bluuebunny/crossref_metadata_2025 huggingface dataset:
Historical Landscape Use of Migratory Caribou: New Insights From Old Antlers
Authors: Miller Joshua H. , Crowley Brooke E. , Bataille Clément P. , Wald Eric J. , Kelly Abigail , Gaetano Madison , Bahn Volker , Druckenmiller Patrick
Published: January 2021

Accumulations of shed caribou antlers (Rangifer tarandus) are valuable resources for expanding the temporal scope with which we evaluate seasonal landscape use of herds. Female caribou shed their antlers within days of giving birth, thus marking calving ground locations. Antler geochemistry (87Sr/86Sr) reflects the isotopic signature of regions used during antler growth, thereby providing data on a second component of seasonal landscape use. Here, we evaluate shed caribou antlers from the Coastal Plain of the Arctic National Wildlife Refuge, Alaska. The Central and Eastern regions of the Coastal Plain are calving grounds for the Porcupine Caribou Herd, while the Western Coastal Plain supports calving by the Central Arctic Herd. We found that antler 87Sr/86Sr from the Central and Eastern Coastal Plain were isotopically indistinguishable, while antler 87Sr/86Sr from the Western Coastal Plain was significantly smaller. For each region, we compared isotopic data for “recent” antlers, which overlap the bulk of standardized state and federal caribou monitoring (early 1980s and younger), with “historical” antlers shed in years predating these records (from the 1300s to the 1970s). For Porcupine Herd females calving in the Arctic Refuge, comparisons of antler 87Sr/86Sr through time indicate that summer ranges have been consistent since at least the 1960s. However, changes between historical and recent antler 87Sr/86Sr for the Central Arctic Herd indicate a shift in summer landscape use after the late 1970s. The timing of this shift is coincident with multiple factors including increased infrastructural development in their range related to hydrocarbon extraction. Accumulations of shed caribou antlers and their isotope geochemistry extend modern datasets by decades to centuries and provide valuable baseline data for evaluating potential anthropogenic and other influences on caribou migration and landscape use.
Mapping the Establishment and Invasiveness Potential of Rainbow Trout (Oncorhynchus mykiss) in Turkey: With Special Emphasis on the Conservation of Native Salmonids
Authors: Yoğurtçuoğlu Baran , Bucak Tuba , Ekmekçi Fitnat Güler , Kaya Cüneyt , Tarkan Ali Serhan
Published: January 2021

Rainbow trout (Oncorhynchus mykiss) has become by far the most frequently farmed freshwater fish species in Turkey, whereas very little is known about its establishment and invasiveness potential. We explored this potential through a combination of Maxent habitat suitability model and the Aquatic Species Invasiveness Screening Kit (AS-ISK) on the river basin scale by generating an overall risk score (ORS). The outcome of this approach was also incorporated with the spatial analysis of native salmonid species by generating a relative vulnerability score (RVS) to prioritize susceptibility of native species (or populations) and to propose risk hotspots by identifying their potential geographic overlap and interaction with O. mykiss. Results suggest that the northern basins (Eastern Black Sea, Western Black Sea and Marmara basins) are the most suitable basins for O. mykiss. According to the Basic Risk Assessment (BRA) threshold scores, O. mykiss is classified as “high risk” for 3 (12.0%) of the 25 river basins screened (Western Black Sea, Eastern Black Sea and Maritza-Ergene), and as “medium risk” for the remaining basins. The climate change assessment (CCA) scores negatively contributed the overall invasiveness potential of O. mykiss in 22 (88.0%) of the river basins and resulted in zero contribution for the remaining three, namely Aras-Kura, Çoruh river and Eastern Black Sea. The ORS score of river basins was lowest for Orontes and highest for Western Black Sea, whereas it was lowest for Konya-closed basin and highest for Eastern Black Sea, when CCA was associated. The micro-basins occupied by Salmo rizeensis had the highest mean habitat suitability with O. mykiss. Among the all species, S. abanticus had the highest RVS, followed by S. munzuricus and S. euphrataeus. The overall outcome of the present study also suggests that the establishment and invasiveness potential of O. mykiss may decrease under future (climate warmer) in Turkey, except for the northeast region. This study can provide environmental managers and policy makers an insight into using multiple tools for decision-making. The proposed RVS can also be considered as a complementary tool to improve IUCN red list assessment protocols of species.
Climate Effects on Prey Vulnerability Modify Expectations of Predator Responses to Short- and Long-Term Climate Fluctuations
Authors: Morin Aïssa , Chamaillé-Jammes Simon , Valeix Marion
Published: January 2021

