bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low sample volume origami-paper-based graphene-modified aptasensors for label-free electrochemical detection of cancer biomarker-EGFR
Authors: Wang Yang , Sun Shuai , Luo Jinping , Xiong Ying , Ming Tao , Liu Juntao , Ma Yuanyuan , Yan Shi , Yang Yue , Yang Zhugen , Reboud Julien , Yin Huabing , Cooper Jonathan M. , Cai Xinxia 
Published: May 2020

AbstractIn this work, an electrochemical paper-based aptasensor was fabricated for label-free and ultrasensitive detection of epidermal growth factor receptor (EGFR) by employing anti-EGFR aptamers as the bio-recognition element. The device used the concept of paper-folding, or origami, to serve as a valve between sample introduction and detection, so reducing sampling volumes and improving operation convenience. Amino-functionalized graphene (NH2-GO)/thionine (THI)/gold particle (AuNP) nanocomposites were used to modify the working electrode not only to generate the electrochemical signals, but also to provide an environment conducive to aptamer immobilization. Electrochemical characterization revealed that the formation of an insulating aptamer–antigen immunocomplex would hinder electron transfer from the sample medium to the working electrode, thus resulting in a lower signal. The experimental results showed that the proposed aptasensor exhibited a linear range from 0.05 to 200 ngmL−1 (R2 = 0.989) and a detection limit of 5 pgmL−1 for EGFR. The analytical reliability of the proposed paper-based aptasensor was further investigated by analyzing serum samples, showing good agreement with the gold-standard enzyme-linked immunosorbent assay.
A phylogenetically novel cyanobacterium most closely related to Gloeobacter
Authors: Grettenberger Christen L , Sumner Dawn Y , Wall Kate , Brown C Titus , Eisen Jonathan A , Mackey Tyler J , Hawes Ian , Jospin Guillaume , Jungblut Anne D 
Published: May 2020

Abstract
Clues to the evolutionary steps producing innovations in oxygenic photosynthesis may be preserved in the genomes of organisms phylogenetically placed between non-photosynthetic Vampirovibrionia (formerly Melainabacteria) and the thylakoid-containing Cyanobacteria. However, only two species with published genomes are known to occupy this phylogenetic space, both within the genus Gloeobacter. Here, we describe nearly complete, metagenome-assembled genomes (MAGs) of an uncultured organism phylogenetically placed near Gloeobacter, for which we propose the name Candidatus Aurora vandensis {Au’ro.ra. L. fem. n. aurora, the goddess of the dawn in Roman mythology; van.de’nsis. N.L. fem. adj. vandensis of Lake Vanda, Antarctica}. The MAG of A. vandensis contains homologs of most genes necessary for oxygenic photosynthesis including key reaction center proteins. Many accessory subunits associated with the photosystems in other species either are missing from the MAG or are poorly conserved. The MAG also lacks homologs of genes associated with the pigments phycocyanoerethrin, phycoeretherin and several structural parts of the phycobilisome. Additional characterization of this organism is expected to inform models of the evolution of oxygenic photosynthesis.
Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium
Authors: Tee H S , Waite D , Payne L , Middleditch M , Wood S , Handley K M 
Published: May 2020

Abstract
Freshwater cyanobacterial blooms have increased worldwide, channeling organic carbon into these systems, and threatening animal health through the production of cyanotoxins. Both toxic and nontoxic Microcoleus proliferations usually occur when there are moderate concentrations of dissolved inorganic nitrogen, but when phosphorus is scarce. In order to understand how Microcoleus establishes thick biofilms (or mats) on riverbeds under phosphorus-limiting conditions, we collected Microcoleus-dominated biofilms over a 19-day proliferation event for proteogenomics. A single pair of nitrogen-dependent Microcoleus species were consistently present in relatively high abundance, although each followed a unique metabolic trajectory. Neither possessed anatoxin gene clusters, and only very low concentrations of anatoxins (~2 µg kg−1) were detected, likely originating from rarer Microcoleus species also present. Proteome allocations were dominated by photosynthesizing cyanobacteria and diatoms, and data indicate biomass was actively recycled by Bacteroidetes and Myxococcales. Microcoleus likely acquired nutrients throughout the proliferation event by uptake of nitrate, urea, and inorganic and organic phosphorus. Both species also harbored genes that could be used for inorganic phosphate solubilization with pyrroloquinoline quinone cofactors produced by cohabiting Proteobacteria. Results indicate that Microcoleus are equipped with diverse mechanisms for nitrogen and phosphorus acquisition, enabling them to proliferate and out-compete others in low-phosphorus waters.
The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities
Authors: Krug Lisa , Erlacher Armin , Markut Katharina , Berg Gabriele , Cernava Tomislav 
Published: May 2020

