nils-herrmann/clean_scirepeval huggingface dataset:
Bioinformatics Analysis Reveals Biomarkers With Cancer Stem Cell Characteristics in Lung Squamous Cell Carcinoma

Tumor stem cells play important roles in the survival, proliferation, metastasis and recurrence of tumors. We aimed to identify new prognostic biomarkers for lung squamous cell carcinoma (LUSC) based on the cancer stem cell theory.  RNA-seq data and relevant clinical information were downloaded from The Cancer Genome Atlas (TCGA) database. Weighted gene coexpression network analysis (WGCNA) was applied to identify significant modules and hub genes, and prognostic signatures were constructed with the prognostic hub genes.  LUSC patients in the TCGA database have higher mRNA expression-based stemness index (mRNAsi) in tumor tissue than in adjacent normal tissue. In addition, some clinical features and outcomes were highly correlated with the mRNAsi. WGCNA revealed that the pink and yellow modules were the most significant modules related to the mRNAsi; the top 10 hub genes in the pink module were enriched mostly in epidermal development, the secretory granule membrane, receptor regulator activity and the cytokine-cytokine receptor interaction. The protein–protein interaction (PPI) network revealed that the top 10 hub genes were significantly correlated with each other at the transcriptional level. In addition, the top 10 hub genes were all highly expressed in LUSC, and some were differentially expressed in different TNM stages. Regarding the survival analysis, the nomogram of a prognostic signature with three hub genes showed high predictive value.  mRNAsi-related hub genes could be a potential biomarker of LUSC.

Field of study: Biology
Cyclotriphosphazene, an old compound applied to the synthesis of smart dendrimers with tailored properties

The versatile reactivity of hexachlorocyclotriphosphazene (N3P3Cl6) has been developed for the synthesis of specifically engineered dendrimers. Dendrimers are hyperbranched macromolecules built by concentric layers constituted of associated monomeric units. Many of the properties of dendrimers depend on the type of their surface (terminal) functions, which are generally all identical. For some specific purposes, it is desirable to have one function that is different at the level of the core. Hexachlorocyclotriphosphazene offers the possibility to differentiate the reactivity of one (or more) Cl from the others, for producing specifically engineered dendritic tools. These specific reactions on N3P3Cl6 have produced highly dense dendrimers, Janus dendrimers (two faces), tools for functionalizing materials, with uses as catalysts, as chemical sensors, for trapping CO2, for the culture of cells, or for imaging biological events. These properties will be emphasized in this review.

Field of study: Chemistry
Coherent categorification of quantum loop algebras : the $SL(2)$ case

We construct an equivalence of graded Abelian categories from a category of representations of the quiver-Hecke algebra of type $A_1^{(1)}$ to the category of equivariant perverse coherent sheaves on the nilpotent cone of type $A$. We prove that this equivalence is weakly monoidal. This gives a representation-theoretic categorification of the preprojective K-theoretic Hall algebra considered by Schiffmann-Vasserot. Using this categorification, we compare the monoidal categorification of the quantum open unipotent cells of type $A_1^{(1)}$ given by Kang-Kashiwara-Kim-Oh-Park in terms of quiver-Hecke algebras with the one given by Cautis-Williams in terms of equivariant perverse coherent sheaves on the affine Grassmannians.

Field of study: Mathematics
Joint optimisation convex-negative matrix factorisation for multi-modal image collection summarisation based on images and tags

Image collection summarisation aims to represent a large-scale multi-modal collection with a small subset of images and tags, helping navigate a large image dataset. Most extant methods leverage the contributions of text-to-visual summaries, ignoring the visual contribution to the textual topic. When the tags are weakly labelled, the textual topic cannot accurately reflect the visual summary. To solve this, the authors propose a novel model, joint optimisation of convex non-negative matrix factorisation, which incorporates images and tags in a beneficial way. The objective function contains visual and textual error functions, sharing the same indicator matrix, connecting different modal relations. Then, they propose an iterative algorithm to optimise the proposed model. Finally, they explore the effects of different visual feature representations (e.g. bag-of-words and deep learning) on multi-modal collection summary. Our proposed method is then compared with state-of-the-art algorithms using two multi-modal datasets (i.e. MIRFlickr and NUS-WIDE-SCENE). Experimental results demonstrate the effectiveness of their proposed approach.

