bluuebunny/crossref_metadata_2025_split huggingface dataset:
Core functional nodes and sex-specific pathways in human ischaemic and dilated cardiomyopathy
Authors: Li Mengbo , Parker Benjamin L. , Pearson Evangeline , Hunter Benjamin , Cao Jacob , Koay Yen Chin , Guneratne Oneka , James David E. , Yang Jean , Lal Sean , O’Sullivan John F. 
Published: June 2020

AbstractPoor access to human left ventricular myocardium is a significant limitation in the study of heart failure (HF). Here, we utilise a carefully procured large human heart biobank of cryopreserved left ventricular myocardium to obtain direct molecular insights into ischaemic cardiomyopathy (ICM) and dilated cardiomyopathy (DCM), the most common causes of HF worldwide. We perform unbiased, deep proteomic and metabolomic analyses of 51 left ventricular (LV) samples from 44 cryopreserved human ICM and DCM hearts, compared to age-, gender-, and BMI-matched, histopathologically normal, donor controls. We report a dramatic reduction in serum amyloid A1 protein in ICM hearts, perturbed thyroid hormone signalling pathways and significant reductions in oxidoreductase co-factor riboflavin-5-monophosphate and glycolytic intermediate fructose-6-phosphate in both; unveil gender-specific changes in HF, including nitric oxide-related arginine metabolism, mitochondrial substrates, and X chromosome-linked protein and metabolite changes; and provide an interactive online application as a publicly-available resource.
Modeling mitigation of influenza epidemics by baloxavir
Authors: Du Zhanwei , Nugent Ciara , Galvani Alison P. , Krug Robert M. , Meyers Lauren Ancel 
Published: June 2020

AbstractInfluenza viruses annually kill 290,000–650,000 people worldwide. Antivirals can reduce death tolls. Baloxavir, the recently approved influenza antiviral, inhibits initiation of viral mRNA synthesis, whereas oseltamivir, an older drug, inhibits release of virus progeny. Baloxavir blocks virus replication more rapidly and completely than oseltamivir, reducing the duration of infectiousness. Hence, early baloxavir treatment may indirectly prevent transmission. Here, we estimate impacts of ramping up and accelerating baloxavir treatment on population-level incidence using a new model that links viral load dynamics from clinical trial data to between-host transmission. We estimate that ~22 million infections and >6,000 deaths would have been averted in the 2017–2018 epidemic season by administering baloxavir to 30% of infected cases within 48 h after symptom onset. Treatment within 24 h would almost double the impact. Consequently, scaling up early baloxavir treatment would substantially reduce influenza morbidity and mortality every year. The development of antivirals against the SARS-CoV2 virus that function like baloxavir might similarly curtail transmission and save lives.
Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition
Authors: Stopfer Lauren E. , Mesfin Joshua M. , Joughin Brian A. , Lauffenburger Douglas A. , White Forest M. 
Published: June 2020

AbstractPeptides bound to class I major histocompatibility complexes (MHC) play a critical role in immune cell recognition and can trigger an antitumor immune response in cancer. Surface MHC levels can be modulated by anticancer agents, altering immunity. However, understanding the peptide repertoire’s response to treatment remains challenging and is limited by quantitative mass spectrometry-based strategies lacking normalization controls. We describe an experimental platform that leverages recombinant heavy isotope-coded peptide MHCs (hipMHCs) and multiplex isotope tagging to quantify peptide repertoire alterations using low sample input. HipMHCs improve quantitative accuracy of peptide repertoire changes by normalizing for variation across analyses and enable absolute quantification using internal calibrants to determine copies per cell of MHC antigens, which can inform immunotherapy design. Applying this platform in melanoma cell lines to profile the immunopeptidome response to CDK4/6 inhibition and interferon-γ — known modulators of antigen presentation — uncovers treatment-specific alterations, connecting the intracellular response to extracellular immune presentation.
Durable and controlled depletion of neutrophils in mice
Authors: Boivin Gael , Faget Julien , Ancey Pierre-Benoit , Gkasti Aspasia , Mussard Julie , Engblom Camilla , Pfirschke Christina , Contat Caroline , Pascual Justine , Vazquez Jessica , Bendriss-Vermare Nathalie , Caux Christophe , Vozenin Marie-Catherine , Pittet Mikael J. , Gunzer Matthias , Meylan Etienne 
Published: June 2020

