bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross-scale neutral ecology and the maintenance of biodiversity
Authors: O’Dwyer James P. , Cornell Stephen J. 
Published: June 2018

AbstractOne of the first successes of neutral ecology was to predict realistically-broad distributions of rare and abundant species. However, it has remained an outstanding theoretical challenge to describe how this distribution of abundances changes with spatial scale, and this gap has hampered attempts to use observed species abundances as a way to quantify what non-neutral processes are needed to fully explain observed patterns. To address this, we introduce a new formulation of spatial neutral biodiversity theory and derive analytical predictions for the way abundance distributions change with scale. For tropical forest data where neutrality has been extensively tested before now, we apply this approach and identify an incompatibility between neutral fits at regional and local scales. We use this approach derive a sharp quantification of what remains to be explained by non-neutral processes at the local scale, setting a quantitative target for more general models for the maintenance of biodiversity.
Biomimetic materials assembled on a photovoltaic cell as a novel biosensing approach to cancer biomarker detection
Authors: Moreira Felismina T. C. , Truta Liliana A. A. N. A. , Sales M. Goreti F. 
Published: June 2018

AbstractThis work describes for the first time the integration of Dye Sensitized Solar Cell (DSSC) technology in biosensors and biomimetic materials, opening doors towards a new dimension of autonomous screening devices that may be used in point-of-care, with zero-power requirements. DSSCs are fabricated with a counter electrode (CE) of polypyrrole (PPy) that was made responsive to a specific protein by biomimetic material (BM) technology. Carcinogenic embryonic antigen (CEA) was selected as target protein. The resulting BM-PPy film acted as biomimetic artificial antibody for CEA. Rebinding of CEA into this film changed its intrinsic electrical properties and the subsequent electrical output of the DSSC using it as CE. The quantity of CEA in solution was deduced by I-V and electrochemical impedance spesctroscopy (EIS). Linear responses to CEA were observed down to 0.25 pg/mL, with 0.13 pg/mL detection limit. Control films of PPy (prepared without CEA in the electropolymerization step) confirmed the ability of the BM material to recognize the target protein. Accurate results were obtained in the analysis of urine samples. Further developments into this ground-breaking self-powered biosensor will display a huge impact in point-to-care medical applications, which may be extended to other fields of knowledge.
Juvenile bovine bone is an appropriate surrogate for normal and reduced density human bone in biomechanical testing: a validation study
Authors: Fletcher J. W. A. , Williams S. , Whitehouse M. R. , Gill H. S. , Preatoni E. 
Published: June 2018

AbstractOrthopaedic research necessitates accurate and reliable models of human bone to enable biomechanical discoveries and translation into clinical scenarios. Juvenile bovine bone is postulated to be a potential model of normal human bone given its dimensions and comparatively reduced ethical restrictions. Demineralisation techniques can reduce bone density and alter bone properties, and methods to model osteoporotic bone using demineralised juvenile bovine bone are investigated. Juvenile bovine long bones were quantitatively CT scanned to assess bone density. Demineralisation using hydrochloric acid (0.6, 1.2 and 2.4 M) was performed to create different bone density models which underwent biomechanical validation for normal and osteoporotic bone models. All long bones were found to have comparable features to normal human bone including bone density (1.96 ± 0.08 gcm−3), screw insertion torque and pullout strength. Demineralisation significantly reduced bone density and pullout strength for all types, with 0.6 M hydrochloric acid creating reductions of 25% and 71% respectively. Juvenile bovine bone is inexpensive, easy to source and not subject to extensive ethical procedures. This study establishes for the first time, the use of its long bones as surrogates for both normal and osteoporotic human specimens and offers preliminary validation for its use in biomechanical testing.
A new approach of gene co-expression network inference reveals significant biological processes involved in porcine muscle development in late gestation
Authors: Marti-Marimon M. , Vialaneix N. , Voillet V. , Yerle-Bouissou M. , Lahbib-Mansais Y. , Liaubet L. 
Published: June 2018

