Miracle-dz/UniFAR-FTUs huggingface dataset:
Vitamin D Deficiency in a Multiethnic Healthy Control Cohort and Altered Immune Response in Vitamin D Deficient European-American Healthy Controls

Objective In recent years, vitamin D has been shown to possess a wide range of immunomodulatory effects. Although there is extensive amount of research on vitamin D, we lack a comprehensive understanding of the prevalence of vitamin D deficiency or the mechanism by which vitamin D regulates the human immune system. This study examined the prevalence and correlates of vitamin D deficiency and the relationship between vitamin D and the immune system in healthy individuals. Methods Healthy individuals (n = 774) comprised of European-Americans (EA, n = 470), African–Americans (AA, n = 125), and Native Americans (NA, n = 179) were screened for 25-hydroxyvitamin D [25(OH)D] levels by ELISA. To identify the most noticeable effects of vitamin D on the immune system, 20 EA individuals with severely deficient (<11.3 ng/mL) and sufficient (>24.8 ng/mL) vitamin D levels were matched and selected for further analysis. Serum cytokine level measurement, immune cell phenotyping, and phosphoflow cytometry were performed. Results Vitamin D sufficiency was observed in 37.5% of the study cohort. By multivariate analysis, AA, NA, and females with a high body mass index (BMI, >30) demonstrate higher rates of vitamin D deficiency (p<0.05). Individuals with vitamin D deficiency had significantly higher levels of serum GM-CSF (p = 0.04), decreased circulating activated CD4+ (p = 0.04) and CD8+ T (p = 0.04) cell frequencies than individuals with sufficient vitamin D levels. Conclusion A large portion of healthy individuals have vitamin D deficiency. These individuals have altered T and B cell responses, indicating that the absence of sufficient vitamin D levels could result in undesirable cellular and molecular alterations ultimately contributing to immune dysregulation.
Function and 3D Structure of the N-Glycans on Glycoproteins

Glycosylation is one of the most common post-translational modifications in eukaryotic cells and plays important roles in many biological processes, such as the immune response and protein quality control systems. It has been notoriously difficult to study glycoproteins by X-ray crystallography since the glycan moieties usually have a heterogeneous chemical structure and conformation, and are often mobile. Nonetheless, recent technical advances in glycoprotein crystallography have accelerated the accumulation of 3D structural information. Statistical analysis of “snapshots” of glycoproteins can provide clues to understanding their structural and dynamic aspects. In this review, we provide an overview of crystallographic analyses of glycoproteins, in which electron density of the glycan moiety is clearly observed. These well-defined N-glycan structures are in most cases attributed to carbohydrate-protein and/or carbohydrate-carbohydrate interactions and may function as “molecular glue” to help stabilize inter- and intra-molecular interactions. However, the more mobile N-glycans on cell surface receptors, the electron density of which is usually missing on X-ray crystallography, seem to guide the partner ligand to its binding site and prevent irregular protein aggregation by covering oligomerization sites away from the ligand-binding site.
Semantic resource management for the web: an e-learning application

Topics in education are changing with an ever faster pace. ELearning resources tend to be more and more decentralized. Users increasingly need to be able to use the resources of the web. For this, they should have tools for finding and organizing information in a decentralized way. In this paper, we show how an ontologybased tool suite allows to make the most of the resources available on the web.
The Electrophysiologic Time‐Course of Acute Myocardial Ischemia and the Effects of Early Coronary Artery Reperfusion

Bipolar potentials were recorded from intramural electrodes located within areas of acute myocardial ischemia in dogs. Alterations in bipolar potential electromotive force (EMF) and local activation times were measured at predetermined intervals up to 12 hours after coronary occlusion. Histochemical stains were used to correlate structural-biochemical changes with sites of electrophysiologic changes. In severely ischemic areas, bipolar potentials lost 50% of their preocclusion EMF within 30 min and 95% within six hours at which time all parameters stabilized. Lesser decreases in bipolar potential EMF were recorded in the peripheral areas of the infarct. Bipolar potential EMF increased at the junction of ischemic and normal myocardium. Activation time was delayed in ischemic areas but no correlation between the magnitude of delay and the degree of tissue ischemia could be established. Coronary reperfusion after 30 min, one hr, two hr and six hr of occlusion resulted in some return in bipolar potential EMF, decreasing as a function of duration between occlusion and reperfusion.Variation in the degree of ischemia of different zones of injury within an acute myocardial infarction, as well as a different response of those zones to the return of blood flow, was shown.
Bayesian gene/species tree reconciliation and orthology analysis using MCMC

