bluuebunny/crossref_metadata_2025 huggingface dataset:
Urine metabolome of tuberculosis patients receiving intensive phase of treatment show diurnal variations
Authors: Faruquee Hossain Md. , Meitei Heikrujam Nilkanta , Pandey Anupama , Pahwa Falak , Thokchom Maria , Sonia Athokpam , Chaudhary Shweta , Gupta Dinesh , Singh Huidrom Lokhendro , Haobam Sunita , Haobam Reena , Nanda Ranjan Kumar
Published: April 2021

Diurnal variation in biofluid metabolome as observed in a healthy human may alter in perturbed conditions. Biofluids like urine are rich in molecular constituents including metabolites, and infectious disease conditions like tuberculosis (TB) may influence diurnal differences for which limited reports are available in the literature. In this study, we present an optimized gas chromatography coupled to a quadrupole mass spectrometry (GC-MS) method to analyze processed and trimethylsilyl (TMS) derivatized urine metabolites. Urine samples were collected at four time points (0, 6, 12 and 24 hours) of study subjects [n=15; mean age 37 (24-70) in years] including controls [n=7; mean age 29.3 (24-35) years] and culture-confirmed active TB patients [ATB; n=8; mean age 43.7 (25-70) years] receiving treatment in the intensive phase. Global urine metabolite profiling was carried out using the optimized GC-MS method. Higher urine analyte diversity was observed in ATB patients (74) than in controls (36) during the day. Diurnal variations of the parent anti-TB drugs and their breakdown products (pyrazinamide, pyrazinoic acid, 5-hydroxy pyrazinoic acid, isonicotinic acid and alpha amino butyric acid) were observed with maximum abundance at 6 h. Interestingly, urine of ATB subjects at 6 h showed the highest metabolic diversity, whereas it was at 12 h in controls. Many analytes including glycine and alanine amino-acids showed diurnal variation in ATB and controls. These changes could be attributed to the altered host metabolic activities due to disease, treatment-associated decrease in total body bacterial burden and gut microbiota dysbiosis. And the optimized spiked-in internal standard, urine sample volume and GC-MS method could be used for global urine metabolome analysis in healthy and different perturbed conditions.

“For Table of Contents Only”
Denoising physiological data collected during multi-band, multi-echo EPI sequences
Authors: Bottenhorn Katherine L. , Salo Taylor , Riedel Michael C. , Sutherland Matthew T. , Robinson Jennifer L. , Musser Erica D. , Laird Angela R.
Published: April 2021

Collecting physiological data during fMRI experiments can improve fMRI data cleaning and contribute to our understanding of psychophysiological processes; however, these recordings are frequently fraught with artifacts from the MRI pulse sequence. Here, we assess data from BIOPAC Systems, Inc., one of the more widely-used manufacturers of physiological monitoring equipment, and evaluate their recommendations for filtering such artifacts from electrocardiogram and electrodermal activity data collected during single-band, single-echo fMRI sequences and extend these recommendations to address artifacts associated with multiband, multi-echo fMRI sequences. While the magnitude and frequencies of artifacts differ with these aspects of pulse sequences, their effects can be mitigated via application of digital filters incorporating slice collection, multiband factor, and repetition time. The implementation of these filters is provided both in interactive online notebooks and an open source denoising tool.
Tripartite networks show that keystone species can multitask
Authors: Timóteo Sérgio , Albrecht Jörg , Rumeu Beatriz , Norte Ana C. , Traveset Anna , Frost Carol M. , Marchante Elizabete , López-Núñez Francisco A. , Peralta Guadalupe , Memmott Jane , Olesen Jens M. , Costa José M. , da Silva Luís P. , Carvalheiro Luísa G. , Correia Marta , Staab Michael , Blüthgen Nico , Farwig Nina , Hervías-Parejo Sandra , Mironov Sergei , Rodríguez-Echeverría Susana , Heleno Ruben
Published: April 2021

Keystone species are disproportionately important for ecosystem functioning (1,2). However, while all species engage in multiple interaction types with other species, the importance of keystone species is often defined based on a single dimension of their Eltonian niche (3), that is, one type of interaction (e.g., keystone predator). Therefore, it remains unclear whether the importance of keystone species is unidimensional or if it extends across interaction types. We conducted a meta-analysis of tripartite interaction networks to examine whether species importance in one dimension of their niche is mirrored in other niche dimensions, and whether this is associated with interaction outcome, intimacy, or species richness. We show that keystone species importance is positively associated across multiple ecological niche dimensions, independently of species’ abundance, and find no evidence that multidimensionality of keystone species is influenced by the explanatory variables. We propose that the role of keystone species extends across multiple ecological niche dimensions, with important implications for ecosystem resilience and conservation.

