Miracle-dz/UniFAR-FTUs huggingface dataset:
Locomotor adaptations in the Early Miocene species Diamantomys luederitzi (Rodentia, Mammalia) from Uganda (Napak)

The study of morphological adaptations to different ecological parameters among fossil vertebrates has been an important challenge in recent decades. In this paper, we focus on the link between morphological traits and locomotor behavior such as terrestriality, fossoriality and arboreality (including gliding). One of the most diverse groups in which various locomotor habits are represented is rodents, occupying a wide range of ecological niches. This work highlights morphological variations in skulls and humerus in extant rodents with varying locomotion, to predict this parameter in the extinct species Diamantomys luederitzi (Early Miocene, Napak, Uganda). Linear discriminant analysis and phylogenetic flexible discriminant analysis are used to analyze datasets obtained via traditional morphometry (measurements) and geometric morphometrics (landmarks). The results show good discrimination between locomotor groups for both structures in extant species: the skull has a wider and longer rostrum in terrestrial and fossorial taxa compared to arboreal rodents, is also higher and posteriorly wider in fossorial taxa; the distal humerus shows elongation of the trochlea and capitulum and a higher trochlea in fossorial and terrestrial species, allowing an increase of stability instead of mobility, which is more important in arboreal taxa for movement in trees. In D. luederitzi, all skull analyses except one predicted it as a terrestrial species, the other prediction as a glider was possibly linked to the diet. For the distal humerus, this species has been predicted as a terrestrial, fossorial and arboreal taxon in differing analyses, reflected by morphological traits represented in these different locomotor categories. These varying predictions could highlight the intraspecific variation in this fossil species as well as its locomotor repertoire, raising a discussion about the use of different methods in such analyses. In addition to these predictions, several issues are discussed, such as the presence of locomotor signal in the skull and its validity in locomotor studies, as well as the relevance of the use of fragmentary material in such analyses. The results obtained in this work highlight the importance of the locomotor signal in these structures, as well as the possibility of taking into account poorly preserved material, in particular the distal humerus.
Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM

Abstract Genomic regions with high guanine content can fold into non-B form DNA four-stranded structures known as G-quadruplexes (G4s). Extensive in vivo investigations have revealed that promoter G4s are transcriptional regulators. Little structural information exists for these G4s embedded within duplexes, their presumed genomic environment. Here, we report the 7.4 Å resolution structure and dynamics of a 28.5 kDa duplex-G4-duplex (DGD) model system using cryo-EM, molecular dynamics, and small-angle X-ray scattering (SAXS) studies. The DGD cryo-EM refined model features a 53° bend induced by a stacked duplex-G4 interaction at the 5’ G-tetrad interface with a persistently unstacked 3’ duplex. The surrogate complement poly dT loop preferably stacks onto the 3’ G-tetrad interface resulting in occlusion of both 5’ and 3’ tetrad interfaces. Structural analysis shows that the DGD model is quantifiably more druggable than the monomeric G4 structure alone and represents a new structural drug target. Our results illustrate how the integration of cryo-EM, MD, and SAXS can reveal complementary detailed static and dynamic structural information on DNA G4 systems.
Ecotoxicological Studies Indicate That Sublethal and Lethal Processes Limit Insect‐Mediated Contaminant Flux

Merolimnic insects can accumulate and transport considerable amounts of aquatic contaminants to terrestrial systems. The rate of contaminant biotransport, termed insect‐mediated contaminant flux (IMCF), depends on emergent insect biomass and contaminant accumulation, both functions of environmental concentration. We developed a mathematical model of IMCF and apply it to three ecotoxicological studies obtained through the US Environmental Protection Agency's ECOTOX database to determine at which concentration maximum IMCF occurs. Model results demonstrate that the maximum IMCF depends on competing rates of biomass loss and contaminant accumulation and does not necessarily occur at the highest insect or environmental contaminant concentration. In addition, modeling results suggest that sublethal contaminant effects (e.g., decreased growth) on insect biomass can be an important and potentially underappreciated control on IMCF. Environ Toxicol Chem 2023;42:1982–1992. © 2023 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
Limited effects of inbreeding on breeding coloration

