bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation of raptor diversity in Europe: linking speciation with climate changes and the ability to migrate
Authors: Negro Juan J. , Rodríguez-Rodríguez Eduardo , Rodríguez Airam , Bildstein Keith 
Published: March 2022

AbstractAimEurope should be considered as a diversity hotspot for diurnal raptors, but just during the breeding season, as it holds the higher proportion of transcontinental migratory species of any landmass, and the area becomes depleted during the winter period. This study will test the hypothesis that the high diversification of the raptor assemblage in Europe is a recent event, occurring mainly during the Quaternary, and that closely related species sharing the same trophic niches can only coexist in sympatry during the breeding period, when food availability is higher.LocationContinental Europe.TaxonDiurnal birds of prey (Accipitriformes and Falconiformes).MethodsA consensus molecular phylogeny for the 38 regular breeding species of raptors in Europe was obtained from BirdTree. For the same species, a trophic niche cluster dendrogram was constructed. Size and migratory strategy were introduced in the resulting phylogeny, where trophic groups were also identified.ResultsA total of 16 trophic groups were identified. Multispecific trophic groups tended to be composed of reciprocal sister species, while monospecific groups (only three) were composed of highly specialized species. According to time calibrated phylogenies, the speciation events took place during the glacial cycles of the Quaternary period in a majority of cases. During the non-breeding season, the smaller species in every trophic group migrate to sub-Saharan Africa, whereas larger species are either non-migratory or perform shorter migrations within Europe and/or northern Africa.Main conclusionsThis investigation illustrates how the rich assemblage of diurnal birds of prey in Europe, more diverse and more migratory than the North American assemblage at equivalent latitudes, has emerged recently due to the multiplication of look-alike species with similar trophic ecologies, mainly in climate refugia during cold periods. In the non-breeding season, when shared food resources are limited, smaller species migrate to Africa and alleviate competition.
PPAR-γ activation promotes xenogenic bioroot regeneration by attenuating the xenograft induced-oxidative stress
Authors: Lan Tingting , Bi Fei , Xu Yuchan , Yin Xiaoli , Chen Jie , Han Xue , Guo Weihua 
Published: March 2022

Objectivexenogenic organ transplantation has been considered the most promising strategy in providing possible subtitutes with physiological function of the failing organs as well as solving the problem of insufficient donor sources. However, the xenograft, suffered from immune rejection and ischemia-reperfusion injury (IRI), causes massive ROS expression and the subsequent cell apoptosis, leading to the xenograft failure. Our previous study found a positive role of PPAR-γ in anti-inflammation through its immunomodulation effects, which inspires us to apply PPAR-γ agonist rosiglitazone (RSG) to address survival issue of xenograft with the potential to eliminate the excessive ROS.MethodsXenogenic bioroot was constructed by wrapping the dental follicle cells (DFC) with porcine extracellular matrix (pECM). The hydrogen peroxide (H2O2)-induced DFC was pretreated with RSG to observe its protection on the damaged biological function. Immunoflourescence staining and transmission electron microscope were used to detect the intracellular ROS level. SD rat orthotopic transplantation model and SOD1 knockout mice subcutaneous transplantation model were applied to explore the regenerative outcome of the xenograft.ResultsRSG pretreatment significantly reduced the adverse effects of H2O2 on DFC with decreased intracellular ROS expression and alleviated mitochondrial damage. In vivo results confirmed RSG administration substantially enhanced the host’s antioxidant capacity with reduced osteoclasts formation and increased periodontal ligament like tissue regeneration efficiency, maximumly maintaining the xenograft function.ConclusionsRSG preconditioning could preserve the biological properties of the transplanted stem cells under OS microenvironment and promote organ regeneration by attenuating the inflammatory reaction and OS injury.
Repeated ethanol exposure and withdrawal alters ACE2 expression in discrete brain regions: Implications for SARS-CoV-2 infection
Authors: Balasubramanian Nagalakshmi , James Thomas D , Pushpavathi Selvakumar Govindhasamy , Marcinkiewcz Catherine A. 
Published: March 2022

