bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of a multi-layer hamming network in problems for recognition dry areas of agricultural crops
Authors: Tokareva Yu M , Tokarev K E , Kuzmin V A , Pleshenko T V , Aleksandrina N A 
Published: October 2021

Abstract
The article discusses the possibilities of using the mathematical and instrumental enhancement of the multilayer Hamming network in the tasks of recognizing aerial photographs, in particular, the advantages of the neuromodel for implementing further research to solve the problems of increasing crop yield based on monitoring and segmentation of dry crop areas are highlighted.
Comparing different bulk radiation damage models in TCAD simulations of small-pitch 3D Si sensors
Authors: Boughedda A. , Lakhdara M. , Latreche S. , Mendicino R. , Dalla Betta G.-F. 
Published: October 2021

Abstract
Small-pitch, thin 3D Si sensors have been developed for the ATLAS and CMS experiment upgrades at the High Luminosity LHC. The pixel sizes are 50 × 50 µm2 with 1 readout column, and 25 × 100 µm2 with 1 or 2 readout columns (1E and 2E). Owing to the small inter-electrode distance, ranging from ∼28 µm to ∼51 µm in the considered layouts, these devices are expected to be extremely radiation hard. TCAD simulations by Synopsys Sentaurus, incorporating advanced radiation damage models, have been used for the design/optimization of these new 3D pixel sensors. In this study, we have compared the accuracy of different bulk damage models in predicting the signal efficiency of small-pitch 3D sensors irradiated at large fluences and its evolution with the bias voltage at different positions within the 3D cell. Selected simulation results will be reported in comparison to experimental data.
The IceCube-Gen2 Neutrino Observatory
Authors: Clark B.A. 
Published: October 2021

Abstract
The IceCube Neutrino Observatory opened the window on neutrino astronomy by discovering high-energy astrophysical neutrinos in 2013 and identifying the first compelling astrophysical neutrino source, the blazar TXS0506 + 056, in 2017. In this proceeding, we will discuss the science reach and ongoing development of the IceCube-Gen2 facility, which is the planned extension to IceCube. IceCube-Gen2 will increase the rate of observed cosmic neutrinos by an order of magnitude, be able to detect five-times fainter neutrino sources, and extend the measurement of astrophysical neutrinos several orders of magnitude higher in energy. We will discuss the envisioned design of the instrument, which will include an enlarged in-ice optical array, a surface array for the study of cosmic-rays, and a shallow radio array to detect ultra-high energy (>100 PeV) neutrinos. We will also highlight ongoing efforts to develop and test new instrumentation for IceCube-Gen2.
Toolbox for non-classical state calculations
Authors: Roux Filippus S 
Published: October 2021

Abstract
Computational challenges associated with the use of Wigner functions to identify non-classical properties of states are addressed with the aid of generating functions. It allows the computation of the Wigner functions of photon-subtracted states for an arbitrary number of subtracted photons. Both the formal definition of photon-subtracted states in terms of ladder operators and the experimental implementation with heralded photon detections are analyzed. These techniques are demonstrated by considering photon subtraction from squeezed thermal states as well as squeezed Fock states. Generating functions are also used for the photon statistics of these states. These techniques reveal various aspects of the parameter dependences of these states.
sAMP-PFPDeep: Improving accuracy of short antimicrobial peptides prediction using three different sequence encodings and deep neural networks
Authors: Hussain Waqar 
Published: October 2021

