Miracle-dz/UniFAR-FTUs huggingface dataset:
One Tree to Link Them All: A Phylogenetic Dataset for the European Tetrapoda

Since the ever-increasing availability of phylogenetic informative data, the last decade has seen an upsurge of ecological studies incorporating information on evolutionary relationships among species. However, detailed species-level phylogenies are still lacking for many large groups and regions, which are necessary for comprehensive large-scale eco-phylogenetic analyses. Here, we provide a dataset of 100 dated phylogenetic trees for all European tetrapods based on a mixture of supermatrix and supertree approaches. Phylogenetic inference was performed separately for each of the main Tetrapoda groups of Europe except mammals (i.e. amphibians, birds, squamates and turtles) by means of maximum likelihood (ML) analyses of supermatrix applying a tree constraint at the family (amphibians and squamates) or order (birds and turtles) levels based on consensus knowledge. For each group, we inferred 100 ML trees to be able to provide a phylogenetic dataset that accounts for phylogenetic uncertainty, and assessed node support with bootstrap analyses. Each tree was dated using penalized-likelihood and fossil calibration. The trees obtained were well-supported by existing knowledge and previous phylogenetic studies. For mammals, we modified the most complete supertree dataset available on the literature to include a recent update of the Carnivora clade. As a final step, we merged the phylogenetic trees of all groups to obtain a set of 100 phylogenetic trees for all European Tetrapoda species for which data was available (91%). We provide this phylogenetic dataset (100 chronograms) for the purpose of comparative analyses, macro-ecological or community ecology studies aiming to incorporate phylogenetic information while accounting for phylogenetic uncertainty.
Factors related to retention of community health workers in a trial on community-based management of fever in children under 5 years in the Dangme West District of Ghana.

BACKGROUND In resource-constrained settings of developing countries, promotion of community-based health interventions through community health workers (CHWs) is an important strategy to improve child health. However, there are concerns about the sustainability of such programmes owing to the high rate of CHW attrition. This study examined factors influencing retention of volunteer CHWs in a cluster randomised trial on community management of under-5 fever in a rural Ghanaian district. METHODS Data were obtained from structured interviews (n=520) and focus group discussions (n=5) with CHWs. Factors influencing CHWs' decisions to remain or leave the programme were analysed using a probit model, and focus group discussion results were used to elucidate the findings. RESULTS The attrition rate among CHWs was 21.2%. Attrition was comparatively higher in younger age groups (25.9% in 15-25 years group, 18.2% in 26-45 years group and 16.5% in ≥46 years group). Approval of a CHW by the community (p<0.001) and the CHW's immediate family (p<0.05) were significant in influencing the probability of remaining in the programme. Motivation for retention was related to the desire to serve their communities as well as humanitarian and religious reasons. CONCLUSION The relatively moderate rate of attrition could be attributed to the high level of community involvement in the selection process as well as other aspects of the intervention leading to high community approval and support. Attention for these aspects could help improve CHW retention in community-based health interventions in Ghana, and the lessons could be applied to countries within similar settings.
Tollip and Tom1 Form a Complex and Recruit Ubiquitin-conjugated Proteins onto Early Endosomes*

Tom1 (target of Myb1) is a protein of unknown function. Tom1 and its relative Tom1L1 have an N-terminal VHS (Vps27p/Hrs/Stam) domain followed by a GAT (GGA and Tom1) domain, both of which are also found in the GGA (Golgi-localizing, γ-adaptin ear domain homology, ADP-ribosylation factor-binding protein) family of proteins. Although the VHS and GAT domains of GGA proteins bind to transmembrane cargo proteins and the small GTPase ADP-ribosylation factor, respectively, the VHS and GAT domains of Tom1 are unable to interact with these proteins. In this study, we show that the GAT domains of Tom1 and Tom1L1 interact with ubiquitin and Tollip (Toll-interacting protein). Ubiquitin bound the GAT domains of Tom1, Tom1L1, and GGA proteins, whereas Tollip interacted specifically with Tom1 and Tom1L1. Ubiquitin and Tollip bound to an overlapping region of the Tom1-GAT domain in a mutually exclusive manner. Tom1 was predominantly cytosolic when expressed in cells. On the other hand, Tollip was localized on early endosomes and recruited Tom1 and ubiquitinated proteins. These observations suggest that Tollip and Tom1 form a complex and regulate endosomal trafficking of ubiquitinated proteins.
The recognition of facial expressions: An investigation of the influence of age and cognition

