bluuebunny/crossref_metadata_2025 huggingface dataset:
Microsurgical Management of Fourth Ventricle Lesions Via the Median Suboccipital Keyhole Telovelar Approach
Authors: Wang Jianpeng , Wang Xu , Xu Jian , Wu Zeyu , Dou Yihe
Published: August 2022

In this 2-year retrospective analysis, 13 patients with fourth ventricle lesions who underwent microsurgical resection via the midline suboccipital keyhole telovelar approach were analyzed. This is the first study to investigate the surgical outcome and complications of using this approach to resect various types of lesions in the fourth ventricle. We aimed to clarify whether this approach has met its promise of lesion dissection. Three patients (23.1%) had intraoperative extraventricular drains. There were no immediate postoperative deaths. Gross total resection was achieved in 84.6% of the cases. The Fisher exact test showed there was no statistically significant correlation between lesion location, lesion size, brainstem invasion, and extent of resection. About two third (69.2%) of the cases were free of complications. New or worsening gait/focal motor disturbance (15.4%) was the most common neurological deficit in the immediate postoperative period. One patient (7.7%) had worse gait disturbance/motor deficit following surgical intervention. Two patients (15.4%) developed meningitis. Two patients (15.4%) required postoperative cerebrospinal fluid diversion after tumor resection, of these 2 patients, 1 (7.7%) eventually needed a permanent shunt. There were no cases of cerebellar mutism and bulbar paralysis. The median suboccipital keyhole telovelar approach provides relative wide access to resect most fourth ventricle tumors completely and with satisfactory results. In contrast, this requires the appropriate patient selection and skilled surgeons.
A Reversal Forehead Free Flap Transplantation Without Interrupted Perfusion for Esthetic Repairing the Mentocervical Scar Deformity
Authors: Cao Zilong , Liu Liqiang , Jiao Hu , Zhang Tiran , Zhou Lu
Published: August 2022

The forehead flap is widely used to repair facial defects. The traditional method would transfer some hair to the recipient area, where the reconstructed beard lies in a misplaced position. The authors designed a reversal forehead free flap method that transposed the flap to 180 degrees, rebuilding the reconstructed beard in the normal position. In addition, the authors used the frontal branches of the superficial temporal vessels on both sides to anastomose with the contralateral parietal branches to lengthen the pedicle and avoid ischemia-reperfusion injury.

Level of Evidence: 4.
Assessing the Relationship Between Molecular Rejection and Parenchymal Injury in Heart Transplant Biopsies
Authors: Madill-Thomsen Katelynn S. , Reeve Jeff , Aliabadi-Zuckermann Arezu , Cadeiras Martin , Crespo-Leiro Marisa G. , Depasquale Eugene C. , Deng Mario , Goekler Johannes , Kim Daniel H. , Kobashigawa Jon , Macdonald Peter , Potena Luciano , Shah Keyur , Stehlik Josef , Zuckermann Andreas , Halloran Philip F.
Published: August 2022

Background.

The INTERHEART study (ClinicalTrials.gov #NCT02670408) used genome-wide microarrays to detect rejection in endomyocardial biopsies; however, many heart transplants with no rejection have late dysfunction and impaired survival. We used the microarray measurements to develop a molecular classification of parenchymal injury.

Methods.

In 1320 endomyocardial biopsies from 645 patients previously studied for rejection-associated transcripts, we measured the expression of 10 injury-induced transcript sets: 5 induced by recent injury; 2 reflecting macrophage infiltration; 2 normal heart transcript sets; and immunoglobulin transcripts, which correlate with time. We used archetypal clustering to assign injury groups.

Results.

Injury transcript sets correlated with impaired function. Archetypal clustering based on the expression of injury transcript sets assigned each biopsy to 1 of 5 injury groups: 87 Severe-injury, 221 Late-injury, and 3 with lesser degrees of injury, 376 No-injury, 526 Mild-injury, and 110 Moderate-injury. Severe-injury had extensive loss of normal transcripts (dedifferentiation) and increase in macrophage and injury-induced transcripts. Late-injury was characterized by high immunoglobulin transcript expression. In Severe- and Late-injury, function was depressed, and short-term graft failure was increased, even in hearts with no rejection. T cell–mediated rejection almost always had parenchymal injury, and 85% had Severe- or Late-injury. In contrast, early antibody-mediated rejection (AMR) had little injury, but late AMR often had the Late-injury state.

Conclusions.

Characterizing heart transplants for their injury state provides new understanding of dysfunction and outcomes and demonstrates the differential impact of T cell–mediated rejection versus AMR on the parenchyma. Slow deterioration from AMR emerges as a major contributor to late dysfunction.
Design, implementation, and functional validation of a new generation of microneedle 3D high-density CMOS multi-electrode array for brain tissue and spheroids
Authors: Mapelli Lisa , Dubochet Olivier , Tedesco Mariateresa , Sciacca Giacomo , Ottaviani Alessandra , Monteverdi Anita , Battaglia Chiara , Tritto Simona , Cardot Francis , Surbled Patrick , Schildknecht Jan , Gandolfo Mauro , Imfeld Kilian , Cervetto Chiara , Marcoli Manuela , D’Angelo Egidio , Maccione Alessandro
Published: August 2022