AbstractShort antimicrobial peptides (sAMPs) belong to a significant repertoire of antimicrobial agents and are known to possess enhanced antimicrobial activity, higher stability and less toxicity to human cells, as well as less complex than other large biological drugs. As these molecules are significantly important, herein, a prediction method for sAMPs (with a sequence length ≤ 30 residues) is proposed for accurate and efficient prediction of sAMPs instead of laborious and costly experimental approaches. Benchmark dataset was collected from a recently reported study and sequences were converted into three channel images comprising information related to the position, frequency and sum of 12 physiochemical features as the first, second and third channels, respectively. Two image-based deep neural networks (DNNs), i.e. RESNET-50 and VGG-16 were trained and evaluated using various metrics while a comparative analysis with previous techniques was also performed. Validation of sAMP-PFPDeep was also performed by using molecular docking based analysis. The results showed that VGG-16 provided more accurate results, i.e. 98.30% training accuracy and 87.37% testing accuracy for predicting sAMPs as compared to those of RESNET-50 having 96.14% training accuracy and 83.87% testing accuracy. However, the comparative analysis revealed that both these models outperformed previously reported state-of-the-art methods. Based on the results, it is concluded that sAMP-PFPDeep can help identify antimicrobial peptides with promising accuracy and efficiency. It can help biologists and scientists to identify antimicrobial peptides, by further aiding the computer-aided drug design and discovery, as well as virtual screening protocols against various pathologies. sAMP-PFPDeep is available at (https://github.com/WaqarHusain/sAMP-PFPDeep).
CpG Transformer for imputation of single-cell methylomes
Authors: De Waele Gaetan , Clauwaert Jim , Menschaert Gerben , Waegeman Willem 
Published: October 2021

Abstract

Motivation
The adoption of current single-cell DNA methylation sequencing protocols is hindered by incomplete coverage, outlining the need for effective imputation techniques. The task of imputing single-cell (methylation) data requires models to build an understanding of underlying biological processes.

Results
We adapt the transformer neural network architecture to operate on methylation matrices through combining axial attention with sliding window self-attention. The obtained CpG Transformer displays state-of-the-art performances on a wide range of scBS-seq and scRRBS-seq datasets. Furthermore, we demonstrate the interpretability of CpG Transformer and illustrate its rapid transfer learning properties, allowing practitioners to train models on new datasets with a limited computational and time budget.

Availability and implementation
CpG Transformer is freely available at https://github.com/gdewael/cpg-transformer.

Supplementary information
Supplementary data are available at Bioinformatics online.
Functional segregation within the dorsal frontoparietal network: a multimodal dynamic causal modeling study
Authors: Raffin Estelle , Witon Adrien , Salamanca-Giron Roberto F , Huxlin Krystel R , Hummel Friedhelm C 
Published: October 2021

AbstractDiscrimination and integration of motion direction requires the interplay of multiple brain areas. Theoretical accounts of perception suggest that stimulus-related (i.e., exogenous) and decision-related (i.e., endogenous) factors affect distributed neuronal processing at different levels of the visual hierarchy. To test these predictions, we measured brain activity of healthy participants during a motion discrimination task, using electroencephalography (EEG) and functional magnetic resonance imaging (fMRI). We independently modeled the impact of exogenous factors (task demand) and endogenous factors (perceptual decision-making) on the activity of the motion discrimination network and applied Dynamic Causal Modeling (DCM) to both modalities. DCM for event-related potentials (DCM-ERP) revealed that task demand impacted the reciprocal connections between the primary visual cortex (V1) and medial temporal areas (V5). With practice, higher visual areas were increasingly involved, as revealed by DCM-fMRI. Perceptual decision-making modulated higher levels (e.g., V5-to-Frontal Eye Fields, FEF), in a manner predictive of performance. Our data suggest that lower levels of the visual network support early, feature-based selection of responses, especially when learning strategies have not been implemented. In contrast, perceptual decision-making operates at higher levels of the visual hierarchy by integrating sensory information with the internal state of the subject.
Real-World Impact of the Accelerate PhenoTest BC Kit on Patients With Bloodstream Infections in the Improving Outcomes and Antimicrobial Stewardship Study: A Quasiexperimental Multicenter Study
Authors: Bhalodi Amira A , MacVane Shawn H , Ford Bradley , Ince Dilek , Kinn Patrick M , Percival Kelly M , Bremmer Derek N , Carr Dustin R , Walsh Thomas L , Bhatti Micah M , Shelburne Samuel A , Humphries Romney M , Wolfe Kaleb , Rosenbaum Eric R , Dare Ryan K , Kolev Johann , Madhusudhan Meghan , Ben-Aderet Michael A , Morgan Margie A 
Published: October 2021

Abstract

Background
Bloodstream infections (BSIs) are a leading cause of morbidity and mortality. The Improving Outcomes and Antimicrobial Stewardship study seeks to evaluate the impact of the Accelerate PhenoTest BC Kit (AXDX) on antimicrobial use and clinical outcomes in BSIs.

