bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatio-temporal variability of tidal-stream energy in north-western Europe
Authors: Guillou Nicolas , Neill Simon P. , Thiébot Jérôme
Published: July 2020

Initial selection of tidal stream energy sites is primarily based on identifying areas with the maximum current speeds. However, optimal design and deployment of turbines requires detailed investigations of the temporal variability of the available resource, focusing on areas with reduced variability, and hence the potential for more continuous energy supply. These aspects are investigated here for some of the most promising sites for tidal array development across the north-western European shelf seas: the Alderney Race, the Fromveur Strait, the Pentland Firth and the channels of Orkney. Particular attention was dedicated to asymmetry between the flood and ebb phases of the tidal cycle (due to the phase relationship between M
2
and M
4
constituents), and spring-neap variability of the available resource (due to M
2
and S
2
compound tides). A series of high-resolution models were exploited to (i) produce a detailed harmonic database of these three components, and (ii) characterize, using energy resource metrics, temporal variability of the available power density. There was a clear contrast between the Alderney Race, with reduced temporal variability over semi-diurnal and fortnightly time scales, and sites in western Brittany and North Scotland which, due to increased variability, appeared less attractive for optimal energy conversion.

This article is part of the theme issue ‘New insights on tidal dynamics and tidal energy harvesting in the Alderney Race’.
Surface currents in the Alderney Race from high-frequency radar measurements and three-dimensional modelling
Authors: Lopez G. , Bennis A.-C. , Barbin Y. , Sentchev A. , Benoit L. , Marié L.
Published: July 2020

Two weeks of high-frequency radar measurements collected at the Alderney Race are compared with the results of a three-dimensional fully coupled wave–current model. Spatial current measurements are rare in this site, otherwise well investigated through modelling. Thus, the radar measurements offer a unique opportunity to examine the spatial reliability of numerical results, and can help to improve our understanding of the complex currents in the area. Comparison of observed and modelled surface current velocities showed a good agreement between the methods, represented by root mean squared errors ranging from 14 to 40 cm s
−1
and from 18 to 60 cm s
−1
during neap and spring tides, respectively. Maximum errors were found in shallow regions with consistently high current velocities, represented by mean neap and spring magnitudes of 1.25 m s
−1
and 2.7 m s
−1
, respectively. Part of the differences between modelled and observed surface currents in these areas are thought to derive from limitations in the k-epsilon turbulence model used to simulate vertical mixing, when the horizontal turbulent transport is high. In addition, radar radial currents showed increased variance over the same regions, and might also be contributing to the discrepancies found. Correlation analyses yielded magnitudes above 0.95 over the entire study area, with better agreement during spring than during neap tides, probably because of an increase in the phase lag between radar and model velocities during the latter.

This article is part of the theme issue ‘New insights on tidal dynamics and tidal energy harvesting in the Alderney Race’.
One year of measurements in Alderney Race: preliminary results from database analysis
Authors: Furgerot L. , Sentchev A. , Bailly du Bois P. , Lopez G. , Morillon M. , Poizot E. , Méar Y. , Bennis A.-C.
Published: July 2020

The Alderney Race is assumed to have the largest tidal-stream energy potential in the north-western European coastal seas. Interaction of the powerful tidal stream with strong wind, high waves and irregular bathymetry creates hydrodynamic conditions of extreme complexity, with high levels of turbulence. A comprehensive dataset has been created to improve the understanding of physical processes, turbulence, tidal stream and resource variability at the site. The database contains a large amount of oceanographic and meteorological measurements acquired in Alderney Race in 2017–2018. This exceptionally long period of observations (nearly one year) became possible due to modern tools and strategies of data acquisition. The paper presents some significant results from the database analysis. Among many results, we would like to underline the following: (i) a wide range of variability of mean flow and sea state parameters was documented; (ii) exceptionally large values of current velocity (7 m s
−1
) and significant wave height (8 m) were measured during extreme meteorological conditions; (iii) high-frequency variability of current speed during storm events was also found to be very large, with the standard deviation of velocity reaching 0.3 m s
−1
in the bottom boundary layer, and 0.6 m s
−1
in the surface layer; and (iv) predominant wind and wave direction relative to the flow impacts the wave height and significantly increases the turbulence kinetic energy of the flow. To our knowledge, this is the largest multi-variable database available on potential tidal energy sites. The results of database analysis can represent a significant advance in environmental conditions and resource characterization and provide advanced information to turbine developers.

This article is part of the theme issue ‘New insights on tidal dynamics and tidal energy harvesting in the Alderney Race’.
Phosphoproteomic Identification of Vasopressin-Regulated Protein Kinases in Collecting Duct Cells
Authors: Datta Arnab , Yang Chin-Rang , Salhadar Karim , Chou Chung-Lin , Raghuram Viswanathan , Knepper Mark A.
Published: July 2020

Background and Purpose

The peptide hormone vasopressin regulates water transport in the renal collecting duct largely via the V2 receptor, which triggers a cAMP-mediated activation of a protein kinase A (PKA)-dependent signaling network. The protein kinases downstream from PKA have not been fully identified or mapped to regulated phosphoproteins.

