Miracle-dz/UniFAR-FTUs huggingface dataset:
EXPLORING PATTERNS OF INTERSPECIFIC VARIATION IN QUANTITATIVE TRAITS USING SEQUENTIAL PHYLOGENETIC EIGENVECTOR REGRESSIONS

A number of metrics have been developed for estimating phylogenetic signal in data and to evaluate correlated evolution, inferring broad‐scale evolutionary and ecological processes. Here, we proposed an approach called phylogenetic signal‐representation (PSR) curve, built upon phylogenetic eigenvector regression (PVR). In PVR, selected eigenvectors extracted from a phylogenetic distance matrix are used to model interspecific variation. In the PSR curve, sequential PVR models are fitted after successively increasing the number of eigenvectors and plotting their R2 against the accumulated eigenvalues. We used simulations to show that a linear PSR curve is expected under Brownian motion and that its shape changes under alternative evolutionary models. The PSR area, expressing deviations from Brownian motion, is strongly correlated (r= 0.873; P < 0.01) with Blomberg's K‐statistics, so nonlinear PSR curves reveal if traits are evolving at a slower or higher rate than expected by Brownian motion. The PSR area is also correlated with phylogenetic half‐life under an Ornstein‐Uhlenbeck process, suggesting how both methods describe the shape of the relationship between interspecific variation and time since divergence among species. The PSR curve provides an elegant exploratory method to understand deviations from Brownian motion, in terms of acceleration or deceleration of evolutionary rates occurring at large or small phylogenetic distances.
Emotional complexity and its effect on psychological distress as a function of chronological age and subjective distance-to-death

Objectives: In light of mixed evidence regarding the associations between age, emotional complexity, and psychological distress, this study examined emotional complexity and its effect on psychological distress as a function of age and subjective distance-to-death. Method: A sample of 188 participants (age range = 29–100) rated their subjective distance-to-death and psychological distress, and reported their emotions across 14 days. Results: Emotional complexity was unrelated to age, but negatively related to feeling closer to death. Moreover, emotional complexity was negatively related to psychological distress among those feeling closer to death. Conclusion: Results suggest that when death is perceived to be nearer, emotional complexity is hampered, yet becomes relevant in buffering psychological distress.
“I'm a Health Nut!” Street Drug Users' Accounts of Self-Care Strategies

This qualitative study analyzes data from in-depth interviews to describe self-care strategies among chronic and injecting drug users. While the types of strategies varied from participant to participant, the theme of proactive self-care remained strong throughout the data. Researchers identified five self-care domains discussed by the study participants. The self-care domains include strategies to improve nutrition, increase physical activity, address medical concerns, regulate substance use, and reduce sexual risk. Overall, these data indicate that chronic drug users are actively involved in managing and improving their health and attempt to take self-protective actions, even while continuing to engage in active drug use. These findings are particularly relevant for primary care providers, walk-in clinics, drug treatment programs, outreach workers and those engaged in harm reduction efforts. Recognizing that drug users are actively involved in taking care of their health can be an important strategy to build into any intervention or risk reduction program.
The Effect of Metabolic Syndrome and Diabetes Mellitus Type 2 on the Arterial Reactivity of Hypertensive Patients during Cold Pressor Test

Background: Arterial hypertension (AH), metabolic syndrome (MS) and diabetes mellitus type 2 (DM2) are interrelated metabolic disorders. The aim of our study was to evaluate how the coexistence of MS or DM2 with AH influences arterial reactivity during cold pressor test (CPT). Methods: We studied 102 patients, 32 with AH (Group A), 38 with AH and MS (Group B) and 32 with AH and DM2 (Group C). All patients underwent full laboratory evaluation and measurement of systolic and diastolic blood pressure (SBP and DBP), heart rate (HR) and carotid-femoral pulse wave velocity (PWVc-f) before and during CPT. Results: During CPT PWVc-f, SBP, DBP and HR were increased significantly in all studied groups, but the change of PWVc-f and HR during CPT was significantly greater in group A compared to group C. On the contrary, the coexistence of MS or DM2 with AH does not alter the response of BP to CPT. Conclusion: The increase of CV risk resulting from the coexistence of MS or DM2 with AH, is best expressed by PWVc-f, while the change of the former and HR during CPT possibly reflects dysfunction of the autonomic nervous system.
COMPARING EVOLVABILITIES: COMMON ERRORS SURROUNDING THE CALCULATION AND USE OF COEFFICIENTS OF ADDITIVE GENETIC VARIATION

