nils-herrmann/clean_scirepeval huggingface dataset:
Ultrasound assessment for grading structural tendon changes in supraspinatus tendinopathy: an inter rater reliability study
Venue: BMJ Open

To evaluate the inter rater reliability of measuring structural changes in the tendon of patients, clinically diagnosed with supraspinatus tendinopathy (cases) and healthy participants (controls) on ultrasound (US) images captured by standardised procedures.  A total of 40 participants (24 patients) were included for assessing inter rater reliability of measurements of fibrillar disruption, neovascularity, as well as the number and total length of calcifications and tendon thickness. Linear weighted k, intraclass correlation (ICC) SEM, limits of agreement (LOA) and minimal detectable change (MDC) were used to evaluate reliability. Results 'Moderate almost perfect' k was found for grading fibrillar disruption, neovascularity and number of calcifications (k 0.60 0.96) For total length of calcifications and tendon thickness, ICC was 'excellent' (0.85 0.90) with SEM(Agreement) ranging from 0.63 to 2.94 mm and MDC(group) ranging from 0.28 to 1.29 mm. In general, SEM, LOA and MDC showed larger variation for calcifications than for tendon thickness.  Inter rater reliability was moderate to almost perfect when a standardised procedure was applied for measuring structural changes on captured US images and movie sequences of relevance for patients with supraspinatus tendinopathy. Future studies should test intra rater and inter rater reliability of the method in vivo for use in clinical practice, in addition to validation against a gold standard, such as MRI.
Unconstrained Sleep Stage Estimation Based on Respiratory Dynamics and Body Movement.
Venue: Methods of information in medicine

The aim of this study is to establish a sleep monitoring method that can classify sleep into four stages in an unconstrained manner using a polyvinylidene fluoride (PVDF) sensor for continuous and accurate estimation of sleep stages.  The study participants consisted of 12 normal subjects and 13 obstructive sleep apnea (OSA) patients. The physiological signals of the subjects were unconstrainedly measured using the PVDF sensor during polysomnography. The respiration and body movement signals were extracted from the PVDF data. Rapid eye movement (REM) sleep was estimated based on the average rate and variability of the respiratory signal. Wakefulness was detected based on the body movement signal. Variability of the respiratory rate was chosen as an indicator for slow wave sleep (SWS) detection. Sleep was divided into four stages (wake, light, SWS, and REM) based on the detection results.  The performance of the method was assessed by comparing the results with a manual scoring by a sleep physician. In an epoch by epoch analysis, the method classified the sleep stages with an average accuracy of 70.9 and kappa statistics of 0.48. No significant differences were observed in the detection performance between the normal and OSA groups.  The developed system and methods can be applied to a home sleep monitoring system.
A CCaMK CYCLOPS DELLA Complex Activates Transcription of RAM1 to Regulate Arbuscule Branching
Venue: Current Biology

Intracellular arbuscular mycorrhiza symbiosis between plants and glomeromycotan fungi leads to formation of highly branched fungal arbuscules that release mineral nutrients to the plant host. Their development is regulated in plants by a mechanistically unresolved interplay between symbiosis, nutrient, and hormone (gibberellin) signaling. Using a positional cloning strategy and a retrotransposon insertion line, we identify two novel alleles of Lotus japonicus REDUCED ARBUSCULAR MYCORRHIZA1 (RAM1) encoding a GRAS protein. We confirm that RAM1 is a central regulator of arbuscule development: arbuscule branching is arrested in L. japonicus ram1 mutants, and ectopic expression of RAM1 activates genes critical for arbuscule development in the absence of fungal symbionts. Epistasis analysis places RAM1 downstream of CCaMK, CYCLOPS, and DELLA because ectopic expression of RAM1 restores arbuscule formation in cyclops mutants and in the presence of suppressive gibberellin. The corresponding proteins form a complex that activates RAM1 expression via binding of CYCLOPS to a cis element in the RAM1 promoter. We thus reveal a transcriptional cascade in arbuscule development that employs the promoter of RAM1 as integrator of symbiotic (transmitted via CCaMK and CYCLOPS) and hormonal (gibberellin) signals.
Growth of Shockley type stacking faults upon forward degradation in 4H SiC p i n diodes