In the last decades, planar multi-electrode arrays (MEAs) have been widely used to record activity from in vitro neuronal cell cultures and tissue slices. Though successful, this technique bears some limitations, particularly relevant when applied to three-dimensional (3D) tissue, such as brain slices, spheroids or organoids. For example, planar MEAs signals are informative on just one side of a 3D-organized structure. This limits the interpretation of the results in terms of network functions in a complex structured and hyperconnected brain tissue. Moreover, the side in contact with the MEAs often shows lower oxygenation rates and related vitality issues. To overcome these problems, we empowered a CMOS high-density multi-electrode array (HD-MEA) with thousands of microneedles (μneedles) of 65-90 μm height, able to penetrate and record in-tissue signals, providing for the first time a 3D HD-MEA chip. We propose a CMOS-compatible fabrication process to produce arrays of μneedles of different widths mounted on large pedestals to create microchannels underneath the tissue. By using cerebellar and cortico-hippocampal slices as a model, we show that the μneedles efficiently penetrate the 3D tissue while the microchannels allow the flowing of maintenance solutions to increase tissue vitality in the recording sites. These improvements are reflected by the increase in electrodes sensing capabilities, the number of sampled neuronal units (compared to matched planar technology), and the efficiency of compound effects. Importantly, each electrode can also be used to stimulate the tissue with optimal efficiency due to the 3D structure. Furthermore, we demonstrate how the 3D HD-MEA can efficiently penetrate and get outstanding signals from in vitro 3D cellular models as brain spheroids. In conclusion, we describe a new recording device characterized by the highest spatio-temporal resolution reported for a 3D MEA and significant improvements in the quality of recordings, with a high signal-to-noise ratio and improved tissue vitality. The applications of this game-changing technique are countless, opening unprecedented possibilities in the neuroscience field and beyond.
L-Fucose is a candidate monosaccharide neuromodulator and mitigates Alzheimer’s synaptic deficits
Authors: Lucente Jacopo Di , Tena Jennyfer , Mendiola Ulises R. , Chen Xi , Lebrilla Carlito B. , Maezawa Izumi , Jin Lee-Way
Published: August 2022

We identified a novel signaling function of L-fucose, a structurally unique monosaccharide. We showed that L-fucose enhanced excitatory neurotransmission and long-term potentiation (LTP) in Schaffer-collateral-CA1 synapses. L-fucose was released by neurons in an activity- and store-dependent manner, and induced rapid signaling changes to enhance presynaptic release. Such effects required L-fucose metabolism through the salvage pathway driven by fucokinase (FUK). Thus, L-fucose could be the first described monosaccharide neuromodulator affecting a metabolic-signaling mechanism. Human Alzheimer’s disease (AD) and 5xFAD mouse brains showed signs of fucose hypometabolism with impaired L-fucose signaling. Such abnormalities could be corrected by exogenous L-fucose, exemplified by rectification of LTPdeficits in 5xFAD hippocampus. Dietary L-fucose supplement, which increased cerebral free L-fucose levels and upregulated FUK to drive the salvage pathway, mitigated synaptic and behavioral deficits of 5xFAD mice. Our data reveals a therapeutic potential of oral L-fucose for AD, which is safe and easy to comply with.
Genome-wide association analysis of hyperspectral reflectance data to dissect growth-related traits genetic architecture in maize under inoculation with plant growth-promoting bacteria
Authors: Yassue Rafael Massahiro , Galli Giovanni , Chen Chun-Peng James , Fritsche-Neto Roberto , Morota Gota
Published: August 2022

Plant growth-promoting bacteria (PGPB) may be of use for increasing crop yield and plant resilience to biotic and abiotic stressors. Using hyperspectral reflectance data to assess growth-related traits may shed light on the underlying genetics as such data can help assess biochemical and physiological traits. This study aimed to integrate hyperspectral reflectance data with genome-wide association analyses to examine maize growth-related traits under PGPB inoculation. A total of 360 inbred maize lines with 13,826 single nucleotide polymorphisms (SNPs) were evaluated with and without PGPB inoculation; 150 hyperspectral wavelength reflectances at 386–1,021 nm and 131 hyperspectral indices were used in the analysis. Plant height, stalk diameter, and shoot dry mass were measured manually. Overall, hyperspectral signatures produced similar or higher genomic heritability estimates than those of manually measured phenotypes, and they were genetically correlated with manually measured phenotypes. Furthermore, several hyperspectral reflectance values and spectral indices were identified by genome-wide association analysis as potential markers for growthrelated traits under PGPB inoculation. Eight SNPs were detected, which were associated with manually measured and hyperspectral phenotypes. Moreover, the hyperspectral phenotypes were associated with genes previously reported as candidates for nitrogen uptake efficiency, tolerance to abiotic stressors, and kernel size. In addition, a Shiny web application was developed to explore multi-phenotype genome-wide association results interactively. Taken together, our results demonstrate the usefulness of hyperspectral-based phenotyping for studying maize growth-related traits in response to PGPB inoculation.
Automatic detection, identification and counting of anguilliform fish using in situ acoustic camera data: development of a cross-camera morphological analysis approach
Authors: Le Quinio Azénor , De Oliveira Eric , Girard Alexandre , Guillard Jean , Roussel Jean-Marc , Zaoui Fabrice , Martignac François
Published: August 2022

