Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of oxidised oil and vitamin E on performance and some blood traits of heat-stressed male broilers

The present study was conducted so that the possible effects of thermally-oxidised dietary oil and vitamin E supplementation could be determined on the performance, lipid peroxidation, antioxidant defence system and some blood and meat quality traits of broilers. Broilers were fed grower diets containing fresh or oxidised oil, supplemented with and without vitamin E (200 mg/kg) from four to six weeks of age. Neither oxidised dietary oil nor vitamin E supplementation had any adverse effect on weight gain, feed consumption or feed conversion ratio. However, the broilers that received oxidised oil had lower levels of plasma cholesterol and triglyceride compared to the control. The glucose level was neither influenced by oxidised oil nor by vitamin E supplementation. The plasma malondialdehyde level increased slightly in broilers fed oxidised oil, indicating increased lipid peroxidation. Higher glutathione peroxidise (GSH–Px) activity observed in the broilers fed oxidised oil suggests greater oxidative stress. Vitamin E supplementation partly depressed GSH–Px activity in broilers fed oxidised oil. This depression in enzyme activity might be the result of homeostatic compensation. The uric acid concentration was not affected by oxidised oil and vitamin E supplementation. Feeding oxidised oil did not cause a marked discolouration in breast meat. Vitamin E supplementation had some beneficial effects on colour measurements. Keywords: Lipid peroxidation, oxidative stress, poultry, performance, meat colour
Molecular insights into the assembly and diversity of the outer core oligosaccharide in lipopolysaccharides from Escherichia coli and Salmonella

In the Enterobacteriaceae, the core oligosaccharide provides the junction between the highly conserved lipid A and the remarkably diverse polysaccharide O antigen. The basic structure of the inner (lipid A-proximal) core is well conserved, perhaps reflecting constraints imposed by its involvement in the structural integrity of the outer membrane. However, non-stoichiometric modifications do create some structural variants. The outer core may show more variation. Efforts to develop immunoprophylactic strategies based on the core oligosaccharide require a detailed understanding of core immunochemistry, the accessibility of specific epitopes in the LPS, and the distribution of specific structures within natural populations. The availability of sequences for the waa (core biosynthesis) loci and functional data for the gene products provide a molecular basis for the known structural diversity in Escherichia coli and Salmonella core oligosaccharide. Surveys of waa-locus organization have established the distribution of these core types in natural populations and have identified genetic variants that provide candidates for additional novel structures.
Effect of Ginkgo biloba (EGb 761) on Treadmill Walking Time Among Adults With Peripheral Artery Disease: A RANDOMIZED CLINICAL TRIAL

PURPOSE Medical therapies for treatment of peripheral artery disease (PAD) are limited. Ginkgo biloba has been reported to increase maximal and pain-free walking distance among patients with PAD; however, the evidence is inconsistent. The objective of this study was to compare the effects of 300 mg/d of Ginkgo biloba (EGb 761) versus placebo on treadmill walking time and related cardiovascular measures among patients with PAD. METHODS A double-blind, placebo-controlled, parallel design trial with a 4-month duration was used. Participants were 62 adults, aged 70 ± 8 years (mean ± SD), with claudication symptoms of PAD. The primary study outcomes were maximal and pain-free walking time on a treadmill. Secondary outcomes included flow-mediated vasodilation, a measure of antioxidant status as assessed by determining antibody levels to epitopes of oxidized low-density lipoprotein, and questionnaires addressing walking impairment and quality of life. RESULTS Maximal treadmill walking time increased by 20 ± 80 and 91 ± 242 seconds in the placebo and the EGb 761 groups, respectively (P = .12). Pain-free walking time increased by 15 ± 31 and 21 ± 43 seconds, respectively (P = .28). No significant differences were detected between groups for any of the secondary outcomes. CONCLUSIONS In older adults with PAD, Ginkgo biloba produced a modest but insignificant increase in maximal treadmill walking time and flow-mediated vasodilation. These data do not support the use of Ginkgo biloba as an effective therapy for PAD, although a longer duration of use should be considered in any future trials.
Post-stroke fatigue and its association with poor functional outcome after stroke in young adults

