bluuebunny/crossref_metadata_2025 huggingface dataset:
A systems approach discovers the role and characteristics of seven LysR type transcription factors inEscherichia coli
Authors: Rodionova Irina A. , Gao Ye , Monk Jonathan , Wong Nicholas , Szubin Richard , Lim Hyun Gyu , Rodionov Dmitry A. , Zhang Zhongge , Saier Milton H. , Palsson Bernhard O.
Published: December 2021

AlthoughEscherichia coliK-12 strains represent perhaps the best known model bacteria, we do not know the identity or functions of all of their transcription factors (TFs). It is now possible to systematically discover the physiological function of TFs inE. coliBW25113 using a set of synergistic methods; including ChIP-exo, growth phenotyping, conserved gene clustering, and transcriptome analysis. Among 47 LysR-type TFs (LTFs) found on theE. coliK-12 genome, many regulate nitrogen source utilization or amino acid metabolism. However, 19 LTFs remain unknown. In this study, we elucidated the regulation of seven of these 19 LTFs: YbdO, YbeF, YgfI, YiaU, YneJ, YcaN, YbhD. We show that: 1) YbdO regulation has an effect on bacterial growth at low pH with citrate supplementation. YbdO is a repressor of theybdNMoperon and is implicated in the regulation of citrate lyase genes (citCDEFG); 2) YgfI activates thedhaKLMoperon that encodes the phosphotransferase system involved in glycerol and dihydroxyacetone utilization; 3) YiaU regulates theyiaTgene encoding an outer membrane protein, andwaaPSBOJYZUoperon is also important in determining cell density at the stationary phase; 4) YneJ, re-named here as PtrR, directly regulates the expression of the succinate-semialdehyde dehydrogenase, Sad (also known as YneI), and is a predicted regulator offnrS(a small RNA molecule). PtrR is important for bacterial growth in the presence of L-glutamate and putrescine as nitrogen sources; and 5) YbhD and YcaN regulate adjacent y-genes on the genome and YbeF is involved in flagella gene regulation. We have thus established the functions for four LTFs and identified the target genes for three LTFs.

IMPORTANCE

The reconstruction of the transcriptional regulatory network (TRN) is important for gram-negative bacteria such asE. coli. LysR-type TFs are abundant in Enterobacteria, but many LTF functions still remain unknown. Here we report putative functions of uncharacterized TFs based on multi-omics data related to L-threonine, L-glutamate, and putrescine utilization. Amino acids (AAs) and polyamines are important sources of nitrogen for many microorganisms, but the increase in one amino acid or putrescine concentration in a minimal medium also induces stress. Although polyamine metabolism has been studied, the TRN that controls the putrescine (Ptr) and AA utilization at minimal medium conditions are still poorly understood. The function of previously uncharacterized transcriptional regulators YbdO, YgfI, and YneJ (PtrR) were identified inEscherichia coli. PtrR is important for Ptr and L-glutamate utilization, while YgfI transcriptional regulation was found to be important for growth on L-threonine and glycerol as a carbon source.
Coupled protein quality control during nonsense mediated mRNA decay
Authors: Inglis Alison J. , Guna Alina , Merchán Ángel Gálvez , Pal Akshaye , Esantsi Theodore K. , Keys Heather R. , Frenkel Evgeni M. , Oania Robert , Weissman Jonathan S. , Voorhees Rebecca M.
Published: December 2021

Translation of mRNAs containing premature termination codons (PTCs) can result in truncated protein products with deleterious effects. Nonsense-mediated decay (NMD) is a surveillance path-way responsible for detecting and degrading PTC containing transcripts. While the molecular mechanisms governing mRNA degradation have been extensively studied, the fate of the nascent protein product remains largely uncharacterized. Here, we use a fluorescent reporter system in mammalian cells to reveal a selective degradation pathway specifically targeting the protein product of an NMD mRNA. We show that this process is post-translational, and dependent on an intact ubiquitin proteasome system. To systematically uncover factors involved in NMD-linked protein quality control, we conducted genome-wide flow cytometry-based screens. Our screens recovered known NMD factors, and suggested a lack of dependence on the canonical ribosome-quality control (RQC) pathway. Finally, one of the strongest hits in our screens was the E3 ubiquitin ligase CNOT4, a member of the CCR4-NOT complex, which is involved in initiating mRNA degradation. We show that CNOT4 is involved in NMD coupled protein degradation, and its role depends on a functional RING ubiquitin ligase domain. Our results demonstrate the existence of a targeted pathway for nascent protein degradation from PTC containing mRNAs, and provide a framework for identifying and characterizing factors involved in this process.
Comparison of Three Individual Identification Algorithms for Sperm Whales (Physeter macrocephalus) after Automated Detection
Authors: Blount Drew , Holmberg Jason , Parham Jason , Gero Shane , Gordon Jonathan , Levenson J. Jacob
Published: December 2021