Acoustic cameras are increasingly used in monitoring studies of diadromous fish populations, even though analyzing them is time-consuming. In complex in situ contexts, anguilliform fish may be especially difficult to identify automatically using acoustic camera data because the undulation of their body frequently results in fragmented targets. Our study aimed to develop a method based on a succession of computer vision techniques, in order to automatically detect, identify and count anguilliform fish using data from multiple models of acoustic cameras. Indeed, several models of cameras, owning specific technical characteristics, are used to monitor fish populations, causing major differences in the recorded data shapes and resolutions. The method was applied to two large datasets recorded at two distinct monitoring sites with populations of European eels with different length distributions. The method yielded promising results for large eels, with more than 75% of eels automatically identified successfully using datasets from ARIS and BlueView cameras. However, only 42% of eels shorter than 60 cm were detected, with the best model performances observed for detection ranges of 4-9 m. Although improvements are required to compensate for fish-length limitations, our cross-camera method is promising for automatically detecting and counting large eels in long-term monitoring studies in complex environments.
CD98 is critical for a conserved inflammatory response to diverse injury stimuli relevant to IPF exacerbations and COVID pneumonitis
Authors: Stylianou Panayiota , Rushwan Sara , Wang Wei , Miah M. Azim , Darweesh Omeed , Mackinnon Alison , Roach Katy M. , Hitchman Charles J. , Gonchar Oksana , Thorpe Stephen , Harris Christopher , Haigh Richard , Richards David F , Snetkov Vladimir , Beasley Jessica , Cleary Simon J , Barer Michael , Ward Jeremy PT , Rooney Claire , McCaughan Frank , Bradding Peter , Beale Richard , Knight Martin M , Sethi Tariq , Gooptu Bibek
Published: August 2022

Progressive fibrosing interstitial lung diseases (PFILDs) cause substantial morbidity and mortality. Antifibrotic agents slow progression, but most of the clinical need remains unmet. The archetypal PFILD is idiopathic pulmonary fibrosis (IPF). Chronic progression is driven by transforming growth factor (TGF-)β1 signalling. It is punctuated by inflammatory flares known as acute exacerbations (AE-IPF), which are associated with accelerated decline and high mortality. We hypothesized that acute injury responses underlying exacerbations and the mechanisms of chronic fibrosis overlap at the molecular level, via a cell surface assembly nucleated by galectin-3 that we term the ‘gal-3-fibrosome’. We focused upon a putative pro-inflammatory galectin-3 ligand, the CD98:integrin complex. Our data indicate CD98 and β1-integrin co-localise with galectin-3 within epithelial cells in IPF lung tissue, and within 40 nm in human lung tissue treated with TGF-β1 compared to controls. CD98 is required for interleukin (IL-)6 and IL-8 responses to biochemical and biophysical conditions mimicking stimuli of AE-IPF in vivo, ex vivo and in cells, and for an interstitial neutrophilic response in a mouse model. We demonstrate this pathway progresses via intracellular influx of Ca2+ mediated by TRPV4, and NF-κB activation, operating in positive feedback. Lastly we show the CD98- and galectin-3-dependence of IL-6 and IL-8 responses to the SARS-CoV-2 spike protein receptor binding domain and the conservation of this response pattern between lung epithelial cells and monocyte-derived macrophages. Taken together our findings identify CD98 as a key mediator of both pro-fibrotic and acute inflammatory responses in the lung with relevance to AE- and chronic progression of IPF, and the priming of fibrotic lungs for acute inflammatory responses. They similarly implicate CD98 and galectin-3 as mediators of COVID pneumonitis and worse outcomes in ILD patients with COVID.
A human tubular aggregate myopathy mutation unmasks STIM1-independent rapid inactivation of Orai1 channels
Authors: Yeung Priscilla S.-W. , Yamashita Megumi , Prakriya Murali
Published: August 2022

Ca2+ release-activated Ca2+ (CRAC) channels are activated by direct physical interactions between Orai1, the channel protein, and STIM1, the endoplasmic reticulum Ca2+ sensor. A hallmark of CRAC channels is fast Ca2+-dependent inactivation (CDI) which provides negative feedback to limit Ca2+ entry through CRAC channels. Although STIM1 is thought to be essential for mediating CDI, the molecular mechanism of CDI remains largely unknown. Here, we examined a gain-of-function (GOF) human Orai1 disease mutation, L138F, that causes tubular aggregate myopathy (TAM). Through pairwise mutational analysis, we determine that large amino acid substitutions at either L138 or the neighboring T92 locus evoke highly Ca2+-selective currents in the absence of STIM1. We find that the GOF phenotype arises due to steric clash between L138 on TM2 and T92 located on the pore helix. Surprisingly, strongly activating L138 and T92 mutations also show CDI in the absence of STIM1, contradicting prevailing views that STIM1 is required for inactivation. CDI of constitutively open T92W and L138F mutants occurred with similar kinetics as WT Orai1 but showed enhanced intracellular Ca2+ sensitivity, which could be normalized by the addition of STIM1. Truncation of the Orai1 C-terminus reduced T92W CDI consistent with a key role for the Orai1 C-terminus for CDI. Overall, these results elucidate the molecular basis of the human TAM-linked mutation and indicate that CDI of CRAC channels is mediated by an Orai1-intrinsic mechanism with STIM1 tuning the calcium sensitivity of CDI.
DrosophilapVALIUM10 TRiP RNAi lines cause undesired silencing of Gateway-based transgenes
Authors: Stanković Dimitrije , Csordás Gábor , Uhlirova Mirka
Published: August 2022

