bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semantic and Physical Properties of Peripheral Vision Are Used for Scene Categorization in Central Vision
Authors: Peyrin Carole , Roux-Sibilon Alexia , Trouilloud Audrey , Khazaz Sarah , Joly Malena , Pichat Cédric , Boucart Muriel , Krainik Alexandre , Kauffmann Louise 
Published: February 2021

Abstract
Theories of visual recognition postulate that our ability to understand our visual environment at a glance is based on the extraction of the gist of the visual scene, a first global and rudimentary visual representation. Gist perception would be based on the rapid analysis of low spatial frequencies in the visual signal and would allow a coarse categorization of the scene. We aimed to study whether the low spatial resolution information available in peripheral vision could modulate the processing of visual information presented in central vision. We combined behavioral measures (Experiments 1 and 2) and fMRI measures (Experiment 2). Participants categorized a scene presented in central vision (artificial vs. natural categories) while ignoring another scene, either semantically congruent or incongruent, presented in peripheral vision. The two scenes could either share the same physical properties (similar amplitude spectrum and spatial configuration) or not. Categorization of the central scene was impaired by a semantically incongruent peripheral scene, in particular when the two scenes were physically similar. This semantic interference effect was associated with increased activation of the inferior frontal gyrus. When the two scenes were semantically congruent, the dissimilarity of their physical properties impaired the categorization of the central scene. This effect was associated with increased activation in occipito-temporal areas. In line with the hypothesis of predictive mechanisms involved in visual recognition, results suggest that semantic and physical properties of the information coming from peripheral vision would be automatically used to generate predictions that guide the processing of signal in central vision.
Functional Context Affects Scene Processing
Authors: Aminoff Elissa M. , Tarr Michael J. 
Published: February 2021

AbstractRapid visual perception is often viewed as a bottom–up process. Category-preferred neural regions are often characterized as automatic, default processing mechanisms for visual inputs of their categorical preference. To explore the sensitivity of such regions to top–down information, we examined three scene-preferring brain regions, the occipital place area (OPA), the parahippocampal place area (PPA), and the retrosplenial complex (RSC), and tested whether the processing of outdoor scenes is influenced by the functional contexts in which they are seen. Context was manipulated by presenting real-world landscape images as if being viewed through a window or within a picture frame—manipulations that do not affect scene content but do affect one's functional knowledge regarding the scene. This manipulation influences neural scene processing (as measured by fMRI): The OPA and the PPA exhibited greater neural activity when participants viewed images as if through a window as compared with within a picture frame, whereas the RSC did not show this difference. In a separate behavioral experiment, functional context affected scene memory in predictable directions (boundary extension). Our interpretation is that the window context denotes three-dimensionality, therefore rendering the perceptual experience of viewing landscapes as more realistic. Conversely, the frame context denotes a 2-D image. As such, more spatially biased scene representations in the OPA and the PPA are influenced by differences in top–down, perceptual expectations generated from context. In contrast, more semantically biased scene representations in the RSC are likely to be less affected by top–down signals that carry information about the physical layout of a scene.
Diagnosing Subsurface Vertical Velocities from High-Resolution Sea Surface Fields
Authors: Liu Lei , Xue Huijie , Sasaki Hideharu 
Published: February 2021

AbstractUsing the extended “interior + surface quasigeostrophic” method from the 2019 study by Liu et al. (hereafter L19), subsurface density and horizontal velocities can be reconstructed from sea surface buoyancy and surface height. This study explores the potential of L19 for diagnosing the upper-ocean vertical velocity w field from high-resolution surface information, employing the 1/30° horizontal resolution OFES model output. Specifically, we employ the L19-reconstructed density and horizontal velocity fields in a diabatic version of the omega equation that incorporates a simplified parameterization for turbulent vertical mixing. The w diagnosis is evaluated against OFES output in the Kuroshio Extension region of the North Pacific, and the result indicates that the L19 method constitutes an effective framework. Statistically, the OFES-simulated and L19-diagnosed w fields have a 2-yr-averaged spatial correlation of 0.42–0.51 within the mixed layer and 0.51–0.67 throughout the 1000-m upper ocean below the mixed layer. Including the diabatic turbulent mixing effect has improved the w diagnoses inside the mixed layer, particularly for the cold-season days with the largest correlation improvement reaching 0.31. Our encouraging results suggest that the L19 method can be applied to the high-resolution sea surface height data from the forthcoming Surface Water and Ocean Topography (SWOT) satellite mission for reconstructing 3D hydrodynamic conditions of the upper ocean.
Ocean Conditions and the Intensification of Three Major Atlantic Hurricanes in 2017
Authors: Domingues Ricardo , Le Hénaff Matthieu , Halliwell George , Zhang Jun A. , Bringas Francis , Chardon Patricia , Kim Hyun-Sook , Morell Julio , Goni Gustavo 
Published: February 2021

