bluuebunny/crossref_metadata_2025 huggingface dataset:
In situnovel environment assay reveals acoustic exploration as a repeatable behavioral response in migratory bats
Authors: Schabacker Theresa , Lindecke Oliver , Rizzi Sofia , Marggraf Lara , Pētersons Gunārs , Voigt Christian C. , Snijders Lysanne
Published: April 2021

Integrating information on species-specific sensory perception together with spatial activity provides a high-resolution understanding of how animals explore environments, yet frequently used exploration assays commonly ignore sensory acquisition as a measure for exploration. Echolocation is an active sensing system used by hundreds of mammal species, primarily bats. As echolocation call activity can be reliably quantified, bats present an excellent animal model to investigate intra-specific variation in environmental cue sampling. Here, we developed anin situroost-like novel environment assay for tree-cave roosting bats. We repeatedly tested 52 individuals of the migratory bat species,Pipistrellus nathusii, across 24 hours, to examine the role of echolocation when crawling through a maze-type arena and test for consistent intra-specific variation in sensory-based exploration. We reveal a strong correlation between echolocation call activity and spatial activity. Moreover, we show that during the exploration of the maze, individuals consistently differed in spatial activity as well as echolocation call activity given their spatial activity, a behavioral response we term ‘acoustic exploration’. Acoustic exploration was correlated with other exploratory behaviors, but not with emergence latency. We here present a relevant new measure for exploration behavior and provide evidence for consistent (short-term) intra-specific variation in the level at which wild bats collect information from a novel environment.
Miami-Dade: A Case Study of Domestic Violence Arrests During the COVID-19 Pandemic
Authors: Kurland Justin , Piquero Alex R. , Piquero Nicole Leeper
Published: April 2021

The global health crisis that started early in 2020 has triggered a surge of interest in the effect (if any) of COVID-19 on patterns of domestic violence.1 The first systematic review and meta-analysis examining domestic violence during the pandemic revealed quite a lot of diversity in the approaches used to measure potential effects. Drawing on the time series forecasting literature, this brief report contributes to the growing body of evidence around the issue of domestic violence during the pandemic. Arrest data from Miami-Dade County (US) are leveraged along with a robust approach towards model identification, which is used to generate a suitably accurate forecast against which the observed pandemic period domestic violence data can be compared. The pattern uncovered for Miami-Dade County was similar what was found in other U.S. cities that during the pandemic experienced spikes (+95 CI) in the level of domestic violence arrests that were greater than expected. Interestingly these spikes appeared shortly after dips (−95 CI) in observed arrests fell below the expected level.
The dark side of SARS-CoV-2 rapid antigen testing: screening asymptomatic patients
Authors: Caruana Giorgia , Lebrun Laure-Line , Aebischer Oriane , Opota Onya , Urbano Luis , de Rham Mikael , Marchetti Oscar , Greub Gilbert
Published: April 2021

Most of the reports describing SARS-CoV-2 rapid antigen tests (RATs) performances derive from COVID-19 symptomatic subjects in outpatient settings during periods of highest incidence of infections and high rates of hospital admissions. Here we investigated the role of RATs in an Emergency Department, as a screening tool before admission for COVID-19 asymptomatic patients. Each patient was screened with two simultaneous nasopharyngeal swabs: one immediately analyzed at the bedside using RAT and the other sent to the laboratory for RT-PCR analysis. A total of 116 patients were screened at hospital admission in a 250-bed community hospital in Morges (EHC), Switzerland. With a disease prevalence of 6% based on RT-PCR results, RAT detected only two out of seven RT-PCR positive patients (sensitivity 28.6%) and delivered two false positive results (specificity 98.2%), thus resulting not fiable enough to be used as a screening method in this clinical scenario.
Sex differences in TB treatment outcomes: Retrospective cohort study and meta-analysis
Authors: Chidambaram Vignesh , Tun Nyan Lynn , Majella Marie Gilbert , Castillo Jennie Ruelas , Ayeh Samuel K. , Kumar Amudha , Neupane Pranita , Sivakumar Ranjith Kumar , Win Ei Phyo , Abbey Enoch J. , Wang Siqing , Zimmerman Alyssa , Blanck Jaime , Gupte Akshay , Wang Jann-Yuan , Karakousis Petros C.
Published: April 2021

Rationale

Although the incidence of tuberculosis (TB) is higher in males compared to females, the relationship of sex with TB treatment outcomes has not been adequately studied.

Objectives and Methods

We performed a retrospective cohort study and a systematic review and meta-analysis of observational studies during the last 10 years to assess the sex differences in clinical and microbiological outcomes in tuberculosis.

Measurements and Main Results

In our cohort of 2,894 patients with drug-susceptible pulmonary TB (1,975 males and 919 females), males had higher adjusted hazards of mortality due to all causes (HR 1·43,95%CI 1.03-1.98) and infections (HR 1.70, 95%CI 1.09-2.64) at 9 months and higher adjusted odds ratio for sputum culture (OR 1.56,95%CI 1.05-2.33) and similar odds ratio for smear positivity (OR 1.27, 0.71-2.27) at 2 months compared to females. Among 7896 articles retrieved, 398 articles were included in our systematic review with a total of 3,957,216 patients. The odds of all-cause mortality was higher in males compared to females in the pooled unadjusted (OR 1.26, 95%CI 1.19-1.34) and adjusted (OR 1.31, 95%CI 1.18-1.45) analyses. Relative to females, males had higher pooled odds of sputum culture (OR 1.44,95% CI 1.14-1.81) and sputum smear (OR 1.58,95%CI 1.41-1.77) positivity at the end of the intensive phase, and upon completion of treatment.