Field of study: Computer science
Experimental studies on coupling characteristics of rectangular slot

This paper experimentally studies the coupling coefficient of microwaves into rectangular slots. The frequency range is from 2 to 18GHz. The experimental method is presented, and the experimental setup is established. The experimental results show that the resonant effect will take place if the microwave wavelength is twice about the side length of the rectangular slot, and if the direction of the incident electric field is perpendicular to the long side of the slot. There is a strong coupling band near the resonant frequency, around which the enhancement effect can take place.

Field of study: Physics
Gamification in software engineering education: A systematic mapping

The potential of gamification in education is based on the hypothesis that it supports and motivates students and can thus lead to enhanced learning processes and outcomes. Gamification in software engineering (SE) education is in its infancy. However, as SE educators we are particularly interested in understanding how gamification is pollinating our field and the extent to which the above claim is valid in our context. A systematic literature mapping has underscored the difficulty in fully corroborating the above claim because few empirical data are available so far. However, key trends and challenges have been identified. We found that the purpose of applying gamification in the SE field is mostly directly related to improving student engagement and, to a lesser extent, to improving student knowledge, although other targets are the application of SE best practices and socialization. We have also discussed insightful issues regarding the implementation cost of gamification, patterns in the most often used gamification elements, and the SE processes and teaching activities addressed. Of the identified challenges, we should highlight the complexity of deciding which gamification approach to follow, the lack of information for choosing gamification elements and the need to control the impact of gamification.

Field of study: Computer science, Engineering
Tree LANs with Collision Avoidance: Station and Switch Protocols

Packet collisions and their resolution create a performance bottleneck in random access LANs. A hardware solution to this problem is to use collision avoidance switches. These switches allow the implementation of random access protocols without the penalty of collisions among packets. We describe some tree LANs that use collision avoidance switches. These LANs have the potential of combining the benefits of random access (low delay when traffic is light; simple, distributed, and therefore robust, protocols) with concurrency of transmission and excellent network utilization. The collision avoidance LANs we describe are broadcast star, CASB Tree (Collision Avoidance Single Broadcast Tree), CAMB Tree (Collision Avoidance Multiple Broadcast Tree), and Tinker Tree.

Field of study: Computer science
Electrodeposited cobalt coating on Crofer22APU steels for interconnect applications in solid oxide fuel cells

A gas-tight cobalt-based protective coating was successfully applied by electroplating and subsequent oxidation. The coating covered all the surfaces of the machined gas channels of the metallic interconnect and adhered well to this substrate. Such a gas-tight coating offers effective blocking of Cr diffusion or evaporation from the interconnect and hence a reliable protection against Cr poisoning of the SOFC cathode. Chemical interactions were observed between the cobalt coating and the LSM contact layer, resulting in layer spallation during oxidation under pressureless conditions. Applying a pressure to the layers, spallation was effectively prevented. Although the area specific resistance (ASR) of the coated interconnect was higher than the uncoated one, it decreased steadily with time within the measurement period. The ASR was 28 mΩ cm 2 after an exposure of 1170 h. It seems thus that electroplating followed by oxidation is a promising method for the fabrication of spinel protective coatings for SOFC interconnects or other balance-of-plant components with complicated gas flow paths.