The growth of Shockley type stacking faults in p i n diodes fabricated on the C face of 4H SiC during forward current operation was investigated using Berg Barrett X ray topography and photoluminescence imaging. After forward current experiment, Shockley type stacking faults were generated from very short portions of basal plane dislocations lower than the conversion points to threading edge dislocations in the epitaxial layer. The growth behavior of Shockley type stacking faults was discussed. Growth of stacking faults in the substrates was not observed.
Solid solution strengthening of hexagonal titanium alloys: Restoring forces and stacking faults calculated from first principles

The solid solution strengthening of a Ti was investigated in respect of dislocation nucleation and dissociation in all four active glide modes. A series of Ti+X alloys (X Al, Sn, V, Zr and O) was selected to analyze the impact of solute valence structure (Al, Sn p type elements, V, Zr d type elements) and lattice site (interstitial O) on the mechanisms responsible for variation of mechanical properties. The computational procedure relied on the generalized stacking fault energy (GSFE) concept combined with the nudged elastic band method that enables full atomic relaxation and determination of the true, minimum energy GSFE path. Additionally, various concentrations of solutes and their distance to the glide plane were considered as well. Our study revealed a strong, nonlinear influence of X position on GSFE and migration of O atoms during the crystal slip. These new phenomena allowed one to determine three solution strengthening mechanisms: (I) hindrance of prismatic dislocation emission and reconfiguration of 1/3 2 0> screw dislocation cores (p type solutes) (II) hindrance of prismatic dislocation emission (V) and SFE reduction in other modes (both d type solutes) and (III) suppression of dislocation nucleation in all modes caused by O. We found that the stacking faults formed by the single partial dislocations have a thickness of few atomic layers and exhibit a highly non uniform structure. Their ability to accommodate the lattice deformation introduced by solute elements greatly affects the stacking fault energies of the a Ti alloys.
Theoretical investigation of the formation of basal plane stacking faults in heavily nitrogen doped 4H SiC crystals

The formation of basal plane stacking faults in heavily nitrogen doped 4H SiC crystals was theoretically investigated. A novel theoretical model based on the so called quantum well action mechanism was proposed; the model considers several factors, which were overlooked in a previously proposed model, and provides a detailed explanation of the annealing induced formation of double layer Shockley type stacking faults in heavily nitrogen doped 4H SiC crystals. We further revised the model to consider the carrier distribution in the depletion regions adjacent to the stacking fault and successfully explained the shrinkage of stacking faults during annealing at even higher temperatures. The model also succeeded in accounting for the aluminum co doping effect in heavily nitrogen doped 4H SiC crystals, in that the stacking fault formation is suppressed when aluminum acceptors are co doped in the crystals.
Pulse electrosynthesis of novel wormlike gadolinium oxide nanostructure and its nanocomposite with conjugated electroactive polymer as a hybrid and high efficient electrode material for energy storage device.
Venue: Journal of colloid and interface science

An effective approach for increasing the life cycle of pure p type conductive polymers is combining conventional conductive polymers and nanomaterials to fabricate hybrid electrodes. In this paper, Gadolinium oxide (Gd2O3) has first been synthesized using pulse electrochemical approach. Hybrid POAP/Gd2O3 films have then been fabricated by POAP electropolymerization in the presence of Gd2O3 nanoparticles as active electrodes for electrochemical supercapacitors. Surface and electrochemical analyses have been used for characterization of Gd2O3 and POAP/Gd2O3 composite films. Different electrochemical methods including galvanostatic charge discharge experiments, cyclic voltammetry and electrochemical impedance spectroscopy have been applied to study the system performance. Specific capacitance, specific energy and specific power of the composite film are calculated 300F*g 1, 41.66Wh*kg 1 and 833.22W*kg 1 respectively. This work introduces new nanocomposite materials for electrochemical redox capacitors with such advantages as the ease of synthesis, high active surface area and stability in an aqueous electrolyte.
Poster Abstract: Edge Caches for Vision Applications
Venue: 2016 IEEE/ACM Symposium on Edge Computing (SEC)

