bluuebunny/crossref_metadata_2025_split huggingface dataset:
Habitat-use influences severe disease-mediated population declines in two of the most common garden bird species in Great Britain
Authors: Hanmer Hugh J. , Cunningham Andrew A. , John Shinto K. , Magregor Shaheed K. , Robinson Robert A. , Seilern-Moy Katharina , Siriwardena Gavin M. , Lawson Becki 
Published: September 2022

AbstractThe influence of supplementary feeding of wildlife on disease transmission and its consequent impacts on population dynamics are underappreciated. In Great Britain, supplementary feeding is hypothesised to have enabled the spread of the protozoan parasite, Trichomonas gallinae, from columbids to finches, leading to epidemic finch trichomonosis and a rapid population decline of greenfinch (Chloris chloris). More recently, chaffinch (Fringilla coelebs), has also declined markedly from the second to fifth commonest bird in Britain. Using citizen science data, we show that both declines were driven primarily by reduced adult survival, with the greatest reductions occurring in peri-domestic habitats, where supplementary food provision is common. Post-mortem examinations showed a proportional increase in chaffinch trichomonosis cases, near-contemporaneous with its population decline. Like greenfinches, chaffinches often use supplementary food, but are less associated with human habitation. Our results support the hypothesis that supplementary feeding can increase parasite transmission frequency within and between common species. However, the dynamics behind resultant population change can vary markedly, highlighting the need for integrating disease surveillance with demographic monitoring. Other species susceptible to T. gallinae infection may also be at risk. Supplementary feeding guidelines for wildlife should include disease mitigation strategies to ensure that benefits to target species outweigh risks.
A novel scaled-gamma-tanh (SGT) activation function in 3D CNN applied for MRI classification
Authors: Khagi Bijen , Kwon Goo-Rak 
Published: September 2022

AbstractActivation functions in the neural network are responsible for ‘firing’ the nodes in it. In a deep neural network they ‘activate’ the features to reduce feature redundancy and learn the complex pattern by adding non-linearity in the network to learn task-specific goals. In this paper, we propose a simple and interesting activation function based on the combination of scaled gamma correction and hyperbolic tangent function, which we call Scaled Gamma Tanh (SGT) activation. The proposed activation function is applied in two steps, first is the calculation of gamma version as y = f(x) = axα for x < 0 and y = f(x) = bxβ for x ≥ 0, second is obtaining the squashed value as z = tanh(y). The variables a and b are user-defined constant values whereas $$\alpha$$
α
and $$\beta$$
β
are channel-based learnable parameters. We analyzed the behavior of the proposed SGT activation function against other popular activation functions like ReLU, Leaky-ReLU, and tanh along with their role to confront vanishing/exploding gradient problems. For this, we implemented the SGT activation functions in a 3D Convolutional neural network (CNN) for the classification of magnetic resonance imaging (MRIs). More importantly to support our proposed idea we have presented a thorough analysis via histogram of inputs and outputs in activation layers along with weights/bias plot and t-SNE (t-Distributed Stochastic Neighbor Embedding) projection of fully connected layer for the trained CNN models. Our results in MRI classification show SGT outperforms standard ReLU and tanh activation in all cases i.e., final validation accuracy, final validation loss, test accuracy, Cohen’s kappa score, and Precision.
Tyrosine phosphatase activity is restricted by basic charge substituting mutation of substrates
Authors: Huang Che-Fan , Gottardi Cara J. , Mrksich Milan 
Published: September 2022

AbstractPhosphorylation controls important cellular signals and its dysregulation leads to disease. While most phospho-regulation studies are focused on kinases, phosphatases are comparatively overlooked. Combining peptide arrays with SAMDI mass spectrometry, we show that tyrosine phosphatase activity is restricted by basic amino acids adjacent to phosphotyrosines. We validate this model using two β-catenin mutants associated with cancer (T653R/K) and a mouse model for intellectual disability (T653K). These mutants introduce a basic residue next to Y654, an established phosphorylation site where modification shifts β-catenin from cell–cell adhesions and towards its essential nuclear role as Wnt-signaling effector. We show that T653-basic mutant β-catenins are less efficiently dephosphorylated by phosphatases, leading to sustained Y654 phosphorylation and elevated Wnt signals, similar to those observed for Y654E phospho-mimic mutant mice. This model rationalizes how basic mutations proximal to phosphotyrosines can restrict counter-regulation by phosphatases, providing new mechanismistic and treatment insights for 6000+ potentially relevant cancer mutations.
Development of Safirinium dyes for new applications: fluorescent staining of bacteria, human kidney cells, and the horny layer of the epidermis
Authors: Fedorowicz Joanna , Bazar Dagmara , Brankiewicz Wioletta , Kapica Hanna , Ciura Krzesimir , Zalewska-Piątek Beata , Piątek Rafał , Cal Krzysztof , Mojsiewicz-Pieńkowska Krystyna , Sączewski Jarosław 
Published: September 2022