AbstractMajor Atlantic hurricanes Irma, Jose, and Maria of 2017 reached their peak intensity in September while traveling over the tropical North Atlantic Ocean and Caribbean Sea, where both atmospheric and ocean conditions were favorable for intensification. In situ and satellite ocean observations revealed that conditions in these areas exhibited (i) sea surface temperatures above 28°C, (ii) upper-ocean heat content above 60 kJ cm−2, and (iii) the presence of low-salinity barrier layers associated with a larger-than-usual extension of the Amazon and Orinoco riverine plumes. Proof-of-concept coupled ocean–hurricane numerical model experiments demonstrated that the accurate representation of such ocean conditions led to an improvement in the simulated intensity of Hurricane Maria for the 3 days preceding landfall in Puerto Rico, when compared to an experiment without the assimilation of ocean observations. Without the assimilation of ocean observations, upper-ocean thermal conditions were generally colder than observations, resulting in reduced air–sea enthalpy fluxes—enthalpy fluxes are more realistically simulated when the upper-ocean temperature and salinity structure is better represented in the model. Our results further showed that different components of the ocean observing system provide valuable information in support of improved TC simulations, and that assimilation of underwater glider observations alone enabled the largest improvement over the 24 h time frame before landfall. Our results, therefore, indicated that ocean conditions were relevant for more realistically simulating Hurricane Maria’s intensity. However, further research based on a comprehensive set of hurricane cases is required to confirm robust improvements to forecast systems.
Fluorescence visualization of the intersegmental plane by bronchoscopic instillation of indocyanine green into the targeted segmental bronchus: determination of the optimal settings
Authors: Anayama Takashi , Hirohashi Kentaro , Miyazaki Ryohei , Okada Hironobu , Yamamoto Marino , Orihashi Kazumasa 
Published: February 2021

Objective To determine the appropriate amount of indocyanine green for bronchial insufflation. Methods We enrolled 20 consecutive patients scheduled for anatomical segmentectomy in the Kochi Medical School Hospital. After inducing general anesthesia, 6 to 60 mL of 200-fold-diluted indocyanine green (0.0125 mg/mL) was insufflated into the subsegmental bronchi in the targeted pulmonary segmental bronchus. The volume of the targeted pulmonary segments was calculated using preoperative computed tomography. Fluorescence spread in the segmental alveoli was visualized using a dedicated near-infrared thoracoscope. Results The targeted segment was uniformly visualized by indocyanine green fluorescence in 16/20 (80.0%) cases after insufflating indocyanine green. A receiver operating characteristic curve indicated that the area under the curve was 0.984; the optimal cut-off volume of diluted indocyanine green for insufflation was 8.91% of the calculated targeted pulmonary segment volume. Conclusions The setting for indocyanine green insufflation was optimized for near-infrared fluorescence image-guided anatomical segmentectomy. By injecting the correct amount of indocyanine green, fluorescence-guided anatomical segmentation may be performed more appropriately.
Examining frequent emergency department use among children and adolescents with autism spectrum disorder
Authors: Beverly Judith , Giannouchos Theodoros , Callaghan Timothy 
Published: February 2021

