Miracle-dz/UniFAR-FTUs huggingface dataset:
Radiative hydrodynamics simulations of red supergiant stars - I. interpretation of interferometric observations

Context. It has been proposed that convection in red supergiant (RSG) stars produces large-scale granules causing observable surface inhomogeneities. This convection is also extremely vigorous and is suspected to be one of the main causes of mass-loss in RSGs. It should thus be understood in detail. Evidence has accumulated of asymmetries in the photospheres of RSGs, but detailed studies of granulation are still lacking. Interferometric observations provide an innovative way of addressing this question, but they are still often interpreted using smooth symmetrical limb-darkened intensity distributions, or simple, spotted, ad hoc models. Aims. We explore the impact of the granulation on visibility curves and closure phases using the radiative transfer code OPTIM3D. We simultaneously assess how 3D simulations of convection in RSG with CO 5 BOLD can be tested by comparing with these observations. Methods. We use 3D radiative hydrodynamical (RHD) simulations of convection to compute intensity maps at various wavelengths and time, from which we derive interferometric visibility amplitudes and phases. We study their behaviour with time, position angle, and wavelength, and compare them to observations of the RSG α Ori. Results. We provide average limb-darkening coefficients for RSGs. We describe the prospects for the detection and characterization of granulation (i.e., contrast, size) on RSGs. We demonstrate that our RHD simulations provide an excellent fit to existing interferometric observations of α Ori, in contrast to limb darkened disks. This confirms the existence of large convective cells on the surface of Betelgeuse.
Progesterone counteracts estrogen-induced increases in neurotrophins in the aged female rat brain

Neurotrophin alterations have been associated with normal aging and age-related neurodegenerative disease, as well as cognitive status. Estrogen influences expression of mRNA and protein of neurotrophins and their receptors, and affects cognitive performance in young ovariectomized (Ovx) rats. The current investigation evaluated whether estrogen or estrogen plus progesterone affects neurotrophin protein levels in cognitive brain regions in the aged Ovx rat. While estrogen treatment increased BDNF, NGF, and NT3 levels in entorhinal cortex, progesterone abated the effects of estrogen resulting in neurotrophin levels comparable to aged Ovx rats not given hormone. Our findings suggest that the aged female brain is responsive to estrogen in cognitive brain regions, and that progesterone can reverse these estrogen effects.
Association Between Low Plasma Levels of Cholesterol and Relapse in Cocaine Addicts

Objective In light of recent studies suggesting the existence of associations between low concentrations of cholesterol and various psychiatric disorders, we decided to explore relationships between cholesterol levels and relapse rates in a group of cocaine addicts who had undergone inpatient detoxification. Methods The total cholesterol levels of 38 non–opiate-dependent and non–alcohol-dependent cocaine addicts were determined while they were hospitalized. Drug use was subsequently assessed 3, 6, and 12 months after patients were discharged from the hospital. Results Comparisons of the cholesterol levels (obtained during hospitalization) of relapsers and nonrelapsers by analyses of covariance with age and weight as covariates revealed significantly lower cholesterol values in patients who relapsed at 3 months (p = .046), 6 months (p = .030), and 12 months (p = .019) after discharge. Conclusions This study showed an association between a low total cholesterol level and relapse rates in detoxified cocaine addicts. Reasons for the predictive value of low cholesterol levels for relapse for up to 1 year after cholesterol measurements were made are unclear. These data are preliminary and in need of replication.
The release element of the yeast polymerase I transcription terminator can function independently of Reb1p

The Saccharomyces cerevisiae polymerase I (polI) transcription terminator utilizes a DNA-binding protein (Reb1p) as part of a signal that causes the polymerase to pause prior to release from the template. To study the release element of the terminator, independent of the Reb1p pause signal, we have replaced the Reb1p binding site with the binding site for the lac repressor, which acts as a self-contained heterologous pause signal for polI. Release efficiency is maximal when the lac repressor causes polI to pause in exactly the same position that Reb1p would have caused it to pause, suggesting that polI must be precisely positioned for transcript release to occur. Mutational analysis shows that the release element is a region rich in T residues which codes for the extreme 3' end of the transcript and which has no apparent ability to form hairpins when transcribed into RNA. We discuss possible mechanisms whereby this polI release element might function.
ThermoSense: Occupancy Thermal Based Sensing for HVAC Control