Significance Statement

Keystone species are often identified by focusing on a single type of interaction (e.g., predation, pollination, herbivory) which contrasts with the multiple roles that species play in biological communities. We conducted a meta-analysis of 18 tripartite interaction networks to explore if keystonness is correlated across the multiple dimensions of species Eltonian niches. Our results suggest that species importance tends to span across multiple interaction types, independently from abundance, which can be key to understand community resilience and collapse in face of multiple threats.
Bipedalism in Mexican Albian lizard (Squamata) and the locomotion type in other Cretaceous lizards
Authors: Villaseñor-Amador Damián , Suárez Nut Xanat , Cruz J. Alberto
Published: April 2021

Representative locomotion types in lizards include terrestrial, arboreal, grass swimmer, sand swimmer and bipedal. Few studies explain the locomotion habit of extinct lizards, and even less asses those of bipedal ones. Here, we use quantitative methods to infer the type of locomotion of two Albian Mexican lizards (Lower Cretaceous) and three Cretaceous lizards from Brazil, North America and Spain, assessing the similarities of the hindlimb-forelimb length ratio amongst extinct and extant species. Additionally, an ancestral character state reconstruction analysis was performed, to evaluate the evolution of lizard locomotion habits. The speciesHuehuecuetzpalli mixtecuswas bipedal whileTijubina ponteiwas facultative bipedal,Hoyalacerta sanzi, Tepexisaurus tepexiiandPolyglyphanodon sternbergicannot be differentiated amongst terrestrial or arboreal with the approach used in this work. The ancestral character state reconstruction analysis showed a terrestrial ancestral locomotion type, with a basal character state of hindlimbs longer than forelimbs. Equal length between hind and forelimbs appear to be a derivate state that evolved multiple times in lizard evolutionary history.
Transient induction of cell cycle promoter Fam64a improves cardiac function through regulating Klf15-dependent cardiomyocyte differentiation in mice
Authors: Hashimoto Ken , Kodama Aya , Ohira Momoko , Kimoto Misaki , Nakagawa Reiko , Usui Yuu , Ujihara Yoshihiro , Hanashima Akira , Mohri Satoshi
Published: April 2021

The introduction of fetal or neonatal signatures such as cell cycle promoting genes into damaged adult hearts has been vigorously pursued as a promising strategy for stimulating proliferation and regeneration of adult cardiomyocytes, which normally cannot divide. However, cell division of cardiomyocytes requires preceding dedifferentiation with sarcomere disassembly and calcium dysregulation, which, in principle, compromises contractile function. To overcome this intrinsic dilemma, we explored the feasibility of optimizing the induction protocol of the cell cycle promoter in mice. As a model of this approach, we used Fam64a, a fetal-specific cardiomyocyte cell cycle promoter that we have recently identified. We first analyzed transgenic mice maintaining long-term cardiomyocyte-specific expression of Fam64a after birth, when endogenous expression was abolished. Despite having an enhanced proliferation of postnatal cardiomyocytes, these mice showed age-related cardiac dysfunction characterized by sustained cardiomyocyte dedifferentiation, which was reminiscent of the dilemma. Mechanistically, Fam64a inhibited glucocorticoid receptor-mediated transcriptional activation of Klf15, a key regulator that drives cardiomyocyte differentiation, thereby directing cardiomyocytes toward immature undifferentiated states. In contrast, transient induction of Fam64a in cryoinjured wildtype adult mice hearts improved functional recovery with augmented cell cycle activation of cardiomyocytes. These data indicate that optimizing the intensity and duration of the stimulant to avoid excessive cardiomyocyte dedifferentiation could pave the way toward developing efficient strategy for successful heart regeneration.
Alveolar macrophages strictly rely on GM-CSF from alveolar epithelial type 2 cells before and after birth
Authors: Gschwend Julia , Sherman Samantha , Ridder Frederike , Feng Xiaogang , Liang Hong-Erh , Locksley Richard M. , Becher Burkhard , Schneider Christoph
Published: April 2021

Programs defining tissue-resident macrophage identity depend on local environmental cues. For alveolar macrophages (AMs), these signals are provided by immune and non-immune cells, and include GM-CSF (CSF2). However, evidence to functionally link components of this intercellular crosstalk remains scarce. We thus developed new transgenic mice to profile pulmonary GM-CSF expression, which we detected in both immune cells, including group 2 innate lymphoid cells and γδ T cells, as well as AT2s. AMs were unaffected by constitutive deletion of hematopoieticCsf2and basophil depletion. Instead, AT2 lineage-specific constitutive and inducibleCsf2deletion revealed the non-redundant function of AT2-derived GM-CSF in instructing AM fate, establishing the postnatal AM compartment, and maintaining AMs in adult lungs. This AT2-AM relationship begins during embryogenesis, where nascent AT2s timely induce GM-CSF expression to support the proliferation and differentiation of fetal monocytes contemporaneously seeding the tissue, and persists into adulthood, when epithelial GM-CSF remains restricted to AT2s.
Technical advances in the development of zonation liverin vitrosystems that incorporate localized Wnt activating signals
Authors: Valle-Encinas Eider , Dawes Michael , Martinez Carmen Velasco , McSweeney Kate , Müller Miryam , Bird Tom , Dale Trevor
Published: April 2021

