nils-herrmann/clean_scirepeval huggingface dataset:
What does the Josephson effect tell us about the superconducting state of the cuprates

We review the recent measurements of the current-phase relation in cuprate Josephson junctions. Special attention is paid to 45 degree grain boundary junctions and to c-axis junctions between YBCO and Nb. It is shown that the anomalous properties of such junctions which have been found experimentally (large second harmonic of the current phase relation, sign change of the first harmonic as a function of temperature) are qualitatively consistent with the d-wave symmetry of pairing in the cuprates. It is argued that in order to describe the data quantitatively, quantum fluctuations of the order parameter need to be taken into account. It is pointed out that the Josephson effect is an ideal tool for measuring the reduced phase stiffness in the cuprates.

Field of study: Physics
Personalized medicine: factors influencing reimbursement.

Personalized medicine (PM) has attracted tremendous interest, but yielded few marketed products. We examined factors influencing the reimbursement of existing PM technologies.



We conducted six case studies of the following paired genetic tests and treatments: HER2/neu with trastuzumab (Herceptin); hepatitis C genotyping with ribavirin/pegylated interferon; Oncotype DX with chemotherapy; UGT1A1 with irinotecan (Camptosar); VKORC1/CYP2C9 with warfarin; BRCA1/2 with prophylactic surgical measures; and Oncotype DX with chemotherapy. We developed a framework for categorizing PM technology, and assessed factors influencing reimbursement, including quality of evidence, type of regulatory oversight, presence of clinical guidelines, and cost-effectiveness.



PM is not a monolithic concept, but rather encompasses different types of technology. The strength of evidence available for existing PM technology varies widely and, along with endorsement of clinical guidelines, appears to be the strongest predictor of reimbursement. In the absence of reimbursement, direct-to-consumer marketing has continued for some PM technology. The type of regulatory oversight and the results of cost-effectiveness analysis do not appear to be associated with reimbursement to date.



To date, the promise and hype of PM has outpaced its evidentiary support. In order to achieve favorable coverage and reimbursement and to support premium prices for PM, manufacturers will need to bring better clinical evidence to the marketplace and better establish the value of their products.

Field of study: Medicine, Political science
Response of bacterioplankton community structures to hydrological conditions and anthropogenic pollution in contrasting subtropical environments.

Bacterioplankton community structures under contrasting subtropical marine environments (Hong Kong waters) were analyzed using 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) and subsequent sequencing of predominant bands for samples collected bimonthly from 2004 to 2006 at five stations. Generally, bacterial abundance was significantly higher in the summer than in the winter. The general seasonal variations of the bacterial community structure, as indicated by cluster analysis of the DGGE pattern, were best correlated with temperature at most stations, except for the station close to a sewage discharge outfall, which was best explained by pollution-indicating parameters (e.g. biochemical oxygen demand). Anthropogenic pollutions appear to have affected the presence and the intensity of DGGE bands at the stations receiving discharge of primarily treated sewage. The relative abundance of major bacterial species, calculated by the relative intensity of DGGE bands after PCR amplification, also indicated the effects of hydrological or seasonal variations and sewage discharges. For the first time, a systematic molecular fingerprinting analysis of the bacterioplankton community composition was carried out along the environmental and pollution gradient in a subtropical marine environment, and it suggests that hydrological conditions and anthropogenic pollutions altered the total bacterial community as well as the dominant bacterial groups.

Field of study: Biology, Environmental science
Another class of quadratic APN binomials over F2n: the case n divisible by 4

We exhibit an infinite class of almost perfect nonlinear quadratic binomials from F2n to F2n with n = 4k and k odd. We prove that these functions are CCZinequivalent to known APN power functions when k 6= 1. In particular it means that for n = 12, 20, 28, they are CCZ-inequivalent to any power function.

Field of study: Computer science, Mathematics
Review of and expectation for the development of enterprises with a sports brand in Jinjiang city.