MOTIVATION Comparative genomics in general and orthology analysis in particular are becoming increasingly important parts of gene function prediction. Previously, orthology analysis and reconciliation has been performed only with respect to the parsimony model. This discards many plausible solutions and sometimes precludes finding the correct one. In many other areas in bioinformatics probabilistic models have proven to be both more realistic and powerful than parsimony models. For instance, they allow for assessing solution reliability and consideration of alternative solutions in a uniform way. There is also an added benefit in making model assumptions explicit and therefore making model comparisons possible. For orthology analysis, uncertainty has recently been addressed using parsimonious reconciliation combined with bootstrap techniques. However, until now no probabilistic methods have been available. RESULTS We introduce a probabilistic gene evolution model based on a birth-death process in which a gene tree evolves 'inside' a species tree. Based on this model, we develop a tool with the capacity to perform practical orthology analysis, based on Fitch's original definition, and more generally for reconciling pairs of gene and species trees. Our gene evolution model is biologically sound (Nei et al., 1997) and intuitively attractive. We develop a Bayesian analysis based on MCMC which facilitates approximation of an a posteriori distribution for reconciliations. That is, we can find the most probable reconciliations and estimate the probability of any reconciliation, given the observed gene tree. This also gives a way to estimate the probability that a pair of genes are orthologs. The main algorithmic contribution presented here consists of an algorithm for computing the likelihood of a given reconciliation. To the best of our knowledge, this is the first successful introduction of this type of probabilistic methods, which flourish in phylogeny analysis, into reconciliation and orthology analysis. The MCMC algorithm has been implemented and, although not yet being in its final form, tests show that it performs very well on synthetic as well as biological data. Using standard correspondences, our results carry over to allele trees as well as biogeography.
Building an efficient P2P overlay for energy-level queries in sensor networks

After the debunking of some myths about why P2P overlays are not feasible in sensornets, many such solutions have been proposed. None of the existing P2P overlays for sensornets provide "Energy-Level Application and Services". On this purpose and based on the efficient P2P method presented in [16], we design a novel P2P overlay for Energy Level discovery in a sensornet, the so-called ELDT (Energy Level Distributed Tree). Sensor nodes are mapped to peers based on their energy level. As the energy levels change, the sensor nodes would have to move from one peer to another and this oparation is the most crucial for the efficient scalability of the proposed system. Similarly, as the energy level of a sensor node becomes extremelly low, that node may want to forward it's task to another node with the desired energy level. The adaptation of the P2P index presented in [16] quarantees the best-known query performance of the above operation. We experimentally verify this performance via an appropriate simulator we have designed for this purpose.
Short‐term effects in a reduced flow stretch: The case of the Antas River in South Brazil

The building of adduction channels (penstocks) that conduct water from reservoirs to turbines, which are located kilometres from the dam, is becoming common, optimizing the electricity generation in small dams. This design creates a river stretch with reduced discharge between the dam and the powerhouse. This study evaluates the short‐term impacts of the below‐dam decrease in river flow on fish assemblages. Samples were collected in the reduced flow stretch of the Castro Alves Hydropower Plant (Antas River, Rio Grande do Sul, Brazil) before the reservoir started operating (January 2008; mean discharge of 103.7 m3/s) and immediately after operation began (March 2008; mean discharge of 12.4 m3/s). Sampling was conducted in distinct habitats of the reduced flow stretch (slow waters—gillnets, sand beaches—seining nets, structured littoral—electrofishing, and fast waters—cast nets) with a strongly standardized effort. The attributes of the fish assemblages were not negatively affected by the flow reduction in any habitat sampled. However, distinct changes in the spatial structure were observed considering the different types of habitat predominantly used by the species, which represents an entire reorganization of the fish assemblages in the short term. It is fundamental that these short‐term aspects be considered in the licensing of hydropower plants in addition to the long‐term changes.
A pivotal role of phosphatidylinositol 3-kinase in delaying of methyl jasmonate-induced leaf senescence

ABSTRACT Phosphatidylinositol 3-kinase (PI3K) and its product PI3P are involved in plant development and stress responses. Our recent report has suggested that down-regulation of PI3K activity accelerated leaf senescence induced by methyl jasmonate (MeJA) and suppressed the activation of vacuolar H+-ATPase (V-ATPase). In vitro and in vivo experiment revealed that PI3K interact with VHA-B2. The inhibition of V-ATPase activity suppressed the vacuolar acidification and enhanced the stomatal opening, thereby accelerating MeJA-induced leaf senescence. It was shown that there is close relationship between PI3K and V-ATPase. However, the factor which initiates the PI3K-V-ATPase pathway needs further improvement, and the domain of VHA-B that binds to PI3K is still not clear enough. By using the Arabidopsis and MeJA as the research model, studies have been performed to investigate the upstream regulation of PI3K and downstream function of PI3K-V-ATPase pathway in the plant senescence.
EMG pattern analysis for patient-responsive control of FES in paraplegics for walker-supported walking

