bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classification of hand‐wrist maturity level based on similarity matching
Authors: Mao Keji , Chen Lijian , Wang Minhao , Xu Ruiji , Zhao Xiaomin 
Published: June 2021

AbstractJudging the maturity level of each hand‐wrist reference bone is the core issue in bone age assessment. Relying on the superiority of convolutional neural networks in feature representation, deep learning is widely studied for the automatic bone age assessment. However, an efficient but complex deep learning network requests a large dataset with bone‐maturity‐level labels for training, restricting its large‐scale application in bone maturity classification. For this reason, we transform the bone‐maturity‐level classification problem into the similarity matching problem. Also, we propose a general structure based on Siamese network by merging two inputs into a two‐channel input and introducing a dual attention mechanism, to create an Attentional Two‐Channel Network (ATC‐Net). This paper takes the intermediate phalanges III as an example to assess the performance of the similarity matching method and the ATC‐Net. Experiments show that our method can perform better on small datasets, which effectively makes up for the data shortage problem. The ATC‐Net used for classification significantly reduces the evaluation time compared with other classical networks. It reduces the time of assessing one sample by about 49% as compared to VGG‐16. And more importantly, it achieves the highest classification accuracy of 92.74% among all investigated networks.
High‐frequency measurement of dielectric permittivity and antimicrobial properties of polyaniline and graphite oxide nanocomposites
Authors: L.N. Shubha , Putta ChandraBabu 
Published: June 2021

AbstractThe polyaniline/graphite oxide (PANI/GO) nanocomposite was prepared by the in situ chemical polymerisation method. The synthesis involved the formation of dark green coloured polyaniline/graphite oxide composite. The crystalline structure and morphology of the composite were studied using UV‐visible spectroscopy (UV), X‐ray diffraction (XRD) and transmission electron microscopy (TEM).The characteristic peaks in XRD and UV‐visible spectra confirmed the formation of the PANI/GO nanocomposite. DC conductivity measurements were performed using a two‐probe method. Dielectric responses of the composites were investigated in the frequency range100 MHz to 3 GHz by the RF impedance analyser. The dielectric constant ϵ′(w) and dielectric loss ϵ′′(w) were investigated. It was observed that the dielectric constant ϵ′(w) and dielectric loss ϵ′′(w) decreased with an increase in frequencies (for different wt % of GO). The antibacterial activity of this composite was examined.
Effects of sampling frequency on the proper orthogonal decomposition based reconstruction of a wind turbine wake
Authors: Wang Yan , Wang Liang , Hu RuiFeng , Kong LingXuan , Cheng Jie 
Published: June 2021

AbstractThe effects of sampling frequency on the efficacy of the POD technique for reconstructing the flow field of a wind turbine wake are studied in a neutral atmospheric boundary layer (ABL) using large eddy simulations (LES) coupled with an actuator disk model. The objective of this paper is to study how the sampling frequency over a fixed period of time affects the POD modes. The results showed that sampling frequency has little influence on the convergence of POD modes and the extraction of large‐scale coherent structures. Meanwhile, sampling frequency has negligible influence on the kinetic energy contained in each mode of the first 25 modes. When the mode number is greater than 25, it affects the distributed energy in each mode and the accumulative energy in a given number of modes, and the accuracy of the reconstructed flow field. In present study, the flow field reconstructed using the smallest sampling frequency can be as accurate as that with the largest sampling frequency, while the former can save about 86% of the computational cost. For a given number of POD modes, a smaller sampling frequency may lead to more accurate flow field reconstruction. The sampling frequency mainly affects the small‐scale structures.
Ultrasound Elastography in the Diagnosis of Malignant Cervical Lymphadenopathy in Children: Can It Replace Surgical Biopsy?
Authors: Elgendy Ahmed , Elhawary Eslam , Shareef Mohamed M. , Romeih Marwa , Ebeed Ahmed 
Published: June 2021

