bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antigen Discovery, Bioinformatics and Biological Characterization of Novel Immunodominant Babesia microti Antigens
Authors: Verma Nitin , Puri Ankit , Essuman Edward , Skelton Richard , Anantharaman Vivek , Zheng Hong , White Siera , Gunalan Karthigayan , Takeda Kazuyo , Bajpai Surabhi , Lepore Timothy J. , Krause Peter J. , Aravind L. , Kumar Sanjai 
Published: June 2020

AbstractBabesia microti is an intraerythrocytic parasite and the primary causative agent of human babesiosis. It is transmitted by Ixodes ticks, transfusion of blood and blood products, organ donation, and perinatally. Despite its global public health impact, limited progress has been made to identify and characterize immunodominant B. microti antigens for diagnostic and vaccine use. Using genome-wide immunoscreening, we identified 56 B. microti antigens, including some previously uncharacterized antigens. Thirty of the most immunodominant B. microti antigens were expressed as recombinant proteins in E. coli. Among these, the combined use of two novel antigens and one previously described antigen provided 96% sensitivity and 100% specificity in identifying B. microti antibody containing sera in an ELISA. Using extensive computational sequence and bioinformatics analyses and cellular localization studies, we have clarified the domain architectures, potential biological functions, and evolutionary relationships of the most immunodominant B. microti antigens. Notably, we found that the BMN-family antigens are not monophyletic as currently annotated, but rather can be categorized into two evolutionary unrelated groups of BMN proteins respectively defined by two structurally distinct classes of extracellular domains. Our studies have enhanced the repertoire of immunodominant B. microti antigens, and assigned potential biological function to these antigens, which can be evaluated to develop novel assays and candidate vaccines.
Graphene oxide integrated silicon photonics for detection of vapour phase volatile organic compounds
Authors: Leo Tsui H. C. , Alsalman Osamah , Mao Boyang , Alodhayb Abdullah , Albrithen Hamad , Knights Andrew P. , Halsall Matthew P. , Crowe Iain F. 
Published: June 2020

AbstractThe optical response of a graphene oxide integrated silicon micro-ring resonator (GOMRR) to a range of vapour phase Volatile Organic Compounds (VOCs) is reported. The response of the GOMRR to all but one (hexane) of the VOCs tested is significantly higher than that of the uncoated (control) silicon MRR, for the same vapour flow rate. An iterative Finite Difference Eigenmode (FDE) simulation reveals that the sensitivity of the GO integrated device (in terms of RIU/nm) is enhanced by a factor of ~2, which is coupled with a lower limit of detection. Critically, the simulations reveal that the strength of the optical response is determined by molecular specific changes in the local refractive index probed by the evanescent field of the guided optical mode in the device. Analytical modelling of the experimental data, based on Hill-Langmuir adsorption characteristics, suggests that these changes in the local refractive index are determined by the degree of molecular cooperativity, which is enhanced for molecules with a polarity that is high, relative to their kinetic diameter. We believe this reflects a molecular dependent capillary condensation within the graphene oxide interlayers, which, when combined with highly sensitive optical detection, provides a potential route for discriminating between different vapour phase VOCs.
Systematic Evaluation of PKH Labelling on Extracellular Vesicle Size by Nanoparticle Tracking Analysis
Authors: Dehghani Mehdi , Gulvin Shannon M. , Flax Jonathan , Gaborski Thomas R. 
Published: June 2020

AbstractExtracellular vesicles (EVs) are membrane vesicles secreted by cells and can modulate biological activities by transferring their content following uptake into recipient cells. Labelling of EVs is a commonly used technique for understanding their cellular targeting and biodistribution. A reliable fluorescent technique needs to preserve the size of EVs since changes in size may alter their uptake and biodistribution. Lipophilic fluorescent dye molecules such as the PKH family have been widely used for EV labelling. Here, the effect of PKH labelling on the size of EVs was systematically evaluated using nanoparticle tracking analysis (NTA), which is a widely used technique for determining the size and concentration of nanoparticles. NTA analysis showed a size increase in all the PKH labelling conditions tested. As opposed to lipophilic dye molecules, no significant shift in the size of labelled EVs was detected with luminal binding dye molecules such as 5-(and-6)-carboxyfluorescein diacetate succinimidyl ester (CFDA-SE, hereinafter CFSE). This finding suggests that PKH labelling may not be a reliable technique for the tracking of EVs.
Splice-specific deficiency of the PTSD-associated gene PAC1 leads to a paradoxical age-dependent stress behavior
Authors: Biran Jakob , Gliksberg Michael , Shirat Ido , Swaminathan Amrutha , Levitas-Djerbi Talia , Appelbaum Lior , Levkowitz Gil 
Published: June 2020

