nils-herrmann/clean_scirepeval huggingface dataset:
Elements: In this month's issue.

I would like to draw your attention to some of the varied content within this month's issue of QJM.

The review article by Noble and colleagues provides a helpful overview of what is a complex topic that is nevertheless the focus of much current research and attention. The term “glycocalyx” (literally “sugary coat”) has many interpretations within the biomedical literature. In this context however it refers to the outer component of vascular cells. The glycoclayx is thought to provide protection against atherosclerotic disease. The mechanisms whereby it achieves this is discussed in detail. The multifaceted relationships between the glycocalyx, nitric oxide, hyperglycaemia and other risk factors are explored. The authors argue that dysfunction of the glycocalyx in arteries (for whatever cause) may be the first step in the atherothrombotic process. This may be a simplistic model and may provoke discussion.

Of the original research papers this month, several focus on evaluation of the outcomes of several clinical services. For example, there is another paper that assesses the impact of a medical admission unit (MAU) on clinical care. St Noble et al. describe the establishment of a MAU. This required substantial changes in consultant and junior doctor working patterns. A …

Field of study: Medicine
Effect of treatment with adsorbent resin on the volatile profile and physicochemical characteristics of clarified cashew apple juice

Increased preference for healthy and functional foods could be an opportunity to increase the consumption of clarified cashew apple juice. Given its level of fructose, glucose, and vitamin C, it can be used as a base in blends. However, its characteristic odor can interfere with the acceptance of these formulations, especially by consumers who are not familiar with cashew aroma. The aim of this study was to evaluate the effect of treatment with macroporous resins (FPA54, FPX66, XAD761, and XAD4) on the volatile profile and physicochemical characteristics of clarified cashew apple juice. After the treatment with the resins, the volatile profile was evaluated using solid-phase microextraction (SPME) and gas chromatography/mass spectrometry (GC/MS). The physicochemical analyses performed were: pH, soluble solids (oBrix), total titrable acidity, reducing sugars, and vitamin C. Gas chromatography analyses showed that XAD4 and FPX66 led to a reduction of the initial amount of volatile compounds to 14.05% and 15.72%, respectively. These two resins also did not affect the physicochemical characteristics of the clarified cashew apple juice.

Field of study: Agricultural and Food sciences
Computer Simulation of Electron Spin Resonance Spectra of Ge25S75and Ge30S70 Bulk Glasses

The electron spin resonance (ESR) spectra of bulk glasses of the chemical composition Ge25S75 and Ge30S70 were measured at liquid nitrogen temperature and subjected to computerized separation. The complex ESR spectra of both glasses were found to represent a superposition of three paramagnetic defect spectra, two with orthorhombic tensors g and one with the axial tensor g . The former two paramagnetic centers can be related to a two-atomic defect of the sulfur-sulfur type, the latter to a germanium-sulfur defect. The experimental results are in a good agreement with the non-dangling bond model of paramagnetic defects in Ge-S glasses.

Field of study: Chemistry
Representing the Internet as a succinct forest

Effective placement of resources used to support distributed services in the Internet depends on an accurate representation of Internet topology and routing. Representations of autonomous system (AS) topology derived solely from routing tables show only a subset of the connections that actually get used. However, in many cases, missing connections can be discovered by simple traceroutes. In addition, the differences between customer-to-provider links, peer-to-peer links, and sibling-to-sibling links are useful distinctions. We first apply a clustering algorithm to simplify the AS graph to an AS forest. Then we use two complementary mechanisms to improve accuracy of an AS forest as a predictor of packet paths. One mechanism uses recent insights that packets flow unidirectionally across customer-provider inter-AS links. Annotations are added to the AS forest to indicate links that appear to be peering versus those that appear to be customer-provider links. The other mechanism provides links between trees by remembering the most recently seen similar traceroute.

Field of study: Computer science
Automating linear accelerator quality assurance.