Experimental Approach

We carried out systems-level analysis of large-scale phosphoproteomic data quantifying vasopressin-induced changes in phosphorylation in aquaporin-2-expressing cultured collecting duct cells (mpkCCD). Quantification was done using stable isotope labeling (SILAC method).

Key Results

9640 phosphopeptides were quantified. Stringent statistical analysis identified significant changes in response to vasopressin in 429 of these phosphopeptides. The corresponding phosphoproteins were mapped to known vasopressin-regulated cellular processes. The vasopressin-regulated sites were classified according to the sequences surrounding the phosphorylated amino acids giving 11 groups distinguished predominantly by the amino acids at positions +1, −3, −2 and −5 relative to the phosphorylated amino acid. Among the vasopressin-regulated phosphoproteins were 25 distinct protein kinases. Among these, six of them plus PKA appeared to account for phosphorylation of more than 80% of the 313 vasopressin-regulated phosphorylation sites. The six downstream kinases were salt-inducible kinase 2 (Sik2), cyclin-dependent kinase 18 (PCTAIRE-3, Cdk18), calmodulin-dependent kinase kinase 2 (Camkk2), protein kinase D2 (Prkd2), mitogen-activated kinase 3 (ERK1; Mapk3), and myosin light chain kinase (Mylk).

Conclusion and Implications

In V2 receptor-mediated signaling, PKA is at the head of a complex network that includes at least 6 downstream vasopressin-regulated protein kinases that are prime targets for future study. The extensive phosphoproteomic data generated in this study is provided as a web-based data resource for future studies of G-protein coupled receptors.
G-CSF Secreted by Epigenetically Reprogrammed Mutant IDH1 Glioma Stem Cells Reverses the Myeloid Cells’-Mediated Immunosuppressive Tumor Microenvironment
Authors: Alghamri Mahmoud S , Avvari Ruthvik P , Thalla Rohit , Kamran Neha , Zhang Li , Ventosa Maria , Taher Ayman , Faisal Syed Mohd , Núñez Felipe J. , Garcia-Fabiani María Belén , Haase Santiago , Carney Stephen , Orringer Daniel , Hervey-Jumper Shawn , Heth Jason , Patil Parag G , Al-Holou Wajd N , Eddy Karen , Merajver Sophia , Ulintz Peter J , Welch Joshua , Gao Chao , Liu Jialin , Núñez Gabriel , Hambardzumyan Dolores , Lowenstein Pedro R , Castro Maria G
Published: July 2020

Mutation in isocitrate dehydrogenase (mIDH) is a gain of function mutation resulting in the production of the oncometabolite, R-2-hydroxyglutarate, that inhibits DNA and histone demethylases. The resultant hypermethylation phenotype reprograms the glioma cells’ transcriptome and elicits profound effects on glioma immunity. We report that in mouse models and human gliomas,mIDH1in the context ofATRXandTP53inactivation results in global expansion of the granulocytic myeloid cells’ compartment. Single-cell RNA-sequencing coupled with mass cytometry analysis revealed that these granulocytes are mainly non-immunosuppressive neutrophils and pre-neutrophils; with a small fraction of polymorphonuclear myeloid-derived suppressor cells. The mechanism ofmIDH1mediated pre-neutrophils expansion involves epigenetic reprogramming which leads to enhanced expression of the granulocyte colony-stimulating factor (G-CSF). Blocking G-CSF restored the inhibitory potential of PMN-MDSCs and enhanced tumor progression. Thus, G-CSF induces remodeling of the inhibitory PMN-MDSCs inmIDH1glioma rendering them non-immunosuppressive; and having significant therapeutic implications.

SIGNIFICANCE

mIDH1is the most common mutation in gliomas associated with improved prognosis. Gliomas harboringmIDH1, together withATRXandTP53inactivation, exhibit higher circulating levels of G-CSF, ensuing the recruitment and expansion of non-suppressive neutrophils, pre-neutrophils and small fraction of PMN-MDSCs to the TME leading to an immune permissive phenotype.
Single-cell classification using learned cell phenotypes
Authors: Chen Yang , Lakshmikanth Tadepally , Mikes Jaromir , Brodin Petter
Published: July 2020

Single-cell methods such as flow cytometry, Mass cytometry and single-cell mRNA sequencing collect high-dimensional data on thousands to millions of individual cells. An important aim during the analysis of such data is to classify cells into known categories and cell types. One commonly used approach towards this is clustering of cells with similar features followed by manual annotation of clusters in relation to known biology. A second approach, commonly used for cytometry data relies on manual sorting or “gating” of cells, often based on pairwise combinations of measurements used in a stepwise and very tedious process of cell annotation. Both of these approaches require manual inspection and annotation of every new dataset generated, a process that is not only time consuming but also subjective and surely influential for the conclusions drawn. The manual annotation is also difficult to reproduce by other researchers with a different perception of features that signify their cells of interest. Here we propose an alternative strategy based on machine learning of known phenotypes from manually curated, high-dimensional data and thereby enabling rapid classification of subsequent datasets in a more reproducible manner. This simple approach increases both throughput, reproducibility and simplicity of cell classification in single-cell biology.
The glycoprotease CpaA secreted by medically relevantAcinetobacterspecies targets multipleO-linked host glycoproteins
Authors: Haurat M. Florencia , Scott Nichollas E. , Di Venanzio Gisela , Lopez Juvenal , Pluvinage Benajmin , Boraston Alisdair B. , Ferracane Michael J. , Feldman Mario F.
Published: July 2020

