bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracking Closely Related Enteric Bacteria at High Resolution in Fecal Samples of Premature Infants Using a Novel rRNA Amplicon
Authors: Graf J. , Ledala N. , Caimano M. J. , Jackson E. , Gratalo D. , Fasulo D. , Driscoll M. D. , Coleman S. , Matson A. 
Published: September 2020

AbstractIdentifying and tracking microbial strains as microbiomes evolve is a major challenge in the field of microbiome research. Longitudinal microbiome samples of co-admitted twins from two different neonatal intensive care units (NICUs) were analyzed using a ∼2,500 base amplicon that spans the 16S and 23S rRNA genes, and mapped to a new 16S-23S rRNA database. Amplicon Sequence Variants inferred using DADA2 provided sufficient resolution for differentiation of rRNA variants from closely related, but not previously sequenced Klebsiella, E. coli, and Enterobacter, among the first bacteria colonizing the gut of these infants after admission to the NICU. Distinct ASV groups (fingerprints) were followed between co-admitted twins over time, demonstrating the potential to track the source and spread of both commensals and pathogens.The high-resolution taxonomy obtained from long amplicon sequencing enable tracking of strains temporally and spatially as microbiomes are established in infants in the hospital environment.
A Multi-center Study of COVID-19 with Multivariate Prognostic Analysis
Authors: Zeng Wen , Feng Xin , Huang Jie , Du Chuan , Qu Dongming , Zhang Xiang , Zhang Jianquan 
Published: September 2020

AbstractPurposeCoronavirus disease (COVID-19) pandemic is now a global health concern. However, there is no detailed analysis of the factors related to patients’ improvement.Patients and methodsWe compared the clinical characteristics, laboratory findings, CT images, and treatment of COVID-19 patients from two different cities in China. One hundred and sixty-nine patients were recruited from January 27 to March 17, 2020 at five hospitals in Hubei and Guangxi. They were divided into four groups according to age and into two groups according to presence of comorbidities. Multivariate statistical analyses were performed for the prognosis of the disease.ResultsFifty-two patients (30.8%) had comorbidities, and the percentage of critical COVID-19was higher in the comorbidities group (11.6%vs.0.9%, p<0.05). Older patients had higher proportion of severe or critical disease. The results showed that lymphocyte count was significantly associated with the number of days from positive COVID-19 nucleic acid test to negative test; number of days from onset of symptoms to confirmation of diagnosis was significantly associated with the time it took for symptoms to improve; and number of days from onset of symptoms to confirmation of diagnosis and disease severity were significantly associated with chest computed tomography improvement.ConclusionsAge, comorbidities, lymphocyte count, and SpO2 may predict the risk of severity of COVID-19. Early isolation, early diagnosis, and early initiation of management can slow down the progression and spread of COVID-19.Key PointsAge and comorbidities can predict the risk of severity of COVID-19, Lymphocyte count and SpO2 may predict the risk of severity of COVID-19. Early isolation, Early diagnosis can slow down the progression of COVID-19
Urbanization alters ecological and evolutionary interactions between Darwin’s finches andTribulus cistoideson the Galápagos Islands
Authors: Rivkin L. Ruth , Johnson Reagan A. , Chaves Jaime A. , Johnson Marc T.J. 
Published: September 2020

AbstractEmerging evidence suggests that urbanization shapes the ecology and evolution of species interactions. Islands are particularly susceptible to urbanization due to the fragility of their ecosystems; however, few studies have examined the effects of urbanization on species interactions on islands. To address this gap, we studied the effects of urbanization on interactions between Darwin’s finches and its key food resource,Tribulus cistoides, in three towns on the Galápagos Islands. We assessed the effects of urbanization on seed and mericarp removal, mericarp morphology, and finch community composition using natural population surveys, experimental manipulations, and finch observations. We found that both seed and fruit removal rates were higher in urban compared to non-urban populations in the natural and experimental populations, and that urbanization modified selection on mericarp size and defense. Urban environments supported smaller and less diverse finch communities than non-urban environments. Together, our results suggest that urbanization can dramatically alter ecological interactions between Darwin’s finches andT. cistoides, leading to modified selection onT. cistoidespopulations. Our study demonstrates that urban development on islands can have profound effects on the ecology and evolution of trophic interactions.
Enhanced retinoid response by a combination of the vitamin A ester retinyl propionate with niacinamide and a flavonoid containingCeratonia siliquaextract in retinoid responsivein vitromodels
Authors: Lam Eric C.S. , Li Rui , Rodrigues MyriamRubecca , Vires Laura , Adams Rachel L. , Sherrill Joseph D. , Oblong John E. 
Published: September 2020