Abstract Animal color signals may function as indicators of fighting ability when males compete for access to females. This allows opponents to settle aggressive interactions before they escalate into physical combat and injury. Thus, there may be strong directional selection on these traits, toward enhanced signal quality. This renders sexually selected traits particularly susceptible to inbreeding depression, due to relatively low ratios of additive genetic variance to dominance variance. We measured the effects of inbreeding on an intrasexually selected color signal (the badge) in a population of Swedish sand lizards (Lacerta agilis) using the Rhh software based on 17 to 21 microsatellites. Males of this sexually dichromatic species use the badge during aggressive interactions to display, and assess, fighting ability. We found negative effects of homozygosity on badge size, saturation, and brightness. However, no such effects were observed on color hue. Pairwise correlations between badge size, hue, and saturation were all statistically significant. Thus, the sand lizard “badge” is a multicomponent signal with variation explained by covariation in badge size, saturation, and color hue. Body mass corrected for skeletal size (body condition) positively predicted badge size and saturation, encouraging future research on the extent that sexual signals may convey information on multigene targets (i.e. “genic capture”).
Does the loss of diadromy imply the loss of salinity tolerance? A gene expression study with replicate nondiadromous populations of Galaxias maculatus

The recurrent colonization of freshwater habitats and subsequent loss of diadromy is a major ecological transition that has been reported in many ancestrally diadromous fishes. Such residency is often accompanied by a loss of tolerance to seawater. The amphidromous Galaxias maculatus has repeatedly colonized freshwater streams with evidence that freshwater‐resident populations exhibit stark differences in their tolerance to higher salinities. Here, we used transcriptomics to gain insight into the mechanisms contributing to reduced tolerance to higher salinities in freshwater resident populations. We conducted an acute salinity challenge (0 ppt to 23–25 ppt) and measured osmoregulatory ability (muscle water content) over 48 h in three populations: diadromous, saltwater intolerant resident (Toltén), and saltwater tolerant resident (Valdivia). RNA sequencing of the gills identified genes that were differentially expressed in association with the salinity change and associated with the loss of saltwater tolerance in the Toltén population. Key genes associated with saltwater acclimation were characterized in diadromous G. maculatus individuals, some of which were also expressed in the saltwater tolerant resident population (Valdivia). We found that some of these “saltwater acclimation” genes, including the cystic fibrosis transmembrane conductance regulator gene (CFTR), were not significantly upregulated in the saltwater intolerant resident population (Toltén), suggesting a potential mechanism for the loss of tolerance to higher salinities. As the suite of differentially expressed genes in the diadromous‐resident comparison differed between freshwater populations, we hypothesize that diadromy loss results in unique evolutionary trajectories due to drift, so the loss of diadromy does not necessarily lead to a loss in upper salinity tolerance.
A Staphylococcal Glucosaminidase Drives Inflammatory Responses by Processing Peptidoglycan Chains to Physiological Lengths

The peptidoglycan of Staphylococcus aureus is a critical cell envelope constituent and virulence factor that subverts host immune defenses and provides protection against environmental stressors. Peptidoglycan chains of the S. aureus cell wall are processed to characteristically short lengths by the glucosaminidase SagB. ABSTRACT The peptidoglycan of Staphylococcus aureus is a critical cell envelope constituent and virulence factor that subverts host immune defenses and provides protection against environmental stressors. Peptidoglycan chains of the S. aureus cell wall are processed to characteristically short lengths by the glucosaminidase SagB. It is well established that peptidoglycan is an important pathogen-associated molecular pattern (PAMP) that is recognized by the host innate immune system and promotes production of proinflammatory cytokines, including interleukin-1β (IL-1β). However, how bacterial processing of peptidoglycan drives IL-1β production is comparatively unexplored. Here, we tested the involvement of staphylococcal glucosaminidases in shaping innate immune responses and identified SagB as a mediator of IL-1β production. A ΔsagB mutant fails to promote IL-1β production by macrophages and dendritic cells, and processing of peptidoglycan by SagB is essential for this response. SagB-dependent IL-1β production by macrophages is independent of canonical pattern recognition receptor engagement and NLRP3 inflammasome-mediated caspase activity. Instead, treatment of macrophages with heat-killed cells from a ΔsagB mutant leads to reduced caspase-independent cleavage of pro-IL-1β, resulting in accumulation of the pro form in the macrophage cytosol. Furthermore, SagB is required for virulence in systemic infection and promotes IL-1β production in a skin and soft tissue infection model. Taken together, our results suggest that the length of S. aureus cell wall glycan chains can drive IL-1β production by innate immune cells through a previously undescribed mechanism related to IL-1β maturation.
Three years on, COVID-19 is still relevant

