nils-herrmann/clean_scirepeval huggingface dataset:
Integrating multi-omic features exploiting Chromosome Conformation Capture data

The representation, integration, and interpretation of omic data is a complex task, in particular considering the huge amount of information that is daily produced in molecular biology laboratories all around the world. The reason is that sequencing data regarding expression profiles, methylation patterns, and chromatin domains is difficult to harmonize in a systems biology view, since genome browsers only allow coordinate-based representations, discarding functional clusters created by the spatial conformation of the DNA in the nucleus. In this context, recent progresses in high throughput molecular biology techniques and bioinformatics have provided insights into chromatin interactions on a larger scale and offer a formidable support for the interpretation of multi-omic data. In particular, a novel sequencing technique called Chromosome Conformation Capture allows the analysis of the chromosome organization in the cell’s natural state. While performed genome wide, this technique is usually called Hi–C. Inspired by service applications such as Google Maps, we developed NuChart, an R package that integrates Hi–C data to describe the chromosomal neighborhood starting from the information about gene positions, with the possibility of mapping on the achieved graphs genomic features such as methylation patterns and histone modifications, along with expression profiles. In this paper we show the importance of the NuChart application for the integration of multi-omic data in a systems biology fashion, with particular interest in cytogenetic applications of these techniques. Moreover, we demonstrate how the integration of multi-omic data can provide useful information in understanding why genes are in certain specific positions inside the nucleus and how epigenetic patterns correlate with their expression.

Field of study: Biology
Tangential derivatives and higher-order regularizing properties of the double layer heat potential

We prove an explicit formula for the tangential derivatives of the double layer heat potential. By exploiting such a formula, we prove the validity of a regularizing property for the integral operator associated to the double layer heat potential in spaces of functions with high-order derivatives in parabolic Hölder spaces defined on the boundary of parabolic cylinders which are unbounded in the time variable.

Field of study: Philosophy
Microstructure of Rings After Cold Ring Rolling and Its Mechanical Property After Quenching and Tempering

By comparing the microstructures of rings before and after deformation and measuring the values of microhardness after heat treatment,the effects of cold ring rolling deformation on microstructure of rings and its mechanical property after quenching and tempering were discussed.The carbide particles in the structure of ring are found smaller and more even in the process of cold rolling,and so the general mechanical property improves after heat treatment.The analysis shows that the process of cold rolling mainly influences the velocity of carbides dissolution during the period of quenching and tempering and leads to different proportion of martensite between deformed and undeformed structure.The changing trend of microhardness exactly presents the distinction.

Field of study: Materials science
Daniel Maira.Typosine, la dixième muse: Formes éditoriales descanzonierifrançais (1544–1560). Travaux d'Humanisme et Renaissance 185. Geneva: Librairie Droz S.A., 2007. 512 pp. + 63 b/w pls. index. append. illus. chron. bibl. $109.20. ISBN: 978–2–600–01138–9.


Field of study: History
More effort is needed to implement and disseminate soil protection measures for tropical soils

Soils are a finite resource paramount to delivering environmental goods that are inextricably linked to Sustainable Development Goals and vital for human well-being. Yet soils, particularly in tropical zones, are being degraded and thus the soil ecosystem services (SES) they deliver are being impaired. Considering Brazil as a case study, we developed a soil-centric ecosystem services approach that may be used to translate and communicate the importance of soils to a range of stakeholders. We propose a plan of action, focused on a communication strategy, which includes dissemination of soil monetary and non-monetary values, and we outline steps that should be incorporated by a range of stakeholders to ensure that soils are understood as pivotal resources to be protected for current and future generations. We call on the international research community, especially in tropical countries, to seize the opportunity to embrace and disseminate this soil-centric approach and to arrest the continuous over-exploitation of soil resources.

