bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering ecological state dynamics with hidden Markov models
Authors: McClintock Brett T. , Langrock Roland , Gimenez Olivier , Cam Emmanuelle , Borchers David L. , Glennie Richard , Patterson Toby A. 
Published: October 2020

AbstractEcological systems can often be characterised by changes among a finite set of underlying states pertaining to individuals, populations, communities or entire ecosystems through time. Owing to the inherent difficulty of empirical field studies, ecological state dynamics operating at any level of this hierarchy can often be unobservable or ‘hidden’. Ecologists must therefore often contend with incomplete or indirect observations that are somehow related to these underlying processes. By formally disentangling state and observation processes based on simple yet powerful mathematical properties that can be used to describe many ecological phenomena, hidden Markov models (HMMs) can facilitate inferences about complex system state dynamics that might otherwise be intractable. However, HMMs have only recently begun to gain traction within the broader ecological community. We provide a gentle introduction to HMMs, establish some common terminology, review the immense scope of HMMs for applied ecological research and provide a tutorial on implementation and interpretation. By illustrating how practitioners can use a simple conceptual template to customise HMMs for their specific systems of interest, revealing methodological links between existing applications, and highlighting some practical considerations and limitations of these approaches, our goal is to help establish HMMs as a fundamental inferential tool for ecologists.
Parenting–Acculturation Match and Psychosocial Adjustment for Academically Gifted Chinese American Adolescents
Authors: Chang Tzu‐Fen , Qin Desiree B. , Wu Ivan H. C. 
Published: October 2020

ObjectiveGrounded in person–environment fit theory, we examine how different levels of parenting–acculturation match are associated with gifted Chinese American students' psychosocial adjustment. This study identifies parenting profiles indicated by psychological control and decisional autonomy granting and adolescents' acculturation profiles indicated by mainstream American culture and Chinese culture orientations.BackgroundAccording to person–environment fit theory, optimal adjustment occurs when there is a match between individuals' environments and needs. However, it remains understudied whether academically gifted Chinese American adolescents have optimal psychosocial adjustment when their acculturation orientation matches with their family's parenting profile.MethodUsing self‐report questionnaires, this study assessed 222 academically gifted Chinese American adolescents' perceptions of parental psychological control and autonomy granting, American and Chinese culture orientation, and psychosocial adjustment (depression, anxiety, social acceptance, and self‐esteem). Latent profile analysis was used to identify parenting and acculturation‐orientation profiles.ResultsThree parenting profiles were identified: high control oriented (14.9%; i.e., high in psychological control and low in decisional autonomy granting), slight control oriented (44.6%; i.e., psychological control slightly exceeding decisional autonomy granting), and child oriented (40.5%; i.e., low in psychological control and high in decisional autonomy granting). Given that all the adolescents in the sample slightly preferred mainstream American culture to Chinese culture, three levels of parenting–acculturation match were identified: a strong match (for those in child‐oriented families), moderate match (for those in slight‐control‐oriented families), and weak match (for those in high‐control‐oriented families).ConclusionThe adolescents with a strong parenting–acculturation match reported lower anxiety and higher social acceptance and self‐esteem than those with a weak match.ImplicationsPractitioners working with academically gifted Chinese American adolescents should seek to understand adolescents' acculturation and the parenting practices in their families and acknowledge how their psychosocial problems are associated with a mismatch in adolescent acculturation and parenting. Strategies for mitigating psychosocial problems in relation to an acculturation–parenting mismatch are discussed.
Heated rivalries: Phenological variation modifies competition for pollinators among arctic plants
Authors: Tiusanen Mikko , Kankaanpää Tuomas , Schmidt Niels M. , Roslin Tomas 
Published: October 2020

AbstractWhen plant species compete for pollinators, climate warming may cause directional change in flowering overlap, thereby shifting the strength of pollinator‐mediated plant–plant interactions. Such shifts are likely accentuated in the rapidly warming Arctic. Targeting a plant community in Northeast Greenland, we asked (a) whether the relative phenology of plants is shifting with spatial variation in temperature, (b) whether local plants compete for pollination, and (c) whether shifts in climatic conditions are likely to affect this competition. We first searched for climatic imprints on relative species phenology along an elevational gradient. We then tested for signs of competition with increasing flower densities: reduced pollinator visits, reduced representation of plant species in pollen loads, and reduced seed production. Finally, we evaluated how climate change may affect this competition. Compared to a dominant species, Dryas integrifolia × octopetala, the relative timing of other species shifted along the environmental gradient, with Silene acaulis and Papaver radicatum flowering earlier toward higher elevation. This shift resulted in larger niche overlap, allowing for an increased potential for competition for pollination. Meanwhile, Dryas emerged as a superior competitor by attracting 97.2% of flower visits. Higher Dryas density resulted in reduced insect visits and less pollen of S. acaulis being carried by pollinators, causing reduced seed set by S. acaulis. Our results show that current variation in climate shifts the timing and flowering overlap between dominant and less‐competitive plant species. With climate warming, such shifts in phenology within trophic levels may ultimately affect interactions between them, changing the strength of competition among plants.
Partial breakage of a tunneled dialysis catheter: An uncommon finding
Authors: Letachowicz Krzysztof , Gołębiowski Tomasz , Miś Marcin , Wolańczyk Michał , Zmonarski Sławomir , Krajewska Magdalena 
Published: October 2020

