nils-herrmann/clean_scirepeval huggingface dataset:
The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance
Venue: BMC Biology

BackgroundThe whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) is among the 100 worst invasive species in the world. As one of the most important crop pests and virus vectors, B. tabaci causes substantial crop losses and poses a serious threat to global food security.ResultsWe report the 615 Mb high quality genome sequence of B. tabaci Middle East Asia Minor 1 (MEAM1) the first genome sequence in the Aleyrodidae family, which contains 15,664 protein coding genes. The B. tabaci genome is highly divergent from other sequenced hemipteran genomes, sharing no detectable synteny. A number of known detoxification gene families, including cytochrome P450s and UDP glucuronosyltransferases, are significantly expanded in B. tabaci. Other expanded gene families, including cathepsins, large clusters of tandemly duplicated B. tabaci specific genes, and phosphatidylethanolamine binding proteins (PEBPs) were found to be associated with virus acquisition and transmission and/or insecticide resistance, likely contributing to the global invasiveness and efficient virus transmission capacity of B. tabaci. The presence of 142 horizontally transferred genes from bacteria or fungi in the B. tabaci genome, including genes encoding hopanoid/sterol synthesis and xenobiotic detoxification enzymes that are not present in other insects, offers novel insights into the unique biological adaptations of this insect such as polyphagy and insecticide resistance. Interestingly, two adjacent bacterial pantothenate biosynthesis genes, panB and panC, have been co transferred into B. tabaci and fused into a single gene that has acquired introns during its evolution.ConclusionsThe B. tabaci genome contains numerous genetic novelties, including expansions in gene families associated with insecticide resistance, detoxification and virus transmission, as well as numerous horizontally transferred genes from bacteria and fungi. We believe these novelties likely have shaped B. tabaci as a highly invasive polyphagous crop pest and efficient vector of plant viruses. The genome serves as a reference for resolving the B. tabaci cryptic species complex, understanding fundamental biological novelties, and providing valuable genetic information to assist the development of novel strategies for controlling whiteflies and the viruses they transmit.
Relationship of Physician identified Patient Race and Ethnicity to Use of Computed Tomography in Pediatric Blunt Torso Trauma.
Venue: Academic emergency medicine official journal of the Society for Academic Emergency Medicine

The objective was to determine whether a child's race or ethnicity as determined by the treating physician is independently associated with receiving abdominal computed tomography (CT) after blunt torso trauma.  We performed a planned secondary analysis of a prospective observational cohort of children 18 years old presenting within 24 hours of blunt torso trauma to 20 North American emergency departments (EDs) participating in a pediatric research network, 2007 2010. Treating physicians documented race/ethnicity as white non Hispanic, black non Hispanic, or Hispanic. Using a previously derived clinical prediction rule, we classified each child's risk for having an intra abdominal injury undergoing acute intervention to define injury severity. We performed multivariable analyses using generalized estimating equations to control for confounding and for clustering of children within hospitals.  Among 12,044 enrolled patients, treating physicians documented race/ethnicity as white non Hispanic (n 5,847, 54.0% black non Hispanic (n 3,687, 34.1% or Hispanic of any race (n 1,291, 11.9% Overall, 51.8% of white non Hispanic, 32.7% of black non Hispanic, and 44.2% of Hispanic children underwent abdominal CT imaging. After age, sex, abdominal ultrasound use, risk for intra abdominal injury undergoing acute intervention, and hospital clustering were adjusted for, the likelihood of receiving an abdominal CT was lower (odds ratio [OR] 0.8, 95% confidence interval [CI] 0.7 to 0.9) for black non Hispanic than for white non Hispanic children. For Hispanic children, the likelihood of receiving an abdominal CT did not differ from that observed in white non Hispanic children (OR 0.9, 95% CI 0.8 to 1.1)  After blunt torso trauma, pediatric patients identified by the treating physicians as black non Hispanic were less likely to receive abdominal CT imaging than those identified as white non Hispanic. This suggests that nonclinical factors influence clinician decision making regarding use of abdominal CT in children. Further studies should focus on explaining how patient race can affect provider choices regarding ED radiographic imaging.
Paleoecology, biogeography, and evolution of reef ecosystems in the Panthalassa Ocean during the Late Triassic: Insights from reef limestone of the Sambosan Accretionary Complex, Shikoku, Japan