Field of study: Materials science
Charge Expulsion, Spin Meissner Effect, and Charge Inhomogeneity in Superconductors

Superconductivity occurs in systems that have a lot of negative charge: the highly negatively charged (CuO2)= planes in the cuprates, negatively charged (FeAs)− planes in the iron arsenides, and negatively charged B− planes in magnesium diboride. And, in the nearly filled (with negative electrons) bands of almost all superconductors, as evidenced by their positive Hall coefficient in the normal state. No explanation for this charge asymmetry is provided by the conventional theory of superconductivity, within which the sign of electric charge plays no role. Instead, the sign of the charge carriers plays a key role in the theory of hole superconductivity, according to which metals become superconducting because they are driven to expel negative charge (electrons) from their interior. This is why NIS tunneling spectra are asymmetric, with larger current for negatively biased samples. The theory also offers a compelling explanation of the Meissner effect: as electrons are expelled towards the surface in the presence of a magnetic field, the Lorentz force imparts them with azimuthal velocity, thus generating the surface Meissner current that screens the interior magnetic field. In type II superconductors, the Lorentz force acting on expelled electrons that do not reach the surface gives rise to the azimuthal velocity of the vortex currents. In the absence of applied magnetic field, expelled electrons still acquire azimuthal velocity, due to the spin–orbit interaction, in opposite direction for spin-up and spin-down electrons: the “Spin Meissner effect.” This results in a macroscopic spin current flowing near the surface of superconductors in the absence of applied fields, of magnitude equal to the critical charge current (in appropriate units). Charge expulsion also gives rise to an interior outward-pointing electric field and to excess negative charge near the surface. In strongly type II superconductors this physics should give rise to charge inhomogeneity and spin currents throughout the interior of the superconductor, to large sensitivity to (non-magnetic) disorder and to a strong tendency to phase separation.

Field of study: Physics
Derivatives of 1,4-diaryl-5,6,7,8-tetrahydro-2,2a,8a-triazacyclopenta[c,d]azulene

Derivatives of the previously unknown heterocyclic system 2,2a,8a-triazacyclopenta[c,d] azulene were synthesized by condensation of 3-aryl-4,5-pentamethylene-1,2,4-triazoles or 2-(β-aroylhydrazin)-l-aza-Δ-cycloheptene with α-halogeno ketones, followed by cyclization of the intermediate products in alkaline media.

Field of study: Chemistry
The British Tariff and Industrial Protection in the 1930s: An A Iternative Model

I n his recent article, Dr Capie used an effective protection model to derive conclusions about the resource flows induced by industrial protection in the I 930s.2 The Building Industry, widely believed to be a major stimulus to the upswing of economic activity in the thirties, was surprisingly found to have been adversely affected by the I 932 tariff, and the Iron and Steel Trades, previously thought to have greatly benefited from protection, were shown to be among the industries least effected. The purpose of this note is to question some of Capie's revisionist conclusions by drawing attention to some omissions and inadequacies of the model used. In section I evidence is adduced to suggest an implicit assumption of Capie's method is inconsistent with historical experience. The second section proposes an alternative model of the substitution effects of the tariff, which is not open to the same objection. It is also shown that Prof. Richardson's earlier method of assessing the impact of the tariff is a special case of the analysis presented  Section III supplements the substitution effects model of the tariff with an assessment of the influence of protection on aggregate income and employment.

Field of study: Economics, History
Concentrations of Polybrominated Diphenyl Ethers, Hexabromocyclododecanes and Tetrabromobisphenol-A in Breast Milk from United Kingdom Women Do Not Decrease over Twelve Months of Lactation.

Conflicting evidence exists about whether concentrations of persistent organic chemicals in human milk decrease over the course of lactation. This has implications for the timing of sampling human milk for exposure assessment purposes. We examined this issue by measuring concentrations of polybrominated diphenyl ethers (PBDEs), hexabromocyclododecanes (HBCDs), the HBCD degradation products tetrabromocyclododecenes (TBCDs), and tetrabromobisphenol-A (TBBP-A) in human milk collected in 2010-2011 from 10 first-time mothers from Birmingham, UK. To evaluate whether concentrations varied significantly over the first 12 months postpartum, 12 samples were taken-one per month-from each mother, amounting to 120 samples overall. While concentrations of most of our target contaminants displayed no significant variation (p > 0.1) over the duration of our study, significant increases were detected in concentrations of ∑TBCDs (p = 0.029, average increase 1.4%/month) and BDE-153 (p = 0.058, average increase 4.2%/month). When compared to data obtained from a different set of UK mothers from a related but geographically wider catchment area sampled contemporaneously to this study, the ratio of median concentrations of BDE-153 to BDE-99 was markedly lower in the current study (0.46 compared to 1.32). This may reflect unidentified differences in exposure of the participants in the two studies.

