bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular detection and phylogenetic analysis of lumpy skin disease virus from outbreaks in Uganda 2017–2018
Authors: Ochwo Sylvester , VanderWaal Kimberly , Ndekezi Christian , Nkamwesiga Joseph , Munsey Anna , Witto Sarah Gift , Nantima Noelina , Mayanja Franklin , Okurut Anna Rose Ademun , Atuhaire David Kalenzi , Mwiine Frank Norbert 
Published: February 2020

Abstract
Background
Lumpy skin disease (LSD) is an infectious viral disease of cattle caused by a Capripoxvirus. LSD has substantial economic implications, with infection resulting in permanent damage to the skin of affected animals which lowers their commercial value. In Uganda, LSD is endemic and cases of the disease are frequently reported to government authorities. This study was undertaken to molecularly characterize lumpy skin disease virus (LSDV) strains that have been circulating in Uganda between 2017 and 2018. Secondly, the study aimed to determine the phylogenetic relatedness of Ugandan LSDV sequences with published sequences, available in GenBank.

Results
A total of 7 blood samples and 16 skin nodule biopsies were screened for LSDV using PCR to confirm presence of LSDV nucleic acids. PCR positive samples were then characterised by amplifying the GPCR gene. These amplified genes were sequenced and phylogenetic trees were constructed. Out of the 23 samples analysed, 15 were positive for LSDV by PCR (65.2%). The LSDV GPCR sequences analysed contained the unique signatures of LSDV (A11, T12, T34, S99, and P199) which further confirmed their identity. Sequence comparison with vaccine strains revealed a 12 bp deletion unique to Ugandan outbreak strains. Phylogenetic analysis indicated that the LSDV sequences from this study clustered closely with sequences from neighboring East African countries and with LSDV strains from recent outbreaks in Europe. It was noted that the sequence diversity amongst LSDV strains from Africa was higher than diversity from Eurasia.

Conclusion
The LSDV strains circulating in Uganda were closely related with sequences from neighboring African countries and from Eurasia. Comparison of the GPCR gene showed that outbreak strains differed from vaccine strains. This information is necessary to understand LSDV molecular epidemiology and to contribute knowledge towards the development of control strategies by the Government of Uganda.
Systematic identification of long intergenic non-coding RNAs expressed in bovine oocytes
Authors: Wang Jian , Koganti Prasanthi P. , Yao Jianbo 
Published: February 2020

Abstract
Background
Long non-coding RNAs (lncRNAs) are key regulators of diverse cellular processes. Although a number of studies have reported the identification of bovine lncRNAs across many tissues, very little is known about the identity and characteristics of lncRNAs in bovine oocytes.

Methods
A bovine oocyte cDNA library was constructed and sequenced using the Illumina HiSeq 2000 sequencing system. The oocyte transcriptome was constructed using the ab initio assembly software Scripture and Cufflinks. The assembled transcripts were categorized to identify the novel intergenic transcripts, and the coding potential of these novel transcripts was assessed using CPAT and PhyloCSF. The resulting candidate long intergenic non-coding RNAs (lincRNAs) transcripts were further evaluated to determine if any of them contain any known protein coding domains in the Pfam database. RT-PCR was used to analyze the expression of oocyte-expressed lincRNAs in various bovine tissues.

Results
A total of 85 million raw reads were generated from sequencing of the bovine oocyte library. Transcriptome reconstruction resulted in the assembly of a total of 42,396 transcripts from 37,678 genomic loci. Analysis of the assembled transcripts using the step-wide pipeline resulted in the identification of 1535 oocyte lincRNAs corresponding to 1183 putative non-coding genes. A comparison of the oocyte lincRNAs with the lncRNAs reported in other bovine tissues indicated that 970 of the 1535 oocyte lincRNAs appear to be unique to bovine oocytes. RT-PCR analysis of 5 selected lincRNAs showed either specific or predominant expression of 4 lincRNAs in the fetal ovary. Functional prediction of the oocyte-expressed lincRNAs suggested their involvement in oogenesis through regulating their neighboring protein-coding genes.

