bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chiral Surface Characterisation and Reactivity Toward H–D Exchange of a Curved Platinum Crystal
Authors: Roorda Tycho , Auras Sabine V. , Juurlink Ludo B. F. 
Published: October 2020

AbstractUnderstanding heterogeneous catalysis at the atomic level requires detailed knowledge of the reactivity of different surface sites toward specific bond breaking and bond making events. We illustrate a new method in such investigations. We use a macroscopically curved Pt single crystal containing a large variation in density of highly kinked steps of two different chiralities. Scanning tunneling microscopy maps the entire range of surface structures present on the 31° section surrounding the Pt(111) apex. Whereas most of the surface shows the expected characteristic arrays of parallel steps, hexagonally-shaped, single-atom deep pits remain after cleaning procedures near the apex. Their orientation is indicative of the different chiralities present on the two sides of the crystal’s apex. These unintended defects locally raise the surface defect concentration, but are of little consequence to subsequent reactivity measurements for $$\text {D}_2$$

D
2

dissociation and H–D exchange as probed by supersonic molecular beam techniques. We quantify absolute elementary dissociation and relative isotopic exchange rates across the surface with high spatial resolution. At low incident energies, elementary dissociation of the homonuclear isotoplogues is dominated by the kinked steps. H–D exchange kinetics depend also mostly linearly on step density. The changing ratio of D2 dissociation to H–D formation, however, suggests that anisotropic diffusion of H(D) atoms is of influence to the measured HD production rate.
Retrospective in silico evaluation of optimized preoperative planning for temporal bone surgery
Authors: Fauser Johannes , Bohlender Simon , Stenin Igor , Kristin Julia , Klenzner Thomas , Schipper Jörg , Mukhopadhyay Anirban 
Published: October 2020

Abstract
Purpose
Robot-assisted surgery at the temporal bone utilizing a flexible drilling unit would allow safer access to clinical targets such as the cochlea or the internal auditory canal by navigating along nonlinear trajectories. One key sub-step for clinical realization of such a procedure is automated preoperative surgical planning that incorporates both segmentation of risk structures and optimized trajectory planning.

Methods
We automatically segment risk structures using 3D U-Nets with probabilistic active shape models. For nonlinear trajectory planning, we adapt bidirectional rapidly exploring random trees on Bézier Splines followed by sequential convex optimization. Functional evaluation, assessing segmentation quality based on the subsequent trajectory planning step, shows the suitability of our novel segmentation approach for this two-step preoperative pipeline.

Results
Based on 24 data sets of the temporal bone, we perform a functional evaluation of preoperative surgical planning. Our experiments show that the automated segmentation provides safe and coherent surface models that can be used in collision detection during motion planning. The source code of the algorithms will be made publicly available.

Conclusion
Optimized trajectory planning based on shape regularized segmentation leads to safe access canals for temporal bone surgery. Functional evaluation shows the promising results for both 3D U-Net and Bézier Spline trajectories.
Buffering Academic Stress during the COVID-19 Pandemic Related Social Isolation: Grit and Growth Mindset as Protective Factors against the Impact of Loneliness
Authors: Mosanya Magdalena 
Published: October 2020

AbstractThe pandemic of the SARS CoV-2 virus, which causes COVID-19 sickness, constitutes a global challenge to well-being. Positive psychology constructs of grit and growth mindset may offer a solution to this challenge as both are associated with psychological resilience. A growth mindset describes the underlying beliefs people have about the malleability of intelligence, and grit refers to dedication to long-term goals. The present study explored whether such constructs could constitute protective factors against the academic stress associated with loneliness and perceived lack of control among international students (n = 170) during social isolation, induced by COVID-19 restrictions. The results of a hierarchical multiple regression model explained 36% of the variance in academic stress with a perceived lack of control (ß = .53, p < .001) and growth mindset (ß = −.22, p < .001) being significant direct predictors. Moderation analysis explained 17% of the variance and confirmed that a level of dispositional grit moderated the detrimental influence loneliness had on academic stress. Simple slopes analysis revealed a significant effect for moderate (β = .07, p = .01) and high (β = .16, p = .001) levels of grit. Our findings suggest that grit and growth mindset, as dynamic variables, could be taught to students as resilience-building prevention of academic stress during the COVID-19 pandemic. Lastly, our results have shown that parents (37%) and friends (32%) were most frequently identified by students as supporters during the COVID-19 pandemic with minimal reported support from universities (2.5%).
Evaluation of a Concept Mapping Task Using Named Entity Recognition and Normalization in Unstructured Clinical Text
Authors: Trivedi Sapna , Gildersleeve Roger , Franco Sandra , Kanter Andrew S. , Chaudhry Afzal 
Published: October 2020

