nils-herrmann/clean_scirepeval huggingface dataset:
[Identification of KI polyomavirus in children with lower respiratory tract infections from Zhejiang region of China].

KI polyomavirus, which was firstly discovered in 2007, is a new human polyomavirus belonging to Polyomaviridae and containing circular double-strand genomic DNA. This study was based on identification assay of KI polyomavirus reported. Total 2293 clinical sputum specimens from children under 3-years-old were collected and screened from Wenzhou Medical College affiliated Wenling Hospital, Zhejiang Province. A KI polyomavirus was detected and identified, the positive rate was 0.04%. The sequences of PCR products was identical to that of the viral capsid protein (VP1) gene derived from KI polyomavirus. The results strongly suggested that the KI polyomavirus was found firstly in Chinese children with acute lower respiratory tract infections from Zhejiang region. This study provided new information for further investigation of etiopathogenisis and diagnosis in children with lower respiratory tract infections.

Field of study: Biology
Boundary Inheritance Codec for high-accuracy structured light three-dimensional reconstruction with comparative performance evaluation.

This paper presents a new method of structured light-based 3D reconstruction, referred to here as Boundary Inheritance Codec, that provides high accuracy and low noise in projector-camera correspondence. The proposed method features (1) real-boundary recovery: the exact locations of region boundaries, defined by a coded pattern, are identified in terms of their real coordinates on the image plane. To this end, a radiance independent recovery of accurate boundaries and a disambiguation of true and false boundaries are presented. (2) Boundary inheritance: the consistency among the same boundaries of different layers in pattern hierarchy is exploited to further enhance the accuracy of region correspondence and boundary estimation. Extensive experimentations are carried out to verify the performance of the proposed Boundary Inheritance Codec, especially, in comparison with a number of well-known methods currently available, including Gray-code (GC) plus line/phase shift (LS/PS). The results indicate that the proposed method of recovering real boundaries with boundary inheritance is superior in accuracy and robustness to Gray-code inverse (GCI), GC+LS/PS. For instance, the error standard deviation and the percentile of outliers of the proposed method were 0.152 mm and 0.089%, respectively, while those of GCI were 0.312 mm and 3.937%, respectively, and those of GC+LS/PS were 0.280/0.321 mm and 0.159/7.074%, respectively.

Field of study: Physics
Fever of Unknown Origin in Carcinoma of the Colon

To report a case of fever of unknown origin in a patient with carcinoma of the colon but without gastrointestinal symptoms.  A 65-year-old man presented with a long-standing fever (of 38°C, about two months’ duration), night sweats, fatigue, malaise and anxiety. General physical examination including rectum, radiographic examinations of the chest, abdomen and bones (including ultrasonography and CT scanning) was normal. Biochemistry profile as well as other laboratory studies including blood, urine and stool cultures were normal except for erythrocyte sedimentation rate, which was 105 mm/h. A barium enema showed a rectosigmoid carcinoma. A left sigmoidal colectomy was performed. The patient recovered quickly and remained well for eight years postoperatively.  This case shows that carcinoma of the colon should be included in the differential diagnosis of patients with fever of unknown origin.

Field of study: Medicine
The role of a native tussock grass (Paspalum quadrifarium Lam.) in structuring plant communities in the Flooding Pampa grasslands, Argentina

The patches of Paspalum quadrifarium-dominated grasslands found atpresent could be remnants of the vegetation that defined the Pampas landscape inthe past. The mere presence of such physical structures should lead to systemsin which many other species are dependent upon both the autogenic creation ofsurface area for living space and the autogenic and allogenic modulation ofresources controlled by these structures. We carried out amensurative–comparative study in naturally occurring sites dominated byP. quadrifarium that occupy different positions within thelandscape in the Flooding Pampa. We found different species assemblages in thesestructurally homogeneous stands, related to the edaphic and topographicgradients. The comparison with sites from similar positions in the landscapewhere this native tussock-grass was absent showed that the dominance ofP. quadrifarium is a minor determinant of floristicdifferences, which are mainly controlled by abiotic factors. We assigned thesedominated grassland stands to previously delimited vegetation units for theFlooding Pampa grasslands and we compared them with the vegetation unitsassigned, in terms of composite properties of the community that may beindicators of ecosystem processes, such as biological invasions andproductivity. Our results show that this native tussock grass is associated withhigher floristic richness, higher representation of perennials and grasses andlower presence of alien plants. This homogeneous pattern of variation across thevegetation units would suggest that, despite the absence of dramatic changes incommunity composition, the dominance of this tussock grass plays an importantrole in structuring species diversity patterns.