In 1992, David Houle showed that measures of additive genetic variation standardized by the trait mean, CVA (the coefficient of additive genetic variation) and its square (IA), are suitable measures of evolvability. CVA has been used widely to compare patterns of genetic variation. However, the use of CVAs for comparative purposes relies critically on the correct calculation of this parameter. We reviewed a sample of quantitative genetic studies, focusing on sire models, and found that 45% of studies use incorrect methods for calculating CVA and that practices that render these coefficients meaningless are frequent. This may have important consequences for conclusions drawn from comparative studies. Our results are suggestive of a broader problem because miscalculation of the additive genetic variance from a sire model is prevalent among the studies sampled, implying that other important quantitative genetic parameters might also often be estimated incorrectly. We discuss the most prominent issues affecting the use of CVA and IA, including scale effects, data transformation, and the comparison of traits with different dimensions. Our aim is to increase awareness of the potential mistakes surrounding the calculation and use of evolvabilities, and to compile general guidelines for calculating, reporting, and interpreting these useful measures in future studies.
INCREASED ENERGY PROMOTES SIZE‐BASED NICHE AVAILABILITY IN MARINE MOLLUSKS

Variation in chemical energy, that is food availability, is posited to cause variation in body size. However, examinations of the relationship are rare and primarily limited to amniotes and zooplankton. Moreover, the relationship between body size and chemical energy may be impacted by phylogenetic history, clade‐specific ecology, and heterogeneity of chemical energy in space and time. Considerable work remains to both document patterns in body size over gradients in food availability and understanding the processes potentially generating them. Here, we examine the functional relationship between body size and chemical energy availability over a broad assortment of marine mollusks varying in habitat and mobility. We demonstrate that chemical energy availability is likely driving body size patterns across habitats. We find that lower food availability decreases size‐based niche availability by setting hard constraints on maximum size and potentially on minimum size depending on clade‐specific ecology. Conversely, higher food availability promotes greater niche availability and potentially promotes evolutionary innovation with regard to size. We posit based on these findings and previous work that increases in chemical energy are important to the diversification of Metazoans through size‐mediated niche processes.
ON THE EVOLUTIONARY DYNAMICS OF PATHOGENS WITH DIRECT AND ENVIRONMENTAL TRANSMISSION

A number of ecologically and economically important pathogens exhibit a complex transmission dynamics that involves distinct transmission modes. In this paper, we study the evolutionary dynamics of pathogens for which transmission includes direct host‐to‐host as well as indirect environmental transmission. Different routes of infection spread require specific adaptations of the parasite, which may result in conflicting selection pressures. Using the framework of Adaptive dynamics, we investigate how these conflicting selection pressures are resolved in the course of evolution and determine the conditions for evolutionary diversification of pathogen strains. We show that evolutionary branching and subsequent evolution of specialist strains occurs in wide parameter regions but evolutionary bistability and evolution of generalist pathogens are possible as well. Our analysis reveals that the relative contributions of direct and environmental transmission, as well as the underlying ecological dynamics, play a crucial role in shaping the course of pathogen evolution. Our findings may explain the coexistence of high and low virulence strains observed in several pathogenic organisms using different transmission modes (e.g., influenza viruses) and highlight the importance of considering ecological dynamics in virulence management.
Pain severity, interference, and prescription analgesic use among depressed, low-income homebound older adults

