bluuebunny/crossref_metadata_2025 huggingface dataset:
Beet production using vermiculite incorporated with Dystrophic Red Latosol (Oxisol)
Authors: Aguilar Ariel Santivañez , Vasque Henrique , Cardoso Antonio Ismael Inácio , Bardiviesso Estefânia Martins , Pelvine Raíra Andrade , Bezerra Sara Raissa Brito , Nasser Maurício Dominguez , Putti Fernando Ferrari , Lemes Ernane Miranda
Published: January 2021

Vermiculite is an expansive material that can be used for crop production. However, information about the use of vermiculite in vegetable production is scarce. Thus, this study's objective was to evaluate the effects of vermiculite levels incorporated into the soil (Red Latosol Dystrophic) for beet (Beta vulgaris L.) crop production. The experiment was performed during spring using the beet cultivar 'Early Wonder Tall Top' and 0, 2, 4, 6, 8, and 10 t∙ha-1 of vermiculite incorporated into the soil before seedling planting. The increase of the vermiculite doses caused a linear decrease of the fresh root and leaf weight. The yield reductions were due to the great water holding capacity of the vermiculite and the consequent high incidence of cercosporiosis (Cercospora beticola Saac).
Protective Effect of Ginsenoside against Acute Renal Failure
and Expression of Tyrosine Hydroxylase in the Locus Coeruleus
Authors: Zhang H A , Wang M , Zhou J , Yao Q Y , Ma J M , Jiang C L
Published: January 2021

Acute renal failure (ARF) is mainly characterized by acute tubular
necrosis. No significant change was found for mortality rates over
the past few decades despite significant advances in supportive
care. In recent years, great effort has been focused on traditional
and herbal medicine, which is much less toxic than those agents
conventionally used and which is nowadays considered as a novel
therapeutic agent for ARF. However, the effect of ginsenosides
(GS) administered orally on ARF has not been reported yet and
little is known about its cellular and molecular mechanism. The
purpose of the study is to investigate the protective effect of
ginsenoside in rats with ARF on the changes of tyrosine
hydroxylase immunoreactivity (TH-IR) as well as on the
involvement of mitogen-activated protein kinases (MAPK) in the
locus coeruleus. In our assay, glycerol-induced acute renal failure
in rats was employed to study the protective effects of
ginsenoside. Our results indicated that the treatment of ARF rats
with ginsenosides for 48 h significantly reduced the serum blood
urea nitrogen, creatinine level, and lipid peroxidation, restored
the GSH level and the normal renal morphology. Immunohistochemistry showed that an obvious increase of TH-IR was further
enhanced in ARF+GS group. The same effect was also observed
in the changes of p-ERK1/2-IR in the locus coeruleus. Our results
suggest that ginsenoside administered orally may have a strong
renal protective effect against glycerol-induced ARF, and
ginsenoside can also activate the brain catecholaminergic
neurons in the locus coeruleus. Our future attention will be
focused to the question whether there is a correlation between
the renal protective effect of ginsenosides against acute renal
failure and the activation of tyrosine hydroxylase in the locus
coeruleus.
New insights into mechanisms of atrial fibrillation
Authors: Aldhoon B , Melenovský V , Peichl P , Kautzner J
Published: January 2021

Although atrial fibrillation (AF) is the most common cardiac arrhythmia in clinical practice, precise mechanisms that lead to the onset and persistence of AF have not completely been elucidated. Over the last decade, outstanding progress has been made in understanding the complex pathophysiology of AF. The key role of ectopic foci in pulmonary veins as a trigger of AF has been recognized. Furthermore, structural remodeling was identified as the main mechanism for AF persistence, confirming predominant role of atrial fibrosis. Systemic inflammatory state, oxidative stress injury, autonomic balance and neurohormonal activation were discerned as important modifiers that affect AF susceptibility. This new understanding of AF pathophysiology has led to the emergence of novel therapies. Ablative interventions, renin-angiotensin system blockade, modulation of oxidative stress and targeting tissue fibrosis represent new approaches in tackling AF. This review aims to provide a brief summary of novel insights into AF mechanisms and consequent therapeutic strategies.
Adenosine A1, A2a, A2b, and A3 Receptors in Hematopoiesis.
2. Expression of Receptor mRNA in Resting and LipopolysaccharideActivated Mouse RAW 264.7 Macrophages
Authors: Štreitová D , Hofer M , Holá J , Vacek A , Pospíšil M
Published: January 2021

Expression of mRNA for adenosine receptor subtypes A1, A2a, A2b,
and A3 in normal and lipopolysaccharide (LPS)-activated murine
RAW 264.7 macrophages has been investigated using the
method of quantitative real-time polymerase chain reaction. The
results have shown a very low, unquantifiable expression of
adenosine A1 receptor mRNA in both normal and LPS-activated
macrophages. The other three adenosine receptor mRNAs have
been found to be expressed at various but always quantifiable
levels. Activation of the macrophages by LPS induced
upregulation of the expression of adenosine receptor A2a and A2b
mRNA, whereas the expression of adenosine receptor A3 mRNA
was downregulated. Unstimulated macrophages exhibited a high
expression of the A2b adenosine receptor mRNA. The findings are
discussed from the point of view of the antiinflammatory and
hematopoiesis-stimulating roles of the adenosine receptor
signaling.
Geoactive Zones and the Structure of Plant Communities in Connection With New Discoveries in Space Geology
Authors: Rogozin M.
Published: January 2021