AbstractInfections and dysfunction are the most common complications related to catheter use. Here we describe a case of catheter rupture on the course of subcutaneous channel. Catheter fractures are relatively rare, but potentially hazardous complications. In case of partial breakage, a catheter exchange should be a simple solution.
Effects of in vitro simulated digestion on the free and bound phenolic content and antioxidant activity of seven species of seaweeds
Authors: Huang Zhiting , Chen Qiqi , Hu Kaixi , Zhang Ruifen , Yuan Yang , He Shan , Zeng Qingzhu , Su Dongxiao 
Published: October 2020

SummaryThe effects of simulated gastrointestinal digestion on the content and antioxidant activity of phenolics of seven seaweeds were investigated: Two methods of digestion were used – simulated gastric fluid (SGF) and simulated intestinal fluid (SIF) to mimic the stomach and upper intestinal environment. Results showed that SIF can significantly increase the free phenolic content of all tested seaweeds. The total phenolic content of the seaweeds increased in range from 4.16 to 17.24 mg GAE/g before simulated digestion to 4.08 to 40.37 mg GAE/g after digestion. The antioxidant activity of seaweed‐bound phenolics was superior to that of free phenolics. Among the seven varieties of seaweeds, Sargassum thunbergii and Sargassum kjellmanianum contained the highest content of bound phenolics after SGF digestion. Bound phenolics of Undaria pinnatifida and Sargassum thunbergii showed the highest in vitro ABTS+ free radical scavenging ability, while Sargassum thunbergii and Sargassum fusiforme showed the highest in vitro FRAP antioxidant activity.
Autoregressive single‐step model for genomic evaluation of longitudinal reproductive traits in portuguese holstein cattle
Authors: Silva Hugo Teixeira , Lopes Paulo Sávio , Costa Claudio Nápolis , Silva Alessandra Alves , Silva Delvan Alves , Silva Fabyano Fonseca , Veroneze Renata , Thompson Gertrude , Carvalheira Júlio 
Published: October 2020

AbstractWe investigated the applicability of ssGBLUP methodology under the autoregressive model (H‐AR) for genomic evaluation of longitudinal reproductive traits in Portuguese Holstein cattle. The genotype data of 1,230 bulls and 1,645 cows were considered in our study. The reproductive traits evaluated were interval from calving to first service (ICF), calving interval (CI) and daughter pregnancy rate (DPR) measured during the first four parities. Reliability and rank correlation were used to compare the H‐AR with the traditional pedigree‐based autoregressive models (A‐AR). In addition, a validation study was performed considering different scenarios. Higher genomic estimated breeding values (GEBV) reliabilities were obtained for genotyped bulls when evaluated under the H‐AR model, with emphasis on bulls with less than 9 daughters. For this group, the averages of GEBV reliabilities corresponded to 0.62, 0.69 and 0.62 for ICF, CI and DPR, respectively, while the averages obtained by the A‐AR model were 0.27, 0.15 and 0.16. The validation study was favourable to H‐AR. The best results were observed in the scenario where genotyped cows were combined with contributing bulls (genotyped bulls with daughter or relationship information in the population). Overall, the results suggest that ssGBLUP methodology under the autoregressive model is a feasible and applicable approach to be used in genomic analyses of longitudinal reproductive traits in Portuguese Holstein cattle.
Do ecological specialization and functional traits explain the abundance–frequency relationship? Arable weeds as a case study
Authors: Fried Guillaume , Armengot Laura , Storkey Jonathan , Bourgeois Bérenger , Gaba Sabrina , Violle Cyrille , Munoz François 
Published: October 2020