The authors reviewed and collated the nearly 30-year course of development of enterprises with a sports brand in Jinjiang city,which "went from imitation and OEM to independent brand,and now gets on the track of capital operation",summed up successful experiences in such aspects as marketing strategies and sales modes: the integrated marketing of "star speakers + ads on CCTV + game sponsors" ensured the effective communication of brands;the sale mode of wholesale was selected at the pioneering stage;"specialized and chained sales" were adopted at the development stage;"direct network sale" that keeps up the pace of times is not only in conformity with the characteristics of times,but also fitting into the pace of enterprise development.In the near future,Jinjiang will surely become the world sports brand base,give birth to a great number of enterprises with a truly global sports brand,and set the trend of consumption based on technical innovation.The author also put forward the following proposals: make long term strategic plans,grasp market patterns,set the trend of consumption,and create consump-tion growth points;constantly enhance the competitive strength of groups,strengthen industrial chain construction within groups,and create a win-win situation of cooperation.

Field of study: Education
Induction of interleukins IL‐6 and IL‐8 by siRNA

The HIV‐1 co‐receptor CCR5 has been thought a relevant target for small interfering RNA (siRNA)‐based therapeutics. However, recent findings suggest that siRNA can stimulate innate cytokine responses in mammals. All siRNA agents tested were able to down‐regulate the expression of CCR5, albeit with different efficiency (51–74% down‐regulation), block HIV‐induced syncytia formation between HIV‐1 BaL‐infected and uninfected CD4+ cells or block single‐round HIV‐1 infection as measured by a luciferase reporter assay (46–83% inhibition). Conversely, siRNA directed against CCR5 did not affect replication of a vesicular stomatitis virus (VSV) pseudotyped virus, suggesting that inhibition of HIV replication was specific to CCR5 down‐regulation. However, two of four siRNA tested were able to induce the production of interleukin (IL) IL‐6 (sixfold induction) and IL‐8 (ninefold induction) but no interferon (IFN)‐α, IFN‐β, IFN‐γ, tumour necrosis factor (TNF)‐α, monocyte chemoattractant protein (MCP)‐1, macrophage inflammatory protein (MIP)‐1α, MIP‐1β, RANTES, IL‐1β, IL‐10 or IL‐12p70 cytokine induction was noted. In the absence of detectable IFN‐α, IL‐6 or IL‐8 may represent markers of non‐specific effects triggered by siRNA.

Field of study: Biology, Medicine
Persistent cold air outbreaks over North America in a warming climate

This study examines future changes of cold air outbreaks (CAOs) using a multi-model ensemble of global climate simulations from the Coupled Model Intercomparison Project Phase 5 and high resolution regional climate simulations. Overall, climate models agree on a dip in CAO duration across North America, but the percentage change is consistently smaller from western Canada to the upper mid-western US with historically more frequent CAO. By decomposing the changes of the probability density function of daily surface temperature into changes due to mean warming and changes in standard deviation (std) and skewness/higher order moments, the contributions of each factor to CAO changes are quantified. Results show that CAO changes can be explained largely by the mean warming, but the decrease in temperature std contributes to about 20% reduction of CAO from Alaska to northeastern US and eastern Canada possibly due to the Arctic amplification and weakening of storm track. A thermodynamical modulation of the skewness called the ?0 ?C mode? effect is found to operate prominently along the 0 ?C isotherm hemispherically and reduce CAO in western and northeastern US with winter snow cover by up to 10%. This effect also produces a manifold increase in CAO events over the Arctic sea ice. An increased frequency in atmospheric blocking also contributes to increases in CAO duration over Alaska and the Arctic region. Regional simulations revealed more contributions of existing snowpack to CAO in the near future over the Rocky Mountain, southwestern US, and Great Lakes areas through surface albedo effects. Overall, the multi-model projections emphasize that cold extremes do not completely disappear in a warming climate. Concomitant with the relatively smaller reduction in CAO events in northwestern US, the top five most extreme CAO events may still occur, and wind chill will continue to have societal impacts in that region.

