nils-herrmann/clean_scirepeval huggingface dataset:
Distinguishable Prognostic Signatures of Left- and Right-Sided Colon Cancer: a Study Based on Sequencing Data

Left- and right-sided colon cancers are considered to be two different diseases and have altered outcomes. However, specific molecules to predict the prognosis of left- and right-sided colon cancers are currently lacking.  Expression profiling of colon cancer were downloaded from The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) of left- and right-sided colon cancers were compared by DESeq analysis. The prognostic values of DEGs were assessed by univariate and multivariate Cox regression. Prognostic index models of two side colon cancers were conducted with prognostic values genes, respectively. Interaction of DEGs was then analyzed by the protein-protein interaction (PPI). Different biology function of two sides of colon cancer was assessed by Gene Set Enrichment Analysis (GSEA).  A total of 167 DEGs were identified between left- and right-sided colon cancers based on TCGA data. Using univariate COX regression analysis, five genes (PHACTR3, CKMT2, CYP2W1, ERFE, HOXC4) were related to overall survival in left-sided, and eight distinguishable genes (EREG, ERFE, HOXC6, SLC22A31, TFF1, GFI1, ZG16, RASL10B) in right-sided. Further, left-sided prognostic model was established with PHACTR3 and CKMT2 (HR=2.040; 95%CI=1.004-4.145; P=0.049). Distinguishable prognostic signature for right-sided colon cancer was established based on EREG, ERFE, GFI1, and RASL10B (HR=3.530; 95%CI: 1.934-6.444; P< 0.001) in multivariate analysis. PPI analysis of 167 DEGs showed that CCL5, GNG4, GNLY, GZMH, DRD2, and FASLG genes were at the core of interaction network. In GSEA function analysis, four pathways, including antigen processing and presentation, natural killer cell mediated cytotoxicity, intestinal immune network for Iga production, and type I diabetes mellitus, were significantly enriched in the DEGs of the right-sided colon cancer.  This study constructs a panel of potential prognostic model of left- and right-sided colon cancers, respectively. We also provide molecular biological alterations between left- and right-sided colon cancers.

Field of study: Biology, Chemistry
Croatian Black Hole School 2010 lecture notes on IMBHs in GCs

Black holes are fascinating objects. As a class of solutions to the Einstein equations they have been studied a great deal, yielding a wealth of theoretical results. But do they really exist? What do astronomers really mean when they claim to have observational evidence of their existence? To answer these questions, I will focus on a particular range of black-hole masses, approximately from 100 to 10000 solar masses. Black holes of this size are named Intermediate Mass Black Holes (IMBHs) and their existence is still heavily disputed, so they will be perfect for illustrating the observational challenges faced by a black hole hunter

Field of study: Physics
Study of Homologous Autoimplantation Therapy for Treatment of Multiple Warts in Patients Attending the Dermatology out Patient Department

Warts are benign tumours that commonly involve skin and other epithelial tissues. There is no single treatment modality that is 100% effective. In multiple warts, especially on face, palms, and soles destructive procedure are inappropriate and impractical. Homologous autoimplantation is a simple technique, which helps in inducing cell mediated response, causing clearance of warts.  To evaluate the effect of homologous autoimplantation therapy in treatment of multiple warts. To study the untoward effects of this treatment.  A total of 49 patients of viral warts were included in study. Homologous autoimplantation of wart was done and regular follow up was done to see the result.  Out of 49 patients, in 24 patients there was good response, 14 showed moderate response, 5 showed poor response and in 6 patients there was no response.  Homologous autoimplantation is an easy, minimally invasive technique which clears multiple, recurrent and recalcitrant warts.

Field of study: Medicine
A comprehensive simulation analysis of LTE Discontinuous Reception (DRX)

In an LTE cell, Discontinuous Reception (DRX) allows the central base station to configure User Equipments for periodic wake/sleep cycles, so as to save energy. DRX operations depend on several parameters, which can be tuned to achieve optimal performance with different traffic profiles (i.e., CBR vs. bursty, periodic vs. sporadic, etc.). This work investigates how to configure these parameters and explores the trade-off between power saving, on one side, and per-user QoS, on the other. Unlike previous work, chiefly based on analytical models neglecting key aspects of LTE, our evaluation is carried out via simulation. We use a fully-fledged packet simulator, which includes models of all the protocol stack, the applications and the relevant QoS metrics, and employ factorial analysis to assess the impact of the many simulation factors in a statistically rigorous way. This allows us to analyze a wider spectrum of scenarios, assessing the interplay of the LTE mechanisms and DRX, and to derive configuration guidelines.