Conclusions

During TB treatment, males have higher all-cause-, infection- and TB-related mortality, as well as higher rates of sputum smear and culture positivity, both after the intensive phase and at the completion of TB treatment, after adjusting for confounding factors.
Stingless bee floral visitation in the global tropics and subtropics
Authors: Garcia Bulle Bueno Francisco , Kendall Liam , Araujo Alves Denise , Lequerica Tamara Manuel , Heard Tim , Latty Tanya , Gloag Rosalyn
Published: April 2021

Bees play a key role in maintaining healthy terrestrial ecosystems by pollinating plants. Stingless bees (Apidae: Meliponini) are a diverse clade of social bees (>500 species) with a pantropical distribution spanning South and Central America, Africa, India, Australia and Asia. They are garnering increasing attention as commercially-beneficial pollinators of some crops, yet their contribution to the pollination of native plants in the tropics and subtropics remains poorly understood. Here we conduct a global review of the plants visited by stingless bees. We compile a database of reported associations (flower visits) between stingless bees and plants, from studies that have made either direct observations of foraging bees or analysed the pollen stored in nests. Worldwide, we find stingless bees have been reported to visit the flowers of plants from at least 220 different families and 1465 genera, with frequently reported interactions for many of the tropic’s most species-diverse plant families including Fabaceae, Asteraceae, Rubiaceae, Malvaceae, Lamiaceae, Arecaceae, Euphorbiaceae, Poaceae, Apocinaceae, Bignoniaceae, Melastomataceae and Myrtaceae. The list of commonly-visited plant families was similar for the stingless bee fauna of each of three major biogeographic regions (Neotropical, Afrotropical and Indo-Malayan-Australasian), though we detected differences in the proportional use of plant families by the stingless bees of the Indo-Malayan-Australasian and Neotropical regions, likely reflecting differences in the available flora of those regions. Stingless bees in all regions visit a range of exotic species in their preferred plant families (crops, ornamental plants and weeds), in addition to native plants. Although most reports of floral visitation on wild plants do not confirm effective pollen transfer, it is likely that stingless bees make at least some contribution to pollination for the majority of plants they visit. In all, our database supports the view that stingless bees play an important role in the ecosystems of the global tropics and subtropics as pollinators of an exceptionally large and diverse number of plants. This database also highlights important gaps in our knowledge of stingless bee resource use that may help focus future research efforts.
Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA
Authors: Paget Max , Cadena Cristhian , Ahmad Sadeem , Wang Hai-Tao , Jordan Tristan X. , Kim Ehyun , Koo Beechui , Lyons Shawn M. , Ivanov Pavel , tenOever Benjamin , Mu Xin , Hur Sun
Published: April 2021

Proper defense against microbial infection depends on the controlled activation of the immune system. This is particularly important for the RIG-I-like receptors (RLRs), which recognize viral dsRNA and initiate antiviral innate immune responses with the potential of triggering systemic inflammation and immunopathology. Here we show that stress granules (SGs), molecular condensates that form in response to various stresses including viral dsRNA, play key roles in controlled activation of RLR signaling. Without the SG nucleators G3BP1/2 and UBAP2L, dsRNA triggers excessive inflammation and immune-mediated apoptosis. In addition to exogenous dsRNA, we find that host-derived dsRNA generated in response to ADAR1 deficiency is also controlled by SG biology. Intriguingly, SGs can function beyond immune control by suppressing viral replication independent of the RLR pathway. These observations thus highlight the multi-functional nature of SGs as cellular “shock absorbers” that converge on protecting cell homeostasis–by dampening both toxic immune response and viral replication.
Surface-Shaving Proteomics ofMycobacterium marinumIdentifies Biofilm Subtype-Specific Changes Affecting Virulence, Tolerance and Persistence
Authors: Savijoki Kirsi , Myllymäki Henna , Luukinen Hanna , Paulamäki Lauri , Vanha-aho Leena-Maija , Svorjova Aleksandra , Miettinen Ilkka , Fallarero Adyary , Ihalainen Teemu O. , Yli-Kauhaluoma Jari , Nyman Tuula A. , Parikka Mataleena
Published: April 2021