Photo-identification of individual sperm whales (Physeter macrocephalus) is the primary technique for mark-recapture-based population analyses for the species The visual appearance of the fluke — with its distinct nicks and notches — often serves as the primary visual differentiator, allowing humans to make recorded sightings of specific individuals. However, the advent of digital photography and the significant increase in volume of images from multiple projects in combination with pre-existing historical catalogs has made applying the method more challenging.with the required human labor for de-duplication (reduction of Type II errors) and reconciliation of sightings between large datasets too cost- and time-prohibitive. To address this, we trained and evaluated the accuracy of PIE v2 (a triplet loss network) along with two existing fluke trailing edge-matching algorithms, CurvRank v2 and Dynamic Time Warping (DTW), as a mean to speed comparison among a high volume of photographs. Analyzed data were collected from a curated catalog of well-known sperm whales sighted across years (2005-2018) off the island of Dominica. The newly-trained PIE model outperformed the older CurvRank and DTW algorithms, and PIE provided the following top-k individual ID matching accuracy on a standard min-3/max-10 sighting training data set: Rank-1: 87.0%, Rank-5: 90.5%, and Rank-12: 92.5%. An essential aspect of PIE is that it can learn new individuals without network retraining, which can be immediately applied in the presence of (and for the resolution of) duplicate individuals in overlapping catalogs. Overall, our results recommend the use of PIE v2 and CurvRank v2 for ID reconciliation in combination due to their complementary performance.
Habitat deterioration despite protection: long-term declines of littoral area of fishponds in Czech nature reserves
Authors: Kolar Vojtech , Francová Kateřina , Vrba Jaroslav , Grill Stanislav , Boukal David S.
Published: December 2021

Fishponds play a key role in current pondscapes in many developed countries. Their littoral areas, supporting multiple ecosystem functions including the maintenance of aquatic and riparian biodiversity, have been adversely affected by the move shift towards more intensive aquaculture and widespread eutrophication in the middle 20th century. To counteract these changes, many fishponds received some protection, but its long-term efficiency has not been studied. Here we focus on the role of conservation status in protecting the area of littoral areas of fishponds in Czechia between the years 1950 and 2019. We found that the conservation status of these fishponds did not prevent habitat deterioration in most of the fishponds, especially during the second half of the 20th century. Moreover, we detected no significant effects of the reserve establishment year, fishpond area and conservation target on the littoral areas. This suggests that the conservation measures are insufficient across fishpond reserve types. We attribute the negative trends to persisting high fish stocks, especially of common carp, and eutrophication resulting from additional feeding, pond manuring, and ongoing nutrient inputs from the pond catchments. Sediment dredging and high grazing pressure by waterfowl in some reserves can further aggravate the situation. We conclude that effective protection of the littoral areas requires a paradigm shift towards less intensive fish stock management, more frequent summer drainage, and effective reduction of all nutrient inputs to increase the water quality. Such measures can help recover the littoral areas and the associated biota.

Graphical abstract

Highlights

Littoral vegetation in ponds supports high biodiversity but often lacks protection.

We evaluated long-term changes in the littoral areas of fishponds in Czechia.

The areas decreased markedly in both protected and unprotected ponds since 1950.

Reserve duration, fishpond area and conservation target did not affect the trends.

Changes in fishpond management are recommended for littoral area recovery.
BK channels of five different subunit combinations underlie the de novo KCNMA1 G375R channelopathy
Authors: Geng Yanyan , Li Ping , Butler Alice , Wang Bill , Salkoff Lawrence , Magleby Karl L.
Published: December 2021

The molecular basis of a severe developmental and neurological disorder associated with a de novo G375R variant of the tetrameric BK channel is unknown. Here we address this question by recording from single BK channels expressed for a heterozygous G375R mutation. Five different types of functional BK channels were observed: 3% were WT, 12% were homomeric mutant, and 85% were three different types of hybrid channels. All channel types except WT showed a marked gain-of-function in voltage activation and a smaller loss-of-function in single channel conductance, with both becoming more pronounced as the number of mutant subunits per tetrameric channel increased. The molecular phenotype suggested codominance for the two homomeric channels and partial dominance for the hybrid channels. A model in which BK channels are randomly assembled from mutant and WT subunits, with each subunit contributing increments of activation and conductance, approximated the molecular phenotype of the heterozygous G375R mutation.
De novo serine biosynthesis from glucose predicts sex-specific response to antifolates in non-small cell lung cancer cell lines
Authors: Sponagel Jasmin , Devarakonda Siddhartha , Rubin Joshua B. , Luo Jingqin , Ippolito Joseph E.
Published: December 2021

Lung cancer is the leading cause of cancer-related death. Intriguingly, males with non-small cell lung cancer (NSCLC), the most common type of lung cancer, have a higher mortality rate than females. Here, we investigated the role of serine metabolism as a predictive marker for sensitivity to the antifolate pemetrexed in male and female NSCLC cell lines. Using [13C6] glucose tracing in NSCLC cell lines, we found that male cells generated significantly more serine from glucose than female cells. Higher serine biosynthesis was further correlated with increased sensitivity to pemetrexed in male cells only. Concordant sex differences in metabolic gene expression were evident in NSCLC and pan-cancer transcriptome datasets, suggesting a potential mechanism with wide-reaching applicability. These data were further validated by integrating antifolate drug cytotoxicity and metabolic pathway transcriptome data from pan-cancer cell lines. Together, these findings highlight the importance of considering sex differences in cancer metabolism to improve treatment for all patients.
Bridging functional annotation gaps in non-model plant genes with AlphaFold, DeepFRI and small molecule docking
Authors: Stephan Georgie , Dugdale Benjamin , Deo Pradeep , Harding Rob , Dale James , Visendi Paul
Published: December 2021