The purpose of this study was 2-fold. One purpose was to develop an automated, streamlined quality assurance (QA) program for use by multiple centers. The second purpose was to evaluate machine performance over time for multiple centers using linear accelerator (Linac) log files and electronic portal images. The authors sought to evaluate variations in Linac performance to establish as a reference for other centers.



The authors developed analytical software tools for a QA program using both log files and electronic portal imaging device (EPID) measurements. The first tool is a general analysis tool which can read and visually represent data in the log file. This tool, which can be used to automatically analyze patient treatment or QA log files, examines the files for Linac deviations which exceed thresholds. The second set of tools consists of a test suite of QA fields, a standard phantom, and software to collect information from the log files on deviations from the expected values. The test suite was designed to focus on the mechanical tests of the Linac to include jaw, MLC, and collimator positions during static, IMRT, and volumetric modulated arc therapy delivery. A consortium of eight institutions delivered the test suite at monthly or weekly intervals on each Linac using a standard phantom. The behavior of various components was analyzed for eight TrueBeam Linacs.



For the EPID and trajectory log file analysis, all observed deviations which exceeded established thresholds for Linac behavior resulted in a beam hold off. In the absence of an interlock-triggering event, the maximum observed log file deviations between the expected and actual component positions (such as MLC leaves) varied from less than 1% to 26% of published tolerance thresholds. The maximum and standard deviations of the variations due to gantry sag, collimator angle, jaw position, and MLC positions are presented. Gantry sag among Linacs was 0.336 ± 0.072 mm. The standard deviation in MLC position, as determined by EPID measurements, across the consortium was 0.33 mm for IMRT fields. With respect to the log files, the deviations between expected and actual positions for parameters were small (<0.12 mm) for all Linacs. Considering both log files and EPID measurements, all parameters were well within published tolerance values. Variations in collimator angle, MLC position, and gantry sag were also evaluated for all Linacs.



The performance of the TrueBeam Linac model was shown to be consistent based on automated analysis of trajectory log files and EPID images acquired during delivery of a standardized test suite. The results can be compared directly to tolerance thresholds. In addition, sharing of results from standard tests across institutions can facilitate the identification of QA process and Linac changes. These reference values are presented along with the standard deviation for common tests so that the test suite can be used by other centers to evaluate their Linac performance against those in this consortium.

Field of study: Medicine, Physics
Nonlinear Dynamic Characteristics of PZT/Polymer Gripper

A kind of PZT/polymer gripper is proposed in this paper and its nonlinear dynamic response in bounded noise is described. In this paper, a polymer piezoelectric material is applied in gripper to substitute the traditional PZT to improve the response range. Nonlinear differential items are introduced to interpret the hysteretic phenomena of the PZT/polymer piezoelectric composites material, and the nonlinear dynamic model of the PZT/polymer gripper in bounded noise is developed. The dynamic response of the system is obtained, and the bifurcation characteristics of the system are analyzed. The results of numerical simulation and experiments show that the stochastic noise intensity has important influence on the system's dynamical response, and the stochastic resonance phenomenon occurs with the stochastic noise intensity variety.

Field of study: Materials science
Investigation of diffused strip waveguides in glass

Methods for fabricating strip diffused waveguides in glass and for determining their parameters were developed. A study was made of the mode composition of the radiation in strip waveguides of different width and the results were used to determine the refractive index profile across the depth and width of the strip waveguides. It was found that metal ions diffused under a mask and this altered the dimensions of strip waveguides.

Field of study: Engineering, Physics
Isotopic composition and origin of lacustrine brines in the Arctic

Meromictic lakes in the Arctic Archipelago were analyzed to determine whether the isotope content of the water molecule might confirm their oceanic origin. The 25 m bottom layer of Lake Garrow, on Little Cornwallis Island, is filled with a homogeneous sodium chloride solution with 2.6 times the chloride concentration of seawater (52 g L−1). Its δ18O value is around −10‰ with respect to V-SMOW, and its δ2H is eight times the oxygen value (~ −85‰). In Lake Sophia on Cornwallis Island, the deep stratum (25 m thick) is less concentrated (35 g L−1 Cl−1) and shows slightly higher δ18O and δ2H values (−9 and −75‰, respectively).Chemocline and surficial waters result from mixing between bottom waters and meteoric waters. The chemical and isotopic signals are interpreted as evidence of diagenesis through subpermafrost or intrapermafrost freezing of aquifers once filled with seawater, at some time during postglacial emergence.