Upper Triassic reefs from the Panthalassa Ocean have been understudied in comparison to their Tethyan counterparts and are therefore pivotal to understanding the global reef evolution during the Late Triassic. To fill this gap, Upper Triassic reef limestone from ten localities of the Sambosan Accretionary Complex at Shikoku Island (Japan) has been investigated. Biotic assemblages, quantitative microfacies analysis, and integrated biostratigraphy allow us to characterize two types of reefs, those attributed to the Ladinian? Early Carnian and those attributed to the Late Carnian Rhaetian? At the regional scale, our data refine the biostratigraphic framework of the Upper Triassic Sambosan limestone. At the global scale, multivariate analyses support a strong paleobiogeographic affinity of the Western Panthalassa reef biota with those of the South Tethys Ocean during the Ladinian Carnian and Norian Rhaetian. Additionally, they indicate connections with East Panthalassa reefs during the Norian Rhaetian.
Sedimentary history and biota of the Zechstein Limestone (Permian, Wuchiapingian) of the Jablonna Reef in Western Poland

The Jablonna Reef, one of the reefs formed in Wuchiapingian time in the western part of the Wolsztyn palaeo High (SW Poland) is characterized by quite irregular outlines and consists of three separate reef bodies (ca. 0.5 1.5 km 2 each; the thickness of the reef complex is usually >60 m) It is penetrated by four boreholes, which show two distinct phases of bryozoan reef development during deposition of the the Zechstein Limestone. The first one occurred early in the depositional history and botryoidal aragonitic cementation played a very important role in reef formation. This phase of bryozoan reef development terminated suddenly; one possible reason was that a relative change of sea level first a fall and then a rise disturbed the upwelling circulation. Consequently, bioclastic deposition predominated for a relatively long time until the second phase of bryozoan reef development occurred, but the latter was not accompanied by dubious early cementation. During this second phase, reticular fenestellid bryozoans were predominant. Subsequently, microbial reefs developed and abound in the upper part of the Zechstein Limestone sections. The general shallowing upward nature of deposition in the Jablonna Reef area resulted in reef flat conditions with ubiquitous, microbial deposits, in the central part of the Jablonna Reef. Then, the reef flat started to prograde and eventually the entire Jablonna Reef area became the site of very shallow, subaqueous deposition. Five biofacies are distinguished in the Jablonna Reef sections: the Acanthocladia biofacies at the base, then mollusc crinoid, brachiopod bryozoan, Rectifenestella and at the top, stromatolite biofacies. They represent a shallowing upward cycle, possibly with some important fluctuation recorded as the distinctive lithofacies boundary, corresponding to the Acanthocladia/mollusc crinoid biofacies boundary. The d 13 C curves of the Jablonna 2 and Jablonna 4 boreholes permit correlation of the trends in the middle parts of both sections and confirm the strong diachroneity of the biofacies boundaries, with the exception of the roughly isochronous Acanthocladia/ mollusc crinoid biofacies boundary. The presence of echinoderms and strophomenid brachiopods indicates that until deposition of the lower part of the Rectifenestella biofacies, conditions were clearly stenohaline. The subsequent elimination of stenohaline organisms and progressively poorer taxonomic differentiation of the faunal assemblage are characteristic for a slight, gradual rise in salinity. The taxonomic composition of organisms forming the Jablonna Reef shows a similarity to reefs described from England and Germany, as well as the marginal carbonate platform of SW Poland. Filled fissures were recorded in the lower part of the Jablonna Reef. The aragonite cementation recorded in some fissure fillings implies that they originated in rocks exposed on the sea floor and are neptunian dykes.
Electrostatic catalysis of a Diels Alder reaction
Venue: Nature

It is often thought that the ability to control reaction rates with an applied electrical potential gradient is unique to redox systems. However, recent theoretical studies suggest that oriented electric fields could affect the outcomes of a range of chemical reactions, regardless of whether a redox system is involved. This possibility arises because many formally covalent species can be stabilized via minor charge separated resonance contributors. When an applied electric field is aligned in such a way as to electrostatically stabilize one of these minor forms, the degree of resonance increases, resulting in the overall stabilization of the molecule or transition state. This means that it should be possible to manipulate the kinetics and thermodynamics of non redox processes using an external electric field, as long as the orientation of the approaching reactants with respect to the field stimulus can be controlled. Here, we provide experimental evidence that the formation of carbon carbon bonds is accelerated by an electric field. We have designed a surface model system to probe the Diels Alder reaction, and coupled it with a scanning tunnelling microscopy break junction approach. This technique, performed at the single molecule level, is perfectly suited to deliver an electric field stimulus across approaching reactants. We find a fivefold increase in the frequency of formation of single molecule junctions, resulting from the reaction that occurs when the electric field is present and aligned so as to favour electron flow from the dienophile to the diene. Our results are qualitatively consistent with those predicted by quantum chemical calculations in a theoretical model of this system, and herald a new approach to chemical catalysis.
UAV path planning using artificial potential field method updated by optimal control theory
Venue: Int. J. Syst. Sci.