Introduction Post-stroke fatigue negatively influences short-term functional outcome in older stroke survivors. In young adults, in the midst of their active working and family life, this influence may even be more pronounced. However, there are only few studies on this topic in young patients with stroke. Therefore, we investigated the long-term prevalence of post-stroke fatigue in patients with a young transient ischaemic attack (TIA) or ischaemic stroke and its association with functional outcome. Methods This study is part of a large cohort study among 511 stroke survivors with a first-ever TIA or ischaemic stroke, aged 18–50 years. After a mean follow-up of 9.8 (SD 8.4) years, we assessed the presence of fatigue with the fatigue subscale of the Checklist Individual Strength questionnaire and functional outcome. Prevalence of fatigue between young patients with stroke and 147 stroke-free sex-matched and age-matched controls was compared. OR's for poor functional outcome on modified Rankin Score (mRS>2) and Instrumental Activities of Daily Living (IADL<8) and cognitive performance were calculated using logistic regression analysis. Results Of the young patients with stroke, 41% experienced symptoms of fatigue, versus 18.4% in controls (p 0.0005). Fatigue was associated with a poor functional outcome, as assessed by the mRS (OR 4.0 (95% CI 1.6 to 9.6), IADL (OR 2.2 (95% CI 1.1 to 4.6), and impairment in speed of information processing (OR 2.2 (95% CI 1.3 to 3.9). Conclusions Fatigue was very common in young stroke survivors and was associated with a poor functional outcome, even after almost a decade of follow-up.
Modélisation grande échelle de réseaux biologiques :vérification par contraintes booléennes de la cohérence des données. (Large-scale modeling of biological networks: checking data consistency using boolean constraints)

Les techniques de biologie moleculaire dites haut-debit permettent de mesurer un grand nombre de variables simultanement. Elles sont aujourd'hui couramment utilisees et produisent des masses importantes de donnees. Leur exploitation est compliquee par le bruit generalement observe dans les mesures, et ce d'autant plus que ces dernieres sont en general trop onereuses pour etre suffisamment reproduites. La question abordee dans cette these porte sur l'integration et l'exploitation des donnees haut-debit : chaque source de donnees mesurant un aspect du fonctionnement cellulaire, comment les combiner dans un modele et en tirer des conclusions pertinentes sur le plan biologique ? Nous introduisons un critere de consistance entre un modele graphique des regulations cellulaires et des donnees de deplacement d'equilibre. Nous montrons ensuite comment utiliser ce critere comme guide pour formuler des predictions ou proposer des corrections en cas d'incompatibilite. Ces differentes tâches impliquent la resolution de contraintes a variables sur domaines finis, pour lesquelles nous proposons deux approches complementaires. La premiere est basee sur la notion de diagramme de decision, qui est une structure de donnees utilisee pour la verification des circuits ; la deuxieme fait appel a des techniques recentes de programmation logique. L'utilisation de ces techniques est illustree avec des donnees reelles sur la bacterie "E. coli" et sur la levure. Les reseaux etudies comportent jusqu'a plusieurs milliers de genes et de regulations. Nous montrons enfin, sur ces donnees, comment notre critere de consistance nous permet d'arriver a des predictions robustes, ainsi que des corrections pertinentes du modele etudie.
Effective cognitive modeling in an intelligent tutoring system for cardiovascular physiology

CIRCSIM-TUTOR, an intelligent tutoring system (ITS), combines both the overlay approach (used to detect declarative errors) and a bug library (for recognizing misconceptions in problem solving). The student modes in most ITSs evaluate the student's current response and store an analysis. However, both earlier responses and immediate ones should be taken into account. It should also be recognized that students may show inconsistent behavior. Exploring initial implementation of CIRCSIM-TUTOR shows that this is a better approach to tutoring first-year medical students about the causal relationships between parameters in the cardiovascular system involved in regulating blood pressure using complex negative feedback process. <<ETX>>
Hamiltonian Monte Carlo estimator for abrupt motion tracking

In this paper, we propose a Hamiltonian Markov Chain Monte Carlo based tracking algorithm for abrupt motion tracking within the Bayesian filtering framework. In this tracking scheme, the object states are augmented by introducing a momentum item and the Hamiltonian Dynamics (HD) is integrated into the traditional MCMC based tracking method. The HD has some excellent properties which are crucial in constructing MCMC updates. A new object state is proposed through constructing a trajectory according to HD, implemented using the Leapfrog method. And the state proposed by the HD can keep a certain distant from the current object state but nevertheless have a high acceptance probability, which consequently bypass the slow exploration of the state space suffered by traditional random-walk proposal distribution. Experimental results reveal that our approach is efficient and effective in handling various types of abrupt motions compared to several alternatives.
Functions of Mature Mammalian Astrocytes: A Current View