Glycans decorate proteins and affect their biological function, including protection against proteolytic degradation. However, pathogenic, and commensal bacteria have evolved specific glycoproteases that overcome the steric impediment posed by carbohydrates, cleaving glycoproteins precisely at their glycosylation site(s). Medically relevantAcinetobacterstrains employ their type II secretion system (T2SS) to secrete the glycoprotease CpaA, which contributes to virulence. Previously, CpaA was shown to cleave twoO-linked glycoproteins, factors V and XII, leading to reduced blood coagulation. In this work, we show that CpaA cleaves a broader range ofO-linked human glycoproteins, including several glycoproteins involved in complement activation, such as CD55 and CD46. However, only CD55 was removed from the cell surface, while CD46 remained unaltered during theA. nosocomialisinfection assay. We show that CpaA has a unique consensus target sequence that consists of a glycosylated serine or threonine residue after a proline residue (P-S/T), and its activity is not affected by sialic acids. Molecular modeling and mutagenesis analysis of CpaA suggest that the indole ring of Trp493 and the ring of the Pro residue in the substrate form a key interaction that contributes to CpaA sequence selectivity. Similar bacterial glycoproteases have recently gained attention as tools for proteomic analysis of human glycoproteins, and CpaA appears to be a robust and attractive new component of the glycoproteomics toolbox. Combined, our work provides insight into the function and possible application of CpaA, a member of a widespread class of broad-spectrum bacterial glycoproteases involved in host-pathogen interactions.

IMPORTANCE

CpaA is a glycoprotease expressed by members of theAcinetobacter baumannii-calcoaceticuscomplex and it is the firstbona fidesecreted virulence factor identified in these species. Here, we show that CpaA cleaves multiple targets precisely atO-glycosylation sites preceded by a Pro residue. This feature, together with the observation that sialic acid does not impact CpaA activity, makes of this enzyme an attractive tool for the analysis ofO-linked human protein for biotechnical and diagnostic purposes. Previous work identified proteins involved in blood coagulation as targets of CpaA. Our work broadens the set of targets of CpaA, pointing towards additional roles in bacteria-host interactions. We propose that CpaA belongs to an expanding class of functionally-defined glycoproteases that targets multipleO-linked host glycoproteins.
Dual-purpose isocyanides produced byAspergillus fumigatuscontribute to cellular copper sufficiency and exhibit antimicrobial activity
Authors: Raffa Nicholas , Won Tae Hyung , Sukowaty Andrew , Candor Kathleen , Cui Chengsen , Halder Saayak , Dai Mingji , Figueroa Julio Landero , Schroeder Frank C. , Keller Nancy
Published: July 2020

The maintenance of sufficient but non-toxic pools of metal micronutrients is accomplished through diverse homeostasis mechanisms in fungi. Siderophores play a well-established role for iron homeostasis; however, no copper-binding analogs have been found in fungi. Here we demonstrate that inAspergillus fumigatusisocyanides derived from thexanbiosynthetic gene cluster (BGC) bind copper, impact cellular copper content, and have significant metal-dependent antimicrobial properties.xanBGC-derived isocyanides are secreted and bind copper as visualized by a chrome azurol S (CAS) assay and inductively coupled plasma-mass spectrometry (ICP-MS) analysis ofA. fumigatusintracellular copper pools demonstrated a role forxancluster metabolites in the accumulation of copper.A. fumigatuscoculture withA. nidulans, Candida albicansand a variety of pathogenic bacteria establish copper-dependent antimicrobial properties ofxanBGC metabolites including inhibition of laccase activity. Similarly, inhibition ofPseudomonas aeruginosaby low concentrations of thexanisocyanide xanthocillin was copper-dependent. Other metals also reduced xanthocillin’s antimicrobial properties, but less efficiently than copper. As variations of thexanBGC exist in other filamentous fungi, we suggest that xanthocillin-like natural products represent a first example for fungal small molecules that serve to maintain copper sufficiency and mediate interactions with competing microbes.

Significance

Metal homeostasis is an integral part of metabolism for any organism. A vast array of small molecules are already known to mediate metal homeostasis in fungi and bacteria; however, unlike their bacterial counterparts, to-date there are no known fungal small molecules that function to maintain copper homeostasis. Discovery of copper binding small molecules produced byA. fumigatusgives insight into mechanisms other than the extensively studied copper transporters or metalloproteins for how fungi can regulate copper. This has important ecological implications as securing scarce nutrients is central for fitness and survival. Additionally, studying this mechanism inA. fumigatusprovides a basis for investigation of copper regulation pathways in other fungi.
The genetic architecture of the sexually selected sword ornament and its evolution in hybrid populations
Authors: Powell Daniel L. , Payne Cheyenne , Keegan Mackenzie , Banerjee Shreya M. , Cui Rongfeng , Andolfatto Peter , Schumer Molly , Rosenthal Gil G.
Published: July 2020