Abstract
Mutualistic interactions within microbial assemblages provide a survival strategy under extreme conditions; however, little is known about the complexity of interaction networks in multipartite, free-living communities. In the present study, the interplay within algae-dominated microbial communities exposed to harsh environmental influences in the Austrian Alps was assessed in order to reveal the interconnectivity of eukaryotic and prokaryotic inhabitants. All analyzed snowfields harbored distinct microbial communities. Network analyses revealed that mutual exclusion prevailed among microalgae in the alpine environment, while bacteria were mainly positively embedded in the interaction networks. Especially members of Proteobacteria, with a high prevalence of Oxalobacteraceae, Pseudomonadaceae, and Sphingomonadaceae showed genus-specific co-occurrences with distinct microalgae. Co-cultivation experiments with algal and bacterial isolates confirmed beneficial interactions that were predicted based on the bioinformatic analyses; they resulted in up to 2.6-fold more biomass for the industrially relevant microalga Chlorella vulgaris, and up to 4.6-fold increase in biomass for the cryophilic Chloromonas typhlos. Our findings support the initial hypothesis that microbial communities exposed to adverse environmental conditions in alpine systems harbor inter-kingdom supportive capacities. The insights into mutualistic inter-kingdom interactions and the ecology of microalgae within complex microbial communities provide explanations for the prevalence and resilience of such assemblages in alpine environments.
Lake characteristics influence how methanogens in littoral sediments respond to terrestrial litter inputs
Authors: Yakimovich Kurt M , Orland Chloé , Emilson Erik J S , Tanentzap Andrew J , Basiliko Nathan , Mykytczuk Nadia C S 
Published: May 2020

Abstract
Shallow lake sediments harbor methanogen communities that are responsible for large amounts of CH4 flux to the atmosphere. These communities play a major role in degrading in-fluxed terrestrial organic matter (t-OM)—much of which settles in shallow near-shore sediments. Little work has examined how sediment methanogens are affected by the quantity and quality of t-OM, and the physicochemical factors that shape their community. Here, we filled mesocosms with artificial lake sediments amended with different ratios and concentrations of coniferous and deciduous tree litter. We installed them in three boreal lakes near Sudbury, Canada that varied in trophic status and water clarity. We found that higher endogenous nutrient concentrations led to greater CH4 production when sediment solar irradiance was similar, but high irradiance of sediments also led to higher CH4 concentrations regardless of nutrient concentrations, possibly due to photooxidation of t-OM. Sediments with t-OM had overall higher CH4 concentrations than controls that had no t-OM, but there were no significant differences in CH4 concentrations with different t-OM compositions or increasing concentrations over 25%. Differences among lakes also explained variation in methanogen community structure, whereas t-OM treatments did not. Therefore, lake characteristics are important modulators of methanogen communities fueled by t-OM.
EMQN best practice guidelines for genetic testing in dystrophinopathies
Authors: Fratter Carl , Dalgleish Raymond , Allen Stephanie K. , Santos Rosário , Abbs Stephen , Tuffery-Giraud Sylvie , Ferlini Alessandra 
Published: May 2020