Field of study: Environmental science
Service Learning in English Composition: A Case Study.

Although service learning has gone a long way since the time when, until the mid-1980, it was practically unknown as a pedagogical practice beyond a closed circle of practitioners, in many higher education institutions it still remains a domain of few faculty interested in integrating service learning in their disciplines. While experimenting with teaching English 191 Composition course at St. Cloud State University in Minnesota and searching for a way to relate the abstractions of my discipline to the realities of the world, I stumbled into service learning and created a course that truly convinced me of the revolutionary potential of service learning in transforming the stale educational practice. This article will record my experience with the course and the lessons I learned from it.

Field of study: Education
Synthesis and special features of the structure of 6(7)-aminoperimidine derivatives

A method of synthesizing 6(7)-aminoperimidines has been developed based on the electrophilic amination of perimidines with sodium azide in PPA. The corresponding amides were synthesized by acylation and were also obtained by the Schmidt reaction from 6(7)-acetyl(or benzoyl)perimidines. A special feature of the structure of the 2-substituted amines and amides is the presence of annular tautomerism slow in NMR time.

Field of study: Chemistry
Petrology and Chemistry of the Rock Creek Flow, Columbia River Basalt, Idaho

A detailed re-examination of the Rock Creek flow, one of the thickest known pre-Yakima basalt flows of the Columbia Plateau, includes 5 wet-chemical and 55 rapid x-ray fluorescent analyses for major elements. The samples were collected at regular intervals from five sections through the flow over a distance of ~ 20 mi. A revised description of the flow9s field characteristics and petrography is included. The Rock Creek flow is typical of the pre-Yakima basalt in most of its field, petrographic, and chemical properties and is quite distinct in all these properties from the Yakima basalt. It differs from the Picture Gorge basalt type in its higher olivine, TiO 2 ; and K 2 O content, and is regarded as a member of a discrete Rock Creek basalt type which will form a valuable marker horizon in the southeast part of the plateau. In the Whitebird Creek section, the lower part of the Rock Creek flow cooling unit is formed from a different chemical type with a different mineralogy, similar to the Roza and Frenchman Springs chemical types as defined by Wright and others (1973). The mineralogy of the main part of the flow is typical of alkali basalt. Plagioclase and olivine were stable before eruption and were joined by a high-calcium pyroxene soon after eruption. Olivine continued to crystallize with the plagioclase and pyroxene, which were later joined by ilmenite and then apatite. Late chabazite and secondary analcite occur in the scoria. Lack of crystal settling and the high potassium content of the unusually thick scoriaceous top, which is locally replaced by a pyroclastic capping, may be associated with exceptionally vigorous degassing of the magma. Chemically, the Rock Creek flow is an olivine tholeiite, but its alkali basalt mineralogy makes either of these terms misleading. Together with many other basalts possessing a similar combination of mineralogy and chemistry, it is classified as a transitional basalt. The mineralogy of the residual material suggests a peralkaline composition.

Field of study: Geology
Assessing potential reinforcement-like effects of brief stimuli unrelated to food reinforcers.