In order to achieve sustainability, steps must be taken to reduce energy consumption. In particular, heating, cooling, and ventilation systems, which account for 42% of the energy consumed by US buildings in 2010 [8], must be made more efficient. In this paper, we demonstrate ThermoSense, a new system for estimating occupancy. Using this system we are able to condition rooms based on usage. Rather than fully conditioning empty or partially filled spaces, we can control ventilation based on near real-time estimates of occupancy and temperature using conditioning schedules learned from occupant usage patterns. ThermoSense uses a novel multisensor node that utilizes a low-cost, low-power thermal sensor array along with a passive infrared sensor. By using a novel processing pipeline and sensor fusion, we show that our system is able measure occupancy with a RMSE of only ≈0.35 persons. By conditioning spaces based on occupancy, we show that we can save 25% energy annually while maintaining room temperature effectiveness.
Continuous Deep Q-Learning with Model-based Acceleration

Model-free reinforcement learning has been successfully applied to a range of challenging problems, and has recently been extended to handle large neural network policies and value functions. However, the sample complexity of modelfree algorithms, particularly when using high-dimensional function approximators, tends to limit their applicability to physical systems. In this paper, we explore algorithms and representations to reduce the sample complexity of deep reinforcement learning for continuous control tasks. We propose two complementary techniques for improving the efficiency of such algorithms. First, we derive a continuous variant of the Q-learning algorithm, which we call normalized advantage functions (NAF), as an alternative to the more commonly used policy gradient and actor-critic methods. NAF representation allows us to apply Q-learning with experience replay to continuous tasks, and substantially improves performance on a set of simulated robotic control tasks. To further improve the efficiency of our approach, we explore the use of learned models for accelerating model-free reinforcement learning. We show that iteratively refitted local linear models are especially effective for this, and demonstrate substantially faster learning on domains where such models are applicable.
Aspirin intolerance and the cyclooxygenase-leukotriene pathways.

PURPOSE OF REVIEW In up to 10% of patients with bronchial asthma, aspirin and other nonsteroidal antiinflammatory drugs precipitate asthmatic attacks. This is a hallmark of a distinct clinical syndrome that develops according to a characteristic sequence of symptoms. Here we discuss its clinical picture and management as related to the abnormalities in arachidonic acid transformations. RECENT FINDINGS At the biochemical level, the characteristic feature is profound alteration in eicosanoid biosynthesis and metabolism. Major advances in the molecular biology of eicosanoids, exemplified by the cloning of cysteinyl-leukotriene receptors and discovery of a whole family of cyclooxygenase enzymes, offer new insights into mechanisms operating in aspirin-induced asthma. Clinical interest has been enhanced by the introduction into therapy of highly specific cyclooxygenase-2 inhibitors and antileukotriene drugs. SUMMARY Recent studies have improved our understanding of mechanisms operating in asthma and unvieled the role of eicosanoid mediators in pulmonary disease.
Computational protein design: Software implementation, parameter optimization, and performance of a simple model

