Miracle-dz/UniFAR-FTUs huggingface dataset:
Receptor Guanylyl Cyclases in Sensory Processing

Invertebrate models have generated many new insights into transmembrane signaling by cell-surface receptors. This review focuses on receptor guanylyl cyclases (rGCs) and describes recent advances in understanding their roles in sensory processing in the nematode, Caenorhabditis elegans. A complete analysis of the C. elegans genome elucidated 27 rGCs, an unusually large number compared with mammalian genomes, which encode 7 rGCs. Most C. elegans rGCs are expressed in sensory neurons and play roles in sensory processing, including gustation, thermosensation, olfaction, and phototransduction, among others. Recent studies have found that by producing a second messenger, guanosine 3′,5′-cyclic monophosphate, some rGCs act as direct sensor molecules for ions and temperatures, while others relay signals from G protein-coupled receptors. Interestingly, genetic and biochemical analyses of rGCs provide the first example of an obligate heterodimeric rGC. Based on recent structural studies of rGCs in mammals and other organisms, molecular mechanisms underlying activation of rGCs are also discussed in this review.
One-dimensional quantum transport in the presence of traps.

On etudie la probabilite de survie P(t) pour une particule se deplacant de maniere coherente sur une chaine a une dimension ordonnee contenant des pieges irreversibles places aleatoirement de concentration q. On considere deux modeles separes de processus de piegeage, en se focalisant sur la limite de longue duree de chacun
Parameterized average-case complexity of the hypervolume indicator

The hypervolume indicator (HYP) is a popular measure for the quality of a set of <i>n</i> solutions in ℜR<i><sup>d</sup></i>. We discuss its asymptotic worst-case runtimes and several lower bounds depending on different complexity-theoretic assumptions. Assuming that P ≠ NP, there is no algorithm with runtime poly(<i>n,d</i>). Assuming the exponential time hypothesis, there is no algorithm with runtime <i>n</i><i><sup>o</sup></i><sup>(<i>d</i>)</sup>. In contrast to these worst-case lower bounds, we study the average-case complexity of HYP for points distributed i.i. d. at random on a <i>d</i>-dimensional simplex. We present a general framework which translates any algorithm for HYP with worst-case runtime <i>n <sup>f</sup></i><sup>(<i>d</i>)</sup> to an algorithm with worst-case runtime <i>n <sup>f</sup></i><sup>(<i>d</i>)+1</sup> and fixed-parameter-tractable (FPT) average-case runtime. This can be used to show that HYP can be solved in expected time <i>O</i>(<i>d</i> <sup><i>d</i>2/2</sup>, <i>n</i> + <i>d, n</i><sup>2</sup>), which implies that HYP is FPT on average while it is W[1]-hard in the worst-case. For constant dimension <i>d</i> this gives an algorithm for HYP with runtime <i>O</i>(<i>n</i><sup>2</sup>) on average. This is the first result proving that HYP is asymptotically easier in the average case. It gives a theoretical explanation why most HYP algorithms perform much better on average than their theoretical worst-case runtime predicts.
The checkpoint clamp, Rad9-Rad1-Hus1 complex, preferentially stimulates the activity of apurinic/apyrimidinic endonuclease 1 and DNA polymerase β in long patch base excision repair