Conclusions
This study provides a starting point for future research aimed at understanding the roles of lncRNAs in controlling oocyte development and early embryogenesis in cattle.
Proposing a re-conceptualisation of competency framework terminology for health: a scoping review
Authors: Mills Jody-Anne , Middleton James W. , Schafer Alison , Fitzpatrick Siobhan , Short Stephanie , Cieza Alarcos 
Published: February 2020

AbstractBackgroundCompetency frameworks are being taken up by a growing number of sectors and for a broad range of applications. However, the topic of competency frameworks is characterised by conceptual ambiguity, misunderstanding and debate. Lack of consistency in the conceptualisation and use of key terminology creates a barrier to research and development, consensus, communication and collaboration, limiting the potential that competency frameworks have to deal with real workforce challenges. This paper aims to advance the field by conducting a detailed review of the literature to understand the underlying causes of conceptual differences and divergent views and proposing a re-conceptualisation of competency framework terminology for use by the health sector.MethodsA broad scoping review of literature was conducted to identify publications relating to the conceptualisation of competency frameworks and key terms, examine how they are conceptualised and determine how this evolved. In addition, a purposive sample of health-related competency frameworks was chosen to illustrate how the terms and concepts are currently being applied in the health context.ResultsOf the 4 155 records identified, 623 underwent text searches and broad quantitative analysis, and 70 were included for qualitative analysis. Quantitative analysis identified 26 key terms, which were coded under six thematic headings. Qualitative analysis using the thematic areas revealed two distinct conceptualisations of competency frameworks and their terminology emerging concurrently in the education and employment sectors, with different underpinnings and purposes. As competency frameworks have developed, these two conceptualisations intertwined, resulting in the same terms being used to convey different concepts. Examination of health-related frameworks showed that this merging of concepts is prominent, with lack of consistency in definitions and use of key terms even within a single organisation.Discussion and conclusionsBuilding on previous efforts to address the lack of conceptual clarity surrounding competency frameworks, this paper proposes a re-conceptualisation of the terminology that encompasses two distinct competency framework interpretations, using a glossary of mutually exclusive terms to differentiate concepts. The re-conceptualisation holds relevance for multiple competency framework applications within health, enabling harmonisation, clear communication, consensus-building and effective implementation of competency frameworks.
Assessment of arthroscopic shavers: a comparison test of resection performance and quality
Authors: Liang Peng , Zhao Gaiping , Gu Xuelian , Chen Zhi , Xu Shaorong , Lai Weiguo , Liu Wentao 
Published: February 2020

Abstract
Background
Arthroscopic shavers play an indispensable role in arthroscopic debridement. They have exquisite structures and similar designs. The purpose of this study was to establish a reproducible testing protocol to compare the resection performance and the quality (tensile strength, torsional strength, and corrosion resistance) of different arthroscopic shavers with comparable designs. We hypothesized that there could be little difference in resection performance and quality between these shavers.

Methods
Incisor Plus Blade (IPB; Smith & Nephew, Andover, MA) and Double Serrated Plus Blade (DSPB; BJKMC, Shanghai, China) were selected for resection performance and quality test. For resection performance testing, the resection torque, which is the minimum torque required to cut off silicone blocks with the same cross-sectional area, was measured to evaluate the resection performance of shaver blades when the other factors remain the same. For quality testing, tensile and torsion tests of the shavers’ joint part were performed, and ultimate failure load and maximum torque were measured and compared. The corrosion resistance of these blades was assessed by the boiling water test based on the ISO13402.

Results
No significant difference existed in the resection torque between the shaver blades of IPB and DSPB (P = 0.54). To the failure load of shavers’ joint parts, IPB was significantly higher than DSPB, both in the outer and inner blades (P < 0.0001). The maximum torque of the joint part had no significant difference between IPB and DSPB (for inner blades P = 0.60 and outer blades P = 0.94). The failure load (for both IPB and DSPB P < 0.0001) and maximum torque (for IPB P = 0.0475 and DSPB P = 0.015) of the inner blades were higher than those of the outer blades. No blemishes were observed on the surface of the blades after corrosion resistance tests.

