bluuebunny/crossref_metadata_2025_split huggingface dataset:
‘Barcode fishing’ for archival DNA from historical type material overcomes taxonomic hurdles, enabling the description of a new frog species
Authors: Scherz Mark D. , Rasolonjatovo Safidy M. , Köhler Jörn , Rancilhac Loïs , Rakotoarison Andolalao , Raselimanana Achille P. , Ohler Annemarie , Preick Michaela , Hofreiter Michael , Glaw Frank , Vences Miguel 
Published: November 2020

AbstractTaxonomic progress is often hindered by intrinsic factors, such as morphologically cryptic species that require a broad suite of methods to distinguish, and extrinsic factors, such as uncertainties in the allocation of scientific names to species. These uncertainties can be due to a wide variety of factors, including old and poorly preserved type specimens (which contain only heavily degraded DNA or have lost important diagnostic characters), inappropriately chosen type specimens (e.g. juveniles without diagnostic characters) or poorly documented type specimens (with unprecise, incorrect, or missing locality data). Thanks to modern sequencing technologies it is now possible to overcome many such extrinsic factors by sequencing DNA from name-bearing type specimens of uncertain assignment and assigning these to known genetic lineages. Here, we apply this approach to frogs of theMantidactylus ambreensiscomplex, which was recently shown to consist of two genetic lineages supported by concordant differentiation in mitochondrial and nuclear genes. These lineages co-occur on the Montagne dʼAmbre Massif in northern Madagascar but appear to have diverged in allopatry. We use a recently published bait set based on three mitochondrial markers from all known Malagasy frog lineages to capture DNA sequences from the 127-year-old holotype ofMantidactylus ambreensisMocquard, 1895. With the obtained sequences we are able to assign the nameM. ambreensisto the lowland lineage, which is rather widespread in the rainforests of northern Madagascar, leaving the microendemic high-elevation lineage on Montagne d’Ambre in north Madagascar in need of description. We describe this species asMantidactylus ambonysp. nov., differing fromM. ambreensisin call parameters and a smaller body size. Thus, using target enrichment to obtain DNA sequence data from this old specimen, we were able to resolve the extrinsic (nomenclatural) hindrances to taxonomic resolution of this complex. We discuss the broad-scale versatility of this ‘barcode fishing’ approach, which can draw on the enormous success of global DNA barcoding initiatives to quickly and efficiently assign type specimens to lineages.
Gene expression of the heat stress response in bovine peripheral white blood cells and milk somatic cells in vivo
Authors: Garner J. B. , Chamberlain A. J. , Vander Jagt C. , Nguyen T. T. T. , Mason B. A. , Marett L. C. , Leury B. J. , Wales W. J. , Hayes B. J. 
Published: November 2020

AbstractHeat stress in dairy cattle leads to reduction in feed intake and milk production as well as the induction of many physiological stress responses. The genes implicated in the response to heat stress in vivo are not well characterised. With the aim of identifying such genes, an experiment was conducted to perform differential gene expression in peripheral white blood cells and milk somatic cells in vivo in 6 Holstein Friesian cows in thermoneutral conditions and in 6 Holstein Friesian cows exposed to a short-term moderate heat challenge. RNA sequences from peripheral white blood cells and milk somatic cells were used to quantify full transcriptome gene expression. Genes commonly differentially expressed (DE) in both the peripheral white blood cells and in milk somatic cells were associated with the cellular stress response, apoptosis, oxidative stress and glucose metabolism. Genes DE in peripheral white blood cells of cows exposed to the heat challenge compared to the thermoneutral control were related to inflammation, lipid metabolism, carbohydrate metabolism and the cardiovascular system. Genes DE in milk somatic cells compared to the thermoneutral control were involved in the response to stress, thermoregulation and vasodilation. These findings provide new insights into the cellular adaptations induced during the response to short term moderate heat stress in dairy cattle and identify potential candidate genes (BDKRB1andSNORA19) for future research.
Genetic and non-genetic factors associated with the phenotype of exceptional longevity & normal cognition
Authors: Han Bin , Chen Huashuai , Yao Yao , Liu Xiaomin , Nie Chao , Min Junxia , Zeng Yi , Lutz Michael W. 
Published: November 2020