Climate changes affect the distribution and abundance of organisms, often via changes in species interactions. Most animals experience predation, and a number of models have investigated how climate fluctuations can influence predator–prey dynamics by affecting prey abundance through changes in resource availability. However, field studies have shown that prey vulnerability is a key feature determining the outcome of predator–prey interactions, which also varies with climatic conditions,viachanges in prey body condition or in habitat characteristics (e.g. vegetation cover). In this theoretical work, we explore, with large mammals of African savannas in mind, how the interplay between climate-induced changes in prey abundance and climate-induced changes in prey vulnerability affects the immediate and long-term responses of predator populations. We account for prey body condition and habitat effects on prey vulnerability to predation. We show that predictions on how predator abundance responds to climate fluctuations differ depending on how climate influences prey vulnerability (habitat characteristics vs. prey body condition). We discuss how species traits influence the relative importance of the different sources of vulnerability. For example, our results suggest that populations of cursorial predators (such as spotted hyaenas) are expected to fare better than populations of ambush predators (such as African lions) in African ecosystems that will be characterised by an aridification. This study highlights the importance of understanding, and accounting for, the vulnerability factors associated to a given predator–prey pair, and improves our comprehension of predator–prey relationships in a changing climate.
Consistency of Social Interactions in Sooty Mangabeys and Chimpanzees
Authors: Mielke Alexander , Preis Anna , Samuni Liran , Gogarten Jan F. , Lester Jack D. , Crockford Catherine , Wittig Roman M.
Published: January 2021

Predictability of social interactions can be an important measure for the social complexity of an animal group. Predictability is partially dependent on how consistent interaction patterns are over time: does the behavior on 1 day explain the behavior on another? We developed a consistency measure that serves two functions: detecting which interaction types in a dataset are so inconsistent that including them in further analyses risks introducing unexplained error; and comparatively quantifying differences in consistency within and between animal groups. We applied the consistency measure to simulated data and field data for one group of sooty mangabeys (Cercocebus atys atys) and to groups of Western chimpanzees (Pan troglodytes verus) in the Taï National Park, Côte d'Ivoire, to test its properties and compare consistency across groups. The consistency measures successfully identified interaction types whose low internal consistency would likely create analytical problems. Species-level differences in consistency were less pronounced than differences within groups: in all groups, aggression and dominance interactions were the most consistent, followed by grooming; spatial proximity at different levels was much less consistent than directed interactions. Our consistency measure can facilitate decision making of researchers wondering whether to include interaction types in their analyses or social networks and allows us to compare interaction types within and between species regarding their predictability.
Effects of Soil Nutrient Heterogeneity on the Growth and Invasion Success of Alien Plants: A Multi-Species Study
Authors: Gao Fang-Lei , He Qiao-Sheng , Zhang Yi-Dan , Hou Jia-Hui , Yu Fei-Hai
Published: January 2021

Spatial heterogeneity in soil nutrient availability can influence performance of invasive plant species under competition-free environments. However, little was known about whether invasive plants perform better under heterogeneous than under homogeneous soil nutrient conditions in competition with native plant communities. We conducted a multi-species greenhouse experiment to test the effect of soil nutrient heterogeneity on the growth and invasion success of alien plants in a native plant community. We grew ten alien invasive plant species that are common in China under a homogeneous or heterogeneous environment alone or together with a community consisting of six native plant species from China. Compared with the homogeneous soil condition, the heterogeneous soil condition significantly increased aboveground biomass of the invasive plants. However, soil nutrient heterogeneity did not affect the relative abundance of the invasive species, as measured by the ratio of aboveground biomass of the invasive species to total aboveground biomass of the whole community. There were no significant interactive effects of soil nutrient heterogeneity and competition from the native community on aboveground biomass of the invasive plants and also no significant effects of soil nutrient heterogeneity on its relative abundance. Our results indicate that soil nutrient heterogeneity has a positive effect on the growth of invasive plants in general, but do not support the idea that soil nutrient heterogeneity favors the invasion success of exotic plant species in native plant communities.
Independent Validation of Genomic Prediction in Strawberry Over Multiple Cycles
Authors: Osorio Luis F. , Gezan Salvador A. , Verma Sujeet , Whitaker Vance M.
Published: January 2021

The University of Florida strawberry (Fragaria×ananassa) breeding program has implemented genomic prediction (GP) as a tool for choosing outstanding parents for crosses over the last five seasons. This has allowed the use of some parents 1 year earlier than with traditional methods, thus reducing the duration of the breeding cycle. However, as the number of breeding cycles increases over time, greater knowledge is needed on how multiple cycles can be used in the practical implementation of GP in strawberry breeding. Advanced selections and cultivars totaling 1,558 unique individuals were tested in field trials for yield and fruit quality traits over five consecutive years and genotyped for 9,908 SNP markers. Prediction of breeding values was carried out using Bayes B models. Independent validation was carried out using separate trials/years as training (TRN) and testing (TST) populations. Single-trial predictive abilities for five polygenic traits averaged 0.35, which was reduced to 0.24 when individuals common across trials were excluded, emphasizing the importance of relatedness among training and testing populations. Training populations including up to four previous breeding cycles increased predictive abilities, likely due to increases in both training population size and relatedness. Predictive ability was also strongly influenced by heritability, but less so by changes in linkage disequilibrium and effective population size. Genotype by year interactions were minimal. A strategy for practical implementation of GP in strawberry breeding is outlined that uses multiple cycles to predict parental performance and accounts for traits not included in GP models when constructing crosses. Given the importance of relatedness to the success of GP in strawberry, future work could focus on the optimization of relatedness in the design of TRN and TST populations to increase predictive ability in the short-term without compromising long-term genetic gains.
Genetic Diversity of Bubalus bubalis in Germany and Global Relations of Its Genetic Background
Authors: Noce Antonia , Qanbari Saber , González-Prendes Rayner , Brenmoehl Julia , Luigi-Sierra María Gracia , Theerkorn Michael , Fiege Marc-André , Pilz Heike , Bota Adrian , Vidu Livia , Horwath Csaba , Haraszthy László , Penchev Pencho , Ilieva Yordanka , Peeva Tzonka , Lüpcke Wolfgang , Krawczynski René , Wimmers Klaus , Thiele Manfred , Hoeflich Andreas
Published: January 2021