The complex cell wall and biofilm matrix (ECM) act as key barriers to antibiotics in mycobacteria. Here, the ECM-proteins ofMycobacterium marinumATCC927, a non-tuberculous mycobacterial model, was monitored over three months by label-free proteomics and compared with cell-surface proteins on planktonic cells to uncover pathways leading to virulence, tolerance, and persistence. We show that ATCC927 forms pellicle-type (PBFs) and submerged-type (SBFs) biofilms after two weeks and two days of growth, respectively, and that the increased CelA1 synthesis in this strain prevents biofilm formation and leads to reduced rifampicin tolerance. The proteomic data suggests that specific changes in mycolic acid synthesis (cord factor), Esx1-secretion, and cell-wall adhesins explain the appearance of PBFs as ribbon-like cords and SBFs as lichen-like structures. A subpopulation of cells resisting the 64 × MIC rifampicin (persisters) were detected in both biofilm subtypes, and already in one-week-old SBFs. The key forces boosting their development could include subtype-dependent changes in asymmetric cell division, cell wall biogenesis, tricarboxylic acid/glyoxylate cycle activities, and energy/redox/iron metabolisms. The effect of varying ambient oxygen tensions on each cell type and non-classical protein secretion are likely factors explaining majority of the subtype-specific changes. The proteomic findings also imply that Esx1-type protein secretion is more efficient in PL and PBF cells, while SBF may prefer both the Esx5- and non-classical pathways to control virulence and prolonged viability/persistence. In conclusion, this study reports a first proteomic insight into aging mycobacterial biofilm-ECMs and indicates biofilm subtype-dependent mechanisms conferring increased adaptive potential and virulence on non-tuberculous mycobacteria.

IMPORTANCE

Mycobacteria are naturally resilient and mycobacterial infections are notoriously difficult to treat with antibiotics, with biofilm formation being the main factor complicating the successful treatment of TB. The present study shows that non-tuberculousMycobacterium marinumATCC927 forms submerged- and pellicle-type biofilms with lichen- and ribbon-like structures, respectively, as well as persister cells under the same conditions. We show that both biofilm subtypes differ in terms of virulence-, tolerance- and persistence-conferring activities, highlighting the fact that both subtypes should be targeted to maximize the power of antimycobacterial treatment therapies.
In vitroefficacy of gentamicin against multidrug-resistantNeisseria gonorrhoeae: synergy of three gentamicin antimicrobial combinations
Authors: Li Xuechun , Le Wenjing , Lou Xiangdi , Wang Biwei , Genco Caroline A. , Rice Peter A. , Su Xiaohong
Published: April 2021

Objectives

To determinein vitroactivities of gentamicin alone and in combination with ceftriaxone, ertapenem and azithromycin against multidrug-resistant (MDR)N. gonorrhoeaeisolates.

Methods

407 isolates from Nanjing, China, obtained in 2016 and 2017, had minimum inhibitory concentrations (MICs) determined for gentamicin using the agar dilution method. Antimicrobial combinations were also tested in 97 MDR strains using the antimicrobial gradient epsilometer test (Etest); results ranging from synergy to antagonism were interpreted using the fractional inhibitory concentration (FICI).

Results

All 407 gonococcal isolates were susceptible to gentamicin. MICs ranged from 2 mg/L to 16 mg/L. Synergy was demonstrated in 16.5%(16/97), 27.8%(27/97) and 8.2%(8/97) MDR strains when gentamicin was combined with ceftriaxone [geometric mean (GM) FICI; 0.747], ertapenem (GM FICI; 0.662) and azithromycin (GM FICI; 1.021), respectively. No antimicrobial antagonism was observed with any combination. The three antimicrobial combinations were indifferent overall. The overall GM MICs of gentamicin were reduced by 2.63-, 3.80- and 1.98-fold when tested in combination with ceftriaxone, ertapenem and azithromycin, respectively. The GM MICs of the three antimicrobials by themselves were reduced by 3-, 2.57- and 1.98-fold respectively, when each was tested in combination with gentamicin. No antimicrobial antagonism was observed with any combination.

Conclusions

Gentamicin alone was effectivein vitroagainst MDRN. gonorrhoeaeand in combination with ceftriaxone, ertapenem or azithromycin. Combination testing of resistant strains, overall, showed lower effective MICs against gentamicin itself and each of the three antimicrobials when used in combination with gentamicin.
A Stable Nano-Vaccine for the Targeted Delivery of Tumor-Associated Glycopeptide Antigens
Authors: Trabbic Kevin R. , Kleski Kristopher A. , Barchi Joseph J
Published: April 2021

We have developed a novel antigen delivery system based on polysaccharide-coated gold nanoparticles (AuNPs) targeted to antigen presenting cells (APCs) expressing Dectin-1. AuNPs were synthesized de-novo using yeast-derived β-1,3-glucans (B13Gs) as the reductant and passivating agent in a microwave-catalyzed procedure yielding highly uniform and serum-stable particles. These were further functionalized with both peptides and glycopeptides from the tandem repeat sequence of mucin 4 (MUC4), a glycoprotein overexpressed in pancreatic tumors. The glycosylated sequence contained the Thomsen-Friedenreich disaccharide, a pan-carcinoma, Tumor-Associated Carbohydrate Antigen (TACA), which has been a traditional target for antitumor vaccine design. These motifs were prepared with a cathepsin B protease cleavage site (Gly-Phe-Leu-Gly), loaded on the B13Gs-coated particles and these constructs were examined for Dectin-1 binding, APC processing and presentation in a model in vitro system and for immune responses in mice. We showed that these particles elicit strong in vivo immune responses through the production of both high-titer antibodies and priming of antigen-recognizing T-cells. Further examination showed that a favorable antitumor balance of expressed cytokines was generated, with limited expression of immunosuppressive Il-10. This system is modular in that any range of antigens can be conjugated to our particles and efficiently delivered to APCs expressing Dectin-1.
From musk to body odor: decoding olfaction through genetic variation
Authors: Li Bingjie , Kamarck Marissa L. , Peng Qianqian , Lim Fei-Ling , Keller Andreas , Smeets Monique A.M. , Mainland Joel D. , Wang Sijia
Published: April 2021