It is widely assumed that reinforcers are biologically relevant stimuli, or stimuli that have been associated with biologically relevant stimuli. However, brief, arbitrary stimuli have also been reported to have reinforcement-like effects, despite being unrelated to biologically relevant stimuli like food. The present study explored the potential reinforcement-like effects of brief stimuli across 5 experiments. In Experiments 1 through 4, pigeon subjects responded for food reinforcement and brief stimulus presentations in a 2-component multiple schedule. Neither baseline response rates nor resistance to change during disruption tests were systematically greater in a component with versus without brief stimulus presentations. Increasing the rate and duration of brief stimulus presentations in Experiment 4 did not reveal reinforcement-like effects when compared directly with food. In Experiment 5, pigeons chose between independent terminal links in a concurrent-chains procedure. Across conditions, varying the location, duration, and rate of brief stimulus presentations in the terminal links had no systematic effects on preference. In contrast, varying rates of food reinforcers resulted in large and reliable shifts in preference. Therefore, the present study found no systematic evidence that brief stimuli unrelated to food reliably increase response rates, resistance to change, or preference. These data demonstrate the value of systematic replication, and a behavioral momentum approach to assessing potential reinforcement-like effects.

Field of study: Biology, Psychology
Semi-empirical modeling and analysis of oil flooded R410A scroll compressors with liquid injection for use in vapor compression systems

Oil flooding is a technique that can be utilized in compression systems to achieve near-isothermal compression. This can lead to a boost in system efficiency and a reduction in compressor power consumption. In this paper a semi-empirical model for oil flooded compressors using liquid injection was developed. The model is validated with experimental data and integrated into a thermodynamic model of a vapor compression system with oil flooding and regeneration. The performance of the heat pump system is predicted and the semi-empirical model is used to identify and estimate the magnitude of the irreversibilities during the compression process. A method for generalizing the model for different working fluids is also presented. Using this model, design recommendations are made to improve the efficiency of the studied liquid flooded compressors for heat pump applications.

Field of study: Engineering
The role of functional magnetic resonance imaging in brain surgery.

New functional neuroimaging techniques are changing our understanding of the human brain, and there is now convincing evidence to move away from the classic and clinical static concepts of functional topography. In a modern neurocognitive view, functions are thought to be represented in dynamic large-scale networks. The authors review the current (limited) role of functional MR imaging in brain surgery and the possibilities of new functional MR imaging techniques for research and neurosurgical practice. A critique of current clinical gold standard techniques (electrocortical stimulation and the Wada test) is given.

Field of study: Medicine
Study on the Noise Reduction Effect of Sound Absorption Barrier in Different Frequency Bands

Due to the sound absorption coefficient of the sound absorption barrier in different frequency range is different, so the effect of noise reduction are also different. Simply improving sound absorption coefficient in the low frequency band does not necessarily improve the effect of noise reduction. To want to achieve overall good noise reduction effect need considering the influence of sound absorption coefficient in each frequency band and the noise spectrum distribution in an actual road section, different sound barrier used in conjunction. In this paper, the change of the sound absorption coefficient and the noise reduction effect for the different sound absorption materials is compared by the calculation of the theoretical formula in the different noise frequency band, and get some conclusions.

Field of study: Engineering
Linking taphonomy to community-level abundance: Insights into compositional fidelity of the Upper Triassic shell concentrations (Eastern Alps)

Although actualistic live/dead comparisons lead to robust estimates of fidelity of modern death assemblages, quantitative evaluation of fidelity of fossil assemblage remains uncertain. In this paper, effects of storm reworking on compositional fidelity of the Upper Triassic shell concentrations (Eastern Alps, Austria) are evaluated. An exploratory approach is based on comparison of reworked and non-reworked assemblages in ordination analyses. Non-reworked assemblages of one or more communities provide a baseline for evaluation of fidelity of reworked assemblages. In siliciclastic-rich intervals of the Kossen Formation, shell concentrations are represented by (1) packstones with small, shallow infaunal bivalves, (2) floatstones and pavements with large semi-infaunal bivalves, and (3) bioclastic marlstones. In carbonate-rich intervals, bioclastic floatstones with bivalves and brachiopods occur. Analyzing all shell concentrations, eight sample groups sharing similar species composition are discriminated. Limited effect of storm reworking on composition of shell concentrations is indicated by (1) a general persistence of six sample groups when only non-reworked assemblages are analyzed, (2) similarity in composition between reworked and non-reworked assemblages within sample groups, and (3) compositional segregation between non-reworked assemblages of distinctive sample groups, mostly without any reworked assemblages of intermediate composition. Depth-related variations in dead-shell production, shell destruction and body size governed preservation and distribution of the shell concentrations along onshore-offshore gradient in the Kossen Basin. First, at times when environmental conditions were unfavorable for shell producers, coupled with high background shell destruction rates, limestone beds formed during storm events were shell-poor. Second, less common shell concentrations in upper than in lower parts of siliciclastic intervals can be related to higher environmental stress in shallower habitats. Third, the difference between shell concentrations dominated by small and large bivalves is driven by between-habitat differences in body size and is not due to a differential sorting of small and large shells. Combining community analysis based on species abundances with taphonomic analysis can thus be helpful in tracking fidelity of fossil assemblages.

