nils-herrmann/clean_scirepeval huggingface dataset:
A Novel Urine Exosome Gene Expression Assay to Predict High grade Prostate Cancer at Initial Biopsy.
Venue: JAMA oncology

Overdiagnosis and overtreatment of indolent prostate cancer (PCA) is a serious health issue in most developed countries. There is an unmet clinical need for noninvasive, easy to administer, diagnostic assays to help assess whether a prostate biopsy is warranted.  To determine the performance of a novel urine exosome gene expression assay (the ExoDx Prostate IntelliScore urine exosome assay) plus standard of care (SOC) (ie, prostate specific antigen [PSA] level, age, race, and family history) vs SOC alone for discriminating between Gleason score (GS)7 and GS6 and benign disease on initial biopsy.  In training, using reverse transcriptase polymerase chain reaction (PCR) we compared the urine exosome gene expression assay with biopsy outcomes in 499 patients with prostate specific antigen (PSA) levels of 2 to 20 ng/mL. The derived prognostic score was then validated in 1064 patients from 22 community practice and academic urology clinic sites in the United States. Eligible participants included PCA free men, 50 years or older, scheduled for an initial or repeated prostate needle biopsy due to suspicious digital rectal examination (DRE) findings and/or PSA levels (limit range, 2.0 20.0 ng/mL) MAIN OUTCOMES AND MEASURES Evaluate the assay using the area under receiver operating characteristic curve (AUC) in discrimination of GS7 or greater from GS6 and benign disease on initial biopsy.  In 255 men in the training target population (median age 62 years and median PSA level 5.0 ng/mL, and initial biopsy) the urine exosome gene expression assay plus SOC was associated with improved discrimination between GS7 or greater and GS6 and benign disease: AUC 0.77 (95% CI, 0.71 0.83) vs SOC AUC 0.66 (95% CI, 0.58 0.72) (P .001) Independent validation in 519 patients' urine exosome gene expression assay plus SOC AUC 0.73 (95% CI, 0.68 0.77) was superior to SOC AUC 0.63 (95% CI, 0.58 0.68) (P .001) Using a predefined cut point, 138 of 519 (27% biopsies would have been avoided, missing only 5% of patients with dominant pattern 4 high risk GS7 disease.  This urine exosome gene expression assay is a noninvasive, urinary 3 gene expression assay that discriminates high grade =GS7) from low grade (GS6) cancer and benign disease. In this study, the urine exosome gene expression assay was associated with improved identification of patients with higher grade prostate cancer among men with elevated PSA levels and could reduce the total number of unnecessary biopsies.
A Highly Sensitive and Quantitative Test Platform for Detection of NSCLC EGFR Mutations in Urine and Plasma
Venue: Journal of thoracic oncology official publication of the International Association for the Study of Lung Cancer

In approximately 60% of patients with NSCLC who are receiving EGFR tyrosine kinase inhibitors, resistance develops through the acquisition of EGFR T790M mutation. We aimed to demonstrate that a highly sensitive and quantitative next generation sequencing analysis of EGFR mutations from urine and plasma specimens is feasible.  Short footprint mutation enrichment next generation sequencing assays were used to interrogate EGFR activating mutations and the T790M resistance mutation in urine or plasma specimens from patients enrolled in TIGER X (NCT01526928) a phase 1/2 clinical study of rociletinib in previously treated patients with EGFR mutant positive advanced NSCLC.  Of 63 patients, 60 had evaluable tissue specimens. When the tissue result was used as a reference, the sensitivity of EGFR mutation detection in urine was 72% (34 of 47 specimens) for T790M, 75% (12 of 16) for L858R, and 67% (28 of 42) for exon 19 deletions. With specimens that met a recommended volume of 90 to 100 mL, the sensitivity was 93% (13 of 14 specimens) for T790M, 80% (four of five) for L858R, and 83% (10 of 12) for exon 19 deletions. A comparable sensitivity of EGFR mutation detection was observed in plasma: 93% (38 of 41 specimens) for T790M, 100% (17 of 17) for L858R, and 87% (34 of 39) for exon 19 deletions. Together, urine and plasma testing identified 12 additional T790M positive cases that were either undetectable or inadequate by tissue test. In nine patients monitored while receiving treatment with rociletinib, a rapid decrease in urine T790M levels was observed by day 21.  DNA derived from NSCLC tumors can be detected with high sensitivity in urine and plasma, enabling diagnostic detection and monitoring of therapeutic response from these noninvasive "liquid biopsy" samples.
Breast parenchymal patterns in processed versus raw digital mammograms: A large population study toward assessing differences in quantitative measures across image representations.
Venue: Medical physics