Growing evidence suggests that the Rad9-Rad1-Hus1 complex (the 9-1-1 complex), besides its functions in DNA damage sensing and signaling pathways, plays also a direct role in various DNA repair processes. Recent studies have demonstrated that the 9-1-1 complex physically and functionally interacts with several components of the base excision repair (BER) machinery namely DNA polymerase β (Pol β), flap endonuclease 1 (Fen 1), DNA ligase I (Lig I) and the MutY homologue of Schizosaccharomyces pombe. In this work, we found for the first time that the 9-1-1 complex interacts in vitro and in vivo with the apurinic/apyrimidinic endonuclease 1 (APE 1), an early component of BER, and can stimulate its AP-endonuclease activity. Moreover, we show that the 9-1-1 complex possesses a stimulatory effect on long patch base excision repair (LP-BER) reconstituted in vitro. The enhancement of LP-BER activity is due to the specific stimulation of the two early components of the repair machinery, namely APE 1 and Pol β, suggesting a hierarchy of interactions between the 9-1-1 complex and the BER proteins acting in the repairosome. Overall, our results indicate that the 9-1-1 complex is directly involved in LP-BER, thus providing a possible link between DNA damage checkpoints and BER.
A prospective study on the effectiveness of ketamine and diazepam used for conscious sedation in paediatric dental patients' management.

AIM The need to manage children using safe, effective and inexpensive conscious sedation materials and techniques in paediatric dentistry is high. This study evaluated the safety and effectiveness of a combination of low dose ketamine (5 mg/kg) and diazepam (0.2 mg/kg) used for conscious sedation in healthy children undergoing paediatric dental procedures at a paediatric dental outpatient clinic over a 3-year period. MATERIALS AND METHODS All children who were scheduled for conscious sedation between 2009 and 2012 were included in the study. All children received ketamine 5 mg/kg body weight in combination with diazepam 0.2 mg/kg body weight in a single oral dose for use as conscious sedation. Patients were considered sedated when the Ramsey Score was 2 or 3. Time of onset and duration of surgical procedures were recorded. Side effects during and after discharge were recorded. RESULTS Twenty five patients participated in the study. The effectiveness of the sedation was 84.0%. The mean time of onset of action was 10.5 ± 7.2 minutes. All cases that needed additional sedation needed this after 35? 36 minutes. Three cases (12.0%) developed high temperature in the night of the day of the procedure. There was a case (4.0%) of hallucination. CONCLUSION Ketamine and diazepam as medication for conscious sedation was considered effective. The duration of effectiveness appears to be 35 minutes. The combination is considered safe for use for conscious sedation in healthy paediatric dental outpatients undergoing minor oral surgical procedures.
Task Context and Frontal Lobe Activation in the Stroop Task

The ability to step outside a routine—to select a new response over a habitual one—is a cardinal function of the frontal lobes. A large body of neuroimaging work now exists pointing to increased activation within the anterior cingulate when stimuli evoke competing responses (incongruent trials) relative to when responses converge (congruent trials). However, lesion evidence that the ACC is necessary in this situation is inconsistent. We hypothesized that this may be a consequence of different task procedures (context) used in lesion and neuroimaging studies. The present study attempted to reconcile the lesion and the fMRI findings by having subjects perform clinical and experimental versions of the Stroop task during BOLD fMRI acquisition. We examined the relationship of brain activation patterns, specifically within the anterior cingulate and left dorsolateral frontal regions, to congruent and incongruent trial types in different task presentations or contexts. The results confirmed our hypothesis that ACC activity is relatively specific to unblocked–uncued incongruent Stroop conditions that have not been used in large neuropsychological studies. Moreover, the size of the behavioral Stroop interference effect was significantly correlated with activity in ACC and left dorsolateral regions, although in different directions. The current results are discussed in terms of previous proposals for the functional roles of these regions in activating, monitoring, and task setting, and the relation of these findings to the disparate reports in recent case series is considered.
Global spectrum fluctuations for the β-Hermite and β-Laguerre ensembles via matrix models

We study the global spectrum fluctuations for β-Hermite and β-Laguerre ensembles via the tridiagonal matrix models introduced previously by the present authors [J. Math. Phys. 43, 5830 (2002)], and prove that the fluctuations describe a Gaussian process on polynomials. We extend our results to slightly larger classes of random matrices.
Fatal Fentanyl Patch Misuse in a Hospitalized Patient with a Postmortem Increase in Fentanyl Blood Concentration