AbstractThe pituitary adenylate cyclase-activating polypeptide receptor (PAC1, also known as ADCYAP1R1) is associated with post-traumatic stress disorder and modulation of stress response in general. Alternative splicing of PAC1 results in multiple gene products, which differ in their mode of signalling and tissue distribution. However, the roles of distinct splice variants in the regulation of stress behavior is poorly understood. Alternative splicing of a short exon, which is known as the “hop cassette”, occurs during brain development and in response to stressful challenges. To examine the function of this variant, we generated a splice-specific zebrafish mutant lacking the hop cassette, which we designated ‘hopless’. We show that hopless mutant larvae display increased anxiety-like behavior, including reduced dark exploration and impaired habituation to dark exposure. Conversely, adult hopless mutants displayed superior ability to rebound from an acute stressor, as they exhibited reduced anxiety-like responses to an ensuing novelty stress. We propose that the developmental loss of a specific PAC1 splice variant mimics prolonged mild stress exposure, which in the long term, predisposes the organism’s stress response towards a resilient phenotype. Our study presents a unique genetic model demonstrating how early-life state of anxiety paradoxically correlates with reduced stress susceptibility in adulthood.
The tumor immune microenvironmental analysis of 2,033 transcriptomes across 7 cancer types
Authors: Kim Sungjae , Kim Ahreum , Shin Jong-Yeon , Seo Jeong-Sun 
Published: June 2020

AbstractUnderstanding the tumor microenvironment is important to efficiently identify appropriate patients for immunotherapies in a variety of cancers. Here, we presented the tumor microenvironmental analysis of 2,033 cancer samples across 7 cancer types: colon adenocarcinoma, skin cutaneous melanoma, kidney renal papillary cell carcinoma, sarcoma, pancreatic adenocarcinoma, glioblastoma multiforme, and pheochromocytoma / paraganglioma from The Cancer Genome Atlas cohort. Unsupervised hierarchical clustering based on the gene expression profiles separated the cancer samples into two distinct clusters, and characterized those into immune-competent and immune-deficient subtypes using the estimated abundances of infiltrated immune and stromal cells. We demonstrated differential tumor microenvironmental characteristics of immune-competent subtypes across 7 cancer types, particularly immunosuppressive tumor microenvironment features in kidney renal papillary cell carcinoma with significant poorer survival rates and immune-supportive features in sarcoma and skin cutaneous melanoma. Additionally, differential genomic instability patterns between the subtypes were found across the cancer types, and discovered that immune-competent subtypes in most of cancer types had significantly higher immune checkpoint gene expressions. Overall, this study suggests that our subtyping approach based on transcriptomic data could contribute to precise prediction of immune checkpoint inhibitor responses in a wide range of cancer types.
Crepidtumines A and B, Two Novel Indolizidine Alkaloids from Dendrobium crepidatum
Authors: Xu Xiaolin , Chen Xingyue , Yang Runmei , Li Zesheng , Zhou Houguang , Bai Yanbing , Yu Meng , Li Biao , Ding Gang 
Published: June 2020

AbstractTwo new indolizidine alkaloids crepidatumines A (1) and B (2) together with the stereoisomer of dendrocrepidine B (3) and known analog dendrocrepine (4) were isolated from D. crepidatum. Their structures were determined by HR-ESI-MS, NMR, and Electronic Circular Dichroism (ECD) experiments together with comparison of analogues. Compound (1) possess a (5/6/6/5) tetra-hetero-cyclic ring, whereas compound (2) contains a tricyclic system with an unusual bridged ring, which are the first report in Nature. The biological evaluation revealed that dendrocrepine (4) displayed a potent hypoglycemic effect in vitro.
Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato
Authors: Sharma Bhaskar , Taganna Joemar 
Published: June 2020