Field of study: Environmental science, Geography
Low-noise slot antenna SIS mixers

We describe quasi-optical SIS mixers operating in the submillimeter band (500-750 GHz) which have very low noise, around 5 h/spl nu//k/sub B/ for the double-sideband receiver noise temperature. The mixers use a twin-slot antenna, Nb/Al-Oxide/Nb tunnel junctions fabricated with optical lithography, a two-junction tuning circuit, and a silicon hyperhemispherical lens with a novel antireflection coating to optimize the optical efficiency. We have flown a submillimeter receiver using these mixers on the Kuiper Airborne Observatory, and have detected a transition of H/sub 2//sup 18/O at 745 GHz. This directly confirms that SIS junctions are capable of low-noise mixing above the gap frequency.<<ETX>>

Field of study: Physics
Detection of Avian Influenza A Virus Using Pyrosequencing

A pyrosequencing method was developed for rapidly detecting avian influenza A virus and predicting the pathogenicity. The avian influenza A virus and its subtype were preliminarily determined by PCR on a species-specific sequence of the M gene and a subtype-specific sequence of the HA gene containing a cleaving site, respectively. The results obtained by PCR were further validated via the pyrosequencing method. As apyrase and Klenow play an important role in pyrosequencing, their concentrations were optimized. The results indicate that the nonspecific signals were effectively suppressed using 1.6 U ml−1 apyrase, and a readable sequence length of 33 bases was obtained with 90 U ml−1 Klenow. On the basis of the optimum pyrosequencing system, four specimens including an H5N1 subtype with high pathogenicity and three specimens of avian influenza A H9N2 subtype with low pathogenicity were confirmed. This method is accurate, fast, and can be used efficiently for identifying the pathogenicity of the avian influenza A virus.

Field of study: Chemistry
Non-conforming finite element discretisations of a class of non-Newtonian flows

We study an approximation for a class of non-Newtonian model, based on the general Ladyzhenskaya law for continuous and non-linear kinematic viscosity functions of the fluid. We introduce a non-conforming finite element approximation of non-linear Stokes problem; we give existence, uniqueness results and optimal error estimates under minimal regularity assumptions. Finally, we introduce a post-processing to obtain conforming approximation of stress, which allow to derive various equivalence with two or three field mixed dual approximations of non-linear Stokes problem.

Field of study: Mathematics
Thermodynamic Origin of Structural Superlubricity: Entropy Matters.

Structural superlubricity, a state of vanishing friction between two incommensurate contact surfaces, is a fascinating phenomenon in modern tribology and shows attractive applications in the fields of sliding devices. Here, we reveal that structural superlubricity intrinsically originates from the configurational entropy of atoms in the incommensurate contact surfaces, based on which, we firstly developed a concise thermodynamic model for the structural superlubricity. The model can universally explain the reported experimental observations in superlubricity very well. Most critically, our model analytically correlates the friction ({\tau}) with sample size (R), twisted angle ({\theta}) and temperature (T) simply as {\tau}=3kTcot({\theta}/2)/(2{\pi}R^3), which not only provides the physical foundation for structural superlubricity, but could also facilitate the development of new superlubric materials as well as extending their applications at extreme temperatures and normal loads.

Field of study: Physics
Cloning and characterization of a novel variant of rat GABA(B)R1 with a truncated C-terminus.