AbstractIn this study, we split 2156 individuals from the Chinese Longitudinal Healthy Longevity Survey (CLHLS) data into two groups, establishing a phenotype of exceptional longevity & normal cognition versus cognitive impairment. We conducted a genome-wide association study (GWAS) to identify significant genetic variants and biological pathways that are associated with cognitive impairment and used these results to construct polygenic risk scores. We elucidated the important and robust factors, both genetic and non-genetic, in predicting the phenotype, using several machine learning models. The GWAS identified 28 significant SNPs at p-value $$< 3 \times 10^{-5}$$

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significance level and we pinpointed four genes, ESR1, PHB, RYR3, GRIK2, that are associated with the phenotype though immunological systems, brain function, metabolic pathways, inflammation and diet in the CLHLS cohort. Using both genetic and non-genetic factors, four machine learning models have close prediction results for the phenotype measured in Area Under the Curve: random forest (0.782), XGBoost (0.781), support vector machine with linear kernel (0.780), and $$\ell _2$$

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penalized logistic regression (0.780). The top four important and congruent features in predicting the phenotype identified by these four models are: polygenic risk score, sex, age, and education.
Soil quality parameters vis-a-vis growth and yield attributes of sugarcane as influenced by integration of microbial consortium with NPK fertilizers
Authors: Shukla S. K. , Sharma Lalan , Jaiswal V. P. , Pathak A. D. , Tiwari Raghvendra , Awasthi S. K. , Gaur Asha 
Published: November 2020

AbstractIntensive agriculture involving high crop intensity, unavailability of organics, and higher use of straight fertilizers causes imbalanced use and deficiencies of several other macro and micronutrients. Nutrients supply through the integration of microbial consortium containing Gluconacetobater diazotrophicus, Trichoderma harzianum, and Pseudomonas fluorescens can reduce the requirements on the one hand and can also increase the response of chemical fertilizers. Thus we had planned the present experiment with the objectives (i) to determine the effect of integrated application of microbial consortium (MC) and NPK fertilizer on soil quality parameters and crop growth and yield attributes and (ii) to assess the effect of integration on agronomic efficiency of N, P and K and find out the possibilities for reduction in applied doses of NPK, if any. Five treatments viz., T1; N0P0K0; T2: N75P13K25; T3: N150P26K50; T4: N75P13K25 + microbial consortium and T5: N150P26K50 + microbial consortium containing new strains of Trichoderma harzianum, Gluconcetobacter diazotrophicus, and Pseudomonas fluorescens (CFU 109–10 per ml liquid culture) were evaluated under four replications in a randomized block design (RBD). Experimental results indicated that integrating microbial consortium and NPK fertilizers' application proved effective in improving soil organic carbon, soil microbial population, microbial biomass carbon, microbial biomass nitrogen, and soil respiration. Integrated use of microbial consortium with NPK also improved the cation exchange capacity of soil and roots. However, the growth and yield attributes, nutrients uptake, sugarcane, and sugar yields also revealed a positive effect of microbial consortium's integrated application with NPK. The integration of MC and NPK also improved the agronomic efficiency of applied nutrients (NPK). Reduction of 50% NPK with these microbial consortia (Trichoderma harzianum, Gluconcetobacter diazotrophicus, and Pseudomonas fluorescens) was found better than the application of full NPK through chemical fertilizers. Thus application of N150P26K50 with microbial consortium can sustain soil fertility besides improving sugarcane and sugar yields in subtropical Indian conditions.
Influenza virus infection augments susceptibility to respiratory Yersinia pestis exposure and impacts the efficacy of antiplague antibiotic treatments
Authors: Vagima Yaron , Gur David , Erez Noam , Achdout Hagit , Aftalion Moshe , Levy Yinon , Zauberman Ayelet , Tidhar Avital , Gutman Hila , Lazar Shlomi , Israely Tomer , Paran Nir , Melamed Sharon , Brosh-Nissimov Tal , Chitlaru Theodor , Sagi Irit , Mamroud Emanuelle 
Published: November 2020