Biologists since Darwin have been fascinated by the evolution of sexually selected ornaments, particularly those that reduce viability. Uncovering the genetic architecture of these traits is key to understanding how they evolve and are maintained. Here, we investigate the genetic architecture of a sexually selected ornament, the “sword” fin extension that characterizes many species of swordtail fish (Xiphophorus). Using sworded and swordless sister species ofXiphophorus, we generated a mapping population and show that the sword ornament is polygenic – with ancestry across the genome explaining substantial variation in the trait. After accounting for the impacts of genome-wide ancestry, we identify one major effect QTL that explains ∼5% of the overall variation in the trait. Using a series of approaches, we narrow this large QTL interval to a handful of likely candidate genes, including the genesp8. Notably,sp8plays a regulatory role in fin regeneration and harbors several derived substitutions that are predicted to impact protein function in the species that has lost the sword ornament. Furthermore, we find evidence of selection on ancestry atsp8in four natural hybrid populations, consistent with selection against the sword in these populations.
Computer vision approach to characterize size and shape phenotypes of horticultural crops using high-throughput imagery
Authors: Haque Samiul , Lobaton Edgar , Nelson Natalie , Yencho G Craig , Pecota Kenneth V , Mierop Russell , Kudenov Michael W , Boyette Mike , Williams Cranos M
Published: July 2020

For many horticultural crops, variation in quality (e.g., shape and size) contribute significantly to the crop’s market value. Metrics characterizing less subjective harvest quantities (e.g., yield and total biomass) are routinely monitored. In contrast, metrics quantifying more subjective crop quality characteristics such as ideal size and shape remain difficult to characterize objectively at the production-scale due to the lack of modular technologies for high-throughput sensing and computation. Several horticultural crops are sent to packing facilities after having been harvested, where they are sorted into boxes and containers using high-throughput scanners. These scanners capture images of each fruit or vegetable being sorted and packed, but the images are typically used solely for sorting purposes and promptly discarded. With further analysis, these images could offer unparalleled insight on how crop quality metrics vary at the industrial production-scale and provide further insight into how these characteristics translate to overall market value. At present, methods for extracting and quantifying quality characteristics of crops using images generated by existing industrial infrastructure have not been developed. Furthermore, prior studies that investigated horticultural crop quality metrics, specifically of size and shape, used a limited number of samples, did not incorporate deformed or non-marketable samples, and did not use images captured from high-throughput systems. In this work, using sweetpotato (SP) as a use case, we introduce a computer vision algorithm for quantifying shape and size characteristics in a high-throughput manner. This approach generates 3D model of SPs from two 2D images captured by an industrial sorter 90 degrees apart and extracts 3D shape features in a few hundred milliseconds. We applied the 3D reconstruction and feature extraction method to thousands of image samples to demonstrate how variations in shape features across sweetptoato cultivars can be quantified. We created a sweetpotato shape dataset containing sweetpotato images, extracted shape features, and qualitative shape types (U.S. No. 1 or Cull). We used this dataset to develop a neural network-based shape classifier that was able to predict Cull vs. U.S. No. 1 sweetpotato with 84.59% accuracy. In addition, using univariate Chi-squared tests and random forest, we identified the most important features for determining qualitative shape (U.S. No. 1 or Cull) of the sweetpotatoes. Our study serves as the first step towards enabling big data analytics for sweetpotato agriculture. The methodological framework is readily transferable to other horticultural crops, particularly those that are sorted using commercial imaging equipment.
Inducing highly physiologically relevant phenotypes of human vascular smooth muscle cells via 3D printing
Authors: Zhu Peiran , Li Xuzhao , Xin Wang , Wang Menglin , Yin Chengzhen , Li Jinze , Chen Hangyu , Zhu Hengjia , Sun Yubing , Jia Jiemin , Zhou Nanjia
Published: July 2020

Vascular smooth muscle cells (vSMCs) are one of the essential cell types in blood vessel walls. A significant vSMC phenotype characteristic is that they collectively wrap around the outer layer of the healthy blood vessels with spindle-like morphology and help maintain the vascular tones and regulate the blood flow. Both physiological and biomedical research are impeded by the standard 2D cell culture approaches which do not createin vivolike microenvironment. Here, we systematically investigated the vSMCs culturing within 3D printed geometrical constraints and on printed microfilaments. Based on these models, we demonstrate a simple bioprinting approach for fast manufacturing vessel architectures with micro-grooved surfaces for vSMCs alignment. We validated that the vSMCs cultured on the printed vessel with microfilaments (VWMF) present a more physiologically relevant morphological phenotype and gene expression profile, and they are considerably more active in wound healing and ischemia than conventional planarly cultured vSMCs.
Transcriptomic Response of Brain Tissue to Focused Ultrasound-Mediated Blood-Brain Barrier Disruption Depends Strongly on Anesthesia
Authors: Mathew A.S. , Gorick C.M. , Thim E.A. , Garrison W.J. , Klibanov A.L. , Miller G.W. , Sheybani N.D. , Price R.J.
Published: July 2020