The purpose of the work is to find out how plants react to such zones and whether their phytoindication is possible. Two territories of the Perm territory were studied: the Vishersky Nature Reserve and forests near Perm. The research methodology included lineament and geostructurometric analysis of space images and special maps using ring structures discovered on the Earth’s surface by Yu. I. Fivenskii, as well as phyto- and bioindication of small geoactive zones. It was found that in the forests near Perm favorable zones of such zones occupy 1.44% of the territory and within their limits the safety of common pine (Pinus sylvestris L.) is 29–42 times higher. Phytoindication of small geoactive zones of 1.0 and 3.0 m by common pine was shown in the zones of influence of these zones: 0–18 cm — the radius of inhibition with the absence of trees; 19–29 cm — the depression zone with small trees; 30–48 cm — the comfort zone with medium and large trees. Two types of networks formed by zones of 1.0 and 8.0 m in size near Perm (on the plain) and in the reserve (in the mountains) were compared. In the mountains, with high geodynamic activity of territories, the networks are oriented in one direction, while on the plain their orientation is misaligned by 30°. In the reserve, large trees of Siberian spruce (Picea obovata Ledeb.) were located on small geoactive zones of 1.0 and 8.0 m, and trees of Siberian pine (Pinus sibirica Du Tour) — on zones 1.0 and 3.0 m in combination with zones 16, 32 and 55 m. In the subgolets zone, ring structures of perennial plants were also found on the first two types of zones. In addition, along the edges of the swamps, chains of trees were found whose direction coincides with ring faults, and the chains themselves are similar to the structure of small geoactive zones networks, and this fractality requires field verification. The hypothesis recharge of plants within geoactive zones is proposed, which also explains the successful growth of trees on rocks, where the amount of available soil is minimal.
Broad-Based Stakeholder Ownership in Journalism: ESOPs, Co-ops, Blockchains
Authors: Schneider Nathan
Published: January 2021

This article presents a survey of broad-based stakeholder-ownership models for journalism. The models considered are forms of ownership by employees, associations, audiences, and blends of these. Some of the examples are so new that they have not been, and cannot yet be, comprehensively studied. Yet they bear unique promise for addressing the dual challenges of economic sustainability and perceived accountability that bedevil news media today. Such promise, however, does not guarantee success. While broad-based stakeholder ownership in the news business shows considerable capacity for public accountability, as well as some promise for business sustainability, it is ill-equipped to compete in markets organized to favor investor owners with far greater capital access. Such ownership models, therefore, will likely require additional policy support in order to gain and maintain significant market share.
Rapid Detection of Pomelo Fruit Quality Using Near-Infrared Hyperspectral Imaging Combined With Chemometric Methods
Authors: Chen Huazhou , Qiao Hanli , Feng Quanxi , Xu Lili , Lin Qinyong , Cai Ken
Published: January 2021

Pomelo is an important agricultural product in southern China. Near-infrared hyperspectral imaging (NIRHI) technology is applied to the rapid detection of pomelo fruit quality. Advanced chemometric methods have been investigated for the optimization of the NIRHI spectral calibration model. The partial least squares (PLS) method is improved for non-linear regression by combining it with the kernel Gaussian radial basis function (RBF). In this study, the core parameters of the PLS latent variables and the RBF kernel width were designed for grid search selection to observe the minimum prediction error and a relatively high correlation coefficient. A deep learning architecture was proposed for the parametric scaling optimization of the RBF-PLS modeling process for NIRHI data in the spectral dimension. The RBF-PLS models were established for the quantitative prediction of the sugar (SU), vitamin C (VC), and organic acid (OA) contents in pomelo samples. Experimental results showed that the proposed RBF-PLS method performed well in the parameter deep search progress for the prediction of the target contents. The predictive errors for model training were 1.076% for SU, 41.381 mg/kg for VC, and 1.136 g/kg for OA, which were under 15% of their reference chemical measurements. The corresponding model testing results were acceptably good. Therefore, the NIRHI technology combined with the study of chemometric methods is applicable for the rapid quantitative detection of pomelo fruit quality, and the proposed algorithmic framework may be promoted for the detection of other agricultural products.
Chondroitin Sulfate as a Potential Modulator of the Stem Cell Niche in Cornea
Authors: Ashworth Sean , Harrington Jodie , Hammond Greg M. , Bains Kiranjit K. , Koudouna Elena , Hayes Anthony J. , Ralphs James R. , Regini Justyn W. , Young Robert D. , Hayashi Ryuhei , Nishida Kohji , Hughes Clare E. , Quantock Andrew J.
Published: January 2021

Chondroitin sulfate (CS) is an important component of the extracellular matrix in multiple biological tissues. In cornea, the CS glycosaminoglycan (GAG) exists in hybrid form, whereby some of the repeating disaccharides are dermatan sulfate (DS). These CS/DS GAGs in cornea, through their presence on the proteoglycans, decorin and biglycan, help control collagen fibrillogenesis and organization. CS also acts as a regulatory ligand for a spectrum of signaling molecules, including morphogens, cytokines, chemokines, and enzymes during corneal growth and development. There is a growing body of evidence that precise expression of CS or CS/DS with specific sulfation motifs helps define the local extracellular compartment that contributes to maintenance of the stem cell phenotype. Indeed, recent evidence shows that CS sulfation motifs recognized by antibodies 4C3, 7D4, and 3B3 identify stem cell populations and their niches, along with activated progenitor cells and transitional areas of tissue development in the fetal human elbow. Various sulfation motifs identified by some CS antibodies are also specifically located in the limbal region at the edge of the mature cornea, which is widely accepted to represent the corneal epithelial stem cell niche. Emerging data also implicate developmental changes in the distribution of CS during corneal morphogenesis. This article will reflect upon the potential roles of CS and CS/DS in maintenance of the stem cell niche in cornea, and will contemplate the possible involvement of CS in the generation of eye-like tissues from human iPS (induced pluripotent stem) cells.
Autophagy and Exosomes Relationship in Cancer: Friends or Foes?
Authors: Colletti Marta , Ceglie Donatella , Di Giannatale Angela , Nazio Francesca
Published: January 2021