With raw digital mammograms (DMs) which retain the relationship with x ray attenuation of the breast tissue, not being routinely available, processed DMs are often the only viable means to acquire imaging measures. The authors investigate differences in quantitative measures of breast density and parenchymal texture, shown to have value in breast cancer risk assessment, between the two DM representations.  The authors report data from 8458 pairs of bilateral raw "FOR PROCESSING" and processed "FOR PRESENTATION" DMs acquired from 4278 women undergoing routine screening evaluation, collected with DM units from two different vendors. Breast dense tissue area and percent density (PD) as well as a range of quantitative descriptors of breast parenchymal texture (statistical, co occurrence, run length, and structural descriptors) were measured using previously validated, fully automated software. Feature measurements were compared using matched pairs Wilcoxon signed ranks test, correlation (r) and linear mixed effects (LME) models, where potential interactions with woman and system specific factors were also assessed. The authors also compared texture feature correlations with the established risk factors of the Gail lifetime risk score (rG) and breast PD (rPD) and evaluated the within woman intraclass feature correlation (ICC) a measure of bilateral breast tissue symmetry, in raw versus processed images.  All density measures and most of the texture features were strongly (r 0.6) or moderately (0.4 r 0.6) correlated between raw and processed images. However, measurements were significantly different between the two imaging formats (Wilcoxon signed ranks test, pw 0.05) The association between measurements varied across features and vendors, and was substantially modified by woman and system specific image acquisition factors, such as age, BMI, and mAs/kVp, respectively. The strongest correlation, combined with minimal LME model interactions, was observed for structural texture features. Overall, texture measures from either image representation were weakly associated with Gail lifetime risk 0.2 rG 0.2) weakly to moderately associated with breast PD 0.6 rPD 0.6) and had overall strong bilateral symmetry (ICC 0.6)  Differences in measures from processed versus raw DM depend highly on the feature, the DM vendor, and image acquisition settings, where structural features appear to be more robust across the different DM settings. The reported findings may serve as a reference in the design of future large scale studies on mammographic features and breast cancer risk assessment involving multiple DM representations.
Climate engineering by mimicking natural dust climate control: the iron salt aerosol method

Power stations, ships and air traffic are among the most potent greenhouse gas emitters and are primarily responsible for global warming. Iron salt aerosols (ISAs) composed partly of iron and chloride, exert a cooling effect on climate in several ways. This article aims firstly to examine all direct and indirect natural climate cooling mechanisms driven by ISA tropospheric aerosol particles, showing their cooperation and interaction within the different environmental compartments. Secondly, it looks at a proposal to enhance the cooling effects of ISA in order to reach the optimistic target of the Paris climate agreement to limit the global temperature increase between 1.5 and 2 degC. Mineral dust played an important role during the glacial periods; by using mineral dust as a natural analogue tool and by mimicking the same method used in nature, the proposed ISA method might be able to reduce and stop climate warming. The first estimations made in this article show that by doubling the current natural iron emissions by ISA into the troposphere, i.e. by about 0.3 Tg Fe yr 1, artificial ISA would enable the prevention or even reversal of global warming. The ISA method proposed integrates technical and economically feasible tools.
Does the "Silver Bullet" Lose its Shine Over the Time? Assessment of Loss of Lithium Response in a Preliminary Sample of Bipolar Disorder Outpatients
Venue: Clinical practice and epidemiology in mental health CP EMH

