nils-herrmann/clean_scirepeval huggingface dataset:
Spectroscopic Analysis of Chloride Ion-induced Structural Change of Bacillus Amyloliquefaciens α-Amylase

The structural change of Bacillus amyloliquefaciens α-amylase (Ba α-amylase) induced by chloride ion was studied by fluorescence spectra, Fourier-transformation infrared (FT-IR) spectroscopy and circular dichroism (CD) spectroscopy. It was found that when chloride ion concentration was below 20.0 mM, the Ba α-amylase was activated by increasing chloride ion concentration; when chloride ion concentration was over 20.0 mM, the biological activity of Ba α-amylase was inhibited by increasing chloride ion concentration. The spectroscopic analyses illustrated that the change in Ba α-amylase biological activity was caused by the alteration in secondary structure of Ba α-amylase. When chloride ion showed activation effect to Ba α-amylase, part of the random coils in Ba α-amylase gradually transformed to α-helix and β-sheet with increasing chloride ion concentration and the Ba α-amylase transited from relatively disordered conformation to relatively ordered one. Whereas when chloride ion showed inhibition effect on the biological activity of Ba α-amylase, part of α-helix and β-sheet in Ba α-amylase gradually transformed to random coil with increasing chloride ion concentration and the Ba α-amylase went back from the relatively ordered conformation to the relatively disordered one. This work shows the dependency of change in biological activity to alteration in secondary structure of protein molecule, which may provide some useful information in the actual application and exploration on action mechanism of proteins.

Field of study: Chemistry
Interest Groups and the White House under Roosevelt and Truman

As an institution, the American presidency is shaped by a wide range of influences, some contemporary in nature while others are embodied in precedents derived from earlier administrations. Analysts, therefore, are confronted by the need to work within multiple time frames.' What appears to be an innovative departure in the structure or operations of the presidency may, in fact, be an extension of practices developed by earlier administrations. The emergence of public liaison as a White House staff specialization illustrates this analytic problem. Early in the presidency of Gerald Ford, White House assistants responsible for liaison with a variety of separate interest-group constituencies were relocated into a single Office of Public Liaison (OPL). This new office included aides assigned to work with blacks, white ethnic Catholics, women, youth, Jews,  The Carter White House adopted a different structure for assigning specialists to work with virtually the same range of organized interests, but Ronald Reagan reestablished much of the original OPL structure upon assuming office. As a new component of the White House staff, public liaison has not yet developed as clearly articulated a role as the press office or congressional relations, but its staff has concentrated on several activities: linking White House policy makers with knowledgeable spokespersons of organized interests, particularly those likely to be affected by policy

Field of study: Political science
The Representation of Radical Islamists in the NYC and USA Today American Newspapers: A Critical Discourse Analysis Study

This study fulfills a critical discourse analysis study of the radical Islamist news in American New York Times and USA Today newspapers. The study aims to find how the radical Islamist are represented in American newspapers and whether those newspapers manipulate the language used to serve certain purposes and how this effect on Muslims in general. The hypotheses proposed to achieve the aims of this study are; American newspapers manipulate the language for ideological purposes and that the way radical Islamist are presented effects on moderate Muslims. Moreover, the study presents a brief theoretical background about critical discourse analysis. The model eclectics for this analysis, is made up of van Dijk (1988) for the linguistic level, and van Dijk’s Ideological Square (1998) and Yul’s (1986) presupposition triggers for the ideological level. The analysis of the data leads to the following conclusions; American newspapers do manipulate the language of the articles and that no difference is made between Radical and moderated Muslims, this effect on moderated Muslims in a negative way.  CDA, radical Islamists, NYC, USA Today

Field of study: Education
Is Shia-Sunni Violence on the Rise? Exploring New Data on Intra-Muslim Organised Violence 1989-2017

This data study provides the first comprehensive empirical overview of organised violence across the Shia and Sunni Muslim divide, 1989–2017. We present a conceptual framework of sectarian dimensions of armed conflicts: sectarian identities; sectarian ideologies; and sectarian alliances. Our analysis demonstrates the extent to which organised violence has been fought across the Shia-Sunni divide. We also explore the sectarian identity dimension in non-state armed conflicts and one-sided violence. Overall, our study shows that most of the organised violence across the Shia-Sunni divide is driven by states, rebel groups, and militias, rather than communities.

