bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon
Authors: Sultana Nusrat , Menzel Gerhard , Seibt Kathrin M. , Garcia Sònia , Weber Beatrice , Serçe Sedat , Heitkam Tony 
Published: July 2021

ABSTRACTBACKGROUNDLong terminal repeat (LTR) retrotransposons are widespread in plant genomes and play a large role in the generation of genomic variation. Despite this, their identification and characterization remains challenging, especially for non-model genomes. Hence, LTR retrotransposons remain undercharacterized in Vaccinium genomes, although they may be beneficial for current berry breeding efforts.OBJECTIVEExemplarily focusing on the genome of American cranberry (Vaccinium macrocarpon Aiton), we aim to generate an overview of the LTR retrotransposon landscape, highlighting the abundance, transcriptional activity, sequence, and structure of the major retrotransposon lineages.METHODSGraph-based clustering of whole genome shotgun Illumina reads was performed to identify the most abundant LTR retrotransposons and to reconstruct representative in silico full-length elements. To generate insights into the LTR retrotransposon diversity in V. macrocarpon, we also queried the genome assembly for presence of reverse transcriptases (RTs), the key domain of LTR retrotransposons. Using transcriptomic data, transcriptional activity of retrotransposons corresponding to the consensuses was analyzed.RESULTSWe provide an in-depth characterization of the LTR retrotransposon landscape in the V. macrocarpon genome. Based on 475 RTs harvested from the genome assembly, we detect a high retrotransposon variety, with all major lineages present. To better understand their structural hallmarks, we reconstructed 26 Ty1-copia and 28 Ty3-gypsy in silico consensuses that capture the detected diversity. Accordingly, we frequently identify association with tandemly repeated motifs, extra open reading frames, and specialized, lineage-typical domains. Based on the overall high genomic abundance and transcriptional activity, we suggest that retrotransposons of the Ale and Athila lineages are most promising to monitor retrotransposon-derived polymorphisms across accessions.CONCLUSIONSWe conclude that LTR retrotransposons are major components of the V. macrocarpon genome. The representative consensuses provide an entry point for further Vaccinium genome analyses and may be applied to derive molecular markers for enhancing cranberry selection and breeding.
Revealing Protein-Level Functional Redundancy in the Human Gut Microbiome using Ultra-deep Metaproteomics
Authors: Li Leyuan , Ning Zhibin , Zhang Xu , Butcher James , Simopoulos Caitlin , Mayne Janice , Stintzi Alain , Mack David R. , Liu Yang-Yu , Figeys Daniel 
Published: July 2021

SummaryFunctional redundancy is a key property of ecosystems and represents the fact that phylogenetically unrelated taxa can play similar functional roles within an ecosystem. The redundancy of potential functions of human microbiome has been recently quantified using metagenomics data. Yet, the redundancy of functions which are actually expressed within the human microbiome remains largely unexplored. Here, we quantify the protein-level functional redundancy in the human gut microbiome using metaproteomics and network approaches. In particular, our ultra-deep metaproteomics approach revealed high protein-level functional redundancy and high nestedness in proteomic content networks - bipartite graphs that connect taxa with their expressed functions. We further examined multiple metaproteomics datasets and showed that various environmental factors, including individuality, biogeography, xenobiotics, and disease, significantly altered the protein-level functional redundancy. Finally, by projecting the bipartite proteomic content networks into unipartite weighted genus networks, functional hub genera across individual microbiomes were discovered, suggesting that there may be a universal principle of functional organization in microbiome assembly.HighlightsUltra-deep metaproteomics reveals high protein-level functional redundancy in the human gut microbiomeWithin-sample proteomic content networks display universal topologyVarious environmental factors influence the redundancy of expressed functionsFunctional hub genera are present across different datasets
Accurate prediction of functional states of cis-regulatory modules reveals the common epigenetic rules in humans and mice
Authors: Ni Pengyu , Moe Joshua , Su Zhengchang 
Published: July 2021