The unmanned aerial vehicle (UAV) path planning problem is an important assignment in the UAV mission planning. Based on the artificial potential field (APF) UAV path planning method, it is reconstructed into the constrained optimisation problem by introducing an additional control force. The constrained optimisation problem is translated into the unconstrained optimisation problem with the help of slack variables in this paper. The functional optimisation method is applied to reform this problem into an optimal control problem. The whole transformation process is deduced in detail, based on a discrete UAV dynamic model. Then, the path planning problem is solved with the help of the optimal control method. The path following process based on the six degrees of freedom simulation model of the quadrotor helicopters is introduced to verify the practicability of this method. Finally, the simulation results show that the improved method is more effective in planning path. In the planning space, the length of the calculated path is shorter and smoother than that using traditional APF method. In addition, the improved method can solve the dead point problem effectively.
Understanding computational web archives research methods using research objects
Venue: 2016 IEEE International Conference on Big Data (Big Data)

Use of computational methods for exploration and analysis of web archives sources is emerging in new disciplines such as digital humanities. This raises urgent questions about how such research projects process web archival material using computational methods to construct their findings. This paper aims to enable web archives scholars to document their practices systematically to improve the transparency of their methods. We adopt the Research Object framework to characterize three case studies that use computational methods to analyze web archives within digital history research. We then discuss how the framework can support the characterization of research methods and serve as a basis for discussions of methods and issues such as reuse and provenance. The results suggest that the framework provides an effective conceptual perspective to describe and analyze the computational methods used in web archive research on a high level and make transparent the choices made in the process. The documentation of the research process contributes to a better understanding of the findings and their provenance, and the possible reuse of data, methods, and workflows.
Integrating qualitative research methods into care improvement efforts within a learning health system: addressing antibiotic overuse
Venue: Health Research Policy and Systems

BackgroundDespite reports advocating for integration of research into healthcare delivery, scant literature exists describing how this can be accomplished. Examples highlighting application of qualitative research methods embedded into a healthcare system are particularly needed. This article describes the process and value of embedding qualitative research as the second phase of an explanatory, sequential, mixed methods study to improve antibiotic stewardship for acute sinusitis.MethodsPurposive sampling of providers for in depth interviews improved understanding of unwarranted antibiotic prescribing and elicited stakeholder recommendations for improvement. Qualitative data collection, transcription and constant comparative analyses occurred iteratively.ResultsEmerging themes and sub themes identified primary drivers of unwarranted antibiotic prescribing patterns and recommendations for improving practice. These findings informed the design of a health system intervention to improve antibiotic stewardship for acute sinusitis. Core components of the intervention are also described.ConclusionQualitative research can be effectively applied in learning healthcare systems to elucidate quantitative results and inform improvement efforts.
Non alcoholic fatty liver disease.
Venue: Nursing standard (Royal College of Nursing (Great Britain) 1987)

Essential facts Non alcoholic fatty liver disease (NAFLD) is an excess of fat in the liver that is not the result of excessive alcohol consumption or other secondary causes, such as hepatitis C. According to the National Institute for Health and Care Excellence, fatty liver steatosis affects between 20% and 30% of the population and its prevalence is increasing.
On a two sector endogenous growth model with quasi geometric discounting

We study a two sector endogenous growth model with quasi geometric discounting in which human capital is the engine of growth. We show that a planning economy welfare dominates a competitive economy and time consistent government policy is welfare improving if the agents are sufficiently patient. The government policy consists of a tax on physical capital income and a subsidy on human capital accumulation. Our results differ from those of existing one sector models with quasi geometric discounting in which a competitive economy always outperforms a planning economy and the government's time consistent tax policies reduce equilibrium welfare.
Large single crystal growth of MnWO4 type materials from high temperature solutions

A simple high temperature growth apparatus was constructed to obtain large crystals of chemically gradient (In, Na) doped MnWO4 solid solutions. This paper presents the crystal growth and characterization of both MnWO4 and epitaxially grown (In, Na):MnWO4 crystals on MnWO4. These large monolithic crystals were made in two steps: A MnWO4 crystal was grown in the crystallographic main direction [001] applying the Czochralski method, followed by the top seeded growth of (In, Na):MnWO4 solid solutions with an oriented seed crystal of MnWO4. Such a monolithic crystal will serve to fundamental investigation of coupling properties at boundaries between various multiferroic MnWO4 type solid solutions.
Effect of Frozen Storage on the Chemical Stability, Functional and Sensory Properties of 'Ogbono' Irvingiagarbonensis var. excelsa and 'Egusi' Citrullus vulgaris schrad Seed Flours