AbstractEmerging evidence suggests that people with alcohol use disorders are at higher risk for SARS-CoV-2. SARS-CoV-2 engages angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) receptors for cellular entry. While ACE2 and TMPRSS2 genes are upregulated in the cortex of alcohol-dependent individuals, information on expression in specific brain regions and neural populations implicated in SARS-CoV-2 neuroinvasion, particularly monoaminergic neurons, is limited. We sought to clarify how chronic alcohol exposure affects ACE2 and TMPRSS2 expression in monoaminergic brainstem circuits and other putative SARS-CoV-2 entry points. C57BL/6J mice were exposed to chronic intermittent ethanol (CIE) vapor for 4 weeks and brains were examined using immunofluorescence. We observed increased ACE2 levels in the olfactory bulb and hypothalamus following CIE, which are known to mediate SARS-CoV-2 neuroinvasion. Total ACE2 immunoreactivity was also elevated in the raphe magnus (RMG), raphe obscurus (ROB), and locus coeruleus (LC), while in the dorsal raphe nucleus (DRN), ROB, and LC we observed increased colocalization of ACE2 with monoaminergic neurons. ACE2 also increased in the periaqueductal gray (PAG) and decreased in the amygdala. Whereas ACE2 was detected in most brain regions, TMPRSS2 was only detected in the olfactory bulb and DRN but was not significantly altered after CIE. Our results suggest that previous alcohol exposure may increase the risk of SARS-CoV-2 neuroinvasion and render brain circuits involved in cardiovascular and respiratory function as well as emotional processing more vulnerable to infection, making adverse outcomes more likely. Additional studies are needed to define a direct link between alcohol use and COVID-19 infection.
A Quantitative Modelling Approach for DNA Repair on a Population Scale
Authors: Zeitler Leo , Wilkes Cyril Denby , Goldar Arach , Soutourina Julie 
Published: March 2022

AbstractDespite intensive research of DNA repair after UV in eukaryotes, a framework to quantitatively describe the dynamics in vivo is still lacking. We developed a new data-driven approach to analyse CPD repair kinetics over time in Saccharomyces cerevisiae. In contrast to other studies that consider sequencing signals as an average behaviour, we introduce a hidden axis representing independent cells where loci can transition from damaged to repaired. This permits the application of the Kolmogorov-Johnson–Mehl–Avrami model to find a region-specific and continuous representation of the entire temporal process. We correlated the parameters via a k-nearest neighbour approach to a variety of genomic features, including transcription rate and nucleosome density. The clearest link was found for the gene size, which has been unreported for budding yeast to our knowledge. The framework hence allows a comprehensive analysis of nuclear processes on a population scale.Author SummaryAs DNA encodes our very identity, it has been subject to a plethora of studies over the last century. The advent of new technologies that permit rapid sequencing of large DNA and RNA samples opened doors to before unknown mechanisms and interactions on a genomic scale. This led to an in-depth analysis of several nuclear processes, including transcription of genes and lesion repair. However, the applied protocols do mostly not allow a high temporal resolution. Quite the contrary, the experiments yield often only some few data signals over several hours. Missing dynamics between time points are chiefly ignored, implicitly assuming that they straightforwardly transition from one to another. Here, we show that such an understanding can be flawed. We use the repair process of UV-induced DNA damage as an example to present a quantitative analysis framework that permits the representation of the entire temporal process with only three parameters. We subsequently describe how they can be linked to other heterogeneous data sets. Consequently, we evaluate a correlation to the whole kinetic process rather than to a single time point. Although the approach is exemplified using DNA repair, it can be readily applied to any other mechanism and sequencing data that represents a state transition between two states, such as damaged and repaired.
MultiHeadGAN: A Deep Learning Method for Low Contrast Retinal Pigment Epithelium Cells Segmentation in Fluorescent Flatmount Microscopy Images
Authors: Yu Hanyi , Wang Fusheng , Theodoro George , Nickerson John , Kong Jun 
Published: March 2022

