bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pocket MUSE: an affordable, versatile and high performance fluorescence microscope using a smartphone
Authors: Liu Yehe , Rollins Andrew M. , Levenson Richard M. , Fereidouni Farzad , Jenkins Michael W. 
Published: September 2020

AbstractSmartphone microscopes can be effective tools for a broad range of imaging applications. In this manuscript, we demonstrate the first practical implementation of Microscopy with Ultraviolet Surface Excitation (MUSE) in a compact smartphone microscope called Pocket MUSE, resulting in a remarkably effective design. Fabricated with parts from consumer electronics that are readily available at low cost, the small optical module attaches directly over the rear lens in a smartphone and enables high quality multichannel fluorescence microscopy with submicron resolution over a 10X equivalent field of view. In addition to the novel optical configuration, Pocket MUSE is compatible with a series of simple, portable and user-friendly sample preparation strategies that can be directly implemented for various microscopy applications for point-of-care diagnostics, at-home health monitoring, plant biology, STEM education, environmental studies, etc.
Clinical Feasibility and Preliminary Outcomes of a Novel Mixed Reality Based System to Manage Phantom Pain for Patients with Lower Limb Amputation.: A Pilot Study
Authors: Annaswamy M. , Bahirat Kanchan , Raval Gargi , Chung Yu Yen , Prabhakaran Balakrishnan 
Published: September 2020

AbstractObjectiveThis report describes the details of Mr. MAPP, a virtual mirror therapy system and the results of a clinical feasibility and evaluation study of a pilot sample of patients with history of lower limb amputation and phantom limb pain.Materials and MethodsMr. MAPP system uses a Kinect V2 RGB-D camera to capture the patient, generates a live interactive 3D model, and incorporates it into a virtual exergame. Mr. MAPP mirrors their preserved limb and allows participants to visualize their amputated limb virtually and perform their prescribed exercise program. Mr. MAPP creates a digital diary of their therapy sessions by recording game performance and errors. Ten consecutive patients with history of limb loss and phantom pain were targeted for this pilot study. They received a Mr. MAPP system and a laptop for home use for 1-month. Outcome measures including pain intensity and pain interference measured on Numerical Rating Scale (NRS) and McGill Pain Questionnaire (MPQ) as well as functional outcomes measured on Patient Specific Functional Scale (PSFS) were obtained at baseline, and after 1-month.ResultsSeven participants were enrolled, out of which four completed the study. The study was temporarily suspended due to restrictions imposed during the COVID-19 public health emergency. In-game performance data showed a trend towards improvement in most participants. Compared to baseline, NRS and MPQ scores at 1-month showed no clear trends. PSFS scores improved for 1 participant and remained unchanged for others.ConclusionGamified home exercises performed via a novel, mixed-reality system—Mr. MAPP— using which virtual mirror therapy was delivered, is feasible and has potential to improve pain and pain related function in patients with lower limb amputations and phantom limb pain.
Virtual metabolic human dynamic model for pathological analysis and therapy design for diabetes
Authors: Kurata Hiroyuki 
Published: September 2020

AbstractA virtual metabolic human model is a valuable complement to experimental biology and clinical studies, becausein vivoresearch involves serious ethical and technical problems. I have proposed a multi-organ and multi-scale kinetic model that formulates the reactions of enzymes and transporters with the regulation of enzyme activities and hormonal actions under prandial and rest conditions. The model consists of 202 ordinary differential equations for metabolites with 217 reaction rates and 1132 kinetic parameter constants. It is the most comprehensive, largest and highly predictive model of the whole-body metabolism. Use of the model revealed the mechanisms by which individual disorders, such as steatosis, β cell dysfunction and insulin resistance, were combined to cause type 2 diabetes. The model predicted a glycerol kinase inhibitor to be an effective medicine for type 2 diabetes, which not only decreased hepatic triglyceride but also reduced plasma glucose. The model also enabled us to rationally design combination therapy.
De novogenome assembly of the Tobacco Hornworm moth (Manduca sexta)
Authors: Gershman Ariel , Romer Tatiana Gelaf , Fan Yunfan , Razaghi Roham , Smith Wendy A. , Timp Winston 
Published: September 2020