Conclusions
This study provided some new methods to evaluate the resection performance and quality of different shavers. The resection performance, the torsional strength of the joint part, and the corrosion resistance of IPB and DSPB may show comparable properties, whereas the tensile strength of the shavers’ joint part showed some level of difference.
Rosai-Dorfman disease with pulmonary involvement mimicking bronchogenic carcinoma
Authors: Al-Maghrabi Haneen , Elmahrouk Ahmed , Feteih Maun , Jamjoom Ahmed , Al-Maghrabi Jaudah 
Published: February 2020

Abstract
Background
Rosai-Dorfman disease is a histiocytic lesion that affects lung rarely.

Case presentation
We present a 52-year-old female diagnosed with right intrabronchial mass invading the bronchial wall and the extrabronchial tissues with lymphadenopathy. Multiple bronchoscopic biopsies were not diagnostic. Pneumonectomy was performed and postoperative histology revealed marked mucin impaction and bronchial dilatation. The pulmonary tissue showed areas of hemorrhage and chronic inflammation. The mass exhibited an excessive number of lymphocytes, plasma cells, and numerous histiocytes engulfing them (lymphocytophagocytosis). These histiocytes were S100 protein and CD68 positive. These features are consistent with Rosai-Dorfman disease.

Conclusion
Rosai-Dorfman Disease with pulmonary affection can be misdiagnosed as malignancy. Careful histological examination of the specimen for emperipolesis or lymphocytophagocytosis together with S100 protein and CD68 positivity are the clue for proper diagnosis.
Equivocal expression of emotions in children with Prader-Willi syndrome: what are the consequences for emotional abilities and social adjustment?
Authors: Famelart Nawelle , Diene Gwenaelle , Çabal-Berthoumieu Sophie , Glattard Mélanie , Molinas Catherine , Guidetti Michèle , Tauber Maithe 
Published: February 2020

Abstract
Background
People with Prader-Willi Syndrome (PWS) experience great difficulties in social adaptation that could be explained by disturbances in emotional competencies. However, current knowledge about the emotional functioning of people with PWS is incomplete. In particular, despite being the foundation of social adaptation, their emotional expression abilities have never been investigated. In addition, motor and cognitive difficulties - characteristic of PWS - could further impair these abilities.

Method
To explore the expression abilities of children with PWS, twenty-five children with PWS aged 5 to 10 years were assessed for 1) their emotional facial reactions to a funny video-clip and 2) their ability to produce on demand the facial and bodily expressions of joy, anger, fear and sadness. Their productions were compared to those of two groups of children with typical development, matched to PWS children by chronological age and by developmental age. The analyses focused on the proportion of expressive patterns relating to the target emotion and to untargeted emotions in the children’s productions.

Results
The results showed that the facial and bodily emotional expressions of children with PWS were particularly difficult to interpret, involving a pronounced mixture of different emotional patterns. In addition, it was observed that the emotions produced on demand by PWS children were particularly poor and equivocal.

Conclusions
As far as we know, this study is the first to highlight the existence of particularities in the expression of emotions in PWS children. These results shed new light on emotional dysfunction in PWS and consequently on the adaptive abilities of those affected in daily life.
Biclique: an R package for maximal biclique enumeration in bipartite graphs
Authors: Lu Yuping , Phillips Charles A. , Langston Michael A. 
Published: February 2020

Abstract
Objective
Bipartite graphs are widely used to model relationships between pairs of heterogeneous data types. Maximal bicliques are foundational structures in such graphs, and their enumeration is an important task in systems biology, epidemiology and many other problem domains. Thus, there is a need for an efficient, general purpose, publicly available tool to enumerate maximal bicliques in bipartite graphs. The statistical programming language R is a logical choice for such a tool, but until now no R package has existed for this purpose. Our objective is to provide such a package, so that the research community can more easily perform this computationally demanding task.