AbstractAimThe abundance–frequency relationship (AFR) is among the most‐investigated patterns in biogeography, yet the relative contributions of niche‐based processes related to ecological strategies, and of neutral processes related to spatial colonization–extinction dynamics, remains uncertain. Here, we tested the influences of ecological specialization and functional traits on local abundance and regional frequency, to determine the contribution of niche‐based processes.LocationFrance and the UK.TaxonVascular plants.MethodsWe used two arable weed surveys covering 1,544 fields in Western Europe (France, UK), along with functional traits related to resource acquisition, resource requirements, flowering phenology and dispersal. We quantified specialization both to arable habitat and to individual crop types, and performed phylogenetic path analyses to test competing models accounting for direct and indirect relationships between traits, specialization, abundance and frequency. We performed the analyses for all species in each country, as well as for a subset of the most abundant species.ResultsLocal abundance of weeds increased with their regional frequency, but the relationship became negative or null when considering only the most abundant weeds. Specialization to arable habitat and to individual crop type either had a similar or opposite effect on regional frequency and local abundance explaining these positive and negative relationships, respectively. Regional frequency was not directly explained by any trait but indirectly by resource requirement traits conferring specialization to the arable habitat. Conversely, high local abundance was directly related to low seed mass, high SLA, early and short flowering.Main conclusionsDirect/indirect effects of functional traits on local abundance/regional frequency, respectively, supports a significant role of niche‐based processes in AFR. Neutral spillover dynamics could further explain a direct linkage of abundance and frequency. Similar causal paths and consistent influences of traits on specialization and abundance in the two studied regions suggest genericity of these findings.
Simultaneous Constrained Adaptive Item Selection for Group‐Based Testing
Authors: Bengs Daniel , Kroehne Ulf , Brefeld Ulf 
Published: October 2020

AbstractBy tailoring test forms to the test‐taker's proficiency, Computerized Adaptive Testing (CAT) enables substantial increases in testing efficiency over fixed forms testing. When used for formative assessment, the alignment of task difficulty with proficiency increases the chance that teachers can derive useful feedback from assessment data. The application of CAT to formative assessment in the classroom, however, is hindered by the large number of different items used for the whole class; the required familiarization with a large number of test items puts a significant burden on teachers. An improved CAT procedure for group‐based testing is presented, which uses simultaneous automated test assembly to impose a limit on the number of items used per group. The proposed linear model for simultaneous adaptive item selection allows for full adaptivity and the accommodation of constraints on test content. The effectiveness of the group‐based CAT is demonstrated with real‐world items in a simulated adaptive test of 3,000 groups of test‐takers, under different assumptions on group composition. Results show that the group‐based CAT maintained the efficiency of CAT, while a reduction in the number of used items by one half to two‐thirds was achieved, depending on the within‐group variance of proficiencies.
Proposed protocol for performing MIC testing to determine the antimicrobial susceptibility of Renibacterium salmoninarum in Chilean salmon farms
Authors: Grandón Maritza , Irgang Rute , Saavedra José , Mancilla Marcos , Avendaño‐Herrera Ruben 
Published: October 2020

AbstractSurveillance of antibiotic resistance is of paramount importance for animal welfare and production. Despite aquaculture being a main source of animal protein, studies on antibiotic susceptibility in fish pathogens are scarce. Renibacterium salmoninarum, the aetiological agent of bacterial kidney disease (BKD), is one of the most common bacterial pathogens affecting salmon farming. In this work, we present an analysis of susceptibility patterns using determinations of minimum inhibitory concentration (MIC) for 65 field isolates, which were collected over seven years (2013–2019) from Atlantic salmon (Salmo salar) and coho salmon (Oncorhynchus kisutch) farms across southern Chile. The MIC protocol described by the Clinical Laboratory Standards Institute (CLSI) was used, but with microdilution instead of macrodilution and eight instead of four days of incubation. Two laboratories independently conducted analyses to provide data on the epidemiological cut‐off values for R. salmoninarum to florfenicol, oxytetracycline and erythromycin. By using two calculation methods, our results provide evidence for an evolving subpopulation of non‐wild‐type isolates for the macrolide erythromycin, which is consistent with the respective treatment frequencies prescribed against BKD. Contrasting with what was expected, R. salmoninarum isolates were most susceptible to florfenicol and oxytetracycline, both of which are widely used antibiotics currently used in the Chilean salmon industry. The presented findings can serve as a reference for national or international antibiotic surveillance programmes, for both MIC interpretation and to identify emerging resistance to the conventional drugs used in BKD management. Finally, our results indicate that an 8‐day incubation period for establishing MIC values of R. salmoninarum should be considered in a future revision of the CLSI guidelines.
AC joint osteoarthritis: The role of genetics. An MRI evaluation of asymptomatic elderly twins
Authors: Candela Vittorio , Villani Ciro , Preziosi Standoli Jacopo , Scacchi Marco , Gumina Stefano 
Published: October 2020