Though often perceived as a "silver bullet" treatment for bipolar disorder (BD) lithium has seldom reported to lose its efficacy over the time.  The aim of the present study was to assess cases of refractoriness toward restarted lithium in BD patients who failed to preserve maintenance.  Treatment trajectories associated with re instituted lithium following loss of achieved lithium based maintenance in BD were retrospectively reviewed for 37 BD I patients (median age 52 years; F:M=17:20 or 46% of the total) over an 8.1 month period on average.  In our sample only 4 cases (roughly 11% of the total, of whom F:M=2:2) developed refractoriness towards lithium after its discontinuation. Thirty three controls (F:M=15:18) maintained lithium response at the time of re institution. No statistically significant difference between cases and controls was observed with respect to a number of demographic and clinical features but for time spent before first trial ever with lithium in life (8.5 vs. 3 years; U=24.5, Z= 2.048, p=.041) and length of lithium discontinuation until new therapeutic attempt (5.5 vs. 2 years; U=8, Z= 2.927, p=.003) between cases vs. controls respectively. Tapering off of lithium was significantly faster among cases vs. controls (1 vs. 7 days; U=22, Z= 2.187) though both subgroups had worrisome high rates of poor adherence overall.  Although intrinsic limitations of the present preliminary assessment hamper the validity and generalizability of overall results, stating the clinical relevance of the topic further prospective research is warranted. The eventual occurrence of lithium refractoriness may indeed be associated with peculiar course trajectories and therapeutic outcomes ultimately urging the prescribing clinicians to put efforts in preserving maintenance of BD in the absence of any conclusive research insight on the matter.
An Accurate and Robust Artificial Marker Based on Cyclic Codes
Venue: IEEE Transactions on Pattern Analysis and Machine Intelligence

Artificial markers are successfully adopted to solve several vision tasks, ranging from tracking to calibration. While most designs share the same working principles, many specialized approaches exist to address specific application domains. Some are specially crafted to boost pose recovery accuracy. Others are made robust to occlusion or easy to detect with minimal computational resources. The sheer amount of approaches available in recent literature is indeed a statement to the fact that no silver bullet exists. Furthermore, this is also a hint to the level of scholarly interest that still characterizes this research topic. With this paper we try to add a novel option to the offer, by introducing a general purpose fiducial marker which exhibits many useful properties while being easy to implement and fast to detect. The key ideas underlying our approach are three. The first one is to exploit the projective invariance of conics to jointly find the marker and set a reading frame for it. Moreover, the tag identity is assessed by a redundant cyclic coded sequence implemented using the same circular features used for detection. Finally, the specific design and feature organization of the marker are well suited for several practical tasks, ranging from camera calibration to information payload delivery.
Pixel Recurrent Neural Networks
Venue: ICML

Modeling the distribution of natural images is a landmark problem in unsupervised learning. This task requires an image model that is at once expressive, tractable and scalable. We present a deep neural network that sequentially predicts the pixels in an image along the two spatial dimensions. Our method models the discrete probability of the raw pixel values and encodes the complete set of dependencies in the image. Architectural novelties include fast two dimensional recurrent layers and an effective use of residual connections in deep recurrent networks. We achieve log likelihood scores on natural images that are considerably better than the previous state of the art. Our main results also provide benchmarks on the diverse ImageNet dataset. Samples generated from the model appear crisp, varied and globally coherent.
Image denoising using the Gaussian curvature of the image surface

A number of high order variational models for image denoising have been proposed within the last few years. The main motivation behind these models is to fix problems such as the staircase effect and the loss of image contrast that the classical Rudin Osher Fatemi model [Leonid I. Rudin, Stanley Osher and Emad Fatemi, Nonlinear total variation based noise removal algorithms, Physica D 60 (1992) pp. 259 268] and others also based on the gradient of the image do have. In this work, we propose a new variational model for image denoising based on the Gaussian curvature of the image surface of a given image. We analytically study the proposed model to show why it preserves image contrast, recovers sharp edges, does not transform piecewise smooth functions into piecewise constant functions and is also able to preserve corners. In addition, we also provide two fast solvers for its numerical realization. Numerical experiments are shown to illustrate the good performance of the algorithms and test results.
Dynamic Computation Offloading for Mobile Edge Computing With Energy Harvesting Devices
Venue: IEEE Journal on Selected Areas in Communications