The olfactory system combines input from multiple receptor types to represent odor information, but there are few explicit examples relating olfactory receptor (OR) activity patterns to odor perception. To uncover these relationships, we performed genome-wide scans on odor-perception phenotypes for ten odors in 1003 Han Chinese and validated results for six of these odors in an ethnically diverse population (n=364). In both populations, we replicated three previously reported associations (β-ionone/OR5A, androstenone/OR7D4, cis-3-hexen-1-ol/OR2J3 LD-band), suggesting that olfactory phenotype/genotype studies are robust across populations. Two novel associations between an OR and odor perception contribute to our understanding of olfactory coding. First, we found a SNP in OR51B2 that associated with trans-3-methyl-2-hexenoic acid, a key component of human underarm odor. Second, we found two linked SNPs associated with the musk Galaxolide in a novel musk receptor, OR4D6, which is also the first OR shown to drive specific anosmia to a musk compound. We also found that the derived alleles of the SNPs reportedly associated with odor perception tend to reduce odor intensity, supporting the hypothesis that the primate olfactory gene repertoire has degenerated over time. This study provides information about coding for human body odor, and gives us insight into broader mechanisms of olfactory coding, such as how differential OR activation can converge on a similar percept.
Quantification of volumetric morphometry and optical property in the cortex of human cerebellum at micrometer resolution
Authors: Liu Chao J. , Ammon William , Siless Viviana , Fogarty Morgan , Wang Ruopeng , Atzeni Alessia , Aganj Iman , Iglesias Juan Eugenio , Zöllei Lilla , Fischl Bruce , Schmahmann Jeremy D. , Wang Hui
Published: April 2021

The surface of the human cerebellar cortex is much more tightly folded than the cerebral cortex. Volumetric analysis of cerebellar morphometry in magnetic resonance imaging studies suffers from insufficient resolution, and therefore has had limited impact on disease assessment. Automatic serial polarization-sensitive optical coherence tomography (as-PSOCT) is an emerging technique that offers the advantages of microscopic resolution and volumetric reconstruction of large-scale samples. In this study, we reconstructed multiple cubic centimeters ofex vivohuman cerebellum tissue using as-PSOCT. The morphometric and optical properties of the cerebellar cortex across five subjects were quantified. While the molecular and granular layers exhibited similar mean thickness in the five subjects, the thickness varied greatly between the crown of the folium and the depth of the fissure in the granular layer within subjects. Layer-specific optical property remained homogenous within individual subjects but showed higher cross-subject variability than layer thickness. High-resolution volumetric morphometry and optical property maps of human cerebellar cortex revealed by as-PSOCT have great potential to advance our understanding of cerebellar function and diseases.

Highlights

We reconstructed cubic centimeters of human cerebellar samples at micrometer resolution in five subjects.

Thickness of the granular layer varies greatly between the crowns and depths of cerebellar fissures.

Cross-subject variability is higher in optical property than cortical morphology.

Our results suggest homogenous cell and myelin density in the cortical layers of human cerebellum despite the highly convoluted folding patterns.
Olfactory receptor-dependent receptor repression inDrosophila
Authors: Mika Kaan , Cruchet Steeve , Chai Phing Chian , Prieto-Godino Lucia L. , Auer Thomas O. , Pradervand Sylvain , Benton Richard
Published: April 2021

In olfactory systems across phyla, most sensory neurons transcribe a single olfactory receptor gene selected from a large genomic repertoire. We describe novel receptor gene-dependent mechanisms that ensure singular expression of receptors encoded by a tandem gene array inDrosophila. Transcription from upstream genes in the cluster runs through the coding region of downstream loci to inhibit their expression incis, via transcriptional interference. Moreover, one receptor blocks expression of other receptor proteins intransthrough a post-transcriptional mechanism. These repression mechanisms operate in endogenous neurons to ensure their unique expression. Our data provide evidence for inter-olfactory receptor regulation in invertebrates, and highlight unprecedented, but potentially widespread, mechanisms for ensuring exclusive expression of chemosensory receptors, and other protein families, encoded by tandemly-arranged genes.
CYCLeR– a novel tool for the full isoform assembly and quantification of circRNAs
Authors: Stefanov Stefan R. , Meyer Irmtraud M.
Published: April 2021

Splicing is one key mechanism determining the state of any eukaryotic cell. Apart from linear splice variants, circular splice variants (circRNAs) can arise via non-canonical splicing involving aback-splice junction(BSJ). Most existing methods only identifycircRNAs via the corresponding BSJ, but do not aim to estimate their full sequence identity or to identify different, alternatively spliced circular isoforms arising from the same BSJ. We here present CYCLeR, the first computational method for identifying the full sequence identify of new and alternatively splicedcircRNAs and their abundances while simultaneously co-estimating the abundances of known linear splicing isoforms. We show that CYCLeR significantly out-performs existing methods in terms of sensitivity, precision and quantification of transcripts. When analysingD. melanogasterdata, CYCLeR uncovers biological patterns of circRNA expression that other methods fail to observe.
Nasal BCG Exposure Accelerates Dural Lymphatics Development via Macrophages’ Role in Newborn Mice
Authors: Yang Junhua , Yuan Lifang , Song Linyang , Qi Fangfang , Zuo Zejie , Xu Jie , Yao Zhibin
Published: April 2021

