bluuebunny/crossref_metadata_2025_split huggingface dataset:
The prediction of swarming in honeybee colonies using vibrational spectra
Authors: Ramsey Michael-Thomas , Bencsik Martin , Newton Michael Ian , Reyes Maritza , Pioz Maryline , Crauser Didier , Delso Noa Simon , Le Conte Yves 
Published: June 2020

AbstractIn this work, we disclose a non-invasive method for the monitoring and predicting of the swarming process within honeybee colonies, using vibro-acoustic information. Two machine learning algorithms are presented for the prediction of swarming, based on vibration data recorded using accelerometers placed in the heart of honeybee hives. Both algorithms successfully discriminate between colonies intending and not intending to swarm with a high degree of accuracy, over 90% for each method, with successful swarming prediction up to 30 days prior to the event. We show that instantaneous vibrational spectra predict the swarming within the swarming season only, and that this limitation can be lifted provided that the history of the evolution of the spectra is accounted for. We also disclose queen toots and quacks, showing statistics of the occurrence of queen pipes over the entire swarming season. From this we were able to determine that (1) tooting always precedes quacking, (2) under natural conditions there is a 4 to 7 day period without queen tooting following the exit of the primary swarm, and (3) human intervention, such as queen clipping and the opening of a hive, causes strong interferences with important mechanisms for the prevention of simultaneous rival queen emergence.
The ecological significance of birds feeding from the hand of humans
Authors: Møller Anders Pape , Xia Canwei 
Published: June 2020

AbstractAnimals keep a safe distance to humans and thus humans rarely physically encounter wild animals. However, birds have been known to feed from the hand of humans. Such behaviour must reflect the trade-off between acquisition of food and the risk of being captured by a potential predator feeding from the hand. Relying on YouTube, an international video-sharing platform, we found 36 European bird species recorded feeding from the hand of humans. We compared ecological traits between these species and all other 490 European bird species, which were not recorded as feeding from a human hand. We found that species with a large number of innovative behaviours, a higher rate of introduction success, larger breeding range, larger population size, and urban tolerance have a higher probability of feeding from the hand of a human. These associations were also supported after control for the similarity among taxa due to common phylogenetic descent. In conclusion, these findings suggest that frequent feeding from the hand of a human results in the transition from natural environments to novel urbanized environments with consequences for population size increasing and range expansion.
Genome Diversity and the Origin of the Arabian Horse
Authors: Cosgrove Elissa J. , Sadeghi Raheleh , Schlamp Florencia , Holl Heather M. , Moradi-Shahrbabak Mohammad , Miraei-Ashtiani Seyed Reza , Abdalla Salma , Shykind Ben , Troedsson Mats , Stefaniuk-Szmukier Monika , Prabhu Anil , Bucca Stefania , Bugno-Poniewierska Monika , Wallner Barbara , Malek Joel , Miller Donald C. , Clark Andrew G. , Antczak Douglas F. , Brooks Samantha A. 
Published: June 2020

AbstractThe Arabian horse, one of the world’s oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ancestry in Arabian horses from the Middle East region. Also, contrary to popular belief, we could detect no significant genomic contribution of the Arabian breed to the Thoroughbred racehorse, including Y chromosome ancestry. However, we found strong evidence for recent interbreeding of Thoroughbreds with Arabians used for flat-racing competitions. Genetic signatures suggestive of selective sweeps across the Arabian breed contain candidate genes for combating oxidative damage during exercise, and within the “Straight Egyptian” subgroup, for facial morphology. Overall, our data support an origin of the Arabian horse in the Middle East, no evidence for reduced global genetic diversity across the breed, and unique genetic adaptations for both physiology and conformation.
Increased expression of PD-1 and PD-L1 in oral lesions progressing to oral squamous cell carcinoma: a pilot study
Authors: Dave Kanan , Ali Aiman , Magalhaes Marco 
Published: June 2020

