Miracle-dz/UniFAR-FTUs huggingface dataset:
State-behavior feedbacks suppress personality variation in boldness during foraging in sticklebacks

Consistent inter-individual variation within a population, widely referred to as personality variation, can be affected by environmental context. Feedbacks between an individual’s personality and state can strengthen (positive feedback) or weaken (negative feedback) individual differences when experiences such as predator encounters or winning contests are dependent on personality type. We examined the influence of foraging on individual-level consistency in refuge use (a measure of risk-taking, i.e. boldness) in three-spined sticklebacks, Gasterosteus aculeatus, and particularly whether changes in refuge use depended on boldness measured under control conditions. In the control treatment trials with no food, individuals were repeatable in refuge use across repeated trials, and this behavioral consistency did not differ between the start and end of these trials. In contrast, when food was available, individuals showed a higher degree of consistency in refuge use at the start of the trials versus controls but this consistency significantly reduced by the end of the trials. The effect of the opportunity to forage was dependent on personality, with bolder fish varying more in their refuge use between the start and the end of the feeding trials than shyer fish. This suggests a state-behavior feedback, but there was no overall trend in how individuals changed their behavior, with some individuals spending more, and others less, time in the refuge area at the end than at the start of the trials. Our study shows that personality variation can be suppressed in foraging contexts and a potential but unpredictable role of feedbacks between state and behavior.
Selective behavioral deficits from focal inactivation of primate inferior temporal (IT) cortex: a new quantitative constraint for models of core object recognition

Primate core visual object recognition is thought to rely on the ventral visual stream, a hierarchy of cortical areas culminating in inferior temporal (IT) cortex. Previous work has shown that the IT population responses accurately predict primate object recognition behavior, suggesting that these IT codes underlie these behaviors. However, direct causal evidence for this decoding hypothesis has been equivocal at best, especially beyond the specific case of face-selective sub-regions of IT. Here, we tested the general causal role of IT in core object recognition by reversibly inactivating individual, millimeter-scale regions of IT via injection of muscimol while monkeys performed several binary object discrimination tasks, interleaved trial-by-trial. Our results show that inactivating different millimeter-scale sub-regions of primate IT resulted in different patterns of task deficits. These results provide new constraints for computational models of the ventral stream and this behavior. To this end, we tested state-of-the-art deep convolutional neural network models by constructing topographic deep artificial neural networks (TDANNs) on which we simulated inactivation experiments. Our results show that TDANNs recapitulated first-order experimental phenomena slightly better than randomly mapped deep artificial neural network models. Taken together, these results establish and test a new class of experimental constraints for computational models of core object recognition.
The Influence of Fire and Other Environmental Factors on Terrestrial Gastropod Species Composition in an Oak-Hickory Woodland of West-Central Illinois

Abstract: Terrestrial gastropods are important herbivores, prey, and as decomposers in woodlands of the Midwestern USA. Vegetation structure and composition are dynamic and may influence gastropod abundance and distribution, but relationships among gastropod communities and environmental variables are understudied. We burned three treatment units in an oak-hickory woodland during 2004 and conducted additional burns on two of those treatment units, one in 2014 and the other in 2015. In May and August 2016, we collected leaf litter containing gastropods from transects within these three burn treatment units and used 19 environmental variables that were potentially important to gastropods. Environmental variables were associated with herbaceous and woody vegetation, ground cover, physiography, and burn history. We identified 14 species of gastropods at the study site. No significant environmental models were found for gastropod abundance, richness, effective number of species (based on Shannon entropy), or effective number of species (based on the Gini-Simpson index). Statistically significant associations among gastropods and environmental variables were seen in three species. Euchemotrema leaii was associated with areas having low coverage of shrubs and other perennials, and abundant leaf litter, whereas Neohelix alleni was positively associated with leaf litter and was abundant in areas with low total cover. Glyphyalinia indentata was associated with higher elevation transects, may be impacted by recent burning, and was found in areas with greater amounts of grasses and vines.
Dual-purpose isocyanides produced by Aspergillus fumigatus contribute to cellular copper sufficiency and exhibit antimicrobial activity

