Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of postural diversity in primates as reflected by the size and shape of the medial tibial facet of the talus.

OBJECTIVES Comprehensive quantification of the shape and proportions of the medial tibial facet (MTF) of the talus (=astragalus) has been lacking for Primates and their closest relatives. In this study, aspects of MTF form were quantified and employed to test hypotheses about their functional and phylogenetic significance. The following hypotheses influence perceptions of primate evolutionary history but are due for more rigorous assessment: 1) A relatively large MTF distinguishes "prosimians" (strepsirrhines and tarsiers) from anthropoids and non-primate euarchontans; 2) the distinctive form of the "prosimian" MTF is a correlate of locomotor tendencies that emphasize use of vertical and small diameter supports in conjunction with inverted, abducted foot postures; and 3) the "prosimian" MTF form arose along the primate stem lineage and was present in the euprimate common ancestor. METHODS Three-dimensional (3D) scanning was used to create scale digital models of tali (n = 378 specimens, 122 species) from which three types of variables capturing aspects of MTF form were computed: 1) MTF area relative to body mass and ectal facet area; 2) MTF shape (elliptical vs. non-elliptical); and 3) MTF dorsal restriction on the talar body (i.e., extensive vs. minimal exposure of non-articular area). Data were analyzed using both phylogenetic and traditional comparative methods including Phylogenetic Generalized Least Squares, Ordinary Least Squares, ANCOVA, ANOVA, and Bayesian Ancestral State Reconstruction (ASR). RESULTS Extant "prosimians" are generally distinct from anthropoids and non-primate euarchontans in our quantitative representations of MTF form. MTF area (but not shape or dorsal restriction) correlates with fibular facet angle (FFa) of the talus, which has also been argued to reflect habitual pedal inversion. Among strepsirrhines, taxa that engage in grasp-leaping more frequently/effectively appear to have a relatively larger MTF than less acrobatic taxa. Directional models of evolutionary change better describe the phylogenetic distribution of MTF variation than do other models. ASR shows 1) little change in the MTF along the primate stem, 2) independent evolution of relatively large and dorsoplantarly deep MTFs in basal haplorhines and strepsirrhines, and 3) re-evolution of morphologies similar to non-euprimates in anthropoids. CONCLUSIONS Results support the hypothesis that differences in MTF form between anthropoids and "prosimians" reflect greater use of inverted foot postures and grasp-leaping in the latter group. Although fossil "prosimians" do not have the extreme MTF dimensions that characterize many extant acrobatic leapers, these variables by themselves provide little additional behavioral resolution at the level of individual fossils due to strong phylogenetic signal. ASR suggests that some specialization for use of inverted foot postures (as required in a fine-branch niche) and modifications for grasp-leaping evolved independently in basal strepsirrhine and haplorhine lineages.
Early growth and childhood adiposity. The Generation R Study

The World Health Organization defines overweight and obesity as abnormal or excessive accumulation of adipose tissue, which is an established risk factor for harmful health. Common health consequences of overweight and obesity include cardiometabolic diseases – mainly diabetes, stroke and heart diseases – orthopedical disorders and some cancers such as breast- and colon cancer. Currently, overweight and obesity are the fifth leading cause of global deaths.The burden of diabetes and ischemic heart disease are for 44% and 23% attributable to overweight and obesity, respectively. Overall, in 2008 more than 1.4 billion adults in the world were overweight.1 The dramatic increase in the worldwide prevalence of overweight and obesity might be designated as a ‘global epidemic’. Also, children with overweight or obesity experience more often inhalation difficulties, non-alcoholic fatty liver disease, adverse lipid profile, hypertension, insulin resistance, and depression and other psychological effects. In 2010, more than 40 million children worldwide under the age of 5 years were estimated as overweight. In the Netherlands, the prevalence of childhood overweight and obesity is fluctuating, but has an overall increasing trend. In 2010, 13.7% and 13.0% of the boys and girls in the Netherlands, respectively, were overweight. On average, the percentage of overweight in young persons has been increased with 40% in the last 30 years. Also, the prevalence of cardiometabolic risk factors associated with overweight and obesity is increasing in children. Childhood overweight and obesity are important risk factors for overweight and obesity in adulthood. The concept of persistence or relative stability of overweight over time is often referred to as ‘tracking’. Tracking is the phenomenon that children keep their body mass index (BMI) position in the population distribution from childhood into adulthood.Several studies have demonstrated that overweight in childhood tracks into adolescence and adulthood. It has also been suggested that clustered cardiometabolic risk factors associated with overweight and obesity track from childhood into adolescence.
Emotions and the heart: psychological risk factors for cardiovascular disease