Field of study: Environmental science
The Abecedario and A Check-List of Mexican Inquisition Documents at the Henry E. Huntington Library

I N 1907 Walter Douglas purchased forty-six volumes of Mexican Inquisition documents for $1,500 from Michael Blake, a dealer in old books and manuscripts in Mexico City. Mr. Douglas bequeathed these to the Henry E. Huntington Library and Art Gallery of San Marino, California. Previously, they had been offered for sale to Henry C. Lea.' Thirtyone volumes of the forty-seven had been offered by E. Nott Anable to Elken N. Adler of England. Mr. Adler published a partial description of them as an Appendix to his Auto de Fe and Jew.2 No check-list has heretofore been published of the contents of the forty-six volumes. This article will discuss some of the findings to be adduced from volume 2, "Abecedario" and its relationship to volume 1, "List of Inquisition Trials from 1525 to 1811." There is considerable inaccuracy and lack of concern for detail and consistency, resulting in many omissions in both volumes and variances between them. The secretariat and other officialdom of the Inquisition paid little heed to spelling, dates, and chronological order. The "Abecedario" is not a running account kept by each secretary of the Inquisition, but was compiled sometime after 1715. The "List" was supposedly prepared at divers times over the course of the three centuries it covers. The "Abecedario " has only ten entries after 1700 and none after 1709. For some unexplained reason the secretariat was directed to prepare the "alphabetical" summary. One conjecture was that about 1720 a visitador came to New Spain to investigate the affairs of the Inquisition. The list may have been prepared for him. The "Abecedario" is not an alphabetical list in our sense of the word. Under each letter the names appear in (more or less) chrono-

Field of study: History
Unique clusters of Archaea in Salar de Huasco, an athalassohaline evaporitic basin of the Chilean Altiplano.

Analyses of clone libraries from water and sediments of different sites from Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano, revealed the presence of five unique clusters of uncultured Archaea that have not been previously reported or specifically assigned. These sequences were distantly related (83-96% sequence identity) to a limited number of other clone sequences and revealed no identity to cultured Archaea. The abundance of Archaea and Bacteria was estimated using qPCR and community composition was examined through the construction of clone libraries of archaeal 16S rRNA gene. Archaea were found to be dominant over Bacteria in sediments from two saline sites (sites H4: 6.31 x 10(4) and site H6: 1.37 x 10(4) microS cm(-1)) and in one of the water samples (freshwater from site H0: 607 muS cm(-1)). Euryarchaeotal sequences were more abundant than crenarchaeotal sequences. Many of the clone sequences (52%) were similar to uncultured archaeal groups found in marine ecosystems having identity values between 99% and 97%. A major fraction of the sequences (40%) were members of Methanobacteria, while others were included in the Marine Benthic Groups B and D, the Miscellaneous Crenarchaeotic Group, the Terrestrial Miscellaneous Euryarchaeotal Group, Marine Group I and Halobacteria. The presence of uncultured archaeal groups in Salar de Huasco extends their known distribution in inland waters, providing new clues about their possible function in the environment.

Field of study: Biology, Environmental science
Modeling grain drying as discharge of an RC electrical circuit

This work presents a grain–drying model based on the hypothesis that the grain–drying process is similar to the 
discharge of an electric system formed of RC circuits arranged in parallel. The model for moisture removal can be represented 
by a sum of exponential terms, adjusted to the experimental data from the dehydration of the product under investigation. 
Using this analogy, physical meaning was attributed to each parameter involved in the drying equation. The number of RC 
circuit branches in the electric system is equal to the number of exponential terms of the drying equation. In the cases 
investigated (soybean and sunflower seed), the adjusted equations to express the time variations of the product moisture were 
composed of the sum of two exponential terms, which are equivalent to the removal of two types of water during the drying process.

Field of study: Agricultural and Food sciences
Characteristics of Regulatory T cells

Regulatory T cells (Tregs) is heterogenic subpopulation of T cells that is able to suppress function of effector cells during the immune response. Among them are natural (nTreg) and induced Treg (Tr1, Th3, CD4 + CD25 - ). CD25, CD45Ro, CD152, GITR, LAG-3, several adhesion molecules, chemokine receptors as well as Toll-like receptors are present on the surface of Treg. Mechanism of suppression used by nTreg is not completely understood.