Computational protein design will continue to improve as new implementations and parameterizations are explored. An automated protein design procedure is implemented and applied to the full redesign of 16 globular proteins. We combine established but simple ingredients: a molecular mechanics description of the protein where nonpolar hydrogens are implicit, a simple solvent model, a folded state where the backbone is fixed, and a tripeptide model of the unfolded state. Sequences are selected to optimize the folding free energy, using a simple heuristic algorithm to explore sequence and conformational space. We show that a balanced parametrization, obtained here and in our previous work, makes this procedure effective, despite the simplicity of the ingredients. Calculations were done using our Proteins @ Home distributed computing platform, with the help of several thousand volunteers. We describe the software implementation, the optimization of selected terms in the energy function, and the performance of the method. We allowed all amino acids to mutate except glycines, prolines, and cysteines. For 15 of the 16 test proteins, the scores of the computed sequences were comparable to those of natural homologues. Using the low energy computed sequences in a BLAST search of the SWISSPROT database, we could retrieve natural sequences for all protein families considered, with no high‐ranking false‐positives. The good stability of the designed sequences was supported by molecular dynamics simulations of selected sequences, which gave structures close to the experimental native structure. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Early reduction of the over‐expression of CD40L, OX40 and Fas on T cells in HIV‐1 infection during triple anti‐retroviral therapy: possible implications for lymphocyte traffic and functional recovery

Fas, CD40L and OX40 are members of the tumour necrosis factor (TNF) receptor superfamily with critical roles in T cell activation and death, B cell function, dendritic cell maturation and leucocyte traffic regulation. The aim of this study was to evaluate the effects of anti‐retroviral therapy (HAART) on CD40L, OX40 and Fas expression on freshly isolated peripheral blood T cells by three‐colour flow cytometry and compare them with lymphoproliferative responses, peripheral blood cell counts and viral load. Fourteen asymptomatic HIV‐1+ patients treated with Lamivudine, Stavudine and Nelfinavir were prospectively investigated sequentially for 48 weeks. At baseline, patients exhibited significantly enhanced proportions and counts of CD40L+ and OX40+ cells within the CD4 subset which were corrected by weeks 8–16 of HAART. Interestingly, in the five patients showing viral load rebound during therapy in spite of increasing CD4 counts, the reduction of the levels of these costimulatory molecules was similarly maintained. Therapy induced a decrease in the over‐expression of Fas, particularly in the CD4 subset where normal levels were reached at week 8. This reduction occurred in parallel with the major recovery of lymphoproliferative responses. Higher basal levels and lower reduction of Fas were associated with suboptimal suppression of viraemia. In conclusion, this previously undescribed increased expression of CD40L and OX40 may play a role in the HIV‐associated pan‐immune activation and represent a possible target for immunointervention, as suggested for several immunologically mediated diseases. Moreover, HAART induced an early correction of the over‐expression of Fas, CD40L and OX40 in CD4 T cells which could be involved in the recovery of the cell traffic disturbances and in the T cell renewal capacity.
Examining the Relationship between Heavy Alcohol Use and Assaults: With Adjustment for the Effects of Unmeasured Confounders

Background. Experimental studies suggest that alcohol can lead to aggression in laboratory settings; however, it is impossible to test the causal relationship between alcohol use and real-life violence among humans in randomized clinical trials. Objectives. (i) To examine the relationship between heavy alcohol use and assaults in a population based study; (ii) to demonstrate the proxy outcome method, as a means of controlling the effects of unknown/unmeasured confounders in observational studies. Methods. This study used data collected from three waves of the National Survey on Drug Use and Health (NSDUH). The effects of heavy alcohol use on assault were measured using multivariable logistic regressions in conjunction with the proxy outcome method. Results. Application of the proxy outcome method indicated that effect sizes of heavy alcohol use on the risk of assault were overestimated in the standard models. After adjusting for the effects of unknown/unmeasured confounders, the risk of assault remained 43% and 63% higher (P < 0.05) among participants who consumed 5+ drinks/day for 5–8 days/month and 9–30 days/month, respectively. Conclusions. Even after adjustment for unknown/unmeasured confounders the association between heavy alcohol use and risk of violence remained significant. These findings support the hypothesis that heavy alcohol use can cause violence.
Population parameters, genetic differentiation and socio-economics of sardinella aurita (valenciennes 1847) and pseudotolithus senegalensis (valenciennes 1833) in south coast, Liberia

