nils-herrmann/clean_scirepeval huggingface dataset:
Functional Interaction Between BRCA1 and DNA Repair in Yeast May Uncover a Role of RAD50, RAD51, MRE11A, and MSH6 Somatic Variants in Cancer Development

In this study, we determined if BRCA1 partners involved in DNA double-strand break (DSB) and mismatch repair (MMR) may contribute to breast and ovarian cancer development. Taking advantage the functional conservation of DNA repair pathways between yeast and human, we expressed several BRCA1 missense variants in DNA repair yeast mutants to identify functional interaction between BRCA1 and DNA repair in BRCA1-induced genome instability. The pathogenic p.C61G, pA1708E, p.M775R, and p.I1766S, and the neutral pS1512I BRCA1 variants increased intra-chromosomal recombination in the DNA-repair proficient strain RSY6. In the mre11, rad50, rad51, and msh6 deletion strains, the BRCA1 variants p.C61G, pA1708E, p.M775R, p.I1766S, and pS1215I did not increase intra-chromosomal recombination suggesting that a functional DNA repair pathway is necessary for BRCA1 variants to determine genome instability. The pathogenic p.C61G and p.I1766S and the neutral p.N132K, p.Y179C, and p.N550H variants induced a significant increase of reversion in the msh2Δ strain; the neutral p.Y179C and the pathogenic p.I1766S variant induced gene reversion also, in the msh6Δ strain. These results imply a functional interaction between MMR and BRCA1 in modulating genome instability. We also performed a somatic mutational screening of MSH6, RAD50, MRE11A, and RAD51 genes in tumor samples from 34 patients and identified eight pathogenic or predicted pathogenic rare missense variants: four in MSH6, one in RAD50, one in MRE11A, and two in RAD51. Although we found no correlation between BRCA1 status and these somatic DNA repair variants, this study suggests that somatic missense variants in DNA repair genes may contribute to breast and ovarian tumor development.

Field of study: Biology
Evaluation of Five Discrimination Procedures for Binary Variables

Five procedures for discrimination with binary variables and small samples are discussed and evaluated. Two procedures are specific for binary variables and are based on first and second order approximations to multinomial probabilities. The third procedure, based on the full multinomial model, is completely general. The fourth and fifth procedures are the linear and quadratic discriminants. Evaluation is in terms of mean actual error and mean correlation between observed and true log likelihood ratios determined by Monte Carlo sampling. The concept of a “reversal” in log likelihood ratios is introduced to explain the results.

Field of study: Mathematics
Effects of sex and estrogen on tyrosine hydroxylase mRNA in cultured embryonic rat mesencephalon.

In order to elucidate cellular events responsible for sex differentiation of the nigro-striatal system, we studied the influence of estrogen on the expression of tyrosine hydroxylase (TH) in sex-specific dissociated cell cultures of embryonic day 14 rat mesencephalon. Cultures were raised in the absence or presence of 17 beta-estradiol (10(-12) M) and hybridized with a [35S]oligonucleotide specific to TH. Cultured cells and tissues were probed for estrogen receptor (ER) transcripts by hemi-nested PCR. More TH mRNA containing cells were present in control cultures from female than from male donors. Estrogen treatment resulted in an up-regulation of TH expression in male cells only and induced a reversal of the sex difference in TH mRNA levels present in early control cultures. ER message was detectable in hypothalamic and uterine tissues but not in mesencephalic tissue or cultured cells. Estrogen exposure failed to induce ER expression in cultured mesencephalic cells. It is concluded that there are sex differences in TH mRNA expression of developing midbrain dopaminergic neurons which are independent of the steroid environment. Estrogen can up-regulate TH mRNA in a sex-specific fashion by modulating signal transduction mechanisms other than the classical nuclear receptor pathway.

Field of study: Biology
Adrien Delmas.Les Voyages de l’écrit: Culture écrite et expansion européenne à l’époque moderne; essais sur la Compagnie Hollandaise des Indes Orientales. L’Atelier des voyages 8. Paris: Honoré Champion Éditeur, 2013. 286 pp. €60. ISBN: 978-2-7453-2310-1.