This is the first study to explore the genetic diversity and population structure of domestic water buffalo (Bubalus bubalis) in Germany and their potential relations to herds in other parts of Europe or worldwide. To this end, animals from different herds in Germany, Bulgaria, Romania, and Hungary were genotyped and compared to genotypes from other populations with worldwide distribution and open to the public. The pilot study analyzed population structure, phylogenetic tree, and inbreeding events in our samples. In buffalos from Germany, a mixed genetic make-up with contributions from Bulgaria (Murrah breed), Romania, and Italy was found. All in all, a high degree of genetic diversity was identified in European buffalos, and a novel genotype was described in Hungarian buffalos by this study. We demonstrate that European buffalos stand out from other buffalo populations worldwide, supporting the idea that buffalos have not completely disappeared from the European continent during the late Pleistocene. The high genetic diversity in European buffalos seems to be an excellent prerequisite for the establishment of local breeds characterized by unique traits and features. This study may also be considered as an initial step on the way to genome characterization for the sustainable development of the buffalo economy in Germany and other parts of Europe in the future.
Technological Innovations for Improving Cassava Production in Sub-Saharan Africa
Authors: Mbanjo Edwige Gaby Nkouaya , Rabbi Ismail Yusuf , Ferguson Morag Elizabeth , Kayondo Siraj Ismail , Eng Ng Hwa , Tripathi Leena , Kulakow Peter , Egesi Chiedozie
Published: January 2021

Cassava is crucial for food security of millions of people in sub-Saharan Africa. The crop has great potential to contribute to African development and is increasing its income-earning potential for small-scale farmers and related value chains on the continent. Therefore, it is critical to increase cassava production, as well as its quality attributes. Technological innovations offer great potential to drive this envisioned change. This paper highlights genomic tools and resources available in cassava. The paper also provides a glimpse of how these resources have been used to screen and understand the pattern of cassava genetic diversity on the continent. Here, we reviewed the approaches currently used for phenotyping cassava traits, highlighting the methodologies used to link genotypic and phenotypic information, dissect the genetics architecture of key cassava traits, and identify quantitative trait loci/markers significantly associated with those traits. Additionally, we examined how knowledge acquired is utilized to contribute to crop improvement. We explored major approaches applied in the field of molecular breeding for cassava, their promises, and limitations. We also examined the role of national agricultural research systems as key partners for sustainable cassava production.
Exploring Prediction of Antimicrobial Resistance Based on Protein Solvent Accessibility Variation
Authors: Marini Simone , Oliva Marco , Slizovskiy Ilya B. , Noyes Noelle Robertson , Boucher Christina , Prosperi Mattia
Published: January 2021

Antimicrobial resistance (AMR) is a significant and growing public health threat. Sequencing of bacterial isolates is becoming more common, and therefore automatic identification of resistant bacterial strains is of pivotal importance for efficient, wide-spread AMR detection. To support this approach, several AMR databases and gene identification algorithms have been recently developed. A key problem in AMR detection, however, is the need for computational approaches detecting potential novel AMR genes or variants, which are not included in the reference databases. Toward this direction, here we study the relation between AMR and relative solvent accessibility (RSA) of protein variants from an in silico perspective. We show how known AMR protein variants tend to correspond to exposed residues, while on the contrary their susceptible counterparts tend to be buried. Based on these findings, we develop RSA-AMR, a novel relative solvent accessibility-based AMR scoring system. This scoring system can be applied to any protein variant to estimate its propensity of altering the relative solvent accessibility, and potentially conferring (or hindering) AMR. We show how RSA-AMR score can be integrated with existing AMR detection algorithms to expand their range of applicability into detecting potential novel AMR variants, and provide a ten-fold increase in Specificity. The two main limitations of RSA-AMR score is that it is designed on single point changes, and a limited number of variants was available for model learning.
Does Antigen Glycosylation Impact the HIV-Specific T Cell Immunity?
Authors: Olvera Alex , Cedeño Samandhy , Llano Anuska , Mothe Beatriz , Sanchez Jorge , Arsequell Gemma , Brander Christian
Published: January 2021