Before the roles of normal, mature astrocytes in the mammalian CNS can be discussed, we first need to define these cells. A definition proposed here is that such a class is best defined as consisting of the protoplasmic and fibrous astrocytes of the gray and white matter, respectively, the Bergmann glia of the molecular layer of the cerebellum, and the Muller cells of the retina. It is concluded that the established properties and functions of these mature astrocytes are essential support for neuronal activity, in the sense of Claude Bernard’s principle of maintaining “la fixité du milieu intérieur. ” This milieu would be the extracellular space common to astrocytes and neurons. More specialized roles, such as the recently described “light guides” for retinal Muller cells can also be viewed as support and facilitation. The ECS is also, of course, common to all other neural cells, but here, I limit the discussion to perturbations of the ECS caused only by neuronal activities and the resolution of these perturbations by astrocytes, such as control of increases in extracellular K+, uptake of excitatory amino acids, and alterations in blood vessel diameter and therefore blood flow. It is also proposed how this fits into the current morphological picture for the protoplasmic astrocytes as having small cell bodies with up to 100,000 process endings that occupy separate territories on which the processes of neighboring astrocytes scarcely intrude.
Interactions between the mu opioid agonist DAMGO and substance P in regulation of the ventral pallidum

Substance P (SP) increases, and the mu‐specific opioid agonist DAMGO decreases neuronal firing within ventral pallidum (VP) of the basal forebrain. This study investigated a possibility that some VP neurons are oppositionally co‐regulated by SP and DAMGO using microiontophoresis combined with the extracellular electrophysiological recordings from chloral hydrate‐anesthetized rats. SP altered DAMGO's ejection current‐response curve, decreasing Emax and slope, and increasing the Ecu50 (ejection current level at which 50% of the maximal response was obtained). The modulation was observed even at low ejection current levels that, when applied alone, were not sufficient to alter neuronal activity (i.e., subthreshold). Also, DAMGO altered the Emax and slope of SP's ejection current‐response curve. DAMGO induced these effects even at subthreshold ejection current levels. The responses to each peptide were blocked by a receptor‐specific antagonist. These findings demonstrate that SP and mu‐activating opioids antagonize each other's effects on VP neuronal firing. Thus, they may interact as physiological antagonists in the regulation of VP‐associated functions. © 1996 Wiley‐Liss, Inc.
Clonidine and Cirazoline Inhibit Activation of Nicotinic Channels in PC‐12 Cells fn1

Clonidine and cirazoline bind with high affinity to a nonadrenergic site in the brain stem, the so-called imidazoline I1 receptor. Our aim was to determine the mechanism by which these receptors act and their possible linkage to signal-transducing heterotrimeric G-proteins. We examined the effects of clonidine and cirazoline on PC-12 cells, a neuronal cell line that is reported to possess the I1 site and have no alpha 2-adrenoceptors. In undifferentiated PC-12 cells loaded with the Ca2+ indicator dye fura-2, clonidine and cirazoline (10-100 microM) inhibited the increase in [Ca2+]i produced by nicotine (10 microM). This inhibition was not reversed by yohimbine (100 microM), and adrenaline and BHT 920 were ineffective at 100 microM. This effect was not inhibited by pretreatment with pertussis toxin (24 hours, 100 ng/ml) and not modulated by pretreatment with IBMX (100 microM). The nicotine-induced increase in [Ca2+]i is apparently due to Ca2+ entering via the intrinsic ion channel of the nicotinic acetylcholine receptor. Clonidine and cirazoline inhibited the inward current produced by nicotine (10 microM) as measured by the whole cell patch-clamp technique in differentiated PC-12 cells, recorded at a holding potential of -60 mV. In agreement with the results found with fura-2, inhibition of inward current was concentration dependent and not blocked by yohimbine (100 microM) or mimicked by adrenaline (100 microM). Pretreatment of PC-12 cells with pertussis toxin or infusion of GDP-beta-S (2 mM) via the patch pipette did not alter the inhibition of the nicotine-induced inward current by clonidine or cirazoline. Clonidine and cirazoline, but not adrenaline, displayed [3H]phencyclidine from Torpedo electroplaque membranes enriched in nicotinic acetylcholine receptors in a concentration-dependent manner (10-100 microM). Taken together, these results suggest that clonidine and cirazoline inhibit Na+ and Ca2+ entry through the nicotinic acetylcholine receptor via a nonadrenergic mechanism that is independent of G-proteins and cyclic nucleotides, presumably by direct blockade of the intrinsic ion channel of the nicotinic acetylcholine receptor.
Fluid‐deposited graphite and its geobiological implications in early Archean gneiss from Akilia, Greenland

