia is now set at 52. Some changes in species distribution and frequencies were detected comparing the published data with new records. Some data about habitat preferences of the more common species are also given. The majority of species have a western Palaearctic distribution, while six species are at the northern limit of their ranges.
Improving Fully Convolution Network for Semantic Segmentation
Venue: ArXiv
Year: 2016

Fully Convolution Networks (FCN) have achieved great success in dense prediction tasks including semantic segmentation. In this paper, we start from discussing FCN by understanding its architecture limitations in building a strong segmentation network. Next, we present our Improved Fully Convolution Network (IFCN) In contrast to FCN, IFCN introduces a context network that progressively expands the receptive fields of feature maps. In addition, dense skip connections are added so that the context network can be effectively optimized. More importantly, these dense skip connections enable IFCN to fuse rich scale context to make reliable predictions. Empirically, those architecture modifications are proven to be significant to enhance the segmentation performance. Without engaging any contextual post processing, IFCN significantly advances the state of the arts on ADE20K (ImageNet scene parsing) Pascal Context, Pascal VOC 2012 and SUN RGBD segmentation datasets.