xviii CHAPTER ONE . 1 1.0 INTRODUCTION . 1 1.1 Problem statement . 2 1.3 Justification . 2 1.4 Aims of the study . 4 1.4. 1 General Objective of the study . 4 1.4. 2 Specific Objectives of the study . 4 1.4. 3 Hypothesis . 4 CHAPTER TWO . 5 2.0 LITERATURE REVIEW . 5 2.1 Distribution of Sardinella aurita: . 7 2.2 Distribution of Pseudotolithus senegalensis (Cassava croaker): . 8 CHAPTER THREE . 9 3.0 MATERIALS AND METHODS . 9
Structure and expression of fibulin-2, a novel extracellular matrix protein with multiple EGF-like repeats and consensus motifs for calcium binding

A new protein, fibulin-2, was predicted from sequence analysis of cDNA clones obtained from a mouse fibroblast library. This protein consists of a 1195-residue polypeptide preceded by a 26-residue signal peptide. The COOH-terminal region of 787 amino acids contained three anaphylatoxin-related segments (domain I), 11 EGF-like repeats (domain II), 10 of which had a consensus motif for calcium-binding, and a 115- residue globular domain III. Except for two additional EGF-like repeats, this COOH-terminal region showed 43% sequence identity with the previously described fibulin-1 (BM-90). The NH2-terminal 408 residues, unique to fibulin-2, showed no sequence homology to other known proteins and presumably form two additional domains that differ in their cysteine content. Recombinant fibulin-2 was produced and secreted by human cell clones as a disulfide-bonded trimer. Rotary shadowing visualized the protein as three 40-45 nm long rods which are connected at one end in a globe-like structure. No significant immunological cross-reaction could be detected between fibulin-1 and fibulin-2. Production of the fibulin-2 was demonstrated by Northern blots and radioimmunoassay in fibroblasts but not in several tumor cell lines. Together with the observation that the serum level of fibulin-2 is 1,000-fold lower than that of fibulin-1, the data indicate that these two isoforms are not always coordinately expressed. This is also suggested by Northern blots of tissue mRNAs and by immunofluorescence localizations using mouse tissues. The latter studies also demonstrated an extracellular localization for fibulin-2 in basement membranes and other connective tissue compartments.
Fused (Stk36) is a ciliary protein required for central pair assembly and motile cilia orientation in the mammalian oviduct

Background: Motile cilia on the inner lining of the oviductal epithelium play a central role in ovum transport toward the uterus and subsequent fertilization by sperm. While the basic ultrastructure of 9+2 motile cilia (nine peripheral microtubule doublets surrounding a central pair) has been characterized, many important steps of ciliogenesis remain poorly understood. Results: Our previous studies on mammalian Fused (Fu) (Stk36), a putative serine‐threonine kinase, reveal a critical function of Fu in central pair construction and cilia orientation of motile cilia that line the tracheal and ependymal epithelia. These findings identify a novel regulatory component for these processes. In this study, we show that Fu is expressed in the multi‐ciliated oviductal epithelium in several vertebrates, suggesting a conserved function of Fu in the oviduct. In support of this, analysis of Fu‐deficient mouse oviducts uncovers a similar role of Fu in central pair construction and cilia orientation. We also demonstrate that Fu localizes to motile cilia and physically associates with kinesin Kif27 located at the cilium base and known central pair components Spag16 and Pcdp1. Conclusions: Our results delineate a novel pathway for central pair apparatus assembly and add important insight to the biogenesis and function of oviductal motile cilia. Developmental Dynamics 242:1307–1319, 2013. © 2013 Wiley Periodicals, Inc.
Identification of Proanthocyanidins from Litchi (Litchi chinensis Sonn.) Pulp by LC-ESI-Q-TOF-MS and Their Antioxidant Activity