AbstractThe Tobacco hornworm,Manduca sexta,is a lepidopteran insect that is used extensively as a model system for studying insect biology, development, neuroscience and immunity. However, current studies rely on the highly fragmented reference genome Msex_1.0, which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. We present the new reference genome forM. sexta, JHU_Msex_v1.0, applying a combination of modern technologies in ade novoassembly to increase continuity, accuracy, and completeness. The assembly is 470 Mb and is ~20x more continuous than the original assembly, with scaffold N50 >14 Mb. We annotated the assembly by lifting over existing annotations and supplementing with additional supporting RNA-based data for a total of 25,256 genes. The new reference assembly is accessible in annotated form for public use. We demonstrate that improved continuity of theM. sextagenome improves resequencing studies and benefits future research onM. sextaas a model organism.
EEG Artifact to Signal: Predicting Horizontal Gaze Position from SOBI-DANS Identified Ocular Artifact Components
Authors: Sun Rui , Chan Cynthia , Hsiao Janet , Tang Akaysha C. 
Published: September 2020

AbstractOcular artifact in EEG has long been viewed as a problem for interpreting EEG data in basic and applied research. The removal of such artifacts has been an on-going effort over many decades. We have recently introduced a hybrid method combining second-order blind identification (SOBI) with DANS, a novel automatic identification method, to extract components containing specifically signals associated with horizontal and vertical saccadic eye movements (H and V Comps) and found that these components’ event-related potentials in response to saccadic eye movement are systematically modulated by movement directions and distances. Here in a case study, taking advantage of signals about gaze positions contained in the ocular artifact components, we introduced a novel concept of EEG-based virtual eye tracking (EVET) and presented its first prototype. Specifically, we determined (1) the amount of data needed for constructing models of horizontal gaze positions; (2) the asymptotic performance levels achieved with such models. We found that for the specific calibration task, 4 blocks of data (4 saccades per target position) are needed for reaching an asymptotic performance with a prediction accuracy of 0.44 and prediction reliability of 1.67. These results demonstrated that it is possible to track horizontal gaze position via EEG alone, ultimately enabling coregistration of eye movement and the neural signals.
Species and intra-specific competition affect growth in greenhouse more than mycorrhizal colonization onQuercus rubraandAcer rubrumseedlings
Authors: Maier Michael 
Published: September 2020

AbstractAimsDistributions of mycorrhizal guilds correlate with differences in soil nutrient availability and tend to predominate ecosystems where plant growth and development are limited by either soil phosphorus (AM, arbuscular mycorrhiza) or nitrogen (EM, ectomycorrhiza) (Read, 1991). In an effort to characterize functional trait differences, we designed a common garden greenhouse experiment to measure growth and colonization responses between two tree seedling species (Acer rubrumandQuercus rubra) that associate with the two major mycorrhizal guilds.MethodsIn a fully factorial, 12-week greenhouse common garden experiment, seedlings were treated to three levels of nitrogen and phosphorus availability, and grown under inter- and intra-species competition. Change in heights and stem diameters were tracked and mycorrhizal colonization was quantified by percent of total and morphology.ResultsRelative growth rates were higher forAcer rubrumseedlings across treatments and intra-species competition had a strong negative effect on height and stem diameter, especially forQuercus rubra. Both species were highly colonized (>50%) by typically endomycorrhizal forms (arbuscules and vesicles) but varied in the distribution of morphological forms present in cells.ConclusionsThis study highlights the plasticity of tree seedling symbiosis during early developmental stages and challenges the strict static categorization of plant species associations with particular mycorrhizal guilds.
Methylene Blue Inhibits In Vitro the SARS-CoV-2 Spike – ACE2 Protein-Protein Interaction – A Mechanism That Can Contribute to Its Antiviral Activity Against COVID-19
Authors: Bojadzic Damir , Alcazar Oscar , Buchwald Peter 
Published: September 2020