AbstractIn this pilot study, we explore the feasibility and accuracy of using a query in a commercial natural language processing engine in a named entity recognition and normalization task to extract a wide spectrum of clinical concepts from free text clinical letters. Editorial guidance developed by two independent clinicians was used to annotate sixty anonymized clinic letters to create the gold standard. Concepts were categorized by semantic type, and labels were applied to indicate contextual attributes such as negation. The natural language processing (NLP) engine was Linguamatics I2E version 5.3.1, equipped with an algorithm for contextualizing words and phrases and an ontology of terms from Intelligent Medical Objects to which those tokens were mapped. Performance of the engine was assessed on a training set of the documents using precision, recall, and the F1 score, with subset analysis for semantic type, accurate negation, exact versus partial conceptual matching, and discontinuous text. The engine underwent tuning, and the final performance was determined for a test set. The test set showed an F1 score of 0.81 and 0.84 using strict and relaxed criteria respectively when appropriate negation was not required and 0.75 and 0.77 when it was. F1 scores were higher when concepts were derived from continuous text only. This pilot study showed that a commercially available NLP engine delivered good overall results for identifying a wide spectrum of structured clinical concepts. Such a system holds promise for extracting concepts from free text to populate problem lists or for data mining projects.
Quantitative analysis of optimum corrective fuel tax for road vehicles in Bangladesh: achieving the greenhouse gas reduction goal
Authors: Kamruzzaman Mohammad Haider , Mizunoya Takeshi 
Published: October 2020

AbstractThis study estimates optimum corrective fuel taxes for Bangladesh and correlates them with climate change policy. First, we use the European road transport emission model (COPERT IV) to precisely estimate the externalities. Second, using the same model, we also estimate the reduction in greenhouse gas emissions caused by the fuel tax. Finally, we develop a correlation between the fuel tax rate and emissions reduction. Our benchmark calculation of the optimum corrective tax is US$0.94 per gallon for gasoline and US$1.46 per gallon for diesel (in 2016 prices). We find that congestion and accident externalities are the two main fuel tax components for Bangladesh. We also find that the net social welfare gain per year is US$302.11 million and the net revenue gain per year is 3.59% of GDP. The corrective diesel tax reduces fuel consumption by 18.10% and increases fuel efficiency by 12.53%. In the benchmark case, corrective fuel taxes reduce GHG emissions by 5.77%. With the combination of the existing gasoline tax and a diesel tax of US$1.20 per gallon, the country’s greenhouse gas reduction goal can be achieved. Policymakers can use fuel taxes to support climate change policy.
Newborn Screening for Spinal Muscular Atrophy: Ontario Testing and Follow-up Recommendations
Authors: McMillan Hugh J. , Kernohan Kristin D. , Yeh Ed , Amburgey Kim , Boyd Jennifer , Campbell Craig , Dowling James J. , Gonorazky Hernan , Marcadier Janet , Tarnopolsky Mark A. , Vajsar Jiri , MacKenzie Alex , Chakraborty Pranesh 
Published: October 2020

ABSTRACT:Background:Spinal muscular atrophy (SMA) is characterized by the progressive loss of motor neurons causing muscle atrophy and weakness. Nusinersen, the first effective SMA therapy was approved by Health Canada in June 2017 and has been added to the provincial formulary of all but one Canadian province. Access to this effective therapy has triggered the inclusion of SMA in an increasing number of Newborn Screening (NBS) programs. However, the range of disease-modifying SMN2 gene copy numbers encountered in survival motor neuron 1 (SMN1)-null individuals means that neither screen-positive definition nor resulting treatment decisions can be determined by SMN1 genotype alone. We outline an approach to this challenge, one that specifically addresses the case of SMA newborns with four copies of SMN2.Objectives:To develop a standardized post-referral evaluation pathway for babies with a positive SMA NBS screen result.Methods:An SMA NBS pilot trial in Ontario using first-tier MassARRAY and second-tier multi-ligand probe amplification (MLPA) was launched in January 2020. Prior to this, Ontario pediatric neuromuscular disease and NBS experts met to review the evidence regarding the diagnosis and treatment of children with SMA as it pertained to NBS. A post-referral evaluation algorithm was developed, outlining timelines for patient retrieval and management.Conclusions:Ontario’s pilot NBS program has created a standardized path to facilitate early diagnosis of SMA and initiation of treatment. The goal is to provide timely access to those SMA infants in need of therapy to optimize motor function and prolong survival.
Enhancing industrial X-ray tomography by data-centric statistical methods
Authors: Suuronen Jarkko , Emzir Muhammad , Lasanen Sari , Särkkä Simo , Roininen Lassi 
Published: October 2020