Field of study: Environmental science
A device for sampling the mud-water interface in eutrophic lakes and bogs for residue analysis

A tubular device has been developed making it possible to obtain layered samples of loosely aggregated, flocculent material from bogs or eutrophic lakes. The samples are up to 50 cm long and 15 cm in diameter. The sampler is free from protuberances and intact, layered samples can be taken. The tubular part of the sampler is about 85 em long, the walls of the lower 25‐cm portion harbouring a pneumatic closing mechanism which is controlled from above the water surface. An extendible handle for manipulating the sampler and for guiding it into place, is fastened to the upper end of the sampling tube. The performance and the operation of the sampler in the field are described.

Field of study: Agricultural and Food sciences
Paleomagnetism and U–Pb geochronology of the 2.17 Ga Biscotasing dyke swarm, Ontario, Canada: evidence for vertical-axis crustal rotation across the Kapuskasing Zone

UPb dates on baddeleyite yield ages of 2167.8 ± 2.2 and 2171.6 ± 1.2 Ma on two northeast-trending dykes west of the Kapuskasing Zone in Ontario, Canada. These ages identify the dykes as belonging to the Biscotasing dyke swarm east of the Kapuskasing Zone, which was previously dated at 2166.7 ± 1.4 Ma by UPb on baddeleyite and zircon. The new dates show that the Biscotasing swarm was emplaced over an area of at least 300 000 km2, much larger than hitherto suspected, and in a geologically short period of time of about 5 million years. A comparison of paleomagnetic data from Biscotasing and 2.45 Ga Matachewan dykes on either side of the Kapuskasing Zone suggests that the western half of the Superior Province has rotated about 10°20° counterclockwise relative to the eastern half across the Kapuskasing Zone. This movement may have been accompanied by rifting farther north which ultimately led to the Paleoproterozoic embayment, underlying Hudson Bay, that gives the Superior Province its characteristic butter...

Field of study: Environmental science
Valley-polarized metals and quantum anomalous Hall effect in silicene.

Silicene is a monolayer of silicon atoms forming a two-dimensional honeycomb lattice, which shares almost every remarkable property with graphene. The low-energy structure of silicene is described by Dirac electrons with relatively large spin-orbit interactions due to its buckled structure. The key observation is that the band structure is controllable by applying electric field to silicene. We explore the phase diagram of silicene together with exchange field M and by applying electric field E(z). A quantum anomalous Hall (QAH) insulator, valley polarized metal (VPM), marginal valley polarized metal (M-VPM), quantum spin Hall insulator, and band insulator appear. They are characterized by the Chern numbers and/or by the edge modes of a nanoribbon. It is intriguing that electrons have been moved from a conduction band at the K point to a valence band at the K' point for E(z) > 0 in the VPM. We find in the QAH phase that almost flat gapless edge modes emerge and that spins form a momentum-space Skyrmion to yield the Chern number. It is remarkable that a topological quantum phase transition can be induced simply by changing electric field in a single silicene sheet.

Field of study: Physics
PERIODIC TOPOLOGY OPTIMIZATION DESIGN FOR THERMAL CONDUCTIVE STRUCTURE USING ICM METHOD

To obtain the optimal topological configuration for thermal conductive microstructures of composite materials, a topological optimization model of the periodic structure is established by the Independent Continuous Mapping method. In this model, minimized weight is taken as the objective and thermal compliance is the constraint condition. The thermal compliance constraint is approximately formulated using a first-order Taylor expansion. The image-filtering method is implemented by a partial differential equation to eliminate checkerboard patterns and mesh-dependence problems. To satisfy the periodic constraint, the designable domain is divided into a certain number of identical subdomains and the contribution coefficients of thermal compliance are redistributed. Optimal topological configurations with different periodic numbers and different loading conditions are compared and analyzed. Numerical results verify the validity of the proposed topology optimization method in designing the microstructures of composite materials for thermal conduction.