Field of study: History, Sociology
Variability of Deeply Embedded Protostars: A New Direction for Star Formation?

The formation of a star is a dynamic process fed by the gravitational collapse of a molecular cloud core. Theoretical models and observations suggest that the majority of this infalling material settles into a protoplanetary disk before reaching the (proto)star and therefore that disk accretion processes are responsible for the rate at which the (proto)star grows. There is no fundamental reason why infall and disk accretion need to be instantaneously identical. Indeed, even within the disk it might be anticipated that there are regions of strong and weak accretion. Together these facts suggest that (proto)stellar mass assembly should be both secular and stochastic and that the underlying physical processes leading to these time-variable accretion rates should manifest in observable time-dependent accretion luminosity variations.

Field of study: Physics
Life-cycle greenhouse gas emissions of shale gas, natural gas, coal, and petroleum.

The technologies and practices that have enabled the recent boom in shale gas production have also brought attention to the environmental impacts of its use. It has been debated whether the fugitive methane emissions during natural gas production and transmission outweigh the lower carbon dioxide emissions during combustion when compared to coal and petroleum. Using the current state of knowledge of methane emissions from shale gas, conventional natural gas, coal, and petroleum, we estimated up-to-date life-cycle greenhouse gas emissions. In addition, we developed distribution functions for key parameters in each pathway to examine uncertainty and identify data gaps such as methane emissions from shale gas well completions and conventional natural gas liquid unloadings that need to be further addressed. Our base case results show that shale gas life-cycle emissions are 6% lower than conventional natural gas, 23% lower than gasoline, and 33% lower than coal. However, the range in values for shale and conventional gas overlap, so there is a statistical uncertainty whether shale gas emissions are indeed lower than conventional gas. Moreover, this life-cycle analysis, among other work in this area, provides insight on critical stages that the natural gas industry and government agencies can work together on to reduce the greenhouse gas footprint of natural gas.

Field of study: Environmental science
Low-loss tunable metamaterials using superconducting circuits with Josephson junctions

We report on experiments with superconducting metamaterials containing Josephson junctions. In these structures, split-ring resonators used in conventional metamaterials are replaced by superconducting loops that are interrupted by Josephson junctions, so called rf-SQUIDs. Like the split-ring resonators, these elements can be seen as LC-resonators that couple to the magnetic field. The advantage of superconducting thin-film metamaterials is that, due to the tunable intrinsic inductance of the Josephson junction, the resonance frequency of the rf-SQUID can be changed by applying an external dc magnetic field. We present experimental results that demonstrate the tunability of the resonance frequency of these devices.

Field of study: Physics
Different approaches of molecular scanning of point mutations in genetic diseases

Several advanced techniques to detect mutations have been developed during the last years. Scanning procedures can be classified as "physical" and "cleavage" methodologies. Physical methods include Denaturing Gradient Gel Electrophoresis, Single-Strand Conformation Polymorphism and Heteroduplex Analysis while cleavage methods include RNAse A Cleavage, Chemical Mismatch Cleavage and Enzyme Mismatch Cleavage. A related technique, Protein Truncation Test, has been recently introduced.