AbstractVarious respiratory viral infections in general and seasonal influenza in particular may increase the susceptibility to bacterial infections. Plague caused by Yersinia pestis endangers large populations during outbreaks or bioterrorism attacks. Recommended antibiotic countermeasures include well-established protocols based on animal studies and corroborated by effective treatment of human cases. Until now, prior exposure to viral respiratory infections was not taken into consideration when selecting the appropriate treatment for plague. Here, we show that as late as 25 days after exposure to influenza virus, convalescent mice still exhibited an increased susceptibility to sublethal doses of Y. pestis, presented with aberrant cytokine expression, and impaired neutrophil infiltration in the lungs. Increased levels of M2 alveolar macrophages and type II epithelial cells, as well as induction in metalloproteases expression and collagen and laminin degradation, suggested that the previous viral infection was under resolution, correlating with enhanced susceptibility to plague. Surprisingly, postexposure prophylaxis treatment with the recommended drugs revealed that ciprofloxacin was superior to doxycycline in mice recovering from influenza infection. These results suggest that after an influenza infection, the consequences, such as impaired immunity and lung tissue remodeling and damage, should be considered when treating subsequent Y. pestis exposure.
A rational experimental approach to identify correctly the working voltage window of aqueous-based supercapacitors
Authors: Nunes Willian G. , Freitas Bruno G. A. , Beraldo Renato M. , Filho Rubens Maciel , Da Silva Leonardo M. , Zanin Hudson 
Published: November 2020

AbstractIt is common to find in the literature different values for the working voltage window (WVW) range for aqueous-based supercapacitors. In many cases, even with the best intentions of the widening the operating voltage window, the measured current using the cyclic voltammetry (CV) technique includes a significant contribution from the irreversible Faradaic reactions involved in the water-splitting process, masked by fast scan rates. Sometimes even using low scan rates is hard to determine precisely the correct WVW of the aqueous-based electrochemical capacitor. In this sense, we discuss here the best practices to determine the WVW for capacitive current in an absence of water splitting using complementary techniques such as CV, chronoamperometry (CA), and the electrochemical impedance spectroscopy (EIS). To accomplish this end, we prepare and present a model system composed of multiwalled carbon nanotubes buckypaper electrodes housed in the symmetric coin cell and soaked with an aqueous-based electrolyte. The system electrochemical characteristics are carefully evaluated during the progressive enlargement of the cell voltage window. The presence of residual Faradaic current is verified in the transients from the CA study, as well as the impedance changes revealed by EIS as a function of the applied voltage, is discussed. We verify that an apparent voltage window of 2.0 V determined using the CV technique is drastically decreased to 1.2 V after a close inspection of the CA findings used to discriminate the presence of a parasitic Faradaic process. Some orientations are presented to instigate the establishment in the literature of some good scientific practices concerned with the reliable characterization of supercapacitors.
Historically unprecedented Northern Gulf of Mexico hurricane activity from 650 to 1250 CE
Authors: Rodysill Jessica R. , Donnelly Jeffrey P. , Sullivan Richard , Lane Philip D. , Toomey Michael , Woodruff Jonathan D. , Hawkes Andrea D. , MacDonald Dana , d’Entremont Nicole , McKeon Kelly , Wallace Elizabeth , van Hengstum Peter J. 
Published: November 2020