A Wnt microenvironment sustained by the hepatic central vein is essential for the segregation of liver functions into zones. Current liver culture systems lack localized Wnt cues and as a consequence fail to maintain the hepatocyte functional heterogeneity that is observed in the intact organ. In this study, organoid models and 2D-culture systems were used to identify cellular sources and Wnt presentation methods that could support the future development of zonated liverin vitrosystems. Using soluble ligands, we show that primary hepatocyte (PH)-derived organoids but not bile duct (BD)-derived organoids may be used to recapitulate the resting liver. We provide evidence that differentiation of PH-organoids in the presence of Wnt9b and Rspo3 induce pericentral maturation. Finally, we show that immobilization of Rspo3 onto beads in combination with soluble Wnt9b may be a valid strategy to recreate the central vein Wnt microenvironmentin vitro.
The natural design for harvesting far-red light: the antenna increases both absorption and quantum efficiency of Photosystem II
Authors: Mascoli Vincenzo , Bhatti Ahmad Farhan , Bersanini Luca , van Amerongen Herbert , Croce Roberta
Published: April 2021

Cyanobacteria carry out photosynthetic light-energy conversion using phycobiliproteins for light harvesting and the chlorophyll-rich photosystems for photochemistry. While most cyanobacteria only absorb visible photons, some of them can acclimate to harvest far-red light (FRL, 700-800 nm) by integrating chlorophyllfanddin their photosystems and producing red-shifted allophycocyanin. Chlorophyllfinsertion enables the photosystems to use FRL but slows down charge separation, reducing photosynthetic efficiency. Here we demonstrate with time-resolved fluorescence spectroscopy that charge separation in chlorophyll-f-containing Photosystem II becomes faster in the presence of red-shifted allophycocyanin antennas. This is different from all known photosynthetic systems, where additional light-harvesting complexes slow down charge separation. Based on the available structural information, we propose a model for the connectivity between the phycobiliproteins and Photosystem II that qualitatively accounts for our spectroscopic data. This unique design is probably important for these cyanobacteria to efficiently switch between visible and far-red light.
Pigs as a new behavioral model for studying Pavlovian eyeblink conditioning
Authors: Boele Henk-Jan , Joung Sangyun , Fil Joanne E. , Mudd Austin T. , Fleming Stephen A. , Koekkoek Sebastiaan K. E. , Dilger Ryan N.
Published: April 2021

Intro

Pigs have been an increasingly popular preclinical model in nutritional neuroscience, as their anatomy, physiology, and nutrition requirements are highly comparable to those of humans. Eyeblink conditioning is one of the most well-validated behavioral paradigms in neuroscience to study underlying mechanisms of learning and memory formation in the cerebellum. Eyeblink conditioning has been performed in many species but has never been done on young pigs. Therefore, our aim here was to develop and validate an eyeblink conditioning paradigm in young pigs.

Method

Eighteen intact male pigs were artificially reared from postnatal day 2 to 30. The eyeblink conditioning setup consisted of a sound-damping box with a hammock that pigs were placed in, which allowed the pig to remain comfortable yet maintain a typical range of head motion. In a delay conditioning paradigm, the conditional stimulus (CS) was a 550 ms blue light-emitting diode (LED), the unconditional stimulus (US) was a 50 ms eye air-puff, the CS-US interval was 500 ms. Starting at postnatal day 14, pigs were habituated for five days to the eyeblink conditioning setup, followed by 5 daily sessions of acquisition training (40 paired CS-US trials each day).

Results

The group-averaged amplitude of eyelid responses gradually increased over the course of the five days of training, indicating that pigs learned to make the association between the LED light CS and the air-puff US. A similar increase was found for the conditioned response (CR) probability: the group-averaged CR probability on session 1 was about 12% and reached a CR probability of 55% on day 5. The latency to CR peak time lacked a temporal preference in the first session, but clearly showed preference from the moment that animals started to show more CRs in session 2 and onwards whereby the eyelid was maximally closed exactly at the moment that the US would be delivered.

Conclusion

We concluded that 4-week-old pigs have the capability of performing in a cerebellar classical association learning task, demonstrating for the first time that eyeblink conditioning in young pigs has the potential to be a valuable behavioral tool to measure neurodevelopment.
Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development
Authors: Bresciani Erica , Carrington Blake , Yu Kai , Kim Erika M. , Zhen Tao , Guzman Victoria Sanchez , Broadbridge Elizabeth , Bishop Kevin , Kirby Martha , Harper Ursula , Wincovitch Stephen , Dell’Orso Stefania , Sartorelli Vittorio , Sood Raman , Liu Paul
Published: April 2021

RUNX1 is essential for the generation of hematopoietic stem cells (HSCs).Runx1null mouse embryos lack definitive hematopoiesis and die in mid-gestation. However, even though zebrafish embryos with arunx1W84X mutation have defects in early definitive hematopoiesis, somerunx1W84X/W84Xembryos can develop to fertile adults with blood cells of multi-lineages, raising the possibility that HSCs can emerge without RUNX1. Here, using three new zebrafishrunx1-/-lines we uncovered the compensatory mechanism forrunx1-independent hematopoiesis. We show that, in the absence of a functionalrunx1, acd41-GFP+population of hematopoietic precursors still emerge from the hemogenic endothelium and can colonize the hematopoietic tissues of the mutant embryos. Single-cell RNA sequencing of thecd41-GFP+cells identified a set ofrunx1-/--specific signature genes during hematopoiesis. Significantly,gata2b, which normally acts upstream ofrunx1for the generation of HSCs, was increased in thecd41-GFP+cells inrunx1- /-embryos. Interestingly, genetic inactivation of bothgata2band its paralog,gata2a, did not affect hematopoiesis. However, knocking outrunx1and any three of the four alleles ofgata2aandgata2babolished definitive hematopoiesis.Gata2expression was also upregulated in hematopoietic cells inRunx1-/-mice, suggesting the compensatory mechanism is conserved. Our findings indicate that RUNX1 and GATA2 serve redundant roles for HSC production, acting as each other’s safeguard.