Graphite, interpreted as altered bioorganic matter in an early Archean, ca. 3.83‐Ga‐old quartz‐amphibole‐pyroxene gneiss on Akilia Island, Greenland, has previously been claimed to be the earliest trace of life on Earth. Our petrographic and Raman spectroscopy data from this gneiss reveal the occurrence of graphitic material with the structure of nano‐crystalline to crystalline graphite in trails and clusters of CO2, CH4 and H2O bearing fluid inclusions. Irregular particles of graphitic material without a fluid phase, representing decrepitated fluid inclusions are common in such trails too, but occur also as dispersed individual or clustered particles. The occurrence of graphitic material associated with carbonic fluid inclusions is consistent with an abiologic, fluid deposited origin during a poly‐metamorphic history. The evidence for fluid‐deposited graphitic material greatly complicates any claim about remnants of early life in the Akilia rock.
Correcting for Noncompliance and Dependent Censoring in an AIDS Clinical Trial with Inverse Probability of Censoring Weighted (IPCW) Log‐Rank Tests

Summary. AIDS Clinical Trial Group (ACTG) randomized trial 021 compared the effect of bactrim versus aerosolized pentamidine (AP) as prophylaxis therapy for pneumocystis pneumonia (POP) in AIDS patients. Although patients randomized to the bactrim arm experienced a significant delay in time to POP, the survival experience in the two arms was not significantly different (p= .32). In this paper, we present evidence that bactrim therapy improves survival but that the standard intent‐to‐treat comparison failed to detect this survival advantage because a large fraction of the subjects either crossed over to the other therapy or stopped therapy altogether. We obtain our evidence of a beneficial bactrim effect on survival by artificially regarding the subjects as dependently censored at the first time the subject either stops or switches therapy; we then analyze the data with the inverse probability of censoring weighted Kaplan‐Meier and Cox partial likelihood estimators of Robins (1993, Proceedings of the Biopharmaceutical Section, American Statistical Association, pp. 24–33) that adjust for dependent censoring by utilizing data collected on time‐dependent prognostic factors.
SiteGuide: An Example-based Approach to Web Site Development Assistance

We present ‘SiteGuide’, a tool that helps web designers to decide which information will be included in a new web site and how the information will be organized. SiteGuide takes as input URLs of web sites from the same domain as the site the user wants to create. It automatically searches the pages of these example sites for common topics and common structural features. On the basis of these commonalities it creates a model of the example sites. The model can serve as a starting point for the new website. Also, it can be used to check whether important elements are missing in a concept version of the new site. Evaluation shows that SiteGuide is able to detect a large part of the common topics in example sites and to present these topics in an understandable form to its users.
Lock-Polymorphic Behaviour Inference for Deadlock Checking