AbstractDue to our interest in the chemical space of organic dyes to identify potential small-molecule inhibitors (SMIs) for protein-protein interactions (PPIs), we initiated a screen of such compounds to assess their inhibitory activity against the interaction between SARS-CoV-2 spike protein and its cognate receptor ACE2, which is the first critical step initiating the viral attachment and entry of this coronavirus responsible for the ongoing COVID-19 pandemic. As part of this, we found that methylene blue, a tricyclic phenothiazine compound approved by the FDA for the treatment of methemoglobinemia and used for other medical applications (including the inactivation of viruses in blood products prior to transfusion when activated by light), inhibits this interaction. We confirmed that it does so in a concentration-dependent manner with a low micromolar half-maximal inhibitory concentration (IC50= 3 μM) in our protein-based ELISA-type setup, while chloroquine, siramesine, and suramin showed no inhibitory activity in this assay. Erythrosine B, which we have shown before to be a promiscuous SMI of PPIs, also inhibited this interaction with an activity similar, possibly slightly higher, than those found for it for other PPIs. This PPI inhibitory activity of methylene blue could contribute to its antiviral activity against SARS-CoV-2 even in the absence of light by blocking its attachment to ACE2-expressing cells and making this inexpensive and widely available drug potentially useful in the prevention and treatment of COVID-19 as an oral or inhaled medication.
Synaptic Zn2+potentiates the effects of cocaine on striatal dopamine neurotransmission and behavior
Authors: Gomez Juan L. , Bonaventura Jordi , Keighron Jacqueline , Wright Kelsey M. , Marable Dondre L. , Rodriguez Lionel A. , Lam Sherry , Carlton Meghan L. , Ellis Randall J. , Jordan Chloe , Bi Guo-hua , Solis Oscar , Pignatelli Marco , Bannon Michael J. , Xi Zheng-Xiong , Tanda Gianluigi , Michaelides Michael 
Published: September 2020

AbstractCocaine binds to the dopamine (DA) transporter (DAT) to regulate cocaine reward and seeking behavior. Zinc (Zn2+) also binds to the DAT, but thein vivorelevance of this interaction is unknown. We found that Zn2+concentrations in postmortem brain (caudate) tissue from humans who died of cocaine overdose were significantly lower than in control subjects. Moreover, the level of striatal Zn2+content in these subjects negatively correlated with plasma levels of benzoylecgonine, a cocaine metabolite indicative of recent use. In mice, repeated cocaine exposure increased synaptic Zn2+concentrations in the caudate putamen (CPu) and nucleus accumbens (NAc). Cocaine-induced increases in Zn2+were dependent on the Zn2+transporter 3 (ZnT3), a neuronal Zn2+transporter localized to synaptic vesicle membranes, as ZnT3 knockout (KO) mice were insensitive to cocaine-induced increases in striatal Zn2+. ZnT3 KO mice showed significantly lower electrically-evoked DA release and greater DA clearance when exposed to cocaine compared to controls. ZnT3 KO mice also displayed significant reductions in cocaine locomotor sensitization, conditioned place preference (CPP), self-administration, and reinstatement compared to control mice and were insensitive to cocaine-induced increases in striatal DAT binding. Finally, dietary Zn2+deficiency in mice resulted in decreased striatal Zn2+content, cocaine locomotor sensitization, CPP, and striatal DAT binding. These results indicate that cocaine increases synaptic Zn2+release and turnover/metabolism in the striatum, and that synaptically-released Zn2+potentiates the effects of cocaine on striatal DA neurotransmission and behavior and is required for cocaine-primed reinstatement. In sum, these findings reveal new insights into cocaine’s pharmacological mechanism of action and suggest that Zn2+may serve as an environmentally-derived regulator of DA neurotransmission, cocaine pharmacodynamics, and vulnerability to cocaine use disorders.
Morphological plasticity inChlamydomonas reinhardtiiand acclimation to micropollutant stress
Authors: Cheloni Giulia , Slaveykova Vera I. 
Published: September 2020