Field of study: Medicine
Convergence Acceleration of Iterative Modal Reduction Methods

An accelerated method is presented for the iterative condensation of eigenproblems. The present study was motivated by the improved reduction system and the succession-level approximate reduction (SAR). The reduction procedures are supplemented with the second-order approximation in the series expansion of the system transformation. The reduced equation of an equivalent system and the transformation matrix are updated in an iterative manner.In addition,systematicderivation andcomparisonoftheequationsinvolvedin variouscondensationshave been sought.Thematrixupdateincorporatesnotonlyinverseiteration butalsosubspacetransformation implicitly. Theseriesexpansion canbeconsideredasrepeatedupdatesofthetransformationmatrixthroughinverseiteration. The solution accuracy is sensitive to the selection of the degrees of freedom, for which sequential elimination or energy method may be preferable. When a poor selection causes a sudden failure of the updatemethod, the hybrid dynamic condensation can be used. The method of SAR is closely related to the hybrid dynamic condensation. Nomenclature [As] = [kss] i 1 [mss] in Eq. (10) [Bpp],[Bsp] = submatrices for inertia force in Eq. (68) [DG] = [MG] i 1 [KG] dynamic matrix in Eq. (13) [Ke], [Me] = equivalent structural matrices in Eq. (26) [KG],[MG] = reduced matrices in Guyan’ s condensation [Kr], [Mr] = structural matrices reduced through [Tr] [KX], [MX] = structural matrices reduced through [TX] [k], [ka b ] = stiffness matrix and submatrices [m], [ma b ] = mass matrix and submatrices p = number of primary degrees of freedom [Q pp] = modal matrix for generalized coordinates {R} = residual error in eigenproblem s = number of secondary degrees of freedom [T] = exact transformation matrix in Eq. (22) [Ti] = matrices in series of Eqs. (15) and (18) [Tp] = system transformation matrix [Tr] = approximate transformation matrix [TX] = improved transformation matrix in Eq. (40) [T0] = transformation in Guyan’ s condensation [T(k )] = frequency-dependent transformation in Eq. (3) [X p] = improved modal matrix [X pp],[Xsp] = submatrices of [X p] e = convergence tolerance [K p]

Field of study: Physics
Assessment of single-sided ventilation with acoustic shutters on windows

Despite natural ventilation has shown great potential and noticeable efficiency in terms of indoor air quality and energy demand, it usually causes external noise entrance by the openings. The use of shutters can reduce this drawback but also the ventilation performance. The paper proves the feasibility of the use of shutters from the viewpoints of both noise and single-sided ventilation rate. It first assesses the acoustic performances of an optimized shutter. Then, using tracer gas methods, the air change rate is measured in a test-room holding this shutter on the window. Results show that the use of an optimized shutter can provide about 4 h-1 average ACR which is largely acceptable for ventilating buildings. The measurement results are then compared to correlations of natural ventilation and provided good agreement.

Field of study: Engineering
Pigeons (Columba livia) approach Nash equilibrium in experimental Matching Pennies competitions.

The game of Matching Pennies (MP), a simplified version of the more popular Rock, Papers, Scissors, schematically represents competitions between organisms with incentives to predict each other's behavior. Optimal performance in iterated MP competitions involves the production of random choice patterns and the detection of nonrandomness in the opponent's choices. The purpose of this study was to replicate systematic deviations from optimal choice observed in humans when playing MP, and to establish whether suboptimal performance was better described by a modified linear learning model or by a more cognitively sophisticated reinforcement-tracking model. Two pairs of pigeons played iterated MP competitions; payoffs for successful choices (e.g., "Rock" vs. "Scissors") varied within experimental sessions and across experimental conditions, and were signaled by visual stimuli. Pigeons' behavior adjusted to payoff matrices; divergences from optimal play were analogous to those usually demonstrated by humans, except for the tendency of pigeons to persist on prior choices. Suboptimal play was well characterized by a linear learning model of the kind widely used to describe human performance. This linear learning model may thus serve as default account of competitive performance against which the imputation of cognitively sophisticated processes can be evaluated.