Key points

Existence of RUNX1-independent mechanisms for the generation of HSCs and the development of functional definitive hematopoietic cells

GATA2 and RUNX1 functionally complement each other for their respective roles during hematopoiesis
Stratification of Risk of Progression to Colectomy in Ulcerative Colitis using Measured and Predicted Gene Expression
Authors: Mo Angela , Nagpal Sini , Gettler Kyle , Haritunians Talin , Giri Mamta , Haberman Yael , Karns Rebekah , Prince Jarod , Arafat Dalia , Hsu Nai-Yun , Chuang Ling-Shiang , Argmann Carmen , Kasarskis Andrew , Suarez-Farinas Mayte , Gotman Nathan , Mengesha Emebet , Venkateswaran Suresh , Rufo Paul A. , Baker Susan S. , Sauer Cary G. , Markowitz James , Pfefferkorn Marian D. , Rosh Joel R. , Boyle Brendan M. , Mack David R. , Baldassano Robert N. , Shah Sapana , LeLeiko Neal S. , Heyman Melvin B. , Griffiths Anne M. , Patel Ashish S. , Noe Joshua D. , Thomas Sonia Davis , Aronow Bruce J. , Walters Thomas D. , McGovern Dermot P. B. , Hyams Jeffrey S. , Kugathasan Subra , Cho Judy H. , Denson Lee A. , Gibson Greg
Published: April 2021

An important goal of clinical genomics is to be able to estimate the risk of adverse disease outcomes. Between 5% and 10% of ulcerative colitis (UC) patients require colectomy within five years of diagnosis, but polygenic risk scores (PRS) utilizing findings from GWAS are unable to provide meaningful prediction of this adverse status. By contrast, in Crohn’s disease, gene expression profiling of GWAS-significant genes does provide some stratification of risk of progression to complicated disease in the form of a Transcriptional Risk Score (TRS). Here we demonstrate that both measured (TRS) and polygenic predicted gene expression (PPTRS) identify UC patients at 5-fold elevated risk of colectomy with data from the PROTECT clinical trial and UK Biobank population cohort studies, independently replicated in an NIDDK-IBDGC dataset. Prediction of gene expression from relatively small transcriptome datasets can thus be used in conjunction with transcriptome-wide association studies to stratify risk of disease complications.
Gene expression inLucilia sericata(Diptera: Calliphoridae) larvae exposed toPseudomonas aeruginosaandAcinetobacter baumaniiidentifies shared and microbe-specific induction of immune genes
Authors: McKenna C.H. , Asgari D. , Crippen T.L. , Zheng L. , Sherman R.A. , Tomberlin J.K. , Meisel R.P. , Tarone A.M.
Published: April 2021

Antibiotic resistance is a continuing challenge in medicine. There are various strategies for expanding antibiotic therapeutic repertoires, including the use of blow flies. Their larvae exhibit strong antibiotic and antibiofilm properties that alter microbiome communities. One species,Lucilia sericata, is used to treat problematic wounds due to its debridement capabilities and its excretions and secretions that kill some pathogenic bacteria. There is much to be learned about howL. sericatainteracts with microbiomes at the molecular level. To address this deficiency, gene expression was assessed after feeding exposure (1 hour or 4 hours) to two clinically problematic pathogens:Pseudomonas aeruginosaandAcinetobacter baumanii. The results identified immunity related genes that were differentially expressed when exposed to these pathogens, as well as non-immune genes possibly involved in gut responses to bacterial infection. There was a greater response toP. aeruginosathat increased over time, while few genes responded toA. baumaniiexposure and expression was not time-dependent. The response to feeding on pathogens indicates a few common responses and features distinct to each pathogen, which is useful in improving wound debridement therapy and helps develop biomimetic alternatives.
Guidelines for obtaining an absolute blood flow index with laser speckle contrast imaging
Authors: Sunil Smrithi , Zilpelwar Sharvari , Boas David A. , Postnov Dmitry D.
Published: April 2021

Laser speckle contrast imaging (LSCI) is a technique broadly applied in research and clinical settings for full-field characterization of tissue perfusion. It is based on the analysis of speckle pattern contrast, which can be theoretically related to the decorrelation time - a quantitative measure of dynamics. A direct contrast to decorrelation time conversion, however, requires prior knowledge of specific parameters of the optical system and scattering media and thus is often impractical. For this reason, and because of the nature of some of the most common applications, LSCI is historically used to measurerelativeblood flow change. Over time, the belief that the absolute blood flow index measured with LSCI is not a reliable metric and thus should not be used has become more widespread. This belief has resulted from the use of LSCI to compare perfusion in different animal models and to obtain longitudinal blood flow index observations without proper consideration given to the stability of the measurement. Here, we aim to clarify the issues that give rise to variability in the repeatability of the quantitative blood flow index and to present guidelines on how to make robust absolute blood flow index measurements with conventional single-exposure LSCI. We also explain how to calibrate contrast to compare measurements from different systems and show examples of applications that are enabled by high repeatability.
Quantitative resistance loci to southern rust mapped in a temperate maize diversity panel
Authors: Sun Guangchao , Mural Ravi V. , Turkus Jonathan D. , Schnable James C.
Published: April 2021