AbstractX-ray tomography has applications in various industrial fields such as sawmill industry, oil and gas industry, as well as chemical, biomedical, and geotechnical engineering. In this article, we study Bayesian methods for the X-ray tomography reconstruction. In Bayesian methods, the inverse problem of tomographic reconstruction is solved with the help of a statistical prior distribution which encodes the possible internal structures by assigning probabilities for smoothness and edge distribution of the object. We compare Gaussian random field priors, that favor smoothness, to non-Gaussian total variation (TV), Besov, and Cauchy priors which promote sharp edges and high- and low-contrast areas in the object. We also present computational schemes for solving the resulting high-dimensional Bayesian inverse problem with 100,000–1,000,000 unknowns. We study the applicability of a no-U-turn variant of Hamiltonian Monte Carlo (HMC) methods and of a more classical adaptive Metropolis-within-Gibbs (MwG) algorithm to enable full uncertainty quantification of the reconstructions. We use maximum a posteriori (MAP) estimates with limited-memory BFGS (Broyden–Fletcher–Goldfarb–Shanno) optimization algorithm. As the first industrial application, we consider sawmill industry X-ray log tomography. The logs have knots, rotten parts, and even possibly metallic pieces, making them good examples for non-Gaussian priors. Secondly, we study drill-core rock sample tomography, an example from oil and gas industry. In that case, we compare the priors without uncertainty quantification. We show that Cauchy priors produce smaller number of artefacts than other choices, especially with sparse high-noise measurements, and choosing HMC enables systematic uncertainty quantification, provided that the posterior is not pathologically multimodal or heavy-tailed.
Towards identifying malnutrition among infants under 6 months: a mixed-methods study of South-Sudanese refugees in Ethiopia
Authors: Moore Laura , O’Mahony Sinead , Shevlin Mark , Hyland Philip , Barthorp Hatty , Vallières Frédérique 
Published: October 2020

AbstractObjectives:To determine (i) whether distinct groups of infants under 6 months old (U6M) were identifiable as malnourished based on anthropometric measures and if so to determine the probability of admittance to GOAL Ethiopia’s Management of At Risk Mothers and Infants (MAMI) programme based on group membership; (ii) whether there were discrepancies in admission using recognised anthropometric criteria, compared with group membership and (iii) the barriers and potential solutions to identifying malnutrition within U6M.Design:Mixed-methods approaches were used, whereby data collected by GOAL Ethiopia underwent: factor mixture modelling,χ2analysis and logistic regression analysis. Qualitative analysis was performed through coding of key informant interviews.Setting:Data were collected in two refugee camps in Ethiopia. Key informant interviews were conducted remotely with international MAMI programmers and nutrition experts.Participants:Participants were 3444 South-Sudanese U6M and eleven key informants experienced in MAMI programming.Results:Well-nourished and malnourished groups were identified, with notable discrepancies between group membership and MAMI programme admittance. Despite weight for agez-scores (WAZ) emerging as the most discriminant measure to identify malnutrition, admittance was most strongly associated with mid-upper arm circumference (MUAC). Misconceptions surrounding malnutrition, a dearth of evidence and issues with the current identification protocol emerged as barriers to identifying malnutrition among U6M.Conclusions:Our model suggests that WAZ is the most discriminating anthropometric measure for malnutrition in this population. However, the challenges of using WAZ should be weighed up against the more scalable, but potentially overly sensitive and less accurate use of MUAC among U6M.
The Apparent Motion of STEVE and the Picket Fence Phenomena
Authors: Gillies D. M. , Liang J. , Donovan E. , Spanswick E. 
Published: October 2020