Methods
This multicenter, quasiexperimental study compared clinical and antimicrobial stewardship metrics, prior to and after implementation of AXDX, to evaluate the impact this technology has on patients with BSIs. Laboratory and clinical data from hospitalized patients with BSIs (excluding contaminants) were compared between 2 arms, 1 that underwent testing on AXDX (post-AXDX) and 1 that underwent alternative organism identification and susceptibility testing (pre-AXDX). The primary outcomes were time to optimal therapy (TTOT) and 30-day mortality.

Results
A total of 854 patients with BSIs (435 pre-AXDX, 419 post-AXDX) were included. Median TTOT was 17.2 hours shorter in the post-AXDX arm (23.7 hours) compared with the pre-AXDX arm (40.9 hours; P&lt;.0001). Compared with pre-AXDX, median time to first antimicrobial modification (24.2 vs 13.9 hours; P&lt;.0001) and first antimicrobial deescalation (36.0 vs 27.2 hours; P=.0004) were shorter in the post-AXDX arm. Mortality (8.7% pre-AXDX vs 6.0% post-AXDX), length of stay (7.0 pre-AXDX vs 6.5 days post-AXDX), and adverse drug events were not significantly different between arms. Length of stay was shorter in the post-AXDX arm (5.4 vs 6.4 days; P=.03) among patients with gram-negative bacteremia.

Conclusions
For BSIs, use of AXDX was associated with significant decreases in TTOT, first antimicrobial modification, and time to antimicrobial deescalation.
Morphology of the left subclavian artery: implications for single-branched endovascular aortic arch repair
Authors: Kondov Stoyan , Beyersdorf Friedhelm , Braun Nora , Höhn Rene , Schlett Christopher , Rylski Bartosz , Siepe Matthias , Kreibich Maximilian , Gottardi Roman , Czerny Martin 
Published: October 2021

Abstract

OBJECTIVES
Our goal was to evaluate the morphology of the aortic arch, focusing on the left subclavian artery (LSA), and to anticipate implications for single-branched endovascular aortic arch repair.

METHODS
We performed a morphological analysis of computed tomography angiography scans of 322 patients between January 2002 and December 2018. Arch type and distance between arch vessels on the convexity were evaluated. We defined 3 morphological types: U-type distance between the left common carotid artery (LCCA) and LSA offspring &gt;10 mm; V-type distance between the LCCA and LSA offspring &lt;10 mm and W-type isolated left vertebral artery offspring from the aortic arch.

RESULTS
Most patients presented a type III arch [50% (n = 161)]. The median distance from the brachiocephalic trunk offspring to the LCCA offspring measured 2.5 mm (2.0–3.0 mm) and that between the LCCA offspring and the LSA offspring was 6.5 mm (4.0–11.0 mm). We observed no significant difference based on the morphological type (V versus U versus W) in the brachiocephalic trunk–LCCA distance, but there were significant differences in the LCCA–LSA distance between types V and U (P &lt; 0.001) and between types V and W (P &lt; 0.001). Interestingly, we found no significant difference in the LCCA–LSA distance between types U and W. We noted a significant difference in the median diameter of the LSA according to U, V and W types: V type versus U type, 12.5 vs 13.5 mm (P = 0.033) as well as U type versus W type, 13.5 vs 10.5 mm (P &lt; 0.001) and V type versus W type, 12.5 vs 10.5 mm (P &lt; 0.002). The distances between the LSA offspring and left vertebral artery offspring between types U and V did not differ significantly.

CONCLUSIONS
Our categorization of the U, V and W types of the LSA can help us anticipate shapes and distances and thereby function as an initial evaluation tool for predicting single branched endovascular aortic arch repair involving the LSA.
PM10 exposure interacts with abdominal obesity to increase blood triglycerides: a cross-sectional linkage study
Authors: Gaio Vânia , Roquette Rita , Monteiro Alexandra , Ferreira Joana , Lopes Diogo , Dias Carlos Matias , Nunes Baltazar 
Published: October 2021

Abstract

Background
Blood lipids and glucose levels dysregulation represent potential mechanisms intermediating the adverse cardiovascular effects of ambient particulate matter (PM) exposure. This study aims to estimate the effect of long-term PM10 exposure on blood lipids and glucose levels and to assess the potential mediation and/or modification action of abdominal obesity (AO) (waist-to-height ratio).

