bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating 87Sr/86Sr isotope ratios and Sr mass fractions in otoliths of different European freshwater fish species as fishery management tool in an Alpine foreland with limited geological variability
Authors: Zitek Andreas , Oehm Johannes , Schober Michael , Tchaikovsky Anastassiya , Irrgeher Johanna , Retzmann Anika , Thalinger Bettina , Traugott Michael , Prohaska Thomas 
Published: July 2021

AbstractThe focus of this study was to assess the potential of otolith microchemistry as a fishery management tool for different European freshwater fish species in an Alpine foreland with a diverse range of different water bodies but low geological variation. 87Sr/86Sr isotope and Sr/Ca ratios in water samples from 26 habitat sites in a pre-alpine catchment region around lake Chiemsee, Germany, an important region for recreational and economic fisheries, were analysed. 87Sr/86Sr isotope ratios and the Sr mass fractions in otoliths of 246 fish out of 16 species were determined using (laser ablation) inductively coupled plasma mass spectrometry ((LA)-ICP-MS). Habitats could be discriminated into three distinct strontium isotope regions (SIGs) and seven clusters with characteristic 87Sr/86Sr isotope and Sr/Ca ratios. The direct comparison of 87Sr/86Sr isotope ratios in water and otolith samples allowed to identify fish that might have been a) migrating b) transferred from other water bodies or c) stocked from fish farms. Sr/Ca ratios in water and the Sr mass fraction in otoliths were highly correlated, although significant differences between species from the same environment could be documented. Sr mass fractions in sagittae of Perca fluviatilis were about 60 % of those in sagittae of Coregonus spp and of lapilli of roach Rutilus rutilus from the same habitats. Different partition factors for water to otolith Sr/Ca mass fractions were determined for different species. Discrimination of fish otoliths by 87Sr/86Sr isotope ratios and Sr mass fractions according to habitat clusters was possible with success rates ranging from 92 % to 100 % for cyprinids, European perch Perca fluviatilis, whitefish Coregonus spp. and European grayling Thymallus thymallus, and was 74 % for salmonids. Otolith microchemistry proved to have great potential to serve as a fishery management tool at smaller spatial scales such as in the studied Alpine foreland when considering the limited variation of 87Sr/86Sr isotope and Sr/Ca ratios, the type and spatial distribution of habitats, and the species and question under investigation.HighlightsOtolith microchemistry applied in in area with limited geological variabilityFish transferred, stocked or migrated were identifiedRegressions between Sr/Ca ratios in water predict Sr mass fractions in otolithsSpecies specific Sr discrimination from water into otolithsEuropean freshwater fish species assigned to habitat clusters of origin
PatchPerPixMatch for Automated 3d Search of Neuronal Morphologies in Light Microscopy
Authors: Mais Lisa , Hirsch Peter , Managan Claire , Wang Kaiyu , Rokicki Konrad , Svirskas Robert R. , Dickson Barry J. , Korff Wyatt , Rubin Gerald M. , Ihrke Gudrun , Meissner Geoffrey W. , Kainmueller Dagmar 
Published: July 2021

AbstractStudies of individual neurons in the Drosophila nervous system are facilitated by transgenic lines that sparsely and repeatably label respective neurons of interest. Sparsity can be enhanced by means of intersectional approaches like the split-GAL4 system, which labels the positive intersection of the expression patterns of two (denser) GAL4 lines. To this end, two GAL4 lines have to be identified as labelling a neuron of interest. Current approaches to tackling this task include visual inspection, as well as automated search in 2d projection images, of single cell multi-color flip-out (MCFO) acquisitions of GAL4 expression patterns. There is to date no automated method available that performs full 3d search in MCFO imagery of GAL4 lines, nor one that leverages automated reconstructions of the labelled neuron morphologies. To close this gap, we propose PatchPerPixMatch, a fully automated approach for finding a given neuron morphology in MCFO acquisitions of Gen1 GAL4 lines. PatchPerPixMatch performs automated instance segmentation of MCFO acquisitions, and subsequently searches for a target neuron morphology by minimizing an objective that aims at covering the target with a set of well-fitting segmentation fragments. Patch-PerPixMatch is computationally efficient albeit being full 3d, while also highly robust to inaccuracies in the automated neuron instance segmentation. We are releasing PatchPerPixMatch search results for ~30,000 neuron morphologies from the Drosophila hemibrain in ~20,000 MCFO acquisitions of ~3,500 Gen1 GAL4 lines.Codehttps://github.com/Kainmueller-Lab/PatchPerPixMatchResultshttps://pppm.janelia.org
Generalizing Bayesian phylogenetics to infer shared evolutionary events
Authors: Oaks Jamie R. , Wood Perry L. , Siler Cameron D. , Brown Rafe M. 
Published: July 2021