Post-transcriptional gene silencing using double-stranded RNA has revolutionized the field of functional genetics, allowing fast and easy disruption of gene function in various organisms. InDrosophila, many transgenic RNAi lines have been generated in large-scale efforts, including theDrosophilaTransgenic RNAi Project (TRiP), to facilitatein vivoknockdown of virtually anyDrosophilagene with spatial and temporal resolution. The available transgenic RNAi lines represent a fundamental resource for the fly community, providing an unprecedented opportunity to address a vast range of biological questions relevant to basic and biomedical research fields. However, caution should be applied regarding the efficiency and specificity of the RNAi approach. Here, we demonstrate that pVALIUM10-based RNAi lines, representing ~13% of the total TRiP collection (1,808 out of 13,410 TRiP pVALIUM-based RNAi lines), cause unintended off-target silencing of transgenes expressed from Gateway destination vectors generated via site-specific recombination. The silencing is mediated by targeting attB1 and attB2 sequences generated in the recombination reaction and included in the transcribed mRNA. Deleting these attB sites from the Gateway expression vector prevents silencing and restores expected transgene expression.
Attenuated foreign body response to subcutaneous implant in regenerative spiny mice (Acomys)
Authors: Gaire Janak , Dill Michele , Supper Valentina , Simmons Chelsey S.
Published: August 2022

Spiny mice (Acomys) can regenerate after injury with minimal fibrosis. Whether Acomys retains the fibrosis-free feature in response to implanted devices is unknown, so we implanted polydimethylsiloxane (PDMS) subcutaneously in Acomys and Mus, a non-regenerative counterpart. In Acomys, we found reduced myeloid cell infiltration, fibroblast activation, and collagen deposition around the PDMS implant. These results suggest that Acomys can regulate FBR and may hold the key to improving implant lifetime and functionality.
Lipids Maintain Genomic Stability and Developmental Potency of Murine Pluripotent Stem Cells
Authors: Zhong Liangwen , Gordillo Miriam , Wang Xingyi , Qin Yiren , Huang Yuanyuan , Soshnev Alexey , Kumar Ritu , Nanjangud Gouri , James Daylon , Allis C. David , Evans Todd , Carey Bryce , Wen Duancheng
Published: August 2022

Lipids play vital roles in cellular homeostasis and regulate pluripotency of human stem cells. However, the impact of lipids on murine pluripotent stem cells is unclear. While Mek1/2 and Gsk3β inhibition (“2i”) supports the maintenance of murine embryonic stem cells (ESCs) in a homogenous naïve state, prolonged culture in 2i results in aneuploidy and DNA hypomethylation that impairs developmental potential. Additionally, 2i fails to support derivation and culture of fully potent female ESCs. Here we find that mouse ESCs cultured in 2i/LIF supplemented with lipid-rich albumin (AlbuMAX) undergo pluripotency transition yet maintain genomic stability and full potency over long-term culture. Mechanistically, lipids in AlbuMAX impact intracellular metabolism including nucleotide biosynthesis, lipid biogenesis, and TCA cycle intermediates, with enhanced expression of ZCAN4 and DNMT3s that prevent telomere shortening and DNA hypomethylation. In concert with 2i, lipids induce a formative-like pluripotent state through direct stimulation of Mek-mediated Erk2 phosphorylation, which also alleviates X chromosome loss in female ESCs. Importantly, both male and female “all-ESC” mice can be generated fromde novoderived ESCs using AlbuMAX-based media. Our findings underscore the importance of lipids to pluripotency and link nutrient cues to genome integrity in early development.
STAT3 signaling in B cells controls germinal center zone organization and recycling
Authors: Fike Adam J , Chodisetti Sathi Babu , Wright Nathaniel E , Bricker Kristen N , Domeier Phillip P , Maienschein-Cline Mark , Rosenfeld Aaron M , Luckenbill Sara A , Weber Julia L , Choi Nicholas M , Luning Prak Eline T , Mandal Malay , Clark Marcus R , Rahman Ziaur SM
Published: August 2022

Germinal centers (GCs), sites of antibody affinity maturation, are organized into dark (DZ) and light (LZ) zones. Here, we uncovered a B cell intrinsic role for STAT3 in GC DZ and LZ organization. Altered zonal organization of STAT3-deficient GCs dampened GC output of long-lived plasma cells (LL-PCs) but increased memory B cells (MBCs). Tfh-GC B cell interaction drive STAT3 tyrosine 705 and serine 727 phosphorylation in LZ B cells, facilitating their recycling into the DZ. An inducible system confirmed STAT3 is not involved in initiating or maintaining the GC but sustains GC zonal organization by regulating GC B cell recycling. RNAseq and ChIPseq analysis identified genes regulated by STAT3 that are critical for LZ cell recycling and transiting through the DZ proliferation and differentiation phases of the DZ. Thus, STAT3 signaling in B cells controls GC zone organization and recycling, and GC egress of LL-PCs, but negatively regulates MBC output.

Fike et al. describe a previously unrecognized mechanism by which B cell intrinsic STAT3 signaling controls the germinal center (GC) dark and light zone organization, GC B cell recycling, and GC output of long-lived plasma cells but negatively regulates memory B cells.
SIRT-1 is required for release of enveloped enteroviruses
Authors: Jassey Alagie , Logue James , Weston Stuart , Wagner Michael A. , Galitska Ganna , Miller Katelyn , Frieman Matthew B. , Jackson William T.
Published: August 2022