Field of study: Biology, Psychology
Attachment-Security Prime Effect on Skin-Conductance Synchronization in Psychotherapists: An Empirical Study

Physiological synchronization (PS) is a phenomenon of simultaneous activity between two persons’ physiological signals. It has been associated with empathy, shared affectivity, and efficacious therapeutic relationships. The aim of the present study was to explore the possible connections between PS and the attachment system, seeking preliminary evidence of this link by means of an experimental manipulation of the sense of attachment security in psychotherapists according to a protocol by Mikulincer and Shaver (2001), which has been proven to elicit empathetic behavior. We compared the synchronization of skin-conductance signals in brief psychological interviews between 18 psychodynamic therapists and 18 healthy volunteers. A sense of attachment-security priming was administered to half of the therapists, whereas the other half received a positive-affect control prime. Lag analysis was performed to investigate the “leading” or “following” attitudes of the participants in the two conditions. Mixed-model regressions and evidence-ratio model comparisons were used to investigate the effects of the manipulation on PS. Therapist attachment anxiety and avoidance traits were considered covariates. The attachment-security prime showed a significant effect on PS lag dynamics, but not on overall PS amount. Lag analysis showed that the therapists in the attachment-security condition were significantly more prone to assume a leading attitude in the physiological coupling than the therapists in the control condition. Therapist attachment anxiety and avoidance had no apparent effect. Our result paves the way for further exploration of the clinical relationship from a physiological standpoint.

Field of study: Psychology
pH-dependent phosphatization of ZnO nanoparticles and its influence on subsequent lead sorption.

Phosphatization of ZnO nanoparticles (ZNPs) at various pHs and its influence on subsequent lead sorption were investigated. Results showed that, in presence of phosphate, both the chemical speciation and crystalline phase of ZNPs were pH dependent that most of them were converted to crystalline Zn3(PO4)2 at acidic pHs, but only little amorphous hopeites can be formed under alkaline condition. Phosphatization process significantly enhanced subsequent lead sorption with the order of acidic process > alkaline > pristine ZNPs. Spectroscopic analysis including ATR-FTIR and XPS revealed main mechanisms of lead phosphate precipitation and inner-sphere complexes for lead sorption on acidic and alkaline treatment products, respectively. The potential toxicity of ZNPs and heavy metals in eutrophic aquatic ecosystems would thus be reduced due to the ubiquitous phosphatization process. This study highlights the importance of environmental variables in exploring the environmental behavior and fate of heavy metals as well as nanoparticles in natural waters.

Field of study: Environmental science
Quantitative Classification and Chemical Comparison of Common Volcanic Rocks

A simple quantitative method of classification and chemical comparison of the main volcanic rock species has been devised using the three-axis orthogonal plot Na 2 O + K 2 O versus FeO + Fe 2 O 3 + 1/2 (MgO + CaO) versus Al 2 O 3 /SiO 2 , in weight percent. The method combines a new index of basicity with some of the important aspects of variation diagrams proposed by Tilley and Murata. The resulting generalized treatment of major oxide data, which stresses the gross differences in rock composition, has the important advantages of de-emphasizing some of the possible effects of analytical error and requiring a minimum of manipulation and processing of data. Graphs of large numbers of published and unpublished analyses readily discriminate between magma types and trends and reaffirm classical volcanic rock nomenclature. Good correlation is established with the arc fusion determinative procedure of Mathews, thereby increasing the scope and general utility of the method.

Field of study: Geology
Pyrazolopyrimidines Based on 5-Aminopyrazoles Unsubstituted at the Position 1

By condensation of various symmetric β-diketones with a series of 5-aminopyrazoles that are unsubstituted at the position 1, we have obtained a series of pyrazolo[1,5-a]pyrimidines that are of interest as physiologically active compounds. Hexafluoroacetylacetone reacts in another direction, forming pyrazolo[4,5-b]pyridine.