Objectives: Disabled, homebound individuals tend to suffer both chronic pain and depression; however, low-income, homebound older adults have been underexposed in pain and depression research. We examined the extent of pain frequency, intensity, and interference; the relationship between pain and depressive symptoms; and prescription analgesic use and its association with use of antidepressant and anxiolytic medications among these older adults. Method: The data came from the baseline assessment of 215 homebound individuals aged 50+ who were referred to a clinical trial of depression treatment. Bivariate and multivariate analyses were used to examine the research questions. Results: Almost 87% (n = 186) of the participants reported having had chronic pain in the preceding three months. Of the pain reporters, the mean frequency, intensity, and interference of pain were 8.65 ± 2.05, 7.71 ± 2.10, and 7.80 ± 2.82, respectively, on a 1–10 scale, and 61% were taking a prescription analgesic. Analgesic users and nonusers did not differ in depressive symptoms and in pain frequency and intensity, but analgesic users reported higher pain interference than nonusers (8.22 ± 2.46 vs. 7.14 ± 3.22; t = 2.44, df = 184, p = .016). Pain frequency and interference were significantly associated with depressive symptoms, and pain interference was significantly associated with analgesic use in multivariate analysis. Anxiolytic medication use was also correlated with analgesic use. Conclusion: The findings underscore the significant pain-related problems in these vulnerable individuals and the need for recognizing and treating both pain and depression more effectively using both pharmacologic and nonpharmacologic interventions.
VIRULENCE NOT ONLY COSTS BUT ALSO BENEFITS THE TRANSMISSION OF A FUNGAL VIRUS

Current theory suggests that cost–benefit relationships govern the evolution of parasite virulence. The cost of virulence is expected to be high for fungal viruses, which are obligate parasites and completely dependent on their hosts. The majority of fungal viruses infect their hosts without any apparent symptoms. Cryphonectria hypovirus 1 (CHV‐1), in contrast, is virulent and debilitates its host, Cryphonectria parasitica. However, the virulence of CHV‐1 is associated with high costs for virus transmission, such as an attenuated fungal growth and reduced production of the fungal spores spreading the virus. In this study, we tested the hypothesis that virulence may not only have costs but also benefits for transmitting CHV‐1 across vegetative incompatibility barriers between fungi. We investigated viruses with low, medium, and high virulence, and determined their transmission rate per host‐to‐host contact (transmissibility). The average transmission rate across all combinations tested was 53% for the most virulent virus, 37% for the virus with intermediate virulence, and 20% for the virus with lowest virulence. These results showed that increased virulence was strongly correlated with increased transmissibility, potentially counterbalancing virulence costs. This association of virulence and transmissibility may explain why CHV‐1 spread widely and evolved higher virulence than most other fungal viruses.
ANCIENT TEPUI SUMMITS HARBOR YOUNG RATHER THAN OLD LINEAGES OF ENDEMIC FROGS

The flattop mountains (tepuis) of South America are ancient remnants of the Precambrian Guiana Shield plateau. The tepui summits, isolated by their surrounding cliffs that can be up to 1000 m tall, are thought of as “islands in the sky,” harboring relict flora and fauna that underwent vicariant speciation due to plateau fragmentation. High endemicity atop tepui summits support the idea of an ancient “Lost World” biota. However, recent work suggests that dispersal between lowlands and summits has occurred long after tepui formation indicating that tepui summits may not be as isolated from the lowlands as researchers have long suggested. Neither view of the origin of the tepui biota (i.e., ancient vicariance vs. recent dispersal) has strong empirical support owing to a lack of studies. We test diversification hypotheses of the Guiana Shield highlands by estimating divergence times of an endemic group of treefrogs, Tepuihyla. We find that diversification of this group does not support an ancient origin for this taxon; instead, divergence times among the highland species are 2–5 Ma. Our data indicate that most highland speciation occurred during the Pliocene. Thus, this unparalleled landscape known as “The Lost World” is inhabited, in part, not by Early Tertiary relicts but neoendemics.
CORRELATION BETWEEN ANOLIS LIZARD DEWLAP PHENOTYPE AND ENVIRONMENTAL VARIATION INDICATES ADAPTIVE DIVERGENCE OF A SIGNAL IMPORTANT TO SEXUAL SELECTION AND SPECIES RECOGNITION

