nils-herrmann/clean_scirepeval huggingface dataset:
Conventional gene targeting protocols lead to loss of targeted cells when applied to a silent gene locus in primary fibroblasts.

Gene targeting in livestock fibroblasts has proven difficult to achieve, particularly if the target gene is silent. We first tested whether efficient gene targeting at the transcriptionally active ovine alpha1(I) procollagen (COL1A1) locus required the use of a promoter trap vector. We compared gene targeting frequencies at the ovine COL1A1 locus using both a promoter trap and a non-promoter trap selection strategy. We demonstrated that targeted cells could be isolated regardless of whether an enrichment step (promoter trap) was used. Next, we used our optimised protocol to target a non-expressed gene, ovine beta-casein. We obtained clones that were scored positive by PCR for the targeting event, but were negative after cell expansion and Southern analysis. We propose that targeted cells were initially generated but that they were at a selective growth disadvantage during culture. We suggest modifications to the conventional targeting protocol that would prevent such loss of targeted cells.

Field of study: Biology, Engineering
The Development of Welfare States in Europe and America.

This volume seeks to contribute to an interdisci-plinary, comparative, and historical study of Western welfare states. It attempts to link their historical dynamics and contemporary problems in an international perspective. Building on collaboration between European-and American-based research groups, the editors have coordinated contributions by economists, political scientists, sociologists, and historians. The developments they analyze cover a time span from the initiation of modern national social policies at the end of the nineteenth century to the present. The experiences of all the presently existing Western European systems except Spain and Por-tugal are systematically encompassed, with com-parisons developed selectively with the experi-ences of the United States and Canada. The devel-opment of the social security systems, of public expenditures!and taxation, of public education and educational opportunities, and of income inequal-ity are described, compared, and analyzed for varying groupings of the Western European and North American nations. This volume addresses itself mainly to two audi-ences. The first includes all students of policy problems of the welfare states who seek to gain a comparative perspective and historical under-standing. A second group may be more interested in the theory and empirical analysis of long-term societal developments. In this context, the growth of the welfare states ranges as a major departure, along with the development of national states and capitalist economies. The welfare state is interpreted as a general phenomenon of modernization, as a product of the increasing differentiation and the growing size of societies on the one hand, and of processes of social and political mobilization on the other. It is an important element of the structural convergence of modern societies -- by its mere weight in all countries -- and at the same time a source of divergence by the variations within its institutional structure.

Field of study: Political science
Solinas primes of small weight for fixed sizes

We give a list of the Solinas prime numbers of the form f(2 k ) = 2 m 2 n ±1, m � 2000, with small modular reduction weight wt < 15, and k = 8, 16, 32, 64, i.e., k is a multiple of the computer integer arithmetic word size. These can be useful in the construction of cryptographic protocols.

Field of study: Computer science, Mathematics
Pressure dependence of the irreversibility line in Bi/sub 2/Sr/sub 2/CaCu/sub 2/O/sub 8+/spl delta//

One of the important problems of high-temperature superconductivity is to understand and ultimately to control fluxoid motion. We present the results of a new technique for measuring the pressure dependence of the transition to superconductivity in a diamond anvil cell. By measuring the third harmonic of the ac susceptibility, we determine the onset of irreversible flux motion. This enables us to study the effects of pressure on flux motion. The application of pressure changes interplanar spacing, and hence the interplanar coupling, without significantly disturbing the intraplanar superconductivity. Thus we are able to separate the effects of coupling from other properties that might affect the flux motion. Our results directly show the relationship between lattice spacing, effective-mass anisotropy, and the irreversibility line in Bi/sub 2/Sr/sub 2/CaCu/sub 2/O/sub 8+/spl delta//. Our results also demonstrate that an application of 2.5 GPa pressure causes a four-fold decrease in the effective-mass anisotropy.