The past The idea that emotions contribute to heart disease has a long history. In the 18 century John Hunter, the Scottish surgeon and anatomist, and a famously quick tempered man with angina, reportedly said “My life is in hands of any rascal who chooses to tease or annoy me”. He died of a heart attack after losing his temper at a committee meeting in his medical school. Over 100 years ago William Osler, a Canadian physician with a dominant position in Anglo Saxon medicine described the typical heart disease patient as “a keen and ambitious man, the indicator of whose engine is always at ‘full speed ahead’”, i.e., an early recognition of the Type A personality. Today if you ask survivors of myocardial infarction (MI) what they think caused their heart attack, 70% believe that stress is involved (Gudmundsdottir, Johnston, Johnston, & Foulkes, 2001). Despite this long history and the current lay acceptance of the link between emotion and heart disease, the scientific study of the association is comparatively recent. Only 30 years ago, Weiner’s (1977) massive text book on psychosomatics “Psychobiology and Disease” did not include a chapter on heart disease and myocardial infarction (MI) had only two entries in the index. Dorothy Levenson’s (1994) splendidly gossipy history of the American Psychosomatic Society hardly mentioned cardiovascular disorders (CVD) until Type A personality is first mentioned in the 1960s. Perhaps most surprisingly no paper on CVD was included in “Classics from Psychosomatic Medicine, 1959-1979”. There were exceptions to this apparent lack of interest in heart disease. Friedman and Rosenman started their highly influential work in the late 50’s that culminated in the report of the Western Collaborative Group study in 1975 and in 1977, Jim Henry summarised his extensive studies of the effects of stress on the cardiovascular systems of mice and placed it in a wider social and cultural context in his wonderful monograph “Stress, Health and the Social Environment” (Henry & Stevens, 1977). However it is broadly true that the scientific study of the role of emotion as a risk factor for cardiovascular disease is a product of the last forty years.
Isotopic evidence of weaning in hunter-gatherers from the late holocene in Lake Salitroso, Patagonia, Argentina.

OBJECTIVES The timing and duration of breastfeeding and weaning in past hunter-gatherer populations are discussed based on the results of stable carbon and nitrogen isotope analyses undertaken on a Late Holocene skeletal sample from Lake Salitroso in the Patagonian steppe (Argentina). Research in Lake Salitroso is part of a regional project that studies the relationship between hunter-gatherer societies, their organizational systems and the environmental changes during the last 3,000 years in Patagonia. METHODS The sample included 52 individuals: 33 subadults and 19 adults of both sexes. They were recovered from 24 burial stone structures, locally called chenques, with dates ranging from ca. 800 BP to 350 BP. Ribs were selected for collagen extraction and measurement of (13) C/(12) C and (15) N/(14) N ratios. RESULTS A δ(13) C mean value of -18.7‰ ± 0.5‰ was obtained, with a range between -19.8‰ and -17.1‰ whereas δ(15) N recorded a mean of 11.9‰ ± 1.1‰ with a range between 10.1‰ and 14.8‰. δ(15) N data showed an age-related pattern with particularly marked difference between values for subadults under the age of 4 and older individuals. As opposed to δ(15) N, δ(13) C showed little variation with age. CONCLUSIONS An early incorporation of supplementary solid food between 0.75 and 2 years of age and a late cessation of breastfeeding at about 5-6 years of age were inferred. This suggests that among this Patagonian hunter-gatherer population weaning was a gradual and lengthy process. These results are consistent with the patterns observed in cross-cultural studies and archaeological samples of hunter-gatherer groups.
Evidence from a randomized evaluation in Western Kenya