One of the thrusts of mobile and pervasive computing is supporting vision based perception applications. Vision based applications, such as augmented reality, are those that help users augment their understanding of the physical world through the camera(s) on their mobile devices. Such applications need to provide a seamless experience and hence require minimal end to end latency. However, these applications cannot be executed entirely on the devices. The recognition algorithms that these applications utilize, such as feature extraction and matching, need intensive computation and access to "big data" such as large labeled image datasets, for them to be fast and accurate. Such data and computational resources are not available locally on the device. Hence, they rely on offloading intensive tasks to the cloud. The devices send captured images to the cloud, which then executes the recognition algorithms using its computational resources and access to big data. However, the heavy computation and the added communication latency still deter seamless interaction, which is desired for such applications. Thus, there is a need to accelerate the performance of vision based mobile applications. One suggested approach towards fulfilling this need has been to place more compute resources at the edge. We propose to efficiently utilize these edge servers, complement them with mobile edge clouds and vertically integrate mobile, edge and cloud, through dynamic edge caching to deliver low latency vision based perception applications.
A new type of solar system material recovered from Ordovician marine limestone
Venue: Nature communications

From mid Ordovician ~470 Myr old limestone >100 fossil L chondritic meteorites have been recovered, representing the markedly enhanced flux of meteorites to Earth following the breakup of the L chondrite parent body. Recently one anomalous meteorite, Osterplana 065 (Ost 65) was found in the same beds that yield L chondrites. The cosmic ray exposure age of Ost 65 shows that it may be a fragment of the impactor that broke up the L chondrite parent body. Here we show that in a chromium versus oxygen isotope plot Ost 65 falls outside all fields encompassing the known meteorite types. This may be the first documented example of an 'extinct' meteorite, that is, a meteorite type that does not fall on Earth today because its parent body has been consumed by collisions. The meteorites found on Earth today apparently do not give a full representation of the kind of bodies in the asteroid belt ~500 Myr ago.
Onset of main Phanerozoic marine radiation sparked by emerging Mid Ordovician icehouse
Venue: Scientific reports

The Great Ordovician Biodiversification Event (GOBE) was the most rapid and sustained increase in marine Phanerozoic biodiversity. What generated this biotic response across Palaeozoic seascapes is a matter of debate; several intrinsic and extrinsic drivers have been suggested. One is Ordovician climate, which in recent years has undergone a paradigm shift from a text book example of an extended greenhouse to an interval with transient cooling intervals at least during the Late Ordovician. Here, we show the first unambiguous evidence for a sudden Mid Ordovician icehouse, comparable in magnitude to the Quaternary glaciations. We further demonstrate the initiation of this icehouse to coincide with the onset of the GOBE. This finding is based on both abiotic and biotic proxies obtained from the most comprehensive geochemical and palaeobiological dataset yet collected through this interval. We argue that the icehouse conditions increased latitudinal and bathymetrical temperature and oxygen gradients initiating an Early Palaeozoic Great Ocean Conveyor Belt. This fuelled the GOBE, as upwelling zones created new ecospace for the primary producers. A subsequent rise in d13C ratios known as the Middle Darriwilian Isotopic Carbon Excursion (MDICE) may reflect a global response to increased bioproductivity encouraged by the onset of the GOBE.
Pandemic influenza and socioeconomic disparities: Lessons from 1918 Chicago
Venue: Proceedings of the National Academy of Sciences