Enterovirus D68 is a re-emerging enterovirus that causes acute respiratory illness in infants and has recently been linked to Acute Flaccid Myelitis. Here, we show that the histone deacetylase, SIRT-1, is essential for autophagy and EV-D68 infection. Knockdown of SIRT-1 inhibits autophagy and reduces EV-D68 extracellular titers. The proviral activity of SIRT-1 does not require its deacetylase activity or functional autophagy. SIRT-1’s proviral activity is, we demonstrate, mediated through the repression of ER stress. Inducing ER stress through thapsigargin treatment or SERCA2A knockdown in SIRT-1 knockdown cells had no additional effect on EV-D68 extracellular titers. Knockdown of SIRT-1 also decreases poliovirus and SARS-CoV-2 titers but not coxsackievirus B3. In non-lytic conditions, EV-D68 is primarily released in an enveloped form, and SIRT-1 is required for this process. Our data show that SIRT-1, through its translocation to the cytosol, is critical to promote the release of enveloped EV-D68 viral particles.
CGIAR BARLEY BREEDING TOOLBOX: A diversity panel to facilitate breeding and genomic research in the Developing World
Authors: Bouhlal O. , Visioni A. , Verma R.P.S. , Kandil M. , Gyawali S. , Capettini F. , Sanchez-Garcia M.
Published: August 2022

Despite the reduced cost of the new genotyping technologies, many public and private breeding programs, mostly in developing countries, still cannot afford them, hindering their research. The objective of the present study was to identify and assemble an Association Mapping panel of widely diverse barley genotypes to serve as a barley breeding toolbox, especially for the Developing World. The main criteria were: i) to be representative of the germplasm grown in the Developing World; ii) to cover a wide range of genetic variability and iii) to be of public domain. For it, we assembled and genotyped a Global Barley Panel (GBP) of 530 genotypes representing a wide range of row-types, end-uses, growth habits, geographical origins and environmental conditions. The GBP accessions were genotyped using the barley Infinium iSelect 50K chip. A total of 40,342 SNP markers were polymorphic and displayed an average polymorphism information content (PIC) of 0.35, with 66% of them exceeding PIC=0.25. The analysis of the population structure identified 8 sub-populations mostly linked to the geographical origin of the lines (Europe, Australia, USA, Canada, Africa, Latin-America, ICARDA and others), four of them of significant ICARDA origin. The 16 allele combinations at 4 major flowering genes (HvVRN-H3, HvPPD-H1, HvVRN-H1 and HvCEN) explained 11.07% genetic variation and were linked to the geographic origins of the lines studied. Among origins, ICARDA material (n= 257) showed wide diversity as revealed by the highest number of polymorphic loci (99.76% of all polymorphic SNPs in GBP), number of private alleles and Nei’s gene diversity and the fact that ICARDA lines were present in all 8 sub-populations and carried all 16 allelic combinations at phenology genes. Due to their genetic diversity and their representativity of the germplasm adapted to the Developing World, 312 ICARDA lines and cultivated landraces were pre-selected to form the CGIAR Barley Breeding Toolbox (CBBT). Using the genotypic data and the Mean of Transformed Kinships method, we assembled the CBBT, an Association Mapping panel of 250 accessions capturing most of the allelic diversity in the global panel. The CBBT preserves a good balance between row types as well as a good representation of both allelic combinations identified at most important phenological loci and sub-populations of the GBP. The CBBT lines together with their genotypic data will be made available to breeders and researchers worldwide to serve as a collaborative tool to underpin the genetic mechanisms of traits of interest for barley cultivation.
Termite diet rather than geographical origin determines the microbiome composition and functional genetic structure of nests from South American and African representatives, as revealed by a multiomics approach
Authors: González Plaza Juan José , Hradecký Jaromír , Šobotník Jan
Published: August 2022

Termites represent one of the most important insect groups worldwide due to their key role as plant decomposers and proxy of carbon recycling in the tropical rainforest ecosystems. Besides, high relevance in research has been given to these social insects due to a prominent role as urban pests. However, one of the most fascinating aspects of termites are their defence strategies that prevent the growth of detrimental microbiological strains on their nests. One success factor is the key role of the nest allied microbiome. Understanding how beneficial microbial strains aid termites in pathogen biocontrol strategies could provide us with an enhanced repertoire for fighting antimicrobial resistant strains or mine for genes for bioremediation purposes.

We carried out a multiomics approach for dissecting the nest microbiome in a wide range of termite species, covering several feeding habits and three geographical locations at two tropical sides of the Atlantic Ocean, and an African savanna. Our experimental approach included untargeted volatile metabolomics, targeted evaluation of volatile naphthalene, taxonomical profile for bacteria and fungi through amplicon sequencing, and further dive into the genetic repertoire through a metagenomic sequencing approach.

Volatile naphthalene was present in species belonging to the genera Nasutitermes and Cubitermes. We further assessed the apparent differences in terms of bacterial community structure, having found a stronger influence from feeding habits and genera, rather than the geographical location. Lastly, our metagenomic analysis revealed that the gene content provides both soil feeding genera with similar functional profiles, while the wood feeding genus shows a different one. These results seem to be independent of the geographical location, indicating that the nest functional profile is heavily influenced by the diet of the termite inhabiting, building, and maintaining the nest.
Cellular Mechanisms Underlying Embryonic Retinal Waves
Authors: Voufo Christiane , Chen Andy Quaen , Smith Benjamin E. , Feller Marla B. , Tiriac Alexandre
Published: August 2022