Background

Functional annotation assigns descriptive biological meaning to genetic sequences. Limited availability of manually curated or experimentally validated plant genes from a diverse range of taxa poses a significant challenge for functional annotation in non-model organisms. Accurate computational approaches are required. We argue that recent breakthroughs in deep learning have the potential to not only narrow the functional annotation gap between non-model and model plant organisms, but also annotate and reveal novel functions even for genes with no homologs in public databases.

Results

Deep learning models were applied to functionally annotate a set of previously published differentially expressed genes. Predicted protein structures and functional annotations were generated using the AlphaFold protein structure and DeepFRI protein language inference models respectively. The resulting structures and functional annotations were validated using small molecule docking experiments. DeepFRI and AlphaFold models not only correctly annotated differentially expressed genes, but also revealed detailed mechanisms involving protein-protein interactions.

Conclusions

Deep learning models are capable of inferring novel functions and achieving high accuracy in functional annotation. Their increased use in plant research will result in major improvements in annotations for non-model plants that are underrepresented in genome databases. We illustrate how integrating protein structure prediction, functional residue prediction, and small molecule docking can infer plausible protein-protein interactions and yield additional mechanistic insights. This approach will aid in the selection of candidate genes for further study from differential expression studies that generate large gene lists.
Failure to account for behavioral variability significantly compromises accuracy in indirect population monitoring
Authors: Wessling Erin G. , Surbeck Martin
Published: December 2021

Indirect wildlife population surveying largely depends upon counts of artefacts of behavior (e.g., nests or dung). Likelihood to encounter these artefacts is derived from both artefact production and decay, and variability in production behavior is considered to contribute minimally to inaccuracy in wildlife estimation. Here, we demonstrate how ignoring behavioral variability contributes to significant population misestimation, using an example of an endangered ape, the bonobo (Pan paniscus). Until now, a single estimate of nest construction rate has been used to extrapolate bonobo densities, assumed to be broadly representative of bonobo sign production behavior. We estimated nest construction rates across seasons and social groups at the Kokolopori Bonobo Reserve, DRC, and find nest construction rates in bonobos to be highly variable across populations as well as seasonal. Failure to account for this variability led to degradation in the accuracy of bonobo population estimates of abundance, accounting for a likely overestimation of bonobo numbers by 34%, and at worst as high as 80%. With this example, we demonstrate that failure to account for inter- and intra-population behavioral variation compromises the ability to estimate both relative and absolute wildlife abundances. We argue that variation in sign production is but one of several potential ways that behavioral variability can affect conservation monitoring, should be measured across contexts whenever possible, and must be considered in population estimation confidence intervals. With increasing attention to be-havioral variability as a potential tool for conservation, conservationists must also account for the impact that behavioral variability can play upon wildlife population estimation. Our results underline the importance of observational research to wildlife monitoring schemes as a critical component of conservation management. We discuss the avenues through which behavioral variability is likely to impact wildlife monitoring accuracy and precision and propose potential approaches for accounting for behavioral variability in wildlife monitoring.
Remote contextual fear retrieval engages activity from salience network regions in rats
Authors: dos Santos Corrêa Moisés , Grisanti Gabriel David Vieira , Franciscatto Isabelle Anjos Fernandes , Tarumoto Tatiana Suemi Anglas , Tiba Paula Ayako , Ferreira Tatiana Lima , Fornari Raquel Vecchio
Published: December 2021

The ability to retrieve contextual fear memories depends on the coordinated activation of a brain-wide circuitry. Transition from recent to remote memories seems to involve the reorganization of this circuitry, a process called systems consolidation that has been associated with time-dependent fear generalization. However, it is unknown whether emotional memories acquired under different stress levels can undergo different systems consolidation processes. Here, we explored the activation pattern and functional connectivity of key brain regions associated with contextual fear conditioning (CFC) retrieval after recent (2 days) or remote (28 days) memory tests performed in rats submitted to strong (1.0mA footshock) or mild (0.3mA footshock) training. We used brain tissue from Wistar rats from a previous study, where we observed that increasing training intensity promotes fear memory generalization over time, possibly due to an increase in corticosterone (CORT) levels during memory consolidation. Analysis of Fos expression across 8 regions of interest (ROIs) allowed us to identify coactivation between them at both timepoints following memory recall. Our results showed that strong CFC elicits higher Fos activation in the anterior insular and prelimbic cortices during remote retrieval, which was positively correlated with freezing along with the basolateral amygdala. Rats trained either with mild or strong CFC showed broad functional connectivity at the recent timepoint whereas only animals submitted to the strong CFC showed a widespread loss of coactivation during remote retrieval. Post-training plasma CORT levels are positively correlated with FOS expression during recent retrieval in strong CFC, but negatively correlated with FOS expression during remote retrieval in mild CFC. Our findings suggest that increasing training intensity results in differential processes of systems consolidation, possibly associated with increased post-training CORT release, and that strong CFC engages activity from the aIC, BLA and PrL – areas associated with the Salience Network in rats – during remote retrieval.
Using Deep Learning for Gene Detection and Classification in Raw Nanopore Signals
Authors: Nykrynova Marketa , Barton Vojtech , Jakubicek Roman , Bezdicek Matej , Lengerova Martina , Skutkova Helena
Published: December 2021