AbstractOral cancer is a devastating disease and is commonly preceded by a range of oral premalignant disorders. We investigated the expression of PD-1 and PD-L1 in oral epithelial dysplasia (OED) that progressed to oral squamous cell carcinoma (OSCC) compared to non-progressing dysplasia. 49 oral biopsies were analyzed, including 19 progressing cases, 20 cases did not progress, and 10 OSCC. Samples were stained with monoclonal antibodies for PD-1 and PD-L1, followed by conventional peroxidase reaction immunohistochemistry (IHC) imaged under light microscopy or fluorescent immunohistochemistry (FIHC) imaged using a confocal microscope. Images were analyzed using a novel semi-automated analysis protocol. PD-1/PD-L1 expression was assessed at the epithelium/tumor cells (TC) and at inflammatory cells in lamina propria. Our results show a significant increase in PD-L1 expression in progressing compared to non-progressing dysplasia. Using FIHC, we showed increased PD-L1 expression, increased nuclear density in progressing dysplasia and a better interobserver agreement compared with IHC. We developed a new FIHC-based quantitative method to study PD-1/PD-L1 expression in FFPE samples and showed that PD-L1 is highly expressed in premalignant lesions progressing to cancer. Our results suggest that immunomodulation via PD-L1/PD-1 pathway occurs prior to malignant transformation.
Increasing serotonin bioavailability alters gene expression in peripheral leukocytes and lymphoid tissues of dairy calves
Authors: Marrero M. G. , Field S. L. , Skibiel A. L. , Dado-Senn B. , Driver J. P. , Laporta J. 
Published: June 2020

AbstractDairy calves are born with a naïve immune system, making the pre-weaning phase a critical window for immune development. In the U.S., 40–60% of dairy farms feed milk replacer to pre-weaned calves, which are devoid of bioactive factors with immunological roles. Serotonin is a bioactive factor with immunoregulatory properties naturally produced by the calf and present in milk. Human and rodent immune cells express the serotonin machinery, but little is known about the role of serotonin in the bovine immune system. Supplementing milk replacer with 5-hydroxytryptophan (serotonin precursor) or fluoxetine (reuptake inhibitor) increases serotonin bioavailability. We hypothesized that increased serotonin bioavailability promotes serotonergic signaling and modulates the expression of immune related genes in peripheral leukocytes and immune-related tissues of dairy calves. The present experiment targeted candidate genes involved in serotonin production, metabolism, transport, signaling and immune regulation. We established that bovine peripheral leukocytes express all known serotonin receptors, and can synthesize, uptake and degrade serotonin due to the expression of serotonin metabolism-related genes. Indeed, we showed that increasing serotonin bioavailability alters gene expression of serotonin receptors and immune-related genes. Further research will determine whether manipulation of the serotonin pathway could be a feasible approach to bolster dairy calves’ immune system.
The entropy production for thermal operations
Authors: Dolatkhah H. , Salimi S. , Khorashad A. S. , Haseli S. 
Published: June 2020

AbstractAccording to the first and second laws of thermodynamics and the definitions of work and heat, microscopic expressions for the non-equilibrium entropy production have been achieved. Recently, a redefinition of heat has been presented in [Nature Communications volume 8, Article number: 2180 (2017)]. Since thermal operations play an important role in the resource theory of thermodynamics, it would be very interesting to find out the effect of the above-mentioned definition on the expression of the entropy production for these kind of operations. This is one of the aims of the present paper. Using the new definition of heat, it is shown that the entropy production is the same as the mutual information between a system and a bath both for thermal operations and, if the system-bath initial state is factorized, for entropy-preserving operations. It is also discussed that how one can recognize the type of the correlation between a system and a bath through knowledge of the initial state of the system only. It is shown that if the initial state of a system is diagonal in the energy basis, the thermal operations cannot create a quantum correlation between the system and the bath, however, if the system initial state is coherent Gibbs state, there cannot be classical correlation due to the thermal operations.
Detecting quadrupole: a hidden source of magnetic anisotropy for Manganese alloys
Authors: Okabayashi Jun , Miura Yoshio , Kota Yohei , Z. Suzuki Kazuya , Sakuma Akimasa , Mizukami Shigemi 
Published: June 2020

AbstractMn-based alloys exhibit unique properties in the spintronics materials possessing perpendicular magnetic anisotropy (PMA) beyond the Fe and Co-based alloys. It is desired to figure out the quantum physics of PMA inherent to Mn-based alloys, which have never been reported. Here, the origin of PMA in ferrimagnetic Mn3− δ Ga ordered alloys is investigated to resolve antiparallel-coupled Mn sites using x-ray magnetic circular and linear dichroism (XMCD/XMLD) and a first-principles calculation. We found that the contribution of orbital magnetic moments in PMA is small from XMCD and that the finite quadrupole-like orbital distortion through spin-flipped electron hopping is dominant from XMLD and theoretical calculations. These findings suggest that the spin-flipped orbital quadrupole formations originate from the PMA in Mn3− δ Ga and bring the paradigm shift in the researches of PMA materials using x-ray magnetic spectroscopies.
Tunable resistivity of correlated VO2(A) and VO2(B) via tungsten doping
Authors: Choi Songhee , Ahn Gihyeon , Moon Soon Jae , Lee Shinbuhm 
Published: June 2020