Autophagy is an intracellular degradation process involved in the removal of proteins and damaged organelles by the formation of a double-membrane vesicle named autophagosome and degraded through fusion with lysosomes. An intricate relationship between autophagy and the endosomal and exosomal pathways can occur at different stages with important implications for normal physiology and human diseases. Recent researches have revealed that extracellular vesicles (EVs), such as exosomes, could have a cytoprotective role by inducing intracellular autophagy; on the other hand, autophagy plays a crucial role in the biogenesis and degradation of exosomes. Although the importance of these processes in cancer is well established, their interplay in tumor is only beginning to be documented. In some tumor contexts (1) autophagy and exosome-mediated release are coordinately activated, sharing the molecular machinery and regulatory mechanisms; (2) cancer cell-released exosomes impact on autophagy in recipient cells through mechanisms yet to be determined; (3) exosome-autophagy relationship could affect drug resistance and tumor microenvironment (TME). In this review, we survey emerging discoveries relevant to the exosomes and autophagy crosstalk in the context of cancer initiation, progression and recurrence. Consequently, we discuss clinical implications by targeting autophagy-exosomal pathway interaction and how this could lay a basis for the purpose of novel cancer therapeutics.
C-Terminal Peptide Modifications Reveal Direct and Indirect Roles of Hedgehog Morphogen Cholesteroylation
Authors: Manikowski Dominique , Kastl Philipp , Schürmann Sabine , Ehring Kristina , Steffes Georg , Jakobs Petra , Grobe Kay
Published: January 2021

Hedgehog (Hh) morphogens are involved in embryonic development and stem cell biology and, if misregulated, can contribute to cancer. One important post-translational modification with profound impact on Hh biofunction is its C-terminal cholesteroylation during biosynthesis. The current hypothesis is that the cholesterol moiety is a decisive factor in Hh association with the outer plasma membrane leaflet of producing cells, cell-surface Hh multimerization, and its transport and signaling. Yet, it is not decided whether the cholesterol moiety is directly involved in all of these processes, because their functional interdependency raises the alternative possibility that the cholesterol initiates early processes directly and that these processes can then steer later stages of Hh signaling independent of the lipid. We generated variants of the C-terminal Hh peptide and observed that these cholesteroylated peptides variably impaired several post-translational processes in producing cells and Hh biofunction inDrosophila melanogastereye and wing development. We also found that substantial Hh amounts separated from cholesteroylated peptide tagsin vitroandin vivoand that tagged and untagged Hh variants lacking their C-cholesterol moieties remained bioactive. Our approach thus confirms that Hh cholesteroylation is essential during the early steps of Hh production and maturation but also suggests that it is dispensable for Hh signal reception at receiving cells.
What Will B Will B: Identifying Molecular Determinants of Diverse B-Cell Fate Decisions Through Systems Biology
Authors: Mitchell Simon
Published: January 2021

B-cells are the poster child for cellular diversity and heterogeneity. The diverse repertoire of B lymphocytes, each expressing unique antigen receptors, provides broad protection against pathogens. However, B-cell diversity goes beyond unique antigen receptors. Side-stepping B-cell receptor (BCR) diversity through BCR-independent stimuli or engineered organisms with monoclonal BCRs still results in seemingly identical B-cells reaching a wide variety of fates in response to the same challenge. Identifying to what extent the molecular state of a B-cell determines its fate is key to gaining a predictive understanding of B-cells and consequently the ability to control them with targeted therapies. Signals received by B-cells through transmembrane receptors converge on intracellular molecular signaling networks, which control whether each B-cell divides, dies, or differentiates into a number of antibody-secreting distinct B-cell subtypes. The signaling networks that interpret these signals are well known to be susceptible to molecular variability and noise, providing a potential source of diversity in cell fate decisions. Iterative mathematical modeling and experimental studies have provided quantitative insight into how B-cells achieve distinct fates in response to pathogenic stimuli. Here, we review how systems biology modeling of B-cells, and the molecular signaling networks controlling their fates, is revealing the key determinants of cell-to-cell variability in B-cell destiny.
MicroRNA-155 Controls iNKT Cell Development and Lineage Differentiation by Coordinating Multiple Regulating Pathways
Authors: Wang Jie , Li Kai , Zhang Xilin , Li Guihua , Liu Tingting , Wu Xiaojun , Brown Stephen L. , Zhou Li , Mi Qing-Sheng
Published: January 2021