AbstractNeutrophils are an essential part of the innate immune system. To study their importance, experimental studies often aim to deplete these cells, generally by injecting anti-Ly6G or anti-Gr1 antibodies. However, these approaches are only partially effective, transient or lack specificity. Here we report that neutrophils remaining after anti-Ly6G treatment are newly derived from the bone marrow, instead of depletion escapees. Mechanistically, newly generated, circulating neutrophils have lower Ly6G membrane expression, and consequently reduced targets for anti-Ly6G-mediated depletion. To overcome this limitation, we develop a double antibody-based depletion strategy that enhances neutrophil elimination by anti-Ly6G treatment. This approach achieves specific, durable and controlled reduction of neutrophils in vivo, and may be suitable for studying neutrophil function in experimental models.
Stable isotopes show that earthquakes enhance permeability and release water from mountains
Authors: Hosono Takahiro , Yamada Chisato , Manga Michael , Wang Chi-Yuen , Tanimizu Masaharu 
Published: June 2020

AbstractHydrogeological properties can change in response to large crustal earthquakes. In particular, permeability can increase leading to coseismic changes in groundwater level and flow. These processes, however, have not been well-characterized at regional scales because of the lack of datasets to describe water provenances before and after earthquakes. Here we use a large data set of water stable isotope ratios (n = 1150) to show that newly formed rupture systems crosscut surrounding mountain aquifers, leading to water release that causes groundwater levels to rise (~11 m) in down-gradient aquifers after the 2016 Mw 7.0 Kumamoto earthquake. Neither vertical infiltration of soil water nor the upwelling of deep fluids was the major cause of the observed water level rise. As the Kumamoto setting is representative of volcanic aquifer systems at convergent margins where seismotectonic activity is common, our observations and proposed model should apply more broadly.
A new viewpoint on antlers reveals the evolutionary history of deer (Cervidae, Mammalia)
Authors: Samejima Yuusuke , Matsuoka Hiroshige 
Published: June 2020

AbstractRecent molecular phylogeny of deer revealed that the characters of antlers previously focused on are homoplasious, and antlers tend to be considered problematic for classification. However, we think antlers are important tools and reconsidered and analysed the characters and structures to use them for classification. This study developed a method to describe the branching structure of antlers by using antler grooves, which are formed on the antlers by growth, and then projecting the position of the branching directions of tines on the burr circumference. By making diagrams, comparing the branching structure interspecifically, homologous elements (tines, beams, and processes) of the antlers of 25 species of 16 genera were determined. Subsequently, ancestral state reconstruction was performed on the fixed molecular phylogenetic tree. It was revealed that Capreolinae and Cervini gained respective three-pointed antlers independently, and their subclades gained synapomorphous tines. We found new homologous and synapomorphous characters, as the antler of Eld’s deer, which has been classified in Rucervus, is structurally close to that of Elaphurus rather than that of Rucervus, consistent with molecular phylogeny. The methods of this study will contribute to the understanding of the branching structure and phylogeny of fossil species and uncover the evolutionary history of Cervidae.
When Lone Wolf Defectors Undermine the Power of the Opt-Out Default
Authors: Ferguson Eamonn , Shichman Ruslan , Tan Jonathan H. W. 
Published: June 2020

AbstractHigh levels of cooperation are a central feature of human society, and conditional cooperation has been proposed as one proximal mechanism to support this. The counterforce of free-riding can, however, undermine cooperation and as such a number of external mechanisms have been proposed to ameliorate the effects of free-riding. One such mechanism is setting cooperation as the default (i.e., an opt-out default). We posit, however, that in dynamic settings where people can observe and condition their actions on others’ behaviour, ‘lone wolf’ defectors undermine initial cooperation encouraged by an opt-out default, while ‘good shepherds’ defeat the free-riding encouraged by an opt-in default. Thus, we examine the dynamic emergence of conditional cooperation under different default settings. Specifically, we develop a game theoretical model to analyse cooperation under defaults for cooperation (opt-out) and defection (opt-in). The model predicts that the ‘lone wolf’ effect is stronger than the ‘good shepherd’ effect, which – if anticipated by players – should strategically deter free-riding under opt-out and cooperation under opt-in. Our experimental games confirm the existence of both ‘lone wolf’ defectors and ‘good shepherd’ cooperators, and that the ‘lone wolf’effect is stronger in the context of organ donation registration behaviour. We thus show a potential ‘dark side’ to conditional cooperation (‘lone wolf effect’) and draw implications for the adoption of an opt-out organ donation policy.
Constitutive expression of Asparaginase in Gossypium hirsutum triggers insecticidal activity against Bemisia tabaci
Authors: Gul Ambreen , Hussain Ghulam , Iqbal Adnan , Rao Abdul Qayyum , Din Salah ud , Yasmeen Aneela , Shahid Naila , Ahad Ammara , Latif Ayesha , Azam Saira , Samiullah Tahir Rehman , Hassan Samina , Shahid Ahmad Ali , Husnain Tayyab 
Published: June 2020