AbstractE3 ubiquitin ligases are a central modifier of plant signaling pathways that act through targeting proteins to the degradation pathway. U-box E3 ubiquitin ligases are a distinct class of E3 ligases that utilize intramolecular interactions for its scaffold stabilization. U-box E3 ubiquitin ligases are prevalent in plants in comparison to animals. However, the evolutionary aspects, genetic organizations, and functional fate of the U-box E3 gene family in plant development, especially in tomato is not well understood. In the present study, we have performed in-silico genome-wide analysis of the U-box E3 ubiquitin ligase gene family in Solanum lycopersicum. We have identified 62 U-box genes with U-box/Ub Fusion Degradation 2 (UFD2) domain. The chromosomal localization, phylogenetic analysis, gene structure, motifs, gene duplication, syntenic regions, promoter, physicochemical properties, and ontology were investigated. The U-box gene family showed significant conservation of the U-box domain throughout the gene family. Duplicated genes discerned noticeable functional transitions among duplicated genes. The gene expression profiles of U-box E3 family members show involvement in abiotic and biotic stress signaling as well as hormonal pathways. We found remarkable participation of the U-box gene family in the vegetative and reproductive tissue development. It is predicted to be actively regulating flowering time and endosperm formation. Our study provides a comprehensive picture of distribution, structural features, promoter elements, evolutionary relationship, and gene expression of the U-box gene family in the tomato. We predict the crucial participation of the U-box gene family in tomato plant development and stress responses.
Effects of a high fat diet on gut microbiome dysbiosis in a mouse model of Gulf War Illness
Authors: Angoa-Pérez Mariana , Zagorac Branislava , Francescutti Dina M. , Winters Andrew D. , Greenberg Jonathan M. , Ahmad Madison M. , Manning Shannon D. , Gulbransen Brian D. , Theis Kevin R. , Kuhn Donald M. 
Published: June 2020

AbstractGulf War Illness (GWI) is a chronic health condition that appeared in Veterans after returning home from the Gulf War. The primary symptoms linked to deployment are posttraumatic stress disorder, mood disorders, GI problems and chronic fatigue. At first glance, these symptoms are difficult to ascribe to a single pathological mechanism. However, it is now clear that each symptom can be linked individually to alterations in the gut microbiome. The primary objective of the present study was to determine if gut microbiome dysbiosis was evident in a mouse model of GWl. Because the majority of Gulf War Veterans are overweight, a second objective was to determine if a high fat diet (HF) would alter GWI outcomes. We found that the taxonomic structure of the gut microbiome was significantly altered in the GWI model and after HF exposure. Their combined effects were significantly different from either treatment alone. Most treatment-induced changes occurred at the level of phylum in Firmicutes and Bacteroidetes. If mice fed HF were returned to a normal diet, the gut microbiome recovered toward normal levels in both controls and GWI agent-treated mice. These results add support to the hypotheses that dysbiosis in the gut microbiome plays a role in GWI and that life-style risk factors such as an unhealthy diet can accentuate the effects of GWI by impacting the gut microbiome. The reversibility of the effect of HF on the gut microbiome suggests new avenues for treating GWI through dietary intervention.
Met-Flow, a strategy for single-cell metabolic analysis highlights dynamic changes in immune subpopulations
Authors: Ahl Patricia J. , Hopkins Richard A. , Xiang Wen Wei , Au Bijin , Kaliaperumal Nivashini , Fairhurst Anna-Marie , Connolly John E. 
Published: June 2020

AbstractA complex interaction of anabolic and catabolic metabolism underpins the ability of leukocytes to mount an immune response. Their capacity to respond to changing environments by metabolic reprogramming is crucial to effector function. However, current methods lack the ability to interrogate this network of metabolic pathways at single-cell level within a heterogeneous population. We present Met-Flow, a flow cytometry-based method capturing the metabolic state of immune cells by targeting key proteins and rate-limiting enzymes across multiple pathways. We demonstrate the ability to simultaneously measure divergent metabolic profiles and dynamic remodeling in human peripheral blood mononuclear cells. Using Met-Flow, we discovered that glucose restriction and metabolic remodeling drive the expansion of an inflammatory central memory T cell subset. This method captures the complex metabolic state of any cell as it relates to phenotype and function, leading to a greater understanding of the role of metabolic heterogeneity in immune responses.
High-resolution mapping of injury-site dependent functional recovery in a single axon in zebrafish
Authors: Hecker Alexander , Anger Pamela , Braaker Philipp N. , Schulze Wolfram , Schuster Stefan 
Published: June 2020