The gamma-aminobutyric acid B receptor (GABA(B)R) belong to the G-protein-coupled receptor superfamily and has been identified as a mediator in the transmission of slow inhibitory neurotransmission in the mammalian central nervous system. Two types of GABA(B)R have been cloned, GABA(B)R1 and R2. GABA(B)R2 is co-expressed with GABA(B)R1 in many brain regions and inwardly rectifying potassium channels are activated by GABA(B)R agonists only upon co-expression of GABA(B)R1 with GABA(B)R2. Several splice variants of GABA(B)R1 receptors have been cloned from rat brain library. Using a rat hippocampal cDNA library, we have isolated a novel cDNA clone of GABA(B) receptor containing an insert of 124 bp between exon 3 and exon 4. This insert occurred between the regions encoding the Sushi domain and leucine binding protein (LBP)-like domain. The insert and subsequent frame shift generated a cDNA that codes for a truncated polypeptide of 239 amino acids lacking the C-terminus. Analysis of the deduced amino acid sequence of the new cDNA clone, termed GABA(B)R1g, showed that it was identical to the first 157 amino acids of GABA(B)R1a, but diverged thereafter. The C-terminal region of GABA(B)R1g contained two cysteine residues. GABA(B)R1g was expressed in both brain and peripheral tissues. Northern blot analysis demonstrated that two transcripts (4.5 kb and 4.0 kb) exist in hippocampus. In addition, studies of hippocampus in developing animals indicated that the expression of GABA(B)R1g is maximal at postnatal day four. GABA(B)R1g could be generated by alternative splicing of the GABA(B)R1 gene.

Field of study: Biology
Reply to the comment of Fügenschuh et al. on the paper ‘Estimating displacement along the Brenner Fault and orogen-parallel extension in the Eastern Alps’ by Rosenberg and Garcia, Int J Earth Sci (Geol Rundsch) (2011) 100:1129–1145

Fugenschuh et al. (2011) question several aspects of our paper (Rosenberg and Garcia 2011) on the estimate of extension along the Brenner Fault (BF). First, they emphasize the necessity of a two-phase extensional model to understand exhumation of the footwall of the BF; second, they claim that the vertical offsets and extensional displacement calculated by Rosenberg and Garcia (2011) only refer to the brittle phase of the BF; third, they follow the new interpretations of Tochterle et al. (2011), inferring that the continuation of the Brenner ductile mylonites is located along the north-western border of the Tauern Window (TW); fourth, they present a new estimate of extension and of exhumation by folding and erosion based on the quantification of tectonic omissions. We discuss and reply to these four issues below.

Field of study: Environmental science
Geology and Geochemistry of Triassic Diabase in Pennsylvania

Based on chemical composition and mineralogy, three types of Triassic diabase are recognized in Pennsylvania. The probable oldest type (Quarryville type) occurs as an olivine tholeiite dike swarm. The York Haven type is a quartz tholeiite, forming sheets, dikes, and a few flows. The youngest Rossville type is also quartz tholeiite that occurs as sheets and dikes. Within samples of the same type, chemical composition is very uniform. In content of major elements, rare earths, and Ba, the Rossville type resembles island-arc tholeiites. The York Haven type is similar to continental tholeiites. Based on calculated cooling rates and the homogeneity within each type of magma, plus paleomagnetic data, we conclude that each type was emplaced within a relatively short time period, and that all sheets, dikes, and flows of a single compositional type are essentially contemporaneous. The trend of Triassic diabase dikes in Pennsylvania parallels the trend of Precambrian and Paleozoic dikes, suggesting that trends of dikes may reflect pre-existing structural weaknesses in the basement rather than being an exact indicator of stress orientation during Triassic time. The two quartz tholeiites can be formed by crystallization of 30 to 45 percent of the olivine tholeiite magma as olivine, minor clinopyroxene, and plagioclase or spinel, accompanied by assimilation of orthopyroxene, probably from the mantle. Rare-earth and Sr-isotope data suggest that the York Haven type probably assimilated as much as 20 percent crustal material, whereas the Rossville type assimilated little or none. These phenomena of multiple-stage fractionation and reaction of the magma with mantle and crust probably apply to most magmas.

Field of study: Geology