Field of study: Chemistry
Development of a Monte Carlo based model for optimization using the Laguerre‐Gauss Hotelling observer

Accurate measures of both clinical image quality and patient radiation risk are needed for successful optimisation of medical imaging with ionising radiation. Optimisation in diagnostic radiology means finding the image acquisition technique that maximises the perceived information content and minimises the radiation risk or keeps it at a reasonably low level. The assessment of image quality depends on the diagnostic task and may in addition to system and quantum noise also be hampered by overlying projected anatomy. The main objective of this thesis is to develop methods for assessment of image quality in simulations of projection radiography. In this thesis, image quality is quantified by modelling the whole x‐ray imaging system including the x‐ray tube, patient, anti‐scatter device, image detector and the observer. This is accomplished by using Monte Carlo (MC) simulation methods that allow simultaneous estimates of measures of image quality and patient dose. Measures of image quality include the signal‐to‐noise‐ratio, SNR, of pathologic lesions and radiation risk is estimated by using organ doses to calculate the effective dose. Based on high‐resolution anthropomorphic phantoms, synthetic radiographs were calculated and used for assessing image quality with model‐observers (Laguerre‐Gauss (LG) Hotelling observer) that mimic real, human observers. Breast and particularly chest imaging were selected as study cases as these are particularly challenging for the radiologists. In chest imaging the optimal tube voltage in detecting lung lesions was investigated in terms of their SNR and the contrast of the lesions relative to the ribs. It was found that the choice of tube voltage depends on whether SNR of the lesion or the interfering projected anatomy (i.e. the ribs) is most important for detection. The Laguerre‐Gauss (LG) Hotelling observer is influenced by the projected anatomical background and includes this into its figure‐of‐merit, SNRhot,LG. The LG‐observer was found to be a better model of the radiologist than the ideal observer that only includes the quantum noise in its analysis. The measures of image quality derived from our model are found to correlate relatively well with the radiologist’s assessment of image quality. Therefore MC simulations can be a valuable and an efficient tool in the search for dose‐efficient imaging systems and image acquisition schemes.

Field of study: Medicine, Physics
Association of HLA-DRB1 and HLA-DQA1 genes with outcome of hepatitis B virus infection

目的 采用组合分析法探讨中国北方汉族人群HLA-DRB1、-DQA1等位基因与乙型肝炎病毒(hepatitis B virus,HBV)感染不同结局的关系.方法 采用序列特异性引物多聚酶链式反应(PCR-SSP)技术对207名慢性乙型肝炎患者和148名自限性HBV感染者进行HLA-DRB1、-DQA1等位基因的检测,并运用病例对照研究设计和组合分析法比较HLA-DRB1、-DQA1等位基因与HBV感染不同结局的关系.结果 携带HLA-DQA1*0102或HLA-DQA1*0301等位基因者,感染HBV后发展为慢性乙肝的风险显著低于不携带这些等位基因者,比值比(odds ratio,OR)分别为0.23和0.52.用此两个等位基因进行组合分析发现,仅携带HLA-DQA1*0102或HLA-DQA1*0301任何一个等位基因者,较不携带HLA-DQA1*0102和HLA-DQA1*0301两个等位基因者发展为慢性乙肝的风险显著降低(OR=0.28,χ2=31.16,P＜0.0001),而同时携带HLA-DQA1*0102和HLA-DQA1*0301两等位基因者,发展为慢性乙肝的风险降低则更为明显(OR=0.16,χ2=5.86,P=0.02).结论 具有两个保护(或危险)作用的等位基因者比不具有或仅有其中一个等位基因者对HBV感染的结局影响更大。

Field of study: Biology
A Hierarchical Bayesian Approach to Multi-Trait Clinical Quantitative Trait Locus Modeling