The development of invariant natural killer T (iNKT) cells requires a well-attuned set of transcription factors, but how these factors are regulated and coordinated remains poorly understood. MicroRNA-155 (miR-155) is a key regulator of numerous cellular processes that affects cell development and homeostasis. Here, we found that miR-155 was highly expressed in early iNKT cells upon thymic selection, and then its expression is gradually downregulated during iNKT cell development. However, the mice with miR-155 germline deletion had normal iNKT cell development. To address if downregulated miR-155 is required for iNKT cell development, we made a CD4Cre.miR-155 knock-in (KI) mouse model with miR-155 conditional overexpression in the T cell lineage. Upregulated miR-155 led to interruption of iNKT cell development, diminished iNKT17 and iNKT1 cells, augmented iNKT2 cells, and these defects were cell intrinsic. Furthermore, defective iNKT cells in miR-155KI mice resulted in the secondary innate-like CD8 T cell development. Mechanistically, miR-155 modulated multiple targets and signaling pathways to fine tune iNKT cell development. MiR-155 modulated Jarid2, a critical component of a histone modification complex, and Tab2, the upstream activation kinase complex component of NF-κB, which function additively in iNKT development and in promoting balanced iNKT1/iNKT2 differentiation. In addition, miR-155 also targeted Rictor, a signature component of mTORC2 that controls iNKT17 differentiation. Taken together, our results indicate that miR-155 serves as a key epigenetic regulator, coordinating multiple signaling pathways and transcriptional programs to precisely regulate iNKT cell development and functional lineage, as well as secondary innate CD8 T cell development.
Epigenetic Regulation of Adipogenesis in Development of Metabolic Syndrome
Authors: Pant Richa , Firmal Priyanka , Shah Vibhuti Kumar , Alam Aftab , Chattopadhyay Samit
Published: January 2021

Obesity is one of the biggest public health concerns identified by an increase in adipose tissue mass as a result of adipocyte hypertrophy and hyperplasia. Pertaining to the importance of adipose tissue in various biological processes, any alteration in its function results in impaired metabolic health. In this review, we discuss how adipose tissue maintains the metabolic health through secretion of various adipokines and inflammatory mediators and how its dysfunction leads to the development of severe metabolic disorders and influences cancer progression. Impairment in the adipocyte function occurs due to individuals’ genetics and/or environmental factor(s) that largely affect the epigenetic profile leading to altered gene expression and onset of obesity in adults. Moreover, several crucial aspects of adipose biology, including the regulation of different transcription factors, are controlled by epigenetic events. Therefore, understanding the intricacies of adipogenesis is crucial for recognizing its relevance in underlying disease conditions and identifying the therapeutic interventions for obesity and metabolic syndrome.
Mitochondrial Function and Dysfunction in Dilated Cardiomyopathy
Authors: Ramaccini Daniela , Montoya-Uribe Vanessa , Aan Femke J. , Modesti Lorenzo , Potes Yaiza , Wieckowski Mariusz R. , Krga Irena , Glibetić Marija , Pinton Paolo , Giorgi Carlotta , Matter Michelle L.
Published: January 2021

Cardiac tissue requires a persistent production of energy in order to exert its pumping function. Therefore, the maintenance of this function relies on mitochondria that represent the “powerhouse” of all cardiac activities. Mitochondria being one of the key players for the proper functioning of the mammalian heart suggests continual regulation and organization. Mitochondria adapt to cellular energy demands via fusion-fission events and, as a proof-reading ability, undergo mitophagy in cases of abnormalities. Ca2+ fluxes play a pivotal role in regulating all mitochondrial functions, including ATP production, metabolism, oxidative stress balance and apoptosis. Communication between mitochondria and others organelles, especially the sarcoplasmic reticulum is required for optimal function. Consequently, abnormal mitochondrial activity results in decreased energy production leading to pathological conditions. In this review, we will describe how mitochondrial function or dysfunction impacts cardiac activities and the development of dilated cardiomyopathy.
Permafrost Hydrology of the Qinghai-Tibet Plateau: A Review of Processes and Modeling
Authors: Gao Hongkai , Wang Jingjing , Yang Yuzhong , Pan Xicai , Ding Yongjian , Duan Zheng
Published: January 2021

Permafrost extends 40% of the Qinghai-Tibet Plateau (QTP), a region which contains the headwaters of numerous major rivers in Asia. As an aquiclude, permafrost substantially controls surface runoff and its hydraulic connection with groundwater. The freeze–thaw cycle in the active layer significantly impacts soil water movement direction, velocity, storage capacity, and hydraulic conductivity. Under the accelerating warming on the QTP, permafrost degradation is drastically altering regional and even continental hydrological regimes, attracting the attention of hydrologists, climatologists, ecologists, engineers, and decision-makers. A systematic review of permafrost hydrological processes and modeling on the QTP is still lacking, however, leaving a number of knowledge gaps. In this review, we summarize the current understanding of permafrost hydrological processes and applications of some permafrost hydrological models of varying complexity at different scales on the QTP. We then discuss the current challenges and future opportunities, including observations and data, the understanding of processes, and model realism. The goal of this review is to provide a clear picture of where we are now and to describe future challenges and opportunities. We concluded that more efforts are needed to conduct long-term field measurements, employ more advanced observation technologies, and develop flexible and modular models to deepen our understanding of permafrost hydrological processes and to improve our ability to predict the future responses of permafrost hydrology to climate changes.
Increased Expression of TICRR Predicts Poor Clinical Outcomes: A Potential Therapeutic Target for Papillary Renal Cell Carcinoma
Authors: Xia Shuang , Lin Yan , Lin Jiaqiong , Li Xiaoyong , Tan Xuexian , Huang Zena
Published: January 2021

Background: Papillary renal cell carcinoma (PRCC), although the second-most common type of renal cell carcinoma, still lacks specific biomarkers for diagnosis, treatment, and prognosis. TopBP1-interacting checkpoint and replication regulator (TICRR) is a DNA replication initiation regulator upregulated in various cancers. We aimed to evaluate the role of TICRR in PRCC tumorigenesis and prognosis.