Although the importance of signals involved in species recognition and sexual selection to speciation is widely recognized, the processes that underlie signal divergence are still a matter of debate. Several possible processes have been hypothesized, including genetic drift, arbitrary sexual selection, and adaptation to local signaling environments. We use comparative analyses to investigate whether the remarkable geographic variation of dewlap phenotype in a Hispaniolan trunk Anolis lizard (A. distichus) is a result of adaptive signal divergence to heterogeneous environments. We recover a repeated pattern of divergence in A. distichus dewlap color, pattern, and size with environmental variation across Hispaniola. These results are aligned with ecological models of signal divergence and provide strong evidence for dewlap adaptation to local signaling environments. We also find that A. distichus dewlaps vary with the environment in a different manner to other previously studied anoles, thus expanding upon previous predictions on the direction dewlaps will diverge in perceptual color space in response to the environment.
Do determinants of burden and emotional distress in dementia caregivers change over time?†

Objectives: Caring for a patient with dementia is a real challenge and can have considerable psychological consequences in the long run. Many caregivers, mostly relatives, feel highly burdened. To develop effective caregiver support to prevent caregivers from getting overburdened, insight is needed into the determinants of burden. The objective of this study is to explore which patient and caregiver characteristics determine the different kinds of caregiver burden over time, both in the short and in the long run. Method: The study was longitudinal. Data on patients and caregivers, general burden and emotional distress were collected at three times: at baseline, at the end of treatment and at nine months. The study was conducted in a psychiatric skilled nursing home with a unit for integrative reactivation and rehabilitation (IRR) and at different sites of home-/day care, assisted living arrangements and nursing home wards (usual care). Results: General burden is shown to be determined by severity of patient's neuropsychiatric symptoms, caregiver's sense of competence, health-related quality of life. Emotional distress is determined by severity of patient's neuropsychiatric symptoms, caregiver's sense of competence, high affiliation and patient gender. Conclusion: In preventing or treating caregiver burden, professional interventions need to aim specifically at diminishing the neuropsychiatric symptoms in dementia patients and improving the sense of competence in caregivers.
VACCINATION AND REDUCED COHORT DURATION CAN DRIVE VIRULENCE EVOLUTION: MAREK’S DISEASE VIRUS AND INDUSTRIALIZED AGRICULTURE

Marek’s disease virus (MDV), a commercially important disease of poultry, has become substantially more virulent over the last 60 years. This evolution was presumably a consequence of changes in virus ecology associated with the intensification of the poultry industry. Here, we assess whether vaccination or reduced host life span could have generated natural selection, which favored more virulent strains. Using previously published experimental data, we estimated viral fitness under a range of cohort durations and vaccine treatments on broiler farms. We found that viral fitness maximized at intermediate virulence, as a result of a trade‐off between virulence and transmission previously reported. Our results suggest that vaccination, acting on this trade‐off, could have led to the evolution of increased virulence. By keeping the host alive, vaccination prolongs infectious periods of virulent strains. Improvements in host genetics and nutrition, which reduced broiler life spans below 50 days, could have also increased the virulence of the circulating MDV strains because shortened cohort duration reduces the impact of host death on viral fitness. These results illustrate the dramatic impact anthropogenic change can potentially have on pathogen virulence.
Preoperative evaluation of lung cancer: predicting the impact of surgery on physiology and quality of life

Purpose of review To summarize the best clinical evidence published in the last year and regarding the functional evaluation and the residual quality of life after lung resection in patients with lung cancer. Recent findings Recent evidences have shown that predicted postoperative forced expiratory volume in 1 s is not a reliable predictor of complications in patients with obstructive pulmonary disease and that carbon monoxide lung diffusion capacity predicts complications even in patients with normal forced expiratory volume in 1 s. Maximal stair-climbing test appears to discriminate better between complicated and noncomplicated patients compared with traditional split-lung function measures. Patients unable to climb 12 m have 2.5-fold and 13-fold higher complications and mortality rates compared with those able to climb 22 m. Quality of life has been shown to decrease in the first month but to return to preoperative values after 3 months in most of the patients after lung resection. Summary Carbon monoxide lung diffusion capacity and stair-climbing test should be performed routinely in all lung-resection candidates. In those with poor exercise tolerance in stair-climbing test or exercise oxygen desaturation, or candidates to pneumonectomy, the measurement of VO2max is recommended. Quality of life should always be assessed through specific instruments and not inferred by traditional functional tests.
Longitudinal associations between perceived age discrimination and subjective well-being: variations by age and subjective life expectancy