AbstractHurricane Michael (2018) was the first Category 5 storm on record to make landfall on the Florida panhandle since at least 1851 CE (Common Era), and it resulted in the loss of 59 lives and $25 billion in damages across the southeastern U.S. This event placed a spotlight on recent intense (exceeding Category 4 or 5 on the Saffir-Simpson Hurricane Wind Scale) hurricane landfalls, prompting questions about the natural range in variability of hurricane activity that the instrumental record is too short to address. Of particular interest is determining whether the frequency of recent intense hurricane landfalls in the northern Gulf of Mexico (GOM) is within or outside the natural range of intense hurricane activity prior to 1851 CE. In this study, we identify intense hurricane landfalls in northwest Florida during the past 2000 years based on coarse anomaly event detection from two coastal lacustrine sediment archives. We identified a historically unprecedented period of heightened storm activity common to four Florida panhandle localities from 650 to 1250 CE and a shift to a relatively quiescent storm climate in the GOM spanning the past six centuries. Our study provides long-term context for events like Hurricane Michael and suggests that the observational period 1851 CE to present may underrepresent the natural range in landfalling hurricane activity.
Omics approaches for conservation biology research on the bivalve Chamelea gallina
Authors: Carducci Federica , Biscotti Maria Assunta , Trucchi Emiliano , Giuliani Maria Elisa , Gorbi Stefania , Coluccelli Alessandro , Barucca Marco , Canapa Adriana 
Published: November 2020

AbstractThe striped venus (Chamelea gallina) is an important economic resource in the Mediterranean Basin; this species has exhibited a strong quantitative decline in the Adriatic Sea. The aim of this work was to provide a comprehensive view of the biological status ofC. gallinato elucidate the bioecological characteristics and genetic diversity of wild populations. To the best of our knowledge, this investigation is the first to perform a multidisciplinary study onC. gallinabased on two omics approaches integrated with histological, ecotoxicological, and chemical analyses and with the assessment of environmental parameters. The results obtained through RNA sequencing indicated that the striped venus has a notable ability to adapt to different environmental conditions. Moreover, the stock reduction exhibited by this species in the last 2 decades seems not to have negatively affected its genetic diversity. Indeed, the high level of genetic diversity that emerged from our ddRAD dataset analyses is ascribable to the high larval dispersal rate, which might have played a “compensatory role” on local fluctuations, conferring to this species a good adaptive potential to face the environmental perturbations. These findings may facilitate the efforts of conservation biologists to adopt ad hoc management plans for this fishery resource.
Tumor cell MT1-MMP is dispensable for osteosarcoma tumor growth, bone degradation and lung metastasis
Authors: Ingvarsen Signe Z. , Gårdsvoll Henrik , van Putten Sander , Nørregaard Kirstine S. , Krigslund Oliver , Meilstrup Josephine A. , Tran Collin , Jürgensen Henrik J. , Melander Maria C. , Nielsen Carsten H. , Kjaer Andreas , Bugge Thomas H. , Engelholm Lars H. , Behrendt Niels 
Published: November 2020

AbstractThe membrane-anchored matrix metalloprotease MT1-MMP is a potent collagenolytic enzyme with a well-established role in extracellular matrix turnover and cellular invasion into collagen-rich tissues. MT1-MMP is highly expressed in various types of cancer and has been demonstrated to be directly involved in several stages of tumor progression, including primary tumor growth, angiogenesis, invasion and metastasis. Osteosarcoma is the most common type of primary bone cancer. This disease is characterized by invasive tumor growth, leading to extensive bone destruction, and metastasis to the lungs. The tumor cells in human osteosarcoma display a strong expression of MT1-MMP, but the role of MT1-MMP in osteosarcoma progression is currently unknown. In this study, we investigated the role of MT1-MMP during various stages of osteosarcoma development. We utilized an optimized orthotopic murine osteosarcoma model and human osteosarcoma cells in which the MT1-MMP gene was knocked out using CRISPR/Cas9. We observed a strong expression of MT1-MMP in wildtype cells of both primary tumors and lung metastases, but, surprisingly, MT1-MMP deficiency did not affect primary tumor growth, bone degradation or the formation and growth of lung metastases. We therefore propose that, unlike findings reported in other cancers, tumor-expressed MT1-MMP is dispensable for all stages of osteosarcoma progression.
Minimum and maximum energy for crystals of magnetic dipoles
Authors: Batle Josep , Ciftja Orion 
Published: November 2020