Field of study: Chemistry
Optically-facial Identification System on the Optical JTC in Mobile Networks

We have so far designed and constructed a facial recognition system based on the optical parallel Joint Transform Correlator combined with a digital computer. In addition to this, we devices a compact prototype PJTC (COPaC) and examined it for a practical use. According to the guideline for identification using biometrics, we carried out the accuracy evaluation by one-to one collation using 300 facial images. We ascertained its performance to be remarkably precise and thus reliable. In this paper, we proposed the Real-time individual authentication system in the mobile network, which is based on an optical correlation. It was examined for the influence of the camera resolution, image compression and background removal. Consequently, we confirmed that this system is highly robust against these potential influences. Moreover, we tested this in a wireless LAN environment, and verified its high possibility for a further facial identification use.

Field of study: Computer science
Individual Cyber Security: Empowering Employees to Resist Spear Phishing to Prevent Identity Theft and Ransomware Attacks

One of the most difficult challenges in information security today is phishing. Phishing is a difficult problem to address because there are many permutations, messages, and value propositions that can be sent to targets. Spear phishing is also associated with social engineering, which can be difficult for even trained or savvy employees to detect. This makes the user the critical point of entry for miscreants seeking to perpetrate cyber crimes such as identity theft and ransomware propagation, which cause billions of dollars in losses each year. Researchers are exploring many avenues to address this problem, including educating users and making them aware of the repercussions of becoming victims of phishing. The purpose of this study was to interview security professionals to gain better insight on preventing users and employees from succumbing to phishing attack. Seven subject-matter experts were interviewed, revealing nine themes describing traits that identify users as vulnerable to attack or strongly resistive to attack, as well as training suggestions to empower users to resist spear phishing attacks. Suggestions are made for practitioners in the field and future research.

Field of study: Business
Investigation of fatigue.

Fatigue is a very common symptom and the cause can often be determined by careful history and physical examination. Since there is no organic cause for at least half of the cases of fatigue, extensive laboratory and radiological investigation may not be necessary. The minimal laboratory investigation should include a urinalysis, complete blood count, smear, sedimentation rate and chest X-ray. Further investigation will be determined by the presence of localizing symptoms and signs. If these are present, then only limited investigation may be necessary. If it is felt that the cause of the fatigue is organic and there are no localizing features, very extensive laboratory and radiological investigation will be required.

Field of study: Medicine
Transport evidence of asymmetric spin–orbit coupling in few-layer superconducting 1Td-MoTe2

Two-dimensional transition metal dichalcogenides MX2 (M = W, Mo, Nb, and X = Te, Se, S) with strong spin–orbit coupling possess plenty of novel physics including superconductivity. Due to the Ising spin–orbit coupling, monolayer NbSe2 and gated MoS2 of 2H structure can realize the Ising superconductivity, which manifests itself with in-plane upper critical field far exceeding Pauli paramagnetic limit. Surprisingly, we find that a few-layer 1Td structure MoTe2 also exhibits an in-plane upper critical field which goes beyond the Pauli paramagnetic limit. Importantly, the in-plane upper critical field shows an emergent two-fold symmetry which is different from the isotropic in-plane upper critical field in 2H transition metal dichalcogenides. We show that this is a result of an asymmetric spin–orbit coupling in 1Td transition metal dichalcogenides. Our work provides transport evidence of a new type of asymmetric spin–orbit coupling in transition metal dichalcogenides which may give rise to novel superconducting and spin transport properties.Two-dimensional transition metal dichalcogenides with peculiar spin–orbit coupling may lead to exotic phenomena. Here, the authors report a large in-plane upper critical field with a two-fold symmetry, suggesting a novel asymmetric spin–orbit coupling in few-layer 1Td-MoTe2.

Field of study: Physics
Bemerkung zur Theorie der Störungen in Hyperfeinstrukturen

ZusammenfassungEs wird gezeigt, daß die in der vorstehenden Arbeit von Schüler und Jones gefundenen Ergebnisse unvereinbar sind mit der Annahme, daß die Wechsel-wirkung zwischen Kern und Elektronenhülle gleich dem Skalarprodukt zweier Vektoren ist.

Field of study: Physics