AbstractIn non-mammalian vertebrates, some neurons can regenerate after spinal cord injury. One of these, the giant Mauthner (M-) neuron shows a uniquely direct link to a robust survival-critical escape behavior but appears to regenerate poorly. Here we use two-photon microscopy in parallel with behavioral assays in zebrafish to show that the M-axon can regenerate very rapidly and that the recovery of functionality lags by just days. However, we also find that the site of the injury is critical: While regeneration is poor both close and far from the soma, rapid regeneration and recovery of function occurs for injuries between 10% and 50% of total axon length. Our findings show that rapid regeneration and the recovery of function can be studied at remarkable temporal resolution after targeted injury of one single M-axon and that the decision between poor and rapid regeneration can be studied in this one axon.
Membrane protein mediated bilayer communication in networks of droplet interface bilayers
Authors: Haylock Stuart , Friddin Mark S. , Hindley James W. , Rodriguez Enrique , Charalambous Kalypso , Booth Paula J. , Barter Laura M. C. , Ces Oscar 
Published: June 2020

AbstractDroplet interface bilayers (DIBs) are model membranes formed between lipid monolayer-encased water droplets in oil. Compared to conventional methods, one of the most unique properties of DIBs is that they can be connected together to generate multi-layered ‘tissue-like’ networks, however introducing communication pathways between these compartments typically relies on water-soluble pores that are unable to gate. Here, we show that network connectivity can instead be achieved using a water-insoluble membrane protein by successfully reconstituting a chemically activatable mutant of the mechanosensitive channel MscL into a network of DIBs. Moreover, we also show how the small molecule activator can diffuse through an open channel and across the neighbouring droplet to activate MscL present in an adjacent bilayer. This demonstration of membrane protein mediated bilayer communication could prove key toward developing the next generation of responsive bilayer networks capable of defining information flow inside a minimal tissue.
Analogue of electromagnetically induced absorption in the microwave domain using stimulated Brillouin scattering
Authors: A. Siva Shakthi , Yelikar Anjali B. , Pant Ravi 
Published: June 2020

AbstractElectromagnetically induced transparency/absorption (EIT/EIA) tailor the amplitude and phase response of an absorption resonance to create large dispersion, which has been exploited for applications in slow- and fast-light, and quantum information science. Since EIA enhances (induces) absorption of an already existing absorption (transmission) profile, it leads to a significant reduction in output signal power. Induction of a narrow absorption feature within a gain resonance can compensate for the signal loss while creating large dispersion at the EIA feature frequency. However, the demonstration of an analogue of EIA exploiting gain resonances has remained elusive. Here, we exploit coherent interaction between the Brillouin gain resonances in orthogonal polarization states to demonstrate controlled excitation of an analogue of EIA over microwave frequency range of 2.5–43 GHz. We induce a narrow absorption feature (~6 MHz), with controllable depth and frequency, within Brillouin gain resonance, demonstrating a novel technique for microwave photonic processing.
Classification and biological identity of complex nano shapes
Authors: Boselli Luca , Lopez Hender , Zhang Wei , Cai Qi , Giannone Valeria A. , Li Jingji , Moura Alirio , de Araujo João M. , Cookman Jennifer , Castagnola Valentina , Yan Yan , Dawson Kenneth A. 
Published: June 2020

AbstractEverywhere in our surroundings we increasingly come in contact with nanostructures that have distinctive complex shape features on a scale comparable to the particle itself. Such shape ensembles can be made by modern nano-synthetic methods and many industrial processes. With the ever growing universe of nanoscale shapes, names such as “nanoflowers” and “nanostars” no longer precisely describe or characterise the distinct nature of the particles. Here we capture and digitise particle shape information on the relevant size scale and create a condensed representation in which the essential shape features can be captured, recognized and correlated. We find the natural emergence of intrinsic shape groups as well-defined ensemble distributions and show how these may be analyzed and interpreted to reveal novel aspects of our nanoscale shape environment. We show how these ideas may be applied to the interaction between the nanoscale-shape and the living universe and provide a conceptual framework for the study of nanoscale shape biological recognition and identity.
Crosstalk reduction between RF input channels of coherent‐driver‐modulator package by introducing enhanced ground lead structure
Authors: Ozaki J. , Tanobe H. , Ishikawa M. 
Published: June 2020