The use of electromyographic (EMG) pattern analysis to provide upper-motor-neuron paraplegics with patient-responsive control of FES (functional electrical stimulation) for the purpose of walker-supported walking is discussed. The system described uses above-lesion surface EMG signals to activate standing and walking functions in a patient-responsive manner. This system was been experimentally applied to paraplegics since early 1982. Below-lesion response-EMG control from the stimulated sites was added in 1987 to regulate stimuli levels in the face of fatigue. Although transcutaneous FES alone is being used the system is applicable in principle to implantable FES systems. <<ETX>>
Sept ans de suivi de la dynamique de la falaise de glace du lac du Miage (massif du Mont Blanc) par scanner laser terrestre

De juillet 2003 a juin 2010, douze leves par scanner laser terrestre ont ete realises au lac du Miage (massif du Mont Blanc, Italie) pour etudier la dynamique du systeme glacier/lac refletee par l'evolution de la falaise de glace. Du fait de la perturbation du systeme introduite par la vidange rapide du lac de septembre 2004, trois periodes de fonctionnement peuvent etre distinguees : (i) jusqu'en 2004 : fonctionnement 'normal' selon un cycle annuel alternant exondation hivernale du plancher de glace prolongeant la falaise et ablation estivale de celui-ci avec recul marque de la falaise, surtout a l'est ; (ii) 2005-2008 : decouplage entre l'ancienne falaise et le lac, autour duquel une nouvelle se reforme progressivement, plus reduite ; (iii) depuis 2008 : retour au fonctionnement " normal ", avec une extension du lac qui reste reduite.
Benefits of Rebuilding Global Marine Fisheries Outweigh Costs

Global marine fisheries are currently underperforming, largely due to overfishing. An analysis of global databases finds that resource rent net of subsidies from rebuilt world fisheries could increase from the current negative US$13 billion to positive US$54 billion per year, resulting in a net gain of US$600 to US$1,400 billion in present value over fifty years after rebuilding. To realize this gain, governments need to implement a rebuilding program at a cost of about US$203 (US$130–US$292) billion in present value. We estimate that it would take just 12 years after rebuilding begins for the benefits to surpass the cost. Even without accounting for the potential boost to recreational fisheries, and ignoring ancillary and non-market values that would likely increase, the potential benefits of rebuilding global fisheries far outweigh the costs.
Water, land, fire, and forest: Multi‐scale determinants of rainforests in the Australian monsoon tropics

Abstract The small rainforest fragments found in savanna landscapes are powerful, yet often overlooked, model systems to understand the controls of these contrasting ecosystems. We analyzed the relative effect of climatic variables on rainforest density at a subcontinental level, and employed high‐resolution, regional‐level analyses to assess the importance of landscape settings and fire activity in determining rainforest density in a frequently burnt Australian savanna landscape. Estimates of rainforest density (ha/km2) across the Northern Territory and Western Australia, derived from preexisting maps, were used to calculate the correlations between rainforest density and climatic variables. A detailed map of the northern Kimberley (Western Australia) rainforests was generated and analyzed to determine the importance of geology and topography in controlling rainforests, and to contrast rainforest density on frequently burnt mainland and nearby islands. In the northwestern Australian, tropics rainforest density was positively correlated with rainfall and moisture index, and negatively correlated with potential evapotranspiration. At a regional scale, rainforests showed preference for complex topographic positions and more fertile geology. Compared with mainland areas, islands had significantly lower fire activity, with no differences between terrain types. They also displayed substantially higher rainforest density, even on level terrain where geomorphological processes do not concentrate nutrients or water. Our multi‐scale approach corroborates previous studies that suggest moist climate, infrequent fires, and geology are important stabilizing factors that allow rainforest fragments to persist in savanna landscapes. These factors need to be incorporated in models to predict the future extent of savannas and rainforests under climate change.
Music Effects on EEG in Intrusive and Withdrawn Mothers with Depressive Symptoms

Abstract The EEG patterns of 48 intrusive and withdrawn mothers with depressive symptoms were assessed following a 20-minute music session to determine if the music had mood-altering effects. Half the mothers listened to classical music while half listened to rock music. Intrusive mothers were expected to have more positive responses and more symmetrical EEG following the calming classical music, while withdrawn mothers were expected to have a more positive response and symmetrical EEG following the energizing rock music. Although more positive EEGs were noted for rock music in both groups, only the withdrawn mothers showed a significant change in EEG toward symmetry following rock music, and only the intrusive mothers showed a decrease in cortisol levels following the rock music. Their State Anxiety Inventory (STAI) anxiety levels also decreased, while the Profile of Mood States (POMS) depressed mood levels decreased significantly for all four groups following music.
Cost of Antibiotic Resistance and the Geometry of Adaptation