Recently, nanopore sequencing has come to the fore as library preparation is rapid and simple, sequencing can be done almost anywhere, and longer reads are obtained than with next-generation sequencing. The main bottleneck still lies in data postprocessing which consists of basecalling, genome assembly, and localizing significant sequences, which is time consuming and computationally demanding, thus prolonging delivery of crucial results for clinical practice. Here, we present a neural network-based method capable of detecting and classifying specific genomic regions already in raw nanopore signals – squiggles. Therefore, the basecalling process can be omitted entirely as the raw signals of significant genes, or intergenic regions can be directly analysed, or if the nucleotide sequences are required, the identified squiggles can be basecalled, preferably to others. The proposed neural network could be included directly in the sequencing run, allowing real-time squiggle processing.
Dual Passive Reactive Brain Computer Interface: a Novel Approach to Human-Machine Symbiosis
Authors: Dehais Frédéric , Ladouce Simon , Darmet Ludovic , Tran-Vu Nong , Ferraro Giuseppe , Tresols Juan Torre , Velut Sébastien , Labedan Patrice
Published: December 2021

The present study proposes a novel concept of neuroadaptive technology, namely a dual passive-reactive Brain-Computer Interface (BCI), that enables bi-directional interaction between humans and machines. We have implemented such a system in a realistic flight simulator using the NextMind classification algorithms and framework to decode pilots’ intention (reactive BCI) and to infer their level of attention (passive BCI). Twelve pilots used the reactive BCI to perform checklists along with an anti-collision radar monitoring task that was supervised by the passive BCI. The latter simulated an automatic avoidance maneuver when it detected that pilots missed an incoming collision. The reactive BCI reached 100% classification accuracy with a mean reaction time of 1.6s when exclusively performing the checklist task. Accuracy was up to 98.5% with a mean reaction time of 2.5s when pilots also had to fly the aircraft and monitor the anti-collision radar. The passive BCI achieved a F1 − score of 0.94. This first demonstration shows the potential of a dual BCI to improve human-machine teaming which could be applied to a variety of applications.
On the assessment of the sources of inoculum of bacterial wilt in Brazil
Authors: Mizubuti Eduardo S. G. , Yamada Jaqueline K. , Santiago Thaís R. , Lopes Carlos Alberto
Published: December 2021

Dispersal of Ralstonia spp. cells by water and contaminated plant material and the importance of weeds as inoculum sources have been poorly investigated. Water of rivers, soil from fields of diverse crops and areas of natural vegetation both from the Amazônia, Cerrado and Mata Atlântica biomes, besides soil of the rhizosphere of weeds present in tomato fields with records of bacterial wilt were sampled and analyzed to detect Ralstonia spp. Seeds of tomato plants artificially and naturally infected with Ralstonia spp. were also processed. All samples were enriched a priori in selective medium South Africa (SMSA) and colonies were isolated in plates containing solid SMSA. Detection of Ralstonia spp. was confirmed by polymerase chain reaction with specific primers. The Co – operational PCR (CO-PCR) was also used to detect Ralstonia spp. Colonies were obtained from soil samples and from a commercial substrate sample. Five soil samples from eggplant fields, one from coffee field, one substrate from potato seed tuber production, two soil samples from the rhizosphere of Amaranthus spp., one from Bidens pilosa and one from Solanum americanum tested positive for Ralstonia spp. Besides these soil samples, five water samples of rivers were positive for CO-PCR detection: two samples from Amazônia, one from Cerrado and two samples from irrigation water collected from tomato fields located in the Mata Atlântica biome. Ralstonia spp. were not detected in tomato seeds. These results revealed potential inoculum sources, especially weeds, in areas with historical records of bacterial wilt. Additionally, rivers may act as dispersal agents of inoculum of Ralstonia spp.
A spectral demixing method for high-precision multi-color localization microscopy
Authors: Andronov Leonid , Genthial Rachel , Hentsch Didier , Klaholz Bruno P.
Published: December 2021