AbstractIn this study, we present the first data obtained from the new Transition Region Explorer (TREx) RGB Imager and analyze the apparent motion of STEVE and the Picket Fence structures in an event on 31 August 2019. The structures associated with STEVE are found to feature a fast westward motion (~5–10 km/s). This is consistent with the notions that STEVE is colocated with a fast subauroral ion drift (SAID) channel and that SAIDs play a key role in the production of STEVE. The apparent motion of the Picket Fence structures is much slower (~400–600 m/s) and can be both westward and eastward. This implies that either the Picket Fence is located at different magnetic flux tubes from that of STEVE, with much slower plasma convection speed, or that the motion of the Picket Fence does not follow the plasma convection.
Evidence of Phytoplankton Light Acclimation to Periodic Turbulent Mixing Along a Tidally Dominated Tropical Coastline
Authors: McLaughlin M. J. , Greenwood J. , Branson P. , Lourey M. J. , Hanson C. E. 
Published: October 2020

AbstractOne of the largest tropical tidal ranges in the world occurs in King Sound, a semienclosed embayment in the tropical Kimberley region of Western Australia. Incubations of phytoplankton within King Sound displayed reduced photosynthetic efficiency, elevated maximum photosynthetic rates, and no measurable photoinhibition. A response typical of high light adapted phytoplankton despite decreased water clarity and low ambient nutrient concentrations in the estuary. This is in contrast with the adjacent shelf where phytoplankton, associated with a deep chlorophyll maximum, display high photosynthetic efficiency and strong light inhibition typical of low light adaptation. Remote sensing and numerical modeling suggest that spatial and temporal variations in tidal mixing drive changes in light variability and in photoacclimation. In King Sound phytoplankton experience the largest variations in light over short time scales where diatoms dominate since they can rapidly acclimate to water column light conditions by adjusting pigment within the cell. The photophysiological response of the phytoplankton in the Sound suggests that acclimation to alternate weak and strong mixing exposes them to cyclical changes in light intensity delaying the onset of photoinhibition, allowing higher maximum photosynthetic rates to be attained. These findings highlight the importance of a multifaceted approach to understanding the links between physics and photoacclimation strategies employed by phytoplankton to more accurately determine rates of depth‐integrated productivity in complex coastal areas.
Inhibition of Chk1 by miR-320c increases oxaliplatin responsiveness in triple-negative breast cancer
Authors: Lim Sera , Kim Yesol , Lee Soo-Been , Kang Hyeok-Gu , Kim Da-Hyun , Park Jee Won , Chung Daeun , Kong Hyunkyung , Yoo Kyung Hyun , Kim Yonghwan , Han Wonshik , Chun Kyung-Hee , Park Jong Hoon 
Published: October 2020

AbstractCheckpoint kinase 1 (Chk1) expression is enhanced in most cancers owing to oncogenic activation and constant replicative stress. Chk1 inactivation is a promising cancer therapy, as its inactivation leads to genomic instability, chromosomal catastrophe, and cancer cell death. Herein, we observed that miR-320c, downregulated in triple-negative breast cancer (TNBC) patients, can target Chk1. In addition, downregulated miR-320c expression was associated with poor overall survival in TNBC patients. As Chk1 was associated with the DNA damage response (DDR), we investigated the effect of miR-320c on DDR in TNBC cells. To induce DNA damage, we used platinum-based drugs, especially oxaliplatin, which is most effective with miR-320c. We observed that overexpression of miR-320c in TNBC regulated the oxaliplatin responsiveness by mediating DNA damage repair through the negative regulation of Chk1 in vitro. Furthermore, using a xenograft model, a combination of miR-320c mimic and oxaliplatin effectively inhibited tumor progression. These investigations indicate the potential of miR-320c as a marker of oxaliplatin responsiveness and a therapeutic target to increase the efficacy of chemotherapy in TNBC.
Space and patchiness affects diversity–function relationships in fungal decay communities
Authors: O’Leary Jade , Journeaux Katie L , Houthuijs Kas , Engel Jasper , Sommer Ulf , Viant Mark R , Eastwood Daniel C , Müller Carsten , Boddy Lynne 
Published: October 2020