ABSTRACTPhytoplankton are characterized by a great phenotypic plasticity and amazing morphological variability, both playing a primary role in the acclimation to changing environments. However, there is a knowledge gap concerning the role of algal morphological plasticity in stress responses and acclimation to micropollutants. The present study aims examining the palmelloid colony formation of the green alga Chlamydomonas reinhardtii upon micropollutants exposure.Cells were exposed to four micropollutants (MPs) with different modes of action (copper, cadmium, PFOS and paraquat) for a duration of 72h. Effects of MPs on palmelloid formation, growth and physiological traits (chlorophyll fluorescence, membrane integrity and oxidative stress) were monitored via flow cytometry and fluorescence microscopy. Palmelloid formation was observed upon treatment with the four micropollutants. Number of palmelloid colonies and their size were dependent on MP concentration and exposure duration. Cells reverted to their unicellular lifestyle when colonies were harvested and inoculated in fresh medium indicating that palmelloid formation is a plastic response to micropollutants. No physiological effects of these compounds were observed in cells forming palmelloids and palmelloid colonies accumulated lower Cd concentration than unicellularC. reinhardtiisuggesting that colony formation protects the cells form MPs exposure. The results show that colony formation inChlamydomonas reinhardtiiis a stress response strategy activated to face sub-lethal micropollutant concentrations.HIGHLIGHTSSub-lethal concentrations of micropollutants (MPs) induce palmelloid formation inC. reinhardtiiMorphological changes are not associated to adverse effects on algal cellsPalmelloid formation is transitory, cells revert to unicellular lifestyle in the absence of MPsCells within large colonies experience lower Cd exposure than unicellularC. reinhardtiiPalmelloid formation is a morphological stress response that plays a role in cells acclimation to MPs
DiffGR: Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps
Authors: Liu Huiling , Ma Wenxiu 
Published: September 2020

AbstractRecent advances in Hi-C techniques have allowed us to map genome-wide chromatin interactions and uncover higher-order chromatin structures, thereby shedding light on the principles of genome architecture and functions. However, statistical methods for detecting changes in large-scale chromatin organization such as topologically-associating domains (TADs) are still lacking. We proposed a new statistical method, DiffGR, for detecting differentially interacting genomic regions at the TAD level between Hi-C contact maps. We utilized the stratum-adjusted correlation coefficient to measure similarity of local TAD regions. We then developed a non-parametric approach to identify statistically significant changes of genomic interacting regions. Through simulation studies, we demonstrated that DiffGR can robustly and effectively discover differential genomic regions under various conditions. Furthermore, we successfully revealed cell type-specific changes in genomic interacting regions in both human and mouse Hi-C datasets, and illustrated that DiffGR yielded consistent and advantageous results compared with state-of-the-art differential TAD detection methods. The DiffGR R code is published under the GNU GPL ≥ 2 license and is publicly available athttps://github.com/wmalab/DiffGR.
N-glucosyltransferase GbNGT1 fromGinkgocomplement auxin metabolic pathway
Authors: Yin Qinggang , Zhang Jing , Wang Shuhui , Cheng Jintang , Gao Han , Guo Cong , Ma Lianbao , Sun Limin , Chen Shilin , Liu An 
Published: September 2020

AbstractAs a group of the most important phytohormone, auxin homeostasis is regulated in a complex manner. Generally, auxin conjugations especially IAA glucosides are dominant on high auxin level conditions. Former terminal glucosylation researches mainly focus onO-position, while IAA-N-glucoside or IAA-Asp-N-glucoside has been neglected since their found in 2001. In our study, IAA-Asp-N-glucoside was firstly found specifically abundant (as high as 4.13 mg/g) in ginkgo seeds of 58 cultivars from Ginkgo Resource Nursery built in 1990. Furthermore, a novelN-glucosyltransferase GbNGT1, which could catalyze IAA-Asp and IAA to form their correspondingN-glucoside, was identified through differential transcriptome analysis andin vitroenzymatic test. The enzyme was demonstrated to possess specific catalyze capacity toward theN-position of IAA-amino acid or IAA among 52 substrates, and was typical of acid tolerance, metal ion independence and high temperature sensitivity. Docking and site-directed mutagenesis of this enzyme confirmed that E15G mutant could almost abolish enzyme catalytic activity towards IAA-Asp and IAAin vitroandin vivo. The IAA modification of GbNGT1 and GbGH3.5 was verified by transient expression assay inNicotiana benthamiana. In conclusion, our results complement the terminal metabolic pathway of auxin, and the specific catalytic function of GbNGT1 towards IAA-amino acid provide a new way to biosynthesis indole-amide compounds.HighlightThe N-glucosylation of IAA or IAA-amino acids in auxin metabolism had been neglected over decades, our work for GbNGT1 redeems the missing chain of auxin metabolic pathway.
Advanced eMAGE for highly efficient combinatorial editing of a stable genome
Authors: Liang Zhuobin , Metzner Eli , Isaacs Farren J. 
Published: September 2020