Single molecule localization microscopy (SMLM) with a dichroic image splitter can provide invaluable multi-color information regarding colocalization of individual molecules, but it often suffers from technical limitations. So far, demixing algorithms give suboptimal results in terms of localization precision and correction of chromatic aberrations. Here we present an image splitter based multi-color SMLM method (splitSMLM) that offers much improved localization precision & drift correction, compensation of chromatic aberrations, and optimized performance of fluorophores in a specific buffer to equalize their reactivation rates for simultaneous imaging. A novel spectral demixing algorithm, SplitViSu, fully preserves localization precision with essentially no data loss and corrects chromatic aberrations at the nanometer scale. Multi-color performance is further improved by using optimized fluorophore and filter combinations. Applied to three-color imaging of the nuclear pore complex (NPC), this method provides a refined positioning of the individual NPC proteins and reveals that Pom121 clusters act as NPC deposition loci, hence illustrating strength and general applicability of the method.
Correlation of receptor density and mRNA expression patterns in the human cerebral cortex
Authors: Matej Murgaš , Paul Michenthaler , Bruce Reed Murray , Gregor Gryglewski , Rupert Lanzenberger
Published: December 2021

Changes in distribution of associated molecular targets have been reported across several neuropsychiatric disorders. However, the high-resolution topology of most proteins is unknown and simultaneous in vivo measurement in multi-receptor systems is complicated. To account for the missing proteomic information, mRNA transcripts are typically used as a surrogate. Nonetheless, post-transcriptional and post-translational processes might cause the discrepancy between the final distribution of proteins and gene expression patterns. Therefore, this study aims to investigate ex vivo links between mRNA expression and corresponding receptor density in the human cerebral cortex.

To this end, autoradiography data on the density of 15 different receptors in 38 brain regions were correlated with the expression patterns of 50 associated genes derived from microarray data (mA), RNA sequencing data (RNA-Seq) provided by the Allen Human Brain Atlas and predicted mRNA expression patterns (pred-mRNA). Spearman’s rank correlation was used to evaluate the possible links between proteomic data and mRNA expression patterns.

Correlations between mRNA and protein density varied greatly between targets: Positive associations were found for e.g. the serotonin 1A (pred-mRNA: rs = 0.708; mA: rs = 0.601) or kainate receptor (pred-mRNA: rs = 0.655; mA: rs = 0.601; RNA-Seq: rs = 0.575), while most of the investigated target receptors showed low or negative correlations.

The high variability in the correspondence of mRNA expression and receptor warrants caution when inferring the topology of molecular targets in the brain from transcriptome data. This highlights the longstanding value of molecular imaging data and the need for comprehensive proteomic data.
MALDI mass spectrometry imaging of fresh and processed food: constituents, ingredients, contaminants and additives
Authors: Kokesch-Himmelreich Julia , Wittek Oliver , Race Alan M. , Rakete Sophie , Schlicht Claus , Busch Ulrich , Römpp Andreas
Published: December 2021

Mass Spectrometry imaging (MS imaging) provides spatial information for a wide range of compound classes in different sample matrices. We used MS imaging to investigate the distribution of components in fresh and processed food, including meat, dairy and bakery products. The MS imaging workflow was optimized to cater to the specific properties and challenges of the individual samples. We successfully detected highly nonpolar and polar constituents such as beta-carotene and anthocyanins, respectively. For the first time, the distribution of a contaminant and a food additive was visualized in processed food. We detected acrylamide in German gingerbread and investigated the penetration of the preservative natamycin into cheese. For this purpose, a new data analysis tool was developed to study the penetration of analytes from uneven surfaces. Our results show that MS imaging has great potential in food analysis to provide relevant information about components’ distributions, particularly those underlying official regulations.

Highlights

Investigation of fresh and processed food by MALDI mass spectrometry imaging

Visualization of different compound classes in plant and meat-based food

Development of data processing tool for penetration/diffusion analysis (in food)

Natamycin penetration in cheese, first visualization of food additive by MS imaging

Acrylamide in gingerbread, first visualization of contaminant by MS imaging
HuluFISH non-denaturing in situ detection of genomic DNA opened by CRISPR-Cas9 Nickase and Exonuclease
Authors: Han Kang , Liu Sheng , Cheng Yongsheng
Published: December 2021

DNA fluorescence in situ hybridization (FISH) has been widely used in diagnosis and genetic research. Traditional Bacterial artificial chromosome (BAC) or oligonucleotide based probe to detect DNA in situ is only effective when the target is relatively large, usually over 150Kb DNA fragments. And it involves heat denaturation steps to open the DNA for in situ hybridization. The heat process can affect the fine structure of nuclei. Here we reported a novel method based on Cas9 nickase and exonuclease digestion of double strand DNA and permanently mark the DNA in single strand state for FISH. With this novel design, we detected non-repetitive genomic loci as small as 2Kb.
SEX-SPECIFIC TRAJECTORIES OF REELIN-DEPENDENT MATURATION OF DEEP LAYER PREFRONTAL NEURONS
Authors: Silva Hurtado Thenzing Judá , Lassalle Olivier , Ameloot Antoine , Chavis Pascale
Published: December 2021