the CoVid-19 pandemic, and the related public health restrictions imposed to curb the transmission of the virus, have had an unprecedented impact on people across the globe (e.g., Krishnamoorthy et al., 2020; Prati & Mancini, 2021). Multiple waves of the pandemic continue for many nations (reuters, 2022), and there are heightened concerns of multiple and emerging new variants of the virus, while other countries have begun to engage in post-pandemic recovery actions. despite the disruption and uncertainty, understanding of and intervening on human behaviour has had an important role in nearly all aspects of the CoVid-19 pandemic (e.g., Bavel et al., 2020; Betsch, 2020). Early phase research in psychology and health was largely cross-sectional, providing an important yet descriptive comparison of how people were affected differentially by the virus and the imposed restrictions. While this initial research was helpful to provide a snapshot of the effect of the pandemic on health behaviours and outcomes, it lacked an understanding of changes during the pandemic. in this special issue of Psychology and Health, we sought longitudinal research focused on the psychology of physical health and illness related to the SarS-CoV-2 virus across time with the aim to fill a knowledge gap on longer-term impacts and changes on people’s health, wellbeing, and behaviour. to this end, this double-sized special issue features 14 studies, across four continents and samples of people in 10 countries, that have focused on broad themes of 1) longitudinal tracking and/or prediction of CoVid-19 virus transmission behaviours, 2) impacts of CoVid-19 on the psychology and health of people with existing health conditions, and 3) the behavioural and psychological mechanisms moderating well-being during the CoVid-19 pandemic.
Nonlinear magnetoelastic deformations

In this paper we first summarize, in a simple form, the equilibrium equations for a solid material capable of large magnetoelastic deformations. Such equations are needed for the analysis of boundary-value problems for elastomers endowed with magnetic properties by the embedding of distributions of ferrous particles. The general constitutive law for an isotropic material in the presence of a magnetic field is described and expressed in a compact form, with either the magnetic field or the magnetic induction as the independent magnetic variable. The equations are applied, in the case of an incompressible material, to the solution of representative problems involving circular cylindrical geometry, specifically the helical shear of a circular cylindrical tube, its specializations to axial and azimuthal shear, and the problem of extension and torsion of a solid circular cylinder. For each problem a general formulation is afforded without specialization of the (isotropic) constitutive law, and then specific results are discussed briefly for special choices of such laws. It is noted, in particular, that certain restrictions may be placed on the class of constitutive laws for a considered combination of deformation and magnetic field to be admitted.
THE PRE-OUTBURST SPECTRUM OF NOVA DELPHINI 1967