Field of study: Physics
A variational multiscale method with bubble stabilization for the Oseen problem based on two local Gauss integrations

We present a variational multiscale method for the Oseen equation with higher Reynolds number. Based on the mini-element discretization, the stabilization term only depends on bubble functions, and the best algorithmic feature of our method is using two local Gauss integrations to replace projection operator without adding any extra storage. A priori error estimate is proved and the effectiveness of the method is illustrated through several numerical experiments.

Field of study: Mathematics
13C, 17O, and 29Si NMR Spectra and Stabilization of Silylated Ketenes and Bisketenes

The experimental and calculated 13C, 17O, and 29Si NMR chemical shifts of silylated ketenes and bisketenes show trends consistent with charge redistribution resulting from neutral hyperconjugative donation from the R3Si-C bond to the p orbital on the carbonyl carbon, and are supportive of this mechanism for the striking stability of these species.

Field of study: Chemistry
Induction of swelling, synovial hyperplasia and cartilage proteoglycan loss upon intra-articular injection of transforming growth factor beta-2 in the rabbit.

Transforming growth factor beta (TGF-beta) is a multifunctional homodimeric polypeptide with potent actions upon many target cells, including those of mesenchymal and haemopoietic lineage. The recent reports of high levels of the cytokine in rheumatoid synovium and synovial fluid, prompted this study into the effect of intra-articular injection of TGF beta-2 into rabbit knee-joints. Four daily injections of 1 microgram caused swelling, probably as a consequence of prostaglandin E2 production, synovial fibroblastic hyperplasia and a striking loss of femoral condyle proteoglycan. Using the polymerase chain reaction, no evidence could be obtained for the induction of interleukin-1 alpha gene expression in either synovial tissue or synovial fluid cells. These findings suggest that the TGF-beta present in the rheumatoid joint may contribute directly to the pathogenesis of rheumatoid arthritis.

Field of study: Medicine
Diurnal variations of summertime precipitation over the Tibetan Plateau in relation to orographically-induced regional circulations

The diurnal patterns of variation of summertime precipitation over the Tibetan Plateau were first investigated using the TRMM multi-satellite precipitation analysis product for five summer seasons (i.e. June to August for 2002–2006). Both hourly precipitation amount and precipitation frequency exhibit pronounced daily variability with an overall late-afternoon–evening maximum and a dominant morning minimum. A notable exception is the prevalent nocturnal maximum around the periphery of the Plateau. In terms of the normalized harmonic amplitude, the diurnal signal shows significant regional contrast with the strongest manifestation over the central Plateau and the weakest near the periphery. This remarkable spatial dependence in daily rainfall cycles is clear evidence of orographic and heterogeneous land-surface impacts on convective development. Using six-hourly NCEP FNL data, we then examined the diurnal variability in the atmospheric circulation and thermodynamics in this region. The results show that the Plateau heats (cools) the overlying atmosphere during the day (night) more than the surrounding areas, and as a consequence a relatively stronger confluent circulation in this region occurs during the day than during the night, consistent with the diurnal rainfall cycles. Moreover, the regions with large low-level convergence and upper-level divergence correspond to the strong diurnal rainfall variations. The reversed daily alterations of convergence–divergence patterns in the vicinity of the Plateau edges are in agreement with the observed nighttime rainfall peak therein. This study further demonstrates the importance of the Tibetan Plateau in regulating regional circulation and precipitation.

Field of study: Environmental science
Adolescent Perception of Rape in Institution of Higher Learning: Implication for Counselling

Rape has continued to be a wide spread global problem in contemporary times. This study expands the empirical and theoretical understanding of adolescents’ perception of rape in the higher institutions of learning. Six hundred and eighty students from four Universities in South West Nigeria were randomly selected and given questionnaires. The study probed the students’ attitudes towards the perception of rape as a crime, the causative factors of rape, how rape is perpetrated, the psychological effects of rape on the victims and what measures they considered appropriate for curbing rape incidents on campuses. The results demonstrated that a significant proportion of the students perceived rape as a crime and that the moral decadence in the society has aggravated rape incidences while indecent dressing of female students among others factors have also encourage rape. Majority of the participants also held favourable attitudes towards major psychological setbacks on rape victims. There was a unanimous agreement by participants that introducing dressing code for female students and promulgation of stiff penalties for rapists would be effective palliative measures for curbing rape incidents. Counselling implications were thereafter highlighted for all stakeholders.  Rape, Perception, Adolescents, Counselling Implications.