Recent advances in high-throughput genotyping and transcript profiling technologies have enabled the inexpensive production of genome-wide dense marker maps in tandem with huge amounts of expression profiles. These large-scale data encompass valuable information about the genetic architecture of important phenotypic traits. Comprehensive models that combine molecular markers and gene transcript levels are increasingly advocated as an effective approach to dissecting the genetic architecture of complex phenotypic traits. The simultaneous utilization of marker and gene expression data to explain the variation in clinical quantitative trait, known as clinical quantitative trait locus (cQTL) mapping, poses challenges that are both conceptual and computational. Nonetheless, the hierarchical Bayesian (HB) modeling approach, in combination with modern computational tools such as Markov chain Monte Carlo (MCMC) simulation techniques, provides much versatility for cQTL analysis. Sillanpää and Noykova (2008) developed a HB model for single-trait cQTL analysis in inbred line cross-data using molecular markers, gene expressions, and marker-gene expression pairs. However, clinical traits generally relate to one another through environmental correlations and/or pleiotropy. A multi-trait approach can improve on the power to detect genetic effects and on their estimation precision. A multi-trait model also provides a framework for examining a number of biologically interesting hypotheses. In this paper we extend the HB cQTL model for inbred line crosses proposed by Sillanpää and Noykova to a multi-trait setting. We illustrate the implementation of our new model with simulated data, and evaluate the multi-trait model performance with regard to its single-trait counterpart. The data simulation process was based on the multi-trait cQTL model, assuming three traits with uncorrelated and correlated cQTL residuals, with the simulated data under uncorrelated cQTL residuals serving as our test set for comparing the performances of the multi-trait and single-trait models. The simulated data under correlated cQTL residuals were essentially used to assess how well our new model can estimate the cQTL residual covariance structure. The model fitting to the data was carried out by MCMC simulation through OpenBUGS. The multi-trait model outperformed its single-trait counterpart in identifying cQTLs, with a consistently lower false discovery rate. Moreover, the covariance matrix of cQTL residuals was typically estimated to an appreciable degree of precision under the multi-trait cQTL model, making our new model a promising approach to addressing a wide range of issues facing the analysis of correlated clinical traits.

Field of study: Biology
High-temperature reliability of Flip Chip assemblies

Flip Chip technology has been widely accepted within microelectronics as a technology for maximum miniaturization. Typical applications today are mobile products such as cellular phones or GPS devices. For both widening Flip Chip technology’s application range and for addressing the automotive electronics’ volume market, developing assemblies capable of withstanding high temperatures is crucial. A typical scenario for integrating electronics into a car is a control unit within the engine compartment, where ambient temperatures are around 150 °C, package junction temperatures may range from 175 °C to 200 °C and peak temperatures may exceed these values. If Flip Chip technology is used under harsh environment conditions, it is clear that especially the polymeric materials, i.e., underfiller, solder mask or the organic substrate base material, are challenged. Generally, the developmental goal for encapsulants compatible with high-temperature applications are materials with high Tg and low degradation even at temperatures >200 °C. According to these demands, a test group of advanced underfill encapsulants has been used for assembling Flip Chip devices. These test vehicles were built using lead-free and lead-containing solders such as SnAgCu and eutectic PbSn and standard FR4 substrates, for evaluating the reliability potential of state-of-the-art underfillers. Material analysis is performed for studying both material degradation as well as temperature-dependent thermo-mechanical and adhesive properties. For assessing reliability, temperature cycling is performed with different maximum test temperatures ranging from 150 °C to 175 °C. The device status is intermediately analyzed by using electrical measurement for detecting bond integrity and acoustomicroscopy for determining the occurrence and growth of delaminations. Extensive failure analysis is added to investigate device failure mechanisms, especially related to the respective test temperature. In summary, an empirical status of the high-temperature potential of state-of-the-art underfillers and material combinations is attained and an outlook on future demands and developments is provided.

Field of study: Engineering
Monte Carlo evaluation of non-Abelian statistics.

We develop a general framework to (numerically) study adiabatic braiding of quasiholes in fractional quantum Hall systems. Specifically, we investigate the Moore-Read (MR) state at nu=1/2 filling factor, a known candidate for non-Abelian statistics, which appears to actually occur in nature. The non-Abelian statistics of MR quasiholes is demonstrated explicitly for the first time, confirming the results predicted by conformal field theories.