Southern rust is a severe foliar disease of maize resulting from infection with the obligate biotrophic fungus,Puccinia polysora. The disease reduces photosynthetic productivity which reduces yields with the greatest yield losses (up to 50%) associated with earlier onset infections.Puccinia polysoraurediniospores overwinter only in tropical and subtropical regions but cause outbreaks when environmental conditions favor initial infection. Increased temperatures and humidity during the growing season, combined with an increased frequency of moderate winters are likely to increase the frequency of severe southern rust outbreaks in the US corn belt. In summer 2020, a severe outbreak of Southern Rust was observed in eastern Nebraska (NE), USA. Disease incidence severity showed significant variation among maize genotypes. A replicated maize association panel planted in Lincoln, NE was scored for disease severity. Genome wide association studies identified four loci associated with significant quantitative variation in disease severity which were associated with candidate genes with plausible links to quantitative disease resistance and a transcriptome wide association study conducted identified additional associated genes. Together these results indicate substantial diversity in resistance to southern rust exists among current temperate adapted maize germplasm, including several candidate loci which may explain observed variation in resistance to southern rust.
Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data Reveal their Clinical Impact
Authors: Yavuz Bengi Ruken , Tsai Chung-Jung , Nussinov Ruth , Tuncbag Nurcan
Published: April 2021

Background

Transforming patient-specific molecular data into clinical decisions is fundamental to personalized medicine. Despite massive advancements in cancer genomics, to date driver mutations whose frequencies are low, and their observable transformation potential is minor have escaped identification. Yet, when paired with other mutationsin cis, such ‘latent driver’ mutations can drive cancer. Here, we discover potential ‘latent driver’ double mutations.

Method

We applied a statistical approach to identify significantly co-occurring mutations in the pan-cancer data of mutation profiles of ∼80,000 tumor sequences from the TCGA and AACR GENIE databases. The components of same gene doublets were assessed as potential latent drivers. We merged the analysis of the significant double mutations with drug response data of cell lines and patient derived xenografts (PDXs). This allowed us to link the potential impact of double mutations to clinical information and discover signatures for some cancer types.

Results

Our comprehensive statistical analysis identified 228 same gene double mutations of which 113 mutations are cataloged as latent drivers. Oncogenic activation of a protein can be through either single or multiple independent mechanisms of action. Combinations of a driver mutation with either a driver, a weak driver, or a strong latent driver have the potential of a single gene leading to a fully activated state and high drug response rate. Tumor suppressors require higher mutational load to coincide with double mutations compared to oncogenes which implies their relative robustness to losing their functions. Evaluation of the response of cell lines and patient-derived xenograft data to drug treatment indicate that in certain genes double mutations can increase oncogenic activity, hence a better drug response (e.g. in PIK3CA), or they can promote resistance to the drugs (e.g. in EGFR).

Conclusion

Our comprehensive analysis of same allele double mutations in cancer genome landscapes emphasizes that interrogation of big genomic data and integration with the results of large-scale small-molecule sensitivity data can provide deep patterns that are rare; but can still result in dramatic phenotypic alterations, and provide clinical signatures for some cancer types.
Roads as ecological traps for giant anteaters
Authors: Noonan Michael J. , Ascensão Fernando , Yogui Débora R. , Desbiez Arnaud L.J.
Published: April 2021

Wildlife-vehicle collisions (WVC) represent a serious source of mortality for many species, threatening local populations’ persistence while also carrying a high economic and human safety cost. Animals may adapt their behaviour to road associated threats, but roadside resources can act as attractants, providing misleading signals about the quality of roadside habitats, ultimately acting as an ecological trap. Yet, the extent to which individuals modify their behaviour and space use to roads is largely unknown for most taxa. Using fine-scale movement data from 41 giant anteaters (Myrmecophaga tridactyla), tracked in the Brazilian Cerrado, we aimed to identify facets of movement behaviour that might exhibit plasticity to roads and traffic volume. Specifically, the analysis of daily and instantaneous movement speeds, home range characteristics, and crossing rates/times, allowed us to test for an effect of road proximity, traffic volume and natural linear features on movement behaviour. We found no effect of road proximity or traffic volume on space use or movement behaviour. While individuals tended to reduce their movement speed when approaching roads and crossed roads ~3 times less than would have been expected by random chance, none of the highways we monitored were impervious. The majority of tracked anteaters living near roads (<2km) crossed them, with higher crossing rates for males. Consequently, habitat near roads may function as an ecological trap where healthy individuals occupy the territories nearby or bisected by roads but eventually are road-killed given their regular crossings, leaving the territory vacant for subsequent occupation. Crucially, we found no evidence that anteaters actively searched for passage structures to cross the roads. This suggests that crossing structures alone are unlikely to mitigate WVC induced mortality. Our research reinforces the need to implement fencing, properly linked to existing passages, and minimising the amount of night-time driving to reduce the number of WVCs.