Opioid‐related mortality happens, even in healthcare settings. We describe serial postmortem fentanyl blood concentrations in a hospital inpatient who fatally abused transdermal fentanyl. This is a single‐patient case report. A 42‐year‐old man with lymphoma was started on transdermal fentanyl therapy while hospitalized for chronic abdominal pain. The patient was last seen awake 1.3 h prior to being found apneic and cyanotic. During the resuscitation attempt, a small square‐shaped film was removed from the patient's oropharynx. Femoral blood was collected 0.5 and 2 h postmortem, and the measured fentanyl concentration increased from 1.6 to 14 ng/mL. Study limitations include potential laboratory or collection errors and missing data. (i) Providers must be vigilant for signs of fentanyl patch abuse. (ii) Postmortem blood concentrations are not static postmortem, likely secondary to decreasing pH, increased aqueous solubility, and tissue redistribution, and are therefore unlikely to accurately represent antemortem blood concentrations.
Response to Comment on Hillis et al. The Relative and Combined Ability of High-Sensitivity Cardiac Troponin T and N-Terminal Pro-B-Type Natriuretic Peptide to Predict Cardiovascular Events and Death in Patients With Type 2 Diabetes. Diabetes Care 2014;37:295–303

We are grateful to Neuhold et al. (1) for their interest in our article (2) and agree with their insightful comments. They highlight an interesting juxtaposition in the field of preventative medicine. While there is increasing disquiet being aired by many regarding the overdiagnosis and overtreatment of some conditions in developed countries, at the same time guidelines for the prevention of cardiovascular disease in the general populations of these countries …
Coherent reaction

Side effects are both the essence and bane of imperative programming. The programmer must carefully coordinate actions to manage their side effects upon each other. Such coordination is complex, error-prone, and fragile. Coherent reaction is a new model of change-driven computation that coordinates effects automatically. State changes trigger events called reactions that in turn change other states. A coherent execution order is one in which each reaction executes before any others that are affected by its changes. A coherent order is discovered iteratively by detecting incoherencies as they occur and backtracking their effects. Unlike alternative solutions, much of the power of imperative programming is retained, as is the common sense notion of mutable state. Automatically coordinating actions lets the programmer express what to do, not when to do it. Coherent reactions are embodied in the Coherence language, which is specialized for interactive applications like those common on the desktop and web. The fundamental building block of Coherence is the dynamically typed mutable tree. The fundamental abstraction mechanism is the virtual tree, whose value is lazily computed, and whose behavior is generated by coherent reactions.
Effects of Feeding Levels of Starter on Weaning Age, Performance, Nutrient Digestibility and Health Parameters in Holstein Dairy Calves

To evaluate the effects of feeding four different levels of starter in male Holstein dairy calves, a completely randomized study was conducted, using 28 calves with initial body weight of 40.5±2.4 kg. The animals were fed iso-nitrogenous starter and were weaned when they consumed 350, 500, 650 and 800 g/d of starter for 3 d consecutively. Starter and water were available ad-libitum throughout the experiment. Body weight at pre-weaning (less than 5 wk) and post-weaning (8 wk) was lower in calves that received 350 g/d of starter than in the other treatments (p<0.05). Feed conversion ratio (FCR) was the highest among all treatments in pre-weaning period (p<0.05). Dry matter intake (DMI) at weaning and total DMI was higher in that calves received 800 g/d of starter compared with other treatments (p<0.05). Calves fed 350 and 500 g/d of starter were weaned earlier (p<0.05) and showed lower milk consumption (kg, DM) compared with other treatments whereas no significant difference was observed between calves fed 350 and 500 g/d of starter (p>0.05). Dry matter, organic matter and crude protein digestibilities were lower in calves that received 350 g/d of starter compared with other treatments (p<0.05). No differences were observed in acid detergent and neutral detergent fiber digestibility among all treatments (p>0.05). Treatments had no significant effect on time of starting rumination, respiratory score, and days of drug administration for pneumonia. There were no meaningful differences in feces, fecal odor scores, body temperature, and days of drug administration for diarrhea among all treatments (p>0.05). Total dry matter intake at the end of experiment showed no significant difference among calves fed 600 and 800 g/d of starter, but calves fed 350 and 500 g/d of starter showed more dry matter (DM) intake than calves in the 600 and 800 g/d groups (p<0.05).
Bounded Solutions of the Boltzmann Equation in the Whole Space