AbstractWe proposed a two-step approach for predicting active cis-regulatory modules (CRMs) in a cell/tissue type. We first predict a map of CRM loci in the genome using all available transcription factor binding data in the organism, and then predict functional states of all the putative CRMs in any cell/tissue type using few epigenetic marks. We have recently developed a pipeline dePCRM2 for the first step, and now presented machine-learning methods for the second step. Our approach substantially outperforms existing methods. Our results suggest common epigenetic rules for defining functional states of CRMs in various cell/tissue types in humans and mice.
Low dose AKT inhibitor miransertib cures PI3K-related vascular malformations in preclinical models of human disease
Authors: Kobialka Piotr , Sabata Helena , Vilalta Odena , Angulo-Urarte Ana , Muixí Laia , Zanoncello Jasmina , Muñoz-Aznar Oscar , Olaciregui Nagore G. , Lavarino Cinzia , Celis Veronica , Rovira Carlota , López Susana , Baselga Eulàlia , Mora Jaume , Castillo Sandra D. , Graupera Mariona 
Published: July 2021

ABSTRACTLow-flow vascular malformations are congenital overgrowths composed by abnormal blood vessels potentially causing pain, bleeding, and obstruction of different organs. These diseases are caused by oncogenic mutations in the endothelium which result in overactivation of the PI3K/AKT pathway. Lack of robustin vivopreclinical data has prevented the development and translation into clinical trials of specific molecular therapies for these diseases. Here, we describe a new reproducible preclinicalin vivomodel of PI3K-driven vascular malformations using the postnatal mouse retina. This model reproduces human disease withPik3caactivating mutations expressed in a mosaic pattern and vascular malformations formed in veins and capillaries. We show that active angiogenesis is required for the pathogenesis of vascular malformations caused by activatingPik3camutations. Using this model, we demonstrate that low doses of the AKT inhibitor miransertib both prevents and induces the regression of PI3K-driven vascular malformations. We confirmed miransertib efficacy in isolated human endothelial cells with genotypes spanning most of human low-flow vascular malformations.Graphical abstractLow-flow vascular malformations are caused by PI3K signalling overactivation in endothelial cells. We have generated an optimised and robust preclinical system of PI3K-driven vascular malformations by inducing the mosaic expression ofPik3caH1047Rin the retinal angiogenic endothelium. This preclinical model displays traits constituting the main hallmarks of the pathogenesis of low-flow blood vascular malformations: overactivation of PI3K signalling (high phospho-S6), vascular compartment specificity, loss of pericyte coverage, and endothelial cell hyperproliferation. Using this preclinical model we report that low dose AKT inhibitor miransertib prevents and regress PI3K-driven vascular malformations.
Temperature and guanidine hydrochloride effects on the folding thermodynamics of WW domain and variants
Authors: Qin Meng , Denesyuk Natalia , Liu Zhenxing , Wang Wei , Thirumalai D. 
Published: July 2021

AbstractWe used simulations based on an all atom Go model to calculate the folding temperatures (Tfs) and free energies (ΔGs) of two variants of the WW domain, which is a small allβ-sheet protein. The results,without adjusting any parameter, are in good agreement with experiments, thus validating the simulations. We then used the Molecular Transfer Model to predict the changes in the ΔGandTfs as guanidine hydrochloride concentration is varied. The predictions can be readily tested in experiments.
An early-stage project complexity assessment tool for the AEC industry
Authors: Vaz-Serra Paulo , Edwards Peter , Aranda-Mena Guillermo 
Published: July 2021

Purpose
Complex projects require careful management. They may expose stakeholders to greater risks and place additional demands upon resources. In the initial stages of project development, however, little may be known about the nature and magnitude of such complexity. This paper aims to ensure that this gap is at least subjectively assessed and addressed.

Design/methodology/approach
Research, using focus group workshops with a convenience sample of construction professionals, was carried out to test the validity of a Project Early Stage Complexity Assessment Tool (PESCAT). The PESCAT concept brings together selected complexity theories and uses subjectively based measures for assessment.

Findings
The findings confirm that an early-stage project complexity assessment tool is practicable and can contribute to project management practice in the construction industry. It should be applied by individual project stakeholders using small teams of experienced staff. PESCAT explores project complexity through “filter” sets of perspective factors which should be customised to reflect the stakeholder’s role and processes in a project.