AbstractLow-molecular synthetic fluorophores are convenient tools in bioimaging applications. Several derivatives of Safirinium dyes as well as their reactive N-hydroxysuccinimide (NHS) esters bearing diverse substituents were synthesized and evaluated experimentally in terms of their lipophilicity by means of reverse-phase and immobilized artificial membrane high-performance liquid chromatography. Subsequently, the selected compounds were employed as novel cellular imaging agents for staining Gram-positive and Gram-negative bacteria, human kidney cell line, as well as human skin tissue. The analyzed dyes allowed for visualization of cellular structures such as mitochondria, endoplasmic reticulum, and cellular nuclei. They proved to be useful in fluorescent staining of stratum corneum, especially in the aspect of xenobiotic exposure and its penetration into the skin. The best results were obtained with the use of moderately lipophilic NHS esters of Safirinium Q. The development of Safirinium dyes is a promising alternative for commercially available dyes since the reported molecules have low molecular masses and exhibit efficient staining and remarkable water solubility. Moreover, they are relatively simple and low-cost in synthesis.
Decoding spatiotemporal features of emotional body language in social interactions
Authors: Keck Johannes , Zabicki Adam , Bachmann Julia , Munzert Jörn , Krüger Britta 
Published: September 2022

AbstractHow are emotions perceived through human body language in social interactions? This study used point-light displays of human interactions portraying emotional scenes (1) to examine quantitative intrapersonal kinematic and postural body configurations, (2) to calculate interaction-specific parameters of these interactions, and (3) to analyze how far both contribute to the perception of an emotion category (i.e. anger, sadness, happiness or affection) as well as to the perception of emotional valence. By using ANOVA and classification trees, we investigated emotion-specific differences in the calculated parameters. We further applied representational similarity analyses to determine how perceptual ratings relate to intra- and interpersonal features of the observed scene. Results showed that within an interaction, intrapersonal kinematic cues corresponded to emotion category ratings, whereas postural cues reflected valence ratings. Perception of emotion category was also driven by interpersonal orientation, proxemics, the time spent in the personal space of the counterpart, and the motion–energy balance between interacting people. Furthermore, motion–energy balance and orientation relate to valence ratings. Thus, features of emotional body language are connected with the emotional content of an observed scene and people make use of the observed emotionally expressive body language and interpersonal coordination to infer emotional content of interactions.
Development of the shear displacement of sandy soil due to absorption under constant shear stress for creep failure
Authors: Sasahara Katsuo 
Published: September 2022

AbstractMeasurement of the displacement and pore pressure in physical model slopes and natural slopes revealed that not only an accelerative increase up to failure but also a decelerative increase occurred in surface displacement under a constant groundwater level, which could be recognized as creep deformation under constant stress. The displacement increased significantly at first in both types, which made it difficult to evaluate whether the displacement developed to the point of failure at the start of the increase. It was necessary to find an indicator for evaluation as the first step of the prediction of an onset of slope failure. Measurement of shear and normal displacements of the sandy specimen in an inclined direct shear box with increasing water content was conducted to examine the indicator. The increase in the shear displacement was categorized into three types: the accelerative increase up to failure with increasing volumetric water content (VWC), the accelerative increase up to failure under constant VWC just prior to failure, and the decelerative increase under constant VWC. It was recognized that a constant VWC corresponded to constant suction from the experimental data. Shear displacement increased up to failure with the monotonic decrease in void ratio just prior to failure in the case of increasing VWC. The void ratio monotonically decreased under constant VWC in the case of shear displacement termination under constant VWC, while it significantly varied at first and then converged to a constant value just prior to failure in the case of shear displacement increase with constant VWC. The ultimate void ratio under the same stress conditions might have been unique. These facts revealed that the void ratio can be recognized as an indicator of the failure of specimens under creep deformation according to absorption. When the void ratio converges to a constant value under constant VWC, the shear displacement might increase up to failure, while the void ratio varying under constant VWC indicates that the shear displacement terminates before failure.
An almost nontoxic tetrodotoxin analog, 5,6,11-trideoxytetrodotoxin, as an odorant for the grass puffer
Authors: Noguchi Yoshihisa , Suzuki Takehisa , Matsutani Keigo , Sakakibara Ryo , Nakahigashi Ryota , Adachi Masaatsu , Nishikawa Toshio , Abe Hideki 
Published: September 2022