Field of study: History
A Convex Formulation for Mixed Regression: Near Optimal Rates in the Face of Noise

Mixture models represent the superposition of statistical processes, and are natural in machine learning and statistics. Despite the prevalence and importance of mixture models, little is known in the realm of efficient algorithms with strong statistical guarantees. The Expectation-Minimization (EM) approach is perhaps the most popular, yet save for the Gaussian mixture clustering problem, few guarantees exist. For mixed regression in the noiseless setting, in particular, only recently has an EM-like algorithm been able to provide near-tight guarantees. In the noisy setting, tensor approaches have recently succeeded in providing a tractable and statistically consistent approach, but require a sample complexity much higher than the information-theoretic limits. 
We consider the mixed regression problem with two components, under adversarial and stochastic noise. Using a lifting to a higher dimensional space, we give a convex optimization formulation that provably recovers the true solution, with near-optimal sample complexity and error bounds. In the noiseless setting, our results remove the extra log factor from recent (and best-to-date) work, thus achieving exact recovery with order-wise as many samples as the degrees of freedom. In the general setting with noise, our results represent the first (and currently only known) tractable algorithm guaranteeing successful recovery with tight bounds on sample complexity and recovery errors.

Field of study: Computer science
Psychometric Considerations in the Analysis of Reading Skill Hierarchies.

AbstractTheories of reading skill hierarchies postulate that reading comprehension consists of separate, increasingly complex, cumulative skills. Part of the inconsistency in the results from studies investigating such hierarchies is attributed to the analytic techniques most often employed. In the present research, the psychometric models of Rasch and Guttman are used to illustrate contrasting yet complementary approaches to investigating hierarchical structures. The data come from graduate and secondary school students who answered questions written to conform to a reading skills hierarchy. The models share a general conclusion but specific results from the Rasch model underscore its greater potential as a reading skills diagnostic techique.

Field of study: Education
Subduction of the Kula Ridge at the Aleutian Trench

A simple model of the probable topographic and thermal consequences of subducting an oceanic spreading center at an island arc predicts three geologic effects: shoaling and subaerial emergence of the crest of the arc; decrease or cessation of subduction-related magmatism; and regional low-grade thermal metamorphism (..delta..T approximately equal to 100 to 300/sup 0/C) of the arc rocks. All three of these phenomena are recorded in the geology of the Aleutian Islands, and the following sequence of events is indicated: (1) diminution of magmatism on approach of the Kula Ridge in middle Eocene times (approximately equal to 45 m.y. ago), marked by a conformable transition from volcanic-rich to volcanic-poor early-series rocks; (2) shoaling and emergence of the crest of the Aleutian arc in late Eocene to Oligocene time, marked by a deep- to shallow-marine transition in sedimentation and then an arc-wide unconformity above the early series and its probable ''submarine equivalent,'' the now-dissected Aleutian crestal platform; (3) subduction of the Kula Ridge and greenschist metamorphism of the early-series rocks at about 30 to 35 m.y. ago, inferred from K-Ar ages; (4) subsidence of the arc down the south flank of the Kula Ridge in middle Oligocene to Miocene time, as themore » Pacific plate was subducted; and (5) abrupt resumption of arc magmatism 15 m.y. ago. This history of events is consistent with the timing of plate motions in the North Pacific and suggests that there has been essentially continuous underthrusting at the Aleutian Trench since at least 45 to 50 m.y. ago, with subduction of 900 to 1,000 km of ocean floor since 30 to 35 m.y. ago.« less

Field of study: Geology
Research on Construction Process and Strategy Optimization under BIM Technology Background

In recent years, the economy has developed rapidly and the construction industry is an important part of the development of the national economy. The construction of a building is one of the most important steps in the construction process. How to manage the progress of the project scientifically and effectively has become an urgent problem for the current construction industry. The traditional management models are mostly empirical and intuitive management, relying on artificial management planning for construction progress. As a kind of information visualization technology, BIM can simulate every stage of construction and arrange the construction process rationally and effectively. The establishment of a BIM platform enables intuitive and effective sharing of information at all stages. This article is based on BIM technology, and scientifically manages the construction progress of the building. It aims at information management of construction progress, reducing costs and shortening the construction period. It also provides a theoretical basis for building information and the application development of BIM in the construction industry.