We construct bounded classical solutions of the Boltzmann equation in the whole space without specifying any limit behaviors at the spatial infinity and without assuming the smallness condition on initial data. More precisely, we show that if the initial data is non-negative and belongs to a uniformly local Sobolev space in the space variable with Maxwellian type decay property in the velocity variable, then the Cauchy problem of the Boltzmann equation possesses a unique non-negative local solution in the same function space, both for the cutoff and non-cutoff collision cross section with mild singularity. The known solutions such as solutions on the torus (space periodic solutions) and in the vacuum (solutions vanishing at the spatial infinity), and solutions in the whole space having a limit equilibrium state at the spatial infinity are included in our category.
On the use of formal techniques for analyzing dependable real-time protocols

The effective design of composite dependable and real time protocols entails demonstrating their proof of correctness and, in practice, the efficient delivery of services. We focus on these aspects of correctness and efficiency, specifically considering the real time aspects where the need is to ensure satisfaction of stringent timing and operational constraints. We establish the use of mathematically rigorous techniques such as formal methods (FMs) in not only providing for their traditional usage in establishing correctness checks, but also for their capability of assessing and analyzing timing requirements in dependable real time protocols. We present our perspectives in utilizing FMs in developing exact case analyses of fault tolerant and real time protocols. We discuss the insights obtained and flaws identified in the hand analysis over the process of formally analyzing and verifying the correctness of an existing fault tolerant real time scheduling protocol.
An Efficient Low Bit-Rate Information Embedding Costa Based Scheme using a Perceptual Model

In this paper, we propose an audio watermarking scheme based on the scalar Costa scheme specifically calibrated with a perceptual model allowing to increase the embedding power. For our study, this scheme is designed to be efficient for low bit-rate embedding with sufficient robustness to channel degradations. We present here the main characteristics of our scheme and the way for introducing perceptual models in such a Costa based watermarking scheme without introducing any noticeable artifacts. An evaluation of the robustness of the embedding system is also theoretically discussed by the way of the main channel attack : additive noise from low to high level. We illustrate its relevance in practice using Monte Carlo simulations.
Expanding Our Horizons in Teaching the Use of Intelligent Agents for Simulation Modeling of Next Generation Engineering Systems

Multi-agent systems are advocated as a model for designing complex, distributed engineering systems. Yet the practice of teaching the use of intelligent agents in modeling and simulation of next generation open, dynamic, adaptive, and intelligent engineering applications is still in its infancy. In this paper we present a unified and coherent framework for teaching a graduate level agent-directed simulation course for computer science and engineering students. The framework aims to: (1) promote extending our horizons by introducing multiple dimensions for the use of agents in simulation; (2) emphasize focusing on teaching the theory, methodology, and fundamental principles underlying the agent-based modeling framework, and (3) suggest a shift from a predictive modeling worldview toward a new computational epistemology perspective that advocates exploratory experimentation with agent-based models. Based on these premises, a synopsis of the structure, delivery strategy, and the underlying rationale for the design of the course are presented.
Nodulation of Thermopsis lupinoides by a Mesorhizobium huakuii Strain with a Unique nodA Gene in Kamtchatka, Russia

ABSTRACT Very little is known about rhizobia that form nodules on Thermopsis spp. We report the isolation of a Mesorhizobium huakuii strain with a unique nodA gene that form nodules on Thermopsis lupinoides in Kamtchatka, Russia. The isolate did not form nodules on Thermopsis chinensis or Thermopsis caroliniana, which suggests it may be host specific.
Emergent Diversity in an Open-Ended Evolving Virtual Community