AbstractBackgroundRetinal pigment epithelium (RPE) aging is an important cause of vision loss. As RPE aging is accompanied by changes in cell morphological features, an accurate segmentation of RPE cells is a prerequisite to such morphology analyses. Due the overwhelmingly large cell number, manual annotations of RPE cell borders are time-consuming. Computer based methods do not work well on cells with weak or missing borders in the impaired RPE sheet regions.MethodTo address such a challenge, we develop a semi-supervised deep learning approach, namely MultiHeadGAN, to segment low contrast cells from impaired regions in RPE flatmount images. The developed deep learning model has a multi-head structure that allows model training with only a small scale of human annotated data. To strengthen model learning effect, we further train our model with RPE cells without ground truth cell borders by generative adversarial networks. Additionally, we develop a new shape loss to guide the network to produce closed cell borders in the segmentation results.ResultsIn this study, 155 annotated and 1,640 unlabeled image patches are included for model training. The testing dataset consists of 200 image patches presenting large impaired RPE regions. The average RPE segmentation performance of the developed model MultiHeadGAN is 85.4 (correct rate), 88.8 (weighted correct rate), 87.3 (precision), and 80.1 (recall), respectively. Compared with other state-of-the-art deep learning approaches, our method demonstrates superior qualitative and quantitative performance.ConclusionsSuggested by our extensive experiments, our developed deep learning method can accurately segment cells from RPE flatmount microscopy images and is promising to support large scale cell morphological analyses for RPE aging investigations.
Multi-Layered Maps of Neuropil with Segmentation-Guided Contrastive Learning
Authors: Dorkenwald Sven , Li Peter H. , Januszewski Michał , Berger Daniel R. , Maitin-Shepard Jeremy , Bodor Agnes L. , Collman Forrest , Schneider-Mizell Casey M. , da Costa Nuno Maçarico , Lichtman Jeff W. , Jain Viren 
Published: March 2022

AbstractMaps of the nervous system that identify individual cells along with their type, subcellular components, and connectivity have the potential to reveal fundamental organizational principles of neural circuits. Volumetric nanometer-resolution imaging of brain tissue provides the raw data needed to build such maps, but inferring all the relevant cellular and subcellular annotation layers is challenging. Here, we present Segmentation-Guided Contrastive Learning of Representations (“SegCLR”), a self-supervised machine learning technique that produces highly informative representations of cells directly from 3d electron microscope imagery and segmentations. When applied to volumes of human and mouse cerebral cortex, SegCLR enabled the classification of cellular subcompartments (axon, dendrite, soma, astrocytic process) with 4,000-fold less labeled data compared to fully supervised approaches. Surprisingly, SegCLR also enabled inference of cell types (neurons, glia, and subtypes of each) from fragments with lengths as small as 10 micrometers, a task that can be difficult for humans to perform and whose feasibility greatly enhances the utility of imaging portions of brains in which many neuron fragments terminate at a volume boundary. These predictions were further augmented via Gaussian process uncertainty estimation to enable analyses restricted to high confidence subsets of the data. Finally, SegCLR enabled detailed exploration of layer-5 pyramidal cell subtypes and automated large-scale statistical analysis of upstream and downstream synaptic partners in mouse visual cortex.
The sugarless grape trait characterized by single berry phenotyping
Authors: Bigard Antoine , Romieu Charles , Ojeda Hernán , Torregrosa Laurent 
Published: March 2022