AbstractToxic puffers contain the potent neurotoxin, tetrodotoxin (TTX). Although TTX is considered to serve as a defense substance, previous behavioral studies have demonstrated that TTX acts as an attractive pheromone for some toxic puffers. To elucidate the physiological mechanism of putative pheromonal action of TTX, we examined whether grass puffers Takifugu alboplumbeus can detect TTX. Electroolfactogram (EOG) results suggest that the olfactory epithelium (OE) of grass puffers responded to a type of TTX analog (5,6,11-trideoxyTTX), although it did not respond to TTX. We also examined the attractive action of 5,6,11-trideoxyTTX on grass puffers by recording their swimming behavior under dark conditions. Grass puffers preferred to stay on the side of the aquarium where 5,6,11-trideoxyTTX was administered, and their swimming speed decreased. Additionally, odorant-induced labeling of olfactory sensory neurons by immunohistochemistry against neural activity marker (phosphorylated extracellular signal regulated kinase; pERK) revealed that labeled olfactory sensory neurons were localized in the region surrounding “islets” where there was considered as nonsensory epithelium. 5,6,11-trideoxyTTX has been known to accumulate in grass puffers, but its toxicity is much lower (almost nontoxic) than TTX. Our results suggest that toxic puffers may positively use this TTX analog, which has been present in their body with TTX but whose function was unknown, as an odorant for chemical communication or effective TTX accumulation.
Determination of FRET orientation factor between artificial fluorophore and photosynthetic light-harvesting 2 complex (LH2)
Authors: Fujimoto Kazuhiro J. , Miyashita Tomoya , Dewa Takehisa , Yanai Takeshi 
Published: September 2022

AbstractThe orientation factor of fluorescence resonance energy transfer (FRET) between photosynthetic light-harvesting 2 complex (LH2) and artificial fluorophore (Alexa Fluor 647: A647) was theoretically investigated. The orientation factor of 2/3, i.e., the isotropic mean, is widely used to predict the donor–acceptor distance from FRET measurements. However, this approximation seems inappropriate because the movement of A647 is possibly restricted by the bifunctional linker binding to LH2. In this study, we performed molecular dynamics (MD) simulations and electronic coupling calculations on the LH2-A647 conjugate to analyze its orientation factor. The MD results showed that A647 keeps a position approximately 26 Å away from the bacteriochlorophyll (BChl) assembly in LH2. The effective orientation factor was extracted from the electronic coupling calculated using the transition charge from electrostatic potential (TrESP) method. With MD snapshots, an averaged orientation factor was predicted to be 1.55, significantly different from the isotropic mean value. The analysis also suggested that the value of the refractive index employed in the previous studies is not suitable for this system. Furthermore, optimal orientations of A647 with larger orientation factors to improve FRET efficiency were searched using Euler angles. The present approach is useful for extending the applicability of FRET analysis.
Metabolomic changes in crown of alfalfa (Medicago sativa L.) during de-acclimation
Authors: Li Zhensong , He Feng , Tong Zongyong , Li Xianglin , Yang Qingchuan , Hannaway David B. 
Published: September 2022