Methods: Based on the Kidney Renal Papillary cell carcinoma Project (KIRP) on The Cancer Genome Atlas (TCGA) database, we determined the expression of TICRR using the Wilcoxon rank sum test. The biological functions of TICRR were evaluated using the Metascape database and Gene Set Enrichment Analysis (GSEA). The association between TICRR and immune cell infiltration was investigated by single sample GSEA. Logistic analysis was applied to study the correlation between TICRR expression and clinicopathological characteristics. Finally, Cox regression analysis, Kaplan–Meier analysis, and nomograms were used to determine the predictive value of TICRR on clinical outcomes in PRCC patients.

Results:TICRR expression was significantly elevated in PRCC tumors (P < 0.001). Functional annotation indicated enrichment with negative regulation of cell division, cell cycle, and corresponding pathways in the high TICRR expression phenotype. High TICRR expression in PRCC was associated with female sex, younger age, and worse clinical stages. Cox regression analysis revealed that TICRR was a risk factor for overall survival [hazard ratio (HR): 2.80, P = 0.002], progression-free interval (HR: 2.86, P < 0.001), and disease-specific survival (HR: 7.03, P < 0.001), especially in patients with male sex, age below 60 years, clinical stages II–IV and clinical T stage T1–T2.

Conclusion: Increased TICRR expression in PRCC might play a role in tumorigenesis by regulating the cell cycle and has prognostic value for clinical outcomes.
Epigenetic Alteration Shaped by the Environmental Chemical Bisphenol A
Authors: Qin Tengfei , Zhang Xiaoping , Guo Ting , Yang Ting , Gao Yahui , Hao Wei , Xiao XiangFen
Published: January 2021

Bisphenol A (BPA) is extensively used in plastic products and epoxy resins. The epigenetic response to the environmental chemical BPA was involved in multiple dysfunctional categories, such as cancer, the reproductive system, metabolism, pubertal development, peripheral arterial disease, infant and childhood growth, and neurodevelopment outcomes. In this mini-review, we described the recent progress of the epigenetic effects of the environmental chemical BPA, including DNA methylation, histone methylation, and toxic epigenomics. Notably, the histone modification changes under BPA exposure are summarized in this review. DNA methylation accompanied by transcriptional changes in key genes affected by BPA exposure is related to various processes, including neural development, cancer pathways, and generational transmission. In addition, BPA could also affect histone modifications in many species, such as humans, rats, and zebrafish. Finally, we reviewed recent studies of the toxico-epigenomics approach to reveal the epigenetic effect of BPA exposure genome-wide.
Historical Trends of Sperm Whale (Physeter macrocephalus) Distribution in the Phoenix Archipelago
Authors: Kennedy Brian R. C. , Hakam Lara , Witting Jan , Milani Regen , Taei Sue , Smith Tim , Taylor Erin , Teemari Tooreka , Rotjan Randi D.
Published: January 2021

The Phoenix Archipelago in the Central Pacific is situated in what was once one of the most productive areas for capturing sperm whales (Physeter macrocephalus). These whales were the focal targets of American offshore whalers in the mid-19th century along the equator, an area known as the “on-the-line” whaling grounds. Now, as large-scale Marine Protected Areas (MPAs) have provided protection for marine mammals and their food sources, it is important to have a solid understanding of historical baselines so recovery distributions can be compared with pre-whaling distributions. The Phoenix Islands archipelago contains two large MPAs: the Phoenix Islands Protected Area (PIPA), established by Kiribati in 2008, and the Howland/Baker unit of the Pacific Remote Islands Marine National Monument (PRIMNM), established by the United States in 2009. Using historic whaling records from American whaling vessels operated through the wider Phoenix Archipelago region, we reconstructed information about the presence and distribution of P. microcephalus throughout the 1800s within and around PIPA and the Howland/Baker units of the PRIMNM. Historical data analyzed using ArcGIS showed that sperm whales were present year-round within the study area, which is consistent with 20th century records from the Ocean Biogeographic Information System (OBIS). A Getis Ord Gi∗ hotspot analysis also revealed sighting hotspots within PIPA and near Howland and Baker, suggesting that these two areas may be of long-term ecological importance to sperm whales in the central Pacific. The New England whaling fleet ceased whaling effort in the central Pacific in the late 1800s, and publicly available records since that time are scarce. There has been no modern systematic whale survey ever conducted within the Phoenix Archipelago, though anecdotal accounts and sightings have been compiled over the years. These intermittent accounts suggest that though whale populations have not recovered to pre-whaling baselines, large-scale MPAs may play a role in helping to foster a resurgence of marine mammal populations. As the network of large-scale MPAs continue to grow as part of the commitment to ocean conservation set forth by UNESCO, IUCN, and the UN Decade for Ocean Science, historical baselines will be critical as a “yardstick” to measure population resurgence success for each MPA, and for populations overall.
Dynamics and Viability of a Small, Estuarine-Resident Population of Lahille’s Bottlenose Dolphins From Southern Brazil
Authors: Fruet Pedro F. , Möller Luciana M. , Secchi Eduardo R.
Published: January 2021