Field of study: Engineering
Three-dimensional atomic structure of a catalytic subunit mutant of human protein kinase CK2.

The three-dimensional crystal structure of the triple-point mutant of the catalytic subunit of human protein kinase CK2alpha has been determined at 2.4 A resolution. Microcrystals of mutant CK2 catalytic subunit were obtained by a protein-crystallization method based on thin-film nanotechnology. These microcrystals (of about 20 micro m in diameter) were used for diffraction data collection by means of the microfocus beamline at the ESRF synchrotron. A comparison between the human protein kinase CK2alpha and the corresponding enzyme from a lower organism (Zea mays) is made.

Field of study: Chemistry
Study on the extraction technology of polysaccharide from hawthorn leaves

Technology on the extraction and decolorization of polysaccharide from hawthorn leaves were studied in the paper.The optimum conditions were obtained through single factor and orthogonal experiments.The results showed the optimum extraction condition is that hawthorn leaves,of which the ratio to liquids is 1:35,was extracted at 90 ℃ for 3 h,and the water-soluble saccharide yields 6.47%.No absorption of nucleic acid and proteins were found in UV spectra,indicating nearly no presence of the above impurities in product.

Field of study: Agricultural and Food sciences
High Resolution Photofission Measuremfnts Using Proton Capture Gamma Rays

High intensity proton beams from the Dynamitron at Brooklyn College are used to generate monochromatic gamma rays from known (p, r) resonances in various nuclei. The gamma rays, whose energy varies continuously as a function of the angle with the proton beam, are used in turn to measure photofission cross sections in 238U and 232Th. The number of suitable (p, r) resonances is sufficient to cover the 5 - 13 MeV range of excitation energy with an average step of ~ 100 keV. For a resonance of average strength the yield is 103 photons per ¿A of protons on target. The energy spread is typically 20 - 40 keV and a gamma ray energy resolution of 200 eV can easily be reached. This resolution is adequate for investigating structure in the photofission cross sections resulting from class II states in the second well of the fission barrier.

Field of study: Physics
Pretreatment with insulin enhances anticancer functions of 5-fluorouracil in human esophageal and colonic cancer cells

To investigate the effects of insulin on enhancing 5-fluorouracil (5-FU) anti-cancer functions and its mechanisms in the human esophageal cancer cell line (Eca 109) and human colonic cancer cell line (Ls-174-t).Methods:The effect of insulin/5-FU combination treatment on the growth of Eca 109 and Ls-174-t cells was evaluated by 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl-tetrazolium bromide (MTT) assay. After insulin treatment or insulin/5-FU treatment, cell cycle distribution of both cell lines was analyzed by flow cytometry. Western blot assay was used to assess the expression of caspase-3 and thymidylate synthase (TS). Apoptosis was detected by flow cytometry, DNA fragmentation assay, and terminal transferase dUTP nick end labeling assay (TUNEL). Moreover, the changes of 5-FU uptake after insulin pretreatment were detected by HPLC assay and Western blot analysis.We found that insulin enhanced the inhibitory effect of 5-FU on cell proliferation when Eca 109 cells and Ls-174-t cells were pretreated with insulin for the appropriate time. Insulin increased the cell number of the S phase and the uptake of 5-FU. Insulin/5-FU treatment enhanced apoptosis of tumor cells and upregulated the expression of cleaved caspase-3 compared with 5-FU treatment. Moreover, insulin/5-FU treatment induced the changes of free TS and the TS ternary complex level compared with 5-FU treatment in Eca 109 and Ls-174-t cells.These data suggest that insulin enhances anticancer functions of 5-FU when it is treated before 5-FU for the appropriate time in human esophageal and colonic cancer cell lines.