We report results from a randomized evaluation comparing three school-based HIV/AIDS interventions in Kenya: 1) training teachers in the Kenyan Government’s HIV/AIDS-education curriculum; 2) encouraging students to debate the role of condoms and to write essays on how to protect themselves against HIV/AIDS; and 3) reducing the cost of education. Our primary measure of the effectiveness of these interventions is teenage childbearing, which is associated with unprotected sex. We also collected measures of knowledge, attitudes, and behavior regarding HIV/AIDS. After two years, girls in schools where teachers had been trained were more likely to be married in the event of a pregnancy. The program had little other impact on students’ knowledge, attitudes, and behavior, or on the incidence of teen childbearing. The condom debates and essays increased practical knowledge and self-reported use of condoms without increasing self-reported sexual activity. Reducing the cost of education by paying for school uniforms reduced dropout rates, teen marriage, and childbearing.
Match running performance in Spanish elite male rugby union using global positioning system

The aim of this study was to analyze the movement patterns and physiological demands of an international level male Rugby Union team. Fourteen samples of running performance, exercise intensity, acceleration and impacts to the body were taken over the course of 3 games using a GPS device. The players covered a mean distance of 6162 m per game, with the forwards covering 5853 m and the backs 6471 m at average speeds throughout the games of 4.3 km/h and 4.77 km/h, respectively. For more than 75.5% and 68.5% of the game forwards and backs, respectively, were exposed to heart rates above 80% of their maximal heart rate. The player’s time-related work to rest ratio was 1:0.8. Rugby Union can be considered a high intensity intermittent team sport with many and varied non-locomotor activities and actions that occur during the playing of matches. These actions and activities greatly increase the exercise intensity but are registered as being low speed running. Each position in the field requires specific physiological demands.
Comments on "Adjustment for total energy intake in epidemiologic studies"

Willett et al [Am J Clin Nutr 1997;65(suppl): 1220S-8S] reviewed the case for energy adjustment in the analysis of nutritional studies and argued strongly for basing the main analysis on an energy-adjustment statistical model. They recommended focusing attention on a statistical association that represents the change in disease incidence associated with the substitution of energy from a specific nutrient for energy from other nutrient sources, while keeping total energy intake constant. Although we agree with many of the points made in their paper, we recommend assessing and reporting associations representing not only the substitution but also the addition of energy from the specific nutrient. For these addition associations, it is especially important to check for confounding with measures of body size and physical activity. Restricting analyses to substitution associations will confine investigators to estimating the relative effects of one nutrient to another and will preclude investigating the effects of increased intake of a specific nutrient.
Coordination between growth, phenology and carbon storage in three coexisting deciduous tree species in a temperate forest.

In deciduous trees growing in temperate forests, bud break and growth in spring must rely on intrinsic carbon (C) reserves. Yet it is unclear whether growth and C storage occur simultaneously, and whether starch C in branches is sufficient for refoliation. To test in situ the relationships between growth, phenology and C utilization, we monitored stem growth, leaf phenology and stem and branch nonstructural carbohydrate (NSC) dynamics in three deciduous species: Carpinus betulus L. , Fagus sylvatica L. and Quercus petraea (Matt.) Liebl. To quantify the role of NSC in C investment into growth, a C balance approach was applied. Across the three species, >95% of branchlet starch was consumed during bud break, confirming the importance of C reserves for refoliation in spring. The C balance calculation showed that 90% of the C investment in foliage (7.0-10.5 kg tree(-1) and 5-17 times the C needed for annual stem growth) was explained by simultaneous branchlet starch degradation. Carbon reserves were recovered sooner than expected, after leaf expansion, in parallel with stem growth. Carpinus had earlier leaf phenology (by ∼25 days) but delayed cambial growth (by ∼15 days) than Fagus and Quercus, the result of a competitive strategy to flush early, while having lower NSC levels.
Hyaluronic Acid Receptor for Endocytosis (HARE)-mediated Endocytosis of Hyaluronan, Heparin, Dermatan Sulfate, and Acetylated Low Density Lipoprotein (AcLDL), but Not Chondroitin Sulfate Types A, C, D, or E, Activates NF-κB-regulated Gene Expression*