ABSTRACT Objectives: Perceived age discrimination can have negative effects on one's subjective well-being (SWB). The response to age discrimination might differ based on age, and based on perceived longevity, or subjective life expectancy (SLE). These differential effects have not yet been prospectively examined within adult life span samples. Method: We examined the association between perceived age discrimination at baseline (T1) and SWB at follow-up (T2), and the moderation effect of SLE. We compared differences in these effects between middle-aged and older adults. Analyses were based on participants who took part in the 2008 (T1) and 2011 (T2) assessments of the German Ageing Survey (DEAS; listwise N = 1534), a population-based representative sample of the German adult population. Participants were categorized as middle-aged (ages 40–64; n = 919) or older adults (ages 65–93; n = 615). Results: Regression analyses indicated that T1 perceived age discrimination significantly predicts lower T2 SWB among middle-aged, but not among older adults, after adjusting for covariates and T1 SWB. There is a significant interaction between age discrimination and SLE for predicting SWB, only among middle-aged participants, suggesting that age discrimination predicts decreases in SWB for those reporting higher, but not lower levels of SLE. Conclusion: People in the transition from midlife to old age, who hold higher SLE, appear to be more vulnerable to age discrimination. This may be due to the experience of age discrimination as an ‘off-time’, or unexpected event for those in midlife who have a higher expectation to live longer.
Interleukin‐10‐induced MARCH1 mediates intracellular sequestration of MHC class II in monocytes

IL‐10 is a potent anti‐inflammatory cytokine interfering with antigen presentation by inducing the intracellular sequestration of MHC class II (MHC‐II) molecules. Here we studied the contribution of membrane‐associated RING‐CH (MARCH) ubiquitin ligase family members to the IL‐10‐induced down‐regulation of MHC‐II molecules. We found that MARCH1 and MARCH8 proteins are the most potent family members for the down‐regulation of MHC‐II surface expression in transfected cells, but only MARCH1 mRNA expression is strongly induced by IL‐10 in human primary monocytes. We detected mono‐ and poly‐ubiquitinated forms of MHC‐II molecules both in IL‐10‐treated monocytes and in cells transfected with MARCH1. We also show direct interaction between MHC‐II and MARCH1 molecules in co‐immunoprecipitation assays. Finally, we found that siRNA‐mediated knockdown of MARCH1 reverses IL‐10‐induced MHC‐II down‐regulation in primary monocytes. Thus, the immunosuppressive effect of IL‐10 on antigen presentation is mediated through induced expression of MARCH1.
Engagement of Toll‐like receptor 2 in mouse macrophages infected with Mycobacterium avium induces non‐oxidative and TNF‐independent anti‐mycobacterial activity

Toll‐like receptor (TLR) 2 plays an important role in the immune response to mycobacterial infections, being required for optimal immunity against certain virulent Mycobacterium avium strains. Here we analyzed the role of TLR2 in the intra‐macrophagic growth of M. avium, using macrophages from TLR2‐deficient mice. We found that the engagement of TLR2/TLR6 and/or TLR2/TLR1 receptors induced bacteriostasis of M. avium inside bone marrow‐derived macrophages in a MyD88‐dependent way. Additionally, lipoproteins from the cell envelope of M. avium with a molecular mass of 20–25 kDa triggered this TLR2 pathway, leading to a decrease in the growth of the mycobacteria. Although TLR2 engagement induced the production of TNF, this cytokine as well as nitric oxide and superoxide molecules were not necessary for TLR2‐mediated bacteriostasis. Finally, TLR ligation did not induce the expression of the 47‐kDa guanosine triphosphatase (LRG‐47) but it promoted an increased maturation of the phagosome with regards to acquisition of LAMP1. Our data show that triggering TLR2 inhibited M. avium growth by an as‐yet‐unknown mechanism that may involve increased phagosome maturation.