The distribution of effects of beneficial mutations is key to our understanding of biological adaptation. Yet, empirical estimates of this distribution are scarce, and its functional form is largely unknown. Theoretical models of adaptation predict that the functional form of this distribution should depend on the distance to the optimum. Here, we estimate the rate and distribution of adaptive mutations that compensate for the effect of a single deleterious mutation, which causes antibiotic resistance. Using a system with multiple molecular markers, we estimate the distribution of fitness effects of mutations at two distances from the adaptive peak in 60 populations of Escherichia coli. We find that beneficial mutations, which can contribute to compensatory evolution, occur at very high rates, of the order of 10−5 per genome per generation and can be detected within a few tens of generations. They cause an average fitness increase of 2.5% and 3.6%, depending on the cost of resistance, which is expected under Fisher's geometrical model of adaptation. Moreover, we provide the first description of the distribution of beneficial mutations, segregating during the process of compensatory evolution, to antibiotic resistances bearing different costs. Hence, these results have important implications to understanding the spread and maintenance of antibiotic resistance in bacteria.
Phase I Oncology Studies: Evidence That in the Era of Targeted Therapies Patients on Lower Doses Do Not Fare Worse

Purpose: To safely assess new drugs, cancer patients in initial cohorts of phase I oncology studies receive low drug doses. Doses are successively increased until the maximum tolerated dose (MTD) is determined. Because traditional chemotherapy is often more effective near the MTD, ethical concerns have been raised about administration of low drug doses to phase I patients. However, a substantial portion of oncology trials now investigate targeted agents, which may have different dose-response relationships than cytotoxic chemotherapies. Experimental Design: Twenty-four consecutive trials treating 683 patients between October 1, 2004, and June 30, 2008, at MD Anderson Cancer Center were analyzed. Patients were assigned to a low-dose (≤25% MTD), medium-dose (25-75% MTD), or high-dose (≥75% MTD) group, and groups were compared for response rate, time-to-treatment failure, progression-free survival, overall survival, and toxicity. To remove negatively biasing data from the high-dose group, in a second analysis, patients treated above the MTD were excluded (high-dose group, 75-100% MTD). Of the 683 patients, 97.7% received targeted agents. Results: Even when excluding patients above the MTD, there was an early trend favoring the low- versus high-dose group in time-to-treatment failure, with 32.9% versus 25.2% of patients on therapy at 3 months (P = 0.08). In addition, the low-dose group fared at least as well as the other groups in all other outcomes, including response rate, progression-free survival, overall survival, and toxicity. Conclusions: These data may help alleviate concerns that patients who receive low drug doses on contemporary phase I oncology trials fare worse and suggest targeted agents may have different dose-response relationships than cytotoxic chemotherapies. Clin Cancer Res; 16(4); 1289–97
Mechanisms of mechanical signaling in development and disease

The responses of cells to chemical signals are relatively well characterized and understood. Cells also respond to mechanical signals in the form of externally applied force and forces generated by cell–matrix and cell–cell contacts. Many features of cell function that are generally considered to be under the control of chemical stimuli, such as motility, proliferation, differentiation and survival, can also be altered by changes in the stiffness of the substrate to which the cells are adhered, even when their chemical environment remains unchanged. Many examples from clinical and whole animal studies have shown that changes in tissue stiffness are related to specific disease characteristics and that efforts to restore normal tissue mechanics have the potential to reverse or prevent cell dysfunction and disease. How cells detect stiffness is largely unknown, but the cellular structures that measure stiffness and the general principles by which they work are beginning to be revealed. This Commentary highlights selected recent reports of mechanical signaling during disease development, discusses open questions regarding the physical mechanisms by which cells sense stiffness, and examines the relationship between studies in vitro on flat substrates and the more complex three-dimensional setting in vivo.
Maximum likelihood network topology identification from edge-based unicast measurements

Network tomography is a process for inferring "internal" link-level delay and loss performance information based on end-to-end (edge) network measurements. These methods require knowledge of the network topology; therefore a first crucial step in the tomography process is topology identification. This paper considers the problem of discovering network topology solely from host-based, unicast measurements, without internal network cooperation. First, we introduce a novel delay-based measurement scheme that does not require clock synchronization, making it more practical than other previous proposals. In contrast to methods that rely on network cooperation , our methodology has the potential to identify layer two elements (provided they are logical topology branching points and induce some measurable delay). Second, we propose a maximum penalized likelihood criterion for topology identification. This is a global optimality criterion, in contrast to other recent proposals for topology identification that employ suboptimal, pair-merging strategies. We develop a novel Markov Chain Monte Carlo (MCMC) procedure for rapid determination of the most likely topologies. The performance of our new probing scheme and identification algorithm is explored through simulation and Internet experiments.