AbstractThe integration of genetic information in the cellular and nuclear environments is crucial for deciphering the way in which the genome functions under different physiological conditions. Experimental techniques of 3D nuclear mapping, a high-flow approach such as transcriptomic data analyses, and statistical methods for the development of co-expressed gene networks, can be combined to develop an integrated approach for depicting the regulation of gene expression. Our work focused more specifically on the mechanisms involved in the transcriptional regulation of genes expressed in muscle during late foetal development in pig. The data generated by a transcriptomic analysis carried out on muscle of foetuses from two extreme genetic lines for birth mortality are used to construct networks of differentially expressed and co-regulated genes. We developed an innovative co-expression networking approach coupling, by means of an iterative process, a new statistical method for graph inference with data of gene spatial co-localization (3D DNA FISH) to construct a robust network grouping co-expressed genes. This enabled us to highlight relevant biological processes related to foetal muscle maturity and to discover unexpected gene associations between IGF2, MYH3 and DLK1/MEG3 in the nuclear space, genes that are up-regulated at this stage of muscle development.
Genome-Wide Determination of Gene Essentiality by Transposon Insertion Sequencing in Yeast Pichia pastoris
Authors: Zhu Jinxiang , Gong Ruiqing , Zhu Qiaoyun , He Qiulin , Xu Ning , Xu Yichun , Cai Menghao , Zhou Xiangshan , Zhang Yuanxing , Zhou Mian 
Published: June 2018

AbstractIn many prokaryotes but limited eukaryotic species, the combination of transposon mutagenesis and high-throughput sequencing has greatly accelerated the identification of essential genes. Here we successfully applied this technique to the methylotrophic yeast Pichia pastoris and classified its conditionally essential/non-essential gene sets. Firstly, we showed that two DNA transposons, TcBuster and Sleeping beauty, had high transposition activities in P. pastoris. By merging their insertion libraries and performing Tn-seq, we identified a total of 202,858 unique insertions under glucose supported growth condition. We then developed a machine learning method to classify the 5,040 annotated genes into putatively essential, putatively non-essential, ambig1 and ambig2 groups, and validated the accuracy of this classification model. Besides, Tn-seq was also performed under methanol supported growth condition and methanol specific essential genes were identified. The comparison of conditionally essential genes between glucose and methanol supported growth conditions helped to reveal potential novel targets involved in methanol metabolism and signaling. Our findings suggest that transposon mutagenesis and Tn-seq could be applied in the methylotrophic yeast Pichia pastoris to classify conditionally essential/non-essential gene sets. Our work also shows that determining gene essentiality under different culture conditions could help to screen for novel functional components specifically involved in methanol metabolism.
Porcine Alveolar Macrophage-like cells are pro-inflammatory Pulmonary Intravascular Macrophages that produce large titers of Porcine Reproductive and Respiratory Syndrome Virus
Authors: Bordet Elise , Maisonnasse Pauline , Renson Patricia , Bouguyon Edwige , Crisci Elisa , Tiret Mathieu , Descamps Delphyne , Bernelin-Cottet Cindy , Urien Céline , Lefèvre François , Jouneau Luc , Bourry Olivier , Leplat Jean-Jacques , Schwartz-Cornil Isabelle , Bertho Nicolas 
Published: June 2018

AbstractLung inflammation is frequently involved in respiratory conditions and it is strongly controlled by mononuclear phagocytes (MNP). We previously studied porcine lung MNP and described a new population of cells presenting all the features of alveolar macrophages (AM) except for their parenchymal location, that we named AM-like cells. Herein we showed that AM-like cells are macrophages phagocytosing blood-borne particles, in agreement with a pulmonary intravascular macrophages (PIM) identity. PIM have been described microscopically long time ago in species from the Laurasiatheria superorder such as bovine, swine, cats or cetaceans. We observed that PIM were more inflammatory than AM upon infection with the porcine reproductive and respiratory syndrome virus (PRRSV), a major swine pathogen. Moreover, whereas PRRSV was thought to mainly target AM, we observed that PIM were a major producer of virus. The PIM infection was more correlated with viremia in vivo than AM infection. Finally like AM, PIM-expressed genes were characteristic of an embryonic monocyte-derived macrophage population, whose turnover is independent of bone marrow-derived hematopoietic precursors. This last observation raised the interesting possibility that AM and PIM originate from the same lung precursor.
Fuzzy Union to Assess Climate Suitability of Annual Ryegrass (Lolium multiflorum), Alfalfa (Medicago sativa) and Sorghum (Sorghum bicolor)
Authors: Kim Hyunae , Hyun Shin Woo , Hoogenboom Gerrit , Porter Cheryl H. , Kim Kwang Soo 
Published: June 2018