Field of study: Computer science
Screening and characterisation of gamma-aminobutyric acid (GABA) producing lactic acid bacteria isolated from Thai fermented fish (Plaa-som) in Nong Khai and its application in Thai fermented vegetables (Som-pak)

Gamma-aminobutyric acid (GABA) is a non-protein amino acid produced through the decarboxylation of glutamate by glutamate decarboxylase and wildly distributes among animals, plants and microorganisms (Ueno, 2000). GABA possesses well-known beneficial bioactivities such as neurotransmission, the induction of hypertension and a tranquilising effect (Pearl et al., 2006). On addition, it can stimulate immune cells (Dh et al., 2003) and is involved in the treatment of sleeplessness, depression and autonomic disorders (Dkada et al., 2000) as well as the improved prevention of diabetes (Hagiwara et al., 2004). This results in increasing commercial demand and extensive study to synthesis GABA in large amounts (Choi et al., 2006; Plokhov et al., 2000). However, the direct addition of GABA to food is considered unsafe and unnatural, while the utilisation of GABA-rich foods produced by natural techniques is more favourable (Dhakal et al., 2012). Many microorganisms are able to produce GABA, including bacteria, fungi and yeast. Among them, lactic acid bacteria (LAB) have been given more attention in research because of their utilisation in the food industry and the fact they are generally regarded as safe (GRAS) and known as probiotic. The production of GABA by LAB in fermented products can provide alternative, naturally fermented health products.

Field of study: Agricultural and Food sciences
Quantitative Determination of Sequence-specific Nucleic Acid Based on Fluorescent Labeled DNA Probe and Dye SYBR Green I

A synchronous fluorescence spectral method was developed for the quantitative detection of sequence-specific DNA.Graphene oxide was used to quench the fluorescence of the dyes.When the target DNA was added,the fluorescences of the two dyes were recovered due to the formed DNA duplex was far away from graphene oxide.Under the optimum conditions,the linear range was 1×10-10-2×10-9 mol/L,the calibration curve was y=63.388x+9.3862,R2=0.9954.The detection limit of 85 pmol/L was estimated with 3σ(where σ was the relative standard deviation of a blank solution,n=11).This method has good sensitivity,selectivity and accuracy.

Field of study: Chemistry
Mobility particle size spectrometers: harmonization of technical standards and data structure to facilitate high quality long-term observations of atmospheric particle number size distributions

Mobility particle size spectrometers often referred to as DMPS (Differential Mobility Particle Sizers) or SMPS (Scanning Mobility Particle Sizers) have found a wide range of applications in atmospheric aerosol research. However, comparability of measurements conducted world-wide is hampered by lack of generally accepted technical standards and guidelines with respect to the instrumental set-up, measurement mode, data evaluation as well as quality control. Technical standards were developed for a minimum requirement of mobility size spectrometry to perform long-term atmospheric aerosol measurements. Technical recommendations include continuous monitoring of flow rates, temperature, pressure, and relative humidity for the sheath and sample air in the differential mobility analyzer. We compared commercial and custom-made inversion routines to calculate the particle number size distributions from the measured electrical mobility distribution. All inversion routines are comparable within few per cent uncertainty for a given set of raw data. Furthermore, this work summarizes the results from several instrument intercomparison workshops conducted within the European infrastructure project EUSAAR (European Supersites for Atmospheric Aerosol Research) and ACTRIS (Aerosols, Clouds, and Trace gases Research InfraStructure Network) to determine present uncertainties especially of custom-built mobility particle size spectrometers. Under controlled laboratory conditions, the particle number size distributions from 20 to 200 nm determined by mobility particle size spectrometers of different design are within an uncertainty range of around ±10% after correcting internal particle losses, while below and above this size range the discrepancies increased. For particles larger than 200 nm, the uncertainty range increased to 30%, which could not be explained. The network reference mobility spectrometers with identical design agreed within ±4% in the peak particle number concentration when all settings were done carefully. The consistency of these reference instruments to the total particle number concentration was demonstrated to be less than 5%. Additionally, a new data structure for particle number size distributions was introduced to store and disseminate the data at EMEP (European Monitoring and Evaluation Program). This structure contains three levels: raw data, processed data, and final particle size distributions. Importantly, we recommend reporting raw measurements including all relevant instrument parameters as well as a complete documentation on all data transformation and correction steps. These technical and data structure standards aim to enhance the quality of long-term size distribution measurements, their comparability between different networks and sites, and their transparency and traceability back to raw data.

Field of study: Environmental science
Conjunctive use of spectral gamma-ray logs and clay mineralogy in defining late Jurassic–early Cretaceous palaeoclimate change (Dorset, U.K.)