The spectrum of Nova Delphini 1967 * ( Alcock 1967 ) was recorded on two objective-prism plates taken for one of my observing programs seven years before the current outburst. This is the third case of the observation of the pre-outburst spectrum of a nova not known to be recurrent ( cf. Cannon 1920; Stephenson and Herr 1963; Gotz 1965 ), and the first instance in which the pre-outburst spectrum was not badly underexposed. The identification of the pre-outburst spectrum with the nova was accomplished as follows. In the first place, the prenova spectrum shows no discrete spectral features, so that direct measurement of a pre-outburst plate would yield a coordinate of very low precision in the direction parallel to the spectral dispersion. However, the candidate spectrum is that of a star no fainter than twelfth magnitude, and only one star of those shown on the prints of the National Geographic Society-Palomar Observatory Sky Survey could be responsible for the prenova spectral image. This star appears to have about the same photographic magnitude on the prints of the Lick Sky Atlas and FranklinAdams charts that show it; moreover, in agreement with the pre-outburst spectrum, a comparison of the red and blue Palomar prints shows that the star in question was extremely blue. To verify that this star was indeed the prenova, its image and those of four nearby A-type reference stars were measured on a glass contact copy of the blue Palomar print ( print O-831 ) and on a post-outburst objective-prism plate of the nova taken July 13, 1967. On the
Rates and Correlates of Intimate Partner Violence Among Indigenous College Students: A Multi-Campus Study

Research suggests that Indigenous girls, women, and LGBTQ+ Two-Spirit people experience disproportionately high rates of intimate partner violence (IPV), but there is a dearth of research on IPV among Indigenous college students. Therefore, the current study sought to explore rates of IPV victimization and perpetration among Indigenous college students, as well as correlates including depressive and anxious symptoms, emotion dysregulation, on-campus social support, and hazardous drinking. Participants were 230 undergraduate students who identified as American Indian/Alaska Native attending 20 medium- and large-sized universities across the contiguous U.S. Results indicated that 28.9% of Indigenous students reported any type of IPV victimization in the past 6 months (psychological: 24.5%; physical: 9.1%; sexual: 9.8%; coercive control: 12.4%). Further, 18.3% of Indigenous students reported any type of IPV perpetration in the past 6 months (psychological: 16.9%; physical: 4.5%; sexual: 2.6%; coercive control: 7.1%). Anxious and depressive symptoms were related to many forms of IPV victimization; emotion dysregulation was related to all forms of IPV victimization and sexual IPV perpetration; and hazardous drinking was related to most forms of IPV victimization and perpetration. These findings underscore the alarmingly high rates of IPV among Indigenous college students as well as the potential deleterious effects of IPV victimization on psychological functioning, as well as the need to concurrently address hazardous alcohol use in IPV prevention and response efforts.
Long-term Survival Outcomes after Lobe-specific Nodal Dissection in Patients with Early Non-Small Cell Lung Cancer.

OBJECTIVE We investigated the long-term outcomes of lobe-specific and systematic nodal dissection in patients with non-small cell lung cancer. METHODS Patients with c-stage I-II non-small cell lung cancer who underwent lobectomy with mediastinal nodal dissection were retrospectively analysed. After propensity score matching, we assessed the overall survival, recurrence-free survival, and cumulative incidence of death from primary lung cancer and other diseases. RESULTS The median follow-up period was 8.4 years. Among 438 propensity score-matched pairs, overall and recurrence-free survival were similar between the lobe-specific and systematic nodal dissection groups (hazard ratio, 0.979; 95% confidence interval, 0.799-1.199; and hazard ratio, 0.912; 95% confidence interval, 0.762-1.092, respectively), but the LSD group showed a better prognosis after 5 years postoperatively. Cumulative incidence of death from primary lung cancer was similar between the two groups (hazard ratio, 1.239; 95% CI, 0.940-1.633). However, the cumulative incidence of death from other diseases was lower in the lobe-specific nodal dissection group than the systematic nodal dissection group (hazard ratio, 0.702; 95% confidence interval, 0.525-0.938). According to c-stage, the lobe-specific nodal dissection group tended towards worse overall and recurrence-free survival, with higher cumulative incidence of death from primary lung cancer than the systematic nodal dissection group, in patients with c-stage II. CONCLUSIONS Lobe-specific nodal dissection provides acceptable long-term survival for patients with early-stage non-small cell lung cancer. However, lobe-specific nodal dissection may not be suitable for patients with c-stage II non-small cell lung cancer due to the higher mortality risk from primary lung cancer.
Initial calibration and alignment of low‐cost inertial navigation units for land vehicle applications