AbstractIntroduction We aimed to assess the accuracy of ultrasound elastography in detecting pediatric malignant cervical lymph nodes, and if this modality can obviate the need for surgical biopsies.Material and Methods A prospective study from September 2017 to September 2020 included 64 children with persistent cervical lymphadenopathy. Patients were evaluated by meticulous history and physical assessment. B-mode ultrasound, color Doppler, and sonoelastography were conducted thereafter. Elastography scans were classified into five patterns, and patterns from 3 to 5 were considered as malignancies. All children underwent open biopsies followed by pathological examination. Results of tissue diagnosis were compared with patterns of elastography to determine its accuracy.Results Twenty-eight patients (43.8%) had malignant nodes and the remaining 36 (56.2%) were due to benign causes. Elastography patterns of 1 and 2 were documented in 30 patients, and all of them were diagnosed as benign lesions. Patterns of 3 to 5 were demonstrated in 34 patients. Out of them, 28 were confirmed as malignancies, while 6 children were of benign nature (false positive). Ultrasound elastography achieved sensitivity and specificity of 100 and 85.7%, respectively, and an overall accuracy of 90.6% in the differentiation between malignant and benign entities. The overall accuracy of B-mode and color Doppler were 75 and 82.2%, respectively.Conclusion Elastography is a useful tool that should be added to ultrasound modalities during the diagnosis of pediatric cervical lymphadenopathy. Surgical biopsy in eligible patients is imperative to commence proper therapy or to discharge the child. Despite favorable results of elastography, it cannot replace surgical biopsy or change its indications.
DeepSuggest: Using Neural Networks to Suggest Related Keywords for a Comprehensive Search of Clinical Notes
Authors: Moosavinasab Soheil , Sezgin Emre , Sun Huan , Hoffman Jeffrey , Huang Yungui , Lin Simon 
Published: June 2021

Abstract
Objective A large amount of clinical data are stored in clinical notes that frequently contain spelling variations, typos, local practice-generated acronyms, synonyms, and informal words. Instead of relying on established but infrequently updated ontologies with keywords limited to formal language, we developed an artificial intelligence (AI) assistant (named “DeepSuggest”) that interactively offers suggestions to expand or pivot queries to help overcome these challenges.
Methods We applied an unsupervised neural network (Word2Vec) to the clinical notes to build keyword contextual similarity matrix. With a user's input query, DeepSuggest generates a list of relevant keywords, including word variations (e.g., formal or informal forms, synonyms, abbreviations, and misspellings) and other relevant words (e.g., related diagnosis, medications, and procedures). Human intelligence is then used to further refine or pivot their query.
Results DeepSuggest learns the semantic and linguistic relationships between the words from a large collection of local notes. Although DeepSuggest is only able to recall 0.54 of Systematized Nomenclature of Medicine (SNOMED) synonyms on average among the top 60 suggested terms, it covers the semantic relationship in our corpus for a larger number of raw concepts (6.3 million) than SNOMED ontology (24,921) and is able to retrieve terms that are not stored in existing ontologies. The precision for the top 60 suggested words averages at 0.72. Usability test resulted that DeepSuggest is able to achieve almost twice the recall on clinical notes compared with Epic (average of 5.6 notes retrieved by DeepSuggest compared with 2.6 by Epic).
Conclusion DeepSuggest showed the ability to improve retrieval of relevant clinical notes when implemented on a local corpus by suggesting spelling variations, acronyms, and semantically related words. It is a promising tool in helping users to achieve a higher recall rate for clinical note searches and thus boosting productivity in clinical practice and research. DeepSuggest can supplement established ontologies for query expansion.
Effective and Collegial Governance of Digital Tools in Health Care
Authors: Auerbach Andrew , Burke Kay , Khanna Raman 
Published: June 2021

AbstractDigital transformation of health care has provided an opportunity for broad-based innovation using tools and platforms implemented either through electronic health records (EHRs), adding software to EHRs or prescribing the software to patients directly (e.g., mobile apps). Effective use and management of digital health tools requires a coherent governance strategy that incorporates strategic thinking and clear management priorities. This manuscript reviews nine of the authors’ recommendations for achieving this challenging but critical overall goal for digital health.
Bipolaris victoriae (Victoria blight of oats).
Authors: Taylor Philip 
Published: June 2021