AbstractOBJECTIVESRetinoids have been used for decades as efficacious topical agents to treat photoaged skin. The purpose of our present research is to evaluate whether the activity of the Vitamin A ester retinyl propionate (RP) can be enhanced by niacinamide (Nam) and a flavonoid containingCeratonia siliqua(CS) fruit extract in retinoid responsivein vitromodels.METHODSRP was tested alone and in combination with Nam andCSin an RARα reporter cell line for promoter activation and compared totrans-retinoic acid (tRA) activation. These treatments were also tested in keratinocytes for gene expression profiling by qPCR using a panel of 40 retinoid responsive genes.RESULTStRA or RP elicited RARα reporter activation in a dose dependent manner. The combination of 0.5 μM or 2 μM RP with 10 mM Nam had a 56% and 95% signal increase compared to RP, respectively. The addition of 1%CSto 0.5 μM or 2 μM RP with 10 mM Nam elicited a further increase of 114% and 156%, respectively, over RP and Nam combinations. All retinoids elicited an increase in expression of 40 retinoid sensitive genes over control levels. Of the 40 genes 27 were enhanced by either 0.5 μM RP or 2 μM RP with 10 mM Nam and 1%CS. Nam orCShad very modest activity in both models.CONCLUSIONThe combination of RP with Nam andCSshowed a higher retinoid response than RP in two separate retinoid responsivein vitromodels. We hypothesize Nam andCSenhances RP activity by modulating metabolism to tRA via increasing NAD+pools and inhibiting reduction of retinal (RAL) back to retinol, respectively. The findings provide evidence that this combination may have enhanced efficacy for treating the appearance of photoaged skin.
Cytokines (IL-17, IL-23 and IL-33) in Systemic lupus erythematosus in Trinidad and Tobago
Authors: Vaillant Angel Justiz , Akpaka Patrick E 
Published: September 2020

AbstractSystemic lupus erythematosus (SLE) is the most common autoimmune disease. It is characterized by the presence of hundreds of autoantibodies against many organs and tissues, including the presence of a large number of autoantibodies, which are specific to self-antigens mainly of nuclear origin such as Smith antigen, double-stranded DNA (dsDNA), anti-Sjögren’s syndrome-related antigen A and B (SSA/Ro and SSB/La, respectively) and ribonucleoproteins, which are the hallmarks of the disease. Type I and II interferons, interleukin-6 (IL-6), IL-1, tumor necrosis factor-alpha (TNF-α), and immunomodulatory cytokines such as IL-10 and TGF-β are essential players in SLE. Additionally, T-cell-derived cytokines such as IL-17, IL-21, and IL-2 are dysregulated in SLE. In this study among cohorts of 60 individuals attending the hospital clinics in Trinidad and Tobago, blood samples were analyzed and the levels of the essential cytokines were measured using SLE Disease Activity Index (SLEDAI) 2000 score. The results confirmed that serum IL-17 and IL-23 levels were positively correlated with the SLE Disease Activity Index (SLEDAI) 2000 score in these patients. These findings have diagnostic and therapeutic implications. However, more work must be done targeting other cytokines relevant to autoimmunity and SLE in particular. Interleulin-33 is not an SLE marker, as has been noted in other populations.
Transposon- and genome dynamics in the fungal genusNeurospora: insights from nearly gapless genome assemblies
Authors: Nguyen Diem , Peona Valentina , Unneberg Per , Suh Alexander , Jern Patric , Johannesson Hanna 
Published: September 2020