This work presents an efficient initial calibration and alignment algorithm for a 6-degrees of freedom inertial measurement unit (IMU) to be used in land vehicle applications. Error models for the gyros and accelerometers are presented with a study of their perturbation in trajectory prediction. A full inertial error model is also presented to determine the sensors needed for full observability of the different perturbation parameters. Finally, dead-reckoning experimental results are presented based on the initial alignment and calibration parameters obtained with the algorithms presented. The results show that the proposed algorithms provide accurate position and velocity information for an extended period of time using nonaided IMU. ©1999 John Wiley & Sons, Inc.
Red pigments in autumn leaves of Norway maple do not offer significant photoprotection but coincide with stress symptoms

Abstract The reasons behind autumn colors, a striking manifestation of anthocyanin synthesis in plants, are poorly understood. Usually, not all leaves of an anthocyanic plant turn red or only a part of the leaf blade turns red. In the present study, we compared green, red and yellow sections of senescing Norway maple leaves, asking if red pigments offer photoprotection, and if so, whether the protection benefits the senescing tree. Green and senescing maple leaves were illuminated with strong white, green or red light in the absence or presence of lincomycin which blocks photosystem II (PSII) repair. Irrespective of the presence of anthocyanins, senescing leaves showed weaker capacity to repair PSII than green leaves. Furthermore, the rate of photoinhibition of PSII did not significantly differ between red and yellow sections of senescing maple leaves. We also followed pigment contents and photosynthetic reactions in individual leaves, from the end of summer until abscission of the leaf. In maple, red pigments accumulated only during late senescence, but light reactions stayed active until most of the chlorophyll had been degraded. PSII activity was found to be lower and non-photochemical quenching higher in red leaf sections, compared with yellow sections of senescing leaves. Red leaf sections were also thicker. We suggest that the primary function of anthocyanin synthesis is not to protect senescing leaves from excess light but to dispose of carbohydrates. This would relieve photosynthetic control, allowing the light reactions to produce energy for nutrient translocation at the last phase of autumn senescence when carbon skeletons are no longer needed.
Pharmacokinetic/Pharmacodynamic Determination of Systemic MIC Breakpoints for Intermittent, Extended, and Continuous Infusion Dosage Regimens of Mecillinam

Previous studies have shown that intravenous mecillinam might be suitable for treatment of urosepsis. Since multidrug-resistant Enterobacterales are common pathogens in such infections, an effort was made to delineate intermittent, extended, and continuous infusion regimens that could cover pathogens exhibiting relatively higher mecillinam MICs than the wild-type strains. ABSTRACT Intravenous mecillinam has been used for the treatment of urosepsis at several dosing regimens, including a dose of 1,000 mg three times a day (TID). In the current pharmacokinetic/pharmacodynamic (PK/PD) study, we analyzed intermittent, extended, and continuous infusion regimens of mecillinam to provide dosage recommendations to treat infections caused by Enterobacterales exhibiting relatively higher mecillinam MICs than the wild-type strains. Monte Carlo simulation studies indicated that regimens of 1,000 mg TID and 1,000 to 1,200 mg four times a day (QID) are efficacious against wild-type and extended-spectrum β-lactamase-producing Enterobacterales, respectively. Prolonged infusion regimens (extended and continuous) could cover carbapenemase producers with a higher range of MICs (2 to 8 mg/L). IMPORTANCE Previous studies have shown that intravenous mecillinam might be suitable for treatment of urosepsis. Since multidrug-resistant Enterobacterales are common pathogens in such infections, an effort was made to delineate intermittent, extended, and continuous infusion regimens that could cover pathogens exhibiting relatively higher mecillinam MICs than the wild-type strains. Our PK/PD analysis has shown that mecillinam might be considered a valuable therapeutic option for the treatment of systemic infections caused by extended-spectrum β-lactamase- and carbapenemase-producing Enterobacterales exhibiting mecillinam MICs up to 8 mg/L.