Significance Metal homeostasis is an integral part of metabolism for any organism. A vast array of natural products are already known to mediate iron homeostasis in fungi and bacteria; however, unlike their bacterial counterparts, to date, there are no known fungal small molecules that function to maintain copper homeostasis. Discovery of copper-binding xanthocillins produced by Aspergillus fumigatus gives insight into mechanisms other than the extensively studied copper transporters or metalloproteins for how fungi can regulate copper. This has important ecological implications, as securing scarce nutrients is central for fitness and survival. Conservation of the xanthocillin biosynthetic machinery across filamentous fungal taxa offers a new paradigm in eukaryotic metal homeostasis. The maintenance of sufficient but nontoxic pools of metal micronutrients is accomplished through diverse homeostasis mechanisms in fungi. Siderophores play a well established role for iron homeostasis; however, no copper-binding analogs have been found in fungi. Here we demonstrate that, in Aspergillus fumigatus, xanthocillin and other isocyanides derived from the xan biosynthetic gene cluster (BGC) bind copper, impact cellular copper content, and have significant metal-dependent antimicrobial properties. xan BGC-derived isocyanides are secreted and bind copper as visualized by a chrome azurol S (CAS) assay, and inductively coupled plasma mass spectrometry analysis of A. fumigatus intracellular copper pools demonstrated a role for xan cluster metabolites in the accumulation of copper. A. fumigatus coculture with a variety of human pathogenic fungi and bacteria established copper-dependent antimicrobial properties of xan BGC metabolites, including inhibition of laccase activity. Remediation of xanthocillin-treated Pseudomonas aeruginosa growth by copper supported the copper-chelating properties of xan BGC isocyanide products. The existence of the xan BGC in several filamentous fungi suggests a heretofore unknown role of eukaryotic natural products in copper homeostasis and mediation of interactions with competing microbes.
Millimeter-Wave On-Chip Bandpass Filter Based on Spoof Surface Plasmon Polaritons

A gallium arsenide (GaAs)-based millimeter-wave broadband bandpass filter (BPF) is proposed based on slotted half-mode substrate integrated waveguide (HMSIW) spoof surface plasmon polaritons (SSPPs). The center frequency and bandwidth of this SSPP-based on-chip BPF can be easily controlled by tuning the geometry dimensions of the SSPP unit cell, which is attributed to its unique dispersion characteristics. For demonstration, a prototype of the proposed BPF is fabricated and experimentally characterized, with good agreement between the simulated and measured results. Due to the ability of the strong electric field confinement, the proposed on-chip SSPP structure has lower coupling feature with closely-spaced transmission line circuits than its counterpart traditional HMSIW structure.
Distributed Ledgers for Spectrum Authorization

The rising demand for wireless services can only be met if the available spectrum is shared effectively, and spectrum underutilization is avoided. This article examines how a DLT-based spectrum authorization system may be designed considering its protocol, data, and network operational layers. Decentralization, automation, and verifiable trust achieved by this system facilitate spectrum sharing and trading, catering to business objectives in addition to the influences from regulatory and technological developments. To this end, we elaborate on the technical feasibility, scalability, and business incentives for such a system to stimulate the multiple cross-industry stakeholders to use the radio spectrum more efficiently for 5G and beyond.
Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts

The well-established Shine-Dalgarno model suggests that translation initiation in bacteria is regulated via base-pairing between ribosomal RNA (rRNA) and mRNA. However, little is currently known about the contribution of such interactions to the rest of the translation process and to the way bacterial transcript evolve. We used novel computational analyses and modelling of 823 bacterial genomes coupled with experiments to demonstrate that rRNA-mRNA interactions are diverse and regulate not only initiation, but all translation steps from pre-initiation to termination across the many bacterial phyla that have the Shine-Dalgarno sequence. As these interactions dictate translation efficiency, they serve as a driving evolutionary force for shaping transcripts in bacteria. We observed selection for strong rRNA-mRNA interactions in regions where such interactions are likely to enhance initiation, regulate early elongation and ensure the fidelity of translation termination. We discovered selection against strong interactions and for intermediate interactions in coding regions and present evidence that these interactions maximize elongation efficiency while also enhancing initiation by ‘guiding’ free ribosomal units to the start codon. Importance Previous research has reported the significant influence of rRNA-mRNA interactions mainly in the initiation phase of translation. The results reported in this paper suggest that, in addition to the rRNA-mRNA interactions near the start codon that trigger initiation in bacteria, rRNA-mRNA interactions affect all sub-stages of the translation process (pre-initiation, initiation, elongation, termination). In addition, these interactions affect the way evolutionary forces shape the bacterial transcripts while considering trade-offs between the effects of different interactions across different transcript regions on translation efficacy and efficiency. Due to the centrality of the translation process, these findings are relevant to all biomedical disciplines.
Bacterial dormancy: A subpopulation of viable but non-culturable cells demonstrates better fitness for revival