Identifying threatened populations and quantifying their vulnerability is crucial for establishing priorities for conservation and providing robust information for decision-making. Lahille’s bottlenose dolphins have been long subjected to by-catch mortality in gillnet fisheries in coastal waters of southern Brazil, particularly in the Patos Lagoon estuary (PLE) and adjacent coastal waters, where dolphins from three populations (or Management Units) show overlapping home ranges. In this study we used a stage-classified matrix population model to conduct a demographic analysis of the PLE’s population with life-history data estimated through an 8 years mark-recapture study. A population viability analysis (PVA) was used to run a series of simulations where the risk was assessed under different by-catch scenarios, taking into account the effects of parameter uncertainty and stochasticity in the projections. In the absence of by-catch, we estimated that this dolphin population would growth at a rate of about 3% annually (95% CI: 1.2–5.8%). Under current by-catch rates, prognoses indicated high probabilities of viability over the next 60 years. These optimistic prognoses appear to be associated with the high survival of adult females. However, the eventual removal of very few mature females (one every year or two) would result in a prominent likelihood of decline from its current abundance at all pre-specified levels. The viability of the population would be substantially improved if the survival of juveniles/sub-adults could be increased. This may be achieved through the recently implemented dolphin protection area, which prohibits gillnet fisheries in the core area of this population. If the protection area reduces the entanglement rates of the most impacted life-stages (i.e., juvenile/sub-adult dolphins), there would be a substantial chance of the PLE’s dolphin population increasing above 20% of its current size, which is here proposed as conservation goal. If met, this goal has the potential to promote habitat quality, increase genetic diversity and connectivity with adjacent populations, enhancing the ability of bottlenose dolphins in southern Brazil to cope with environmental change and potential disease outbreaks.
The Association Between Handgrip Strength and Predialysis Serum Sodium Level in Patients With Chronic Kidney Disease Stage 5D
Authors: Markaki Anastasia , Kyriazis Periklis , Dermitzaki Eleftheria-Kleio , Maragou Sevasti , Psylinakis Emmanuel , Spyridaki Aspasia , Drosataki Helen , Lygerou Dimitra , Grammatikopoulou Maria G. , Petrakis Ioannis , Stylianou Kostas
Published: January 2021

Purpose: Handgrip strength (HGS) is a useful tool for the systematic assessment of muscle function related to nutritional status. Reduced HGS has been associated with adverse clinical outcomes in chronic kidney disease (CKD) stage 5D patients. In the same patients, predialysis low serum sodium (sNa) has been associated with malnutrition and mortality. Here, we investigated the role of predialysis sNa on muscle function in CKD-5D patients.

Methods: We evaluated 45 patients on hemodialysis (HD) and 28 patients on peritoneal dialysis (PD) with HGS measurement, bioimpedance analysis, anthropometric measures, and malnutrition inflammation score (MIS). According to established diagnostic criteria, reduced HGS was defined as strength below 30 and 20 Kg in men and women, respectively. Predialysis sNa values were defined as the mean of all predialysis measurements during the preceding 6 months. Data analysis was performed separately for each of the HD and PD groups.

Results: The proportions of reduced HGS did not differ between the HD (66%) and PD (54%) groups, respectively. Patients in the HD group as compared to those in the PD group had higher serum albumin and potassium and mid-arm muscle circumference and lower residual renal function (RRF) and residual urine volume. Multivariate logistic analysis, after controlling for muscle mass, nutritional biomarkers, MIS, fluid overload and RRF, showed that for every 1 mmol/l increase of sNa the odds of reduced HGS was decreased by 60% (OR = 0.40, 95% CI: 0.16–0.99) and 42% (OR = 0.58, 95% CI: 0.36–0.93) in HD and PD patients, respectively. However, stratified analysis indicated that lower sNa levels predicted reduced HGS in individuals with a background of malnutrition, inflammation, overhydration and less preserved RRF, representing unfavorable conditions strongly related to muscle wasting in the dialysis setting.

Conclusions: Predialysis sNa is a strong and independent determinant of HGS, a reliable nutritional marker in CKD-5D stage patients. However, according to our findings, lower sNa levels appear to be a marker of underlying unfavorable conditions that are heavily associated with reduced HGS, rather than a causal determinant of reduced HGS. Whether optimizing sNa levels improves patient muscle performance requires further investigations.
Extracorporeal Membrane Oxygenation for SARS-CoV-2 Acute Respiratory Distress Syndrome: A Retrospective Study From Hubei, China
Authors: Yang Xiaobo , Hu Ming , Yu Yuan , Zhang Xijing , Fang Minghao , Lian Yingtao , Peng Yong , Wu Lingling , Wu Yongran , Yi Jun , Zhang Lu , Wang Bing , Xu Zhengqin , Liu Boyi , Yang Yadong , Xiang Xiaowei , Qu Xingguang , Xu Wenhao , Li Hunian , Shen Zubo , Yang Changming , Cao Fengsheng , Liu Jie , Zhang Zhaohui , Li Lianghai , Liu Xiaoyun , Li Ruiting , Zou Xiaojing , Shu Huaqing , Ouyang Yaqi , Xu Dan , Xu Jiqian , Zhang Jiancheng , Liu Hong , Qi Hong , Fan Xuepeng , Huang Chaolin , Yu Zhui , Yuan Shiying , Zhang Dingyu , Shang You
Published: January 2021

Background: The data on long-term outcomes of patients infected by SARS-CoV-2 and treated with extracorporeal membrane oxygenation (ECMO) in China are merely available.