Field of study: Education
Electronic structure of La 1.85 Sr 0.15 CuO 4 : Characterization of a Fermi-level band crossing

We present the results of a Hubbard model for optimally doped ${\mathrm{La}}_{2\ensuremath{-}x}{\mathrm{Sr}}_{x}{\mathrm{CuO}}_{4}.$ This model uses parameters derived from Becke-Lee-Yang-Parr calculations on the cluster ${\mathrm{CuO}}_{6}.$ It explicitly includes the Cu ${d}_{{x}^{2}\ensuremath{-}{y}^{2}}$ and ${d}_{{z}^{2}}$ orbitals, the O ${p}_{\ensuremath{\sigma}}$ orbitals, and the apical O ${p}_{z}$ orbitals. We find that when the mean-field equation is appropriately modified to include a self-interaction correction, a crossing of two bands is observed in the vicinity of the Fermi level for the optimally doped superconductor. This crossing rigorously occurs along the $(0,0)\ensuremath{-}(\ensuremath{\pi}/a,\ensuremath{\pi}/a)$ direction of the two-dimensional (2D) Brillouin zone. The crossing arises due to the overlap of a broad ``${B}_{1g}$'' band dominated by Cu ${d}_{{x}^{2}\ensuremath{-}{y}^{2}}$ character and a narrower ``${A}_{1g}$'' band dominated by Cu ${d}_{{z}^{2}}$ character. We conclude that optimal doping of ${\mathrm{La}}_{2\ensuremath{-}x}{\mathrm{Sr}}_{x}{\mathrm{CuO}}_{4}$ and related materials is achieved when the Fermi level coincides with this crossing. At this point, formation of Cooper pairs between the two bands (i.e., interband pairing or IBP) leads to superconductivity. We further extend our conclusions to ${\mathrm{YBa}}_{2}{\mathrm{Cu}}_{3}{\mathrm{O}}_{6+\mathrm{\ensuremath{\delta}}}$ and offer a simple explanation for the seemingly complex behavior of ${T}_{c}$ as a function of doping in this material. This behavior can be understood on the basis of multiple band crossings predicted from geometric considerations.

Field of study: Physics
Middle Cambrian Formations of the Providence and Marble Mountains, California

The field work on which the following report is based was done in conjunction with a reconnaissance survey of the Bengal quadrangle,[1][1] California, which is now in progress for the California State Division of Mines. Because the work on the Paleozoic rocks of the area has progressed most rapidly in connection with the Middle Cambrian formations, it has been deemed advisable to summarize the results so far obtained. In a sense, this report is a continuation of a paper by Hazzard and Crickmay [2][2] in which the lithology and fauna of the lower portion of the Cambrian succession of this region were discussed.

The Providence and the Marble mountains are about seventy miles west of the Colorado River, within the northern half of the Bengal quadrangle. The Providence Range lies east of Kelso, California; the Marble Mountains are about thirty miles farther south. The writers wish to thank C . . .