Mobile edge computing (MEC) is an emerging paradigm to meet the ever increasing computation demands from mobile applications. By offloading the computationally intensive workloads to the MEC server, the quality of computation experience, e.g. the execution latency, could be greatly improved. Nevertheless, as the on device battery capacities are limited, computation would be interrupted when the battery energy runs out. To provide satisfactory computation performance as well as achieving green computing, it is of significant importance to seek renewable energy sources to power mobile devices via energy harvesting (EH) technologies. In this paper, we will investigate a green MEC system with EH devices and develop an effective computation offloading strategy. The execution cost, which addresses both the execution latency and task failure, is adopted as the performance metric. A low complexity online algorithm is proposed, namely, the Lyapunov optimization based dynamic computation offloading algorithm, which jointly decides the offloading decision, the CPU cycle frequencies for mobile execution, and the transmit power for computation offloading. A unique advantage of this algorithm is that the decisions depend only on the current system state without requiring distribution information of the computation task request, wireless channel, and EH processes. The implementation of the algorithm only requires to solve a deterministic problem in each time slot, for which the optimal solution can be obtained either in closed form or by bisection search. Moreover, the proposed algorithm is shown to be asymptotically optimal via rigorous analysis. Sample simulation results shall be presented to corroborate the theoretical analysis as well as validate the effectiveness of the proposed algorithm.
Flexible and scalable particle in cell methods for massively parallel computations

Particle in cell methods couple mesh based methods for the solution of continuum mechanics problems, with the ability to advect and evolve particles. They have a long history and many applications in scientific computing. However, they have most often only been implemented for either sequential codes, or parallel codes with static meshes that are statically partitioned. In contrast, many mesh based codes today use adaptively changing, dynamically partitioned meshes, and can scale to thousands or tens of thousands of processors. Consequently, there is a need to revisit the data structures and algorithms necessary to use particle methods with modern, mesh based methods. Here we review commonly encountered requirements of particle in cell methods, and describe efficient ways to implement them in the context of large scale parallel finite element codes that use dynamically changing meshes. We also provide practical experience for how to address bottlenecks that impede the efficient implementation of these algorithms and demonstrate with numerical tests both that our algorithms can be implemented with optimal complexity and that they are suitable for very large scale, practical applications. We provide a reference implementation in ASPECT, an open source code for geodynamic mantle convection simulations built on the deal.II library.
Qualitative generalising in accounting research: concepts and strategies

This paper aims to identify and articulate concepts and approaches to qualitative generalisation that will offer qualitative accounting researchers avenues for enhancing and justifying the general applicability of their research findings and conclusions.  The study and arguments draw from multidisciplinary approaches to this issue. Its analysis and theorising is based on published qualitative research literatures from the fields of education, health sciences, sociology, information systems, management and marketing, as well as accounting.  The paper develops two overarching generalisation concepts for application by qualitative accounting researchers. These are built upon a number of qualitative generalisation concepts that have emerged in the multidisciplinary literatures. It also articulates strategies for enhancing the generalisability of qualitative accounting research findings.  The paper provides qualitative accounting researchers with understandings, arguments and justifications for the generalisability of their research and the related potential for wider accounting and societal contributions. It also articulates the key factors that impact on the quality of research generalisation that qualitative researchers can offer.  This paper presents the most comprehensively sourced and developed approach to the concepts, strategies and unique deliverables of qualitative generalising hitherto available in the accounting research literature.
Current status of dental English education in China