Focused ultrasound (FUS) mediated blood brain barrier disruption (BBBD) is a promising strategy for the targeted delivery of systemically-administered therapeutics to the central nervous system (CNS). Pre-clinical investigations of BBBD have been performed on different anesthetic backgrounds; however, the potential influence of the choice of anesthetic on the molecular response to BBBD is unknown, despite its potential to critically affect interpretation of experimental therapeutic outcomes. Here, using bulk RNA sequencing approaches, we comprehensively examined the transcriptomic response of both normal brain tissue and brain tissue exposed to FUS-induced BBBD in mice anesthetized with either isoflurane with medical air (Iso) or ketamine/dexmedetomidine (KD). In normal murine brain tissue, Iso alone elicited minimal differential gene expression (DGE) and repressed pathways associated with neuronal signaling. KD alone, however, led to massive DGE and enrichment of pathways associated with protein synthesis. In brain tissue exposed to BBBD (1 MHz, 0.5 Hz pulse repetition frequency, 0.4 MPa peak-negative pressure), we systematically evaluated the relative effects of anesthesia, microbubbles, and FUS on the transcriptome. Of particular interest, we observed that gene sets associated with sterile inflammatory responses and cell-cell junctional activity were induced by BBBD, regardless of the choice of anesthesia. Meanwhile, gene sets associated with metabolism, platelet activity, tissue repair, and signaling pathways, were differentially affected by BBBD, with a strong dependence on the anesthetic. We conclude that the underlying transcriptomic response to FUS-mediated BBBD may be powerfully influenced by anesthesia. These findings raise considerations for the translation of FUS-BBBD delivery approaches that impact, in particular, metabolism, tissue repair, and intracellular signaling.
Two-dimensional video-based analysis of human gait using pose estimation
Authors: Stenum Jan , Rossi Cristina , Roemmich Ryan T.
Published: July 2020

Walking is the primary mode of human locomotion. Accordingly, people have been interested in studying human gait since at least the fourth century BC. Human gait analysis is now common in many fields of clinical and basic research, but gold standard approaches – e.g., three-dimensional motion capture, instrumented mats or footwear, and wearables – are often expensive, immobile, data-limited, and/or require specialized equipment or expertise for operation. Recent advances in video-based pose estimation have suggested exciting potential for analyzing human gait using only two-dimensional video inputs collected from readily accessible devices (e.g., smartphones, tablets). However, we currently lack: 1) data about the accuracy of video-based pose estimation approaches for human gait analysis relative to gold standard measurement techniques and 2) an available workflow for performing human gait analysis via video-based pose estimation. In this study, we compared a large set of spatiotemporal and sagittal kinematic gait parameters as measured by OpenPose (a freely available algorithm for video-based human pose estimation) and three-dimensional motion capture from trials where healthy adults walked overground. We found that OpenPose performed well in estimating many gait parameters (e.g., step time, step length, sagittal hip and knee angles) while some (e.g., double support time, sagittal ankle angles) were less accurate. We observed that mean values for individual participants – as are often of primary interest in clinical settings – were more accurate than individual step-by-step measurements. We also provide a workflow for users to perform their own gait analyses and offer suggestions and considerations for future approaches.
Causal evidence for a double dissociation between object- and scene-selective regions of visual cortex: A pre-registered TMS replication study
Authors: Wischnewski Miles , Peelen Marius V.
Published: July 2020

Natural scenes are characterized by individual objects as well as by global scene properties such as spatial layout. Functional neuroimaging research has shown that this distinction between object and scene processing is one of the main organizing principles of human high-level visual cortex. For example, object-selective regions, including the lateral occipital complex (LOC), were shown to represent object content (but not scene layout), while scene-selective regions, including the occipital place area (OPA), were shown to represent scene layout (but not object content). Causal evidence for a double dissociation between LOC and OPA in representing objects and scenes is currently limited, however. One TMS experiment, conducted in a relatively small sample (N=13), reported an interaction between LOC and OPA stimulation and object and scene recognition performance (Dilks et al., 2013). Here, we present a high-powered pre-registered replication of this study (N=72, including male and female human participants), using group-average fMRI coordinates to target LOC and OPA. Results revealed unambiguous evidence for a double dissociation between LOC and OPA: Relative to vertex stimulation, TMS over LOC selectively impaired the recognition of objects, while TMS over OPA selectively impaired the recognition of scenes. Furthermore, we found that these effects were stable over time and consistent across individual objects and scenes. These results show that LOC and OPA can be reliably and selectively targeted with TMS, even when defined based on group-average fMRI coordinates. More generally, they support the distinction between object and scene processing as an organizing principle of human high-level visual cortex.

Significance Statement

Our daily-life environments are characterized both by individual objects and by global scene properties. The distinction between object and scene processing features prominently in visual cognitive neuroscience, with fMRI studies showing that this distinction is one of the main organizing principles of human high-level visual cortex. However, causal evidence for the selective involvement of object- and scene-selective regions in processing their preferred category is less conclusive. Here, testing a large sample (N=72) using an established paradigm and a pre-registered protocol, we found that TMS over object-selective cortex (LOC) selectively impaired object recognition while TMS over scene-selective cortex (OPA) selectively impaired scene recognition. These results provide conclusive causal evidence for the distinction between object and scene processing in human visual cortex.
Temporally and Spatially Partitioned Neuropeptide Release from Individual Clock Neurons
Authors: Klose Markus K. , Bruchez Marcel P. , Deitcher David L. , Levitan Edwin S.
Published: July 2020