AbstractEukaryotic multiplex genome engineering (eMAGE) offers a powerful tool to generate precise combinatorial genome modifications inSaccharomyces cerevisiae. We optimize the design of synthetic oligonucleotides and enrichment of edited populations to increase editing frequencies up to 90%, reduce workflow time by 40%, and engineer a tunable mismatch repair system to lower the rate of spontaneous mutations ∼17-fold. These advances transiently evade genome maintenance to introduce multiple edits at high efficiencies in a stable genetic background, expanding utility of eMAGE in eukaryotic cells.
Multi-regional module-based signal transmission in mouse visual cortex
Authors: Jia Xiaoxuan , Siegle Joshua H. , Durand Séverine , Heller Greggory , Ramirez Tamina , Koch Christof , Olsen Shawn R. 
Published: September 2020

AbstractThe visual cortex is organized hierarchically, but the presence of extensive recurrent and parallel pathways make it challenging to decipher how signals flow between neuronal populations. Here, we tracked the flow of spiking activity recorded from six interconnected levels of the mouse visual hierarchy. By analyzing leading and lagging spike-timing relationships among pairs of simultaneously recorded neurons, we created a cellular-scale directed network graph. Using a module-detection algorithm to cluster neurons based on shared connectivity patterns, we uncovered two multi-regional communication modules distributed across the hierarchy. The direction of signal flow between and within these modules, differences in layer and area distributions, and distinct temporal dynamics suggest that one module is positioned to transmit feedforward sensory signals, whereas the other integrates inputs for recurrent processing. These results suggest that multi-regional functional modules may be a fundamental feature of organization beyond cortical areas that supports signal propagation across hierarchical recurrent networks.
Low cost conservation: Fishing gear threats to marine species
Authors: Cashion Tim , Tai Travis C. , Lam Vicky W.Y. , Pauly Daniel , Sumaila U. Rashid 
Published: September 2020

AbstractUnderstanding conflicts between objectives of fisheries and conservation is the key to finding win-win situations for marine biodiversity and fishers. Many marine species are threatened by harmful interactions with fisheries, but the threats they face are associated with the fishing gear used. Here, we undertake a novel analysis of marine species and their gear-specific threats to evaluate conservation-fisheries trade-offs to identify areas with high competing goals. Our analysis suggests that gillnet and longline fisheries pose the greatest risk to marine species yet deliver relatively low profits, emphasizing the inefficiencies of these gears. We find that the majority of the high seas has low economic fisheries benefits with over 25% of the high seas categorized as areas of ‘conservation prioritisation’ over fisheries.
Ebselen derivatives are very potent dual inhibitors of SARS-CoV-2 proteases - PLproand Mproin in vitro studies
Authors: Zmudzinski Mikolaj , Rut Wioletta , Olech Kamila , Granda Jarosław , Giurg Mirosław , Burda-Grabowska Małgorzata , Zhang Linlin , Sun Xinyuanyuan , Lv Zongyang , Nayak Digant , Kesik-Brodacka Malgorzata , Olsen Shaun K. , Hilgenfeld Rolf , Drag Marcin 
Published: September 2020

AbstractProteases encoded by SARS-CoV-2 constitute a promising target for new therapies against COVID-19. SARS-CoV-2 main protease (Mpro, 3CLpro) and papain-like protease (PLpro) are responsible for viral polyprotein cleavage - a process crucial for viral survival and replication. Recently it was shown that 2-phenylbenzisoselenazol-3(2H)-one (ebselen), an organoselenium anti-inflammatory small-molecule drug, is a potent, covalent inhibitor of both the proteases and its potency was evaluated in enzymatic and anti-viral assays. In this study, we screened a collection of 23 ebselen derivatives for SARS-CoV-2 PLproand Mproinhibitors. Our studies revealed that ebselen derivatives are potent inhibitors of both the proteases. We identified three PLproand four Mproinhibitors superior to ebselen. Our work shows that ebselen constitutes a promising platform for development of new antiviral agents targeting both SARS-CoV-2 PLproand Mpro.