Article Impact Statement

Analyses of giant anteater movement show how roads act as ecological traps, reinforcing the need for fencing and reduced night-time driving.
Modeling The Effect of Background Sounds on Human Focus Using Brain Decoding Technology
Authors: Haruvi Aia , Kopito Ronen , Brande-Eilat Noa , Kalev Shai , Kay Eitan , Furman Daniel
Published: April 2021

The goal of this study was to investigate the effect of sounds on human focus and to identify the properties that contribute most to increasing and decreasing focus in people within their natural, everyday environment. Participants (N=62, 18-65y) performed various tasks on a tablet computer while listening to either no background sounds (silence), popular music playlists designed to increase focus (pre-recorded songs in a particular sequence), or engineered soundscapes that were personalized to individual listeners (digital audio composed in real-time based on input parameters such as heart rate, time of day, location, etc.). Sounds were delivered to participants through headphones while simultaneously their brain signals were recorded by a portable electroencephalography headband. Participants completed four one-hour long sessions at home during which different sound content played continuously. Using brain decoding technology, we obtained individual participant focus levels over time and used this data to analyze the effects of various properties of sound. We found that while participants were working, personalized soundscapes increased their focus significantly above silence (p=0.008), while music playlists did not have a significant effect. For the young adult demographic (18-36y), all sound content tested was significantly better than silence at producing focus (p=0.001-0.009). Personalized soundscapes increased focus the most relative to silence, but playlists of pre-recorded songs also increased focus significantly during specific time intervals. Ultimately we found that it is possible to accurately predict human focus levels that will be experienced in response to soundsa prioribased on the sound’s physical properties. We then applied this finding to compare between music genres and revealed that classical music, engineered soundscapes, and natural sounds were the best genres for increasing focus, while pop and hip-hop were the worst. These insights can enable human and artificial intelligence composers to produce increases or decreases in listener focus with high temporal (millisecond) precision. Future research will include real-time adaptation of sound libraries for other functional objectives beyond affecting focus, such as affecting listener enjoyment, stress, and memory.
Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN
Authors: Moeller Nicholas H. , Shi Ke , Demir Özlem , Banerjee Surajit , Yin Lulu , Belica Christopher , Durfee Cameron , Amaro Rommie E. , Aihara Hideki
Published: April 2021

High-fidelity replication of the large RNA genome of coronaviruses (CoVs) is mediated by a 3′-to-5′ exoribonuclease (ExoN) in non-structural protein 14 (nsp14), which excises nucleotides including antiviral drugs mis-incorporated by the low-fidelity viral RNA-dependent RNA polymerase (RdRp) and has also been implicated in viral RNA recombination and resistance to innate immunity. Here we determined a 1.6-Å resolution crystal structure of SARS-CoV-2 ExoN in complex with its essential co-factor, nsp10. The structure shows a highly basic and concave surface flanking the active site, comprising several Lys residues of nsp14 and the N-terminal amino group of nsp10. Modeling suggests that this basic patch binds to the template strand of double-stranded RNA substrates to position the 3′ end of the nascent strand in the ExoN active site, which is corroborated by mutational and computational analyses. Molecular dynamics simulations further show remarkable flexibility of multi-domain nsp14 and suggest that nsp10 stabilizes ExoN for substrate RNA-binding to support its exoribonuclease activity. Our high-resolution structure of the SARS-CoV-2 ExoN-nsp10 complex serves as a platform for future development of anti-coronaviral drugs or strategies to attenuate the viral virulence.
UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues
Authors: Yapp Clarence , Novikov Edward , Jang Won-Dong , Vallius Tuulia , Chen Yu-An , Cicconet Marcelo , Maliga Zoltan , Jacobson Connor A. , Wei Donglai , Santagata Sandro , Pfister Hanspeter , Sorger Peter K.
Published: April 2021

Newly developed technologies have made it feasible to routinely collect highly multiplexed (20-60 channel) images at subcellular resolution from human tissues for research and diagnostic purposes. Extracting single cell data from such images requires efficient and accurate image segmentation, a challenging problem that has recently benefited from the use of deep learning. In this paper, we demonstrate two approaches to improving tissue segmentation that are applicable to multiple deep learning frameworks. The first uses “real augmentations” that comprise defocused and saturated image data collected on the same instruments as the actual data; using real augmentation improves model accuracy to a significantly greater degree than computational augmentation (Gaussian blurring). The second involves imaging the nuclear envelope to better identify nuclear outlines. The two approaches cumulatively and substantially improve segmentation on a wide range of tissue types and provide a set of improved segmentation models. We speculate that the use of real augmentations may have applications in image processing outside of microscopy.
Unbiased clade age estimation using a Bayesian Brownian Bridge
Authors: Silvestro Daniele , Bacon Christine D. , Ding Wenna , Zhang Qiuyue , Donoghue Philip C. J. , Antonelli Alexandre , Xing Yaowu
Published: April 2021