AbstractThe Law of the Minimum is often implemented using t-norm or fuzzy intersection. We propose the use of t-conorm or fuzzy union for climate suitability assessment of a grass species using annual ryegrass (Lolium multiflorumLam.) as an example and evaluate the performance for alfalfa (Medicago sativaL.) and sorghum (Sorghum bicolorL.). The ORFand ANDFmodels, which are fuzzy logic systems based on t-conorm and t-norm between temperature and moisture conditions, respectively, were developed to assess the quality of climate conditions for crops. The parameter values for both models were obtained from existing knowledge, e.g., the EcoCrop database. These models were then compared with the EcoCrop model, which is based on the t-norm. The ORFmodel explained greater variation (54%) in the yield of annual ryegrass at 84 site-years than the ANDFmodel (43%) and the EcoCrop model (5%). The climate suitability index of the ORFmodel had the greatest likelihood of occurrence of annual ryegrass compared to the other models. The ORFmodel also had similar results for alfalfa and sorghum. We emphasize that the fuzzy logic system for climate suitability assessment can be developed using knowledge rather than presence-only data, which can facilitate more complex approaches such as the incorporation of biotic interaction into species distribution modeling.
Male rutting calls synchronize reproduction in Serengeti wildebeest
Authors: Calabrese Justin M. , Moss Clay Allison , Estes Richard D. , Thompson Katerina V. , Monfort Steven L. 
Published: June 2018

AbstractTightly synchronized reproduction in vast wildebeest herds underpins the keystone role this iconic species plays in the Serengeti. However, despite decades of study, the proximate synchronizing mechanism remains unknown. Combining a season-long field experiment with simple stochastic process models, we show that females exposed to playback of male rutting vocalizations are over three times more synchronous in their expected time to mating than a control group isolated from all male stimuli. Additionally, predictions of both mating and calving synchrony based on the playback group were highly consistent with independent data on wildebeest mating and calving synchrony, while control-based predictions were inconsistent with the data. Taken together, our results provide the first experimental evidence that male rutting vocalizations alone could account for the highly synchronized reproduction observed in Serengeti wildebeest. Given anthropogenically driven losses in many areas, a mechanistic understanding of synchrony can highlight additional risks declining wildebeest populations may face.
Preventive treatment with liraglutide protects against development of glucose intolerance in a rat model of Wolfram syndrome
Authors: Toots Maarja , Seppa Kadri , Jagomäe Toomas , Koppel Tuuliki , Pallase Maia , Heinla Indrek , Terasmaa Anton , Plaas Mario , Vasar Eero 
Published: June 2018

AbstractWolfram syndrome (WS) is a rare autosomal recessive disorder caused by mutations in the WFS1 (Wolframin1) gene. The syndrome first manifests as diabetes mellitus, followed by optic nerve atrophy, deafness, and neurodegeneration. The underlying mechanism is believed to be a dysregulation of endoplasmic reticulum (ER) stress response, which ultimately leads to cellular death. Treatment with glucagon-like peptide-1 (GLP-1) receptor agonists has been shown to normalize ER stress response in several in vitro and in vivo models. Early chronic intervention with the GLP-1 receptor agonist liraglutide starting before the onset of metabolic symptoms prevented the development of glucose intolerance, improved insulin and glucagon secretion control, reduced ER stress and inflammation in Langerhans islets in Wfs1 mutant rats. Thus, treatment with GLP-1 receptor agonists might be a promising strategy as a preventive treatment for human WS patients.
Attentional state and brain processes: state-dependent lateralization of EEG profiles in horses
Authors: Rochais C. , Sébilleau M. , Menoret M. , Oger M. , Henry S. , Hausberger M. , Cousillas H. 
Published: June 2018