AbstractThe space in which organisms live determines health and physicality, shaping the way in which they interact with their peers. Space, therefore, is critically important for species diversity and the function performed by individuals within mixed communities. The biotic and abiotic factors defined by the space that organisms occupy are ecologically significant and the difficulty in quantifying space-defined parameters within complex systems limits the study of ecological processes. Here, we overcome this problem using a tractable system whereby spatial heterogeneity in interacting fungal wood decay communities demonstrates that scale and patchiness of territory directly influence coexistence dynamics. Spatial arrangement in 2- and 3-dimensions resulted in measurable metabolic differences that provide evidence of a clear biological response to changing landscape architecture. This is of vital importance to microbial systems in all ecosystems globally, as our results demonstrate that community function is driven by the effects of spatial dynamics.
International Myeloma Working Group risk stratification model for smoldering multiple myeloma (SMM)
Authors: Mateos María-Victoria , Kumar Shaji , Dimopoulos Meletios A. , González-Calle Verónica , Kastritis Efstathios , Hajek Roman , De Larrea Carlos Fernández , Morgan Gareth J. , Merlini Giampaolo , Goldschmidt Hartmut , Geraldes Catarina , Gozzetti Alessandro , Kyriakou Charalampia , Garderet Laurent , Hansson Markus , Zamagni Elena , Fantl Dorotea , Leleu Xavier , Kim Byung-Su , Esteves Graça , Ludwig Heinz , Usmani Saad , Min Chang-Ki , Qi Ming , Ukropec Jon , Weiss Brendan M. , Rajkumar S. Vincent , Durie Brian G. M. , San-Miguel Jesús 
Published: October 2020

AbstractSmoldering multiple myeloma (SMM) is an asymptomatic precursor state of multiple myeloma (MM). Recently, MM was redefined to include biomarkers predicting a high risk of progression from SMM, thus necessitating a redefinition of SMM and its risk stratification. We assembled a large cohort of SMM patients meeting the revised IMWG criteria to develop a new risk stratification system. We included 1996 patients, and using stepwise selection and multivariable analysis, we identified three independent factors predicting progression risk at 2 years: serum M-protein >2 g/dL (HR: 2.1), involved to uninvolved free light-chain ratio >20 (HR: 2.7), and marrow plasma cell infiltration >20% (HR: 2.4). This translates into 3 categories with increasing 2-year progression risk: 6% for low risk (38%; no risk factors, HR: 1); 18% for intermediate risk (33%; 1 factor; HR: 3.0), and 44% for high risk (29%; 2–3 factors). Addition of cytogenetic abnormalities (t(4;14), t(14;16), +1q, and/or del13q) allowed separation into 4 groups (low risk with 0, low intermediate risk with 1, intermediate risk with 2, and high risk with ≥3 risk factors) with 6, 23, 46, and 63% risk of progression in 2 years, respectively. The 2/20/20 risk stratification model can be easily implemented to identify high-risk SMM for clinical research and routine practice and will be widely applicable.
Alcohol consumption, drinking patterns and cancer incidence in an Australian cohort of 226,162 participants aged 45 years and over
Authors: Sarich Peter , Canfell Karen , Egger Sam , Banks Emily , Joshy Grace , Grogan Paul , Weber Marianne F. 
Published: October 2020

AbstractBackgroundAlthough overall alcohol consumption is known to increase the risk of a number of cancers internationally, evidence for Australia and evidence regarding the pattern of drinking and cancer risk is limited.MethodsAdjusted hazard ratios (HR) and 95% confidence intervals (CI) for cancer risk in relation to overall alcohol consumption (drinks/week) and pattern of drinking were calculated using Cox proportional hazard regressions for 226,162 participants aged ≥45 years (2006–2009) in the 45 and Up Study, an Australian prospective cohort study. Incident primary cancer cases were ascertained by linkage to the New South Wales Cancer Registry to 2013 by the Centre for Health Record Linkage.ResultsOver a median of 5.4 years, 17,332 cancers were diagnosed. Increasing levels of alcohol intake were associated with increased risk of cancers of the upper aerodigestive tract (1.19; 1.10–1.29), mouth and pharynx (1.18; 1.08–1.29), oesophagus (1.22; 1.04–1.43), colorectum (1.09; 1.04–1.15), colon (1.13; 1.06–1.20), liver (1.22; 1.04–1.44) and breast (1.11; 1.02–1.21). Breast cancer risk was marginally associated with drinking pattern, with higher risk when intake was concentrated on 1–3 days/week compared to the same amount spread over 4–7 days (Pinteraction = 0.049).ConclusionsAlcohol consumption confers a significant risk of cancer, and drinking pattern may be independently related to breast cancer risk.