AbstractBackgroundA large portion of nuclear DNA is composed of transposable element (TE) sequences, whose transposition is controlled by diverse host defense strategies in order to maintain genomic integrity. One such strategy is the fungal-specific Repeat-Induced Point (RIP) mutation that hyper-mutates repetitive DNA sequences. While RIP is found across Fungi, it has been shown to vary in efficiency. To date, detailed information on the TE landscapes and associated RIP patterns exist only in a few species belonging to highly divergent lineages.ResultWe investigated 18 nearly gapless genome assemblies of tenNeurosporaspecies, which diverged from a common ancestor about 7 MYA, to determine genome-wide TE distribution and their associated RIP patterns. We showed that the TE contents between 8.7-18.9% covary with genome sizes that range between 37.8-43.9 Mb. Degraded copies of Long Terminal Repeat (LTR) retrotransposons were abundant among the identified TEs, and these are distributed across the genome at varying frequencies. In all investigated genomes, TE sequences had signs of numerous C-to-T substitutions, suggesting that RIP occurred in all species. RIP signatures in all genomes correlated with TE-dense regions.ConclusionsEssentially gapless genome assemblies allowed us to identify TEs inNeurosporagenomes, and reveal that TEs contribute to genome size variation in this group. Our study suggests that TEs and RIP are highly correlated inNeurospora, and hence, the pattern of interaction is conserved over the investigated evolutionary timescale. We show that RIP signatures can be used to facilitate the identification of TE-rich region in the genome.
CARMIL3 is important for cell migration and morphogenesis during early development in zebrafish
Authors: Stark Benjamin C. , Gao Yuanyuan , Belk Lakyn , Culver Matthew A. , Hu Bo , Sepich Diane S. , Mekel Marlene , Solnica-Krezel Lilianna , Lin Fang , Cooper John A. 
Published: September 2020

AbstractCell migration is important during early animal embryogenesis. Cell migration and cell shape are controlled by actin assembly and dynamics, which depend on capping proteins, including the barbed-end heterodimeric actin capping protein (CP). CP activity can be regulated by capping-protein-interacting (CPI) motif proteins, including CARMIL (capping protein Arp2/3 myosin-I linker) family proteins. Previous studies of CARMIL3, one of the three highly conserved CARMIL genes in vertebrates, have largely been limited to cells in culture. Towards understanding CARMIL function during embryogenesisin vivo, we analyzed zebrafish lines carrying mutations ofcarmil3. Maternal-zygotic mutants show impaired endodermal migration during gastrulation, along with defects in dorsal forerunner cell (DFC) cluster formation, affecting the morphogenesis of Kupffer’s vesicle (KV). Mutant KVs are smaller and display decreased numbers of cilia, leading to defects in left/right (L/R) patterning with variable penetrance and expressivity. The penetrance and expressivity of the KV phenotype incarmil3mutants correlated well with the L/R heart positioning defect at the end of embryogenesis. This firstin vivoanimal study of CARMIL3 reveals its new role for CARMIL3 during morphogenesis of the vertebrate embryo. This role involves migration of endodermal cells and DFCs, along with subsequent morphogenesis of the KV and L/R asymmetry.
Isoform-specific characterization implicates alternative splicing inAPOBEC3Bas a mechanism restricting APOBEC-mediated mutagenesis
Authors: Banday A. Rouf , Onabajo Olusegun O. , Lin Seraph Han-Yin , Obajemu Adeola , Vargas Joselin M. , Delviks-Frankenberry Krista A. , Lamy Philippe , Bayanjargal Ariunaa , Zettelmeyer Clara , Florez-Vargas Oscar , Pathak Vinay K. , Dyrskjøt Lars , Prokunina-Olsson Ludmila 
Published: September 2020

ABSTRACTAPOBEC3A (A3A) and APOBEC3B (A3B) enzymes drive APOBEC-mediated mutagenesis, but the understanding of the regulation of their mutagenic activity remains limited. Here, we showed that mutagenic and non-mutagenic A3A and A3B enzymes are produced by canonical and alternatively splicedA3AandA3Bisoforms, respectively. Notably, increased expression of the canonicalA3Bisoform, which encodes the mutagenic A3B enzyme, predicted shorter progression-free survival of bladder cancer patients. Expression of the mutagenicA3Bisoform was reduced by exon 5 skipping, generating a non-mutagenicA3Bisoform. The exon 5 skipping, which was dependent on the interaction between SF3B1 splicing factor and weak branch point sites in intron 4, could be enhanced by an SF3B1 inhibitor, decreasing the production of the mutagenic A3B enzyme. Thus, our results underscore the role of A3B, especially in bladder cancer, and implicate alternative splicing ofA3Bas a mechanism and therapeutic target to restrict APOBEC-mediated mutagenesis.
Individual variation in Achilles tendon morphology and geometry changes susceptibility to injury
Authors: Yin Nai-Hao , Fromme Paul , McCarthy Ian , Birch Helen 
Published: September 2020