Background: HARE mediates systemic clearance of 14 ECM- or stress-derived ligands. Hyaluronan uptake activates NF-κB. Results: Heparin, dermatan sulfate, and acetylated LDL also activated NF-κB; chondroitin sulfates types A, C, D, and E did not. Conclusion: A subset of HARE ligands activates signaling and gene expression. Significance: HARE may be a systemic tissue-stress sensor that responds to abnormal ECM turnover and damage. The hyaluronan (HA) receptor for endocytosis (HARE; Stab2) clears 14 systemic ligands, including HA and heparin. Here, we used NF-κB promoter-driven luciferase reporter assays to test HARE-mediated intracellular signaling during the uptake of eight ligands, whose binding sites in the HARE ectodomain were mapped by competition studies (Harris, E. N., and Weigel, P. H. (2008) Glycobiology 18, 638–648). Unique intermediate size Select-HATM, heparin, dermatan sulfate, and acetylated LDL stimulated dose-dependent HARE-mediated NF-κB activation of luciferase expression, with half-maximal values of 10–25 nm. In contrast, chondroitin sulfate types A, C, D, and E did not stimulate NF-κB activation. Moreover, degradation of endogenous IkB-α (an NF-κB inhibitor) was stimulated only by the signaling ligands. The stimulatory activities of pairwise combinations of the four signaling ligands were additive. The four nonstimulatory chondroitin sulfate types, which compete for HA binding, also effectively blocked HA-stimulated signaling. Clathrin siRNA decreased clathrin expression by ∼50% and completely eliminated NF-κB-mediated signaling by all four ligands, indicating that activation of signaling complexes occurs after endocytosis. These results indicate that HARE not only binds and clears extracellular matrix degradation products (e.g. released normally or during infection, injury, tumorigenesis, or other stress situations) but that a subset of ligands also serves as signaling indicator ligands. HARE may be part of a systemic tissue-stress sensor feedback system that responds to abnormal tissue turnover or damage as a danger signal; the signaling indicator ligands would reflect the homeostatic status, whether normal or pathological, of tissue cells and biomatrix components.
Genetic adaptation and phenotypic plasticity contribute to greater leaf hydraulic tolerance in response to drought in warmer climates

The ability of plants to maintain an intact water transport system in leaves under drought conditions is intimately linked to survival and can been be seen as adaptive in shaping species climatic limits. Large differences in leaf hydraulic vulnerability to drought are known among species from contrasting climates, yet whether this trait varies among populations within a single species and, furthermore, whether it is altered by changes in growth conditions, remain unclear. We examined intraspecific variation in both leaf water transport capacity (Kleaf) and leaf hydraulic vulnerability to drought (P50leaf) among eight populations of Corymbia calophylla (R. Br.) K.D. Hill & L.A. S. Johnson (Myrtaceae) from both cool and warm climatic regions grown reciprocally under two temperature treatments representing the cool and warm edge of the species distribution. Kleaf did not vary between cool and warm-climate populations, nor was it affected by variable growth temperature. In contrast, population origin and growth temperature independently altered P50leaf. Using data pooled across growth temperatures, cool-climate populations showed significantly higher leaf hydraulic vulnerability (P50leaf = -3.55 ± 0.18 MPa) than warm-climate populations (P50leaf = -3.78 ± 0.08 MPa). Across populations, P50leaf decreased as population home-climate temperature increased, but was unrelated to rainfall and aridity. For populations from both cool and warm climatic regions, P50leaf was lower under the warmer growth conditions. These results provide evidence of trait plasticity in leaf hydraulic vulnerability to drought in response to variable growth temperature. Furthermore, they suggest that climate, and in particular temperature, may be a strong selective force in shaping intraspecific variation in leaf hydraulic vulnerability to drought.
Stable isotope study on ancient populations of central sudan: Insights on their diet and environment.