Neuropeptides control rhythmic behaviors, but the timing and location of their release within circuits is unknown. Here imaging in the brain shows that synaptic neuropeptide release byDrosophilaclock neurons is diurnal, peaking at times of day that were not anticipated by prior electrical and Ca2+data. Furthermore, hours before peak synaptic neuropeptide release, neuropeptide release occurs at the soma, a neuronal compartment that has not been implicated in peptidergic transmission. The timing disparity between release at the soma and terminals results from independent and compartmentalized mechanisms for daily rhythmic release: consistent with conventional electrical activity-triggered synaptic transmission, terminals require Ca2+influx, while somatic neuropeptide release is triggered by the biochemical signal IP3. Upon disrupting the somatic mechanism, the rhythm of terminal release and locomotor activity period are unaffected, but the number of flies with rhythmic behavior and sleep-wake balance are reduced. These results support the conclusion that somatic neuropeptide release controls specific features of clock neuron dependent behaviors. Thus, compartment specific mechanisms within individual clock neurons produce temporally and spatially partitioned neuropeptide release to expand the peptidergic connectome underlying daily rhythmic behaviors.

Significance Statement

It is believed that electrical activity simultaneously stimulates widespread release sites in single neurons to elicit neuropeptide dependent behaviors. However, optically detecting neuropeptide release in the intact brain shows that clock neurons release neuropeptides from different sites at different times of the day. This is possible because one neuronal compartment, the soma, uses biochemical signaling instead of electrical activity to evoke release. Disrupting somatic release affects specific features of circadian locomotor activity and sleep. Thus, neuropeptide release is elicited by independent triggers from distinct parts of clock neurons to engage different regions of behavior regulating circuitry. This strategy for expanding the connectome may be used for other neuropeptide dependent behaviors, such as feeding and pain perception.
A Wearable Optical Microfibrous Biomaterial with Encapsulated Nanosensors Enables Wireless Monitoring of Oxidative Stress
Authors: Safaee Mohammad Moein , Gravely Mitchell , Roxbury Daniel
Published: July 2020

In an effort to facilitate personalized medical approaches, the continuous and noninvasive monitoring of biochemical information using wearable technologies can enable a detailed understanding of an individual’s physiology. Reactive oxygen species (ROS) are a class of oxygen-containing free radicals which function in a wide range of biological processes. In wound healing applications, the continuous monitoring of ROS through a wearable diagnostics platform is essential for the prevention of chronicity and pathogenic infection. Here, a versatile one-step procedure is utilized to fabricate optical core-shell microfibrous textiles incorporating single-walled carbon nanotubes (SWCNTs) for the real-time optical monitoring of hydrogen peroxide concentrations in wounds. The environmentally sensitive and non-photobleachable fluorescence of SWCNTs enables continuous analyte monitoring without a decay in signal over time. The existence of multiple chiralities of SWCNTs emitting near-infrared fluorescence with narrow bandwidths allows a ratiometric signal readout invariant to the excitation source distance and exposure time. The individual fibers encapsulate the SWCNT nanosensors for at least 21 days without apparent loss in structural integrity. Moreover, the microfibrous textiles can be utilized to spatially resolve peroxide concentrations on a wound surface using a camera and can be integrated into commercial wound bandages without being altered or losing their optical properties.
miRinGO: Prediction of biological processes indirectly targeted by human microRNAs
Authors: Sayed Mohammed , Park Juw Won
Published: July 2020

MicroRNAs are small non-coding RNAs that are known for their role in post-transcriptional regulation of target genes. Typically, their functions are predicted by first identifying their target genes and then finding biological processes enriched in these targets. Current tools for miRNA functional analysis use only genes with physical binding sites as their targets and exclude other genes that are indirectly targeted transcriptionally through transcription factors. Here, we introduce a method to predict gene ontology (GO) annotations indirectly targeted by microRNAs. The proposed method resulted in better performance in predicting known miRNA-GO term associations compared to the canonical approach. To facilitate miRNA GO enrichment analysis, we developed an R Shiny application, miRinGO, that is freely available from GitHub athttps://github.com/Fadeel/miRinGO
A rapid ecological assessment for necrophagous flies (Diptera, Calyptratae) in a mosaic landscape of the Colombian Andes
Authors: Amat Eduardo , Medina Claudia A.
Published: July 2020

A necrophagous flies ensemble (Diptera, Calyptratae) was rapidly assessed in four coverages of an anthropogenic landscape in the east range of the Colombian Andes. Ninetyseven individuals belonging to eight species were collected in only two hours of sampling. The highest diversity values and the occurrence of asynanthropic flies in the forest under conservation management may reflect a positively natural restoration process in the area assessed. Grassland, rural and urban coverages were similarly low in diversity and composition. A brief discussion about the flies’ bionomy and their environment association is offered. Necrophagous flies ensembles by coverage behave as an indicator of the anthropic impact on the landscape.
Minimally-overlapping words for sequence similarity search
Authors: Frith Martin C. , Noé Laurent , Kucherov Gregory
Published: July 2020

Analysis of genetic sequences is usually based on finding similar parts of sequences, e.g. DNA reads and/or genomes. For big data, this is typically done via “seeds”: simple similarities (e.g. exact matches) that can be found quickly. For huge data, sparse seeding is useful, where we only consider seeds at a subset of positions in a sequence.