Abstract

A disease almost unknown prior to 1944 (Romanko, 1957), Bipolaris victoriae is a potentially destructive disease of oats (it reduced the Iowa oat crop by 32% in 1947) (Anon, 1965) that currently has a limited host range and geographical spread. It has been reported from several continents and associated with several crops, however its status as a pathogen on crops could be questioned in all cases with the exception of oats, timothy grass and switch grass. It is seedborne and thus any trade in seed both for cultivation or for livestock feed is a potential means of spread. The virulence of the fungus is due to the production of a peptide often called a host-specific toxin 'victorin'. The disease has generally been controlled through the use of genetically resistant lines but the resistance gene which confers resistance to victorin actually causes plants to become susceptible to crown rust, caused by Puccinia coronata (Lorang et al., 2007).
Fusarium oxysporum f.sp. niveum (Fusarium wilt of watermelon).
Authors: Keinath Anthony 
Published: June 2021

Abstract

Fusarium wilt of watermelon occurs throughout the world and is often a limiting factor in watermelon production. In China, 20-30% of watermelon production is normally lost in infested areas, and 100% mortality has been observed in fields planted with susceptible cultivars in Zhejiang Province (Lin, 1990). In a survey of 62 watermelon crops grown in plastic tunnels throughout the main production area of Cyprus, Fusarium wilt was found in all fields sampled despite the use of resistant cultivars (mainly Crimson Sweet). Mean incidence ranged from 37 to 70% in 1985 and 1986, and mean yields of marketable fruit were 38 and 10 t/ha, respectively (Ioannou and Poullis, 1991). In Aydin Province, Turkey, incidence ranged from 0.2 to 12% in fields in which the pathogen was isolated from symptomatic plants (Erİncİk and Döken, 2018). In Spain, in soil infested with unidentified races of F. oxysporum f.sp. niveum, yield loss in a triploid cultivar was 42 to 68% (Miguel et al., 2004). In South Carolina and Georgia, USA, yield losses in research fields naturally infested with race 2 averaged 62 and 83%, respectively, which represented a 91 and 55% loss in net returns per hectare, respectively, based on an average price of $USD 0.35 per kilogram of seedless watermelon fruit.
Heterodera ustinovi (grass cyst nematode).
Authors: Powers Thomas 
Published: June 2021

Abstract

There is limited evidence available to suggest that H. ustinovi is invasive. The identical COI halpotypes shared between the USA and Europe most likely represent recent introductions. The small amount of genetic information from North America suggests that H. ustinovi is widespread in the south west (Arizona), midwest (Ohio) and New England states, with little genetic differentiation. H. ustinovi has not been found on any plant species in the USA other than introduced Agrostis species and in turf/golf course settings. A lot of nematodes are transported in turf from turf farms. The initial discovery on native Agrostis in the Ukraine would suggest a potential native parasite existing on a native plant species, but, there are very few of samples on which to base these comparisons.
Shall genomic correlation structure be considered in copy number variants detection?
Authors: Qin Fei , Luo Xizhi , Cai Guoshuai , Xiao Feifei 
Published: June 2021

AbstractCopy number variation has been identified as a major source of genomic variation associated with disease susceptibility. With the advent of whole-exome sequencing (WES) technology, massive WES data have been generated, allowing for the identification of copy number variants (CNVs) in the protein-coding regions with direct functional interpretation. We have previously shown evidence of the genomic correlation structure in array data and developed a novel chromosomal breakpoint detection algorithm, LDcnv, which showed significantly improved detection power through integrating the correlation structure in a systematic modeling manner. However, it remains unexplored whether the genomic correlation exists in WES data and how such correlation structure integration can improve the CNV detection accuracy. In this study, we first explored the correlation structure of the WES data using the 1000 Genomes Project data. Both real raw read depth and median-normalized data showed strong evidence of the correlation structure. Motivated by this fact, we proposed a correlation-based method, CORRseq, as a novel release of the LDcnv algorithm in profiling WES data. The performance of CORRseq was evaluated in extensive simulation studies and real data analysis from the 1000 Genomes Project. CORRseq outperformed the existing methods in detecting medium and large CNVs. In conclusion, it would be more advantageous to model genomic correlation structure in detecting relatively long CNVs. This study provides great insights for methodology development of CNV detection with NGS data.
Structural Attributes and Principles of the Neocortical Connectome in the Marmoset Monkey
Authors: Theodoni Panagiota , Majka Piotr , Reser David H , Wójcik Daniel K , Rosa Marcello G P , Wang Xiao-Jing 
Published: June 2021