We analyze the 2011–2016 Healthcare Cost and Utilization Project State Emergency Department Databases and State Inpatient Databases for all emergency department visits by children and adolescents in New York to estimate the association between autism spectrum disorder and frequent emergency department utilization. Our study included 5.9 million individuals with 9.1 million emergency department visits. Of those, 31,682 had autism spectrum disorder (0.5%) accounting for 66,053 (0.7%) emergency department visits. Individuals with autism spectrum disorder had on average 0.6 more emergency department visits per year, were more likely to exhibit frequent emergency department use (⩾4, ⩾6, ⩾8, and ⩾10 emergency department visits/year), and had larger shares of comorbidities and diagnoses related to attention-deficit/hyperactivity disorder, intellectual disability, and epilepsy. These findings highlight the need for patient and family-centered care interventions and emergency department staff education initiatives. Lay abstract This study used data for 5.9 million individuals with 9.1 million emergency department visits from all hospitals in the state of New York to explore frequent emergency department use between children and adolescents with autism spectrum disorders and those without autism spectrum disorders. We found that children and adolescents with autism spectrum disorders had larger shares of comorbidities and diagnoses related to attention-deficit/hyperactivity disorder, intellectual disability, and epilepsy. Children and adolescents with autism spectrum disorders were also more likely to utilize emergency departments and to exhibit frequent use. These results emphasize the need for using family-centered care to improve the care experiences of children and youth with autism spectrum disorders and their families. In addition, the education of emergency department staff of processes and practices as it relates to delivery of care and the care experience.
Molecular determinants of the factor VIII/von Willebrand factor complex revealed by BIVV001 cryo-electron microscopy
Authors: Fuller James R. , Knockenhauer Kevin E. , Leksa Nina C. , Peters Robert T. , Batchelor Joseph D. 
Published: February 2021

AbstractInteraction of factor VIII (FVIII) with von Willebrand factor (VWF) is mediated by the VWF D′D3 domains and thrombin-mediated release is essential for hemostasis after vascular injury. VWF-D′D3 mutations resulting in loss of FVIII binding are the underlying cause of von Willebrand disease (VWD) type 2N. Furthermore, the FVIII–VWF interaction has significant implications for the development of therapeutics for bleeding disorders, particularly hemophilia A, in which endogenous VWF clearance imposes a half-life ceiling on replacement FVIII therapy. To understand the structural basis of FVIII engagement by VWF, we solved the structure of BIVV001 by cryo-electron microscopy to 2.9 Å resolution. BIVV001 is a bioengineered clinical-stage FVIII molecule for the treatment of hemophilia A. In BIVV001, VWF-D′D3 is covalently linked to an Fc domain of a B domain–deleted recombinant FVIII (rFVIII) Fc fusion protein, resulting in a stabilized rFVIII/VWF-D′D3 complex. Our rFVIII/VWF structure resolves BIVV001 architecture and provides a detailed spatial understanding of previous biochemical and clinical observations related to FVIII–VWF engagement. Notably, the FVIII acidic a3 peptide region (FVIII-a3), established as a critical determinant of FVIII/VWF complex formation, inserts into a basic groove formed at the VWF–D′/rFVIII interface. Our structure shows direct interaction of sulfated Y1680 in FVIII-a3 and VWF-R816 that, when mutated, leads to severe hemophilia A or VWD type 2N, respectively. These results provide insight on this key coagulation complex, explain the structural basis of many hemophilia A and VWD type 2N mutations, and inform studies to further elucidate how VWF dissociates rapidly from FVIII upon activation.
ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites
Authors: Liu Pengyu , Song Jiangning , Lin Chun-Yu , Akutsu Tatsuya 
Published: February 2021

Abstract
Background
Human dicer is an enzyme that cleaves pre-miRNAs into miRNAs. Several models have been developed to predict human dicer cleavage sites, including PHDCleav and LBSizeCleav. Given an input sequence, these models can predict whether the sequence contains a cleavage site. However, these models only consider each sequence independently and lack interpretability. Therefore, it is necessary to develop an accurate and explainable predictor, which employs relations between different sequences, to enhance the understanding of the mechanism by which human dicer cleaves pre-miRNA.

Results
In this study, we develop an accurate and explainable predictor for human dicer cleavage site – ReCGBM. We design relational features and class features as inputs to a lightGBM model. Computational experiments show that ReCGBM achieves the best performance compared to the existing methods. Further, we find that features in close proximity to the center of pre-miRNA are more important and make a significant contribution to the performance improvement of the developed method.