It is largely unknown how post-translational protein modifications, including glycosylation, impacts recognition of self and non-self T cell epitopes presented by HLA molecules. Data in the literature indicate thatO- andN-linked glycosylation can survive epitope processing and influence antigen presentation and T cell recognition. In this perspective, we hypothesize that glycosylation of viral proteins and processed epitopes contribute to the T cell response to HIV. Although there is some evidence for T cell responses to glycosylated epitopes (glyco-epitopes) during viral infections in the literature, this aspect has been largely neglected for HIV. To explore the role of glyco-epitope specific T cell responses in HIV infection we conductedin silicoandex vivoimmune studies in individuals with chronic HIV infection. We found thatin silicoviral protein segments with potentially glycosylable epitopes were less frequently targeted by T cells.Ex vivosynthetically added glycosylation moieties generally masked T cell recognition of HIV derived peptides. Nonetheless, in some cases, addition of simple glycosylation moieties produced neo-epitopes that were recognized by T cells from HIV infected individuals. Herein, we discuss the potential importance of these observations and compare limitations of the employed technology with new methodologies that may have the potential to provide a more accurate assessment of glyco-epitope specific T cell immunity. Overall, this perspective is aimed to support future research on T cells recognizing glycosylated epitopes in order to expand our understanding on how glycosylation of viral proteins could alter host T cell immunity against viral infections.
Host Transcriptomic Response Following Administration of Rotavirus Vaccine in Infants’ Mimics Wild Type Infection
Authors: Gómez-Carballa Alberto , Barral-Arca Ruth , Cebey-López Miriam , Currás-Tuala Maria José , Pischedda Sara , Gómez-Rial José , Habgood-Coote Dominic , Herberg Jethro A. , Kaforou Myrsini , Martinón-Torres Federico , Salas Antonio
Published: January 2021

Background

Rotavirus (RV) is an enteric pathogen that has devastating impact on childhood morbidity and mortality worldwide. The immunologic mechanism underlying the protection achieved after RV vaccination is not yet fully understood.

Methods

We compared the transcriptome of children affected by community-acquired RV infection and children immunized with a live attenuated RV vaccine (RotaTeq®).

Results

RV vaccination mimics the wild type infection causing similar changes in children’s transcriptome, including transcripts associated with cell cycle, diarrhea, nausea, vomiting, intussusception, and abnormal morphology of midgut. A machine learning approach allowed to detect a combination of nine-transcripts that differentiates vaccinated from convalescent-naturally infected children (AUC: 90%; 95%CI: 70–100) and distinguishes between acute-infected and healthy control children (in both cases, AUC: 100%; 95%CI: 100–100). We identified a miRNA hsa-mir-149 that seems to play a role in the host defense against viral pathogens and may have an antiviral role.

Discussion

Our findings might shed further light in the understanding of RV infection, its functional link to intussusception causes, as well as guide development of antiviral treatments and safer and more effective vaccines. The nine-transcript signature may constitute a marker of vaccine protection and helps to differentiate vaccinated from naturally infected or susceptible children.
Immune Responses to Plasma-Derived Versus Recombinant FVIII Products
Authors: Peyvandi Flora , Miri Syna , Garagiola Isabella
Published: January 2021

The most severe side effect of hemophilia treatment is the inhibitor development occurring in 30% of patients, during the earliest stages of treatment with factor (F)VIII concentrates. These catastrophic immune responses rapidly inactivate the infused FVIII, rendering the treatment ineffective. This complication is associated with a substantial morbidity and mortality. The risk factors involved in the onset of the inhibitors are both genetic and environmental. The source of FVIII products, i.e. plasma-derived or recombinant FVIII products, is considered one of the most relevant factors for inhibitor development. Numerous studies in the literature report conflicting data on the different immunogenicity of the products. The SIPPET randomized trial showed an increased in the inhibitor rate in patients using recombinant FVIII products than those receiving plasma-derived products in the first exposure days. The SIPPET randomized trial showed an increase in the inhibitor rate in patients using recombinant FVIII products compared to those treated with plasma-derived products in the first days of exposure. The potential increase in the immunogenicity of recombinant products can be attributed to several factors such as: the different post-translational modification in different cell lines, the presence of protein aggregates, and the role played by the chaperon protein of FVIII, the von Willebrand factor, which modulates the uptake of FVIII by antigen presenting cells (APCs). Furthermore, the presence of non-neutralizing antibodies against FVIII has shown to be in increased inhibitor development as demonstrated in a sub-analysis of the SIPPET study. In addition, the presence of the specific subclasses of the immunoglobulins may also be an important biomarker to indicate whether the inhibitor will evolve into a persistent neutralizing antibody or a transient one that would disappear without any specific treatment. Recently, the availability of novel non-replacement therapies as well as emicizumab, administered by weekly subcutaneous infusion, have significantly changed the quality of life of patients with inhibitors showing a considerable reduction of the annual bleeding rate and in most patients the absence of bleeding. Although, these novel drugs improve patients' quality of life, they do not abolish the need to infuse FVIII during acute bleeding or surgery. Therefore, the issue of immunogenicity against FVIII still remains an important side effect of hemophilia treatment.
The Regulatory Role of High-Mobility Group Protein 1 in Sepsis-Related Immunity
Authors: Li Li , Lu Yuan-Qiang
Published: January 2021