Abstract
The marmoset monkey has become an important primate model in Neuroscience. Here, we characterize salient statistical properties of interareal connections of the marmoset cerebral cortex, using data from retrograde tracer injections. We found that the connectivity weights are highly heterogeneous, spanning 5 orders of magnitude, and are log-normally distributed. The cortico-cortical network is dense, heterogeneous and has high specificity. The reciprocal connections are the most prominent and the probability of connection between 2 areas decays with their functional dissimilarity. The laminar dependence of connections defines a hierarchical network correlated with microstructural properties of each area. The marmoset connectome reveals parallel streams associated with different sensory systems. Finally, the connectome is spatially embedded with a characteristic length that obeys a power law as a function of brain volume across rodent and primate species. These findings provide a connectomic basis for investigations of multiple interacting areas in a complex large-scale cortical system underlying cognitive processes.
Preparation and application of 3-(methylene-bis(1′,4′-phenylene)dicarbamate-2,3-bis(3,5-dimethylphenylcarbamate)-amylose)-2-hydroxylpropoxy-propylsilyl-appended silica particles as chiral stationary phase for HPLC
Authors: Xu Lu , Wang Hui , Yi Jingxuan , Meng Min , Sun Jiahui , Yin Xiaoxing , Zhou Xueyan , Yin Jiale , Wang Yinan , Hou Jasmine , Wei Qunli , Gong Yinhan 
Published: June 2021

Abstract
3-(Methylene-bis(1′,4′-phenylene) dicarbamate-2,3-bis(3,5-dimethylphenylcarbamate)-amylose)-2-hydroxylpropoxy-propylsilyl-appended silica particles (DMP-AM-HPS), a new type of 2, 3-regioselectively substituted amylose-immobilized chiral stationary phase (CSP) for high-performance liquid chromatography (HPLC), have been prepared by treatment of 3-(2,3-dihydroxyl-propoxy)-propylsilyl silica particles with 2,3-bis(3,5-dimethylphenylcarbamate)-amylose and 4,4′-diphenylmethane diisocyanate. The chemical characterization of the bonded particles DMP-AM-HPS has been carried out by elemental analysis and Fourier transform infrared spectroscopic analysis. The chromatographic performance of the DMP-AM-HPS has been evaluated in HPLC under multi-mode conditions including normal phase, reversed phase, and polar organic mobile phase conditions. The DMP-AM-HPS phase has exhibited excellent selectivity in separating enantiomers of a wide range of chiral drug compounds. The result also suggests that unsubstituted C6 hydroxyl groups in the regioselectively substituted amylose not only have important contributions to chiral recognitions and chromatographic separations, but also allow the DMP-AM-HPS to be used as a new type of amylose-immobilized CSP under multi-mode mobile phase conditions in HPLC.
Noninvasive Targeted Crohn Disease Management by Combining Endoscopic Healing Index and Therapeutic Drug Monitoring
Authors: Hemperly Amy , Dubinsky Marla C , Yarur Andres , Afzali Anita , Hanauer Stephen , Kugathasan Subra , Long Millie D , Rabizadeh Shervin , Sockolow Robbyn , Okada Lauren , Jain Anjali , Abreu Maria T , Vande Casteele Niels 
Published: June 2021

Abstract

Background and Aims
Therapeutic drug monitoring (TDM) with measurement of serum drug and antidrug antibody concentrations is used to optimize tumor necrosis factor antagonists (anti-TNF). The endoscopic healing index (EHI) is a validated serum-based assay to measure mucosal inflammation in adults with Crohn disease (CD). Our objectives were to evaluate the relationship between EHI and TDM results and to determine the anti-TNF concentration range associated with EHI &lt;20 (consistent with endoscopic remission).

Methods
Adult and pediatric patients with CD (N = 1731) were selected retrospectively from a clinical laboratory cohort. Patients were selected if they had an ICD-10 code for CD and if results for EHI and TDM were available within 30 days of each other. The relationship between EHI and TDM results was examined and the anti-TNF concentration range associated with EHI &lt;20 vs &gt;50 was evaluated.

Results
Median anti-TNF concentration was higher in patients with EHI &lt;20 vs &gt;50 for infliximab (N = 796): 11.1 vs 3.4 µg/mL and for adalimumab (N = 935): 9.2 vs 5.0 µg/mL (P &lt; 0.0001 both drugs). Patients with antibodies to infliximab (12.8%) or adalimumab (14.9%) had lower anti-TNF concentrations (P &lt; 0.001 both drugs) and higher EHI (P &lt; 0.01 both drugs). The concentration range for infliximab: 5–15 µg/mL (5–9 µg/mL in pediatric patients) and for adalimumab: 5–10 µg/mL (8 µg/mL in pediatric patients) best discriminated EHI &lt;20 vs &gt;50.