Methods: A retrospective study included 73 patients infected by SARS-CoV-2 and treated with ECMO in 21 intensive care units in Hubei, China. Data on demographic information, clinical features, laboratory tests, ECMO durations, complications, and living status were collected.

Results: The 73 ECMO-treated patients had a median age of 62 (range 33–78) years and 42 (63.6%) were males. Before ECMO initiation, patients had severe respiratory failure on mechanical ventilation with a median PO2/FiO2 of 71.9 [interquartile range (IQR), 58.6–87.0] mmHg and a median PCO2 of 62 [IQR, 43–84] mmHg on arterial blood analyses. The median duration from symptom onset to invasive mechanical ventilation, and to ECMO initiation was19 [IQR, 15–25] days, and 23 [IQR, 19–31] days. Before and after ECMO initiation, the proportions of patients receiving prone position ventilation were 58.9 and 69.9%, respectively. The median duration of ECMO support was 18.5 [IQR 12–30] days. During the treatments with ECMO, major hemorrhages occurred in 31 (42.5%) patients, and oxygenators were replaced in 21 (28.8%) patients. Since ECMO initiation, the 30-day mortality and 60-day mortality were 63.0 and 80.8%, respectively.

Conclusions: In Hubei, China, the ECMO-treated patients infected by SARS-CoV-2 were of a broad age range and with severe hypoxemia. The durations of ECMO support, accompanied with increased complications, were relatively long. The long-term mortality in these patients was considerably high.
Immunomodulation of J774A.1 Murine Macrophages by Lactiplantibacillus plantarum Strains Isolated From the Human Gastrointestinal Tract and Fermented Foods
Authors: Garcia-Gonzalez Natalia , Nuñez-Sanchez María A. , Villoria Recio Miguel , Battista Natalia , Gahan Cormac G. M. , Corsetti Aldo
Published: January 2021

Lactobacillus plantarum species (recently re-named Lactiplantibacillus (Lpb.) plantarum subsp. plantarum) can be isolated from both either the mammalian gut or specific fermented foods where they may be present at high concentrations. Whilst Lpb. plantarum strains have been proposed as potential probiotic candidates, the ability of resident strains consumed in fermented foods to interact with the host is unclear. The main objective of this study was to investigate the cellular location and ability of three different food-borne Lpb. plantarum strains isolated from different sources (table olives and cheese) to modulate the immune response of a murine macrophage-like cell line (J774A.1). For that purpose, macrophages were exposed to the three different Lpb. plantarum strains for 24 h and the expression of a panel of genes involved in the immune response, including genes encoding pattern-recognition receptors (TLRs and NLRs) and cytokines was evaluated by qRT-PCR. We also utilized chemical inhibitors of intracellular pathways to gain some insight into potential signaling mechanisms. Results showed that the native food strains of Lpb. plantarum were able to modulate the response of J774A.1 murine macrophages through a predominately NOD signaling pathway that reflects the transient intracellular location of these strains within the macrophage. The data indicate the capacity of food-dwelling Lpb. plantarum strains to influence macrophage-mediated host responses if consumed in sufficient quantities.
Extracting the GEMs: Genotype, Environment, and Microbiome Interactions Shaping Host Phenotypes
Authors: Oyserman Ben O. , Cordovez Viviane , Flores Stalin Sarango , Leite Marcio F. A. , Nijveen Harm , Medema Marnix H. , Raaijmakers Jos M.
Published: January 2021

One of the fundamental tenets of biology is that the phenotype of an organism (Y) is determined by its genotype (G), the environment (E), and their interaction (GE). Quantitative phenotypes can then be modeled as Y = G + E + GE + e, where e is the biological variance. This simple and tractable model has long served as the basis for studies investigating the heritability of traits and decomposing the variability in fitness. The importance and contribution of microbe interactions to a given host phenotype is largely unclear, nor how this relates to the traditional GE model. Here we address this fundamental question and propose an expansion of the original model, referred to as GEM, which explicitly incorporates the contribution of the microbiome (M) to the host phenotype, while maintaining the simplicity and tractability of the original GE model. We show that by keeping host, environment, and microbiome as separate but interacting variables, the GEM model can capture the nuanced ecological interactions between these variables. Finally, we demonstrate with an in vitro experiment how the GEM model can be used to statistically disentangle the relative contributions of each component on specific host phenotypes.
How Copepods Can Eat Toxins Without Getting Sick: Gut Bacteria Help Zooplankton to Feed in Cyanobacteria Blooms
Authors: Gorokhova Elena , El-Shehawy Rehab , Lehtiniemi Maiju , Garbaras Andrius
Published: January 2021