The 1918 "Spanish" influenza pandemic holds a particular place in medical history; it wiped out an estimated ~1% of the global population, or ~20 50 million deaths worldwide, and earned the dubious honor of being coined the "mother of all pandemics" (1) Fortunately, important strides have been made in elucidating the emergence of novel pandemic influenza viruses and their impact on human populations since the 1918 pandemic. The field of archeo epidemiology has been particularly active in recent years, thanks to coordinated interdisciplinary efforts involving epidemiologists, virologists, demographers, and medical historians. Their work has paid off to unearth, digitize, and analyze archival disease records sitting in dusty old books, providing a careful description of the mortality and transmissibility patterns of the 1918 influenza pandemic in several areas of the world where little prior quantitative information existed (e.g. refs. 2| 5) In PNAS, Grantz et al. (6) contribute to the growing interest in applying modern analytical tools to epidemiological archives, through the lens of socioeconomic disparities affecting the 1918 influenza pandemic. The role of socioeconomic factors on influenza mortality and morbidity goes back to the early work of Robert Pearl in the years immediately following the 1918 pandemic (7) but has only regained traction among epidemiologists and sociologists in the last decade. In 2006, a seminal study revealed more than 30 fold variation in 1918 pandemic excess mortality rates across a sample of 20 countries, with socioeconomic factors explaining a significant fraction of the observed variation (2) In Latin America, pandemic excess mortality rates varied from 0.4 to 2.9% in national and province level data, a greater than sevenfold variation (4, 8, 9) In contrast, United States and European populations fared relatively well during the pandemic, despite intense disruption at the end of World War I (excess mortality rates of [1]1To whom correspondence should be addressed.  gchowell{at}gsu.edu.  #xref corresp 1 1
Using tropical optimization to solve minimax location problems with a rectilinear metric on the line

Methods of tropical (idempotent) mathematics are applied to the solution of minimax location problems under constraints on the feasible location region. A tropical optimization problem is first considered, formulated in terms of a general semifield with idempotent addition. To solve the optimization problem, a parameter is introduced to represent the minimum value of the objective function, and then the problem is reduced to a parametrized system of inequalities. The parameter is evaluated using existence conditions for solutions of the system, whereas the solutions of the system for the obtained value of the parameter are taken as the solutions of the initial optimization problem. Then, a minimax location problem is formulated to locate a single facility on a line segment in the plane with a rectilinear metric. When no constraints are imposed, this problem, which is also known as the Rawls problem or the messenger boy problem, has known geometric and algebraic solutions. For the location problems, where the location region is restricted to a line segment, a new solution is obtained, based on the representation of the problems in the form of the tropical optimization problem considered above. Explicit solutions of the problems for various positions of the line are given both in terms of tropical mathematics and in the standard form.
Distributive Processing by the Iron(II)/a Ketoglutarate Dependent Catalytic Domains of the TET Enzymes Is Consistent with Epigenetic Roles for Oxidized 5 Methylcytosine Bases.
Venue: Journal of the American Chemical Society

The ten eleven translocation (TET) proteins catalyze oxidation of 5 methylcytosine (5m)C) residues in nucleic acids to 5 hydroxymethylcytosine (5hm)C) 5 formylcytosine (5f)C) and 5 carboxycytosine (5ca)C) These nucleotide bases have been implicated as intermediates on the path to active demethylation, but recent reports have suggested that they might have specific regulatory roles in their own right. In this study, we present kinetic evidence showing that the catalytic domains (CDs) of TET2 and TET1 from mouse and their homologue from Naegleria gruberi, the full length protein NgTET1, are distributive in both chemical and physical senses, as they carry out successive oxidations of a single (5m)C and multiple (5m)C residues along a polymethylated DNA substrate. We present data showing that the enzyme neither retains (5hm)C/(5f)C intermediates of preceding oxidations nor slides along a DNA substrate (without releasing it) to process an adjacent (5m)C residue. These findings contradict a recent report by Crawford et al.  2016 138 730 claiming that oxidation of (5m)C by CD of mouse TET2 is chemically processive (iterative) We further elaborate that this distributive mechanism is maintained for TETs in two evolutionarily distant homologues and posit that this mode of function allows the introduction of (5m)C forms as epigenetic markers along the DNA.
Compact Frequency Reconfigurable Slot Antenna for Wireless Applications
Venue: IEEE Antennas and Wireless Propagation Letters