Content of total proanthocyanidins as well as total phenolics, flavonoids, antioxidant activities were evaluated for litchi (Litchi chinensis Sonn.) pulp of 32 cultivars. One cultivar, Hemaoli, showed the highest total proanthocyanidins and total phenolics, and DPPH or ABTS radical scavenging activities. ESI-MS and NMR analysis of the Hemaoli pulp crude extracts (HPCE) showed that procyandins composed of (epi)catechin unites with degree of polymerization (DP) of 2–6 were dominant proanthocyanidins in HPCE. After the HPCE was fractionated by a Sephadex LH-20 column, 32 procyanidins were identified by LC-ESI-Q-TOF-MS in litchi pulp for the first time. Quantification of individual procyanidin in HPCE indicated that epicatechin, procyanidin B2, procyanidin C1 and A-type procyanidin trimer were the main procyanidins. The radical scavenging activities of different fractions of HPCE as well as six procyanidins standards were evaluated by both DPPH and ABTS assays. HPCE fractions showed similar antioxidant activities with those of Vc and six individual procyanidins, the IC50 of which ranged from 1.88 ± 0.01 to 2.82 ± 0.10 μg/ml for DPPH assay, and from 1.52 ± 0.17 to 2.71 ± 0.15 μg/ml for ABTS assay. Such results indicate that litchi cultivars rich in proanthocyanidins are good resources of dietary antioxidants and have the potential to contribute to human health.
Rapid conservation assessment for endangered species using habitat connectivity models

SUMMARY To avoid extinction of rare species in regions of active environmental change, strategic approaches are needed to manage remaining habitat. When observations of dispersal or metapopulation information are not available, habitat connectivity simulations may offer a valuable alternative source of information to assess threats and evaluate conservation options. For the Critically Endangered San Martin titi monkey (Callicebus oenanthe) in north central Peru, an updated distribution model was generated and land cover in the heavily deforested northern range of the species was mapped. The value of remaining forest fragments was characterized and threats from future land use change were assessed using complementary connectivity models. It is estimated that the species range is less than 14 000 km2. Remote sensing analysis reveals that at least 34% of lowland forest in the northern range has been lost, while nearly 95% of remaining habitat fragments are likely too small to support viable populations and less than 8% of this habitat lies within conservation areas. Areas with the highest modelled connectivity comprise only 10% of the remaining forest in the northern range and small patches may contribute disproportionately to movement; these lands represent opportunities for conservation and reforestation to prevent potentially significant impacts from future mining and urban development. This study prioritized remaining suitable habitat patches using modelled connectivity and local knowledge to gain insight into the status of an understudied species. This approach offers a relatively rapid method to identify potential land use conflicts, and to further focus research and locally appropriate conservation.
New strategies for lowering the costs of antiretroviral treatment and care for people with HIV/AIDS in the United Kingdom

In the UK, the annual cost of treatment and care for people with human immunodeficiency virus (HIV)/acquired immune deficiency virus (AIDS) rose by over 600% from £104 million in 1997 to £762 million in 2010; approximately two-thirds of the £762 million cost of treatment and care in 2010 was for the procurement of antiretrovirals and other related drugs. The number of people accessing care for HIV/AIDS rose from 22,000 in 2000 to 65,000 in 2009. Adoption of “test and treat” guidelines for treating all HIV-infected people with antiretrovirals would further increase the burden of costs. Given the current economic situation, there is now a new focus on strategies for treatment and care of people with HIV-1 infection which can maintain efficacy but at a lower cost. In this review, we propose three strategies which could potentially lower the costs of treatment and care, ie, stopping testing CD4 counts for patients with full HIV RNA suppression on antiretroviral treatment and recent CD4 counts above 350 cells/μL; more widespread use of generic antiretrovirals as replacements for patients currently taking patented versions; and use of darunavir-ritonavir monotherapy as a switch option for patients with full HIV RNA suppression on other antiretrovirals and no history of virological failure. However, it is important that high standards of clinical care are maintained despite cost-saving measures. Antiretrovirals with generic alternatives may have toxicity issues, eg, zidovudine and nevirapine. There could be ethical issues in starting patients on these drugs if they are currently tolerating other treatments. The use of darunavir-ritonavir monotherapy is not consistently recommended in international HIV treatment guidelines.