Field of study: Environmental science
Cenozoic Volcanic Rocks in the Southern Shoshone Mountains and Paradise Range, Nevada

The Cenozoic volcanic rocks in the southern part of the Shoshone Mountains and most of the Paradise Range consist predominantly of lava flows and pyroclastic rocks ranging in composition from rhyolitic to basaltic, and minor volcaniclastic sedimentary rocks. In the Shoshone Mountains, the stratigraphic column is more than 3,000 m thick, of which all but 150 m consist of lava flows and pyroclastic rocks, the remainder being volcaniclastic sediments. New formation names are given to two units in the lower part of the section that are well exposed near Mission Spring and Third Canyon, respectively. In the Paradise Range, lava flows and pyroclastic rocks of rhyolitic to andesitic composition 625 m thick constitute the entire Cenozoic section. In the lower part of the section, only the Third Canyon Formation of the Shoshone Mountains section is recognized in the Paradise Range; it is identified on the basis of stratigraphic position and characteristic propylitic alteration. A prominent ignimbrite unit higher in the section in both ranges is obviously the correlative of the Toiyabe Quartz Latite originally described in the Round Mountain quadrangle.  Dikes and pluglike intrusive rocks range in composition from rhyolite to trachyandesite. The relative position assigned to the various intrusive rocks, purely on the basis of superposition, is in good chemical and mineralogical agreement with the chemistry and mineralogy of the intruded and overlying rocks in each case, suggesting that most dikes and plugs are feeders. Chemical analyses and C.I.P.W. norms for 14 lava flows and pyroclastic and associated intrusive rocks show that all are oversaturated with respect to quartz, all are quartz-hypersthene normative, and all belong to the calc-alkaline suite. Some of the rocks have co-menditic and potassic rhyolite tendencies.

Field of study: Geology
Middle and Upper Ordovician graptolites from the St. Lawrence Lowlands, Quebec, Canada

Eleven species of Middle and Upper Ordovician graptolites are described and illustrated, a lectotype is selected for Orthograptus reudemanni (Gurley) and the occurrence of eighteen other species is recorded. The specimens were collected from sections along the Becancour, Nicolet, Nicolet Sud-Ouest, and St. Francois Rivers of the St. Lawrence Lowlands, Quebec. The graptolite zonal scheme proposed by Riva for eastern North America is reviewed and adopted in the present study.

Field of study: Environmental science
An innovative solution for breast cancer textual big data analysis

The digitalization of stored information in hospitals now allows for the exploitation of medical data in text format, as electronic health records (EHRs), initially gathered for other purposes than epidemiology. Manual search and analysis operations on such data become tedious. In recent years, the use of natural language processing (NLP) tools was highlighted to automatize the extraction of information contained in EHRs, structure it and perform statistical analysis on this structured information. The main difficulties with the existing approaches is the requirement of synonyms or ontology dictionaries, that are mostly available in English only and do not include local or custom notations. In this work, a team composed of oncologists as domain experts and data scientists develop a custom NLP-based system to process and structure textual clinical reports of patients suffering from breast cancer. The tool relies on the combination of standard text mining techniques and an advanced synonym detection method. It allows for a global analysis by retrieval of indicators such as medical history, tumor characteristics, therapeutic responses, recurrences and prognosis. The versatility of the method allows to obtain easily new indicators, thus opening up the way for retrospective studies with a substantial reduction of the amount of manual work. With no need for biomedical annotators or pre-defined ontologies, this language-agnostic method reached an good extraction accuracy for several concepts of interest, according to a comparison with a manually structured file, without requiring any existing corpus with local or new notations.

Field of study: Computer science
Feasibility of a low-energy X-ray free-electron laser.

X-ray free-electron lasers based on self-amplified spontaneous emission promise users unprecedented X-radiation that is extremely bright, extremely short and transversely coherent. However, hard X-ray free-electron laser facilities under construction are all huge and expensive, consisting of high-energy linear accelerators and long undulators. The benefit of hard X-ray free-electron lasers may be limited to only a few regions in the world, unless it is possible to reduce the size. This paper discusses how small a hard X-ray free-electron laser facility can be. It is shown that a 1.5 A X-ray free-electron laser is achievable using electron energy down to 4.5 GeV or lower if we use the third-harmonic radiation, but at the expense of the transverse coherence.