AbstractWhitefly infestation of cotton crop imparts enormous damage to cotton yield by severely affecting plant health, vigour and transmittingCottonLeafCurlVirus (CLCuV). Genetic modification of cotton helps to overcome both the direct whitefly infestation as well as CLCuV based cotton yield losses. We have constitutively overexpressed asparaginase (ZmASN) gene inGossypium hirsutumto overcome the cotton yield losses imparted by whitefly infestation. We achieved 2.54% transformation efficiency in CIM-482 byAgrobacterium-mediated shoot apex transformation method. The relative qRT-PCR revealed 40-fold higher transcripts ofasparaginasein transgenic cotton line vs. non-transgenic cotton lines. Metabolic analysis showed higher contents of aspartic acid and glutamic acid in seeds and phloem sap of the transgenic cotton lines. Phenotypically, the transgenic cotton lines showed vigorous growth and height, greater number of bolls, and yield. Among six representative transgenic cotton lines, line 14 had higher photosynthetic rate, stomatal conductance, smooth fiber surface, increased fiber convolutions (SEM analysis) and 95% whitefly mortality as compared to non-transgenic cotton line. The gene integration analysis by fluorescencein situhybridization showed single copy gene integration at chromosome number 1. Collectively, asparaginase gene demonstrated potential to control whitefly infestation, post-infestation damages and improve cotton plant health and yield: a pre-requisite for farmer’s community.
Pyramidal core-shell quantum dot under applied electric and magnetic fields
Authors: Osorio J. A. , Caicedo-Paredes D. , Vinasco J. A. , Morales A. L. , Radu A. , Restrepo R. L. , Martínez-Orozco J. C. , Tiutiunnyk A. , Laroze D. , Hieu Nguyen N. , Phuc Huynh V. , Mora-Ramos M. E. , Duque C. A. 
Published: June 2020

AbstractWe have theoretically investigated the electronic states in a core/shell pyramidal quantum dot with GaAs core embedded in AlGaAs matrix. This system has a quite similar recent experimental realization through a cone/shell structure [Phys. Status Solidi-RRL 13, 1800245 (2018)]. The research has been performed within the effective mass approximation taking into account position-dependent effective masses and the presence of external electric and magnetic fields. For the numerical solution of the resulting three-dimensional partial differential equation we have used a finite element method. A detailed study of the conduction band states wave functions and their associated energy levels is presented, with the analysis of the effect of the geometry and the external probes. The calculation of the non-permanent electric polarization via the off-diagonal intraband dipole moment matrix elements allows to consider the related optical response by evaluating the coefficients of light absorption and relative refractive index changes, under different applied magnetic field configurations.
Ultrafast reprogrammable multifunctional vanadium-dioxide-assisted metasurface for dynamic THz wavefront engineering
Authors: Shabanpour Javad , Beyraghi Sina , Cheldavi Ahmad 
Published: June 2020