Methods
Our study was based on 2,390 participants of the first Portuguese Health Examination Survey (INSEF, 2015) with available data on blood lipids and glucose parameters and living within a 30-km radius of an air quality monitoring station with available PM10 measurements. PM10 concentrations were acquired from the air quality monitoring network of the Portuguese Environment Agency. Generalized linear models were used to assess the effect of 1-year PM10 exposure on blood lipids and glucose levels. An interaction term was introduced in the models to test the modification action of AO.

Results
We found an association between PM10 and non-fasting blood triglycerides (TG) after adjustment for age, sex, education, occupation, lifestyles-related variables and temperature but only in participants with AO. Per each 1 µg/m3 PM10 increment, there was a 1.84% (95% confidence interval: 0.02–3.69) increase in TG. For the remaining blood lipid and glucose parameters, no associations were found.

Conclusions
Our study demonstrates that even at low levels of exposure, long-term PM10 exposure interacts with AO to increase blood TG. Our findings suggest that reducing both AO prevalence and PM10 below current standards would result in additional health benefits for the population.
Trace Densities and Algebraic Index Theorems for Sheaves of Formal Cherednik Algebras
Authors: Vitanov Alexander 
Published: October 2021

AbstractWe show how a novel construction of the sheaf of Cherednik algebras $\mathscr {H}_{1, c, X, G}$ on a quotient orbifold $Y:=X/G$ in author’s prior work leads to results for $\mathscr {H}_{1, c, X, G}$, which until recently were viewed as intractable. First, for every orbit type stratum in $X$, we define a trace density map for the Hochschild chain complex of $\mathscr {H}_{1, c, X, G}$, which generalizes the standard Engeli–Felder’s trace density construction for the sheaf of differential operators $\mathscr {D}_X$. Second, by means of the newly obtained trace density maps, we prove an isomorphism in the derived category of complexes of $\mathbb {C}_{Y}\llbracket \hbar \rrbracket $-modules, which computes the hypercohomology of the Hochschild chain complex of the sheaf of formal Cherednik algebras $\mathscr {H}_{1, \hbar , X, G}$. We show that this hypercohomology is isomorphic to the Chen–Ruan cohomology of the orbifold $Y$ with values in the ring of formal power series $\mathbb {C}\llbracket \hbar \rrbracket $. We infer that the Hochschild chain complex of the sheaf of skew group algebras $\mathscr {H}_{1, 0, X, G}$ has a well-defined Euler characteristic that is equal to the orbifold Euler characteristic of $Y$. Finally, we prove an algebraic index theorem.
Patients experience more support, information and involvement after first-time hospital accreditation: a before and after study in the Faroe Islands
Authors: Bergholt Maria daniella , Falstie-jensen Anne mette , Brink valentin Jan , Hibbert Peter , Braithwaite Jeffrey , Johnsen Søren paaske , Von plessen Christian 
Published: October 2021

Abstract

Background
The impact of hospital accreditation on the experiences of patients remains a weak point in quality improvement research. This is surprising given the time and cost of accreditation and the fact that patient experiences influence outcomes. We investigated the impact of first-time hospital accreditation on patients’ experience of support from health-care professionals, information and involvement in decisions.

Objective
We aimed to examine the association between first-time hospital accreditation and patient experiences.

Methods
We conducted a longitudinal study in the three Faroese hospitals that, unlike hospitals on the Danish mainland and elsewhere internationally, had no prior exposure to systematic quality improvement. The hospitals were accredited in 2017 according to a modified second version of the Danish Healthcare Quality program. Study participants were 18 years or older and hospitalized for at least 24 h in 2016 before or 2018 after accreditation. We administered the National Danish Survey of Patient Experiences for acute and scheduled hospitalization. Patients rated their experiences of support, information and involvement in decision-making on a 5-point Likert scale. We calculated individual and grouped mean item scores, the percentages of scores ≥4, the mean score difference, the relative risk (RR) for high/very high scores (≥4) using Poisson regression and the risk difference. Patient experience ratings were compared using mixed effects linear regression.