AbstractLateralization of brain functions has been suggested to provide individuals with advantages, such as an increase of neural efficiency. The right hemisphere is likely to be specialized for processing attention for details and the left hemisphere for categorization of stimuli. Thus attentional processes actually may underlie lateralization. In the present study, we hypothesized that the attentional state of horses could be reflected in the lateralization of brain responses. We used i) a recently developed attention test to measure horses’ visual attentional responses towards a standardized stimulus and ii) a recently developed portable EEG telemetric tool to measure brain responses. A particular emphasis was given to the types of waves (EEG power profile) and their side of production when horses were either attentive towards a visual stimulus or quiet standing. The results confirmed that a higher attentional state is associated with a higher proportion of gamma waves. There was moreover an interaction between the attentional state, the hemisphere and the EEG profile: attention towards the visual stimulus was associated with a significant increase of gamma wave proportion in the right hemisphere while “inattention” was associated with more alpha and beta waves in the left hemisphere. These first results are highly promising and contribute to the large debate on functional lateralization.
Paleosecular variation recorded by Quaternary lava flows from Guadeloupe Island
Authors: Ricci Julia , Carlut Julie , Valet Jean-Pierre 
Published: June 2018

AbstractPaleomagnetic directional data were obtained from fourteen 0 to 2 Ma old lava flows at Basse-Terre Island (Guadeloupe, French West Indies). Five reversed polarity flows are consistent with their Matuyama age between 1.6–1.5 Ma and 875–790 ka while the ages of the other nine normal polarity units tie them to the Olduvai subchron and the Brunhes Chron. These directions have been combined with previous results obtained from Basse-Terre Island. The overall mean direction (D = −1.2°, I = 31.4°, α95 = 3.3°) obtained from the 39 non-transitional flows from Basse-Terre Island is indistinguishable from the expected geocentric axial dipole value (D = 0°, I = 29.8°). The dispersion measured from the angular standard deviation of the Virtual Geomagnetic Poles (VGPs) was found to be close to, but smaller than the predictions of geomagnetic models. Together with further directions from the nearby Martinique Island, the 45 directions obtained within the Brunhes chron provide the most robust estimate of the statistical distribution of paleosecular variation (PSV) at this latitude. The sequence of directions shows episodes of high amplitude secular variation that are coeval with several geomagnetic events including the last reversal documented by five transitional directions. Finally, three lava flows have recorded a transitional behavior which could be link to two excursions, the Laguna del Sello (at ~340 ka) and the Pringle Falls (at ~210 ka) events.
Novel biomineralization strategy in calcareous foraminifera
Authors: Borrelli C. , Panieri G. , Dahl T. M. , Neufeld K. 
Published: June 2018

AbstractThis work shows that calcareous benthic foraminifera are capable of agglutinating sedimentary particles also. In particular, we focus on Melonis barleeanus. Traditionally considered a calcareous species, our data revealed the presence of minute (~3 μm) sedimentary particles (silicate grains) inside the chamber walls of the examined shells. These particles were arranged in a definitive and systematic pattern, and the similar grain chemical characterization and size suggested a relatively high degree of selectivity in both modern and fossil specimens. Based on these results, we propose that M. barleeanus is capable of agglutinating sedimentary particles during the formation of a new chamber. The analysis of other calcareous foraminiferal species (e.g., Cassidulina neoteretis, Lobatula lobatula, Nonionella stella) did not reveal the presence of silicate grains in the shell of the specimens analyzed confirming this to be a characteristic of M. barleeanus. Considering that the isotopic and chemical composition of this species is widely used in paleoclimatic and paleoceanographic reconstructions, we used a mixing model to better constrain the influence of sedimentary particles on M. barleeanus δ18O data. Our model showed that the calcite δ18O would increase by ~0.9–2‰ if 10 wt% of feldspars (i.e., anorthite, albite, orthoclase) and quartz, respectively, were included in the analyzed shell. Based on these results, we emphasize that it is of paramount importance to consider M. barleeanus unusual biomineralization strategy during the interpretation of geological records and to investigate the presence of similar processes in other calcareous foraminiferal species.
Improving of hydrolases biosythesis by solid-state fermentation of Penicillium camemberti on rapeseed cake
Authors: Boratyński Filip , Szczepańska Ewa , Grudniewska Aleksandra , Gniłka Radosław , Olejniczak Teresa 
Published: June 2018