Throughout early adulthood, the anatomical and functional maturation of PFC circuitry continues under the influence of multiple extrinsic and intrinsic factors, most notably electrical activity, and molecular cues. We previously showed that the extracellular matrix protein reelin orchestrates the structural and functional maturation of deep layers medial PFC (mPFC) pyramidal neurons. Additionally, we reported that reelin haploinsufficiency is associated to prefrontal disruptions of long-term memory retention thereby illustrating the eminent role of reelin in cognitive maturation of the PFC. Prefrontal maturation follows a sex-specific developmental pattern, supporting the existence of sexual differences in the morphology-functional properties PFC. Here, we interrogated the role of reelin in the functional maturation of excitatory networks in the mPFC. The developmental trajectory of reelin’s expression and deep layer pyramidal neurons synaptic plasticity was tracked in the mPFC of male and female mice, from the juvenile period to adulthood. To assess the role of reelin in both sexes, wild-type and heterozygous reeler mice (HRM) were compared. The results show that the maturational profile of reelin expression in the mPFC is sex-dependent and that the developmental trajectory of long-term potentiation is different between wild-type males and females. These data demonstrate reelin’s influence on prefrontal synapses is sex and period specific.
Comparative assessment of electronic nicotine delivery systems aerosol and cigarette smoke on endothelial cell migration: the Replica Project
Authors: Caruso Massimo , Emma Rosalia , Distefano Alfio , Rust Sonja , Poulas Konstantinos , Giordano Antonio , Volarevic Vladislav , Mesiakaris Konstantinos , Boffo Silvia , Arsenijevic Aleksandar , Karanasios Georgios , Pulvirenti Roberta , Ilic Aleksandar , Canciello Angelo , Zuccarello Pietro , Ferrante Margherita , Polosa Riccardo , Li Volti Giovanni ,   the Replica Project Group
Published: December 2021

Cigarette smoking is associated with impairment of repair mechanisms necessary for vascular endothelium homeostasis. Reducing the exposure to smoke toxicants may result in the mitigation of the harmful effect on the endothelium and cardiovascular disease development. Previous investigations performed by the tobacco industries evaluated in vitro the effect of electronic cigarette (e-cig) compared to cigarette smoke demonstrating a significant reduction in endothelial cell migration inhibition following e-cig aerosol exposure. In the present study, we replicated one of these studies, evaluating the effects of cigarette smoke on endothelial cell migration compared to e-cig and heated tobacco products. We used a multi-center approach (ring-study) to verify the robustness and reliability of the results obtained in the replicated study. Consistently with the original study, we observed a substantial reduction of the effects of e-cig and tobacco heated products on endothelial cell migration compared to cigarette smoke. In conclusion, our study further confirms the importance of e-cig and tobacco heated products as a possible harm reduction strategy for cardiovascular diseases development in smokers.

Highlights

Cigarette smoking is strictly related to impairment of vascular repair mechanisms

Reducing the exposure to toxicants in smoke, could reduce the harm to endothelium

ENDS showed a reduced effect on endothelial cell migration compared to cigarette

These data demonstrated the reduced toxicity of ENDS compared to cigarettes.
Megaherbivores modify forest structure and increase carbon stocks through multiple pathways
Authors: Berzaghi Fabio , Bretagnolle François , Durand-Bessart Clémentine , Blake Stephen
Published: December 2021

Megaherbivores have pervasive ecological effects. In African rainforests, elephants can increase aboveground carbon, though the mechanisms are unclear. Here we combine a large unpublished dataset of forest elephant feeding with published browsing preferences totaling > 120,000 records covering 700 plant species, including nutritional data for 102 species. Elephants increase carbon stocks by: 1) promoting high wood density tree species via preferential browsing on leaves from low wood density species, which are more digestible; 2) dispersing seeds of trees that are relatively large and have the highest average wood density among tree guilds based on dispersal mode. Loss of forest elephants could cause a 5-12% decline in carbon stocks due to regeneration failure of elephant-dispersed trees and an increase in abundance of low wood density trees. These results show the major importance of megaherbivores in maintaining diverse, high-carbon tropical forests. Successful elephant conservation will contribute to climate mitigation at a scale of global relevance.
Reconfigurable microfluidic circuits for isolating and retrieving cells of interest
Authors: Deroy Cyril , Wheeler James H. R. , Rumianek Agata N. , Cook Peter R. , Durham William M. , Foster Kevin , Walsh Edmond J.
Published: December 2021

Microfluidic devices are widely used in many fields of biology, but a key limitation is that cells are typically surrounded by solid walls, making it hard to access those that exhibit a specific phenotype for further study. Here, we provide a general and flexible solution to this problem that exploits the remarkable properties of microfluidic circuits with fluid walls – transparent interfaces between culture media and an immiscible fluorocarbon that are easily pierced with pipets. We provide two proofs-of-concept in which specific cell sub-populations are isolated and recovered: i) murine macrophages chemotaxing towards complement component 5a, and ii) bacteria (Pseudomonas aeruginosa) in developing biofilms that migrate towards antibiotics. We build circuits in minutes on standard Petri dishes, add cells, pump in laminar streams so molecular diffusion creates attractant gradients, acquire time-lapse images, and isolate desired sub-populations in real-time by building fluid walls around migrating cells with an accuracy of tens of micrometres using 3D-printed adaptors that convert conventional microscopes into wall-building machines. Our method allows live cells of interest to be easily extracted from microfluidic devices for downstream analyses.
Low-background neutron reflectometry from solid/liquid interfaces
Authors: Hoogerheide David P. , Dura Joseph A. , Maranville Brian B. , Majkrzak Charles F.
Published: December 2021