Field of study: Geology
Japanese Prayer Below the Equator: How Brazilians Believe in the Church of World Messianity (review)

Research on the Japanese in Latin America has become increasingly specialized during the past decade. While some of this research is becoming redundant, particularly on the experience of the Issei and Nisei generations during World War II, this study by Hideaki Matsuoka provides fresh insights regarding the religious views of recent generations of Japanese Brazilians. Matsuoka, an anthropologist educated at the University of Tokyo and the University of California at Berkeley, conducted the bulk of his research in Sao Paulo during the early 1990s. He argues that new Japanese religions such as World Messianity have arisen during the past century because of crises in Japanese society, especially World War II. These destructive events required spiritual and emotional renewal. One of the most important of these new religions was Omoto, a millenarian belief that proclaimed the need for the complete renewal of the world. World Messianity's founder, Okada Mokichi, drew heavily upon the teachings of Omoto. The early twentieth-century importance of Omoto among a core group of Japanese-Brazilian immigrants laid the groundwork for World Messianity's appeal after World War II in Brazil.

Field of study: History
Molluscan generic diversity of New Zealand Neogene stages: extinction and biostratigraphic events

The Molluscan generic diversity histogram of New Zealand Neogene stages almost parallels the trend of published New Zealand paleotemperature curves. The major exception is very high diversity during the relatively cool Pliocene and Pleistocene stages, attributed to the good preservation at this time of near-shore, mollusc-rich facies. Diversity was lowest during Kapitean (Late Miocene) time, and probably particularly during late Kapitean (Messinian) time; 22.9% of molluscan genera became extinct at the end of the preceding Tongaporutuan Stage. Three major events can be recognised in the Neogene molluscan fauna: (1) a thermal maximum during late Early and early Middle Miocene (coeval around much of the Pacific); (2) the terminal Miocene event, when the most marked Neogene extinction occurred; and (3) the arrival of a cold-water subantarctic fauna in central North Island 2.4 m.y. ago, coeval with the onset of major Northern Hemisphere glaciation.

Field of study: Environmental science, Geography
Microstructure and creep of eutectic indium/tin on copper and nickel substrates

The behavior during creep in shear of eutectic indium-tin joints on copper and nickel substrates was examined in order to determine the effect of creep deformation on the microstructure of the alloy. Primary creep was absent in all the samples tested. The stress exponent at 20° C was much higher for samples on nickel than for those on copper, indicating a different creep deformation mechanism. Also, the microstructure within the indium-tin joints differed significantly with a change of substrate. Samples with a nickel substrate showed a colony microstructure that was not observed in those with a copper substrate. Thus, eutectic morphology is important in determining deformation mechanism during creep. The microstructure within the joints in tested and untested regions of the samples was effectively the same. This is quite distinct from the behavior of eutectic lead-tin observed in previous work. Lead-tin formed a recrystallized band of material along a region of concentrated shear deformation. While the deformation pattern in the indium-tin samples appeared to be the same as for lead-tin, the microstructural changes did not occur. This implies that the behavior observed in lead-tin is not universal to eutectic alloys.

Field of study: Materials science
The influence of antiferromagnetism, soft out-of plane phonons and heavy electrons on the superconducting pairing mechanism of Ba1-xKxFe2As2

Based on ab-initio calculated parameters, we apply a theoretical model on the iron-based BaFe2As2 superconductor that takes into account dramatic enhancements of the electron-phonon coupling of soft transverse phonons in the FeAs layers and antiferromagnetism. Our model is able to reproduce the Tc values of BaFe2As2 found under pressure in experiments. To calculate the Tc of the K-doped Ba1-xKxFe2As2 system as a function of the K content, we additionally consider the experimentally observed effective mass enhancements and Kondo temperatures in the strongly over-doped region (0.8 < x < 1), which decouple the antiferromagnetism and electron-phonon scattering. The highest theoretical Tc at the optimal doping concentration is reproduced after optimization of antiferromagnetic fluctuations and electron-phonon coupling. Our model is also able to reproduce the dip-like structure in Tc in the region where a re-entrant tetragonal phase of C4 symmetry is found (0.24 < x < 0.28) and indicates the weakening effect of local exchange correlation energy as responsible for Tc reduction. Our model thus demonstrates that the high transition temperatures and the exact doping and pressure dependence of this iron-based superconductor can be explained within an extended electron-phonon coupling model in which the structural, magnetic and electronic degrees of freedom are strongly intertwined.