Field of study: Biology, Chemistry, Medicine
Terrestrial flatworm (Platyhelminthes: Tricladida: Terricola) diversity versus man-induced disturbance in an ombrophilous forest in southern Brazil

Terrestrial flatworms, or Terricola, are sensitive to environmentalchanges and therefore might be excellent indicators of the conservation statusof natural habitats. The present study aimed to answer two main questions: (1)is terrestrial planarian diversity affected by human disturbances, and (2) isthere any species or group of species that indicates such disturbance? The studysite, National Forest of São Francisco de Paula, Brazil, was originallycovered by a mixed ombrophilous forest, but successive reforestations andselective logging have modified the original landscape. We studied Terricoladiversity in the four main habitats in the study area: mixed ombrophilous forest(NA), ombrophilous forest with selective Araucariaangustifolia logging (N), A. angustifoliareforestation (A), and reforestation of Pinus elliottii(P). According to an increasing degree of disturbance, the habitats might beordered as follows: (NA)<(N)<(A)<(P). We conducted 24 surveys in eachhabitat over a period of 1 year. Our results indicate that: (1)Terricola diversity is inversely related to the degree of habitat disturbance;(2) there are species (Geoplana franciscana,Geoplana sp. 5, and possibly Geoplanidae 3 andNotogynaphallia guaiana) that prefer habitats located onthe extreme right along the main axis of a detrended correspondence analysisordination and therefore can be considered as indicators of well preserved,natural habitats. On the other hand there are species(Xerapoa sp. 1, Choeradoplanaiheringi, G. marginata sensu Marcus andGeoplana sp. 2) preferring more disturbed habitats, whichmay form biological indicators of such disturbances.

Field of study: Environmental science
Bootstrapping a time series model: some empirical results

The bootstrap is a methodology for estimating standard errors. The idea is to use a Monte Carlo simulation experiment based on a nonparametric estimate of the error distribution. The main objective of this article is to demonstrate the use of the bootstrap to attach standard errors to coefficient estimates in a second-order autoregressive model fitted by least squares and maximum likelihood estimation. Additionally, a comparison of the bootstrap and the conventional methodology is made. As it turns out, the conventional asymptotic formulae (both the least squares and maximum likelihood estimates) for estimating standard errors appear to overestimate the true standard errors. But there are two problems:i. The first two observations y1 and y2 have been fixed, and ii. The residuals have not been inflated. After these two factors are considered in the trial and bootstrap experiment, both the conventional maximum likelihood and bootstrap estimates of the standard errors appear to be performing quite well.

Field of study: Mathematics
The Technology Toolbelt for Teaching

Publisher’s Description: Instructors are pressured to integrate technology into their traditional or online instruction. This book offers a hands-on resource that shows how to integrate technology into lessons and offers information about common technologies, categorizing by groups, and explains the purposes they serve pedagogically as well as how they can be most effectively used in online or face-to-face classrooms. In addition to examples, each chapter will feature a decision making matrix to help instructors decide on whether or not a tool is really needed based on curriculum objectives or a specific organizational or curricular problem.

Field of study: Education
Improving TCP performance over wired-wireless networks

Today there is a growing demand for Internet services over WLAN hotspots. Majority of the Internet services today are based on TCP. However, TCP is not well-suited for heterogeneous networks consisting of wired and wireless networks. Losses in wireless network, which are quite frequent, are often misinterpreted by the TCP sender as loss due to congestion, which leads to poor performance of TCP. Hence, it is important to shield the TCP sender from wireless error. In this paper, we propose an improved method for identifying cases of wireless losses and tackling the loss at the local link level through MAC layer retransmissions. We then evaluate the effect of MAC layer retransmissions on the performance of TCP both analytically and empirically. Our empirical results show that significant improvement in TCP performance is possible through MAC layer retransmission.

Field of study: Computer science