AbstractDystrophinopathies are X-linked diseases, including Duchenne muscular dystrophy and Becker muscular dystrophy, due toDMDgene variants. In recent years, the application of new genetic technologies and the availability of new personalised drugs have influenced diagnostic genetic testing for dystrophinopathies. Therefore, these European best practice guidelines for genetic testing in dystrophinopathies have been produced to update previous guidelines published in 2010.These guidelines summarise current recommended technologies and methodologies for analysis of theDMDgene, including testing for deletions and duplications of one or more exons, small variant detection and RNA analysis. Genetic testing strategies for diagnosis, carrier testing and prenatal diagnosis (including non-invasive prenatal diagnosis) are then outlined. Guidelines for sequence variant annotation and interpretation are provided, followed by recommendations for reporting results of all categories of testing. Finally, atypical findings (such as non-contiguous deletions and dualDMDvariants), implications for personalised medicine and clinical trials and incidental findings (identification ofDMDgene variants in patients where a clinical diagnosis of dystrophinopathy has not been considered or suspected) are discussed.
Tatton-Brown-Rahman syndrome with a novel DNMT3A mutation presented severe intellectual disability and autism spectrum disorder
Authors: Yokoi Takayuki , Enomoto Yumi , Naruto Takuya , Kurosawa Kenji , Higurashi Norimichi 
Published: May 2020

AbstractTatton-Brown-Rahman syndrome is a congenital anomaly syndrome that manifests with overgrowth, macrocephaly, and characteristic facial features. This autosomal dominant disease is caused by a germline mutation in DNMT3A. Some patients with this syndrome develop mild to severe intellectual disability, which is sometimes accompanied by autism spectrum disorder or other developmental disorders. We report a Japanese patient with severe intellectual disability and autism spectrum disorder with a de novo mutation in the active domain of DNMT3A.
Dose-dependent skeletal deficits due to varied reductions in mechanical loading in rats
Authors: Ko Frank C. , Mortreux Marie , Riveros Daniela , Nagy Janice A. , Rutkove Seward B. , Bouxsein Mary L. 
Published: May 2020

AbstractReduced skeletal loading leads to marked bone loss. Animal models of hindlimb suspension are widely used to assess alterations in skeleton during the course of complete unloading. More recently, the effects of partial unloading on the musculoskeletal system have been interrogated in mice and rats, revealing dose-dependent effects of partial weight bearing (PWB) on the skeleton and skeletal muscle. Here, we extended these studies to determine the structural and functional skeletal alterations in 14-week-old male Wister rats exposed to 20%, 40%, 70%, or 100% of body weight for 1, 2, or 4 weeks (n = 11–12/group). Using in vivo pQCT, we found that trabecular bone density at the proximal tibia declined in proportion to the degree of unloading and continued progressively with time, without evidence of a plateau by 4 weeks. Ex vivo measurements of trabecular microarchitecture in the distal femur by microcomputed tomography revealed deficits in bone volume fraction, 2 and 4 weeks after unloading. Histologic analyses of trabecular bone in the distal femur revealed the decreased osteoblast number and mineralizing surface in unloaded rats. Three-point bending of the femoral diaphysis indicated modest or no reductions in femoral stiffness and estimated modulus due to PWB. Our results suggest that this rat model of PWB leads to trabecular bone deterioration that is progressive and generally proportional to the degree of PWB, with minimal effects on cortical bone.
New GMP manufacturing processes to obtain thermostable HIV-1 gp41 virosomes under solid forms for various mucosal vaccination routes
Authors: Amacker Mario , Smardon Charli , Mason Laura , Sorrell Jack , Jeffery Kirk , Adler Michael , Bhoelan Farien , Belova Olga , Spengler Mark , Punnamoottil Beena , Schwaller Markus , Bonduelle Olivia , Combadière Behazine , Stegmann Toon , Naylor Andrew , Johnson Richard , Wong Desmond , Fleury Sylvain 
Published: May 2020

AbstractThe main objective of the MACIVIVA European consortium was to develop new Good Manufacturing Practice pilot lines for manufacturing thermostable vaccines with stabilized antigens on influenza virosomes as enveloped virus-like particles. The HIV-1 gp41-derived antigens anchored in the virosome membrane, along with the adjuvant 3M-052 (TLR7/8 agonist) on the same particle, served as a candidate vaccine for the proof of concept for establishing manufacturing processes, which can be directly applied or adapted to other virosomal vaccines or lipid-based particles. Heat spray-dried powders suitable for nasal or oral delivery, and freeze-dried sublingual tablets were successfully developed as solid dosage forms for mucosal vaccination. The antigenic properties of vaccinal antigens with key gp41 epitopes were maintained, preserving the original immunogenicity of the starting liquid form, and also when solid forms were exposed to high temperature (40 °C) for up to 3 months, with minimal antigen and adjuvant content variation. Virosomes reconstituted from the powder forms remained as free particles with similar size, virosome uptake by antigen-presenting cells in vitro was comparable to virosomes from the liquid form, and the presence of excipients specific to each solid form did not prevent virosome transport to the draining lymph nodes of immunized mice. Virosome integrity was also preserved during exposure to <−15 °C, mimicking accidental freezing conditions. These “ready to use and all-in-one” thermostable needle-free virosomal HIV-1 mucosal vaccines offer the advantage of simplified logistics with a lower dependence on the cold chain during shipments and distribution.
Dissociating the white matter tracts connecting the temporo-parietal cortical region with frontal cortex using diffusion tractography
Authors: Barbeau Elise B. , Descoteaux Maxime , Petrides Michael 
Published: May 2020