Field of study: Engineering
Atomic-scale observation and manipulation of plaquette antiferromagnetic order in iron-based superconductor

The symmetry requirement and the origin of magnetic orders coexisting with superconductivity have been strongly debated issues of iron-based superconductors (FeSCs). Observation of C$_4$-symmetric antiferromagnetism in violation of the inter-band nesting condition of spin-density waves in superconducting ground state will require significant change in our understanding of the mechanism of FeSC. The superconducting material Sr$_2$VO$_3$FeAs, a bulk version of monolayer FeSC in contact with a perovskite layer with its magnetism (T$_N$ ~ 50 K) and superconductivity (T$_c$ ~ 37 K) coexisting at parent state, has no reported structural orthorhombic distortion and thus makes a perfect system to look for theoretically expected C$_4$ magnetisms. Based on variable temperature spin-polarized scanning tunneling microscopy (SPSTM) with newly discovered imaging mechanism that removes the static surface reconstruction (SR) pattern by fluctuating it rapidly with spin-polarized tunneling current, we could visualize underlying C$_4$ symmetric (2$\times$2) magnetic domains and its phase domain walls. We find that this magnetic order is perfectly consistent with the plaquette antiferromagnetic order in tetragonal Fe spin lattice expected from theories based on the Heisenberg exchange interaction of local Fe moments and the quantum order by disorder. The inconsistency of its modulation Q vectors from the nesting condition also implies that the nesting-based C$_2$ symmetric magnetism is not a unique prerequisite of high-T$_c$ FeSC. Furthermore, the plaquette antiferromagnetic domain wall dynamics under the influence of small spin torque effect of spin-polarized tunneling current are shown to be consistent with theoretical simulation based on the extended Landau-Lifshitz-Gilbert equation.

Field of study: Physics
Three Cal Poly Teams Compete in the Ninth ULI - Gerald D. Hines Urban Design Competition

The Urban Land Institute’s Gerald D. Hines Student Urban Design Competition stimulates visioning of innovative built environments. Recognizing that “successful real estate development and design in the 21st century requires intensive collaboration across disciplines and sectors” the Hines competition invites graduate students in the United States or Canada to form a multidisciplinary five-person team to intensively tackle a real land use challenge in a U.S. city.

Field of study: Medicine
Heterogeneous ozonation kinetics of phenanthrene at the air?ice interface

Phenanthrene ozonation kinetics were measured on ice at ?30 and ?10??C, and on a water surface at 22??C using glancing angle laser-induced fluorescence. A Langmuir?Hinshelwood type kinetic mechanism was observed on ice. The maximum ozonation rates were a factor of ten higher on ice than on water. No temperature dependence to the kinetics was observed between ?30 and ?10??C, suggesting that the differences in the rates on ice and water are due to different physical properties at the two surfaces. Fluorescence spectra of phenanthrene show significant self-association on ice that is not observed on water, adding further evidence for the hypothesis that the quasi-liquid layer at the air?ice interface presents a very different environment to liquid water.

Field of study: Environmental science
Phase behaviour of blends of poly(chlorinated-ethyl methacrylate) with poly(styrene-co-acrylonitrile) and with poly(p-methylstyrene-co-acrylonitrile)

The phase behaviour of blends of four poly(chlorinated-ethyl methacrylates) with poly(styrene-co-acrylonitrile) (SAN) and with poly(p-methylstyrene-co-acrylonitrile) (pMSAN) was studied. Poly(1-chloroethyl methacrylate) and poly(2,2-dichloroethyl methacrylate) are miscible with SAN and pMSAN over a certain copolymer composition range, showing miscibility windows. Poly(2,2,2-trichloroethyl methacrylate) (PTCEMA) is miscible with SAN and pMSAN having high acrylonitrile contents, showing miscibility doors. PTCEMA is also miscible with polyacrylonitrile. However, poly(1,2,2,2-tetrachloroethyl methacrylate) is immiscible with any of the SAN and pMSAN samples.