The viable but non culturable (VBNC) state is a condition in which bacterial cells are viable and metabolically active, but resistant to cultivation using a routine growth medium. We investigated the ability of V. parahaemolyticus to form VBNC cells, and to subsequently become resuscitated. The ability to control VBNC cell formation in the laboratory allowed us to selectively isolate VBNC cells using fluorescence activated cell sorting, and to differentiate subpopulations based on their metabolic activity, cell shape and the ability to cause disease in Galleria mellonella. Our results showed that two key subpopulations (P1 and P2) of V. parahaemolyticus VBNC cells exist and can remain dormant in the VBNC state for long periods. The two subpopulations displayed different abilities for revival under favourable conditions. Proteomic analysis of these subpopulations (at two different time points: 12 days (T12) and 50 days (T50) post VBNC) has also revealed that the proteome of P2 was more similar to that of the starting microcosm culture (T0) than the proteome of P1. The proteins that were significantly up and down regulated between the different VBNC populations were determined and significantly regulated proteins were assigned into 23 functional groups, the majority being included in metabolism functional categories. A lactate dehydrogenase (lldD) protein was significantly upregulated in all subpopulations of VBNC cells and is responsible for converting lactate to pyruvate. Deletion of the lactate dehydrogenase (RIMD2210633:ΔlldD) gene causes the cells to enter the VBNC state significantly faster than the wild-type, and exogenously adding lactate to VBNC cells aided resuscitation and extended the resuscitation window. Addition of pyruvate to the RIMD2210633:ΔlldD strain restored the wild-type VBNC formation profile. This study suggests that lactate dehydrogenase plays a putative key role in regulating the VBNC state.
4H-SiC UMOSFET With an Electric Field Modulation Region Below P-Body

In this article, we investigate a novel optimized 4H-SiC U-shaped trench-gate MOSFET (UMOSFET) structure, which features an electric field modulation region below the P-body. This region consists of a p-type region and an n-type region, while the p-type region is wrapped by the n-type region. We use the p-type region to reduce the electric field at the P+ shielding layer and the gate oxide. The reduced electric field increases the breakdown voltage (BV) of the optimized UMOSFET substantially. The n-type region can also improve the ON-state characteristics of the UMOSFET. Under the combined action of the p-type region and the n-type region, the BV and figure of merit increased by 25.2% and 120.5%, respectively. Moreover, the specific ON-resistance dropped by 40.8%.
Space Use and Habitat Selection by Female Louisiana Black Bears in the Tensas River Basin of Louisiana

Abstract Studies of space use and habitat selection of endangered species are useful for identifying factors that influence fitness of individuals and viability of populations. However, there is a lack of published information regarding these behaviors for the federally threatened Louisiana black bear (Ursus americanus luteolus). We documented space use and habitat selection for 28 female black bears in 2 subpopulations of the Tensas River Basin population in northeast Louisiana, USA. The Tensas subpopulation inhabits a relatively large (>300-km2) contiguous area of bottomland hardwood forest, whereas the Deltic subpopulation exists mainly in 2 small (<7-km2) forested patches surrounded by an agricultural matrix. Females on Deltic maintained smaller seasonal and annual home ranges than females on Tensas (all P < 0.04), except for females with cubs during spring. On Tensas, females with cubs maintained smaller home ranges than females without cubs during spring (P = 0.01), but we did not detect this difference on Deltic or in other seasons. Females on Tensas and Deltic exhibited differences in habitat selection when establishing home ranges and within home ranges (P < 0.001). Deltic females selected mature bottomland hardwood forests and avoided agricultural habitats at both spatial scales. Tensas females selected a mixture of swamps, mature and regenerating forests, and exhibited variation in selection across scale, season, and reproductive status. We suggest that differences in space use and habitat selection between Tensas and Deltic are at least partially due to habitat differences at the landscape (i.e., amount of forested habitat) and patch (i.e., food availability) scales. Our results contribute to the understanding of factors that influence space use and habitat selection by black bears and provide specific information on habitat types selected by Louisiana black bears to agencies involved in habitat protection and restoration for this threatened subspecies.
Laminin N-terminus α31 expression during development in an inducible-transgenic mouse model is lethal and causes a multitude of tissue-specific defects

Alternative splicing of the laminin α3 gene gives rise to a netrin-like protein termed LaNt α31, the major structural feature of which is a laminin N-terminal domain. LaNt α31 is expressed across a wide range of tissues, is upregulated in cancers, and ex vivo and in vitro functional studies have indicated that this relatively unstudied protein influences wound repair, stem cell activity, and tumour progression via modifying matrix organisation. However, LaNt α31 functionality has never been investigated in vivo. Here we report the generation and characterisation of the first LaNt α31 transgenic mouse line using the ubiquitin C promoter to drive expression of an expression cassette containing a flox-STOP sequence, the human LaNt α31 coding sequence and a tdTomato reporter. This line was crossed with mice expressing inducible Cre recombinase driven from the Rosa26 locus (R26CreERT2), and double transgenics were given tamoxifen at E15.5 to induce expression. LaNt α31 overexpressing animals were fully formed and intact at birth but were not viable, exhibiting localised regions of erythema. Histological examination revealed numerous striking defects includng extra-vascular erythrocytes across multiple tissues. Widespread disorganisation was apparent in the kidney, with epithelial detachment, tubular dilation, interstitial bleeding observed, and thickening of the kidney tubule basement membranes. In the skin, mice exhibited disruption of the epidermal basal cell layer and hair follicle outer root sheath, with evidence of basement membrane interruption in the interfollicular epidermis. In the liver, there was a ~50% reduction of total cell number, associated with a depletion of hematopoietic erythrocytic foci. In the lungs, there appeared to be a reduction of alveolar epithelial cells accompanied by blood interspersed throughout the tissue. Together, these findings demonstrate that LaNt α31 can influence tissue morphogenesis during development and implicate this new protein as a potentially important mediator of basement membrane assembly.
Cavin3 released from caveolae interacts with BRCA1 to regulate the cellular stress response