AbstractIn this paper, for the first time, a new generation of ultrafast reprogrammable multi-mission bias encoded metasurface is proposed for dynamic terahertz wavefront engineering by employing VO2 reversible and fast monoclinic to tetragonal phase transition. The multi-functionality of our designed VO2 based coding metasurface (VBCM) was guaranteed by elaborately designed meta-atom comprising three-patterned VO2 thin films whose operational statuses can be dynamically tuned among four states of “00”-“11” by merely changing the biasing voltage controlled by an external Field-programmable gate array platform. Capitalizing on such meta-atom design and by driving VBCM with different spiral-like and spiral-parabola-like coding sequences, single vortex beam and focused vortex beam with interchangeable orbital angular momentum modes were satisfactorily generated respectively. Additionally, by adopting superposition theorem and convolution operation, symmetric/asymmetric multiple beams and arbitrarily-oriented multiple vortex beams in pre-demined directions with different topological charges are realized. Several illustrative examples successfully have clarified that the proposed VBCM is a promising candidate for solving crucial terahertz challenges such as high data rate wireless communication where ultrafast switching between several missions is required.
Evaluation of antibiotic resistance dissemination by wastewater treatment plant effluents with different catchment areas in Germany
Authors: Alexander Johannes , Hembach Norman , Schwartz Thomas 
Published: June 2020

AbstractThe study quantified the abundances of antibiotic resistance genes (ARGs) and facultative pathogenic bacteria (FPB) as well as one mobile genetic element in genomic DNA via qPCR from 23 different wastewater treatment plant (WWTP) effluents in Germany. 12 clinically relevant ARGs were categorized into frequently, intermediately, and rarely occurring genetic parameters of communal wastewaters. Taxonomic PCR quantifications of five FPB targeting Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Acinetobacter baumannii, and enterococci were performed. The WWTPs differed in their catchment areas being impacted by hospitals, food processing companies, or housing areas only. The total discharges of the analyzed ARGs and FPB were found to cluster independently of the sizes of the WWTPs with a maximum difference of two log units within one cluster. Initially, quantitative data evaluations revealed no significant difference between ARG categories and WWTP catchment areas. More distinct correlations became obvious with a Pearson correlation approach, where each single taxonomic marker is compared to each ARG target. Here, increased correlation of FPB (i.e. E. coli, K. pneumoniae, P. aeruginosa, and enterococci) with clinically relevant ARGs of the category of rarely occurring resistance genes (blaNDM-1, vanA) was found in WWTP effluents being influenced by hospital wastewaters.
Genomic analyses of early responses to radiation in glioblastoma reveal new alterations at transcription, splicing, and translation levels
Authors: Choudhary Saket , Burns Suzanne C. , Mirsafian Hoda , Li Wenzheng , Vo Dat T. , Qiao Mei , Lei Xiufen , Smith Andrew D. , Penalva Luiz O. 
Published: June 2020

AbstractHigh-dose radiation is the main component of glioblastoma therapy. Unfortunately, radio-resistance is a common problem and a major contributor to tumor relapse. Understanding the molecular mechanisms driving response to radiation is critical for identifying regulatory routes that could be targeted to improve treatment response. We conducted an integrated analysis in the U251 and U343 glioblastoma cell lines to map early alterations in the expression of genes at three levels: transcription, splicing, and translation in response to ionizing radiation. Changes at the transcriptional level were the most prevalent response. Downregulated genes are strongly associated with cell cycle and DNA replication and linked to a coordinated module of expression. Alterations in this group are likely driven by decreased expression of the transcription factor FOXM1 and members of the E2F family. Genes involved in RNA regulatory mechanisms were affected at the mRNA, splicing, and translation levels, highlighting their importance in radiation-response. We identified a number of oncogenic factors, with an increased expression upon radiation exposure, including BCL6, RRM2B, IDO1, FTH1, APIP, and LRIG2 and lncRNAs NEAT1 and FTX. Several of these targets have been previously implicated in radio-resistance. Therefore, antagonizing their effects post-radiation could increase therapeutic efficacy. Our integrated analysis provides a comprehensive view of early response to radiation in glioblastoma. We identify new biological processes involved in altered expression of various oncogenic factors and suggest new target options to increase radiation sensitivity and prevent relapse.
In vivo assessment of foveal geometry and cone photoreceptor density and spacing in children
Authors: Mirhajianmoghadam Hanieh , Jnawali Ashutosh , Musial Gwen , Queener Hope M. , Patel Nimesh B. , Ostrin Lisa A. , Porter Jason 
Published: June 2020