AbstractMany processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a “super-spreading” event, and a geological event fragmenting whole communities of species. It is difficult to test for patterns of shared divergences predicted by such processes, because all phylogenetic methods assume that lineages diverge independently. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. Using simulations, we find the new method accurately infers shared and multifurcating divergence events when they occur, and performs as well as current phylogenetic methods when divergences are independent and bifurcating. We apply our new approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands’ landscape caused bursts of speciation. Unlike our previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences.Significance statementPhylogenetic models have long assumed that lineages diverge independently. Processes of diversification that are of interest in biogeography, epidemiology, and genome evolution, violate this assumption by affecting multiple evolutionary lineages. To relax the assumption of independent divergences and infer patterns of divergences predicted by such processes, we introduce a new way of conceptualizing, modeling, and inferring phylogenetic trees. We apply the new approach to genomic data from geckos distributed across the Philippines, and find support for patterns of shared divergences predicted by repeated fragmentation of the archipelago by interglacial rises in sea level.
The U.S. COVID-19 Trends and Impact Survey, 2020-2021: Continuous real-time measurement of COVID-19 symptoms, risks, protective behaviors, testing and vaccination
Authors: Salomon Joshua A. , Reinhart Alex , Bilinski Alyssa , Chua Eu Jing , La Motte-Kerr Wichada , Rönn Minttu M. , Reitsma Marissa , Morris Katherine Ann , LaRocca Sarah , Farag Tamar , Kreuter Frauke , Rosenfeld Roni , Tibshirani Ryan J. 
Published: July 2021

AbstractThe U.S. COVID-19 Trends and Impact Survey (CTIS) is a large, cross-sectional, Internet-based survey that has operated continuously since April 6, 2020. By inviting a random sample of Facebook active users each day, CTIS collects information about COVID-19 symptoms, risks, mitigating behaviors, mental health, testing, vaccination, and other key priorities. The large scale of the survey – over 20 million responses in its first year of operation – allows tracking of trends over short timescales and allows comparisons at fine demographic and geographic detail. The survey has been repeatedly revised to respond to emerging public health priorities. In this paper, we describe the survey methods and content and give examples of CTIS results that illuminate key patterns and trends and help answer high-priority policy questions relevant to the COVID-19 epidemic and response. These results demonstrate how large online surveys can provide continuous, real-time indicators of important outcomes that are not subject to public health reporting delays and backlogs. The CTIS offers high value as a supplement to official reporting data by supplying essential information about behaviors, attitudes toward policy and preventive measures, economic impacts, and other topics not reported in public health surveillance systems.Significance statementThe U.S. COVID-19 Trends and Impact Survey (CTIS) has operated continuously since April 6, 2020, collecting over 20 million responses. The largest public health survey ever conducted in the United States, CTIS was designed to facilitate detailed demographic and geographic analyses, track trends over time, and accommodate rapid response to emerging priorities. Using examples of CTIS results illuminating trends in symptoms, risks, mitigating behaviors, testing and vaccination in relation to evolving high-priority policy questions over 12 months of the pandemic, we illustrate the value of online surveys for tracking patterns and trends in COVID outcomes as an adjunct to official reporting, and showcase unique insights that would not be visible through traditional public health reporting.
A network-based approach reveals the dysregulated transcriptional regulation in non-alcohol fatty liver disease
Authors: Yang Hong , Arif Muhammad , Yuan Meng , Li Xiangyu , Shong Ko Eun , Turkez Hasan , Nielsen Jens , Uhlén Mathias , Borén Jan , Cheng Zhang , Mardinoglu Adil 
Published: July 2021

ABSTRACTNon-alcohol-related fatty liver disease (NAFLD) is a leading cause of chronic liver disease worldwide. We performed network analysis to investigate the dysregulated biological processes in the disease progression and revealed the molecular mechanism underlying NAFLD. Based on network analysis, we identified a highly conserved disease-associated gene module across three different NAFLD cohorts and highlighted the predominant role of key transcriptional regulators associated with lipid and cholesterol metabolism. In addition, we revealed the detailed metabolic differences between heterogenous NAFLD patients through integrative systems analysis of transcriptomic data and liver-specific genome-scale metabolic model. Furthermore, we identified transcription factors (TFs), including SREBF2, HNF4A, SREBF1, YY1 and KLF13, showing regulation of hepatic expression of genes in the NAFLD-associated modules and validated the TFs using data generated from a mouse NAFLD model. In conclusion, our integrative analysis facilitated our understanding of the regulatory mechanism of these perturbed TFs and associated biological processes.
Role of non-specific interactions in the phase-separation and maturation of macromolecules
Authors: Krishnan Rakesh , Ranganathan Srivastav , Maji Samir K , Padinhateeri Ranjith 
Published: July 2021