Spontaneous activity is a hallmark of developing neural systems. In the retina, spontaneous activity comes in the form of retinal waves, comprised of three stages persisting from embryonic day 16 (E16) to eye opening at postnatal day 14 (P14). Though postnatal retinal waves have been well characterized, little is known about the spatiotemporal properties or the mechanisms mediating embryonic retinal waves, designated Stage 1 waves. Using a custom-built macroscope to record spontaneous calcium transients from whole embryonic retinas, we show that Stage 1 waves are initiated at several locations across the retina and propagate across finite regions of a broad range of areas. A gap junction antagonist, meclofenamic acid, reduced the frequency and size of Stage 1 waves but did not abolish them. The general nAChR antagonist, hexamethonium blocked Stage 1 waves, while they persisted in the presence of α4β2 nAChR antagonist dihydro-ß-erythroidine, indicating that the spatiotemporal properties of Stage 1 waves are mediated by a complex circuitry involving subtypes of nAChRs and gap junctions. Stage 1 waves in mice lacking the β2 subunit of the nAChRs (β2-nAChR-KO) were reduced, but in contrast to WT mice, they persisted in the hexamethonium and were completely blocked by meclofenamic acid. To assay the impact of Stage 1 waves on retinal development, we compared the spatial distribution of a subtype of retinal ganglion cells, intrinsically photosensitive retinal ganglion cells (ipRGCs) in WT and β2-nAChR-KO mice. We found that the developmental decrease of ipRGC density is preserved between WT and β2-nAChR-KO mice, indicating that processes regulating ipRGC distribution are not influenced by spontaneous activity.
Strategic in vitro bioaugmentation of indigenous Actinobacteria isolated from east Kolkata wetlands (Ramsar site) to degrade highly toxic waste engine oil in free and emulsified state
Authors: Bhattacharya Souptik , Putatunda Sirsha , Mazumder Ankita , Sen Dwaipayan , Bhattacharjee Chiranjib
Published: August 2022

The present study investigates the bioremediation of waste engine oil at both dissolved or being suspended in oily wastewater using an actinobacterium, Gordonia terrae DSM 43249 strain isolated from East Kolkata wetlands. The isolated strain was found capable of sustaining in highly toxic oil contaminated wastewater and simultaneously can efficiently biodegrade the pollutants in both simulated fresh and marine water system at optimized environmental conditions. Moreover, in order to understand the effect of physical presence of oil in oily wastewater on the bioremediation process, three types of simulated oil-water forms were studied: water with free waste engine oil, oil-water mixture in the form of coarse emulsion and microemulsion. It was observed that the percentage degradation became maximum with the microemulsion form (72.73%) followed by the coarse one (65.45%). The minimum percentage degradation of 39.74% was seen with the free oil. Statistical interpretation also revalidates the experimental observations, showing that the oil percentage degradation is much sensitive to the oil and water composition in an oily-water system (F=772.64> Fcritical =5.143). Hence, it is presumed from the present study that such a high percentage degradation of oil especially, when oil is thoroughly mixed with water, can be considered as one of the potential applications for oil treatment such as during oil spillage using G.terrae DSM 43249.

Graphical Abstract
Psychophysiological stress induced neurobehavioral changes in adolescent rat and their impact in Adult rat enhanced by cinnamaldehyde
Authors: Keerthi Priya C S , Ravindran R
Published: August 2022

Adolescent is a tricky developmental period were the Physical, cognitive and social changes takes place. Adolescent brain undergoes vigorous maturation and more susceptible to stressors, distresses in the brain development leading to more susceptibility for stress related psychophysiological disorders in later life. The present study explores the association of adolescent stress on same period and on adult. Adolescent rats were restraint to induce psychophysiological stress from PND28 to PND42.Cinnamaldehyde (CA) 25 mg/kg body weight is treated along with the stress. Restraint stress showed more deleterious effect on learning, memory, anxiety, depression and locomotor activity. The result of this study reveal that adolescent stress has impact on that period and even long-lasting impact. But CA may act as antistressor and cognitive enhancer.
Identification of unique α4 chain structure and conserved anti-angiogenic activity of α3NC1 type IV collagen in zebrafish
Authors: LeBleu Valerie S. , Dai Jianli , Tsutakawa Susan , MacDonald Brian A. , Alge Joseph L. , Sund Malin , Xie Liang , Sugimoto Hikaru , Tainer John , Zon Leonard I. , Kalluri Raghu
Published: August 2022

Type IV collagen is an abundant component of basement membranes in all multicellular species and is essential for the extracellular scaffold supporting tissue architecture and function. Lower organisms typically have two type IV collagen genes, encoding α1 and α2 chains, in contrast with the six genes in humans, encoding α1 to α6 chains. The α chains assemble into trimeric protomers, the building blocks of the type IV collagen network. The detailed evolutionary conservation of type IV collagen network remains to be studied. We report on the molecular evolution of type IV collagen genes. The zebrafish α4 non-collagenous (NC1) domain, in contrast with its human ortholog, contains an additional cysteine residue and lacks the M93 and K211 residues involved in sulfilimine bond formation between adjacent protomers. This may alter α4 chain interactions with other α chains, as supported by temporal and anatomic expression patterns of collagen IV chains during zebrafish development. Despite the divergence between zebrafish and human α3 NC1 domain (endogenous angiogenesis inhibitor, Tumstatin), the zebrafish α3 NC1 domain exhibits conserved anti-angiogenic activity in human endothelial cells. Our work supports type IV collagen is largely conserved between zebrafish and humans, with a possible difference involving the α4 chain.
The gut microbiome and child mental health: a population-based study
Authors: Kraaij Robert , Schuurmans Isabel K. , Radjabzadeh Djawad , Tiemeier Henning , Dinan Timothy G. , Uitterlinden André G. , Hillegers Manon , Jaddoe Vincent W.V. , Duijts Liesbeth , Moll Henriette , Rivadeneira Fernando , Medina-Gomez Carolina , Jansen Pauline W. , Cecil Charlotte A.M.
Published: August 2022