Deadlocks are a common problem for concurrent programs with shared resources. According to the classic characterization from [2], a deadlocked state is marked by a number of processes forming a cycle where each process, unwilling to release its own resource, is waiting on the resource held by its neighbor. The inherent non-determinism make deadlocks, as other errors in the presence of concurrency, hard to detect and to reproduce. We present a static analysis using behavioral effects to detect deadlocks in a higher-order concurrent calculus. Deadlock freedom, an important safety property for concurrent programs, is a thread-global property, i.e., the blame for a deadlock in a defective program cannot be put on a single thread, it is two or more processes that share responsibility; the somewhat atypical situation, where a process forms a deadlock with itself, cannot occur in our setting, as we assume re-entrant locks. The approach presented in this paper works in two stages: in a first stage, an effect-type system uses a static behavioral abstraction of the codes’ behavior, concentrating on the lock interactions. To analyze the consequences on the global level, in particular for detecting deadlocks, the combined individual abstract thread behaviors are explored in the second stage. Two challenges need to be tackled to make such a framework applicable in practice. For the first stage on the thread local level, the static analysis must be able to derive the abstract behavior, not just check compliance of the code with a user-provided description. This is the problem of type and effect inference or reconstruction. As usual, the abstract behavior needs to over-approximate the concrete one which means, concrete and abstract description are connected by some simulation relation: everything the concrete system does, the abstract one can do as well (modulo some abstraction function relating the concrete and abstract states). For the second stage, exploring the (abstract) state space on the global level, obtaining finite abstractions is crucial. In our setting, there are four principal sources of infinity: the calculus, 1) allowing recursion, supports 2) dynamic thread creation, 3) dynamic lock creation, and 4) with re-entrant locks, the lock counters are unbounded. Our approach offers sound abstractions for the mentioned sources of unboundedness, except that we do not have an abstraction usable for deadlock detection in the presence of dynamic thread creation. We shortly present in a non-technical manner the ideas behind the abstraction.
Imatinib mesylate in T-cell large granular lymphocyte leukemia associated with chronic graft-versus-host disease

Polyclonal or oligoclonal T-cell large granular lymphocyte (T-LGL) expansion generally occurs in patients with viral infections, autoimmune diseases, malignancies [1], and solid organ [2] or allogeneic hematopoietic stem cell transplant (allo-HSCT) [3,4]. Particularly, Mohty et al. [4] documented T-LGL expansion in 3% of a wide cohort of patients following allo-HSCT. Typically the disorder is indolent, although in rare cases it may be aggressive [1,3]. When treatment is needed, immunosuppressive therapy can be attempted, with variable efficacy [5]. Recently, Yang and colleagues [6] demonstrated that an autocrine platelet-derived growth factor (PDGF) regulatory loop mediates survival of leukemic cells, suggesting that targeting of downstream components of PDGF signaling may be a potential therapy in T-LGL leukemia. Likewise, stimulatory antibodies against the PDGF receptor (PDGFR) have been found in patients developing chronic graftversus-host disease (cGvHD), and these antibodies trigger an intracellular loop involving extracellular signal-regulated kinases 1/2 (ERK1/2) [7]. In our experience, we have diagnosed T-LGL proliferation in 10 of 12 patients with cGvHD. Two of these patients have been successfully treated with imatinib mesylate (IM), a small molecule that antagonizes tyrosine kinases (TKs) involved in fibrotic pathways, including c-Abl and PDGFR [8]. The patients (both male, 39 and 57 years old) underwent allo-HSCT from human leukocyte antigen (HLA)-matched sibling donors for acute myeloid leukemia. After transplant, both patients suffered from sclerodermatous cGvHD associated with an expanded clonal population of CD3þ/CD47/ CD8þ/CD57þ T-cells of donor origin. Clonality was assessed by analyzing the rearrangement of the T-cell receptor (TCR) gamma gene (region VJ-A). Constitutive phosphorylation of ERK1/2, which could be a common signal transduction pathway in T-LGL and GvHD [7,9], was found in the peripheral blood mononuclear cell fraction of whole blood after 2 weeks in culture. In addition, the expression profiles of many genes implicated in apoptosis, including BCL2A1, CASP1, CASP6, EGR1, EGR2, FAS, FOS, TNF, and TNFRSF1A, were dysregulated. Because of their cGvHD, the patients received IM according to the trial ‘Imatinib mesylate in the treatment of refractory extensive cGvHD with scleroderma-like features’ (Eudract no. 2007001508-19). Interestingly, during IM treatment, both patients displayed progressive improvement of cutaneous sclerosis, clearance of the T-LGL clonotype, ERK inactivation, and modulation of genes involved in cell survival. After IM discontinuation, one patient maintained clinical and biological benefit for 8 months (time of last follow-up), while the other quickly experienced a worsening of cGvHD, with T-LGL re-expansion associated with monoclonality of TCR, ERK-autophosphorylation, and deregulation of proand anti-apoptotic gene transcripts. This second patient restarted IM, obtaining clinical and laboratory results similar to those observed after the