Liquid cells are an increasingly common sample environment for neutron reflectometry experiments and are critical for measuring the properties of materials at solid/liquid interfaces. Background scattering determines the maximum useful scattering vector, and hence the spatial resolution, of the neutron reflectometry measurement. The primary sources of background are the liquid in the cell reservoir and the materials forming the liquid cell itself. Thus, characterization and mitigation of these background sources are necessary for improvements in the signal-to-background ratio and resolution of neutron reflectometry measurements employing liquid cells. Single-crystal silicon is a common material used for liquid cells due to its low incoherent scattering cross section for neutrons, and the path lengths of the neutron beam through silicon can be several centimetres in modern cell designs. Here, a liquid cell is constructed with a sub-50 µm thick liquid reservoir encased in single-crystal silicon. It is shown that, at high scattering vectors, inelastic scattering from silicon represents a significant portion of the scattering background and is, moreover, structured, confounding efforts to correct for it by established background subtraction techniques. A significant improvement in the measurement quality is achieved using energy-analyzed detection. Energy-analyzed detection reduces the scattering background from silicon by nearly an order of magnitude, and from fluids such as air and liquids by smaller but significant factors. Combining thin liquid reservoirs with energy-analyzed detection and the high flux of the CANDOR polychromatic reflectometer at the NIST Center for Neutron Research, a background-subtracted neutron reflectivity smaller than 10−8 from a liquid cell sample is reported.
Implementation of cryogenic tender X-ray HR-XANES spectroscopy at the ACT station of the CAT-ACT beamline at the KIT Light Source
Authors: Schacherl Bianca , Prüssmann Tim , Dardenne Kathy , Hardock Kirsten , Krepper Volker , Rothe Jörg , Vitova Tonya , Geckeis Horst
Published: December 2021

The ACT experimental station of the CAT-ACT wiggler beamline at the Karlsruhe Institute of Technology (KIT) Light Source is dedicated to the investigation of radionuclide materials with radioactivities up to 1000000 times the exemption limit by various speciation techniques applying monochromatic X-rays. In this article, the latest technological developments at the ACT station that enable high-resolution X-ray absorption near-edge structure (HR-XANES) spectroscopy for low radionuclide loading samples are highlighted – encompassing the investigation of actinide elements down to 1 p.p.m. concentration – combined with a cryogenic sample environment reducing beam-induced sample alterations. One important part of this development is a versatile gas tight plexiglass encasement ensuring that all beam paths in the five-analyzer-crystal Johann-type X-ray emission spectrometer run within He atmosphere. The setup enables the easy exchange between different experiments (conventional X-ray absorption fine structure, HR-XANES, high-energy or wide-angle X-ray scattering, tender to hard X-ray spectroscopy) and opens up the possibility for the investigation of environmental samples, such as specimens containing transuranium elements from contaminated land sites or samples from sorption and diffusion experiments to mimic the far field of a breached nuclear waste repository.
University business idea incubation and stakeholders' engagement: closing the gap between theory and practice
Authors: Secundo Giustina , Mele Gioconda , Passiante Giuseppina , Albergo Francesco
Published: December 2021

Purpose

The paper aims to contributes on the debates about University Idea Incubation by investigating the role and the engagement of different University's stakeholders in the process of opportunity recognition in an entrepreneurship education program targeted at students with an interdisciplinary background.

Design/methodology/approach

Through a longitudinal case study methodology, the Contamination Lab at University of Salento (Lecce, Italy), the learning approaches and the knowledge process to create an entrepreneurial awareness, mindset and capability in students with different educational background are presented.

Findings

The findings demonstrates the crucial role of stakeholders' engagement for business idea presentation, open innovation challenge, contamination workshop on specialized topics, enterprise projects are important vehicle for effective students' business ideas and innovative projects development in a multidisciplinary environment. The close interaction among students, academia, companies and institutions creates a favourable environment that enables opportunity identification, idea generation through a deep contamination of knowledge, skills and experiences.

Research limitations/implications

Limitations include the need to generalise the results even if this limitation is typical of the case study methodology. Other research is necessary for an in-depth analysis in deep of the other Contamination Lab in Italy and to derive the “invariance traits” of this environment according to the features of the local entrepreneurial ecosystems.

Practical implications

Implications for practices include recommendations for designing innovative programs where the interactions between University-Institutions-Industry are realized.

Originality/value

A conceptual framework is proposed by defining all the entrepreneurial knowledge process and knowledge creation within the Contamination Lab, highlighting the contribution of the stakeholders in each phase and learning initiative of the program.
The administrative state in food policymaking: a fait accompli
Authors: Bancerz Margaret
Published: December 2021

Purpose

This paper analyzes scholarly literature and the development of a nonstate food strategy in Canada, the Conference Board of Canada's Canadian Food Strategy, to explore the role of the administrative state in food policymaking.