In a recent paper1we presented a new model, the Bayesian Brownian Bridge (BBB), to infer clade age based on fossil evidence and modern diversity. We benchmarked the method with extensive simulations, including a wide range of diversification histories and sampling heterogeneities that go well beyond the necessarily simplistic model assumptions. Applying BBB to 198 angiosperm families, we found that their fossil record is compatible with clade origins earlier than most contemporary palaeobotanical interpretations. In particular, we estimated with high probability that crown-angiosperms originated before the Cretaceous (> 145 Ma). Budd and colleagues2critique our study, arguing that the BBB model is biased towards older estimates when fossil data are scarce or absent, that our underlying fossil dataset is unsound, that our clade age estimates are therefore biased by early diverging lineages that are underrepresented in the fossil record, and that pooling of fossil data for analysis at higher taxonomic ranks overcomes these biases. Here, we explore their points and perform new simulations to show that their critique has no merit.
Impaired top-down auditory processing despite extensive single-neuron responses during human sleep
Authors: Hayat Hanna , Marmelshtein Amit , Krom Aaron J. , Sela Yaniv , Tankus Ariel , Strauss Ido , Fahoum Firas , Fried Itzhak , Nir Yuval
Published: April 2021

Sleep in all species is universally defined as a reversible, homeostatically-regulated state of a reduced behavioral responsiveness, with a high arousal threshold in response to external sensory stimulation1. However, it remains unclear whether sleep mainly gates motor output or affects responses along sensory pathways, and whether sleep primarily modulates specific aspects of the sensory response such as feedforward vs. feedback signaling2–7. Here, we simultaneously recorded polysomnography, iEEG, microwire LFPs, and neuronal spiking activity during wakefulness and sleep in 13 epilepsy patients implanted with clinical depth electrodes, while presenting auditory stimuli (e.g. click-trains, words, music). The results revealed robust spiking and induced LFP high-gamma (80-200Hz) power responses during both NREM and REM sleep across the lateral temporal lobe. The magnitude of the responses was only moderately attenuated in sleep, most notably for late responses beyond the early auditory cortex. Nonetheless, sleep responses maintained their tight locking with soundwave envelopes and their information content was only minimally affected. In contrast, a decrease in LFP alpha-beta (10-30Hz) power responses was prevalent in wakefulness but significantly disrupted in sleep. Entrainment to 40 Hz click-trains was comparable across REM sleep and wakefulness, but reduced in NREM sleep. In conclusion, our results establish the presence of extensive and robust auditory responses during sleep while LFP alpha-beta power decrease, likely reflecting top-down processes8–10, is deficient. More broadly, our findings suggest that feedback signalling is key to conscious sensory processing11–13.
Electrical Propagation of Condensed and Diffuse Ions Along Actin Filaments
Authors: Hunley Christian , Marucho Marcelo
Published: April 2021

In this article, we elucidate the role of divalent ion condensation and high polarization of immobile water molecules in the condensed layer on the propagation of ionic calcium waves along actin filaments. We introduced a novel electrical triple layer model and used a non-linear Debye-Huckel theory with a non-linear, dissipative, electrical transmission line model to characterize the physicochemical properties of each monomer in the filament. This characterization is carried out in terms of an electric circuit model containing monomeric flow resistances and ionic capacitances in both the condensed and diffuse layers. In our studies, we characterized the biocylindrical actin filament model using a high resolution molecular structure. We considered resting and excited states of a neuron using representative mono and divalent electrolyte mixtures. Additionally, we used 0.05Vand 0.15Vvoltage inputs to study ionic waves in voltage clamp experiments on actin filaments. Our results reveal that the physicochemical properties characterizing the condensed and diffuse layers lead to different electrical conduction mediums depending on the ionic species and the neuron state. This region specific propagation mechanism provides a more realistic avenue of delivery by way of cytoskeleton filaments for larger charged cationic species. This new direct path for transporting divalent ions might be crucial for many electrical processes that connect different compartments of the neuron to the soma.
Artificial mosaic brain evolution of relative telencephalon size improves cognitive performance in the guppy (Poecilia reticulata)
Authors: Triki Zegni , Fong Stephanie , Amcoff Mirjam , Kolm Niclas
Published: April 2021

The telencephalon is a brain region believed to have played an essential role during cognitive evolution in vertebrates. However, till now, all the evidence on the evolutionary association between telencephalon size and cognition stem from comparative studies. To experimentally investigate the potential evolutionary association between cognitive abilities and telencephalon size, we used male guppies artificially selected for large and small telencephalon relative to the rest of the brain. In a detour task, we tested a functionally important aspect of executive cognitive ability; inhibitory control abilities. We found that males with larger telencephalon outperformed males with smaller telencephalon. They showed faster improvement in performance during detour training and were more successful in reaching the food reward without touching the transparent barrier. Together, our findings provide the first experimental evidence showing that evolutionary enlargements of relative telencephalon size confer cognitive benefits, supporting an important role for mosaic brain evolution during cognitive evolution.
Unveiling the neural correlates of habit in the dorsal striatum
Authors: Vandaele Y. , Janak P.H.
Published: April 2021