Field of study: Physics
Risk-minimizing pricing and hedging foreign currency options under regime-switching jump-diffusion models

This article mainly investigates risk-minimizing European currency option pricing and hedging strategy when the spot foreign exchange rate is driven by a Markov-modulated jump-diffusion model. We suppose the domestic and foreign money market floating interest rates, the drift, and the volatility of the exchange rate dynamics all depend on the state of the economy, which is modeled by a continuous-time hidden Markov chain. The model considered in this article will provide market practitioners with flexibility in characterizing the dynamics of the spot foreign exchange rate. Using the minimal martingale measure, we obtain a system of coupled partial-differential-integral equations satisfied by the currency option price and find the corresponding hedging strategies and the residual risk. According to simulation of currency option prices in the special case of double exponential jump-diffusion regime-switching model, we further discuss and show the effects of the parameters on the prices.

Field of study: Mathematics
The Clarence Ayres Memorial Lecture: The Paradoxes of Happiness in an Old Institutionalist Perspective

In recent years, happiness research has become a strongly recognized new field of economic discourse. This contribution tries to delineate the insights and limitations of this research from a critical institutionalist vantage point. In a couple of articles on happiness research, Thorstein B. Veblen is mentioned. l The theoretical and intellectual affinity between Veblen's theory and path-breaking contributions in happiness research like Tibor Scitovsky's The Joyless Economy (1976), Fred Hirsch's The Social Limits to Growth (1976), and, for example, Robert Frank's Choosing the Right Pond (1985) is obvious. They are all skeptical about the assumption that changes in economic welfare indicate changes in social welfare in the same direction, if not in the same degree. Hirsch's positional goods underline Veblen's insight that economic value also depends on the relative position regarding, for example, the possessions of others. All recent authors refer to some degree to James Duesenberry, whose relative income hypothesis (1949) is directly derived from Veblen's theory of the leisure class. In this contribution I will focus on Veblen's analysis of the paradoxes of happiness in his major work on the leisure class, The Theory of the Leisure Class ([ 1899] 1994). It will be shown that Veblen can be assessed as a neglected founder of happiness research. I cannot describe happiness research in detail  I will only mention the major finding of happiness research: in many countries real income has risen but self-reported subjective well-being has not (substantially) increased (Easterlin 2001). Its research strategy may be described as conceptual individualism; micro happiness functions are derived from the empirical-statistical measuring of the influences of variables on reported subjective statements of well-being.

Field of study: Economics
Evolution, plant breeding and biodiversity

This paper deals with changes in biodiversity during the course of evolution, plant domestication and plant breeding. It shows than man has had a strong influence on the progressive decrease of biodiversity, unconscious at first and deliberate in modern times. The decrease in biodiversity in the agricultures of the North causes a severe threat to food security and is in contrasts with the conservation of biodiversity which is part of the culture of several populations in the South. The concluding section of the paper shows that man could have guided evolution in a different way and shows an example of participatory plant breeding, a type of breeding which is done in collaboration with farmers and is based on selection for specific adaptation. Even though participatory plant breeding has been practiced for only about 20 years and by relatively few groups, the effects on both biodiversity and crop production are impressive. Eventually the paper shows how participatory plant breeding can be developed into ‘evolutionary plant breeding’ to cope in a dynamic way with climate changes.

Field of study: Agricultural and Food sciences
CAUSES OF THE UNUSUALLY DESTRUCTIVE 2004 ATLANTIC BASIN HURRICANE SEASON

The 2004 Atlantic basin hurricane season was one of the most active on record with nine hurricanes and six major hurricanes (maximum sustained winds > 49 ms1) forming during the season. All six major hurricanes formed during August and September, causing this two-month period to be the most active on record. The primary reason the 2004 hurricane season will be remembered, however, is because of the four hurricanes that devastated the Caribbean and the southeastern United States (Hurricanes Charley, Frances, Ivan, and Jeanne). Estimated total U.S. hurricane damage was between $40 and $50 billion, and much additional damage was sustained in the Caribbean. It is shown that a very strong central Atlantic equatorial trough, associated with anomalously warm tropical Atlantic sea surface temperatures and anomalously weak tropospheric vertical wind shear, combined with extremely favorable midlatitude steering conditions to allow many of the Africa-spawned easterly waves to develop into major hurricanes in the cen...

Field of study: Environmental science