AbstractThree major white matter pathways connect the posterior temporal region and the adjacent inferior parietal lobule with the lateral frontal cortex: the arcuate fasciculus (AF), and the second and third branches of the superior longitudinal fasciculus (SLF II and SLF III). These pathways are found also in nonhuman primate brains where they play specific roles in auditory and spatial processing. The precise origin, course, and termination of these pathways has been examined in invasive tract tracing studies in macaque monkeys. Here we use this prior knowledge to improve dissections of these pathways in vivo in the human brain using diffusion Magnetic Resonance Imaging (MRI) tractography. In this study, the AF, originating from the posterior temporal cortex, has been successfully separated from the SLF II and SLF III tracts originating from the angular and supramarginal gyri of the inferior parietal lobule, respectively. The latter two pathways, i.e. SLF II and SLF III, have also been clearly separated from each other. Furthermore, we report for the first time in the human brain the dorsal branch of the AF that targets the posterior dorsolateral frontal region. These improved dissection protocols provide a solid basis for exploring the respective functional roles of these major fasciculi.
Rabies Vaccine Characterization by Nanoparticle Tracking Analysis
Authors: Navarro Sanchez M. E. , Soulet D. , Bonnet E. , Guinchard F. , Marco S. , Vetter E. , Nougarede N. 
Published: May 2020

AbstractThere are concerns that effectiveness and consistency of biopharmaceutical formulations, including vaccines, may be compromised by differences in size, concentration and shape of particles in suspension. Thus, a simple method that can help monitor and characterize these features is needed. Here, nanoparticle tracking analysis (NTA) was used to characterize particle concentration and size distribution of a highly-purified rabies vaccine (RABV), produced in Vero cells without raw materials of animal origin (RMAO). The NTA technique was qualified for characterization of RABV particles by assessing the stability profile of vaccine particles over 5–55 °C. Antigenicity of the viral particle was also monitored with the enzyme-linked immunosorbent assay (ELISA) and NTA. RABV particle size diameters were 100–250 nm (mean:150 nm), similar to sizes obtained when labelled with rabies anti-G D1–25 monoclonal antibody, suggesting mainly antigenic virus-like particles, also confirmed by transmission electron microscopy. Thermal stress at 55 °C decreased the concentration of anti-G D1–25-labelled particles from 144 hours, coherent with conformational changes leading to loss of G protein antigenicity without impacting aggregation. Results from RABV antigenicity assessment during the 24 months monitoring of stability showed good correlation between NTA and ELISA. NTA is a suitable approach for the characterization of biopharmaceutical suspensions.
Nanostructural Diversity of Synapses in the Mammalian Spinal Cord
Authors: Broadhead Matthew J. , Bonthron Calum , Arcinas Lauren , Bez Sumi , Zhu Fei , Goff Frances , Nylk Jonathan , Dholakia Kishan , Gunn-Moore Frank , Grant Seth G. N. , Miles Gareth B. 
Published: May 2020