AbstractApplications of correlated vanadium dioxides VO2(A) and VO2(B) in electrical devices are limited due to the lack of effective methods for tuning their fundamental properties. We find that the resistivity of VO2(A) and VO2(B) is widely tunable by doping them with tungsten ions. When x < 0.1 in V1−xWxO2(A), the resistivity decreases drastically by four orders of magnitude with increasing x, while that of V1−xWxO2(B) shows the opposite behaviour. Using spectroscopic ellipsometry and X-ray photoemission spectroscopy, we propose that correlation effects are modulated by either chemical-strain-induced redistribution of V−V distances or electron-doping-induced band filling in V1−xWxO2(A), while electron scattering induced by disorder plays a more dominant role in V1−xWxO2(B). The tunable resistivity makes correlated VO2(A) and VO2(B) appealing for next-generation electronic devices.
Bayesian Hyper-LASSO Classification for Feature Selection with Application to Endometrial Cancer RNA-seq Data
Authors: Jiang Lai , Greenwood Celia M. T. , Yao Weixin , Li Longhai 
Published: June 2020

AbstractFeature selection is demanded in many modern scientific research problems that use high-dimensional data. A typical example is to identify gene signatures that are related to a certain disease from high-dimensional gene expression data. The expression of genes may have grouping structures, for example, a group of co-regulated genes that have similar biological functions tend to have similar expressions. Thus it is preferable to take the grouping structure into consideration to select features. In this paper, we propose a Bayesian Robit regression method with Hyper-LASSO priors (shortened by BayesHL) for feature selection in high dimensional genomic data with grouping structure. The main features of BayesHL include that it discards more aggressively unrelated features than LASSO, and it makes feature selection within groups automatically without a pre-specified grouping structure. We apply BayesHL in gene expression analysis to identify subsets of genes that contribute to the 5-year survival outcome of endometrial cancer (EC) patients. Results show that BayesHL outperforms alternative methods (including LASSO, group LASSO, supervised group LASSO, penalized logistic regression, random forest, neural network, XGBoost and knockoff) in terms of predictive power, sparsity and the ability to uncover grouping structure, and provides insight into the mechanisms of multiple genetic pathways leading to differentiated EC survival outcome.
Near Zero Index Perfect Metasurface Absorber using Inverted Conformal Mapping
Authors: Swett Dwight W. 
Published: June 2020

AbstractThe geometry of the characteristic element forming the artificial structure of an electromagnetic metamaterial defines the way the metamaterial will interact with electromagnetic waves, and accordingly, how it will transmit, reflect, and absorb electromagnetic energy. Metamaterials have been discovered that can manipulate electromagnetic waves to create perfect absorption of incident electromagnetic energy using relatively simple elemental geometries. But the phenomenon is confined to very narrow frequency bandwidths owing to the mono-resonance characteristics of simple cellular structures. Complex cellular geometries based on the combination of many different fundamental building blocks may be able to constructively couple many more resonances and broaden the perfect absorption bandwidth. We describe here a metasurface based upon geometric inversion of a set of conformal mapping contours. The resulting geometry forms a nearly continuous series of perfect absorption resonances within an ultrathin (λ/165) metasurface to develop broadband absorption in a frequency range of interest for downhole chemical spectroscopy. The metasurface is derived from a geometric inversion of the Rhodonea, or more commonly called four-leaf roses, conformal mapping contours and was found to exhibit a near zero index metamaterial (NZIM) behavior. An uncooled microbolometer design is described that uses the metasurface geometry on a single VO2thermometric substrate leading to an infrared detector with predicted maximum absorption of 99.94% at 4.3μm and an absorption bandwidth of 170% FWHM on 15.8μm center wavelength, coincident with important chemical spectra of downhole hydrocarbons. The infrared detector design has a predicted maximum detectivity D* = 1.5 × 109 cm$$\sqrt{\text{Hz}}$$Hz/W and noise equivalent difference temperature NEDT of 70 mK at a frame rate of 60 Hz. These levels of detector performance conventionally would be achievable only with cryogenically cooled technologies and could represent a significant step in the effort towards deploying an in situ infrared chemical spectroscopy sensor into downhole logging applications.
Metabolomic differences between invasive alien plants from native and invaded habitats
Authors: Skubel Sarah A. , Su Xiaoyang , Poulev Alexander , Foxcroft Llewellyn C. , Dushenkov Vyacheslav , Raskin Ilya 
Published: June 2020