AbstractThe study show usefulness of rapeseed cake, rich in fats and proteins byproduct generated after oil production, which may be used as a microbial medium for lipase and protease biosynthesis. Of 26 different filamentous fungi screened by solid-state fermentation, Penicillium camemberti AM83 was found to abundantly produce lipase and protease. Various process parameters were then optimized to maximize lipase and protease secretion, including carbon and nitrogen source, C/N ratio, metal ions, temperature, moisture content, initial pH, and inoculum size. Lipase production increased approximately 11.2-fold in solid-state cultures on rapeseed cake supplemented with lactose and calcium chloride, alkalinized to pH 8, hydrated to 80%, and inoculated with 1.2 × 106 spores/mL. Similarly, protease production increased approximately 8.4-fold in optimized cultures inoculated with 3.2 × 108 spores/mL, and grown on rapeseed cake with lactose and ammonium sulfate at pH 9 and moisture content 60%. The results highlight the potential economic value of solid-state fermentation on rapeseed cake to produce industrial hydrolases.
Glacial Inception in Marine Isotope Stage 19: An Orbital Analog for a Natural Holocene Climate
Authors: Vavrus Stephen J. , He Feng , Kutzbach John E. , Ruddiman William F. , Tzedakis Polychronis C. 
Published: June 2018

AbstractThe Marine Isotope Stage 19c (MIS19c) interglaciation is regarded as the best orbital analog to the Holocene. The close of MIS19c (~777,000 years ago) thus serves as a proxy for a contemporary climate system unaffected by humans. Our global climate model simulation driven by orbital parameters and observed greenhouse gas concentrations at the end of MIS19c is 1.3 K colder than the reference pre-industrial climate of the late Holocene (year 1850). Much stronger cooling occurs in the Arctic, where sea ice and year-round snow cover expand considerably. Inferred regions of glaciation develop across northeastern Siberia, northwestern North America, and the Canadian Archipelago. These locations are consistent with evidence from past glacial inceptions and are favored by atmospheric circulation changes that reduce ablation of snow cover and increase accumulation of snowfall. Particularly large buildups of snow depth coincide with presumed glacial nucleation sites, including Baffin Island and the northeast Canadian Archipelago. These findings suggest that present-day climate would be susceptible to glacial inception if greenhouse gas concentrations were as low as they were at the end of MIS 19c.
Rbpj direct regulation of Atoh7 transcription in the embryonic mouse retina
Authors: Miesfeld Joel B. , Moon Myung-soon , Riesenberg Amy N. , Contreras Ashley N. , Kovall Rhett A. , Brown Nadean L. 
Published: June 2018

AbstractIn vertebrate retinal progenitor cells, the proneural factor Atoh7 exhibits a dynamic tissue and cellular expression pattern. Although the resulting Atoh7 retinal lineage contains all seven major cell types, only retinal ganglion cells require Atoh7 for proper differentiation. Such specificity necessitates complex regulation of Atoh7 transcription during retina development. The Notch signaling pathway is an evolutionarily conserved suppressor of proneural bHLH factor expression. Previous in vivo mouse genetic studies established the cell autonomous suppression of Atoh7 transcription by Notch1, Rbpj and Hes1. Here we identify four CSL binding sites within the Atoh7 proximal regulatory region and demonstrate Rbpj protein interaction at these sequences by in vitro electromobility shift, calorimetry and luciferase assays and, in vivo via colocalization and chromatin immunoprecipitation. We found that Rbpj simultaneously represses Atoh7 transcription using both Notch-dependent and –independent pathways.