Field of study: Materials science
Quasi-free $\pi^0$ photoproduction from the bound nucleon

Differential cross-sections for quasi-free $\pi^0$ photoproduction from the proton and neutron bound in the deuteron have been measured for $E_\gamma = 200\mbox{--}400$ MeV at $\theta_\gamma^{\rm lab} = 136.2^\circ$ using the Glasgow photon tagger at MAMI, the Mainz 48 cm $\clubsuit\times 64$ cm NaI(Tl) photon detector and the Göttingen SENECA recoil detector. For the proton measurements made with both liquid-deuterium and liquid-hydrogen targets allow direct comparison of “free” $\pi^0$ photoproduction cross-sections as extracted from the bound-proton data with experimental free cross-sections which are found to be in reasonable agreement below 320 MeV. At higher energies the “free” cross-sections extracted from quasi-free data are significantly smaller than the experimental free cross-sections and theoretical predictions based on multipole analysis. For the first time, “free” neutron cross-section have been extracted in the $\Delta$-region. They are also in agreement with the predictions from multipole analysis up to 320 MeV and significantly smaller at higher photon energies.

Field of study: Physics
Estimation and visualization of the fatigue life of Pb-free SAC solder bump joints under thermal cycling

A method for estimating the fatigue life of Pb-free solder (Sn–3.0Ag–0.5Cu) bump joints under thermal cycling is described. The test specimens were 4, 6 and 8 mm chip size packages mounted on printed circuit boards. To develop a semi-analytical model for estimating the thermal fatigue life, thermal cycle tests were carried out on the test specimens and the thermal fatigue life obtained experimentally was compared with the corresponding result from nonlinear, elastic–plastic finite element analysis. It was found that the chip size affected the thermal fatigue life and the strain accumulated in the solder bumps during thermal cycling. This was due to the difference in mechanical boundary conditions around the Si chip. Based on the Coffin–Manson law, an equation for estimating the thermal fatigue life was derived and the predicted fatigue life for various chip sizes and under different rises in temperature were found to be in good agreement with the experimental results. Moreover, a measurable parameter that correlates with the accumulated strain in the solder bumps was introduced for estimating the thermal fatigue life of the test specimens.

Field of study: Engineering
An Analysis on the Modes of Thinking of Jiang Zemin's Idea about Anti-corruption and Advocating Clear Politics

Jiang Zemin's idea about anti-corruption and advocating clear politics has creatively achieved organic combination of dialectical and systematic modes of thinking.In the macioscopical respect,he insists philosophical mode of thinking on the basis of dialectical Maxism,and there is creation and development to the analysis of concrete contradiction categories.In the microscopical respect,he makes full use of the latest achievement in the modern scientific and technological revolution——systematic mode of thinking.This is a distinguished feature in the modes of thinking of Jiang Zemin's idea about anti-corruption and advocating clear politics.

Field of study: Agricultural and Food sciences
Core scheme and depletion analysis of new thorium molten salt reactor

Core layout and depletion features of thorium molten salt reactor(TMSR) are analyzed using the self-developed lattice and core code SONG/TANG-MSR. Based on the results of previous lattice optimization research, fuel salt that contains no BeF2 is adopted, BeO is introduced as moderator instead of graphite, and SiC is chosen as cladding material. According to further lattice analysis at core level, the optimized three-zone layout of core is obtained, with high breeding ratio, negative power coefficient, flat temperature distribution. Thereafter, the depletion calculation and analysis is performed considering the online processing of fuel salt. The results show that the core has high breeding ratio, short doubling time, and long term stable operation. Thus, the design of TMSR has been greatly improved with increased breeding ability and sufficient safety margins.

Field of study: Physics
Fast Qualitative Analysis of Dioxins in Fly Ash by Comprehensive Two Dimensional Gas Chromatography Coupled Time of Fight Mass Spectrometry

Comprehensive two dimensional gas chromatography (GC×GC-TOFMS) has been applied to fast qualitative analysis of 17 polychlorinated dibenzo-p-dioxins and dibenofurans (PCDD/Fs).GC×GC-TOFMS parameters were evaluated and optimized to yield complete separation for 17 PCDD/Fs from interference,and to attain the high sensitivity.After optimization,all 17 PCDD/Fs were separated in 42.5 min.The critical and most toxic tetrachloro-dibenzo-p-dioxin (TCDD) detection was up to 0.5 pg/μL.The method was used to analyze a real fly ash sample.Accurate identification and determination of all analytes were by GC×GC,mass spectrum library and ion ratio.The technique could be a substitute and supplement for high resolution gas chromatography/high resolution mass spectrometry in the field of dioxin analysis.