Originality/value
In the initial complexity assessment model, resolution space and uncertainty were tested as project complexity parameters. However, in subsequent versions of the tool, four measures (differentiation and differentiation uncertainty; interdependency and interdependency uncertainty) are used in an innovative way that focuses users’ attention more clearly and points to a more targeted approach for addressing project complexity. The value of our model lies in its practical application and the project management benefits it can deliver.
A new conceptual framework for memorable Airbnb experiences: guests’ perspectives
Authors: Sthapit Erose , Björk Peter , Coudounaris Dafnis N. , Stone Matthew J. 
Published: July 2021

Purpose
This qualitative study aims to explore the activities that guests perform while staying in Airbnbs, emotions associated with these experiences and the components of memorable Airbnb experiences.

Design/methodology/approach
An empirical study of a qualitative nature was conducted using a self-administered open-ended questionnaire among tourists who had stayed in an Airbnb in the past three years. Data were collected using two different sources for triangulation purposes, referred to as Studies 1 and 2.

Findings
Many respondents reported conducting similar activities while at home and while staying in an Airbnb, supporting Burch’s (1969) spill-over theory. Travellers mostly recalled mundane activities, such as cooking. The results suggest that the spill-over effect is more prevalent in the Airbnb context than in other accommodation types, as one often travels from one’s own home to another’s home. Respondents associated their Airbnb experience with the positive emotion of joy. Respondents mentioned numerous reasons for having felt joy during their Airbnb experiences, such as sharing the trip with travel companions and spending time with friends.

Practical implications
Airbnb should clearly define host’s tasks and responsibilities, hosts should treat guests in a friendly manner, which includes resolving any problems they face in relation to the rental property.

Originality/value
This paper proposes a new conceptual framework for a memorable Airbnb experience, which comprises several components: socialising and bonding with friends and family members, location, the host’s hospitality, a homely feeling, home amenities and negative experiences (the poor condition of the room and a dishonest host).
Can an ecological-transactional systems model in occupational therapy contribute to a social prescribing programme?
Authors: Johansson Erika , Rapo Emil , Nilsson Ingeborg 
Published: July 2021

Purpose
The spread and level of loneliness is today considered a public health issue. Attempts to promote or reduce the level of loneliness have been made, one of which is social prescribing (SP), developed and extensively used. Complex interventions such as SP are advised to be connected to theory.

Design/methodology/approach
For this purpose, the Person-Environment-Occupation-Participation model (PEOP) will be reviewed and used as an example, both as a way of organize occupational knowledge and as a model for practice.

Findings
Occupational therapy underpinned by transactional system theory such as the PEOP model seems to give comprehensive and relevant support in the SP process. Particularly, this model can guide practitioners through crucial phases when assessing needs, matching interests and goals with relevant occupations, as well as understanding of important components embedded in the program.

Originality/value
This opinion piece offers insights in why and how specific components connected to SP needs to be understood by theory and applied by personnel to facilitate a meaningful and sustainable occupational performance for the individuals.
Changing social burden of Japan’s three major diseases including Long-term Care due to aging
Authors: Hirata Koki , Matsumoto Kunichika , Onishi Ryo , Hasegawa Tomonori 
Published: July 2021

PurposeThe purpose of this article is to clarify the social burden of Japan’s three major diseases including Long-term Care (LTC) burden.Design/methodology/approachA modification of the Cost of Illness (COI)—the Comprehensive-COI (C-COI) was utilized to estimate three major diseases: cancer, heart disease, and cerebrovascular diseases (CVD). The C-COI consists of five parts: medical direct cost, morbidity cost, mortality cost, formal LTC cost and informal LTC cost. The latter was calculated by two approaches: opportunity cost approach (OC) and replacement approach (RA), which assumed that informal caregivers were substituted by paid caregivers.FindingsThe C-COI of cancer, heart disease and CVD in 2017 amounted to 10.5 trillion JPY, 5.2 trillion JPY, and 6.7 trillion JPY, respectively (110 JPY= 1 US$). The mortality cost was preponderant for cancer (61 percent) and heart disease (47.9 percent); while the informal LTC cost was preponderant for CVD (27.5 percent). The informal LTC cost of the CVD in OC amounted to 1.8 trillion JPY; while the RA amounted to 3.0 trillion JPY.Social implicationsThe LTC burden accounted for a significant proportion of the social burden of chronic diseases. The informal care was maintained by unsustainable structures such as the elderly providing care for the elderly. This result can affect health policy decisions.Originality/valueThe C-COI is more appropriate for estimating the social burden of chronic diseases including the LTC burden and can be calculated using governmental statistics.
Educators’ experiences in special education institutions during the COVID‐19 outbreak
Authors: Yakut Ayse Dilsad 
Published: July 2021