Results
In total, 400 patients before and 400 after accreditation completed the survey. After accreditation patients reported increased support from health professionals; adjusted mean score difference (adj. mean diff.) = 1.99 (95% confidence interval (CI): 1.89, 2.10), feeling better informed before and during the hospitalization; adj. mean diff. = 1.14 (95% CI: 1.07; 1.20) and more involved in decision-making; adj. mean diff. = 1.79 (95% CI: 1.76; 1.82). Additionally, the RR for a high/very high score (≥4) was significantly greater on 15 of the 16 questionnaire items. The greatest RR for a high/very high score (≥4) after accreditation, was found for the item ‘Have you had a dialogue with the staff about the advantages and disadvantages of the examination/treatment options available?’; RR= 5.73 (95% CI: 4.51, 7.27).

Conclusion
Hospitalized patients experienced significantly more support from health professionals, information and involvement in decision-making after accreditation. Future research on accreditation should include the patients’ perspective.
Timing of prior exposure to antibiotics and failure of Helicobacter pylori eradication: a population-based study
Authors: Guo Chuan-Guo , Jiang Fang , Cheung Ka Shing , Li Bofei , Ooi Poh Hwa , Leung Wai K. 
Published: October 2021

Abstract

Background
The success rate of conventional Helicobacter pylori eradication therapy is declining, due to rising antibiotic resistance.

Objectives
To determine the temporal effects of prior antibiotic exposure on eradication outcome.

Patients and methods
This is a retrospective cohort study including all H. pylori-infected patients who received their first course of clarithromycin-containing triple therapy in 2003–18. Prior antibiotic exposures before H. pylori eradication therapy (up to 180 days, 1 year or 3 years) were retrieved. A logistic regression model was used to evaluate the association between different timings of previous antibiotic exposure, recent (within 30/60 days) or distant period, and the need for retreatment for H. pylori.

Results
A total of 120 787 H. pylori-infected patients were included. Prior exposure to any antibiotics within 180 days was associated with a higher risk of retreatment (OR 1.18, 95% CI 1.13–1.24) and the risk progressively increased with longer duration of antibiotic use. The results were consistent for prior exposure up to 1 year (OR 1.26, 95% CI 1.20–1.31) or 3 years (OR 1.30, 95% CI 1.25–1.35). However, when compared with those without prior antibiotic exposure, recent exposure (within 30 days) did not increase the risk of retreatment, which was consistent for analysis with prior antibiotic exposure up to 3 years. Notably, recent use of cephalosporins within 30/60 days and nitroimidazole within 30 days had significantly lower risks of retreatment.

Conclusions
Any prior antibiotic exposure increased the risk of treatment failure of clarithromycin-containing triple therapy. Recent exposures to some classes of antibiotics may paradoxically increase treatment success.
Genetic control of leaf angle in sorghum and its effect on light interception
Authors: Zhi Xiaoyu , Tao Yongfu , Jordan David , Borrell Andrew , Hunt Colleen , Cruickshank Alan , Potgieter Andries , Wu Alex , Hammer Graeme , George-Jaeggli Barbara , Mace Emma 
Published: October 2021

Abstract
Developing sorghum genotypes adapted to different light environments requires understanding of a plant’s ability to capture light, determined through leaf angle specifically. This study dissected the genetic basis of leaf angle in 3 year field trials at two sites, using a sorghum diversity panel (729 accessions). A wide range of variation in leaf angle with medium heritability was observed. Leaf angle explained 36% variation in canopy light extinction coefficient, highlighting the extent to which variation in leaf angle influences light interception at the whole-canopy level. This study also found that the sorghum races of Guinea and Durra consistently having the largest and smallest leaf angle, respectively, highlighting the potential role of leaf angle in adaptation to distinct environments. The genome-wide association study detected 33 quantitative trait loci (QTLs) associated with leaf angle. Strong synteny was observed with previously detected leaf angle QTLs in maize (70%) and rice (40%) within 10 cM, among which the overlap was significantly enriched according to χ2 tests, suggesting a highly consistent genetic control in grasses. A priori leaf angle candidate genes identified in maize and rice were found to be enriched within a 1-cM window around the sorghum leaf angle QTLs. Additionally, protein domain analysis identified the WD40 protein domain as being enriched within a 1-cM window around the QTLs. These outcomes show that there is sufficient heritability and natural variation in the angle of upper leaves in sorghum which may be exploited to change light interception and optimize crop canopies for different contexts.