Field of study: Physics
Quantification of uncertainty in aerosol optical thickness retrieval arising from aerosol microphysical model and other sources, applied to Ozone Monitoring Instrument (OMI) measurements

Satellite instruments are nowadays successfully utilised for measuring atmospheric aerosol in many applications as well as in research. Therefore, there is a growing need for rigorous error characterisation of the measurements. Here, we introduce a methodology for quantifying the uncertainty in the retrieval of aerosol optical thickness (AOT). In particular, we concentrate on two aspects: uncertainty due to aerosol microphysical model selection and uncertainty due to imperfect forward modelling. We apply the introduced methodology for aerosol optical thickness retrieval of the Ozone Monitoring Instrument (OMI) on board NASA’s Earth Observing System (EOS) Aura satellite, launched in 2004. We apply statistical methodologies that improve the uncertainty estimates of the aerosol optical thickness retrieval by propagating aerosol microphysical model selection and forward model error more realistically. For the microphysical model selection problem, we utilise Bayesian model selection and model averaging methods. Gaussian processes are utilised to characterise the smooth systematic discrepancies between the measured and modelled reflectances (i.e. residuals). The spectral correlation is composed empirically by exploring a set of residuals. The operational OMI multiwavelength aerosol retrieval algorithm OMAERO is used for cloud-free, over-land pixels of the OMI instrument with the additional Bayesian model selection and model discrepancy techniques introduced here. The method and improved uncertainty characterisation is demonstrated by several examples with different aerosol properties: weakly absorbing aerosols, forest fires over Greece and Russia, and Sahara desert dust. The statistical methodology presented is general; it is not restricted to this particular satellite retrieval application.

Field of study: Environmental science
Mechanism-based QSAR approach to the study of the toxicity of endocrine active substances

Mechanism-based QSAR models for interactions between various ligands and the estrogenic receptor are developed by using well-developed physicochemical parameters. Common features of these QSARs are identified, and deficiencies in some datasets are highlighted. The relative binding affinities of various substituted hexestrols to estrogen receptors are examined in terms of their steric, electronic, and hydrophobic attributes. Different QSARs for hexestrols and tamoxifens reveal that steric effects are of overriding importance in variations of binding affinity. In the few cases where a large number of diverse substituents are located on aromatic rings, electronic effects emerge and suggest that electron-donating groups enhance binding to the receptor while hydrophobicity plays a marginal role in decreasing binding affinity. With substituted phenols bearing alkyl-type substituents and substituted hydroxy-biphenyls, the binding is strictly dependent on hydrophobicity and size. These QSAR models are described in detail and examined together to illustrate the utility of lateral validation in mechanistic interpretation.

Field of study: Chemistry
Livelihood improvement of small farmers through family poultry in Bangladesh

The present study was undertaken to examine livelihood improvement of small farmers through family poultry by income and employment generation. The data were collected from 60 family poultry farms families from two upazila of Mymensingh district through direct interview method. As analytical tools simple statistical measures, Cobb Douglas production function was used to observe the impact of explanatory variables on gross return while problem confrontation index (PCI) was calculated in order to ascertain the extent of severity of problems confronted by family poultry farmers. It was found that family poultry farming was chosen by 100% farmers as subsidiary occupation. Small farmers earned an income of Tk. 3705.95 per year as net return from family poultry farming and it generated on average 53.23 working man days per year as employment especially for women. As regards of livelihood improvement, family poultry farming changed food habit, increased knowledge and skill, savings, social status, recreational facility, improved food nutritional condition, family health and sanitation and enhanced women empowerment. Among the explanatory variables observed bird cost, feed cost, labor cost had positive and significant impact on gross return and impact of transportation & marketing cost was positive but insignificant. Outbreak of disease was found as the main setback in family poultry production.