AbstractProperties of many magnetic materials consisting of dipoles depend crucially on the nature of the dipole–dipole interaction. In the present work, we study systems of magnetic dipoles where the dipoles are arranged on various types of one-dimensional, two-dimensional and three-dimensional lattices. It is assumed that we are in the regime of strong dipole moments where a classical treatment is possible. We combine a new classical numerical approach in conjuncture with an ansatz for an energy decomposition method to study the energy stability of various magnetic configurations at zero temperature for systems of dipoles ranging from small to an infinite number of particles. A careful analysis of the data in the bulk limit allows us to identify very accurate minimum and maximum energy bounds as well as ground state configurations corresponding to various types of lattices. The results suggest stabilization of a particularly interesting ground state configuration consisting of three embedded spirals for the case of a two-dimensional hexagonal lattice.
3-O-sulfated heparan sulfate interactors target synaptic adhesion molecules from neonatal mouse brain and inhibit neural activity and synaptogenesis in vitro
Authors: Maïza Auriane , Sidahmed-Adrar Nazha , Michel Patrick P. , Carpentier Gilles , Habert Damien , Dalle Carine , Redouane Walid , Hamza Magda , van Kuppevelt TH , Ouidja Mohand Ouidir , Courty José , Chantepie Sandrine , Papy-Garcia Dulce , Stettler Olivier 
Published: November 2020

AbstractHeparan sulfate (HS) chains, covalently linked to heparan sulfate proteoglycans (HSPG), promote synaptic development and functions by connecting various synaptic adhesion proteins (AP). HS binding to AP could vary according to modifications of HS chains by different sulfotransferases. 3-O-sulfotransferases (Hs3sts) produce rare 3-O-sulfated HSs (3S-HSs), of poorly known functions in the nervous system. Here, we showed that a peptide known to block herpes simplex virus by interfering with 3S-HSs in vitro and in vivo (i.e. G2 peptide), specifically inhibited neural activity, reduced evoked glutamate release, and impaired synaptic assembly in hippocampal cell cultures. A role for 3S-HSs in promoting synaptic assembly and neural activity is consistent with the synaptic interactome of G2 peptide, and with the detection of Hs3sts and their products in synapses of cultured neurons and in synaptosomes prepared from developing brains. Our study suggests that 3S-HSs acting as receptors for herpesviruses might be important regulators of neuronal and synaptic development in vertebrates.
Organophosphorus diisopropylfluorophosphate (DFP) intoxication in zebrafish larvae causes behavioral defects, neuronal hyperexcitation and neuronal death
Authors: Brenet Alexandre , Somkhit Julie , Hassan-Abdi Rahma , Yanicostas Constantin , Romain Christiane , Bar Olivier , Igert Alexandre , Saurat Dominique , Taudon Nicolas , Dal-Bo Gregory , Nachon Florian , Dupuis Nina , Soussi-Yanicostas Nadia 
Published: November 2020

AbstractWith millions of intoxications each year and over 200,000 deaths, organophosphorus (OP) compounds are an important public health issue worldwide. OP poisoning induces cholinergic syndrome, with respiratory distress, hypertension, and neuron damage that may lead to epileptic seizures and permanent cognitive deficits. Existing countermeasures are lifesaving but do not prevent long-lasting neuronal comorbidities, emphasizing the urgent need for animal models to better understand OP neurotoxicity and identify novel antidotes. Here, using diisopropylfluorophosphate (DFP), a prototypic and moderately toxic OP, combined with zebrafish larvae, we first showed that DFP poisoning caused major acetylcholinesterase inhibition, resulting in paralysis and CNS neuron hyperactivation, as indicated by increased neuronal calcium transients and overexpression of the immediate early genes fosab, junBa, npas4b, and atf3. In addition to these epileptiform seizure-like events, DFP-exposed larvae showed increased neuronal apoptosis, which were both partially alleviated by diazepam treatment, suggesting a causal link between neuronal hyperexcitation and cell death. Last, DFP poisoning induced an altered balance of glutamatergic/GABAergic synaptic activity with increased NR2B-NMDA receptor accumulation combined with decreased GAD65/67 and gephyrin protein accumulation. The zebrafish DFP model presented here thus provides important novel insights into the pathophysiology of OP intoxication, making it a promising model to identify novel antidotes.