The teaching of dental English for undergraduate students plays an important role in dental education. Most dental schools or colleges have set up the course of dental English education in China. However, this course lacks of a unified educational plans, contents and goals based on actual situation of dental students, which does not fully achieve the teaching purpose. This study was aimed to explore the developmental direction of the course of dental English education through comparison among different dental schools or colleges in China, in order to find out the teaching mode of dental English education, and promote the teaching effect and cultivation of international dental talents.
[Current status of dental English education in China]
Venue: Shanghai kou qiang yi xue Shanghai journal of stomatology

The teaching of dental English for undergraduate students plays an important role in dental education. Most dental schools or colleges have set up the course of dental English education in China. However, this course lacks of a unified educational plans, contents and goals based on actual situation of dental students, which does not fully achieve the teaching purpose. This study was aimed to explore the developmental direction of the course of dental English education through comparison among different dental schools or colleges in China, in order to find out the teaching mode of dental English education, and promote the teaching effect and cultivation of international dental talents.
Unicorns cartoons: marketing sweet and creamy e juice to youth
Venue: Tobacco Control

In 2009, the Food and Drug Administration (FDA) banned characterising flavours for cigarettes with the exception of menthol and tobacco.1 New regulations, released in May 2016, deemed electronic cigarettes to be tobacco products under the FDA's regulatory  Nicotine containing liquid (e juice) used in e cigarettes is marketed in thousands of flavours. While the initial set of FDA rules did not address e juice flavours, future FDA action may do so. The agency's determination on whether or not e cigarettes should be subject to flavour regulations similar to those already in place for traditional combustible cigarettes will depend on evidence of differential appeal of these products to youth. Unicorns are mythological creatures which permeate popular culture, especially children's literature (eg, The Princess and the Unicorn) television (eg, My Little Pony) and games (eg, Rainbow Unicorn).3 A search for 'unicorn children's' in the Amazon.com book section returned 5223 items (15 May 2016) The number one item is titled: 'Sparkly the Unicorn: Cute Bedtime Story for Kids with a Lesson About Caring and Love' The purpose of this article is to describe unicorn themed flavoured e juice and their associated advertising messaging. In analysing over 12 000 e cigarette advertisements, we have encountered a remarkable assortment of unicorn themed e juice products4 ,5 (table 1) Most illustrations of unicorns show them as happy, playful and cuddly creatures. Unicorn e juice products most often are named after the creature's supposed secretions and excretions: milk, breath, tears, blood, puke, vomit, poop, piss, spew and jizz [sic\ (figures 1| 4) In advertisements, the e juice emanates from the appropriate bodily orifice of the unicorn in the form of an
DESIGN AND IMPLEMENTATION OF CONVEYOR LINE SPEED SYNCHRONISER FOR INDUSTRIAL CONTROL APPLICATIONS: A CASE STUDY OF CHAMPION'S BREWERIES PLC, UYO

This paper presents the mathematical modeling of a conveyor mechanism for control applications with Champion Breweries PLC as a case study. The electrical and mechanical sections were modeled separately and then integrated to obtain one composite system. Due to the lack of synchronisation of the conveyor line speed and the speed of action of the empty bottle inspection (EBI) and the full bottle inspection (FBI) units at Champion Breweries, there exists the problem of residue left over in bottles, cracked bottles on the conveyor line and the non detection of incorrect liquor level in bottles. Therefore a Proportional Integral Derivative(PID) controller was designed to act as a speed synchronizer in order to eliminate the above mentioned problems. http:/dx.doi.org/10.4314/njt.v35i3.21
Optical Coherence Tomography Angiography
Venue: Investigative ophthalmology visual science

Optical coherence tomography angiography (OCTA) is a noninvasive approach that can visualize blood vessels down to the capillary level. With the advent of high speed OCT and efficient algorithms, practical OCTA of ocular circulation is now available to ophthalmologists. Clinical investigations that used OCTA have increased exponentially in the past few years. This review will cover the history of OCTA and survey its most important clinical applications. The salient problems in the interpretation and analysis of OCTA are described, and recent advances are highlighted.