The COVID‐19 outbreak has had a profound impact on education worldwide. As a result of the educational institutions closures, it is likely that the impact on special education would be more detrimental since special education population becomes more vulnerable in the aftermath of an outbreak. In the scope of this study, a researcher created survey was used to examine educators’ teaching experiences and their perceptions about the impact of COVID‐19 outbreak on special education students. The sample included 215 educators working in the Special Education and Rehabilitation Centers (SERCs) in Turkey. Results indicated that a large majority of the SERCs were not able to continue their education during the COVID‐19 outbreak. In addition, there was a difference in educators’ experiences by their educational practices (normal weekly schedule, reduced schedule, most of the educational activities are suspended, and all of the educational activities are suspended). Perceived level of COVID‐19 outbreak impact on special education students were found to be significantly higher for autism spectrum disorders, intellectual disabilities, attention deficit and hyperactivity disorders, visual impairments, hearing impairments, specific learning disabilities and gifted students, respectively. The conclusion highlights the need of global collaboration, disaster preparation and management for students with special needs.
Improving estimates of Medicaid's effect on poverty: Measures and counterfactuals
Authors: Zewde Naomi , Remler Dahlia , Hyson Rosemary , Korenman Sanders 
Published: July 2021

AbstractObjectiveTo re‐evaluate the effect of Medicaid on poverty using a poverty measure that accounts for health insurance needs and benefits and an evaluation approach that reflects disparities in access to alternative coverage.Data SourcesThe Current Population Survey (CPS) for calendar year 2015.Study DesignWe estimate the effect of losing Medicaid on poverty, combining two previous approaches: (1) A propensity impact, which simulates a no‐Medicaid counterfactual incorporating changes to health insurance and medical out‐of‐pocket spending, using the Supplemental Poverty Measure (SPM). This measure does not reflect a need for health care access nor how health benefits meet that need. (2) An accounting impact, which assumes that those losing Medicaid remain uninsured and does not incorporate any behavioral changes, using the health‐inclusive poverty measure (HIPM). This measure includes a need for health insurance in the threshold and health insurance benefits in resources.Data Collection/Extraction MethodsNot applicable.Principal FindingsUsing the propensity‐matched approach, we attributed a 2.5 percentage point reduction in health‐inclusive poverty among those younger than age 65 to the Medicaid program, between the 1.0‐point SPM propensity‐match impact and the 3.9‐point HIPM accounting impact. Medicaid's antipoverty impact and HIPM‐SPM differences are greater among those who would become uninsured. HIPM propensity‐matched estimates reveal much larger impacts of Medicaid on poverty disparities linked to race/ethnicity and single parenthood than SPM‐based propensity estimates.ConclusionsBoth the poverty measure and the method used to estimate the counterfactual make substantial, policy‐relevant differences to estimates of Medicaid's impact on poverty. A poverty measure that fails to incorporate health insurance needs and benefits substantially underestimates Medicaid's effect. Failing to consider adjustments in insurance coverage and out‐of‐pocket spending substantially overestimates Medicaid's effect and underestimates its reduction of disparities.
Prediction in HRM research–A gap between rhetoric and reality
Authors: Sarstedt Marko , Danks Nicholas P. 
Published: July 2021