The link between the gut microbiome and the brain has gained increasing scientific and public interest for its potential to explain psychiatric risk. While differences in gut microbiome composition have been associated with several mental health problems, evidence to date has been largely based on animal models and human studies in small sample sizes. Here, we aimed to systematically characterize associations of the gut microbiome with overall psychiatric symptoms as well as with specific domains of emotional and behavioral problems, assessed via the maternally rated Child Behavior Checklist in 1,784 ten-year-old children from the multi-ethnic, population-based Generation R Study. While we observe lower gut microbiome diversity in case of more overall and specific mental health problems, associations were not significant. Likewise, we did not identify any taxonomic feature associated with mental health problems after multiple testing correction, although nominally significant findings indicated depletion of genera previously associated with psychiatric disorders, including Anaerotruncus, Anaeroplasma, and Hungatella. The identified compositional abundance differences were found to be similar across all mental health problems. Finally, we did not find any specific microbial functions that were enriched in relation to children with mental health problems. In conclusion, based on the largest sample examined to date, we found no clear evidence of associations between gut microbiome diversity, taxonomies or functions and mental health problems in the general pediatric population. In future, the use of longitudinal designs with repeated measurements microbiome and psychiatric outcomes will be critical to clarify any emerging associations between the gut microbiome and mental health from early life to adulthood.
classLog: Logistic regression for the classification of genetic sequences
Authors: Zeller Michael A. , Arendsee Zebulun W. , Smith Gavin J.D. , Anderson Tavis K.
Published: August 2022

Sequencing and phylogenetic classification have become a common task in human and animal diagnostic laboratories. It is routine to sequence pathogens to identify genetic variations of diagnostic significance and to use these data in real-time genomic contact tracing and surveillance. Under this paradigm, unprecedented volumes of data are generated that require rapid analysis to provide meaningful inference. We present a machine learning logistic regression pipeline that can assign classifications to genetic sequence data. The pipeline implements an intuitive and customizable approach to developing a trained prediction model that runs in linear time complexity, generating accurate output more rapidly than other classification methods. Our approach was benchmarked against porcine respiratory and reproductive syndrome virus (PRRSv) and swine H1 influenza A (IAV) datasets. Trained classifiers were tested against sequences and simulated datasets that artificially degraded sequence quality at 0, 10, 20, 30, and 40%. When applied to a poor-quality sequence data, the classifier achieved between >85% to 95% accuracy for the PRRSv and the swine H1 IAV HA dataset and this increased to near perfect accuracy when using the full dataset. The model also identifies amino acid positions used to determine genetic clade identity through a feature selection ranking within the model. These positions can be mapped onto a maximum-likelihood phylogenetic tree, allowing for the inference of clade defining mutations. Our approach is implemented as a python package with code available athttps://github.com/flu-crew/classLog.
Characterizing nanometric thin films with far-field light
Authors: Klimovsky Hodaya , Shavit Omer , Julien Carine , Olevsko Ilya , Hamode Mohamed , Abulafia Yossi , Suaudeau Hervé , Armand Vincent , Oheim Martin , Salomon Adi
Published: August 2022

Ultra-thin, transparent films are being used as protective layers on semiconductors, solar cells, as well as for nano-composite materials and optical coatings. Nano-sensors, photonic devices and calibration tools for axial super-resolution microscopies, all rely on the controlled fabrication and analysis of ultra-thin layers. Here, we describe a simple, non-invasive, optical technique for simultaneously characterizing the refractive index, thickness, and homogeneity of nanometric transparent films. In our case, these layers are made of the biomimetic polymer, My-133-MC, having a refractive index of 1.33, so as to approach the cytosol for biological applications. Our technique is based on the detection in the far field and the analysis of supercritical angle fluorescence (SAF), i.e., near-field emission from molecular dipoles located very close to the dielectric interface. SAF emanates from a 5-nm J-aggregate emitter layer deposited on and in contact with the inspected polymer film. Our results compare favorably to that obtained through a combination of atomic force and electron microscopy, surface-plasmon resonance spectroscopy and ellipsometry. We illustrate the value of the approach in two applications, (i), the measurement of axial fluorophore distance in a total internal reflection fluorescence geometry; and, (ii), axial super-resolution imaging of organelle dynamics in a living biological sample, cortical astrocytes, an important type of brain cell. In the later case, our approach removes uncertainties in the interpretation of the nanometric axial dynamics of fluorescently labeled vesicles. Our technique is cheap, versatile and it has obvious applications in microscopies, profilometry and optical nano-metrology.
Intrinsic Activity Develops Along a Sensorimotor-Association Cortical Axis in Youth
Authors: Sydnor Valerie J. , Larsen Bart , Seidlitz Jakob , Adebimpe Azeez , Alexander-Bloch Aaron , Bassett Dani S. , Bertolero Maxwell A. , Cieslak Matthew , Covitz Sydney , Fan Yong , Gur Raquel E. , Gur Ruben C. , Mackey Allyson P. , Moore Tyler M. , Roalf David R. , Shinohara Russell T. , Satterthwaite Theodore D.
Published: August 2022