AbstractPurposeThe anatomy of the articular surfaces has historically identified as major responsible for acromioclavicular joint osteoarthritis (ACJO). On the other side, the almost 100% prevalence of ACJO in subjects over 50 years old seems to suggest a multifactorial etiology. We compared ACJO between asymptomatic elderly monozygotic (MZ) and dizygotic (DZ) twins to investigate the influence of genetics and environmental factors.Materials and MethodsThirty pairs of twins [15MZ‐15DZ; mean age (SD): 63.70 (3.31); range: 53–72] were retrospectively enrolled. ACJO was evaluated on MRI through a 4‐grade severity scale and ACJ configuration was assessed. Information regarding work activity were obtained. Heritability index was calculated.ResultsThe intraclass correlation coefficient (ICC) value of 0.868 (95% CI; 0.798 to 0.917). An ICC values of 0.889 (95% CI; 0.798 to 0.944) and 0.843 (95% CI, 0.712 to 0.920) were found in the MZ and DZ groups, respectively. The polychoric correlation was 0.857 in the MZ twins and 0.757 in the DZ twins. The calculated heritability index was 0.20 (20%), and the contribution of the shared environment (c2) and unique environment (e2) was 0.66 (66%) and 0.14 (14%), respectively. No relationship between job types and ACJO in both the total cohort (r = 0.089; p = 0.499) and in the monozygotic (r = 0.247; p = 0.187) and the dizygotic twin groups (r = −0.084; p = 0.658) was found.ConclusionsThe role of genetics on ACJO accounts for only 20%; a specific anatomical configuration of the articular surfaces only partially acts on the development of joint osteoarthritis. Environmental factors have the greatest impact.Level of Evidence: IV.
What drives the dynamics of HBV RNA during treatment?
Authors: Gonçalves Antonio , Lemenuel‐Diot Annabelle , Cosson Valérie , Jin Yuyan , Feng Sheng , Bo Qingyan , Guedj Jérémie 
Published: October 2020

AbstractHepatitis B virus RNA (HBV RNA)–containing particles are encapsidated pre‐genomic RNA (pgRNA) detectable in chronically infected patients in addition to virions (HBV DNA) that have been suggested as a marker of the treatment efficacy. This makes promising the use of core protein allosteric modulators, such as RG7907, which disrupt the nucleocapsid assembly and profoundly reduce HBV RNA. Here, we developed a multiscale model of HBV extending the standard viral dynamic models to analyse the kinetics of HBV DNA and HBV RNA in 35 patients treated with RG7907 for 28 days. We compare the predictions with those obtained in patients treated with the nucleotide analog tenofovir. RG7907 blocked 99.3% of pgRNA encapsidation (range: 92.1%–99.9%) which led to a decline of both HBV DNA and HBV RNA. As a consequence of its mode of action, the first phase of decline of HBV RNA was rapid, uncovering the clearance of viral particles with half‐life of 45 min. In contrast, HBV DNA decline was predicted to be less rapid, due to the continuous secretion of already formed viral capsids (t1/2 = 17 ± 6 h). After few days, both markers declined at the same rate, which was attributed to the loss of infected cells (t1/2 ≅ 6 ± 0.8 days). By blocking efficiently RNA reverse transcription but not its encapsidation, nucleotide analog in contrast was predicted to lead to a transient accumulation of HBV RNA both intracellularly and extracellularly. The model brings a conceptual framework for understanding the differences between HBV DNA and HBV RNA dynamics. Integration of HBV RNA in viral dynamic models may be helpful to better quantify the treatment effect, especially in viral‐suppressed patients where HBV DNA is no longer detectable.
Direct examination, histopathology and fungal culture for the diagnosis of onychomycosis: A retrospective, comparative study on 2245 specimens
Authors: Lecerf Pauline , Abdy Salome , Vollono Laura , Pastushenko Ievgenia , Richert Bertrand , André Josette 
Published: October 2020

AbstractBackgroundOnychomycosis affects 5.5% of the general population and represents up to 50% of all nail diseases. Diagnosis and pathogen identification are essential in order to plan an adequate treatment. Many diagnostic techniques are available, and however, no solid data regarding comparison between different techniques over a large number of specimens are available to date.ObjectivesTo compare sensitivity and specificity of direct examination, histopathology and fungal culture in our referral mycology laboratory.MethodsNail specimens received at the cutaneous pathology and mycology laboratory of the University Hospital Saint‐Pierre (Brussels, Belgium) between 1 January and 15 May 2018 were retrospectively analysed. All specimens were submitted to direct examination and culture. In cases of adequate specimen size, histopathology was performed. Fungal culture was considered the gold standard for diagnosis.ResultsA total of 2245 nail samples were included in the study. Onychomycosis was diagnosed in 1266 specimens. Sensitivity and positive predictive value were found to be higher for direct examination compared to histopathology, while sensitivity of direct examination was found to be lower. Combined approach with all the three techniques showed the highest rate of positivity, followed by the association of direct examination and histopathology.ConclusionsTo our knowledge, this study included the largest number of nail specimens to date, allowing a comparison between direct examination, culture and histopathology. Direct examination showed to be the most performing technique in routine practice. Histopathology represents the most effective option in cases where both specimen size and laboratory resources are adequate. Our paper adds to the literature the ‘real‐life’ experience of the mycology laboratory of a referral centre for nail diseases.