AbstractThere are broadly two dimensions on which researchers can evaluate their statistical models: explanatory power and predictive power. Using data on job satisfaction in ageing workforces, we empirically highlight the importance of distinguishing between these two dimensions clearly by showing that a model with a certain degree of explanatory power can produce vastly different levels of predictive power and vice versa—in the same and different contexts. In a further step, we review all the papers published in three top‐tier human resource management journals between 2014 and 2018 to show that researchers generally confuse explanation and prediction. Specifically, while almost all authors rely solely on explanatory power assessments (i.e., assessing whether the coefficients are significant and in the hypothesised direction), they also derive practical recommendations, which inherently result from a predictive scenario. Based on our results, we provide HRM researchers recommendations on how to improve the rigour of their explanatory studies.
Media coverage of industry and the cross‐section of stock returns
Authors: Huang Tao , Zhang Xueyong 
Published: July 2021

AbstractThis paper investigates the cross‐sectional relation between media coverage of industry and expected stock returns. Using abnormal industry‐level news volume as a proxy for industry‐level media coverage, we find that stocks in industries with lower media coverage earn significantly higher future returns than stocks in industries with higher media coverage. This finding is robust even after controlling for well‐known stock characteristics and proxies for stock‐specific attention. Moreover, the return premium of lower industry‐level media coverage experiences continuation in the following 2 months, only to be followed by a reversal in the third month, due to the erosion of media coverage.
Development of a 19‐plex short tandem repeat typing system for individual identification and parentage testing of horses (Equus caballus)
Authors: Shang S. , Jiang R. , Luo R. , Jia S. , Irwin D. M. , Wang Z. , Zhang S. 
Published: July 2021

SummaryIndividual identification of horses for pedigree verification and registration is important for the sustainable development of the horse industry. Horse individual identification and parentage tests commonly use the 17 short tandem repeats (STRs) recommended by the International Society for Animal Genetics (ISAG) and the locus LEX33. While many multiplex STR typing systems have been established for the horse, a sex determining marker is usually absent, and none of them can simultaneously detect all 17 ISAG recommended loci and the locus LEX33. Here, we present a 19‐plex STR typing system that contains the 17 ISAG recommend loci, the locus LEX33 and amelogenin as sex determining loci. The results of our sensitivity, species specificity, stutter analysis and population data analysis, indicate that this system is a specific, sensitive, and robust tool for the identification of individuals, parentage testing and genetic research in the horse.
Circ_0011460 upregulates HTRA1 expression by sponging miR‐762 to suppress HTR8/SVneo cell growth, migration, and invasion
Authors: Fan Zhongyan , Wang Qiming , Deng Hui 
Published: July 2021

AbstractBackgroundAberrant expression of circular RNAs (circRNAs) during placental development could affect fetal growth and contribute to preeclampsia (PE). Circ_0011460 was found to be differentially expressed in placental samples of PE. However, the exact function and mechanism of circ_0011460 in PE process remain largely undefined.MethodsLevels of circ_0011460, microRNA (miR)‐762, and high‐temperature requirement‐A serine peptidase 1 (HTRA1) were detected using quantitative real‐time polymerase chain reaction and Western blot. In vitro experiments in HTR8/SVneo cells were conducted using cell counting kit‐8, wound healing, transwell, flow cytometry and Western blot assays. The direct interactions between miR‐762 and circ_0011460 or HTRA1 were verified using dual‐luciferase reporter, RNA immunoprecipitation (RIP) and RNA pull‐down assays.ResultsCirc_0011460 possessed a loop structure and was highly expressed in placental tissues of PE patients. Overexpression of circ_0011460 greatly suppressed HTR8/SVneo cell proliferation, migration, and invasion, and accelerated cell apoptosis. While circ_0011460 knockdown yielded the opposite trends on above biological behaviors. Mechanistically, we confirmed that circ_0011460 could up‐regulate HTRA1 expression via serving as a sponge of miR‐762. Further rescue studies demonstrated that circ_0011460 exerted its roles via targeting miR‐762, and miR‐762 promoted HTR8/SVneo cell growth, migration and invasion via regulating HTRA1.ConclusionIn all, circ_0011460 suppressed HTR8/SVneo cell growth, migration, and invasion via miR‐762/HTRA1 axis, suggesting a new insight into the pathogenesis of PE.