AbstractFor grape production, an important driver for the selection of varieties better adapted to climate fluctuations, especially warming, is the balance between fruit sugars and acidity. Since the past decades, temperature during ripening has constantly raised causing excessive sugars concentrations and insufficient acidity of the wine grapes in warmest regions. There is thus an increasing interest in breeding new cultivars, able to ripen at lower sugar concentration while preserving fruit acidity. However, the phenotyping of berry composition challenges both methodological and conceptual issues. Indeed, most authors predetermine either average harvest date, ripening duration, thermal time or even hexoses concentration threshold itself, to compare accessions at an hopefully similar ripe stage. Here, we have phenotyped the fruit development and composition of 6 genotypes, including 3 new disease-tolerant varieties known to produce wines with low alcoholic contents. The study was performed at single berry level from the end of green growth stage to the arrest of phloem unloading, when water and solute contents reach a maximum per berry. The results confirmed that sugarless genotypes achieve fruit ripening with 20-30% less hexoses than classical varieties, Grenache N and Merlot N, without impacting berry growth, total acidity or cations accumulation. Sugarless genotypes displayed a higher malic acid/tartaric acid balance than other genotypes with similar sucrose/H+ exchanges at the onset of ripening. Data suggest that sugarless phenotype results from a specific plasticity in the relationship between growth and the turgor imposed by organic acid accumulation and sugar loading. This opens interesting perspectives to understand the mechanism of grapevine berry growth and to breed varieties better coping with climate warming.
Female directors and environmental innovation: is stakeholder orientation a missing link?
Authors: Wang Yu , Chang Xiaoying , Wang Tienan , Wang Shanshan 
Published: March 2022

Purpose
The purpose of this study is to examine the effect of stakeholder orientation in mediating the impact of female directors on environmental innovation. The authors argue that female directors are eco-friendly and more concerned with multi-stakeholder interests and demands. Thus, they promote environmental innovation by including more stakeholder-oriented values and beliefs in firm decision-making.

Design/methodology/approach
As the dependent variable in this study is a nonnegative count variable, the authors use a count data model based on Poisson regression. A sample of Chinese listed firms between 2010 and 2020 is used to test the hypotheses.

Findings
The results of this study show that female directors can enhance environmental innovation. Further, stakeholder orientation represents an intermediate channel that accounts for the effects of female directors on environmental innovation. This suggests that having women on a board can lead to better stakeholder management, which, in turn, positively affects environmental innovation. The authors also reveal that female directors contribute more to stakeholder orientation with the presence of female chairpersons.

Originality/value
A significant limitation in the literature is that little attention has been paid to the mechanisms linking female directors to firm outcomes. In the context of environmental innovation, while previous studies have investigated the influence of female directors on environmental innovation, the underlying channels of that influence remain largely unexplored. Therefore, the findings of this study advance the understanding of the effects of female directors on environmental innovation by revealing an important underlying channel – stakeholder orientation.
Enhancing in-store picking for e-grocery: an empirical-based model
Authors: Seghezzi Arianna , Siragusa Chiara , Mangiaracina Riccardo 
Published: March 2022

PurposeThis paper identifies, configures and analyses a solution aimed at increasing the efficiency of in-store picking for e-grocers and combining the traditional store-based option with a warehouse-based logic (creating a back area dedicated to the most required online items).Design/methodology/approachThe adopted methodology is a multi-method approach combining analytical modelling and interviews with practitioners. Interviews were performed with managers, whose collaboration allowed the development and application of an empirically-grounded model, aimed to estimate the performances of the proposed picking solution in its different configurations. Various scenarios are modelled and different policies are evaluated.FindingsThe proposed solution entails time benefits compared to traditional store-based picking for three main reasons: lower travel time (due to the absence of offline customers), lower retrieval time (tied to the more efficient product allocation in the back) and lower time to manage stock-outs (since there are no missing items in the back). Considering the batching policies, order picking is always outperformed by batch and zone picking, as they allow for the reduction of the average travelled distance per order. Conversely, zone picking is more efficient than batch picking when demand volumes are high.Originality/valueFrom an academic perspective, this work proposes a picking solution that combines the store-based and warehouse-based logics (traditionally seen as opposite/alternative choices). From a managerial perspective, it may support the definition of the picking process for traditional grocers that are offering – or aim to offer – e-commerce services to their customers.
Survey of non‐native small mammals traded in South Africa
Authors: Shivambu Ndivhuwo , Shivambu Tinyiko C. , Downs Colleen T. 
Published: March 2022