The dural lymphatics develop mainly during the first postnatal month. Lymphatics may be shaped by immune activation when bacterial infection happens. BCG, a strong immune activator, is widely injected to newborns. Moreover, human beings are nasally exposed in daily life to bacterial stimuli. These background prompted us to investigate whether neonatal BCG injection combined with nasally exposure exerts an influence on dural lymphatics develop. Here, mice received a single dose intracutaneous (i.c.) BCG injection immediately after birth followed by repeated nasal BCG challenge once a day (i.c./nasal group). These mice had an accelerated dural lymphatics growth and increased levels of several cytokines and VEGFR-3. Furthermore, macrophages were identified as a key mediator of these alterations. Mice that received mere one dose i.c. BCG injection showed no significant alterations in these indexes. Additionally, mere repeated nasal BCG challenge induced similar effects to i.c./nasal challenge but with a slighter extent. Taken together, these findings show that repeated nasal BCG vaccination accelerates dural lymphatics development in neonatal mice, especially in the presence of neonatal i.c. BCG injection.
Panache: a Web Browser-Based Viewer for Linearized Pangenomes
Authors: Durant Éloi , Sabot François , Conte Matthieu , Rouard Mathieu
Published: April 2021

Motivation

Pangenomics evolved since its first applications on bacteria, extending from the study of genes for a given population to the study of all of its sequences available. While multiple methods are being developed to construct pangenomes in eukaryotic species there is still a gap for efficient and user-friendly visualization tools. Emerging graph representations comes with their own challenges, and linearity remains a suitable option for user-friendliness.

Results

We introduce Panache, a tool for the visualization and exploration of linear representations of gene-based and sequence-based pangenomes. It uses a layout similar to genome browsers to display presence absence variations and additional tracks along a linear axis with a pangenomics perspective.

Availability

Panache is available at github.com/SouthGreenPlatform/panache under the MIT License.

Contact

eloi.durant@ird.fr,m.rouard@cgiar.org
Sleep Loss Impacts the Interconnected Brain-Body-Mood Regulation of Cardiovascular Function in Humans
Authors: Krause Adam J. , Vallat Raphael , Simon Eti Ben , Walker Matthew P.
Published: April 2021

Poor sleep is associated with hypertension, a major risk factor for cardiovascular disease1,2. However, the mechanism(s) through which sleep loss impacts blood pressure remain largely unknown, including the inter-related brain and peripheral body systems that regulate vascular function3. In a repeated-measures experimental study of 66 healthy adult participants, we demonstrate four core findings addressing this question. First, a night of sleep loss significantly increased blood pressure—both systolic and diastolic, yet this change in vascular tone was independent of any increase in heart rate. Second, sleep loss compromised functional brain connectivity within regions that regulate vascular tone. Third, sleep-loss related changes in brain connectivity and vascular tone were significantly inter-dependent, with changes in brain nodes explaining the shift towards hypertension. Fourth, sleep-loss related changes in mood, specifically reductions in positive and amplification in negative states, each demonstrated an interaction with the impairments in brain connectivity and blood pressure. Together, these findings support an embodied framework in which sleep loss confers increased risk of cardiovascular disease through interactions between brain homeostatic control, mood-state and blood pressure.
ZGA: a flexible pipeline for read processing, de novo assembly and annotation of prokaryotic genomes
Authors: Korzhenkov A.A.
Published: April 2021

Motivation

Whole genome sequencing (WGS) became a routine method in modern days and may be applied to study a wide spectrum of scientific problems. Despite increasing availability of genome sequencing by itself, genome assembly and annotation could be a challenge for an inexperienced researcher.

Results

ZGA is a computational pipeline to assemble and annotate prokaryotic genomes. The pipeline supports several modern sequencing platforms and may be used for hybrid genome assembling. Resulting genome assembly is ready for deposition to an INSDC database or for further analysis.

Availability

ZGA was written in Python, the source code is freely available athttps://github.com/laxeye/zga/. ZGA can be installed via Anaconda Cloud and Python Package Index.

Contact

oscypek@ya.ru

Supplementary information

Supplementary data are available atBioinformaticsonline.
Shaping information processing: the role of oscillatory dynamics in a working-memory task
Authors: ElShafei Hesham A. , Zhou Ying Joey , Haegens Saskia
Published: April 2021

Neural oscillations are thought to reflect low-level operations that can be employed for higher-level cognitive functions. Here, we investigated the role of brain rhythms in the 1–30 Hz range by recording MEG in human participants performing a visual delayed match-to-sample paradigm in which orientation or spatial frequency of sample and probe gratings had to be matched. A cue occurring before or after sample presentation indicated the to-be-matched feature. We demonstrate that alpha/beta power decrease tracks the presentation of the informative cue and indexes faster responses. Moreover, these faster responses coincided with an augmented phase alignment of slow oscillations, as well as phase-amplitude coupling between slow and fast oscillations. Importantly, stimulus decodability was boosted by both low alpha power and high beta power. In summary, we provide support for a comprehensive framework in which different rhythms play specific roles: slow rhythms control input sampling, while alpha (and beta) gates the information flow, beta recruits task-relevant circuits, and the timing of faster oscillations is controlled by slower ones.