Detrital clay mineralogy is controlled by weathered source rock, climate, transport and deposition that in turn influence the spectral gamma-ray (SGR) response of resultant sediments. Whilst a palaeoclimate signal in clay mineralogy has been established in some ancient successions, the SGR response remains contentious, largely because the data sets have yet to be collected at the same or appropriate vertical scales to allow comparison. In addition, the influence of organic matter on SGR is not always considered. Here, we present clay mineralogical, total organic carbon (TOC) and SGR analyses from the late Jurassic and early Cretaceous of the Wessex Basin, a period of previously documented palaeoclimate change. The aim of this paper is to estimate the sensitivity of SGR as palaeoclimatic tool, SGR and clay mineral data having been collected at the same sample points, making this one of the most rigorous comparison of clay mineral and SGR to date. Overall, the correlation between high thorium/potassium or thorium/uranium and kaolinite associated with a well-established palaeoclimate change shows that elevated thorium may be used as a proxy for humid palaeoweathering, as suggested by few previous studies.

Field of study: Environmental science, Geography
Uniform Deviation Bounds for Unbounded Loss Functions like k-Means

Uniform deviation bounds limit the difference between a model's expected loss and its loss on an empirical sample uniformly for all models in a learning problem. As such, they are a critical component to empirical risk minimization. In this paper, we provide a novel framework to obtain uniform deviation bounds for loss functions which are *unbounded*. In our main application, this allows us to obtain bounds for $k$-Means clustering under weak assumptions on the underlying distribution. If the fourth moment is bounded, we prove a rate of $\mathcal{O}\left(m^{-\frac12}\right)$ compared to the previously known $\mathcal{O}\left(m^{-\frac14}\right)$ rate. Furthermore, we show that the rate also depends on the kurtosis - the normalized fourth moment which measures the "tailedness" of a distribution. We further provide improved rates under progressively stronger assumptions, namely, bounded higher moments, subgaussianity and bounded support.

Field of study: Computer science
Modified maximum likelihood estimation

The problems raised by Chan (1982) of modified maximum likelihood estimation (MMLE) are considered. Using sample moments to reduce the number of parameters in the likelihood function of a statistical model under certain kind of reparametrization, we obtained the MMLE estimates by locating an optimal solution in the reduced parameter space. Conditions under which the MMLE gives consistent and asymptotically normal estimators areconsidered. For symmetric location–scale families, the MMLE for the shape parameter is asymptotically efficient. We also examine an example of twoparameter Weibull distribution on failure times data.

Field of study: Mathematics
The optimization study of α-amylase activity based on central composite design-response surface methodology by dinitrosalicylic acid method.

The optimum conditions of an α-amylase activity were experimentally investigated in details comparing with those of using a response surface methodology (RSM). Its optimum activity was achieved with 0.5 concentration unit of α-amylase and 1.0% (w/v) starch concentration in phosphate buffer solution pH 6.9 at 37°C for 10 min. The α-amylase activity was monitored by dinitrosalicylic acid method based on the measurement of maltose. The enzymatic activity was then statistically optimized using RSM, alternatively to focus on the effects of pH buffer solution, incubation temperature and incubation time on the yield of maltose. A quadratic regression model that related the yield of maltose concentration (response) to three basic factors was developed using Design-Expert software. Regression analysis revealed that the maximum concentration of maltose (0.915 mg/mL) could be reached with the buffer solution pH 7.3 at 39°C for 10 min. The high value of the adjusted R-square of the regression (0.9255) also demonstrates the regression equation providing a good model to fit the data obtained.

Field of study: Agricultural and Food sciences
A simple polarization calibrator.

The theory, design, and performance of a simple polarization calibrator based upon the polarization of specularly reflected light are presented and discussed. A formula is derived for the Rubenson degree of polarization of specularly reflected light in terms of the angle of incidence and the refractive index (real) of the material of the reflector. Criteria are presented for the design of an optimal diaphragm to minimize the depolarizing effects of light that has undergone a single internal reflection inside the body of the reflector.

Field of study: Physics
Impact of Research Training Environment and Holland Personality Type: A 15-Year Follow-Up of Research Productivity.