High-mobility group box 1 (HMGB1), a prototypical damage-associated molecular pattern (DAMP) molecule, participates in multiple processes of various inflammatory diseases through binding to its corresponding receptors. In the early phase, sepsis is mainly characterized as a multi-bacterial-induced complex, excessive inflammatory response accompanied by the release of pro-inflammatory mediators, which subsequently develops into immune paralysis. A growing number of in vivo and in vitro investigations reveal that HMGB1 plays a pivotal role in the processes of inflammatory response and immunosuppression of sepsis. Therefore, HMGB1 exerts an indispensable role in the immune disorder and life-threatening inflammatory syndrome of sepsis. HMGB1 mainly mediate the release of inflammatory factors via acting on immune cells, pyroptosis pathways and phosphorylating nuclear factor-κB. Moreover HMGB1 is also associated with the process of sepsis-related immunosuppression. Neutrophil dysfunction mediated by HMGB1 is also an aspect of the immunosuppressive mechanism of sepsis. Myeloid-derived suppressor cells (MDSCs), which are also one of the important cells that play an immunosuppressive effect in sepsis, may connect with HMGB1. Thence, further understanding of HMGB1-associated pathogenesis of sepsis may assist in development of promising treatment strategies. This review mainly discusses current perspectives on the roles of HMGB1 in sepsis-related inflammation and immunosuppressive process and its related internal regulatory mechanisms.
RANK Signaling in the Differentiation and Regeneration of Thymic Epithelial Cells
Authors: Irla Magali
Published: January 2021

Thymic epithelial cells (TECs) provide essential clues for the proliferation, survival, migration, and differentiation of thymocytes. Recent advances in mouse and human have revealed that TECs constitute a highly heterogeneous cell population with distinct functional properties. Importantly, TECs are sensitive to thymic damages engendered by myeloablative conditioning regimen used for bone marrow transplantation. These detrimental effects on TECs delayde novoT-cell production, which can increase the risk of morbidity and mortality in many patients. Alike that TECs guide the development of thymocytes, reciprocally thymocytes control the differentiation and organization of TECs. These bidirectional interactions are referred to as thymic crosstalk. The tumor necrosis factor receptor superfamily (TNFRSF) member, receptor activator of nuclear factor kappa-B (RANK) and its cognate ligand RANKL have emerged as key players of the crosstalk between TECs and thymocytes. RANKL, mainly provided by positively selected CD4+thymocytes and a subset of group 3 innate lymphoid cells, controls mTEC proliferation/differentiation and TEC regeneration. In this review, I discuss recent advances that have unraveled the high heterogeneity of TECs and the implication of the RANK-RANKL signaling axis in TEC differentiation and regeneration. Targeting this cell-signaling pathway opens novel therapeutic perspectives to recover TEC function and T-cell production.
Carbon Export in the Seasonal Sea Ice Zone North of Svalbard From Winter to Late Summer
Authors: Dybwad Christine , Assmy Philipp , Olsen Lasse M. , Peeken Ilka , Nikolopoulos Anna , Krumpen Thomas , Randelhoff Achim , Tatarek Agnieszka , Wiktor Józef M. , Reigstad Marit
Published: January 2021

Phytoplankton blooms in the Arctic Ocean's seasonal sea ice zone are expected to start earlier and occur further north with retreating and thinning sea ice cover. The current study is the first compilation of phytoplankton bloom development and fate in the seasonally variable sea ice zone north of Svalbard from winter to late summer, using short-term sediment trap deployments. Clear seasonal patterns were discovered, with low winter and pre-bloom phytoplankton standing stocks and export fluxes, a short and intense productive season in May and June, and low Chl a standing stocks but moderate carbon export fluxes in the autumn post-bloom conditions. We observed intense phytoplankton blooms with Chl a standing stocks of >350 mg m−2 below consolidated sea ice cover, dominated by the prymnesiophyte Phaeocystis pouchetii. The largest vertical organic carbon export fluxes to 100 m, of up to 513 mg C m−2 day−1, were recorded at stations dominated by diatoms, while those dominated by P. pouchetii recorded carbon export fluxes up to 310 mg C m−2 day−1. Fecal pellets from krill and copepods contributed a substantial fraction to carbon export in certain areas, especially where blooms of P. pouchetii dominated and Atlantic water advection was prominent. The interplay between the taxonomic composition of protist assemblages, large grazers, distance to open water, and Atlantic water advection was found to be crucial in determining the fate of the blooms and the magnitude of organic carbon exported out of the surface water column. Previously, the marginal ice zone was considered the most productive region in the area, but our study reveals intense blooms and high export events in ice-covered waters. This is the first comprehensive study on carbon export fluxes for under-ice phytoplankton blooms, a phenomenon suggested to have increased in importance under the new Arctic sea ice regime.
Perspectives on Documenting Methods to Create Ocean Best Practices
Authors: Hörstmann Cora , Buttigieg Pier Luigi , Simpson Pauline , Pearlman Jay , Waite Anya M.
Published: January 2021

This perspective outlines how authors of ocean methods, guides, and standards can harmonize their work across the scientific community. We reflect on how documentation practices can be linked to modern information technologies to improve discoverability, interlinkages, and thus the evolution of distributed methods into common best practices within the ocean community. To show how our perspectives can be turned into action, we link them to guidance on using the IOC-UNESCO Ocean Best Practice System to support increased collaboration and reproducibility during and beyond the UN Decade of Ocean Sciences for Sustainable Development.
Traditional Knowledge Aids Description When Resolving the Taxonomic Status of Unsettled Species Using Classical and Molecular Taxonomy: The Case of the Shallow-Water Octopus Callistoctopus furvus (Gould, 1852) From the Western Atlantic Ocean
Authors: Jesus Manuella Dultra , Sales João Bráullio de Luna , Martins Rodrigo Silvestre , Ready Jonathan Stuart , Costa Tarcisio Augusto S. , Ablett Jonathan D. , Schiavetti Alexandre
Published: January 2021