Significance statement

Brain oscillations reflect low-level operations, building blocks, that control the flow of information through the brain. We propose and test a novel comprehensive framework in which slow oscillations control input sampling, alpha gates information flow, beta recruits task-relevant circuits, and the timing of faster oscillations is controlled by slower ones. We collected MEG data while participants performed a visual delayed match-to-sample task with pre- & retro-cues. Phase alignment of slow oscillations, governing input sampling, indexed faster responses. Alpha/beta power, gating information flow, boosted behavior & tracked informative cues. Low alpha (gating) & high beta (circuit-setup) power boosted signal information content. This is an essential step towards a more unified framework regarding the role of oscillatory dynamics in shaping information processing.
GDF8 Contributes to the Adverse Effects of Liver Injury on Skeletal Muscle Homeostasis and Regeneration
Authors: Culver Alexander , Hamang Matthew , Wang Yan , White Emily , Gawrieh Samer , Vuppalanchi Raj K. , Chalasani Naga P. , Dai Guoli , Yaden Benjamin C.
Published: April 2021

Background

An emerging clinical phenomenon in patients with end stage liver disease is progressive skeletal muscle atrophy. This loss in lean mass predicts poor survival outcomes for liver disease patients and highlights an underappreciated crosstalk between injured liver and muscle that lacks defined mediators. The purpose of our study was to identify potential liver-muscle mediator(s) in pre-clinicalin vivomodels of liver injury which may contribute to the muscle loss observed in liver disease.

Methods

Utilizing a mouse model of carbon tetrachloride CCl4-induced liver injury in the presence or absence of cardiotoxin-induced muscle injury, we evaluated whether neutralizing Activin type IIB receptor (ActRIIB) ligands, or specifically growth differentiation factor 8 (Gdf8), could preserve or reverse muscle atrophy associated with liver disease.

Results

We found that hepatic injury via CCl4or bile duct ligation (BDL) similarly caused significant muscle atrophy along with decreased gene expression in key myogenesis markers. This adverse effect of injured liver on muscle were completely prevented and reversed by the intervention of Activin type IIB receptor (ActRIIB)-Fc fusion protein, which neutralizes the ActRIIB ligands, including Activins and growth differentiation factor 8 (Gdf8 or myostatin). The results indicate that ActRIIB ligands promoted muscle atrophy which was manifested in response to hepatic injury/disease and conferred the negative communication of injured liver with muscle. Indeed, direct injection of exogenous Gdf8 protein into muscle along with acute focal muscle injury recapitulated similar dysregulated muscle regeneration as observed with liver injury. Furthermore, we found that hepatocytes produced Gdf8 in response to liver injury in rodents and in patients with end stage liver disease. A neutralizing antibody to Gdf8 attenuated muscle atrophy and unexpectedly ameliorated liver fibrosis in both CCl4and BDL models. Following this observation, we demonstrated Gdf8’s ability to induce fibrogenesis in stellate cells, potentially identifying a novel hepatic role for this protein. Moreover, hepatic Gdf8 promoted muscle wasting in response to liver damage and hindered skeletal muscle regeneration.

Conclusion

Our findings identified Gdf8 as a novel hepatomyokine contributing to injured liver-muscle negative crosstalk and liver injury progression. Moreover, we demonstrated a promising therapeutic strategy for muscle atrophy accompanying liver diseases.
Characterizing interactions between the microtubule-binding protein CLIP-170 and F-actin
Authors: Wu Yueh-Fu O. , Miller Rachel A. , Alberico Emily O. , Nelson Nora T. , Jonasson Erin M. , Goodson Holly V.
Published: April 2021

The cooperation between the actin and microtubule (MT) cytoskeletons is important for cellular processes such as cell migration and muscle cell development. Full understanding of how this cooperation occurs has yet to be sufficiently developed. The MT plus-end tracking protein (+TIP) CLIP-170 has been implicated in this actin-MT coordination by associating with the actin-binding signaling protein IQGAP1, and by promoting actin polymerization through binding with formins. Thus far, CLIP-170’s interactions with actin were assumed to be indirect. Here, we demonstrate that CLIP-170 can bind to filamentous actin (F-actin) directly. The affinity is relatively weak, but is strong enough to be significant in the actin-rich cortex, where actin concentrations can be extremely high. Using CLIP-170 fragments and mutants, we show that the direct CLIP-170:actin interaction is independent of the FEED domain, the region that mediates formin-dependent actin polymerization, and that the CLIP-170 F-actin-binding region overlaps with the MT-binding region. Consistent with these observations,in vitrocompetition assays indicate that CLIP-170:F-actin and CLIP-170:MT interactions are mutually exclusive. Taken together, these observations lead us to speculate that direct CLIP-170:F-actin interactions may function to reduce the stability of MTs in actin-rich regions of the cell, as previously proposed for EB1.
The medial orbitofrontal cortex - basolateral amygdala circuit regulates the influence of reward cues on adaptive behavior and choice
Authors: Lichtenberg Nina T. , Sepe-Forrest Linnea , Pennington Zachary T. , Lamparelli Alexander C. , Greenfield Venuz Y. , Wassum Kate M.
Published: April 2021