Ratings of the research training environment (RTE) and Holland personality type from 325 counseling psychology students who participated in G. M. Royalty, C. J. Gelso, B. Mallinckrodt, and K. Garrett’s (1986) study were examined as predictors of the students’ research productivity 15 years later. Graduates’ research productivity was determined by a search of the PsycLIT database. Results indicated that 2 specific RTE elements were related to productivity for men (faculty modeling and science as a partly social experience) together with the Interpersonal cluster of elements and the total RTE. Only 1 RTE element was related to productivity for women (untying statistics from research). Investigative Holland type was related to productivity for the combined sample of men and women. At a program level, Interpersonal and Instructional RTE ingredients distinguished programs whose graduates had sustained low, moderate, or high levels of research productivity. An important goal of psychology programs that ascribe to the scientist–practitioner training model is to produce doctoral graduates who are interested in research as well as practice and who are able to integrate science and practice into a body of skills, knowledge, and professional attitudes that is greater than the sum of these two parts (Belar, 2000). Gelso and Fretz (2001) suggested that successful scientist–practitioner training is manifested at three ordinal levels: (a) the ability to critically review research produced by others; (b) the ability to apply the rigorous logic of the scientific method to practice activities such as diagnosis, treatment planning, and evaluating the effectiveness of one’s work; and (c) at the highest level, the ability to actually produce scholarly work. Thus, whether the outcome of training is defined in the most demanding terms of producing original scholarship or less rigorously in terms of critical thinking skills, all three levels involve an interest in research and positive attitude toward scholarly activity.

Field of study: Psychology
Quality Control Measures of the Heavy Section Ductile Iron Casting

Since heavy section ductile iron casting is easy to suffer from these defects such as the nodular graphite coarsening, reduction of the nodular graphite, graphite floating, deformation of nodular graphite which leads to engender exploded graphite and chunk graphite, itd production technology is a recognized as a troublesome problem in the field of casting industry. Combined with current production status of heavy section ductile iron castingsat home and abroad, a series of quality control measures is summarized in this paper, forexample, shortening cooling time, strictly controlling composition, adding the trace elements Bi and Sb, using proper nodularizer and inoculant.In the process of production, the heavy sectionductile iron casting could be obtained with good external and internal quality by adopting these quality control measures.

Field of study: Materials science
Social and Dimensional Comparisons in the Formation of German Students’ Language Self-Concepts

This study extended the internal/external reference model to multiple languages including students’ language of instruction, first foreign language, and second foreign language. We examined whether social and dimensional comparisons play similar roles in the formation of students’ self-concept related to different languages and whether dimensional comparisons result in contrast or assimilation effects. All students had German as the language of instruction and English as the first foreign language. Students were divided into a subsample (N = 487) learning French as a second foreign language and a subsample (N = 481) learning Latin. Invariance tests demonstrated that the achievement–self-concept relations were similar across the subsamples, but interesting group differences became apparent when analyzing the French and Latin subsamples separately.

Field of study: Education
Britain Colonized: Hollywood’s Appropriation of British Literature (review)

frame and trajectory: both proved casualties of their liberal foundations" (138). This statement also serves as the conclusion of the study since what follows is, in the author's own words, "more coda than conclusion" (141): a survey of contemporary British novels that use the estate novel formula to represent the missed opportunities of the postwar settlement era in British society. The section includes brief but thought-provoking discussions of Angus Wilson's Setting the World on Fire, Muriel Spark's The Girls of Slender Means, Ian McEwan's Atonement, and Kazuo Ishiguro's The Remains of the Day that could form the basis for further study on the subject. Looking at this last section, if any conclusion is to be drawn from the book, it should be that late modernist writers, who belonged mostly to upper middle classes, were, at best, uncomfortable with the idea of a more democratic distribution of wealth that formed the basis of the postwar settlement in Britain. Therefore, MacKay concludes, the "attack on the humane liberalism of 'the British cultural elite', the intellectual aristocracy of late modernism, found its political corollary in Thatcherite ideology, which welcomed with open arms both its philistinism and its apportioning of blame for industrial decline to the idiocies of the progressively minded" (155). This is a reasonable conclusion; however, MacKay does little to familiarize the reader with the cultural atmosphere of postwar settlement or the ensuing era of Thatcherite regime. MacKay's assumption that the reader is already familiar with this historical context is yet another proof that this book is a particularly valuable addition to the historical study of British culture and the Second World War, but its contribution to literary scholarship is limited: while it has a promising start and shows occasional signs of brilliance, these are not often enough to sustain the interest of the reader looking for more than the historicist approach MacKay employs.

Field of study: Art
A developmental dissociation of context and GABA effects on extinguished fear in rats.

Although extinction has attracted considerable attention in recent years, there has been very little empirical work on extinction during development. Using Pavlovian fear conditioning, the authors provide evidence for developmental differences in extinction. Specifically, Postnatal Day (PND) 23 rats exhibited recovery of an extinguished freezing response to an auditory conditioned stimulus when tested in a context different from that in which extinction occurred (i.e., renewal) or when injected with the gamma-amino butyric acid (GABA) inverse agonist FG7142 prior to test. In contrast, PND 16 rats failed to exhibit either of these effects, although a subsequent experiment demonstrated that FG7142 alleviated spontaneous forgetting in PND 16 rats. Taken together, it appears that there are fundamental differences in the processes involved in extinction across development.

Field of study: Biology, Psychology