Understanding the dynamics of biodiversity has become an important line of research in theoretical ecology and, in particular, conservation biology. However, studying the evolution of ecological communities under traditional modeling approaches based on differential calculus requires species' characteristics to be predefined, which limits the generality of the results. An alternative but less standardized methodology relies on intensive computer simulation of evolving communities made of simple, explicitly described individuals. We study here the formation, evolution, and diversity dynamics of a community of virtual plants with a novel individual-centered model involving three different scales: the genetic, the developmental, and the physiological scales. It constitutes an original attempt at combining development, evolution, and population dynamics (based on multi-agent interactions) into one comprehensive, yet simple model. In this world, we observe that our simulated plants evolve increasingly elaborate canopies, which are capable of intercepting ever greater amounts of light. Generated morphologies vary from the simplest one-branch structure of promoter plants to a complex arborization of several hundred thousand branches in highly evolved variants. On the population scale, the heterogeneous spatial structuration of the plant community at each generation depends solely on the evolution of its component plants. Using this virtual data, the morphologies and the dynamics of diversity production were analyzed by various statistical methods, based on genotypic and phenotypic distance metrics. The results demonstrate that diversity can spontaneously emerge in a community of mutually interacting individuals under the influence of specific environmental conditions.
Theoretical and Practical Arguments for Modeling Labor Supply as a Choice Among Latent Jobs

Models of labor supply derived from stochastic utility representations and discretized sets of feasible hours of work have gained popularity because they are more practical than the standard approaches based on marginal calculus. In this paper we argue that practicality is not the only feature that can be addressed by means of stochastic choice theory. This theory also offers a powerful framework for developing a more realistic model for labor supply choices, founded on individuals having preferences over jobs and facing restrictions on the choice of jobs and hours of work. We discuss and clarify how this modeling framework deviates from both the conventional discrete approach (Van Soest, 1995), as well as the standard textbook approach based on marginal calculus (Hausman, 1985). It is argued that a model based on job choice opens up for a more realistic representation of the choice environment, and consequently offers the possibility of conducting a richer set of simulations of alternative policies.
The immunologic effects of maraviroc intensification in treated HIV-infected individuals with incomplete CD4+ T-cell recovery: a randomized trial.

The CCR5 inhibitor maraviroc has been hypothesized to decrease T-cell activation in HIV-infected individuals, but its independent immunologic effects have not been established in a placebo-controlled trial. We randomized 45 HIV-infected subjects with CD4 counts <350 cells per mm(3) and plasma HIV RNA levels <48 copies per mL on antiretroviral therapy (ART) to add maraviroc vs placebo to their regimen for 24 weeks followed by 12 weeks on ART alone. Compared with placebo-treated subjects, maraviroc-treated subjects unexpectedly experienced a greater median increase in % CD38+HLA-DR+ peripheral blood CD8+ T cells at week 24 (+2.2% vs -0.7%, P = .014), and less of a decline in activated CD4+ T cells (P < .001). The % CD38+HLA-DR+ CD4+ and CD8+ T cells increased nearly twofold in rectal tissue (both P < .001), and plasma CC chemokine receptor type 5 (CCR5) ligand (macrophage-inflammatory protein 1β) levels increased 2.4-fold during maraviroc intensification (P < .001). During maraviroc intensification, plasma lipopolysaccharide declined, whereas sCD14 levels and neutrophils tended to increase in blood and rectal tissue. Although the mechanisms explaining these findings remain unclear, CCR5 ligand-mediated activation of T cells, macrophages, and neutrophils via alternative chemokine receptors should be explored. These results may have relevance for trials of maraviroc for HIV preexposure prophylaxis and graft-versus-host disease. This trial was registered at www.clinicaltrials. gov as #NCT00735072.