Here we study a simple sparse-seeding method: using seeds at positions of certain “words” (e.g.ac, at, gc, orgt). Sensitivity is maximized by using words with minimal overlaps. That is because, in a random sequence, minimally-overlapping words are anti-clumped. We provide evidence that this is often superior to acclaimed “minimizer” sparse-seeding methods. Our approach can be unified with design of inexact (spaced and subset) seeds, further boosting sensitivity. Thus, we present a promising approach to sequence similarity search, with open questions on how to optimize it.
Are Granulins Copper Sequestering Proteins?
Authors: Bhopatkar Anukool A. , Rangachari Vijayaraghavan
Published: July 2020

Granulins (GRN 1-7) are short (∼6 kDa), cysteine-rich proteins that are generated upon the proteolytic processing of progranulin (PGRN). These modules, along with their precursor, have been implicated in multiple pathophysiological roles, especially in neurodegenerative diseases. Our previous investigations into GRN-3 and GRN-5 reveal them to be fully disordered in the reduced form and implicate redox sensitive attributes to the proteins. Such redox-dependent modulation has become associated with proteins involved in oxidative stress regulation and maintaining metal-homeostasis within cells. To probe whether GRNs play a contributory role in such functions, we tested the metal binding potential of the reduced form of GRNs -3 and -5 under neutral and acidic pH mimicking cytosolic and lysosomal conditions, respectively. We found, at neutral pH, both GRNs selectively bind Cu(II) and no other divalent cations. Binding of Cu(II) also partly triggered the oxidative multimerization of GRNs via uncoordinated cystines at both pH conditions. Furthermore, binding did not induce gain in secondary structure and the protein remained disordered. Overall, the results indicate that GRN-3 and -5 have a surprisingly strong affinity for Cu(II) in the pM range, comparable to known copper sequestering proteins. This data also hints at a potential of GRNs to reduce Cu(II) to Cu(I), a process that has significance in mitigating Cu-induced ROS cytotoxicity in cells. Together, this report uncovers a metal-coordinating capability of GRNs for the first time, which could have profound significance in their structure and function.
Direct medium-chain carboxylic-acid oil separation from a bioreactor by an electrodialysis/phase separation cell
Authors: Xu Jiajie , Guzman Juan J.L. , Angenent Largus T.
Published: July 2020

Medium-chain carboxylic acids (MCCAs) are valuable platform chemicals with numerous industrial-scale applications. These MCCAs can be produced from waste biomass sources or syngas fermentation effluent through an anaerobic fermentation process called chain elongation. We have previously demonstrated successful approaches to separate >90%-purity oil with several MCCAs by integrating the anaerobic bioprocess with membrane-based liquid-liquid extraction (pertraction) and membrane electrolysis. However, membrane electrolysis without pertraction was not able to separate MCCA oil. Therefore, we developed an electrodialysis/phase separation cell (ED/PS) and evaluated whether it can function as a stand-alone extraction and separation unit. First, we tested an ED/PS cell, which, when evaluatedin serieswith pertraction, achieved a maximum MCCA-oil flux of 1,665 g d-1per projected area (m2) (19.3 mL oil d-1) and a MCCA-oil transfer efficiency [100%*moles MCCA-oil moles electrons-1] of 74% at 15 A m-2. This extraction system demonstrated a ∼10 times lower electric-power consumption of 1.05 kWh kg-1MCCA oil when compared to membrane electrolysisin serieswith pertration (11.1 kWh kg-1MCCA oil) at 15 A m-2. Second, we evaluated our ED/PS as a stand-alone unit when integrated with the anaerobic bioprocess (without pertraction), and demonstrated that we can selectively extract and separate MCCA oil directly from chain-elongating bioreactor broth with just an abiotic electrochemical cell. We assumed that such a stand-alone unit would reduce capital and operating costs, but electric-power consumption increased considerably due to the lower MCCA concentrations in the bioreactor broth compared to the pertraction broth. Only a full techno-economic analysis will be able to determine whether the use of the ED/PS cell should be as a stand-alone unit or after pertraction.
TheAppNL-G-Fmouse retina is a site for preclinical Alzheimer’s disease diagnosis and research
Authors: Vandenabeele Marjan , Veys Lien , Lemmens Sophie , Hadoux Xavier , Gelders Géraldine , Masin Luca , Serneels Lutgarde , Theunis Jan , Saito Takashi , Saido Takaomi C. , Jayapala Murali , De Boever Patrick , De Strooper Bart , Stalmans Ingeborg , van Wijngaarden Peter , Moons Lieve , De Groef Lies
Published: July 2020

In this study, we report the results of a comprehensive phenotyping of the retina of theAppNL-G-Fmouse. We demonstrate that soluble Aβ accumulation is present in the retina of these mice early in life and progresses to Aβ plaque formation by midlife. This rising Aβ burden coincides with local microglia reactivity, astrogliosis, and abnormalities in retinal vein morphology. Electrophysiological recordings reveal signs of neuronal dysfunction yet no overt neurodegeneration was observed and visual performance outcomes were unaffected in theAppNL-G-Fmouse. Furthermore, we show that hyperspectral imaging can be used to quantify retinal Aβ, underscoring its potential as a biomarker for AD diagnosis and monitoring. These findings suggest that theAppNL-G-Fretina mimics the early, preclinical stages of AD, and, together with retinal imaging techniques, offers unique opportunities for drug discovery and fundamental research into preclinical AD.
NanoReviser: An Error-correction Tool for Nanopore Sequencing Based on a Deep Learning Algorithm
Authors: Wang Luotong , Qu Li , Yang Longshu , Wang Yiying , Zhu Huaiqiu
Published: July 2020