Conclusions
We report the anti-TNF concentration range associated with EHI &lt;20. Combined testing of EHI and TDM is proposed as a noninvasive approach for treat-to-target management which could improve the ability to monitor disease and optimize anti-TNF therapy.
The Great Debate With IBD Biosimilars
Authors: Panaccione Remo 
Published: June 2021

Abstract
The costs associated with biologic therapy in immune-mediated diseases, including inflammatory bowel disease has steadily increased since their introduction over 2 decades ago. The introduction of biosimilars has the promise of cost savings and putting reimbursement pressure on future market entries. However, the interpretation of evidence to support the use of biosimilars either as first line or as part of a nonmedical switch strategy is not straight forward due to low to very low-quality evidence. In particular, switching to a biosimilar is associated with both clinical, ethical, and possibly medicolegal issues. Due to these factors, solutions to address cost efficiency should involve an open, transparent, and collaborative dialogue among the various stakeholders and if at all possible involve strategies that allow patients to remain on originator biologics.
The Polish Panel Survey, POLPAN
Authors: Tomescu-Dubrow Irina , Slomczynski Kazimierz M , Sawiński Zbigniew , Kiersztyn Anna , Janicka Krystyna , Życzyńska-Ciołek Danuta , Wysmułek Ilona , Kotnarowski Michał 
Published: June 2021

AbstractThe Polish Panel Survey POLPAN provides data infrastructure to analyze the dynamics of social inequality from a life-course perspective. Historical events shape the study’s research design. In 1987–1988, 5,817 randomly sampled men and women aged 21–65 are interviewed in what is still state socialist Poland. Soon after, their lives are upended by the profound transformations that the anti-communist revolutions in Eastern Europe triggered. To understand how people transition to the emerging social structure, close to half of the respondents are re-interviewed in 1993. This sample serves as a panel that we follow every 5 years, most recently in 2018. Since 1998, POLPAN waves feature renewal samples of the youngest cohort that become part of the panel. Participants are interviewed face-to-face on a wide range of topics, including educational and occupational careers, psychological functioning, physical and mental health, political behaviours, and social attitudes. These topics address POLPAN’s overarching research problem, how does social position influence individual biographies and social networks, and how do individual choices that peoples’ biographies and networks reflect, in turn influence their later social standing. A multi-dimensional approach to data quality informs POLPAN methodology and the decision to publicly share the project’s products, including datasets and analytic tools.
Origin and Evolution of the Cannabinoid Oxidocyclase Gene Family
Authors: van Velzen Robin , Schranz M Eric 
Published: June 2021

AbstractCannabis is an ancient crop representing a rapidly increasing legal market, especially for medicinal purposes. Medicinal and psychoactive effects of Cannabis rely on specific terpenophenolic ligands named cannabinoids. Recent whole-genome sequencing efforts have uncovered variation in multiple genes encoding the final steps in cannabinoid biosynthesis. However, the origin, evolution, and phylogenetic relationships of these cannabinoid oxidocyclase genes remain unclear. To elucidate these aspects, we performed comparative genomic analyses of Cannabis, related genera within the Cannabaceae family, and selected outgroup species. Results show that cannabinoid oxidocyclase genes originated in the Cannabis lineage from within a larger gene expansion in the Cannabaceae family. Localization and divergence of oxidocyclase genes in the Cannabis genome revealed two main syntenic blocks, each comprising tandemly repeated cannabinoid oxidocyclase genes. By comparing these blocks with those in genomes from closely related species, we propose an evolutionary model for the origin, neofunctionalization, duplication, and diversification of cannabinoid oxidocycloase genes. Based on phylogenetic analyses, we propose a comprehensive classification of three main clades and seven subclades that are intended to aid unequivocal referencing and identification of cannabinoid oxidocyclase genes. Our data suggest that cannabinoid phenotype is primarily determined by the presence/absence of single-copy genes. Although wild populations of Cannabis are still unknown, increased sampling of landraces and wild/feral populations across its native geographic range is likely to uncover additional cannabinoid oxidocyclase sequence variants.