ABSTRACT The present study aimed to investigate changes in facial expression recognition across the lifespan, as well as to determine the influence of fluid intelligence, processing speed, and memory on this ability. Peak performance in the ability to identify facial affect was found to occur in middle-age, with the children and older adults performing the poorest. Specifically, older adults were impaired in their ability to identify fear, sadness, and happiness, but had preserved recognition of anger, disgust, and surprise. Analyses investigating the influence of cognition on emotion recognition demonstrated that cognitive abilities contribute to performance, especially for participants over age 45. However, the cognitive functions did not fully account for the older adults’ impairments on expression recognition. Overall, the age-related deficits in facial expression recognition have implications for older adults’ use of non-verbal communicative information.
HIF display synergistic behaviour during hypoxic inflammation

Title þÿ N F o B a n d H I F d i s p l a y s y n e r g i s t i c b e h a v i o u r d u r i n g h y p o x i c i n f l a m m a t i o n Authors(s) Bruning, Ulrike; Fitzpatrick, Susan F. ; Frank, Till D. ; et al. Publication date 2011-11-09 Publication information Cellular and Molecular Life Sciences, 69 (8): 1319-1329 Publisher Springer-Verlag Item record/more information http://hdl.handle. net/10197/5093 Publisher's statement The final publication is available at www.springerlink. com Publisher's version (DOI) 10.1007/s00018-011-0876-2
Differences in healthy lifestyle characteristics between adults with prehypertension and normal blood pressure

Background Identifying differences in modifiable lifestyle factors between persons with prehypertension and normal blood pressure (BP) can help improve prevention efforts. Methods Data from the 1999–2004 National Health and Nutrition Examination Survey were analyzed (in 2008) for persons aged at least 20 years (n = 11 194). Differences in five healthy lifestyle characteristics were examined by BP status (normal, prehypertension, and hypertension). Additionally, differences in lifestyle characteristics by sex, race/ethnicity, and education among those with prehypertension were analyzed. Results Overall, 32.8% of adults had a normal BMI, 75.3% did not smoke, 31.3% were regularly physically active, 57.7% were moderate drinkers or nondrinkers, and 28.1% had a low sodium intake; only 2% had all five characteristics. Almost 40% had a normal BP and 30.3% were prehypertensive. Those with prehypertension were less likely to have a normal BMI than normotensive individuals [adjusted odds ratio (OR) = 0.63, 95% confidence interval (CI) = 0.56–0.70], to be regularly active (adjusted OR = 0.85, 95% CI = 0.74–0.98), and to moderately/not drink (adjusted OR = 0.88, 95% CI = 0.80–0.97). Those with prehypertension or hypertension were less likely to have at least three or four healthy lifestyle characteristics compared with those with normal BP. Among 3168 persons with prehypertension, some sex, race/ethnic, and education level differences in the prevalence of healthy lifestyles were observed. Conclusion Differences in healthy lifestyle factors were observed by BP status, but the prevalence of healthy lifestyle factors is suboptimal among the population as a whole.
sPECAM-1 and sVCAM-1: role in pathogenesis and diagnosis of chronic hepatitis C and association with response to antiviral therapy