Results
Biclique is an R package that takes as input a bipartite graph and produces a listing of all maximal bicliques in this graph. Input and output formats are straightforward, with examples provided both in this paper and in the package documentation. Biclique employs a state-of-the-art algorithm previously developed for basic research in functional genomics. This package, along with its source code and reference manual, are freely available from the CRAN public repository at https://cran.r-project.org/web/packages/biclique/index.html.
Patient and physician perceptions of seasonal allergic rhinitis and allergen immunotherapy: a parallel physician patient survey
Authors: Ellis Anne K. , Boursiquot Jean , Carr Stuart , Graham François , Masse Marie-Soleil 
Published: February 2020

Abstract
Background
The Allergy Patient Identification for Immunotherapy (AsPIRe) program was a parallel physician and patient survey. The objectives were to examine physician and patient perceptions of seasonal allergy symptoms and their impact on patients, and to examine patient and physician attitudes to allergen immunotherapy (AIT) for seasonal allergies. AsPIRe was led by a steering committee and received research ethics board clearance from Queen’s University.

Methods
Allergists (17) from across Canada enrolled in the AsPIRe program and completed an on-line survey to collect demographic information and baseline perceptions. Allergists then recruited patients and completed paper-based parallel physician and patient questionnaires. Patients received an AIT informational booklet with their questionnaire. Patients who were AIT-naïve with no contraindication to AIT and 12 years of age and older met the inclusion criteria.

Results
The survey was in field from February 2018 to June 2018. A total of 141 allergist surveys and 136 patient surveys were completed. Mean age of patients was 30 years old (range 12–70). Fifty-seven percent of patients reported prior knowledge of AIT. Seventy-two percent of patients reported seasonal allergies of longer than 5 years duration and in this subset of patients, 46% were at their first allergist visit. Seventy-three percent of all patients indicated they would be likely or very likely to try sublingual immunotherapy (SLIT), if recommended by their allergist compared to 36% for subcutaneous immunotherapy (SCIT). Conversely, 10% of patients reported they would be unlikely or very unlikely to try SLIT compared to 46% of patients who would be unlikely or very unlikely to try SCIT if recommended by their allergist.

Conclusions
In this particular study cohort, there was a gap in perception between allergists and their patients as to the impact of allergy symptoms on daily life. Patients reported being more frequently impacted vs. their physician’s assessment. When asked about preference for AIT options, Canadian patients reported they were more likely to follow their allergists’ recommendation for initiation of SLIT compared to SCIT.
Inhibition of growth of Asian keloid cells with human umbilical cord Wharton’s jelly stem cell-conditioned medium
Authors: Arjunan Subramanian , Gan Shu Uin , Choolani Mahesh , Raj Vaishnevi , Lim Jane , Biswas Arijit , Bongso Ariff , Fong Chui Yee 
Published: February 2020