'Ogbono' (Irvingiagarbonensis var. excelsa) and 'egusi' (Citrullusvulgaries Schrad) seed flours were packaged separately in vacuum sealed high density polyethylene bags of 0.7mm thickness and were subjected to frozen storage by storing the packs in a domestic deep freezer for up to four months. Samples were removed at intervals of 0, 1, 2, 3 and 4 months for analysis. The effects of frozen storage on the shelf stability factors (moisture, free fatty acids and peroxide values) selected functional properties of water/oil absorption capacity, foam capacity and viscosity and sensory attributes of the frozen 'ogbono' and 'egusi' samples were investigated. The result of this investigation shows that there was no significant difference (p>0.05) in storage life (shelf stability factors) selected functional and sensory properties of both "ogbono" and 'egusi' seed flours frozen up to three months. However, all the shelf stability properties, selected functional and sensory properties of both flour samples decreased significantly (p<0.05) after four months of frozen storage. Therefore, frozen storage at 18degC could be used to preserve the storage life, functional and sensory properties of vacuum packaged 'ogbono' and 'egusi' seed flours up to three months in moisture/gas impermeable polyethylene packs of 0.7mm thickness without losing its sensory properties.
Between Cold War Imperatives and State Sponsored Terrorism: The United States and "Operation Condor"

Condor was a transnational network of organized state sponsored terrorism that targeted Communist "subversion." It was operational in the second half of the 1970s. The key member countries were Chile, Argentina, Uruguay, Bolivia, Paraguay, and Brazil (Peru and Equador joined the network later on, with a more marginal role) Based on declassified documents from the United Nations High Commissioner for Refugees in Geneva and on U.S. documents of various origin, this article will assess the development of the Condor network and the U.S. reaction to such manifest acts of state sponsored terrorism.
Co occurrence of intimate partner violence and child sexual abuse: Prevalence, risk factors and related issues.
Venue: Child abuse neglect

This article proposes a review of the scientific literature on the cooccurrence of intimate partner violence and intrafamilial child sexual abuse. The review of these two types of violence has evolved in distinct research fields and their cooccurrence has rarely been examined. The objective of this article is to examine the existing knowledge about this cooccurrence. A systematic examination of the scientific literature in several relevant databases was conducted using combinations of 20 keywords so as to identify scientific articles, published between 2003 and 2013, that investigated this cooccurrence. The final sample comprised 10 studies. These studies revealed the presence of much heterogeneity regarding the prevalence of the cooccurrence for intimate partner violence with sexual abuse and other maltreatment (from 12% to 70% The review also highlighted a greater risk for children to be victims of sexual abuse or other maltreatment when exposed to intimate partner violence. The implications of these results and the ensuing recommendations for practice and future research are considered in the discussion section.
Systematic reviews about child abuse and neglect in last 10 years

In this study, we aimed to determine the level of available information and gaps which are related to child abuse and neglect in last ten tears. Literature review made on systematic reviews and meta analysis in Pubmed database that has the " Child abuse and neglect" or "Child maltreatment" keywords. Studies published in English through 1st January 2005 31th March 2015 were reviewed. Totally 112 article were resulted in the search but only 101 of them were full text and also 59 systematic review excluded in the study. 42 articles were examined which are matching the criterias. Articles were classified according to subjects of the articles (identification, prevention, intervention, identification of the relationships, and others) types of child abuse neglect (physical, emotional, sexual and others) Although we reached the systematic reviews related to child neglect and all types of child abuse, systematic reviews about emotional and sexual abuse are inadequate. The studies about intervention and identification of relations are insufficient. We observed the gap in the literature, in this direction. Child abuse and neglect regardless of the kind; create irreversible trauma and also leads to problems in the child's adulthood. Therefore; identification and prevention is a priority, If prevention is impossible; it is a quite vital importance to intervent as soon as possible. Despite the achievement of systematic compilation associated with child neglect and abuse; especially intervention studies about emotional and sexual abuse were found as inadequate.
Measurement results for cooperative device to device communication in cellular networks

Device to Device communication is expected to be a part of future 5G networks. Many researchers have provided solid theoretical concepts to implement it, but a real practical solution is still in dearth. In this work, first the design and development of a proof of concept testbed for single carrier Device to Device (D2D) communication have been done. The results obtained from this testbed can be used to evaluate the subtle design issues associated with the real world deployment of single carrier D2D communication protocols. These issues are often overlooked in a theoretical or simulation framework. The performance of this light weight, readily deployable testbed has been validated by emulating a cellular scenario in which a base station (BTS) and many D2D enabled devices coordinate and communicate with each other to select an optimum communication range, transmit parameters, intracellular localization and mode of communication. Through the experimental results it has been shown that D2D communication can significantly reduce the power consumption of a conventional cellular network. After this, another testbed (Multi carrier) was developed using Software Defined radio which incorporates the concept of Spectrum Sharing through static sub carrier allocation to D2D user by cellular system which will eventually enhance the performance of cellular as well as D2D communication system. Our purposed and deployed protocol have shown significant improvement (10% to 30% on Symbol Error Rate (SER) and Signal to Noise Ratio (SNR) as compared with conventional direct transmission schemes.