Field of study: Chemistry
The age of the “Grande Coupure” mammal turnover: New constraints from the Eocene–Oligocene record of the Eastern Ebro Basin (NE Spain)

The Grande Coupure represents a major terrestrial faunal turnover recorded in Eurasia associated with the overall climate shift at the Eocene–Oligocene transition. During this event, a large number of European Eocene endemic mammals became extinct and new Asian immigrants appeared. The absolute age of the Grande Coupure, however, has remained controversial for decades. The Late Eocene–Oligocene continental record of the Eastern Ebro Basin (NE Spain) constitutes a unique opportunity to build a robust magnetostratigraphy-based chronostratigraphy which can contribute with independent age constraints for this important turnover. This study presents new magnetostratigraphic data of a 495-m-thick section (Moia-Santpedor) that ranges from 36.1 Ma to 33.3 Ma. The integration of the new results with previous litho- bio- and magnetostratigraphic records of the Ebro Basin yields accurate ages for the immediately pre- and post-Grand Coupure mammal fossil assemblages found in the study area, bracketing the Grande Coupure to an age embracing the Eocene–Oligocene transition, with a maximum allowable lag of 0.5 Myr with respect to this boundary. The shift to drier conditions that accompanied the global cooling at the Eocene–Oligocene transition probably determined the sedimentary trends in the Eastern Ebro Basin. The occurrence and expansion of an amalgamated-channel sandstone unit is interpreted as the forced response of the fluvial fan system to the transient retraction of the central-basin lake systems. The new results from the Ebro Basin allow us to revisit correlations for the controversial Eocene–Oligocene record of the Hampshire Basin (Isle of Wight, UK), and their implications for the calibration of the Mammal Palaeogene reference levels MP18 to MP21.

Field of study: Environmental science, Geography
The impact of African-trained neurosurgeons on sub-Saharan Africa.

Sub-Saharan Africa (SSA) represents 17% of the world's land, 14% of the population, and 1% of the gross domestic product. Previous reports have indicated that 81/500 African neurosurgeons (16.2%) worked in SSA-i.e., 1 neurosurgeon per 6 million inhabitants. Over the past decades, efforts have been made to improve neurosurgery availability in SSA. In this study, the authors provide an update by means of the polling of neurosurgeons who trained in North Africa and went back to practice in SSA.



Neurosurgeons who had full training at the World Federation of Neurosurgical Societies (WFNS) Rabat Training Center (RTC) over the past 16 years were polled with an 18-question survey focused on demographics, practice/case types, and operating room equipment availability.



Data collected from all 21 (100%) WFNS RTC graduates showed that all neurosurgeons returned to work to SSA in 12 different countries, 90% working in low-income and 10% in lower-middle-income countries, defined by the World Bank as a Gross National Income per capita of ≤ US$995 and US$996-$3895, respectively. The cumulative population in the geographical areas in which they practice is 267 million, with a total of 102 neurosurgeons reported, resulting in 1 neurosurgeon per 2.62 million inhabitants. Upon return to SSA, WFNS RTC graduates were employed in public/private hospitals (62%), military hospitals (14.3%), academic centers (14.3%), and private practice (9.5%). The majority reported an even split between spine and cranial and between trauma and elective; 71% performed between 50 and more than 100 neurosurgical procedures/year. Equipment available varied across the cohort. A CT scanner was available to 86%, MRI to 38%, surgical microscope to 33%, endoscope to 19.1%, and neuronavigation to 0%. Three (14.3%) neurosurgeons had access to none of the above.



Neurosurgery availability in SSA has significantly improved over the past decade thanks to the dedication of senior African neurosurgeons, organizations, and volunteers who believed in forming the new neurosurgery generation in the same continent where they practice. Challenges include limited resources and the need to continue expanding efforts in local neurosurgery training and continuing medical education. Focus on affordable and low-maintenance technology is needed.

Field of study: Medicine