AbstractAlfalfa is a high-quality forage legume species that is widely cultivated at high latitudes worldwide. However, a decrease in cold tolerance in early spring seriously affects regrowth and persistence of alfalfa. There has been limited research on the metabolomic changes that occur during de-acclimation. In this study, a liquid chromatography–mass spectrometry system was used to compare the metabolites in two alfalfa cultivars during a simulated overwintering treatment. In four pairwise comparisons, 367 differential metabolites were identified, of which 31 were annotated according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Many of these metabolites were peptides, carbohydrates, and lipids. At the subclass level, 17 major pathways were revealed to be significantly enriched (P < 0.05). The main differential metabolites included amino acids, peptides and analogs, carbohydrates, and glycerol phosphocholines. A metabolomic analysis showed that the up-regulation of unsaturated fatty acids and amino acids as well as the enhancement of the related metabolic pathways might be an effective strategy for increasing alfalfa cold tolerance. Furthermore, glycerophospholipid metabolism affects alfalfa cold tolerance in early spring. Study results provide new insights about the changes in alfalfa metabolites that occur during de-acclimation, with potential implications for the selection and breeding of cold-tolerant cultivars.
Molecular characterisation of a novel pathogenic avipoxvirus from an Australian little crow (Corvus bennetti) directly from the clinical sample
Authors: Sarker Subir , Sutherland Michelle 
Published: September 2022

AbstractAvipoxviruses are thought to be restricted to avian hosts and considered significant pathogens that may impact the conservation of many birds. However, reports of avipoxvirus-like viruses from reptiles suggest that cross-species transmission, within birds and other species, may be possible. The vast majority of avipoxviruses in wild birds remain uncharacterised and their genetic variability is unclear. Here, cutaneous pox lesions were used to recover a novel full-length crowpox virus genome from an Australian little crow (Corvus bennetti), followed by the detection of immature and intracellular mature virions using electron microscopy. The CRPV genome was 328,768 bp in length and contained 403 predicted open-reading frames. While 356 of the ORFs of CRPV genome had the greatest similarity with other avipoxviruses gene products, a further 47 ORFs were novel. Subsequent phylogenetic analyses showed that the CRPV was most closely related to other avipoxviruses isolated from passerine and marine bird species and demonstrated the highest sequence similarity with an albatrosspox virus (84.4%). Considering the sequence similarity observed between CRPV and other avipoxviruses and phylogenetic position, this study concluded that the CRPV to be a distinct available candidate of avipoxviruses.
Development of a red fluorescent protein-based cGMP indicator applicable for live-cell imaging
Authors: Takizawa Mai , Osuga Yuri , Ishida Rika , Mita Marie , Harada Kazuki , Ueda Hiroshi , Kitaguchi Tetsuya , Tsuboi Takashi 
Published: September 2022

AbstractCyclic guanosine 3′, 5′-monophosphate (cGMP) is a second messenger that regulates a variety of physiological processes. Here, we develop a red fluorescent protein-based cGMP indicator, “Red cGull”. The fluorescence intensity of Red cGull increase more than sixfold in response to cGMP. The features of this indicator include an EC50 of 0.33 μM for cGMP, an excitation and emission peak at 567 nm and 591 nm, respectively. Live-cell imaging analysis reveal the utility of Red cGull for dual-colour imaging and its ability to be used in conjunction with optogenetics tools. Using enteroendocrine cell lines, Red cGull detects an increase in cGMP following the application of l-arginine. An increase in intracellular cGMP is found to be inhibited by Ca2+, and l-arginine-mediated hormone secretion is not potentiated. We propose that Red cGull will facilitate future research in cell signalling in relation to cGMP and its interplay with other signalling molecules.
Oestrogen-dependent hypothalamic oxytocin expression with changes in feeding and body weight in female rats
Authors: Nishimura Kazuaki , Yoshino Kiyoshi , Ikeda Naofumi , Baba Kazuhiko , Sanada Kenya , Akiyama Yasuki , Nishimura Haruki , Tanaka Kentaro , Sonoda Satomi , Ueno Hiromichi , Yoshimura Mitsuhiro , Maruyama Takashi , Hachisuga Toru , Ueta Yoichi 
Published: September 2022