Nanopore sequencing is regarded as one of the most promising third-generation sequencing (TGS) technologies. Since 2014, Oxford Nanopore Technologies (ONT) has developed a series of devices based on nanopore sequencing to produce very long reads, with an expected impact on genomics. However, the nanopore sequencing reads are susceptible to a fairly high error rate owing to the difficulty in identifying the DNA bases from the complex electrical signals. Although several basecalling tools have been developed for nanopore sequencing over the past years, it is still challenging to correct the sequences after applying the basecalling procedure. In this study, we developed an open-source DNA basecalling reviser, NanoReviser, based on a deep learning algorithm to correct the basecalling errors introduced by current basecallers provided by default. In our module, we re-segmented the raw electrical signals based on the basecalled sequences provided by the default basecallers. By employing convolution neural networks (CNNs) and bidirectional long short-term memory (Bi-LSTM) networks, we took advantage of the information from the raw electrical signals and the basecalled sequences from the basecallers. Our results showed NanoReviser, as a post-basecalling reviser, significantly improving the basecalling quality. After being trained on standard ONT sequencing reads from publicE. coliand human NA12878 datasets, NanoReviser reduced the sequencing error rate by over 5% for both theE. colidataset and the human dataset. The performance of NanoReviser was found to be better than those of all current basecalling tools. Furthermore, we analyzed the modified bases of theE. colidataset and added the methylation information to train our module. With the methylation annotation, NanoReviser reduced the error rate by 7% for theE. colidataset and specifically reduced the error rate by over 10% for the regions of the sequence rich in methylated bases. To the best of our knowledge, NanoReviser is the first post-processing tool after basecalling to accurately correct the nanopore sequences without the time-consuming procedure of building the consensus sequence. The NanoReviser package is freely available athttps://github.com/pkubioinformatics/NanoReviser.
Temperature-dependent competitive outcomes between the fruit fliesDrosophila santomeaandD. yakuba
Authors: Comeault Aaron A. , Matute Daniel R.
Published: July 2020

Changes in temperature associated with climate change can alter species’ distributions, drive adaptive evolution, and, in some cases, cause extinction. Research has tended to focus on the direct effects of temperature, but changes in temperature can also have indirect effects on populations and species. Here we test whether temperature can indirectly affect the fitness ofDrosophila santomeaandD. yakubaby altering interspecific competitive outcomes. We show that, when raised in isolation, bothD. santomeaandD. yakubashow maximal performance at temperatures near 22°C. However, when raised together,D. santomeaoutcompetesD. yakubaat a lower temperature (18°C), whileD. yakubaoutcompetesD. santomeaat a higher temperature (25°C). We then use a ‘coexistence’ experiment to show thatD. santomeais rapidly (within 8 generations) extirpated when maintained withD. yakubaat 25°C. By contrast,D. santomearemains as (or more) abundant thanD. yakubaover the course of ~10 generations when maintained at 18°C. Our results provide an example of how the thermal environment can indirectly affect interspecific competitive outcomes and suggest that changes in the competitive advantage of species can lead to some species becoming more prone to extinction by competitive exclusion.
Microtiter plate-based antibody-competition assay to determine binding affinities and plasma/blood stability of CXCR4 ligands
Authors: Harms Mirja , Gilg Andrea , Ständker Ludger , Beer Ambros J. , Mayer Benjamin , Rasche Volker , Gruber Christian W. , Münch Jan
Published: July 2020

C-X-C chemokine receptor type 4 (CXCR4) is involved in several intractable disease processes, including HIV infection, cancer cell metastasis, leukemia cell progression, rheumatoid arthritis, asthma and pulmonary fibrosis. Thus, CXCR4 represents a promising drug target and several CXCR4 antagonizing agents are in preclinical or clinical development. Important parameters in drug lead evaluation are determination of binding affinities to the receptor and assessment of their stability and activity in plasma or blood of animals and humans. Here, we designed a microtiter plate-based CXCR4 antibody competition assay that enables to measure inhibitory concentrations (IC50values) and affinity constants (Kivalues) of CXCR4 targeting drugs. The assay is based on the observation that most if not all CXCR4 antagonists compete with binding of the fluorescence-tagged CXCR4 antibody 12G5 to the receptor. We demonstrate that this antibody-competition assay allows a convenient and cheap determination of binding affinities of various CXCR4 antagonists in living cells within just 3 hours. Moreover, the assay can be performed in the presence of high concentrations of physiologically relevant body fluids, and thus is a useful readout to evaluate stability (i.e. half-life) of CXCR4 ligands in serum/plasma, and even whole human and mouse bloodex vivo. Thus, this optimized 12G5 antibody competition assay allows a robust and convenient determination and calculation of various important pharmacological parameters of CXCR4 receptor-drug interaction and may not only foster future drug development but also animal welfare by reducing the number of experimental animals.