Adaptive reward-related decision making requires accurate prospective consideration of the specific outcome of each option and its current desirability. Often this information must be inferred based on the presence of predictive environmental events. The basolateral amygdala (BLA) and medial orbitofrontal cortex (mOFC) are two key nodes in the circuitry supporting such outcome expectations, but very little is known about the function of direct connections between these regions. Here, in male rats, we first anatomically confirmed the existence of bidirectional, direct projections between the mOFC and BLA and found that BLA projections to mOFC are largely distinct from those to lateral OFC (lOFC). Next, using pathway-specific chemogenetic inhibition and the outcome-selective Pavlovian-to-instrumental transfer and devaluation tests, we interrogated the function of the bidirectional mOFC-BLA connections in reward-directed behavior. We found evidence that the mOFC→BLA pathway mediates the use of environmental cues to understand which specific reward is predicted, information needed to infer which action to choose, and how desirable that reward is to ensure adaptive responses to the cue. By contrast, the BLA→mOFC pathway is not needed to use the identity of an expected reward to guide choice, but does mediate adaptive responses to cues based on the current desirability of the reward they predict. These functions differ from those we previously identified for the lOFC-BLA circuit. Collectively, the data reveal the mOFC-BLA circuit as critical for the cue-dependent reward outcome expectations that influence adaptive behavior and decision making.

SIGNIFICANCE STATEMENT

To make good decisions we evaluate how advantageous a particular course of action would be. This requires understanding what rewarding outcomes can be expected and how desirable they currently are. Such prospective considerations are critical for adaptive decision making but disrupted in many psychiatric diseases. Here we reveal that direct connections between the medial orbitofrontal cortex and basolateral amygdala mediate these functions. These findings are especially important in light of evidence of dysfunction in this circuit in substance use disorder and mental illnesses marked by poor decision making.
Stochastic Neural Networks for Automatic Cell Tracking in Microscopy Image Sequences of Bacterial Colonies
Authors: Sarmadi Sorena , Winkle James J. , Alnahhas Razan N. , Bennett Matthew R. , Josić Krešimir , Mang Andreas , Azencott Robert
Published: April 2021

We describe an automated analysis method to quantify the detailed growth dynamics of a population of bacilliform bacteria. We propose an innovative approach to frame-sequence tracking of deformable-cell motion by the automated minimization of a new, specific cost functional. This minimization is implemented by dedicated Boltzmann machines (stochastic recurrent neural networks). Automated detection of cell divisions is handled similarly by successive minimizations of two cost functions, alternating the identification of children pairs and parent identification. We validate this automatic cell tracking algorithm using recordings of simulated cell colonies that closely mimic the growth dynamics ofE. coliin microfluidic traps. On a batch of 1100 image frames, cell registration accuracies per frame ranged from 94.5% to 100%, with a high average. Our initial tests using experimental image sequences ofE. colicolonies also yield convincing results, with a registration accuracy ranging from 90% to 100%.
Medial Prefrontal Cortex controlling the immobility of rats in the forced swimming test: a systematic review and meta-analysis
Authors: Domingues K. , Melleu F. F. , Lino de Oliveira C.
Published: April 2021

The medial prefrontal cortex (mPFC) belong to the neural circuitry responsible for the behavioral responses to antidepressants in humans or animals. In the forced swimming (FST), a predictive test for antidepressants in laboratory rodents, inhibition, or stimulation of mPFC may produce antidepressant-like, unlike or no behavioral effect at all. Controversial findings may result from the variety of subregions of mPFC controlling behaviour of rats in the FST. The aim in the present study was to estimate the contribution of subregions of the mPFC to the control of rat behavior in the FST. For an unbiased view and well-powered analysis of the mentioned effects, a systematic review at Medline (Pubmed) followed by a meta-analysis was performed. Compared to other subdivisions, inhibition of prelimbic or infralimbic mPFC caused a significant drop of immobility time in the FST, which is an antidepressant-like effect. Summarizing, prelimbic or infralimbic cortices seem more relevant than other subregions to the control of immobility in the FST underlying the effects of antidepressants on mood and behaviour.
Gazing at Egypt's museums: toward a new internationalism
Authors: El-Ashmouni Marwa M.
Published: April 2021

Purpose

This paper aims to examine the transformation of the concept of cultural tourism within the sociopolitical empowerments, changes of visual realms and normative contexts, which is embedded within museums as institutions.

Design/methodology/approach

These discussions will be conceptualized through investigating the shifts in the metamorphosis of the architectural vocabulary of Egypt's museums between nineteenth and twentieth centuries. This analysis will be highlighted through connecting both the notion of the “tourist reflexivity” of John Urry and Jonas Larsen in The Tourist Gaze 3.0 (2011) and the notion of the “interstitial spaces” and “new internationalism” of Homi Bhabha in The Location of Culture (1994). The analysis expands to interrogate these two notions as prelude for reflecting on representations of colonial and postcolonial museums in Egypt, starting from the Museum of Egyptian Antiquities, Cairo (c. 1863) to the most recent, the Egyptian Grand Museum, Cairo (c. 2002).

Findings

The analysis revealed that while colonial museums endeavored to stage external cultural authority and postcolonial ones staged traditions' liminality through “New internationalism”, they created spatiotemporal interstices. This finding, while is a timely example with the rising global cultural encounters that emerged during this transformative age, it challenges the collective imaginations of architects to liberate from traditional nationalism.