AbstractThe sale of live non‐native animals has become a social norm and is of global concern. The pet trade industry has become one of the main pathways where non‐native small mammals are introduced worldwide. We conducted a questionnaire survey in South African pet shops from September 2018 to September 2019 to gain insights into non‐native small mammalian species trade in South Africa. We also investigated whether the pet shop owners were aware of the South African National Environmental Management: Biodiversity Act (NEM: BA; No. 10 of 2004), which regulates and provides management and conservation of the country's biodiversity. A total of 111 pet shop owners/managers responded to the survey, with 26.6% of the owners reporting the sale of birds, 25.1% of fish and 22.5% of mammals. A total of 16 non‐native small mammalian species were reported sold, with European rabbits (Oryctolagus cuniculus), Norwegian rats (Rattus norvegicus) and house mice (Mus musculus) being the most commonly sold pets. We found that breeders, animal rescues and pet shops were the major suppliers of small mammal pets, and in terms of the regulation, most respondents (67.8%) were aware of NEM: BA. However, despite the knowledge of the regulations, some of the traded species pose a serious invasion threat. As a result, we recommend increased regulation, monitoring and public awareness to prevent the potential negative impacts associated with non‐native mammal species in South Africa.
Comparison of aquatic macroinvertebrate communities of Lake Ahémé (Benin, West Africa) across the short and long wet seasons
Authors: Odountan Olaniran Hamed , Sidi O. I. Massara Nadjib , Janssens de Bisthoven Luc , Bird Matthew S. , Abou Youssouf 
Published: March 2022

AbstractSeldom investigated for its biodiversity, the biomonitoring of Lake Ahémé is expected to increase in future and a prerequisite is the design of an appropriate sampling strategy. Here, we assessed macroinvertebrate assemblages in relation to environmental conditions in Lake Ahémé during the short and long wet seasons (SWS and LWS, respectively). This will help optimise sampling strategies for the future, when sampling only during the SWS or the LWS. A total of 4049 macroinvertebrates from 28 families and 32 genera were collected. Abundance was significantly higher at sites sampled during the SWS. Molluscs were the most dominant taxon and accounted for 92.8% of individuals collected during this study. This was followed by annelids, insects and crustaceans representing 3.7%, 3.2% and 0.3% of the total abundance, respectively. Biodiversity indices showed a significantly higher diversity in the SWS and higher spatial variation in the macroinvertebrate community. The first three axes of the non‐metric multidimensional scaling revealed spatial changes in the macroinvertebrate community during the SWS and LWS. These changes were driven by salinity, conductivity, pH, temperature, dissolved oxygen and water depth. No taxa could be assigned as indicators in the LWS whereas diverse brackish and freshwater species characterised the SWS. As a result, when considering sampling during the wet seasons, SWS sampling should suffice for a qualitative study whereas an accurate ecological investigation requires both SWS and LWS.
The smile curve: Evolving sources of value added in manufacturing
Authors: Baldwin Richard , Ito Tadashi 
Published: March 2022

AbstractA dramatic disordering of global manufacturing has been seen in recent years. Production processes have fragmented, and many production stages have been offshored to developing nations. Organization of this new global supply chain has evolved into what are often called global value chains (GVCs). Less studied, but no less important, is the shift in the sectoral source of value added in manufactured exports. This phenomenon, often called the “smile curve,” involves a swing in the share of value added in manufactured exports that is generated in the manufacturing sector itself instead of, for example, in the pre‐ and post‐fabrication stages. Our paper presents new evidence quantifying the magnitude of the smile curve notion. Using international input–output databases, we find evidence supporting the smile curve at the aggregate level. Specifically, for almost all exporting sectors and nations, we find that the value added to exports has shifted decisively from the manufacturing sector to service sectors. We also find that developing countries reduced their own‐sourcing service value‐added share, while developed countries maintained their relatively high levels of own‐sourcing service value‐added share.