Shallow-water marine invertebrate fauna is diverse in tropical latitudes but generally poorly known. This is in part due the remoteness of many of these regions, and a lack of locally trained taxonomists. In such cases, the ethnoknowledge (i.e., information acquired from the sociocultural references of a given social group) of traditional human populations may be a valuable tool to elucidate gaps in the occurrence of some taxa. In this study, we used a combined approach of ethnoknowledge, classic taxonomy and molecular techniques to describe and diagnose an unsettled species of shallow-water octopus of the genusCallistoctopus. A neotype for the Brazilian eastern octopusCallistoctopus furvus(Gould, 1852) is described along with some ecological notes. Octopuses were collected between April and May 2018 during field trips guided by artisanal octopus fishers of Bahia State (Brazil). A linear discriminant analysis showed that the morphology ofC. furvusoverlapped poorly withCallistoctopussp. from the Caribbean and Macaronesia (Madeira Archipelago) as well as withCallistoctopus macropus stricto sensufrom Mediterranean Sea. Analysis of mitochondrial large ribosomal subunit (rrnL, also known as 16S) gene and cytochrome C oxidase I (COI) showed thatC. furvusdiffers genetically from EuropeanC. macropusand the other species in the genus. In general,C. furvusdiffers from other Atlantic/MediterraneanCallistoctopusspecies in having a slender body shape and longer mantle lengths. As in other species of the genus,C. furvusis nocturnal and inhabits sandy bottoms, seagrass beds and/or low-profile reefs. Interestingly,C. furvusburrows itself into the sand as a defense mechanism. In conclusion, we showed the support of ethnoknowledge for integrative biodiversity assessments in poorly surveyed remote areas in the western tropical Atlantic.
Fluidic Platforms Incorporating Photo-Responsive Soft-Polymers Based on Spiropyran: From Green Synthesis to Precision Flow Control
Authors: Pandurangan Komala , Barrett Ruairi , Diamond Dermot , McCaul Margaret
Published: January 2021

In this paper, we describe how to create simple fluidic systems incorporating soft polymer actuator valves, that can provide highly precise control of flow rates in fluidic channels as an example of a 4D-materials based platform. The particular approach we describe employs photoresponsive gels that swell/contract via a light stimulus, enabling flow behavior to be controlled from outside the fluidic platform in a completely remote and non-contact manner. An improved synthesis of the spiropyran molecular photoswitch that delivers high yields (77%) using scalable green chemistry is described, along with details on how to build the valve structures in custom designed sites within the fluidic system. Fabrication of a demonstrator fluidic system incorporating up to four valves is described, along with electronics and in-house developed PID control software for achieving precise control of flow in the channels using LEDs. The resulting system demonstrates an innovative approach to microfluidics that offers scalability in terms of the number of polymer actuators along with wide variability of actuator form and function.
Practical Considerations Relating to Routine Clinical Biomarker Testing for Non–small Cell Lung Cancer: Focus on Testing for RET Fusions
Authors: Herbst Roy S. , Aisner Dara L. , Sonett Joshua R. , Turk Andrew T. , Weintraub Joshua L. , Lindeman Neal I.
Published: January 2021

For patients with advanced non–small cell lung cancer, genomic profiling of tumors to identify potentially targetable alterations and thereby inform treatment selection is now part of standard care. While molecular analyses are primarily focused on actionable biomarkers associated with regulatory agency-approved therapies, there are a number of emerging biomarkers linked to investigational agents in advanced stages of clinical development will become approved agents. A particularly timely example is the reported data and US Food and Drug Administration approval of highly specific small molecule inhibitors of the proto-oncogene tyrosine-protein kinase receptor RET indicate that testing for tumor RET gene fusions in patients with NSCLC has become clinically important. As the number of biomarkers to be tested in NSCLC grows, it becomes increasingly important to optimize and prioritize the use of biopsy tissue, in order to both continue to allow accurate histopathological diagnosis and also to support concurrent genomic profiling to identify perhaps relatively uncommon genetic events. In order to provide practical expert consensus guidance to optimize processes facilitating genomic testing in NSCLC and to overcome barriers to access and implementation, a multidisciplinary advisory board was held in New York, on January 30, 2019. The panel comprised physicians involved in sample procurement (interventional radiologists and a thoracic surgeon), surgical pathologists specializing in the lung, molecular pathologists, and thoracic oncologists. Particular consideration was given to the key barriers faced by these experts in establishing institutional genomic screening programs for NSCLC. Potential solutions have been devised in the form of consensus opinions that might be used to help resolve such issues.
Development and Validation of a Sepsis Mortality Risk Score for Sepsis-3 Patients in Intensive Care Unit
Authors: Zhang Kai , Zhang Shufang , Cui Wei , Hong Yucai , Zhang Gensheng , Zhang Zhongheng
Published: January 2021

Background: Many severity scores are widely used for clinical outcome prediction for critically ill patients in the intensive care unit (ICU). However, for patients identified by sepsis-3 criteria, none of these have been developed. This study aimed to develop and validate a risk stratification score for mortality prediction in sepsis-3 patients.