AbstractBackgroundKeloid formation occurs in Caucasian, African, and Asian populations and is a severe psychosocial burden on patients. There is no permanent treatment for this problem as its pathogenesis is not properly understood. Furthermore, differences in keloid behavior between ethnic groups are not known. It has been hypothesized that keloids behave like benign tumors because of their uncontrolled growth. The present study evaluated the tumoricidal properties of human Wharton’s jelly stem cell-conditioned medium (hWJSC-CM) on fresh Asian keloid cells (AKCs).MethodsHuman Wharton’s jelly stem cells (hWJSCs) and AKCs were isolated based on our previous methods. hWJSCs and human skin fibroblasts (HSF) (controls) were used to collect hWJSC-CM and HSF-conditioned medium (HSF-CM). AKCs were treated with hWJSC-CM and HSF-CM in vitro and in vivo in a human keloid xenograft SCID mouse model. The inhibitory effect of hWJSC-CM on AKCs was tested in vitro using various assays and in vivo for attenuation/abrogation of AKC tumors created in a xenograft mouse model.ResultsqRT-PCR analysis showed that the genes FN1, MMP1, and VCAN were significantly upregulated in AKCs and ANXA1, ASPN, IGFBP7, LGALS1, and PTN downregulated. AKCs exposed to hWJSC-CM in vitro showed significant decreases in cell viability and proliferation, increases in Annexin V-FITC+ cell numbers, interruptions of the cell cycle at Sub-G1 and G2/M phases, altered CD marker expression, downregulated anti-apoptotic-related genes, and upregulated pro-apoptotic and autophagy-related genes compared to controls. When AKCs were administered together with hWJSC-CM into immunodeficient mice there were no keloid tumors formed in 7 mice (n = 10) compared to the untreated control mice. When hWJSC-CM was injected directly into keloid tumors created in mice there were significant reductions in keloid tumor volumes and weights in 30 days.ConclusionshWJSC-CM inhibited the growth of AKCs in vitro and in xenograft mice, and it may be a potential novel treatment for keloids in the human. The specific molecule(s) in hWJSC-CM that induce the anti-keloid effect need to be identified, characterized, and tested separately in larger preclinical and clinical studies.
A self-attention based message passing neural network for predicting molecular lipophilicity and aqueous solubility
Authors: Tang Bowen , Kramer Skyler T. , Fang Meijuan , Qiu Yingkun , Wu Zhen , Xu Dong 
Published: February 2020

AbstractEfficient and accurate prediction of molecular properties, such as lipophilicity and solubility, is highly desirable for rational compound design in chemical and pharmaceutical industries. To this end, we build and apply a graph-neural-network framework called self-attention-based message-passing neural network (SAMPN) to study the relationship between chemical properties and structures in an interpretable way. The main advantages of SAMPN are that it directly uses chemical graphs and breaks the black-box mold of many machine/deep learning methods. Specifically, its attention mechanism indicates the degree to which each atom of the molecule contributes to the property of interest, and these results are easily visualized. Further, SAMPN outperforms random forests and the deep learning framework MPN from Deepchem. In addition, another formulation of SAMPN (Multi-SAMPN) can simultaneously predict multiple chemical properties with higher accuracy and efficiency than other models that predict one specific chemical property. Moreover, SAMPN can generate chemically visible and interpretable results, which can help researchers discover new pharmaceuticals and materials. The source code of the SAMPN prediction pipeline is freely available at Github (https://github.com/tbwxmu/SAMPN).
Modelling the transmission dynamics of bovine digital dermatitis in New Zealand pastoral dairy production systems
Authors: Yang D. Aaron , Laven Richard A. , Müller Kristina R. , Gates M. Carolyn 
Published: February 2020

AbstractBovine digital dermatitis (DD) is an important infectious cause of cattle lameness worldwide that has become increasingly prevalent in New Zealand pastoral dairy herds. In this study, a simplified DD scoring system after considering both M and Iowa DD scoring systems was applied to explore the transmission dynamics of DD in a typical spring-calving pastoral New Zealand dairy herd. The modified model only included three compartments: normal skin, early stage lesions and advanced lesions. Lesions regressing after treatment were excluded as DD lesions are rarely treated in New Zealand. Furthermore, sub-classes within each lesion class were not defined due to the lack of variability in DD lesion presentations within New Zealand. The model was validated based on longitudinal field data from three dairy herds in the Waikato region during one lactation season (2017–18). The model suggested that in infected dairy herds, although DD prevalence will tend to increase year-on-year it is likely to remain relatively low (< 18%) even after 10 years of within-herd transmission. It is likely that the low transmission rate during the late lactation (model assumption) results in more cases resolving than developing during this period and therefore results in the low prevalence of infectious cattle at the start of each subsequent lactation. Cattle with advanced lesions had a stronger influence on the establishment and maintenance of DD than cattle with early stage lesions highlighting the importance of targeting these animals for intervention. On-going monitoring of DD is highly recommended to assess the long-term progression of the disease in affected dairy herds.