AbstractGlobalization facilitated the spread of invasive alien species (IAS), undermining the stability of the world’s ecosystems. We investigated the metabolomic profiles of three IAS species: Chromolaena odorata (Asteraceae) Datura stramonium (Solanaceae), and Xanthium strumarium (Asteraceae), comparing metabolites of individual plants in their native habitats (USA), to their invasive counterparts growing in and around Kruger National Park (South Africa, ZA). Metabolomic samples were collected using RApid Metabolome Extraction and Storage (RAMES) technology, which immobilizes phytochemicals on glass fiber disks, reducing compound degradation, allowing long-term, storage and simplifying biochemical analysis. Metabolomic differences were analyzed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) of samples eluted from RAMES disks. Partial Least Squares-Discriminant Analysis (PLS-DA) of metabolomes of individual plants allowed statistical separation of species, native and invasive populations of each species, and some populations on the same continent. Invasive populations of all species were more phytochemically diverse than their native counterparts, and their metabolomic profiles were statistically distinguishable from their native relatives. These data may elucidate the mechanisms of successful invasion and rapid adaptive evolution of IAS. Moreover, RAMES technology combined with PLS-DA statistical analysis may allow taxonomic identification of species and, possibly, populations within each species.
TRPA1 and TRPV1 channels participate in atmospheric-pressure plasma-induced [Ca2+]i response
Authors: Kawase Masayoshi , Chen Weijian , Kawaguchi Kota , Nyasha Mazvita R. , Sasaki Shota , Hatakeyama Hiroyasu , Kaneko Toshiro , Kanzaki Makoto 
Published: June 2020

AbstractDespite successful clinical application of non-equilibrium atmospheric pressure plasma (APP), the details of the molecular mechanisms underlying APP-inducible biological responses remain ill-defined. We previously reported that exposure of 3T3L1 cells to APP-irradiated buffer raised the cytoplasmic free Ca2+ ([Ca2+]i) concentration by eliciting Ca2+ influx in a manner sensitive to transient receptor potential (TRP) channel inhibitors. However, the precise identity of the APP-responsive channel molecule(s) remains unclear. In the present study, we aimed to clarify channel molecule(s) responsible for indirect APP-responsive [Ca2+]i rises. siRNA-mediated silencing experiments revealed that TRPA1 and TRPV1 serve as the major APP-responsive Ca2+ channels in 3T3L1 cells. Conversely, ectopic expression of either TRPA1 or TRPV1 in APP-unresponsive C2C12 cells actually triggered [Ca2+]i elevation in response to indirect APP exposure. Desensitization experiments using 3T3L1 cells revealed APP responsiveness to be markedly suppressed after pretreatment with allyl isothiocyanate or capsaicin, TRPA1 and TRPV1 agonists, respectively. APP exposure also desensitized the cells to these chemical agonists, indicating the existence of a bi-directional heterologous desensitization property of APP-responsive [Ca2+]i transients mediated through these TRP channels. Mutational analyses of key cysteine residues in TRPA1 (Cys421, Cys621, Cys641, and Cys665) and in TRPV1 (Cys258, Cys363, and Cys742) have suggested that multiple reactive oxygen and nitrogen species are intricately involved in activation of the channels via a broad range of modifications involving these cysteine residues. Taken together, these observations allow us to conclude that both TRPA1 and TRPV1 channels play a pivotal role in evoking indirect APP-dependent [Ca2+]i responses.
SNP genotyping reveals substructuring in weakly differentiated populations of Atlantic cod (Gadus morhua) from diverse environments in the Baltic Sea
Authors: Wenne Roman , Bernaś Rafał , Kijewska Agnieszka , Poćwierz-Kotus Anita , Strand Jakob , Petereit Christoph , Plauška Kęstas , Sics Ivo , Árnyasi Mariann , Kent Matthew P. 
Published: June 2020