Design/methodology/approach

This research is based on an exploratory case study drawing data from 38 semistructured interviews, including elite interviews. It also draws on policy documents from the nonstate food strategy.

Findings

This paper shows that various nonstate actors, including large food industry players, identify a role for the state in food policy in two ways: as a “conductor,” playing a managing role in the food policy process, and as a “commander,” taking control of policy development and involving nonstate actors when necessary. The complex and wicked aspects of food policy require the administrative state's involvement in food policymaking, while tamer aspects of food policy may be less state-centric.

Originality/value

This paper fills gaps in studies exploring food policymaking processes as well as the administrative state's role in food policymaking in a governance era. It contributes to a better understanding of the state's role in complex and wicked policy domains.
Financial feasibility assessment of adopting active controlled atmosphere containers for exporting highly perishable fruits during COVID-19: case of Taiwanese atemoya
Authors: Huang Wen-Hung , Dy Kenneth Bicol , Chang Ching-Cheng , Hsu Shih-Hsun
Published: December 2021

Purpose

This study deals with attenuating the risk of relying on a single export market, which was heightened by the outbreak of the COVID-19 pandemic. It focuses on Taiwanese atemoya (a fruit with short storage life) and the adoption of active controlled atmosphere (CA) containers, a new technology which lengthens storage time for other export markets. This study looks at the financial feasibility of the technology's first ever use in atemoya exports.

Design/methodology/approach

Apart from the standard financial assessment tools—like net present value (NPV), internal rate of return (IRR), benefit-cost ratio (BCR) and payback period (PBP)—this study calibrated five different scenarios based on data gathered from relevant market agents including suppliers, exporters, customs brokers and technology developer.

Findings

Due to the high profit margin and low investment cost, the use of active CA containers for long-haul exports of this highly perishable fruit is found both technically and financially feasible, despite the generally higher operational cost during the pandemic.

Research limitations/implications

This study looked at three specific export markets: Malaysia, Dubai and Canada. Results here may lack generalizability in other markets, although it is believed that slight deviations would not invalidate the conclusions of this research because short, medium and long distances were all covered therein.

Originality/value

This paper studies the first time that active CA is used for export of atemoyas to expand existing markets.
Role of cloud computing technology in the education sector
Authors: Thavi Riddhi , Jhaveri Rujuta , Narwane Vaibhav , Gardas Bhaskar , Jafari Navimipour Nima
Published: December 2021

Purpose

This paper aims to provide a literature review on the cloud-based platforms for the education sectors. The several aspects of cloud computing adoption in education, remote/distance learning and the application of cloud-based design and manufacturing (CBDM) have been studied and theorised.

Design/methodology/approach

A four-step methodology was adopted to analyse and categorise the papers obtained through various search engines. Out of 429 research articles, 72 papers were shortlisted for the detailed analysis.

Findings

Many factors that influence cloud computing technology adoption in the education sector have been identified in this paper. The research findings on several research items have been tabulated and discussed. Based on the theoretical research done on cloud computing for education, cloud computing for remote/distance learning and CBDM, cloud computing could enhance the educational systems in mainly developing countries and improve the scope for remote/distance learning.

Research limitations/implications

This study is limited to papers published only in the past decade from 2011 to 2020. Besides, this review was unable to include journal articles published in different languages. Nevertheless, for the effective teaching and learning process, this paper could help understand the importance and improve the process of adopting cloud computing concepts in educational universities and platforms.

Originality/value

This study is a novel one as a research review constituting cloud computing applications in education and extended for remote/distance learning and CBDM, which have not been studied in the existing knowledge base.
Teaching for creativity and entrepreneurial intentions: an empirical study
Authors: Nguyen Thuy Thu , Do Diep Ngoc
Published: December 2021

Purpose

This study aims to investigate the structural relationships between pedagogy methods, creativity and entrepreneurial intentions. This study theorizes that work-integrated and active learning methods positively influence personal creativity, which in turn positively influences entrepreneurial intention. Moreover, entrepreneurial inspiration moderates the impact of creativity on entrepreneurial intentions.

Design/methodology/approach

A sample of 701 valid questionnaires from university students is used to investigate the proposed research model empirically. As the methodological approach, structural equation modelling with multigroup analysis is used.

Findings

The statistical results confirm the positive impacts of work-integrated and active learning methods on individual perceived creativity and of creativity on entrepreneurial intentions. Further, inspiration towards entrepreneurship moderates the link between individual creativity and entrepreneurial intentions.

Originality/value

This research fills the gap in the realm of examining the structural relationship among learning methods, creativity and entrepreneurial intentions in an emerging economy context. Specifically, this study confirms experiential teaching methods as important predictors of the development of students’ creativity capability and the moderating role of entrepreneurial inspiration in the relationship between perceived creativity and entrepreneurial intention. These results add to the academic literature on entrepreneurial intentions in emerging economies and provide new insights into how universities in emerging economies can foster the entrepreneurial intentions of their students.