Originality/value

The paper offers novel theoretical and architectural analysis of Egypt's museums through the exigency of nationalism and “new internationalism”. The encounter between both notions is a timely example given the recent involvements by the “Modern State” and the recent pandemic upheaval that revealed the inevitability of globalism and the discursivity of such notions.
Farmer preferences regarding durum wheat contracts in Italy: a discrete choice experiment
Authors: Oliveira Gustavo Magalhães de , Martino Gaetano , Ciliberti Stefano , Frascarelli Angelo , Chiodini Gabriele
Published: April 2021

Purpose

This study aims to investigate farmer preferences regarding sales contracts for durum wheat in Italy.

Design/methodology/approach

The authors consider that contracts are formed by an organisational entity that is in charge of transferring decision and property rights based on reductions in transaction costs. The empirical analysis presents a discrete choice experiment with three distinct models that was performed by a survey of 160 wheat farmers in southern Italy.

Findings

The results show that contractual terms affect the probability of both a contract being signed and allocating decision rights due to their effects on price, technology and quality.

Practical implications

This study provides some insights on which contractual attributes could support the wider use of contracts along the durum wheat supply chain in Italy.

Originality/value

The paper reveals that contracts are relevant not only to the coordination of agri-food chains because of price stabilisation but also due to their impacts on technology and quality strategies.
Trajectory of research on maritime transportation in the era of digitization
Authors: Shankar Sonali , Punia Sushil , Singh Surya Prakash , Dong Jingxin
Published: April 2021

Purpose

The literature on Maritime Transportation (MT) is experiencing a transition phase where the focus of the research is repositioning. It registered steep growth in recent years with its beginning articles on the concepts of cost minimization to the current focus on achieving sustainable operational effectiveness using Information and Communication Technologies (ICTs). Thus, this becomes a right time to investigate the trajectory of research on MT.

Design/methodology/approach

The proposed study aims to explore the potential of data analytics techniques such as data mining and network analytics to reflect the trajectory of research in the maritime supply chain over time. This study identifies the eight main dimensions of the research published under maritime paradigm through network analytics. The in-depth review of these dimensions rendered us to segregate them further into sub-dimensions for the ease of understanding and interpretability. Further, the text mining is employed to extract thematic evolution of the research.

Findings

The evolved themes are completely exclusive from the conventional MT research with artificial intelligence, digital storage, waste management and biofuels emerging as contemporary themes. It is found that although there are a sufficient amount of literature on sustainable port practices but their policy implications are still underexplored. The inter-dimension research is needed to achieve the motive of economic efficiency and environmental sustainability simultaneously.

Originality/value

The study has contributed on the methodology side of conducting literature reviews. The dimensions, sub-dimensions and themes are obtained using data analytics tools and techniques. This omits the possibility of personal bias and thus making the results verifiable.
Crisis, rigidity and nonliberal governance in Japan: the cases of Mitsubishi Motors and Kanebo
Authors: Takeshita Seijiro , Lee Soo Hee , Williams Christopher , You Jacqueline Jing
Published: April 2021

Purpose

The authors examine the nature of institutional rigidity and governance problems contributing to crisis and under-performance of large corporations in Japan during a period of environmental turbulence for corporate Japan.

Design/methodology/approach

Through explorative case studies of Mitsubishi Motors and Kanebo over a 10-year period from the mid-1990s to the mid-2000s the authors see how informal norms deeply embedded in the Japanese business system prevented the adoption of more liberal forms of governance that may have helped to overcome crisis.

Findings

Despite fundamental differences in formal organization between the two cases, there were similar underlying problems in terms of (1) mechanisms for capital investment that would underpin strategic resilience and rejuvenation and (2) management decision-making and strategic control during crisis.

Research limitations/implications

The cases show how normative institutions rather than formal regulative institutions matter to strategic continuity in national business systems that are put under pressure.

Originality/value

The authors link informal norms of governance intrinsic to a country to the issues of strategic resilience and responses during crisis and warn against the retrenching to traditional governance approaches where there has been criticism of alternative governance approaches.
Response of contractor behavior to hierarchical governance: effects on the performance of mega-projects
Authors: Yin Hang , Wang Dan , Yin Yilin , Liu Henry , Deng Binchao
Published: April 2021

Purpose

This study aims to examine the impacts of formal and informal hierarchical governances (HGs) on the performance of mega-projects and the mediating role of contractor behavior (i.e. perfunctory and consummate behaviors) in these relationships.

Design/methodology/approach

A total of 375 valid data entries from managers representing 375 mega-projects were analyzed through path analysis.

Findings

Both formal and informal HGs exert positive effects on the performance of mega-projects. While formal HG positively affects contractor perfunctory behavior and contractor consummate behavior, informal HG affects contractor perfunctory behavior only. Contractor behavior mediates the relationship between formal HG and project performance.

Research limitations/implications

The impacts of potential moderators (e.g. institutional arrangement and complexity) on the relationship between HG and contractor behavior have not been considered in this study.

Practical implications

This study is useful for owners to enhance formal HG to improve contractor perfunctory and consummate behaviors, which in turn can enhance the performance of mega-projects.

Originality/value

This study expands the knowledge of mega-project performance management from the perspective of HG. It also contributes to the literature of contractor behavior within the context of mega-projects.