Field of study: Business
Biodegradation and microbial community changes upon shrimp shell wastes amended in mangrove river sediment

Chitin, a homopolymer of N-acetyl-D-glucosamine (GlcNAc) residues linked by β 1-4 bonds, is the most abundant renewable natural resource after cellulose. It is widely distributed in nature as the integuments of crustaceans and insects and as a component of fungi and algae. This study investigated the effects of a bifunctional chitinase/lysozyme-producing strain, Pseudomonas aeruginosa K-187, on degradation of shrimp shells and the survival conditions of bacterial strains in mangrove river sediment of Tamsui River. The structures of the whole bacterial community of the samples were measured by using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique. Results show that three bacterial strains (Acrobacter sp., Shewanella sp., and Marinobacterium sp.) which originated from the mangrove river sediment were found predominant in the 6 days-incubation sample of P. aeruginosa K-187 amended mangrove river sediment. Meanwhile, biomass, reducing sugar, and total sugar were found highest in the 6 weeks-incubation sample of shrimp shell powder and P. aeruginosa K-187-amended mangrove river sediment. According to the results, we assumed that the amendment of P. aeruginosa K-187 can enhance the biodegradation of shrimp shells in the seawater containing mangrove river sediment. We hope that these findings may provide some useful information for the reclamation of chitin-containing wastes in our environment.

Field of study: Agricultural and Food sciences
Shifting shorelines and political winds – The complexities of implementing the simple idea of shoreline setbacks for oceanfront developments in Maui, Hawaii

Building out of harm's way is a simple, precautionary, logical idea that respects the ocean's power along dynamic coastlines. Maui has more beaches than any island in Hawaii, attracting tourists and oceanfront investment. In the late 1960s, with the islands agrarian economy of sugar cane and pineapple exports faltering, the County's leadership began marketing its coastal resources as a destination economy, beaches chief among them ( Chu, 1965 ). The Island built a destination development economy out of its beaches, unique coastal resources and access to ocean recreation ( HTA, 2005 ). Good planning and foresight by the local municipal county government could have protected these natural assets, thereby sustaining the island's development. Instead, the county relied on a standardized building setback policy that failed to account for erosion prone areas. Four decades later, realizing the impending loss of the island's premier asset, namely beaches and access to the shoreline, the County moved to site-specific erosion-rate based setback policy. Government regulatory action, including setbacks for constructing buildings along the shoreline, form an integral part of the community's response to climate change and sea level rise ( Codiga et al., 2011 ). The erosion-based setback policy, now a decade old, encountered numerous problems with its implementation. This led to delays in government permitting of oceanfront development and a number of time-consuming amendments to revise the policy. Here we present the unanticipated outcomes of the policy's implementation, particularly challenges to demark the shoreline setback area and delineate erosion prone areas. We also discuss the inherent problems encountered when applying the method to properties with ocean on more than one side or irregularly shaped parcels and situations where cliffs or bluffs rise from the sea. With proper foresight, a destination economy can sustain its growth for years to come by prudently planning for coastal hazards while retaining the natural assets that formed the basis of their destination economy. We conclude by offering lessons learned from experience implementing shoreline setbacks that that will help coastal planners, practitioners, regulators and policy makers save time and avoid mistakes and delays when considering oceanfront development policies.

Field of study: Environmental science
Imagery/Concreteness Attributes of Advance Organizers.

The purpose of this study was to examine the attributes of prose passages used in advance organizer studies on an imagery-concreteness scale. Phase I demonstrated significant differences in ratings between organizer, historical, and learning passages using a semantic differential type instrument. A principal components factor analysis of the scale provided evidence of a stable factor structure for the instrument across the three passages. Phase II demonstrated significant differences in retention for the organizer-learning passage combination but no differences when the three passages were examined alone. Results are discussed on the basis of Paivio’s two-process theory, and questions are raised about the role of advance organizers in learning and retention.

Field of study: Education