AbstractThe unique structure of the Achilles tendon, combining three smaller sub-tendons, enhances movement efficiency by allowing individual control from connected muscles. This requires compliant interfaces between sub-tendons, but compliance decreases with age and may account for increased injury frequency. Current understanding of sub-tendon sliding and its role in the whole Achilles tendon function is limited. Here we show changing the degree of sliding greatly affects the tendon mechanical behaviour. Ourin vitrotesting discovered distinct sub-tendon mechanical properties in keeping with their mechanical demands.In silicostudy based on measured properties, subject-specific tendon geometry, and modified sliding capacity demonstrated age-related displacement reduction similar to ourin vivoultrasonography measurements. Peak stress magnitude and distribution within the whole Achilles tendon is affected by individual tendon geometries, the sliding capacity between sub-tendons, and different muscle loading conditions. These results suggest clinical possibilities to identify patients at risk and design personalised rehabilitation protocols.
Ets2frame-shift mutant models express in-frame mRNA by exon skipping that complements Ets2 function in the skin
Authors: Kishimoto Yuki , Nishiura Iori , Yuri Shunsuke , Yamamoto Nami , Ikawa Masahito , Isotani Ayako 
Published: September 2020

AbstractThe Ets2 transcription factor has been implicated in various biological processes. AnEts2mutant model, which lacks the DNA-binding domain (ETS domain), was previously reported to exhibit embryonic lethality caused by a trophoblast abnormality. This phenotype could be rescued by tetraploid complementation, resulting in pups with wavy hair.Here, we generated newEts2mutant models with deletions in exon 8 and with frame-shift mutations using the CRISPR/Cas9 method. Homozygous mutants could not be obtained by natural mating as previously reported. After rescuing with tetraploid complementation, homozygous mutant mice were generated, but these mice did not exhibit wavy hair phenotype. Our newly generated mice exhibited exon 8 skipping, which led to in-frame mutant mRNA expression in the skin and thymus but not in E7.5 embryos. As this in-frame mutation contained the ETS domain, the exon 8-skippedEts2mRNA was likely translated into protein in the skin that complemented the Ets2 function. Thus, theseEts2mutant models, depending on the cell types, exhibited novel phenotypes due to exon skipping and are expected to be useful in several fields of research.Summary statementNew Ets2 mutant models showed embryonic lethal phenotype by a placental abnormality but did not exhibit a wavy hair phenotype as a previous model.
Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy
Authors: Shabalin Ivan G. , Czub Mateusz P. , Majorek Karolina A. , Brzezinski Dariusz , Grabowski Marek , Cooper David R. , Panasiuk Mateusz , Chruszcz Maksymilian , Minor Wladek 
Published: September 2020

Dexamethasone, a widely used corticosteroid, has recently been reported as the first drug to increase the survival chances of patients with severe COVID-19. Therapeutic agents, including dexamethasone, are mostly transported through the body by binding to serum albumin. Here, the first structure of serum albumin in complex with dexamethasone is reported. Dexamethasone binds to drug site 7, which is also the binding site for commonly used nonsteroidal anti-inflammatory drugs and testosterone, suggesting potentially problematic binding competition. This study bridges structural findings with an analysis of publicly available clinical data from Wuhan and suggests that an adjustment of the dexamethasone regimen should be further investigated as a strategy for patients affected by two major COVID-19 risk factors: low albumin levels and diabetes.
The use of the Montreal Cognitive Assessment (MoCA) to assess cognitive impairment in Prader-Willi syndrome
Authors: Chevalère Johann , Laurier Virginie , Tauber Maite , Camblats Anna-Malika , Thuilleaux Denise , Postal Virginie 
Published: September 2020