AbstractAtlantic cod (Gadus morhua) is one of the most important fish species in northern Europe for several reasons including its predator status in marine ecosystems, its historical role in fisheries, its potential in aquaculture and its strong public profile. However, due to over-exploitation in the North Atlantic and changes in the ecosystem, many cod populations have been reduced in size and genetic diversity. Cod populations in the Baltic Proper, Kattegat and North Sea have been analyzed using a species specific single nucleotide polymorphism (SNP) array. Using a subset of 8,706 SNPs, moderate genetic differences were found between subdivisions in three traditionally delineated cod management stocks: Kattegat, western and eastern Baltic. However, an FST measure of population differentiation based on allele frequencies from 588 outlier loci for 2 population groups, one including 5 western and the other 4 eastern Baltic populations, indicated high genetic differentiation. In this paper, differentiation has been demonstrated not only between, but also within western and eastern Baltic cod stocks for the first time, with salinity appearing to be the most important environmental factor influencing the maintenance of cod population divergence between the western and eastern Baltic Sea.
Differential recognition of lipid domains by two Gb3-binding lectins
Authors: Schubert Thomas , Sych Taras , Madl Josef , Xu Maokai , Omidvar Ramin , Patalag Lukas J. , Ries Annika , Kettelhoit Katharina , Brandel Annette , Mely Yves , Steinem Claudia , Werz Daniel B. , Thuenauer Roland , Römer Winfried 
Published: June 2020

AbstractThe two lectins LecA from Pseudomonas aeruginosa and the B-subunit of Shiga toxin from Shigella dysenteriae (StxB) share the glycosphingolipid globotriaosylceramide (Gb3) as receptor. Counterintuitively, we found that LecA and StxB segregated into different domains after recognizing Gb3 at the plasma membrane of cells. We hypothesized that the orientation of the carbohydrate head group of Gb3 embedded in the lipid bilayer differentially influences LecA and StxB binding. To test this hypothesis, we reconstituted lectin-Gb3 interaction using giant unilamellar vesicles and were indeed able to rebuild LecA and StxB segregation. Both, the Gb3 fatty acyl chain structure and the local membrane environment, modulated Gb3 recognition by LecA and StxB. Specifically, StxB preferred more ordered membranes compared to LecA. Based on our findings, we propose comparing staining patterns of LecA and StxB as an alternative method to assess membrane order in cells. To verify this approach, we re-established that the apical plasma membrane of epithelial cells is more ordered than the basolateral plasma membrane. Additionally, we found that StxB recognized Gb3 at the primary cilium and the periciliary membrane, whereas LecA only bound periciliary Gb3. This suggests that the ciliary membrane is of higher order than the surrounding periciliary membrane.
Liver-specific knockout of B cell lymphoma 6 suppresses progression of non-alcoholic steatohepatitis in mice
Authors: Chikada Hiromi , Ida Kinuyo , Nishikawa Yuji , Inagaki Yutaka , Kamiya Akihide 
Published: June 2020

AbstractThe prevalence of non-alcoholic steatohepatitis (NASH) rapidly increases with metabolic disorders such as dyslipidaemia, high blood pressure, and hyperglycaemia. B cell lymphoma 6 (Bcl6), a transcriptional repressor, is essential for the formation of germinal centre B cells. In this study, we analysed the role of Bcl6 in NASH progression-associated pathological changes, such as hepatic lipid accumulation, liver fibrosis, and hepatocarcinogenesis. The roles of Bcl6 in NASH were analysed using liver-specific Bcl6 knockout (Bcl6-LKO) and control wild-type (WT) mice. The murine NASH model was established by feeding the mice with choline-deficient, L-amino-acid-defined, high-fat diet (CDAHFD). Feeding the WT mice with CDAHFD for 7 weeks induced the formation of histopathological features resembling human NASH, such as hepatic lipid accumulation, hepatocellular injury, and fibrosis. These histopathological changes were significantly attenuated in Bcl6-LKO mice. Additionally, feeding the male WT mice with CDAHFD for 38 weeks induced the formation of liver tumours, which was suppressed in Bcl6-LKO mice. These findings indicate that Bcl6 is involved in the progression of NASH and NASH-derived tumours.