Conclusions
The results of this study show that ReCGBM is an interpretable and accurate predictor. Besides, the analyses of feature importance show that it might be of particular interest to consider more informative features close to the center of the pre-miRNA in future predictors.
GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians
Authors: Gangiredla Jayanthi , Rand Hugh , Benisatto Daniel , Payne Justin , Strittmatter Charles , Sanders Jimmy , Wolfgang William J. , Libuit Kevin , Herrick James B. , Prarat Melanie , Toro Magaly , Farrell Thomas , Strain Errol 
Published: February 2021

Abstract
Background
Processing and analyzing whole genome sequencing (WGS) is computationally intense: a single Illumina MiSeq WGS run produces ~ 1 million 250-base-pair reads for each of 24 samples. This poses significant obstacles for smaller laboratories, or laboratories not affiliated with larger projects, which may not have dedicated bioinformatics staff or computing power to effectively use genomic data to protect public health. Building on the success of the cloud-based Galaxy bioinformatics platform (http://galaxyproject.org), already known for its user-friendliness and powerful WGS analytical tools, the Center for Food Safety and Applied Nutrition (CFSAN) at the U.S. Food and Drug Administration (FDA) created a customized ‘instance’ of the Galaxy environment, called GalaxyTrakr (https://www.galaxytrakr.org), for use by laboratory scientists performing food-safety regulatory research. The goal was to enable laboratories outside of the FDA internal network to (1) perform quality assessments of sequence data, (2) identify links between clinical isolates and positive food/environmental samples, including those at the National Center for Biotechnology Information sequence read archive (https://www.ncbi.nlm.nih.gov/sra/), and (3) explore new methodologies such as metagenomics. GalaxyTrakr hosts a variety of free and adaptable tools and provides the data storage and computing power to run the tools. These tools support coordinated analytic methods and consistent interpretation of results across laboratories. Users can create and share tools for their specific needs and use sequence data generated locally and elsewhere.

Results
In its first full year (2018), GalaxyTrakr processed over 85,000 jobs and went from 25 to 250 users, representing 53 different public and state health laboratories, academic institutions, international health laboratories, and federal organizations. By mid-2020, it has grown to 600 registered users and processed over 450,000 analytical jobs. To illustrate how laboratories are making use of this resource, we describe how six institutions use GalaxyTrakr to quickly analyze and review their data. Instructions for participating in GalaxyTrakr are provided.

Conclusions
GalaxyTrakr advances food safety by providing reliable and harmonized WGS analyses for public health laboratories and promoting collaboration across laboratories with differing resources. Anticipated enhancements to this resource will include workflows for additional foodborne pathogens, viruses, and parasites, as well as new tools and services.
Reduced expression of a subunit gene of sucrose non-fermenting 1 related kinase, PpSnRK1βγ, confers flat fruit abortion in peach by regulating sugar and starch metabolism
Authors: Guo Jian , Cao Ke , Yao Jia-Long , Deng Cecilia , Li Yong , Zhu Gengrui , Fang Weichao , Chen Changwen , Wang Xinwei , Wu Jinlong , Guo Wenwu , Wang Lirong 
Published: February 2021

AbstractBackgroundFruit abortion is a major limiting factor for fruit production. In flat peach, fruit abortion is present in the whole tree of some accessions during early fruit development. However, the physiological factors and genetic mechanism underlying flat fruit abortion remain largely elusive.ResultsIn this study, we have revealed that the fertilization process was accomplished and the reduction of sucrose and starch contents might result in flat fruit abortion. By combining association and gene expression analysis, a key candidate gene,PpSnRK1βγ, was identified. A 1.67-Mb inversion co-segregated with flat fruit shape altered the promoter activity ofPpSnRK1βγ, resulting in much lower expression in aborting flat peach. Ectopic transformation in tomato and transient overexpression in peach fruit have shown thatPpSnRK1βγcould increase sugar and starch contents. Comparative transcriptome analysis further confirmed thatPpSnRK1βγparticipated in carbohydrate metabolism. Subcellular localization found that PpSnRK1βγ was located in nucleus.ConclusionsThis study provides a possible reason for flat fruit abortion and identified a critical candidate gene,PpSnRK1βγ, that might be responsible for flat fruit abortion in peach. The results will provide great help in peach breeding and facilitate gene identification for fruit abortion in other plant species.
Ultrasound-guided transmuscular quadratus lumborum block reduced postoperative opioids consumptions in patients after laparoscopic hepatectomy: a three-arm randomized controlled trial
Authors: Pang Mengya , Sun Guoliang , Yao Weifeng , Zhou Shaoli , Shen Ning , Liao Haofeng , Xie Hanbing , Gao Wanling , Ge Mian 
Published: February 2021