Aim: To analyze the relationship between pretreatment clinical or histological features and the levels of soluble platelet-endothelial cell adhesion molecule-1 (sPECAM-1) and soluble vascular cell adhesion molecule-1 (sVCAM-1), to determine their serum concentration in responders and nonresponders, to evaluate the behavior under antiviral therapy, to explain their relationship in response to therapy and to assess the association between these two molecules in chronic hepatitis C (CHC). Methods: The study analyzed 65 CHC patients, including 50 patients (Group 1) with marked fibrosis treated with peginterferon plus ribavirin, 15 patients without fibrosis (Group 2) and 13 healthy volunteers (the control group, Group 3). sPECAM-1 and sVCAM-1 levels were assessed by an immunoenzymatic method (ELISA) before and after therapy. Results: sVCAM-1 and sPECAM-1 serum concentrations increased significantly in CHC patients (p<0.001). sPECAM-1 levels corresponded to inflammatory grade (p = 0.03) and fibrosis stage (p = 0.01). sVCAM-1 increased only in advanced fibrosis. After therapy, sPECAM-1 levels decreased significantly (p<0.001) with no difference between responders and nonresponders. sPECAM-1 correlated positively with inflammatory activity (p = 0.02), fibrosis stage (p<0.001), sVCAM-1 (r = 0.56, p<0.001) and alanine aminotransferase activity (r = 0.30, p = 0.05). Receiver operating characteristic curve analysis showed a good discriminant power of serum sPECAM-1 concentrations for detection of liver fibrosis — stage 0 versus stage 1—3, AUC 0.81; cut-off 221.0 ng/ml and a fair discriminant power for distinguishing bridging fibrosis, AUC 0.78; cut-off 237.1 ng/ml. Conclusions: Hepatitis C virus (HCV) infection results in upregulation of sPECAM-1 and sVCAM-1. sPECAM-1 levels are related to necroinflammatory activity and may also identify patients with advanced fibrosis. The sPECAM-1 value was decreased by therapy but its measurement cannot predict therapy outcome and confirm HCV persistence. sPECAM-1 may influence VCAM-1 expression.
The efferent pathway of epileptic seizures for the face following cortical stimulation differs from that for limbs.

1. Stimulation electrically as well as chemically applied to the motor face area of the cortex produced generalized epileptic seizures in the limbs and face muscles in monkeys as well as in dogs.2. After removing the homolateral leg and arm area, stimulation to the face area produced epileptic seizures only in the contralateral face muscles in monkeys as well as in dogs.3. After the face area of the cortex was removed, stimulation of the limb or arm area produced seizures in all limbs and trunk and in the ipsilateral face muscles in monkeys as well as in dogs.4. Seizures of the homolateral face muscles following stimulation of the face area could not be produced when the contralateral hemisphere, especially, its face area was removed, and also when the homolateral or the contralateral thalamus was removed in dogs.5. Epileptic seizures for the face muscles as well as for limb muscles following cortical stimulation could not appear after the globus pallidus in both sides were removed, on the contrary, the tonic contraction could be produced. Chemical stimulation to the globus pallidus produced epileptic seizures of all limbs, the homolateral face muscles in dogs and of bilateral eyelids and ears.6. Stimulation of the frontal eye field produced a conjugate deviation of the eyes to the opposite side and clonic convulsion of the eyelids and ears. It did not produce seizures of the face muscles nor limb muscles in monkeys as well as in dogs. It was established that the frontal eye field in dogs was situated in the prorea (in front of the gyrus compositus ant.). 7. The efferent pathway of the epileptic seizures for face muscles differed from that for limb muscles. It took the course that the cells of the cortical area for face projected to the homolateral thalamus from which the second neurone to the homolateral globus pallidus. The third neurone started in the globus pallidus, crossed at the level between the thalamus and midbrain and reached the medial side of the substantia nigra and its posterior locus of substantia reticularis, which would be the executing center of an epileptic spasm of the muscles of that half of the face from which the fourth neurone got to the nuclei of the cranial nerves for face muscles.8. The copious secretion of saliva which accompanied the epileptic seizure could not be produced when seizure of the face could not be elicited in monkeys as well as in dogs.
A low-profile unidirectional antenna enabled by interdigital capacitor loaded metasurface

In this paper, a compact footprint and low-profile metasurface-enabled unidirectional antenna that operates from 4.11GHz to 4.26GHz with a center frequency at 4.2GHz is presented. The miniaturized metasurface, which has a reflection phase of -150 degree at 4.2GHz, was made possible by interdigital capacitor loading, resulting in a unit cell with an electrical dimension of only 0. 02λ02. A finite-sized metasurface with two by three elements was integrated with a planar microstrip fed monopole antenna, enabling a total antenna footprint of around 0. 13λ02 and a thickness of 0. 05λ0. Full-wave simulations show that, even with such a small footprint, the antenna achieves a large front-to-back ratio and a high gain within the targeted operational frequency band.
Identity and Diversity of Human Peripheral Th and T Regulatory Cells Defined by Single-Cell Mass Cytometry