Field of study: Environmental science
Normalized protein nitrogen appearance is correlated with hospitalization and mortality in hemodialysis patients with Kt/V greater than 1.20.

Normalized protein nitrogen appearance (nPNA), also known as protein catabolic rate (nPCR), reflects the daily protein intake in maintenance hemodialysis (MHD) patients. Several studies indicate that nPNA and Kt/V correlate with clinical outcome and also with each other. Thus, the relationship between low nPNA and poor outcome could be due to uremia, low Kt/V or due to reported mathematical coupling between nPNA and Kt/V. We therefore investigated whether nPNA is associated with outcome in patients who have adequate or high Kt/V.



Prospective cohort.



Outpatient dialysis unit affiliated with a tertiary-care community medical center.



From a pool of 135 MHD outpatients in one dialysis unit, 122 patients with a delivered, Kt/V(sp)>1.20, independent of their residual renal function, were evaluated. Patients (61 women, 61 men), aged from 23 to 89 years (53.4+/-14.0 years)(+/-SD), had been undergoing MHD for one month to 17 years.



Review of laboratory values and clinical outcome.



Twelve-month mortality and hospitalization.



Delivered Kt/V(sp) ranged from 1.23 to 2.71 (1.77+/-0.34), nPNA from 0.5 to 2.15 (1.13+/-0.29 g/kg/day), and serum albumin, from 1.9 to 4.6 (3.76+/-0.37 g/dL). During the 12-month follow-up, 55 patients were hospitalized overnight at least once; 12 patients died; 5 patients underwent renal transplantation, and 6 patients left the study. The nPNA and Kt/V(sp) did not correlate significantly (r=.09) except when analysis was limited to Kt/V values < 1.5 (r=.54). Serum nPNA and albumin were the only variables with statistically significant correlations with both mortality and 3 measures of hospitalization (H): total days of H (H(D)), total number of H (H(F)), and time to first H (H(T)). The case-mix adjusted correlations for serum albumin and nPNA versus total days (r(HD)) and frequency of H (r(HF)) were significant, and Cox analysis based on H(T) and time to death resulted in significant odds ratios for each standard deviation decrement for both serum albumin and nPNA. Serum total iron binding capacity (TIBC) and creatinine concentrations also correlated with some but not all outcome measures: lower serum concentrations of these values were each significantly associated with poor clinical outcomes.



Both nPNA and serum albumin predict prospective hospitalization and mortality in MHD patients with Kt/V > 1.20. Serum TIBC and creatinine concentrations appear to have association with some outcome measures as well. These data are consistent with the possibility that protein intake affects the clinical course even in the setting of an adequate to high hemodialysis dose. Studies based on randomized assignments to different protein intakes would be helpful to confirm these conclusions.

Field of study: Medicine
Clinicopathologic Characteristics and Therapeutic Outcomes of Primary Gastrointestinal Non-Hodgkin’s Lymphomas: 10 Years of Experience from a Single Center in Eastern Anatolia

The objective of this retrospective study was to report the clinicopathological data and the treatment outcomes in patients with primary gastrointestinal non-Hodgkin’s lymphoma.  We carried out a retrospective analysis of 41 patients (22 females, 18 males, median age 58 and range 18–90 years) who presented to our department with histopathological diagnosis of primary gastrointestinal non-Hodgkin’s lymphoma between 1995 and 2004.  The stomach was the most common extranodal site and was seen in 25 of 41 (61%) patients. At presentation 28 (68.3%) patients had gastrointestinal symptoms while 27 (65.9%) had B symptoms. The range of follow-up was 2–84 months with a median of 9 months. The overall survival rate was 3 years for 25 (61.2%) patients. The 3-year overall survival rate was better in patients with early-stage disease (stages I and II1) who were treated with surgery plus chemotherapy and/or radiation therapy than in those treated with chemotherapy alone (91.6 vs. 50%, p < 0.05). The disease had a significant impact on both the progression-free survival and overall survival rates.  Our data showed that surgical resection prior to postoperative chemotherapy was a better option for patients with early-stage disease with better patient survival.