AbstractFunctionally distinct synapses exhibit diverse and complex organisation at molecular and nanoscale levels. Synaptic diversity may be dependent on developmental stage, anatomical locus and the neural circuit within which synapses reside. Furthermore, astrocytes, which align with pre and post-synaptic structures to form ‘tripartite synapses’, can modulate neural circuits and impact on synaptic organisation. In this study, we aimed to determine which factors impact the diversity of excitatory synapses throughout the lumbar spinal cord. We used PSD95-eGFP mice, to visualise excitatory postsynaptic densities (PSDs) using high-resolution and super-resolution microscopy. We reveal a detailed and quantitative map of the features of excitatory synapses in the lumbar spinal cord, detailing synaptic diversity that is dependent on developmental stage, anatomical region and whether associated with VGLUT1 or VGLUT2 terminals. We report that PSDs are nanostructurally distinct between spinal laminae and across age groups. PSDs receiving VGLUT1 inputs also show enhanced nanostructural complexity compared with those receiving VGLUT2 inputs, suggesting pathway-specific diversity. Finally, we show that PSDs exhibit greater nanostructural complexity when part of tripartite synapses, and we provide evidence that astrocytic activation enhances PSD95 expression. Taken together, these results provide novel insights into the regulation and diversification of synapses across functionally distinct spinal regions and advance our general understanding of the ‘rules’ governing synaptic nanostructural organisation.
RIFTA: A Robust Iterative Fourier Transform-based dwell time Algorithm for ultra-precision ion beam figuring of synchrotron mirrors
Authors: Wang Tianyi , Huang Lei , Kang Hyukmo , Choi Heejoo , Kim Dae Wook , Tayabaly Kashmira , Idir Mourad 
Published: May 2020

AbstractWith the rapid evolution of synchrotron X-ray sources, the demand for high-precision X-ray mirrors has greatly increased. Single nanometer profile error is required to keep imaging capability at the diffraction limit. Ion Beam Figuring (IBF), as a highly deterministic surfacing technique, has been used for ultra-precision finishing of mirrors. One crucial step that guides the IBF process is dwell time calculation. A valid dwell time solution should be non-negative and duplicate the shape of the desired removal map. Another important aspect is to minimize the total dwell time. In this study, we propose a Robust Iterative Fourier Transform-based dwell time Algorithm (RIFTA) that automatically fulfills these requirements. First, the thresholded inverse filtering in Fourier transform-based deconvolution is stabilized and automated by optimizing the threshold value using the Nelder-Mead simplex algorithm. Second, a novel two-level iterative scheme is proposed to guarantee the minimized total dwell time with its non-negativity at each dwell point. Third, a bicubic resampling is employed to flexibly adapt the calculated dwell time map to any IBF process intervals. The performance of RIFTA is first studied with simulation, followed by a comparison with the other state-of-the-art dwell time algorithms. We then demonstrate with an experiment that, using the dwell time calculated by the RIFTA, the total dwell time is shortened by a factor of two and the RMS in a 5 × 50 mm clear aperture was reduced from 3.4 nm to 1.1 nm after one IBF run, which proves the effectiveness and the efficiency of the proposed algorithm.
Determination of the optimal location for constructing solar photovoltaic farms based on multi-criteria decision system and Dempster–Shafer theory
Authors: Mokarram Marzieh , Mokarram Mohammad J. , Khosravi Mohammad R. , Saber Ali , Rahideh Akbar 
Published: May 2020

AbstractConsidering environmental concerns regarding air pollution which is induced by burning fossil fuels to generate electrical power, utilizing solar energy as a green and sustainable energy source is of great interest. This study proposes a novel framework to determine the optimal location for constructing solar photovoltaic (PV) farms. To locate the suitable areas for PV farms, firstly, a fuzzy-based method is utilized to homogenize the input parameters, thereafter, the analytical hierarchy process (AHP) and Dempster-Shafer (DS) methods are independently used. In the AHP method, the proper weight for each input parameter is generated utilizing a pairwise comparison matrix. However, the DS method identifies output in different confident levels. Finally, southeast of Fars province in Iran as a region with high sunny hours in the year is selected, and the applicability of proposed methods is examined. The results show that 32% of the case study is located at high and good suitability classes in the fuzzy_AHP method. However, it is 18.56%, 16.70%, 16.32% according to 95%, 99% and 99.5% confident levels in the fuzzy_DS method, respectively. Comparisons of the fuzzy_AHP and fuzzy_DS methods at 20 points with various solar radiation intensities and the number of dusty days parameters indicate that the fuzzy_DS method can more reliably determine the optimal PV farm locations. Additionally, as the fuzzy_DS method determines the optimal locations with different confident levels, this method can benefit decision-makers to determine the risks associated with selecting a specific site for constructing solar PV farms.