A compact frequency reconfigurable slot antenna for LTE (2.3 GHz) AMT fixed service (4.5 GHz) and WLAN (5.8 GHz) applications is proposed in this letter. A U shaped slot with short ends and an L shaped slot with open ends are etched in the ground plane to realize dual band operation. By inserting two p i n diodes inside the slots, easy reconfigurability of three frequency bands over a frequency ratio of 2.62:1 can be achieved. In order to reduce the cross polarization of the antenna, another L shaped slot is introduced symmetrically. Compared to the conventional reconfigurable slot antenna, the size of the antenna is reduced by 32.5% Simulated and measured results show that the antenna can switch between two single band modes (2.3 and 5.8 GHz) and two dual band modes (2.3/4.5 and 4.5/5.8 GHz) Also, stable radiation patterns are obtained.
Single nucleotide polymorphisms in the mitochondrial displacement loop and age at onset of epithelial ovarian cancer
Venue: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis

The accumulation of the single nucleotide polymorphisms (SNPs) in the mitochondrial displacement loop (D loop) has been reported in many types of cancers. And the association with the risk and prognosis of cancers also has been described extensively. In the present study, we investigated the association between the age at onset and SNPs in the D loop of mitochondria DNA (mtDNA) using a population based series of primary epithelial ovarian cancer (EOC) patients.  The D loop region of mtDNA samples from blood were obtained from 89 patients with primary EOC, who underwent surgery. The age at onset curves were calculated by Kaplan Meier method and compared by the log rank test.  The SNP sites of nucleotide 248, 524 and 16,304 alleles were identified for their association with age at onset by the log rank test. The age at onset of patients with the minor allele 248 G was lower than that of patients with 248 A. The same was seen for the rare allele 16,304 T genotype when compared with matched allele 16,304 C at the 16,304 site. But the age at onset of patients with the minor allele 524 C was higher than that of patients with frequent 524 deletions.  Genetic polymorphisms in the D loop are the predictive markers for age at onset in EOC patients. Accordingly, the analysis of genetic polymorphisms may help identify EOC patient subgroups at high risk of early onset.
Book Review: Digital Labour and Karl Marx

In this book, Fuchs sets out to elucidate Marx's theory of labour and exploitation within the capitalist mode of production and then to apply this theory in an analysis of the role of labour within the various stages of production that result in the delivery of digital media. He claims in particular that only such a theoretical perspective allows us to grasp (a) the way in which users of social media are being exploited to produce surplus value for the owners of services such as Facebook and (b) the need for a classic Marxist proletarian revolution within the field of social media to end this exploitation and replace it with what he calls 'a communications commons' Fuchs places his project within the renewed interest in Marxism inspired by the 2008 financial crisis and explicitly sees it as a continuation of the debate between Cultural Studies and The Political Economy of Communications. Certainly, the book, in its case studies of the labour process and the relations of production within the various stages of global production that underpin, within the International Division of Labour (IDL) our usage of digital devices and network services, serves as a useful reminder, to those with a more benign, idealist view of the digital information revolution, of the very real material costs involved and who bears them. A reminder unfortunately that cannot be reiterated often enough. However, one does not, I think, require the very narrow and dogmatic version of Marxist theory that Fuchs deploys to get this point. Much writing on the Left in response to the 2008 crisis has talked in terms of a return to Marxism. After the years in the wilderness of neo liberal hegemony, the rumbling of capitalist crisis is heard again, and now, perhaps, at last it can be claimed that 'our time has come' One more circumnavigation of the walls of capitalism blowing the trumpets of proletarian revolution and the gates to an unalienated paradise will open to us. The sense of anger and the widespread economic and social distress are, of course, very real. But it is the idea that we should go back to something with which I want to take issue. Particularly to a set of theories of both economy and polity designed for very different conditions. What is required is not a going back but a going beyond which takes into account the very real theoretical inadequacies of Marxism and the lessons learnt by political economists, and citizens at large, from analysing and experiencing 150 years of capitalist development and attempts at socialist transformation. Indeed, in my judgement, the sad irony is that both Marxism and neo liberalism suffer from the same failure, born of the same 19th century model of the world. Both systems of thought believe that the economy is a simple, monolithic system and that therefore there 612543 MCS0010.1177/0163443715612543Media, Culture SocietyBook Review research article2015