Field of study: Medicine
DISCO: a low-energy multipurpose beamline at synchrotron SOLEIL.

DISCO, a novel low-energy beamline covering the spectrum range from the VUV to the visible, has received its first photons at the French synchrotron SOLEIL. In this article the DISCO design and concept of three experimental stations serving research communities in biology and chemistry are described. Emphasis has been put on high flux generation and preservation of polarization at variable energy resolutions. The three experiments include a completely new approach for microscopy and atmospheric pressure experiments as well as a ;classical' synchrotron radiation circular dichroism station. Preliminary tests of the optical design and technical concept have been made. Theoretical predictions of the beam have been compared with the first images produced by the first photons originating from the large-aperture bending-magnet source. Results are also reported concerning the cold finger used to absorb hard X-ray radiation in the central part of the synchrotron beam and to avoid heavy thermal load on the following optics. Wavelength selection using monochromators with different gratings for each experimental set-up as well as beam propagation and conditioning throughout the optical system are detailed. First photons comply very well with the theoretical calculations.

Field of study: Physics
Spontaneous Mental Contrasting and Selective Goal Pursuit

Mental contrasting a desired future with reality is a self-regulation strategy that fosters selective goal pursuit; people pursue goals for which they have high expectations of success, and let go of those for which they have low expectations. Indulging in the future, dwelling on the reality, or contrasting the reality with the future lead to indiscriminate goal pursuit. We developed a content analytic measure to observe spontaneous mental contrasting in people writing about an important wish (Study 1). Just like induced mental contrasting, spontaneous mental contrasting predicted selective goal pursuit measured by self-reported performance (Study 2) and observed performance (Study 3). The developed coding scheme opens the way to investigating situation, person, and cultural predictors of spontaneous mental contrasting.

Field of study: Psychology
Isotopically selective photoionization of calcium atoms

Three-stage selective photoionization of calcium atoms was investigated using cw dye lasers. Selective excitation was due to an intercombination transition 4s2 1S0→4s4p 3P1 (λ = 657.3 nm), additional excitation by a transition 4s4p 3P1→4s5s 3S1 (λ = 612.2 nm), followed by final ionization at λ = 488.0 nm from an argon laser. The photoion currents of different nuclides were determined using an MKh-7303 mass spectrometer. The ratios of the ion currents were used to find the separation coefficients a which were ~ 900 for 48Ca, ~ 1400 for 44Ca, and ~ 5500 for 42Ca.

Field of study: Engineering, Physics
Rachel M. May, Alejandro Schneider and Roberto González Arana, Caribbean Revolutions: Cold War Armed Movements (Cambridge and New York: Cambridge University Press, 2018), pp. x + 165, $24.99; £17.99, pb.

human rights; continental revolution or nationally-bound militancy). These minor criticisms should not hide the fact that Marchesi’s monograph constitutes a major contribution to a nascent, promising historiographical field. The author consolidates a rising but still marginal tendency in Latin American scholarship that breaks not only from nationally-centred narratives, but also from a transnational history of Latin America mainly written through its relations with the United States. In addition, and contrary to many cultural approaches to the Global 1960s, Marchesi always analyses the circulation of ideas in light of specific contexts. There is no doubt that Latin America’s Radical Left is already a benchmark for specialists of the Latin American Global 1960s. Let us hope that this book – and hopefully, the ones that will follow and appear in English translation – will also allow a geographical decentring of the currently dominant historiographical gaze on the Global 1960s.

Field of study: Political science