Human CD3+CD4+ Th cells, FOXP3+ T regulatory (Treg) cells, and T regulatory type 1 (Tr1) cells are essential for ensuring peripheral immune response and tolerance, but the diversity of Th, Treg, and Tr1 cell subsets has not been fully characterized. Independent functional characterization of human Th1, Th2, Th17, T follicular helper (Tfh), Treg, and Tr1 cells has helped to define unique surface molecules, transcription factors, and signaling profiles for each subset. However, the adequacy of these markers to recapitulate the whole CD3+CD4+ T cell compartment remains questionable. In this study, we examined CD3+CD4+ T cell populations by single-cell mass cytometry. We characterize the CD3+CD4+ Th, Treg, and Tr1 cell populations simultaneously across 23 memory T cell–associated surface and intracellular molecules. High-dimensional analysis identified several new subsets, in addition to the already defined CD3+CD4+ Th, Treg, and Tr1 cell populations, for a total of 11 Th cell, 4 Treg, and 1 Tr1 cell subsets. Some of these subsets share markers previously thought to be selective for Treg, Th1, Th2, Th17, and Tfh cells, including CD194 (CCR4)+FOXP3+ Treg and CD183 (CXCR3)+T-bet+ Th17 cell subsets. Unsupervised clustering displayed a phenotypic organization of CD3+CD4+ T cells that confirmed their diversity but showed interrelation between the different subsets, including similarity between Th1–Th2–Tfh cell populations and Th17 cells, as well as similarity of Th2 cells with Treg cells. In conclusion, the use of single-cell mass cytometry provides a systems-level characterization of CD3+CD4+ T cells in healthy human blood, which represents an important baseline reference to investigate abnormalities of different subsets in immune-mediated pathologies.
Decrease in ventricular stroke volume at apnea termination is independent of oxygen desaturation.

Patients with obstructive sleep apnea experience nocturnal hemodynamic oscillations in association with repetitive respiratory events. Apnea termination (recovery) is accompanied by the nadir of arterial O2 saturation (SaO2), changes in intrathoracic pressure, and arousal from sleep. To investigate separately the contributions of hypoxemia and of arousal from sleep to changes in cardiac function, we continuously measured left ventricular stroke volume (LVSV) and mean arterial pressure (MAP) in eight subjects with severe obstructive sleep apnea (apnea-hypopnea index > 30 events/h associated with SaO2 < or = 82%) during two experimental conditions: 1) subjects slept without intervention for 1-2 h and then supplemental O2 was administered to maintain SaO2 > or = 90% (mean SaO2 nadir 92.7%) throughout the apnea-recovery cycle and 2) upper airway obstructions were abolished using nasal continuous positive airway pressure and subjects were aroused from sleep by an auditory signal. Recovery was associated with an increase in MAP and a decrease in LVSV both with and without supplemental O2. Arousal from sleep on nasal continuous positive airway pressure reproduced the postapneic elevation of MAP but not a decrease in cardiac function of the magnitude that occurred at apnea termination. We conclude that elevation of blood pressure and reduction of LVSV that occurred at apnea termination may be due to different physiological mechanisms.
Health risk appraisal in older people 2: the implications for clinicians and commissioners of social isolation risk in older people.

BACKGROUND Social isolation is associated with poorer health, and is seen by the World Health Organisation (WHO) as one of the major issues facing the industrialised world. AIM To explore the significance of social isolation in the older population for GPs and for service commissioners. DESIGN OF STUDY Secondary analysis of baseline data from a randomised controlled trial of health risk appraisal. SETTING A total of 2641 community-dwelling, non-disabled people aged 65 years and over in suburban London. METHOD Demographic details, social network and risk for social isolation based on the 6-item Lubben Social Network Scale, measures of depressed mood, memory problems, numbers of chronic conditions, medication use, functional ability, self-reported use of medical services. RESULTS More than 15% of the older age group were at risk of social isolation, and this risk increased with advancing age. In bivariate analyses risk of social isolation was associated with older age, education up to 16 years only, depressed mood and impaired memory, perceived fair or poor health, perceived difficulty with both basic and instrumental activities of daily living, diminishing functional ability, and fear of falling. Despite poorer health status, those at risk of social isolation did not appear to make greater use of medical services, nor were they at greater risk of hospital admission. Half of those who scored as at risk of social isolation lived with others. Multivariate analysis showed significant independent associations between risk of social isolation and depressed mood and living alone, and weak associations with male sex, impaired memory and perceived poor health. CONCLUSION The risk of social isolation is elevated in older men, older persons who live alone, persons with mood or cognitive problems, but is not associated with greater use of services. These findings would not support population screening for individuals at risk of social isolation with a view to averting service use by timely intervention. Awareness of social isolation should trigger further assessment, and consideration of interventions to alleviate social isolation, treat depression or ameliorate cognitive impairment.
Time domain characterization of finite frequency properties via behavioral approach