Field of study: Physics
What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants

Many problems of modern genetics and functional genomics require the assessment of functional effects of sequence variants, including gene expression changes. Machine learning is considered to be a promising approach for solving this task, but its practical applications remain a challenge due to the insufficient volume and diversity of training data. A promising source of valuable data is a saturation mutagenesis massively parallel reporter assay, which quantitatively measures changes in transcription activity caused by sequence variants. Here, we explore the computational predictions of the effects of individual single-nucleotide variants on gene transcription measured in the massively parallel reporter assays, based on the data from the recent “Regulation Saturation” Critical Assessment of Genome Interpretation challenge. We show that the estimated prediction quality strongly depends on the structure of the training and validation data. Particularly, training on the sequence segments located next to the validation data results in the “information leakage” caused by the local context. This information leakage allows reproducing the prediction quality of the best CAGI challenge submissions with a fairly simple machine learning approach, and even obtaining notably better-than-random predictions using irrelevant genomic regions. Validation scenarios preventing such information leakage dramatically reduce the measured prediction quality. The performance at independent regulatory regions entirely excluded from the training set appears to be much lower than needed for practical applications, and even the performance estimation will become reliable only in the future with richer data from multiple reporters. The source code and data are available at https://bitbucket.org/autosomeru_cagi2018/cagi2018_regsat and .

Field of study: Biology
Edge and shape effects on ant (Hymenoptera: 
Formicidae) species richness and composition 
in forest fragments

In this paper, we tested four hypotheses relative to edge and shape effects on ant communities: (i) forest edges have lower species richness than the remnant core; (ii) species richness increases with distance from the edge; (iii) irregularly shaped remnants have lower species richness than more regular remnants; (iv) there is a higher similarity of species composition between edge and core in irregular than in regular remnants. We sampled litter ant communities on the edge and core of ten remnants, in Viçosa, Minas Gerais, Brazil. Species richness was larger at the forest core than at the edges, although did not increase with distance from the edge. Species richness did not vary with shape complexity. The similarity of species composition between edge and core showed a decreasing trend with remnant area, and did not vary with shape complexity. The observed differences of species richness between forest core and edge may be due to higher harshness of edges, caused by environmental changes. The absence of relationship between species richness and distance from the edge might indicate the range of edge effects, which would be smaller than the smallest distance of core sampled. Therefore, edges would affect litter-dwelling ant species richness in a distance smaller than 50 m. The observation of species composition allowed us to notice an effect of fragmentation that would not be noticed if we were considering only species richness. Edge may serve as step to generalist species, which may use it to colonise forest remnants. Furthermore, small remnants are more colonisation-prone by such species, and have a more homogeneous species composition than large remnants.

Field of study: Environmental science
Wool Trade and Commercial Networks in Buenos Aires, 1840s to 1880s

Between the 185os and i88os, Argentina became one of the chief suppliers of wool to the expanding world markets. Most of this wool was grown in the fertile sheep-runs of the richest province in the country, and was sent to Europe through its capital city and port, Buenos Aires. After the colonial experience of being mainly an entrepot in the legal and contraband trade between the Viceroyalty of the River Plate and the rest of the world, Buenos Aires had seen its commercial opportunities flourish after Independence, and had found in its rural hinterland the staples to export, hides and salted beef. A mercantile class, at the rise of the century more interested in commercial pursuits than in productive activities related to the rural areas, had, nevertheless, sought in the late colonial era the benefits of cattle-raising, which provided the new staples, first to complement and later to replace the chief export of colonial Buenos Aires, bullion from Potosf. A tight intertwining of interests of port and province was the most immediate result of that initial drive, as capital and efforts were turned towards production. From then on, the international market became the main stimulus for the expansion of production in Buenos Aires, but this, in turn, was achieved only by the local development of an economic and social structure that could respond to such an incentive. A long process of capitalist organization of the rural areas was set in motion.

Field of study: Political science