We have recently reported sustained inhibition in the dorsomedial striatum (DMS) and sustained excitation in the dorsolateral striatum (DLS) during execution of a lever press sequence in a discrete-trials task promoting habit. This sustained dorsostriatal activity was present early on, and did not clearly change in step with improved performance over ten training sessions. Early onset of sequence-related neural activity could have resulted from rapid habitual learning promoted by presentation of lever cues, predicting reward availability and delivery. To test this hypothesis, we compared DLS and DMS spiking activity in the discrete trials habit-promoting task with two task variants that promote goal-directed behavior. Comparison of the three tasks revealed that mean neuronal spiking activity was generally sustained across the lever press sequence in the task promoting habit and characterized by overall excitation in DLS and inhibition in DMS relative to baseline. In contrast, mean activity differences in DLS and DMS were much less prominent, and most changes occurred transiently around individual lever presses, in the tasks promoting goal-directed behavior. These results indicate that sequence delineation cues, such as the lever cues in these studies, promote habitual behavior and that this habitual behavior is encoded in the striatum by cue-triggered sustained DLS excitation and DMS inhibition that likely reflects cue-elicited behavioral chunking.
Perfluorooctanoic Acid Induces Liver and Serum Dyslipidemia in Humanized PPARα Mice fed an American Diet
Authors: Schlezinger JJ , Hyötyläinen T , Sinioja T , Boston C , Puckett H , Oliver J , Heiger-Bernays W , Webster TF
Published: April 2021

Per- and polyfluoroalkyl substances (PFAS) are pervasive in the environment resulting in nearly universal detection in people. Human serum PFAS concentrations are strongly associated with increased serum low-density lipoprotein cholesterol (LDL-C), and growing evidence suggests an association with serum triacylglycerides (TG). Here, we tested the hypothesis that perfluorooctanoic acid (PFOA) dysregulates liver and serum triacylglycerides in human peroxisome proliferator activated receptor α (hPPARα)-expressing mice fed an American diet. Mice were exposed to PFOA (3.3 mg/l) in drinking water for 6 weeks resulting in a serum concentration of 48 ± 9 μg/ml. In male and female hPPARα mice, PFOA increased total liver TG and TG substituted with saturated and monounsaturated fatty acids. Lack of expression of hPPARα alone also increased total liver TG, and PFOA treatment had little effect on liver TG in null mice. In hPPARα mice, PFOA neither significantly increased nor decreased serum TG; however, there was a modest increase in TG associated with very low-density cholesterol particles in both sexes. Across studies, a non-monotonic effect of PFOA on serum TG is evident, with the serum PFOA concentration in this study falling near the “null point” between increasing and decreasing serum TG. Intriguingly, in female PPARα null mice, PFOA significantly increased serum TG, with a similar trend in males. PFOA also modified fatty acid and TG homeostasis-related gene expression in liver, in a hPPARα-dependent manner, but not in adipose. The results reveal the importance of context (serum concentration and genotype) in determining the effect of PFOA on lipid homeostasis.
Cobolt: Joint analysis of multimodal single-cell sequencing data
Authors: Gong Boying , Zhou Yun , Purdom Elizabeth
Published: April 2021

A growing number of single-cell sequencing platforms enable joint profiling of multiple omics from the same cells. We present Cobolt, a novel method that not only allows for analyzing the data from joint-modality platforms, but provides a coherent framework for the integration of multiple datasets measured on different modalities. We demonstrate its performance on multi-modality data of gene expression and chromatin accessibility and illustrate the integration abilities of Cobolt by jointly analyzing this multi-modality data with single-cell RNA-seq and ATAC-seq datasets.
Halfway to self-sustainability: Reintroduced migratory European Northern Bald Ibises (Geronticus eremita) still need management interventions for population viability
Authors: Drenske Sinah , Radchuk Viktoriia , Scherer Cédric , Esterer Corinna , Kowarik Ingo , Fritz Johannes , Kramer-Schadt Stephanie
Published: April 2021

Northern Bald Ibis (NBI) have disappeared from Europe already in Middle Age. Since 2003 a migratory population is reintroduced in Central Europe. We conducted demographic analyses of survival and reproduction of 384 NBI over a period of 12 years (2008-2019). These data also formed the basis for a population viability analysis (PVA) simulating the possible future development of the NBI population in different scenarios. We tested life-stage specific survival rates for differences between these stages, raising types and colonies as well as the influence of stochastic events and NBI supplements on the population growth.

Stage specific survival rates ranged from 0.64 to 0.78. 61% of the mature females reproduce with a mean fecundity of 2.15 fledglings per nest. The complementary PVA indicated that the release population is close to self-sustainability with a given lambda 0.95 and 24% extinction probability within 50 years. Of the 326 future scenarios tested, 94 % reached the criteria of <5% extinction probability and population growth rates >1. In case of positive population growth, stochastic events had a limited effect. Of 820 sub-scenarios with different stochastic event frequencies and severities 87 % show population growth despite the occurrence of stochastic events.

Predictions can be made based on the results of the individual-based model as to whether and under what circumstances the reintroduced NBI population can survive. This study shows that a PVA can support reintroduction success that should work closely together with the project in the field for mutual benefit, to optimize future management decisions.