AbstractPhase separation of biomolecules could be mediated by both specific and non-specific interactions. How the interplay between non-specific and specific interactions along with polymer entropy influences phase separation is an open question. We address this question by simulating self-associating molecules as polymer chains with a short core stretch that forms the specifically interacting functional interface, and longer non-core regions that participate in non-specific/promiscuous interactions. Our results show that the interplay of specific (strength, ϵsp) and non-specific interactions (strength, ϵns) could result in phase separation of polymers and its transition to solid-like aggregates (mature state). In the absence of ϵns, the polymer chains do not dwell long enough in the vicinity of each other to undergo phase separation and transition into a mature state. On the other hand, in the limit of strong ϵns, the assemblies cannot transition into the mature state and form a non-specific assembly, suggesting an optimal range of interactions favoring mature multimers. In the scenario where only a fraction (Nfrac) of the non-core regions participate in attractive interactions, we find that a slight modifications to either ϵns or Nfrac can result in a dramatically altered self-assembled states. Using a combination of heterogeneous and homogeneous mix of polymers, we establish how this interplay between interaction energies dictates the propensity of biomolecules to find the correct binding partner at dilute concentrations in crowded environments.Author SummaryBiological function relies on the ability of biomolecules to bind to specific interaction partners. In the crowded cellular milieu, the process of biomolecules binding to specific interaction partners to carry out a function is non-trivial. A mere diffusion-limited meeting of interaction partners in space does not ensure biomolecular function. Rather, even when in contact these molecules have to find the correct orientations to carry out function. Further, for dynamic biomolecules such as polymers, the functional configuration is often one of several possible configurations. In this scenario, assuming the functional configuration after binding involves overcoming of a significant entropic barrier. Therefore, the interacting biomolecules have to dwell in contact long enough before they reorganize to find the functional orientation! While functional contacts offer an enthalpic gain, they are often only a small fraction of all protein-protein interactions. Therefore, in this paper, we study the role played by non-functional, promiscuous interactions in shaping the thermodynamics and kinetics of formation of specific interactions. Our results suggest that there exists an optimal range of non-specific interaction strengths which promotes the process of biomolecular complexes finding the functional configurations.
Estimation of Average Blood Glucose Values Based on Fructosamine Values
Authors: de Oliveira Andrade Luis Jesuino , Vinhaes Bittencourt Alcina Maria , Moreno de Brito Luiz Felipe , de Oliveira Luís Matos , Matos de Oliveira Gabriela Correia 
Published: July 2021

ABSTRACTIntroductionThe fructosamine is originated of the glycation of plasmatic proteins, especially albumin, in addition to immunoglobulins and proteins diverse. It constitutes an alternative biomarker of glycemic control when glycated hemoglobin is not indicated for this purpose.ObjectiveTo define the mathematical relationship between fructosamine and average glucose values.MethodThe study comprised the laboratorial data collected of 1227 diabetic subjects (type 1 and type 2). Fructosamine levels obtained at the end of three weeks and measured were compared with the average glucose levels of the three previous weeks. The average glucose levels were determined by the weighted mean of the daily fasting capillary glucose results performed during the study period, and the plasma glucose taken at the time of the fructosamine.ResultsA total of 9,450 glucoses were performed. Linear regression analysis between the fructosamine and average glucose levels showed that each increase of 1.0 µmol/L in fructosamine increase 0.5mg/dL in the average glucose levels as evidenced in the equation forward: Average glucose levels = 0.5157 x Fructosamine - 20. According to the coefficient of determination (r2 = 0.353492, P < 0.006881), making it possible to calculate the estimated average glucose according to the frutosamine values.ConclusionFructosamine levels can be expressed as average glucose levels for assessing the metabolic control of diabetic patients.
Global protein responses of multi-drug resistant plasmid containing Escherichia coli to ampicillin, cefotaxime, imipenem and ciprofloxacin
Authors: Margalit Anatte , Carolan James C. , Walsh Fiona 
Published: July 2021