OBJECTIVES A contribution to the knowledge of the economy and the environmental surroundings of the populations living along the Nile valley in three different periods. MATERIALS AND METHODS This study reports stable isotope analyses on apatite bone samples of 139 humans, 48 mammals, and 43 fish from the Al Khiday archaeological sites in Sudan. The bones belong to four archaeological periods: pre-Mesolithic, Mesolithic, Neolithic, and Meroitic. Data were processed statistically. RESULTS A significant difference exists between the pre-Mesolithic and Mesolithic mean δ(18) Ow value and the mean of the modern Nile. The mean δ(18) Ow values for the Neolithic humans and bovids are very similar (+1.5‰ ±4‰, and -2‰, respectively) and more positive than the mean values of Mesolithic mammals and Pre-Mesolithic humans. The water ingested by Meroitic humans (+7‰ ± 2.5‰) is enriched in (18) O in respect to the water ingested by the Neolithic population. There is a separation in the δ(13) Cdiet values between the pre-Mesolithic humans (-14‰ ± 1‰) and Mesolithic mammals (-12‰ ± 2‰) group and the Neolithic humans (-18‰ ± 1‰), Meroitic humans (-19‰ ±1‰), Neolithic mammals (-21‰), and the modern (mean δ(13) Cdiet = -19‰ ±2‰) mammal group. DISCUSSION The climate became warmer and more arid from the pre-Mesolithic/Mesolithic to the Meroitic period. The environmental conditions influenced the strategies of subsistence and, in particular, the changes occurring from the pre-Mesolithic to the Neolithic can be considered contemporaneous to the transition from hunting-gathering-fishing to cultivation-herding. Am J Phys Anthropol 160:498-518, 2016. © 2016 Wiley Periodicals, Inc.
Genetic Signatures of HIV-1 Envelope-mediated Bystander Apoptosis

Background: Determinants of HIV-1 Env-mediated apoptosis remain poorly understood. Results: We studied the bystander apoptosis-inducing activity of a panel of primary HIV Envs. Conclusion: Residues Arg-476 and Asn-425 are associated with differences in HIV-1 Env-mediated bystander apoptosis induction. Significance: We identified specific genetic signatures within the HIV-1 Env that are associated with the bystander apoptosis-inducing phenotype. The envelope (Env) glycoprotein of HIV is an important determinant of viral pathogenesis. Several lines of evidence support the role of HIV-1 Env in inducing bystander apoptosis that may be a contributing factor in CD4+ T cell loss. However, most of the studies testing this phenomenon have been conducted with laboratory-adapted HIV-1 isolates. This raises the question of whether primary Envs derived from HIV-infected patients are capable of inducing bystander apoptosis and whether specific Env signatures are associated with this phenomenon. We developed a high throughput assay to determine the bystander apoptosis inducing activity of a panel of primary Envs. We tested 38 different Envs for bystander apoptosis, virion infectivity, neutralizing antibody sensitivity, and putative N-linked glycosylation sites along with a comprehensive sequence analysis to determine if specific sequence signatures within the viral Env are associated with bystander apoptosis. Our studies show that primary Envs vary considerably in their bystander apoptosis-inducing potential, a phenomenon that correlates inversely with putative N-linked glycosylation sites and positively with virion infectivity. By use of a novel phylogenetic analysis that avoids subtype bias coupled with structural considerations, we found specific residues like Arg-476 and Asn-425 that were associated with differences in bystander apoptosis induction. A specific role of these residues was also confirmed experimentally. These data demonstrate for the first time the potential of primary R5 Envs to mediate bystander apoptosis in CD4+ T cells. Furthermore, we identify specific genetic signatures within the Env that may be associated with the bystander apoptosis-inducing phenotype.