AbstractOxytocin (OXT) is produced in the hypothalamic nuclei and secreted into systemic circulation from the posterior pituitary gland. In the central nervous system, OXT regulates behaviours including maternal and feeding behaviours. Our aim is to evaluate whether oestrogen regulates hypothalamic OXT dynamics. Herein, we provide the first evidence that OXT dynamics in the hypothalamus vary with sex and that oestrogen may modulate dynamic changes in OXT levels, using OXT-mRFP1 transgenic rats. The fluorescence intensity of OXT-mRFP1 and expression of the OXT and mRFP1 genes in the hypothalamic nuclei is highest during the oestrus stage in female rats and decreased significantly in ovariectomised rats. Oestrogen replacement caused significant increases in fluorescence intensity and gene expression in a dose-related manner. This is also demonstrated in the rats’ feeding behaviour and hypothalamic Fos neurons using cholecystokinin-8 and immunohistochemistry. Hypothalamic OXT expression is oestrogen-dependent and can be enhanced centrally by the administration of oestrogen.
Making Quality Cosmetics
Authors: Gilchrist Alastair J 
Published: September 2022

Cosmetics manufacture is a dynamic and vibrant industry with companies varying from the very small scale, working in their own home, to much larger enterprises. With such variable companies there is the risk of equally variable quality in manufacturing. The International Organization for Standards (ISO) provides guidelines on good manufacturing processes for the cosmetics industry. However, not everyone working in cosmetics has a scientific or engineering backgrounds and understanding and meeting the ISO requirements can be daunting.
Whether you are a small business just starting out or an established company looking to expand, Making Quality Cosmetics will guide you through the requirements of the ISO standard. Calling on more than 35 years of experience in the cosmetics sector the author covers every aspect of the manufacturing set up and process, as well as discussing other regulations that may need to be considered, especially in larger facilities. With technical advice ranging from choosing equipment and raw materials, to assessing and auditing contractors this book will help you make sure your products are of the highest quality.
Charge detection mass spectrometry for the analysis of viruses and virus-like particles
Authors: Miller Lohra M. , Jarrold Martin F. 
Published: September 2022

AbstractHeterogeneity usually restricts conventional mass spectrometry to molecular weights less than around a megadalton. As a single-particle technique, charge detection mass spectrometry (CDMS) overcomes this limitation. In CDMS, the mass-to-charge (m/z) ratio and charge are measured simultaneously for individual ions, giving a direct mass measurement for each ion. Recent applications include the analysis of viruses, virus-like particles, vaccines, heavily glycosylated proteins, and gene therapy vectors.
PRODIGE – envelope to disk with NOEMA
Authors: Valdivia-Mena M. T. , Pineda J. E. , Segura-Cox D. M. , Caselli P. , Neri R. , López-Sepulcre A. , Cunningham N. , Bouscasse L. , Semenov D. , Henning Th. , Piétu V. , Chapillon E. , Dutrey A. , Fuente A. , Guilloteau S. , Hsieh T. H. , Jiménez-Serra I. , Marino S. , Maureira M. J. , Smirnov-Pinchukov G. V. , Tafalla M. , Zhao B. 
Published: September 2022

Context. In the past few years, there has been a rise in the detection of streamers, asymmetric flows of material directed toward the protostellar disk with material from outside a star’s natal core. It is unclear how they affect the process of mass accretion, in particular beyond the Class 0 phase.
Aims. We investigate the gas kinematics around Per-emb-50, a Class I source in the crowded star-forming region NGC 1333. Our goal is to study how the mass infall proceeds from envelope to disk scales in this source.
Methods. We use new NOEMA 1.3 mm observations, including C18O, H2CO, and SO, in the context of the PRODIGE MPG – IRAM program, to probe the core and envelope structures toward Per-emb-50.
Results. We discover a streamer delivering material toward Per-emb-50 in H2CO and C18O emission. The streamer’s emission can be well described by the analytic solutions for an infalling parcel of gas along a streamline with conserved angular momentum, both in the image plane and along the line-of-sight velocities. The streamer has a mean infall rate of 1.3 × 10−6 M⊙ yr−1, five to ten times higher than the current accretion rate of the protostar. SO and SO2 emission reveal asymmetric infall motions in the inner envelope, additional to the streamer around Per-emb-50. Furthermore, the presence of SO2 could mark the impact zone of the infalling material.
Conclusions. The streamer delivers sufficient mass to sustain the protostellar accretion rate and might produce an accretion burst, which would explain the protostar’s high luminosity with respect to other Class I sources. Our results highlight the importance of late infall for protostellar evolution: streamers might provide a significant amount of mass for stellar accretion after the Class 0 phase.