Animal studies of neurodevelopmental plasticity have shown that intrinsic brain activity evolves from high amplitude and globally synchronized to suppressed and sparse as plasticity declines and the cortex matures. Leveraging resting-state functional MRI data from 1033 individuals (8-23 years), we reveal that this stereotyped refinement of intrinsic activity occurs during human development and provides evidence for a cortical gradient of neurodevelopmental plasticity during childhood and adolescence. Specifically, we demonstrate that declines in the amplitude of intrinsic activity are initiated heterochronously across regions, coupled to the maturation of a plasticity-restricting structural feature, and temporally staggered along a hierarchical sensorimotor-association axis from ages 8 to 18. Youth from disadvantaged environments exhibit reduced intrinsic activity in regions further up the sensorimotor-association axis, suggestive of a reduced level of plasticity in late-maturing cortices. Our results uncover a hierarchical axis of neurodevelopment and offer insight into the temporal sequence of protracted neurodevelopmental plasticity in humans.
Irony detection engages the Precuneus and Inferior Frontal Gyrus and relies on integration of contextual cues and inferential skills
Authors: Valles-Capetillo Elizabeth , Ibarra Cristian D. , Giordano Magda
Published: August 2022

It has been suggested that irony is one of the most challenging forms of communication, consequently, it can be a valuable indicator of communication abilities. An ironic statement transmits the opposite meaning of its literal counterpart. The cognitive processes that may support the interpretation of irony include the Theory of Mind (ToM), executive functions, and processing style. The brain areas associated with irony detection are the medial prefrontal cortex, inferior frontal gyrus (IFG), posterior superior temporal gyrus (pSTG), precuneus, and inferior parietal lobule, among others. This study aims to analyze the cognitive processes and neural correlates involved in irony detection in Mexican adults. Forty-five participants underwent a cognitive assessment and performed a contextual discrepancy task during fMRI acquisition. The behavioral results showed that the detection of nonliteral statements (irony, unrelated, and white lies) requires ToM and verbal abilities. In addition, white lies detection seemed to involve inhibitory control. Ironic statements were the hardest intention to detect, having the lowest percentage of classification and the slowest latency of classification. Irony detection involved brain areas associated with the ToM (i.e., precuneus) and language (i.e., IFG and pSTG) as was expected based on the results of previous studies. The detection of literal and unrelated statements recruited motor areas. No differential activation pattern was found for detection of white lies. Finally, a global perceptual processing style predicted the percent change in the BOLD signal in the IFG for all the nonliteral and literal statements.
Plant species‐dependent transmission of Escherichia coli O157:H7 from the spermosphere to cotyledons and first leaves
Authors: Wright Kathryn Mary , Wright Peter John , Holden Nicola Jean
Published: August 2022

The colonization of six edible plant species: alfalfa, broccoli, coriander, lettuce, parsley and rocket, by the human pathogen Shigatoxigenic Escherichia coli was investigated following two modes of artificial inoculation of seeds, by soaking or watering. The frequency and extent of colonization of cotyledons depended on the mode of inoculation, with three, rapidly germinating species being successfully colonized after overnight soaking, but slower germinating species requiring prolonged exposure to bacteria by watering of the surrounding growth media. Separate analysis of the cotyledons and leaves from individual plants highlighted that successful colonization of the true leaves was also species dependent. For three species, failure of transfer, or lack of nutrients or suitable microhabitat on the leaf surface resulted in infrequent bacterial colonization. Colonization of leaves was lower and generally in proportion to that in cotyledons, if present. The potential risks associated with consumption of leafy produce are discussed.
Hepatic haemophagocytosis in haematology patients with hepatic dysfunction: prognostic impact and contribution of liver biopsy combined with the haemophagocytic syndrome diagnostic score (HScore)
Authors: Bris Pierre‐Nicolas , Gauchez Philippe , Devillier Raynier , Galicier Lionel , Collignon Aude , Piana Gilles , Poizat Flora , Faucher Marion , Hospital Marie‐Anne , Vey Norbert , Gonzalez Frederic , Servan Luca , Chow‐Chine Laurent , Sannini Antoine , Mokart Djamel , Saillard Colombe , Bisbal Magali
Published: August 2022

Hepatic dysfunction (HD) is common in patients with haematological malignancies. Hepatic haemophagocytosis (HH) was detected in >50% of liver biopsies taken when HD remained unresolved after standard examination. We aimed to explore the contribution of liver biopsy in patients with both haematological malignancies and HD, describe the population of patients with HH, assess the prognostic impact of HH, and investigate haemophagocytic syndrome diagnostic score (HScore) utility in patients with HH. Between 2016 and 2019, 116 consecutive liver biopsies (76 transjugular, 40 percutaneous) were taken in 110 patients with haematological malignancy and HD (hyperbilirubinaemia, elevated transaminases, and/or cholestasis) and without a clear diagnosis. Liver biopsies were safe and diagnostically efficient. Predominant diagnoses included: HH (56%), graft‐versus‐host disease (55%), associated infections (24%), sinusoidal obstruction syndrome (15%), and tumoral infiltration (8%). Of patients, 35% were critically ill and 74% were allogeneic haematopoietic stem cell transplantation recipients, while 1‐year overall survival (OS) was 35% with HH versus 58% without HH (p = 0.026). The 1‐year OS was 24% with a HScore of ≥169 versus 50% with a HScore of <169 (p = 0.019). Liver biopsies are feasible in and contribute significantly to haematology patients with HD. HH occurred frequently and was associated with a poor prognosis. Combined with liver biopsy, the HScore may be helpful in refining haemophagocytic syndrome diagnosis.