bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractTermites 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

ABSTRACTSpontaneous 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

AbstractThe 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

ABSTRACTAdolescent 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

AbstractType 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

ABSTRACTThe 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

AbstractSequencing 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

ABSTRACTUltra-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

ABSTRACTAnimal 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

AbstractIt 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

AbstractThe 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

SummaryHepatic 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.
Local adaptation to seasonal cues at the fronts of two parallel, climate‐induced butterfly range expansions
Authors: Ittonen Mats , Hagelin Alexandra , Wiklund Christer , Gotthard Karl 
Published: August 2022

AbstractClimate change allows species to expand polewards, but non‐changing environmental features may limit expansions. Daylength is unaffected by climate and drives life cycle timing in many animals and plants. Because daylength varies over latitudes, poleward‐expanding populations must adapt to new daylength conditions. We studied local adaptation to daylength in the butterfly Lasiommata megera, which is expanding northwards along several routes in Europe. Using common garden laboratory experiments with controlled daylengths, we compared diapause induction between populations from the southern‐Swedish core range and recently established marginal populations from two independent expansion fronts in Sweden. Caterpillars from the northern populations entered diapause in clearly longer daylengths than those from southern populations, with the exception of caterpillars from one geographically isolated population. The northern populations have repeatedly and rapidly adapted to their local daylengths, indicating that the common use of daylength as seasonal cue need not strongly limit climate‐induced insect range expansions.
The building blocks of a supply chain management theory: Using factor market rivalry for supply chain theorizing
Authors: Ralston Peter M. , Schwieterman Matthew , Bell John E. , Ellram Lisa M. 
Published: August 2022

AbstractAs the supply chain discipline matures, opportunities emerge to develop or define theories that are specific to supply chain phenomenon. The current research specifies characteristics that we offer which comprise the building blocks of supply chain theory. These characteristics include the flows of material through a supply chain network, the temporal management of these material flows, the dyadic and triadic interactions of firms within the supply chain network, and the outward focus on supply chain management (SCM), in other words a supply chain orientation, of firms in a supply chain. Further, recognizing that supply chain theories must contain the previously identified characteristics, we offer Factor Market Rivalry (FMR) as a theory of SCM. FMR refers to intense battles for resource positions that are needed to manufacture, provide, or deliver firm products or services. We argue that FMR only occurs within supply chain phenomena. The piece concludes with a future research agenda based upon the practical implications of further developing FMR as a theory of SCM.