PurposeWhen a comprehensive neuropsychological assessment cannot be carried out, a quick and discriminant tool of good psychometric properties can be useful to practitioners. The purpose of this paper is to examine the use of the Montreal Cognitive Assessment (MoCA) in patients with Prader–Willi syndrome (PWS) and to test its reliability for cognitive assessment in a population with intellectual disabilities.Design/methodology/approachThirty-seven adults with PWS took the MoCA. Reliability of the battery was tested using Cronbach’s alphas. The performance of PWS adults in each subtest was then compared to that of a normative population of healthy adults.FindingsThe MoCA was found to be unreliable in PWS. The subtests analyses indicated that the PWS sample underperformed the normative population of healthy adults on most subtests of the MoCA. A sub-sample aged between 17and 29 years showed normal performance on Naming and Memory, and a sub-sample aged from 30 to 39 years showed similar performance on Language, Memory and Orientation relative to age-matched normative healthy adults.Research limitations/implicationsResults showed that the current version of the MoCA, if taken as a whole test for cognitive assessment, does not present with adequate psychometric properties, which the authors interpret as reflecting the heterogeneity in PWS cognitive profiles. If used in PWS, the MoCA may however be useful in examining cognitive functions separately using subtest-based comparisons to normative data.Originality/valueThis research contributes to a better assessment of cognitive profile in PWS and people with learning disabilities by arguing that the use of psychometric tests should depend more on the specificity of the population under evaluation.
The concept of competitive productivity (CP): a linguistic investigation
Authors: Hoadley Susan 
Published: September 2020

PurposeThe paper presents an investigation into the validity and robustness of the concept of competitive productivity (CP) using linguistic analysis and theory to explore the foundational CP concepts and the relationships between them.Design/methodology/approachThe aim of this paper is to make a theoretical contribution to the conceptualisation of CP in order to inform its understanding, measurement and application.FindingsThe investigation indicates the relevance of three dimensions (instantiation, stratification and system) to understand CP as a complex, multidimensional system. Instantiation both clarifies CP as a multilevel system and highlights the need for an additional dimension(s) to understand the relationship between national, firm and individual CP (NCP, FCP and ICP). In combination, the two dimensions of stratification and system model CP as a series of nested strata (theory/models, concepts, constructs, variables and measures) through which marketing and management theory and knowledge is created and demonstrate how the options at each level can be articulated as system networks.Research limitations/implicationsManaging the complexity of CP by mapping different aspects along different dimensions and, in doing so, better understanding the nature of and relationships between different phenomena within the domain can potentially inform future qualitative and quantitative research in business studies and beyond.Originality/valueThe paper uses a novel, interdisciplinary approach to demonstrate the existence of CP as a complex, multidimensional system, where such dimensions inform the understanding, measurement and application of CP, and so is of value to marketing and management researchers and practitioners.
Challenges on contemporary architectural technology on durability of reinforced concrete structures
Authors: Charalambidi Barbara , Markou Panagiotis , Drakakaki Argyro , Oungrinis Konstantinos-Alketas 
Published: September 2020

PurposeThis study aims to discuss the causes of short-lived structuring of contemporary buildings. The life expectancy of structures may be theoretically predefined during the state of the design. This time period, known as the service life of structures, is determined by the load or the deformation level at which irreversible failures of the bearing structure may occur. On the other hand, planned obsolescence and perceived obsolescence, observed in the western world since the first half of 20th century, are currently setting an economic reality and are part of an expanded framework that, apart from architectural structures, extends to all design fields. The effects of short-lived structuring on environmental and energy terms are presented and theoretical and experimental recommendations from the literature are cited, as well as recommendations that have already been successfully applied in some countries.Design/methodology/approachThis study aims to discuss the issues associated with short-lived structuring, durability and obsolescence of contemporary structures. For this purpose, theoretical and experimental recommendations from the literature are cited, via an extensive state of the art research.FindingsShort-lived structuring has been a field of research during recent years. Terms such as durability are being introduced into Design Codes, while trends like perceived obsolescence and environmental impact raise issues for research. Moreover, the results of short-lived structuring are becoming more and more apparent, indicating an unsustainable reality. Issues like maintenance of structures, sustainability in design, corrosion effects, repair techniques and building waste management are an important field of research among the engineering community. In this study, the parameters affecting the lifespan of contemporary structures have been discussed.Originality/valueThe effects of short-lived structuring on environmental and energy terms are presented and theoretical and experimental recommendations from the literature are cited. The parameters studied herein concern material properties and design approach but also environmental and energy-related ones.