This Letter presents a novel RF ground lead structure for surface‐mount‐type optical modules that enables RF crosstalk reduction and bandwidth enhancements. Conventional RF lead‐pins of a surface‐mount‐type optical module have a bent shape that affects on RF ground stability and RF crosstalk between channels. The authors introduced an enhanced ground lead with an optimised shape for RF ground scheme enhancement. They prepared two types of high‐bandwidth coherent driver modulator packages for demonstrating RF performance difference, one with the conventional bent ground lead and the other with the optimum‐shaped ground lead. The measured results of the package with the enhanced ground lead successfully exhibited adjacent far‐end crosstalk reduction of about 5 dB at 50 GHz, and the crosstalk of −30 dB or less up to 58 GHz was confirmed. Moreover, they obtained the improvement in the insertion loss of 1 dB at 54 GHz and the 3‐dB electrical bandwidth enhancement of 2 GHz. These RF performances are sufficient for a high‐bandwidth coherent driver modulator package that allows 96‐GBd class operations.
Microfluidic devices for the generation of centimetre‐long motor nerve organoids derived from iPSCs
Authors: Kaneda Shohei , Kurihara Kohei , Suzuki Kenji , Takanobu Hideaki , Ohka Seii 
Published: June 2020

Although a microfluidic neuronal culture technique that utilised a microchannel structure to generate a motor nerve organoid consisted of neurospheres and fascicles of motor neuronal axons derived from human induced pluripotent stem cells (iPSCs) was reported recently, the lengths of the axonal fascicles were limited to less than 1 cm, which corresponded to the microchannel length. In this study, the authors fabricated microfluidic devices composed of a polydimethylsiloxane chip with a glass substrate and 20‐mm‐long and 150‐μm‐wide microchannels to obtain centimetre‐long axonal fascicles. They investigated the effects of microchannel height on fascicle length by using three different microchannel heights (120, 150, and 220 μm), neurospheres containing 80,000 motor neuronal cells derived from a human iPSCs cell line (409B2), and N2B27 medium. Maximum and average fascicle lengths of 2 and 1.25 cm, respectively, were successfully achieved with 150‐μm‐high microchannels. The fascicles grew in length, with an increase in the number of days spent in the culture (ranging from 0.44 to 0.60 mm per day), growing to over 1 cm around the 23rd day of culture. The difference in fascicle length obtained with 120‐μm and 150‐μm‐high microchannels suggests that height significantly affects the length of the axonal fascicle of the nerve organoid.
Planetary mass–radius relations across the galaxy
Authors: Michel A. , Haldemann J. , Mordasini C. , Alibert Y. 
Published: June 2020

Context. Planet formation theory suggests that planet bulk compositions are likely to reflect the chemical abundance ratios of their host star’s photosphere. Variations in the abundance of particular chemical species in stellar photospheres between different galactic stellar populations demonstrate that there are differences among the expected solid planet bulk compositions.
Aims. We aim to present planetary mass-radius relations of solid planets for kinematically differentiated stellar populations, namely, the thin disc, thick disc, and halo.
Methods. Using two separate internal structure models, we generated synthetic planets using bulk composition inputs derived from stellar abundances. We explored two scenarios, specifically iron-silicate planets at 0.1 AU and silicate-iron-water planets at 4 AU.
Results. We show that there is a persistent statistical difference in the expected mass-radius relations of solid planets among the different galactic stellar populations. At 0.1 AU for silicate-iron planets, there is a 1.51–2.04% mean planetary radius difference between the thick and thin disc stellar populations, whilst for silicate-iron-water planets past the ice line at 4 AU, we calculate a 2.93–3.26% difference depending on the models. Between the halo and thick disc, we retrieve at 0.1 AU a 0.53–0.69% mean planetary radius difference, and at 4 AU we find a 1.24–1.49% difference depending on the model.
Conclusions. Future telescopes (such as PLATO) will be able to precisely characterize solid exoplanets and demonstrate the possible existence of planetary mass-radius relationship variability between galactic stellar populations.