AbstractThe fovea undergoes significant developmental changes from birth into adolescence. However, there is limited data examining cone photoreceptor density, foveal pit shape, and foveal avascular zone (FAZ) size in children. The purpose of this study was to determine whether overall foveal structure differs as a function of age and refractive status in children. Forty-eight healthy children (ages 5.8 to 15.8 years) underwent optical coherence tomography imaging to quantify foveal point thickness and foveal pit diameter, depth, and slope. Adaptive optics scanning laser ophthalmoscope (AOSLO) images of foveal capillaries and cone photoreceptors were acquired in a subset of children to quantify FAZ metrics and cone densities at 0.2, 0.3, and 0.5 mm eccentricities. Results show that foveal pit and FAZ metrics were not related to age, axial length, or refractive status. However, linear cone density was lower in myopic versus non-myopic children at eccentricities of 0.2 mm (mean ± SD = 50,022 ± 5,878 cones/mm2vs 58,989 ± 4,822 cones/mm2,P < 0.001) and 0.3 mm (43,944 ± 5,547 cones/mm2vs 48,622 ± 3,538 cones/mm2,P < 0.001). These results suggest FAZ and foveal pit metrics do not systematically differ with age in children, while myopic eyes have decreased linear cone density near the foveal center.Significance Statement:The development of the fovea begins prior to birth and continues through the early teenage years until it reaches adult-like properties. Although the majority of changes during childhood are related to the maturation and migration of cone photoreceptors,in vivodata describing cone packing in children is limited. We assessed overall foveal structure in children as young as 5.8 years old by quantifying cone density and spacing, foveal avascular zone size, and foveal pit morphometry to investigate potential structural differences as a function of age and refractive status. While foveal avascular zone and foveal pit metrics did not significantly differ with age, results indicate that myopic children have lower linear cone densities close to the foveal center compared to non-myopic children.
Comparative transcriptomics of an arctic foundation species, tussock cottongrass (Eriophorum vaginatum), during an extreme heat event
Authors: Mohl Jonathon E. , Fetcher Ned , Stunz Elizabeth , Tang Jianwu , Moody Michael L. 
Published: June 2020

AbstractTussock cottongrass (Eriophorum vaginatum) is a foundation species for much of the arctic moist acidic tundra, which is currently experiencing extreme effects of climate change. The Arctic is facing higher summer temperatures and extreme weather events are becoming more common. We used Illumina RNA-Seq to analyse cDNA libraries for differential expression of genes from leaves of ecologically well-characterized ecotypes of tussock cottongrass found along a latitudinal gradient in the Alaskan Arctic and transplanted into a common garden. Plant sampling was performed on a typical summer day and during an extreme heat event. We obtained ade novoassembly that contained 423,353 unigenes. There were 363 unigenes up-regulated and 1,117 down-regulated among all ecotypes examined during the extreme heat event. Of these, 26 HSP unigenes had >log2-fold up-regulation. Several TFs associated with heat stress in previous studies were identified that had >log2-fold up- or down-regulation during the extreme heat event (e.g., DREB, NAC). There was consistent variation in DEGs among ecotypes, but not specifically related to whether plants originated from taiga or tundra ecosystems. As the climate changes it is essential to determine ecotypic diversity at the genomic level, especially for widespread species that impact ecosystem function.
Optimization of rGO-PEI/Naph-SH/AgNWs/Frt/GOx nanocomposite anode for biofuel cell applications
Authors: Inamuddin  , Shakeel Nimra 
Published: June 2020

AbstractThe present study reports a new nanocomposite design using surface modified silver nanowires decorated on the surface of polyethyleneimine (PEI), a cationic polymer acting as glue for anchoring nanowires and reduced graphene oxide (rGO). The synthesized nanocomposite was employed as a promising electrode material for immobilization of biomolecules and effective transportation of electron, in enzymatic biofuel cell (EBFCs) application. The synthesized nanocomposite was confirmed by analytical techniques, for instance, Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), transmission electron microscopy (TEM). The electrochemical behaviour of the nanobioelectrocatalysts rGO-PEI/Frt/GOx, rGO-PEI/AgNWs/Frt/GOx, and rGO-PEI/Naph-SH/AgNWs/Frt/GOx was determined by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and linear sweep voltammetry (LSV). The maximum current density obtained by the modified bioanode was found to be 19.9 mA cm−2 at the limiting glucose concentration of 50 mM in PBS (pH 7.0) as supporting electrolyte at a scan rate of 100 mVs−1.