Many of practical design specifications are provided by finite frequency properties described by inequalities over restricted finite frequency intervals. A quadratic differential form (QDF) is a useful algebraic tool when we consider the dissipation theory based on the behavioral approach. In this paper, we consider a time domain characterization of the finite frequency domain inequalities (FFDIs) using QDFs. We first derive an LMI condition which is equivalent to the FFDIs. Using the condition, we derive a time domain characterization of the FFDIs in terms of QDFs as a main result of this paper. This condition recovers the previous result in the sense that our result can characterize the FFDIs for the system of nonproper transfer functions.
Music Therapy in Palliative Care.

BACKGROUND Music therapy has been used successfully for over 30 years as part of palliative care programs for severely ill patients. There is nonetheless a lack of high-quality studies that would enable an evidence-based evaluation of its psychological and physiological effects. METHODS In a randomized controlled trial, 84 hospitalized patients in palliative care were assigned to one of two treatment arms--music therapy and control. The music therapy intervention consisted of two sessions of live music-based relaxation exercises; the patients in the control group listened to a verbal relaxation exercise. The primary endpoints were self-ratings of relaxation, well-being, and acute pain, assessed using visual analog scales. Heart rate variability and health-related quality of life were considered as secondary outcomes. The primary data analysis was performed according to the intention-to-treat principle. RESULTS Analyses of covariance revealed that music therapy was more effective than the control treatment at promoting relaxation (F = 13.7; p <0.001) and well-being (F = 6.41; p = 0.01). This effect was supported by a significantly greater increase in high-frequency oscillations of the heart rate (F = 8.13; p = 0.01). Music therapy did not differ from control treatment with respect to pain reduction (F = 0.4; p = 0.53), but it led to a significantly greater reduction in the fatigue score on the quality-of-life scale (F = 4.74; p = 0.03). CONCLUSION Music therapy is an effective treatment with a low dropout rate for the promotion of relaxation and well-being in terminally ill persons undergoing palliative care.
The Five Near-iron Transporter (NEAT) Domain Anthrax Hemophore, IsdX2, Scavenges Heme from Hemoglobin and Transfers Heme to the Surface Protein IsdC*

Pathogenic bacteria require iron to replicate inside mammalian hosts. Recent studies indicate that heme acquisition in Gram-positive bacteria is mediated by proteins containing one or more near-iron transporter (NEAT) domains. Bacillus anthracis is a spore-forming, Gram-positive pathogen and the causative agent of anthrax disease. The rapid, extensive, and efficient replication of B. anthracis in host tissues makes this pathogen an excellent model organism for the study of bacterial heme acquisition. B. anthracis secretes two NEAT hemophores, IsdX1 and IsdX2. IsdX1 contains a single NEAT domain, whereas IsdX2 has five, a novel property among hemophores. To understand the functional significance of harboring multiple, non-identical NEAT domains, we purified each individual NEAT domain of IsdX2 as a GST fusion and analyzed the specific function of each domain as it relates to heme acquisition and transport. NEAT domains 1, 3, 4, and 5 all bind heme, with domain 5 having the highest affinity. All NEATs associate with hemoglobin, but only NEAT1 and -5 can extract heme from hemoglobin, seemingly by a specific and active process. NEAT1, -3, and -4 transfer heme to IsdC, a cell wall-anchored anthrax NEAT protein. These results indicate that IsdX2 has all the features required to acquire heme from the host and transport heme to the bacterial cell wall. Additionally, these results suggest that IsdX2 may accelerate iron import rates by acting as a “heme sponge” that enhances B. anthracis replication in iron-starved environments.