Methods: In this retrospective cohort study, we employed the Medical Information Mart for Intensive Care III (MIMIC III) database for model development and the eICU database for external validation. We identified septic patients by sepsis-3 criteria on day 1 of ICU entry. The Least Absolute Shrinkage and Selection Operator (LASSO) technique was performed to select predictive variables. We also developed a sepsis mortality prediction model and associated risk stratification score. We then compared model discrimination and calibration with other traditional severity scores.

Results: For model development, we enrolled a total of 5,443 patients fulfilling the sepsis-3 criteria. The 30-day mortality was 16.7%. With 5,658 septic patients in the validation set, there were 1,135 deaths (mortality 20.1%). The score had good discrimination in development and validation sets (area under curve: 0.789 and 0.765). In the validation set, the calibration slope was 0.862, and the Brier value was 0.140. In the development dataset, the score divided patients according to mortality risk of low (3.2%), moderate (12.4%), high (30.7%), and very high (68.1%). The corresponding mortality in the validation dataset was 2.8, 10.5, 21.1, and 51.2%. As shown by the decision curve analysis, the score always had a positive net benefit.

Conclusion: We observed moderate discrimination and calibration for the score termed Sepsis Mortality Risk Score (SMRS), allowing stratification of patients according to mortality risk. However, we still require further modification and external validation.
Inflammatory Cytokines in Diabetic Kidney Disease: Pathophysiologic and Therapeutic Implications
Authors: Donate-Correa Javier , Ferri Carla M. , Sánchez-Quintana Fátima , Pérez-Castro Atteneri , González-Luis Ainhoa , Martín-Núñez Ernesto , Mora-Fernández Carmen , Navarro-González Juan F.
Published: January 2021

Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease and a main contributing factor for cardiovascular morbidity and mortality in patients with diabetes mellitus. Strategies employed to delay the progression of this pathology focus on the control of traditional risk factors, such as hyperglycemia, and elevated blood pressure. Although the intimate mechanisms involved in the onset and progression of DKD remain incompletely understood, inflammation is currently recognized as one of the main underlying processes. Untangling the mechanisms involved in the appearing of a harmful inflammatory response in the diabetic patient is crucial for the development of new therapeutic strategies. In this review, we focus on the inflammation-related pathogenic mechanisms involved in DKD and in the therapeutic utility of new anti-inflammatory strategies.
Use of Synonymous Deoptimization to Derive Modified Live Attenuated Strains of Foot and Mouth Disease Virus
Authors: Diaz-San Segundo Fayna , Medina Gisselle N. , Spinard Edward , Kloc Anna , Ramirez-Medina Elizabeth , Azzinaro Paul , Mueller Steffen , Rieder Elizabeth , de los Santos Teresa
Published: January 2021

Foot-and-mouth disease (FMD) is one of the most economically important viral diseases that can affect livestock. In the last 70 years, use of an inactivated whole antigen vaccine has contributed to the eradication of disease from many developed nations. However, recent outbreaks in Europe and Eastern Asia demonstrated that infection can spread as wildfire causing economic and social devastation. Therefore, it is essential to develop new control strategies that could confer early protection and rapidly stop disease spread. Live attenuated vaccines (LAV) are one of the best choices to obtain a strong early and long-lasting protection against viral diseases. In proof of concept studies, we previously demonstrated that “synonymous codon deoptimization” could be applied to the P1 capsid coding region of the viral genome to derive attenuated FMDV serotype A12 strains. Here, we demonstrate that a similar approach can be extended to the highly conserved non-structural P2 and P3 coding regions, providing a backbone for multiple serotype FMDV LAV development. Engineered codon deoptimized P2, P3 or P2, and P3 combined regions were included into the A24Cruzeiro infectious clone optimized for vaccine production, resulting in viable progeny that exhibited different degrees of attenuation in cell culture, in mice, and in the natural host (swine). Derived strains were thoroughly characterizedin vitroandin vivo. Our work demonstrates that overall, the entire FMDV genome tolerates codon deoptimization, highlighting the potential of using this technology to derive novel improved LAV candidates.
Denitrification, Nitrogen Uptake, and Organic Matter Quality Undergo Different Seasonality in Sandy and Muddy Sediments of a Turbid Estuary
Authors: Bartoli Marco , Nizzoli Daniele , Zilius Mindaugas , Bresciani Mariano , Pusceddu Antonio , Bianchelli Silvia , Sundbäck Kristina , Razinkovas-Baziukas Arturas , Viaroli Pierluigi
Published: January 2021