AbstractAntimicrobial resistance (AMR) and multi-drug resistance (MDR) in pathogenic bacteria are frequently mediated by plasmids. However, plasmids do not exist in isolation but rather require the bacterial host interaction in order to produce the AMR phenotype. This study aimed to utilise mass spectrometry-based proteomics to reveal the plasmid and chromosomally derived protein profile of Escherichia coli under antimicrobial stress. This was achieved by comparing the proteomes of E. coli containing the MDR pEK499 plasmid, under ampicillin, cefotaxime, imipenem or ciprofloxacin stress with the proteomes of these bacteria grown in the absence of antimicrobial. Our analysis identified statistically significant differentially abundant proteins common to groups exposed to the β-lactam antimicrobials but not ciprofloxacin, indicating a β-lactam stress response to exposure from this class of drugs, irrespective of β-lactam resistance or susceptibility. These include ecotin and free methionine-R-sulfoxide reductase. These data also identified distinct differences in the cellular response to each β-lactam. Data arising from comparisons of the proteomes of ciprofloxacin-treated E. coli and controls detected an increase in the relative abundance of proteins associated with ribosomes, translation, the TCA-cycle and several proteins associated with detoxification and a decrease in the relative abundances of proteins associated with stress response, including oxidative stress. We identified changes in proteins associated with persister formation in the presence of ciprofloxacin but not the β-lactams. The plasmid proteome differed across each treatment and did not follow the pattern of antimicrobial – AMR protein associations. For example, a relative increase in the amount of blaCTX-M-15 in the presence of cefotaxime and ciprofloxacin but not the other β-lactams, suggesting regulation of the blaCTX-M-15 protein production. The proteomic data from the this study provided novel insights into the proteins produced from the chromosome and plasmid under different antimicrobial stresses. These data also identified novel proteins not previously associated with AMR or antimicrobials responses in pathogens, which may well represent potential targets of AMR inhibition.
Activity networks and the temporality of urban space: the case of a cul-de-sac square
Authors: Sharif Ahlam Ammar 
Published: July 2021

PurposeThis study draws on recent actor-network theory (ANT) literature to provide a nuanced understanding of the effect of time on activity networks in urban spaces. It investigates the role of time in multiplying these networks and producing urban change, which is limited in similar ANT-related research.Design/methodology/approachThis ethnographic study of a cul-de-sac square within a housing project in the suburb of Dahiyat Al-Hussein in Amman, Jordan, documents the changes in its activity networks when comparing the 1990s with 2019. Data were collected through interviews and site observations covering the two time periods to investigate the different activities that occurred constantly over time, which reflect the temporal network stabilisation within the square.FindingsThe findings demonstrate the profound effect time has on the stability of activity networks related to playing, observing, walking, vending and their interrelations. Their overlaps and conflicts with each other and with other networks in the space were observed. Unpacking the stability of activity networks and their interrelations demonstrates the change in their actor relations and temporalities over time. This is significant in understanding urban change.Originality/valueThe study investigates the importance of time in recognising and extending the multiplicity of urban activities, which suggests new ways of understanding urban change. This exploration highlights new possibilities for creating more adaptable spaces according to residents' long-term needs.
Multilayer DS-MAC with game theory optimization
Authors: S. Radha , Bala G. Josemin , P. Nagabushanam 
Published: July 2021

Purpose
Energy is the major concern in wireless sensor networks (WSNs) for most of the applications. There exist many factors for higher energy consumption in WSNs. The purpose of this work is to increase the coverage area maintaining the minimum possible nodes or sensors.

Design/methodology/approach
This paper has proposed multilayer (ML) nodes deployment with distributed MAC (DS-MAC) in which nodes listen time is controlled based on communication of neighbors. Game theory optimization helps in addressing path loss constraints while selecting path toward base stations (BS).

Findings
The simulation is carried out using NS-2.35, and it shows better performance in ML DS-MAC compared to random topology in DS-MAC with same number of BS. The proposed method improves performance of network in terms of energy consumption, network lifetime and better throughput.

Research limitations/implications
Energy consumption is the major problem in WSNs and for which there exist many reasons, and many approaches are being proposed by researchers based on application in which WSN is used. Node mobility, topology, multitier and ML deployment and path loss constraints are some of the concerns in WSNs.

Practical implications
Game theory is used in different situations like countries whose army race, business firms that are competing, animals generally fighting for prey, political parties competing for vote, penalty kicks for the players in football and so on.

Social implications
WSNs find applications in surveillance, monitoring, inspections for wild life, sea life, underground pipes and so on.

Originality/value
Game theory optimization helps in addressing path loss constraints while selecting path toward BS.
Learning as cognition: a developmental process for organizational learning
Authors: E. Carpenter Rob 
Published: July 2021

Purpose
The aim of this article is to present a viewpoint from learning as individual and group cognition for the benefit of organization learning scholarship.

Design/methodology/approach
Conceptual viewpoint of the author.

Findings
The results demonstrate that perspective of intentionality is important for understanding how learning as cognition develops into organizational learning.

Practical implications
Organizations that recognize perspective as the agency by which learning as cognition develops organizational learning have a better opportunity to remain competitive.

Originality/value
This paper provides a basis to advance understanding on how perspective influences learning as cognition as a developmental process for organizational learning.