Toxin-producing cyanobacteria can be harmful to aquatic biota, although some grazers utilize them with often beneficial effects on their growth and reproduction. It is commonly assumed that gut microbiota facilitates host adaptation to the diet; however, the evidence for adaptation mechanisms is scarce. Here, we investigated the abundance of mlrA genes in the gut of the Baltic copepods Acartia bifilosa and Eurytemora affinis during cyanobacteria bloom season (August) and outside it (February). The mlrA genes are unique to microcystin and nodularin degraders, thus indicating the capacity to break down these toxins by the microbiota. The mlrA genes were expressed in the copepod gut year-round, being >10-fold higher in the summer than in the winter populations. Moreover, they were significantly more abundant in Eurytemora than Acartia. To understand the ecological implications of this variability, we conducted feeding experiments using summer- and winter-collected copepods to examine if/how the mlrA abundance in the microbiota affect: (1) uptake of toxic Nodularia spumigena, (2) uptake of a non-toxic algal food offered in mixtures with N. spumigena, and (3) concomitant growth potential in the copepods. The findings provide empirical evidence that the occurrence of mlrA genes in the copepod microbiome facilitates nutrient uptake and growth when feeding on phytoplankton mixtures containing nodularin-producing cyanobacteria; thus, providing an adaptation mechanism to the cyanobacteria blooms.
Whole Genome Analysis of African G12P[6] and G12P[8] Rotaviruses Provides Evidence of Porcine-Human Reassortment at NSP2, NSP3, and NSP4
Authors: Mokoena Fortunate , Esona Mathew Dioh , Seheri Luyanda Mapaseka , Nyaga Martin Munene , Magagula Nonkululelo Bonakele , Mukaratirwa Arnold , Mulindwa Augustine , Abebe Almaz , Boula Angeline , Tsolenyanu Enyonam , Simwaka Julia , Rakau Kebareng Giliking , Peenze Ina , Mwenda Jason Mathiu , Mphahlele Maphahlaganye Jeffrey , Steele Andrew Duncan ,   African Rotavirus Surveillance Network
Published: January 2021

Group A rotaviruses (RVA) represent the most common cause of pediatric gastroenteritis in children <5 years, worldwide. There has been an increase in global detection and reported cases of acute gastroenteritis caused by RVA genotype G12 strains, particularly in Africa. This study sought to characterize the genomic relationship between African G12 strains and determine the possible origin of these strains. Whole genome sequencing of 34 RVA G12P[6] and G12P[8] strains detected from the continent including southern (South Africa, Zambia, Zimbabwe), eastern (Ethiopia, Uganda), central (Cameroon), and western (Togo) African regions, were sequenced using the Ion Torrent PGM method. The majority of the strains possessed a Wa-like backbone with consensus genotype constellation of G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, while a single strain from Ethiopia displayed a DS-1-like genetic constellation of G12-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. In addition, three Ethiopian and one South African strains exhibited a genotype 2 reassortment of the NSP3 gene, with genetic constellation of G12-P[8]-I1-R1-C1-M1-A1-N1-T2-E1-H1. Overall, 10 gene segments (VP1–VP4, VP6, and NSP1–NSP5) of African G12 strains were determined to be genetically related to cognate gene sequences from globally circulating human Wa-like G12, G9, and G1 strains with nucleotide (amino acid) identities in the range of 94.1–99.9% (96.5–100%), 88.5–98.5% (93–99.1%), and 89.8–99.0% (88.7–100%), respectively. Phylogenetic analysis showed that the Ethiopian G12P[6] possessing a DS-1-like backbone consistently clustered with G2P[4] strains from Senegal and G3P[6] from Ethiopia with the VP1, VP2, VP6, and NSP1–NSP4 genes. Notably, the NSP2, NSP3, and NSP4 of most of the study strains exhibited the closest relationship with porcine strains suggesting the occurrence of reassortment between human and porcine strains. Our results add to the understanding of potential roles that interspecies transmission play in generating human rotavirus diversity through reassortment events and provide insights into the evolutionary dynamics of G12 strains spreading across selected sub-Saharan Africa regions.
Effects of Rare Microbiome Taxa Filtering on Statistical Analysis
Authors: Cao Quy , Sun Xinxin , Rajesh Karun , Chalasani Naga , Gelow Kayla , Katz Barry , Shah Vijay H. , Sanyal Arun J. , Smirnova Ekaterina
Published: January 2021

Background: The accuracy of microbial community detection in 16S rRNA marker-gene and metagenomic studies suffers from contamination and sequencing errors that lead to either falsely identifying microbial taxa that were not in the sample or misclassifying the taxa of DNA fragment reads. Removing contaminants and filtering rare features are two common approaches to deal with this problem. While contaminant detection methods use auxiliary sequencing process information to identify known contaminants, filtering methods remove taxa that are present in a small number of samples and have small counts in the samples where they are observed. The latter approach reduces the extreme sparsity of microbiome data and has been shown to correctly remove contaminant taxa in cultured “mock” datasets, where the true taxa compositions are known. Although filtering is frequently used, careful evaluation of its effect on the data analysis and scientific conclusions remains unreported. Here, we assess the effect of filtering on the alpha and beta diversity estimation as well as its impact on identifying taxa that discriminate between disease states.

Results: The effect of filtering on microbiome data analysis is illustrated on four datasets: two mock quality control datasets where the same cultured samples with known microbial composition are processed at different labs and two disease study datasets. Results show that in microbiome quality control datasets, filtering reduces the magnitude of differences in alpha diversity and alleviates technical variability between labs while preserving the between samples similarity (beta diversity). In the disease study datasets, DESeq2 and linear discriminant analysis Effect Size (LEfSe) methods were used to identify taxa that are differentially abundant across groups of samples, and random forest models were used to rank features with the largest contribution toward disease classification. Results reveal that filtering retains significant taxa and preserves the model classification ability measured by the area under the receiver operating characteristic curve (AUC). The comparison between the filtering and the contaminant removal method shows that they have complementary effects and are advised to be used in conjunction.

Conclusions: Filtering reduces the complexity of microbiome data while preserving their integrity in downstream analysis. This leads to mitigation of the classification methods' sensitivity and reduction of technical variability, allowing researchers to generate more reproducible and comparable results in microbiome data analysis.