Caveolae-associated protein 3 (cavin3), a putative tumor suppressor protein, is inactivated in most cancers. We characterized how cavin3 affects the cellular proteome using genome-edited cells together with label-free quantitative proteomics. These studies revealed a prominent role for cavin3 in DNA repair with BRCA1 and BRCA1 A-complex components being downregulated on cavin3 deletion. Cellular and cell-free expression assays, we show a direct interaction between BRCA1 and cavin3. Association of BRCA1 and cavin3 occurs when cavin3 is released from caveolae that are disassembled in response to UV and mechanical stress. Supporting a role in DNA repair, cavin3-deficient cells were sensitized to the effects of PARP inhibition, which compromises DNA repair, and showed reduced recruitment of the BRCA1 A-complex to UV DNA damage foci. Overexpression and RNAi-depletion revealed that cavin3 sensitized various cancer cells to UV-induced apoptosis. We conclude that cavin3 functions together with BRCA1 in multiple pathways that contribute to tumorigenesis.
Variants at RNF212 and RNF212B are associated with recombination rate variation in Soay sheep (Ovis aries)

Meiotic recombination is a ubiquitous feature of sexual reproduction, ensuring proper disjunction of homologous chromosomes, and creating new combinations of alleles upon which selection can act. By identifying the genetic drivers of recombination rate variation, we can begin to understand its evolution. Here, we revisit an analysis investigating the genetic architecture of gamete autosomal crossover counts (ACC) in a wild population of Soay sheep (Ovis aries) using a much larger dataset (increasing from 3,300 to 7,235 gametes and from ∼39,000 to ∼415,000 SNPs for genome-wide association analysis). Animal models fitting genomic relatedness confirmed that ACC was heritable in both females (h2 = 0.18) and males (h2 = 0.12). Genome-wide association studies identified two regions associated with ACC variation. A region on chromosome 6 containing RNF212 explained 46% of heritable variation in female ACC, but was not associated with male ACC, confirming the previous finding. A region on chromosome 7 containing RNF212B explained 20-25% of variation in ACC in both males and females. Both RNF212 and RNF212B have been repeatedly associated with recombination rate in other mammal species. These findings confirm that moderate to large effect loci can underpin ACC variation in wild mammals, and provide a foundation for further studies on the evolution of recombination rates.
Non-communicable disease and the risk of infection death: a UK Biobank prospective cohort study

Objectives: Non-communicable diseases (NCDs) have recently been highlighted as important risk factors for COVID-19 fatality. We set out to investigate the association between NCDs and the risk of death from any infection in the pre-COVID-19 era. Design: Prospective population-based study Setting: UK Biobank Participants: 493,295 participants Main outcome measures: Infection death prior to December 31st 2019. Results: During 5,277,344 participant-years of follow-up, 1,385 infection deaths occurred, accounting for 5% of all deaths. Competing risks regression revealed that advancing age, male sex, smoking, socio-economic deprivation and all studied NCDs were independently associated with both the risk of infection death and non-infection death; ethnicity was associated with neither. Only smoking, socio-economic deprivation, hypertension, respiratory disease, chronic kidney disease, psychiatric disease and rheumatological disease were associated with greater hazard ratios for infection than non-infection death. Accrual of multimorbidity was also associated with a greater increases in the risk of infection death (HR 9.03 [95% confidence interval 6.61 to 12.34] for 5+ comorbidities versus none; p<0.001), than non-infection death (HR 5.68 [95% confidence interval 5.22 to 6.17] for 5+ comorbidities versus none; p<0.001). Conclusions: Diverse NCDs are associated with increased risk of infection death, suggesting that recently reported associations with COVID-19 death may be non-specific. Moreover, only a subset of NCDs, together with the accrual of multimorbidity, smoking and socio-economic deprivation, are associated with greater relative risks of infection death than other causes of death. Further research is needed to define why these risk factors are biased toward infection death so that more effective preventative strategies can be targeted to high-risk groups.