The interaction between microbial communities and benthic algae as nitrogen (N) regulators in poorly illuminated sediments is scarcely investigated in the literature. The role of sediments as sources or sinks of N was analyzed in spring and summer in sandy and muddy sediments in a turbid freshwater estuary, the Curonian Lagoon, Lithuania. Seasonality in this ecosystem is strongly marked by phytoplankton community succession with diatoms dominating in spring and cyanobacteria dominating in summer. Fluxes of dissolved gas and inorganic N and rates of denitrification of water column nitrate (Dw) and of nitrate produced by nitrification (Dn) and sedimentary features, including the macromolecular quality of organic matter (OM), were measured. Shallow/sandy sites had benthic diatoms, while at deep/muddy sites, settled pelagic microalgae were found. The OM in surface sediments was always higher at muddy than at sandy sites, and biochemical analyses revealed that at muddy sites the OM nutritional value changed seasonally. In spring, sandy sediments were net autotrophic and retained N, while muddy sediments were net heterotrophic and displayed higher rates of denitrification, mostly sustained by Dw. In summer, benthic oxygen demand increased dramatically, whereas denitrification, mostly sustained by Dn, decreased in muddy and remained unchanged in sandy sediments. The ratio between denitrification and oxygen demand was significantly lower in sandy compared with muddy sediments and in summer compared with spring. Muddy sediments displayed seasonally distinct biochemical composition with a larger fraction of lipids coinciding with cyanobacteria blooms and a seasonal switch from inorganic N sink to source. Sandy sediments had similar composition in both seasons and retained inorganic N also in summer. Nitrogen uptake by microphytobenthos at sandy sites always exceeded the amount loss via denitrification, and benthic diatoms appeared to inhibit denitrification, even in the dark and under conditions of elevated N availability. In spring, denitrification attenuated N delivery from the estuary to the coastal area by nearly 35%. In summer, denitrification was comparable (~100%) with the much lower N export from the watershed, but N loss was probably offset by large rates of N-fixation.
Diversity of Fungal DNA Methyltransferases and Their Association With DNA Methylation Patterns
Authors: Nai Yu-Shin , Huang Yu-Chun , Yen Ming-Ren , Chen Pao-Yang
Published: January 2021

DNA methyltransferases (DNMTs) are a group of proteins that catalyze DNA methylation by transferring a methyl group to DNA. The genetic variation in DNMTs results in differential DNA methylation patterns associated with various biological processes. In fungal species, DNMTs and their DNA methylation profiles were found to be very diverse and have gained many research interests. We reviewed fungal DNMTs in terms of their biological functions, protein domain structures, and their associated epigenetic regulations compared to those known in plant and animal systems. In addition, we summarized recent reports on potential RNA-directed DNA methylation (RdDM) related to DNMT5 in fungi. We surveyed up to 40 fungal species with published genome-wide DNA methylation profiles (methylomes) and presented the associations between the specific patterns of fungal DNA methylation and their DNMTs based on a phylogenetic tree of protein domain structures. For example, the main DNMTs in Basidiomycota, DNMT1 with RFD domain + DNMT5, contributing to CG methylation preference, were distinct from RID + Dim-2 in Ascomycota, resulting in a non-CG methylation preference. Lastly, we revealed that the dynamic methylation involved in fungal life stage changes was particularly low in mycelium and DNA methylation was preferentially located in transposable elements (TEs). This review comprehensively discussed fungal DNMTs and methylomes and their connection with fungal development and taxonomy to present the diverse usages of DNA methylation in fungal genomes.
Early Long-Term Memory Impairment and Changes in the Expression of Synaptic Plasticity-Associated Genes, in the McGill-R-Thy1-APP Rat Model of Alzheimer's-Like Brain Amyloidosis
Authors: Habif Martín , Do Carmo Sonia , Báez María Verónica , Colettis Natalia Claudia , Cercato Magalí Cecilia , Salas Daniela Alejandra , Acutain María Florencia , Sister Caterina Laura , Berkowicz Valeria Laura , Canal María Pilar , González Garello Tomás , Cuello A. Claudio , Jerusalinsky Diana Alicia
Published: January 2021

Accruing evidence supports the hypothesis that memory deficits in early Alzheimer Disease (AD) might be due to synaptic failure caused by accumulation of intracellular amyloid beta (Aβ) oligomers, then secreted to the extracellular media. Transgenic mouse AD models provide valuable information on AD pathology. However, the failure to translate these findings to humans calls for models that better recapitulate the human pathology. McGill-R-Thy1-APP transgenic (Tg) rat expresses the human amyloid precursor protein (APP751) with the Swedish and Indiana mutations (of familial AD), leading to an AD-like slow-progressing brain amyloid pathology. Therefore, it offers a unique opportunity to investigate learning and memory abilities at early stages of AD, when Aβ accumulation is restricted to the intracellular compartment, prior to plaque deposition. Our goal was to further investigate early deficits in memory, particularly long-term memory in McGill-R-Thy1-APP heterozygous (Tg+/–) rats. Short-term- and long-term habituation to an open field were preserved in 3-, 4-, and 6-month-old (Tg+/–). However, long-term memory of inhibitory avoidance to a foot-shock, novel object-recognition and social approaching behavior were seriously impaired in 4-month-old (Tg+/–) male rats, suggesting that they are unable to either consolidate and/or evoke such associative and discriminative memories with aversive, emotional and spatial components. The long-term memory deficits were accompanied by increased transcript levels of genes relevant to synaptic plasticity, learning and memory processing in the hippocampus, such as Grin2b, Dlg4, Camk2b, and Syn1. Our findings indicate that in addition to the previously well-documented deficits in learning and memory, McGill-R-Thy1-APP rats display particular long-term-memory deficits and deep social behavior alterations at pre-plaque early stages of the pathology. This highlights the importance of Aβ oligomers and emphasizes the validity of the model to study AD-like early processes, with potentially predictive value.