Abstract
Background
To investigate whether transmuscular quadratus lumborum block (TQLB) combined with oxycodone-based patient-controlled intravenous analgesia (PCIA) compared with sufentanil-based patient-controlled intravenous analgesia could reduce postoperative pain and opioid consumption in patients undergoing laparoscopic hepatectomy.

Methods
Eighty patients undergoing laparoscopic hepatectomy surgery were randomly divided into Group S (Sufentanil for PCIA group), Group O (Oxycodone for PCIA group) and Group QO (transmuscular quadratus lumborum block + oxycodone for PCIA group). Primary outcome was Numerical Rating Scale (NRS) pain score when coughing at 6th hour after the operation. We summarized opioid consumption and recorded complications, opioid drug adverse reaction and analgesia satisfaction.

Results
NRS pain scores were significantly lower in Group QO while patients coughing at 6th hour after the operation compared with Group S and Group O (median (interquartile range [IQR]):Group S vs. Group O vs. Group QO 4.0 [3.0, 5.0] vs. 4.0[3.0,5.0]vs.3.0 [2.0, 3.0], p < 0.05). Within 24 h after surgery, the bolus times of PCIA (patient controlled intravenous analgesia) in the QO group was reduced which was compared with the Group S and Group O (median (interquartile range [IQR]):Group S vs. Group O vs. Group QO 13.0 [10.3, 19.5] vs. 11.5 [7.8, 18.3]vs.6.5[3.5,12.0], p < 0.05). The proportion of patients in the three groups who required additional analgesia was ranked as Group QO < Group O < Group S(p < 0.05). The analgesic satisfaction of patients in Group QO was higher than the Group S (p = 0.001) and Group O (p = 0.012).

Conclusions
TQLB combined with oxycodone-based PCIA provided satisfactory postoperative analgesia and reduced oxycodone consumption in patients following laparoscopic hepatectomy.

Trial registration
ChiCTR1900028467 (22/12/2019).
Anatomical correlation between left atrium pulmonary vein ablation targets of atrial fibrillation and adjacent bronchi and pulmonary arteries by MSCT
Authors: Wang Yan-Jing , Sun Huan , Fan Xiao-Fei , Zhang Meng-Chao , Yang Ping , Zeng Hong , Liu Lin 
Published: February 2021

Abstract
Background
The ablation targets of atrial fibrillation (AF) are adjacent to bronchi and pulmonary arteries (PAs). We used computed tomography (CT) to evaluate the anatomical correlation between left atrium (LA)-pulmonary vein (PV) and adjacent structures.

Methods
Data were collected from 126 consecutive patients using coronary artery CT angiography. The LA roof was divided into three layers and nine points. The minimal spatial distances from the nine points and four PV orifices to the adjacent bronchi and PAs were measured. The distances from the PV orifices to the nearest contact points of the PVs, bronchi, and PAs were measured.

Results
The anterior points of the LA roof were farther to the bronchi than the middle or posterior points. The distances from the nine points to the PAs were shorter than those to the bronchi (5.19 ± 3.33 mm vs 8.62 ± 3.07 mm; P < .001). The bilateral superior PV orifices, especially the right superior PV orifices were closer to the PAs than the inferior PV orifices (left superior PV: 7.59 ± 4.14 mm; right superior PV: 4.43 ± 2.51 mm; left inferior PV: 24.74 ± 5.26 mm; right inferior PV: 22.33 ± 4.75 mm) (P < .001).

Conclusions
The right superior PV orifices were closer to the bronchi and PAs than other PV orifices. The ablation at the mid-posterior LA roof had a higher possibility to damage bronchi. CT is a feasible method to assess the anatomical adjacency in vivo, which might provide guidance for AF ablation.