Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient Reconstruction of Piecewise Constant Images Using Nonsmooth Nonconvex Minimization

We consider the restoration of piecewise constant images where the number of the regions and their values are not fixed in advance, with a good difference of piecewise constant values between neighboring regions, from noisy data obtained at the output of a linear operator (e.g., a blurring kernel or a Radon transform). Thus we also address the generic problem of unsupervised segmentation in the context of linear inverse problems. The segmentation and the restoration tasks are solved jointly by minimizing an objective function (an energy) composed of a quadratic data-fidelity term and a nonsmooth nonconvex regularization term. The pertinence of such an energy is ensured by the analytical properties of its minimizers. However, its practical interest used to be limited by the difficulty of the computational stage which requires a nonsmooth nonconvex minimization. Indeed, the existing methods are unsatisfactory since they (implicitly or explicitly) involve a smooth approximation of the regularization term and often get stuck in shallow local minima. The goal of this paper is to design a method that efficiently handles the nonsmooth nonconvex minimization. More precisely, we propose a continuation method where one tracks the minimizers along a sequence of approximate nonsmooth energies $\{J_\eps\}$, the first of which being strictly convex and the last one the original energy to minimize. Knowing the importance of the nonsmoothness of the regularization term for the segmentation task, each $J_\eps$ is nonsmooth and is expressed as the sum of an $\ell_1$ regularization term and a smooth nonconvex function. Furthermore, the local minimization of each $J_{\eps}$ is reformulated as the minimization of a smooth function subject to a set of linear constraints. The latter problem is solved by the modified primal-dual interior point method, which guarantees the descent direction at each step. Experimental results are presented and show the effectiveness and the efficiency of the proposed method. Comparison with simulated annealing methods further shows the advantage of our method.
The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs

Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNALys3, to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3′-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5′-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNALys3. The importance of individual and combined anticodon modifications to the tRNA/HIV-1 Loop I RNA's interaction was determined. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. The modifications 2-thiouridine, s2U34, and pseudouridine, Ψ39, appreciably stabilized the interaction of the anticodon region with the viral subtype G and B RNAs. The structure of the duplex results in two coaxially stacked A-form RNA stems separated by two mismatched base pairs, U162•Ψ39 and G163•A38, that maintained a reasonable A-form helix diameter. The tRNA's s2U34 stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's Ψ39 stabilized the adjacent mismatched pairs.
Acute Lymphoblastic Leukemia in Early Childhood as the Presenting Sign of Ataxia-Telangiectasia Variant

Ataxia-telangiectasia (A-T), an autosomal recessive disorder is characterized by progressive neurodegeneration, immunodeficiency, sensitivity to ionizing radiation, and predisposition to cancer, especially to lymphoid malignancies. A-T variant is characterized by a milder clinical phenotype and is caused by missense or leaky splice site mutations that produce residual ataxia telangiectasia mutated (ATM) kinase activity. Lymphoid malignancy can precede the diagnosis of A-T, particularly in young children with mild neurological symptoms. We studied a consanguineous family with four A-T variant patients, three of them developed T-ALL at a young age before the diagnosis of A-T was established. ATM mutation analysis detected two new missense mutations both within exon 12: c.1514T>C and c.1547T>C. All four patients are homozygous for the two mutations, while their parents are heterozygous for the mutations. ATM protein level was low in all patients and the response to the radiomimetic agent, neocarzinostatin, was reduced. Leukemic presentation in a young age in three members of consanguineous family led to the identification of a new missense mutation in the ATM gene. The diagnosis of A-T or A-T variant should be considered in children with neurological abnormalities who develop T-ALL at a young age.
Readmission Rates and Long-Term Hospital Costs Among Survivors of an In-Hospital Cardiac Arrest

Background—Although an in-hospital cardiac arrest is common, little is known about readmission patterns and an inpatient resource use among survivors of an in-hospital cardiac arrest. Methods and Results—Within a large national registry, we examined long-term inpatient use among 6972 adults aged ≥65 years who survived an in-hospital cardiac arrest. We examined 30-day and 1-year readmission rates and inpatient costs, overall and by patient demographics, hospital disposition (discharge destination), and neurological status at discharge. The mean age was 75.8±7.0 years, 56% were men, and 12% were black. There were a total of 2005 readmissions during the first 30 days (cumulative incidence rate, 35 readmissions/100 patients; 95% confidence interval, 33–37) and 8751 readmissions at 1 year (cumulative incidence rate, 185 readmissions/100 patients; 95% confidence interval, 177–190). Overall, mean inpatient costs were $7741±$2323 at 30 days and $18 629±$9411 at 1 year. Thirty-day inpatient costs were higher in patients of younger age (≥85 years, $6052 [reference]; 75–84 years, $7444 [adjusted cost ratio, 1.23; 1.06–1.42; 65–74 years, $8291 [adjusted cost ratio, 1.37; 1.19–1.59; both P<0.001) and black race (whites, $7413; blacks, $9044; adjusted cost ratio, 1.22; 1.05–1.42; P<0.001), as well as those discharged with severe neurological disability or to skilled nursing or rehabilitation facilities. These differences in resource use persisted at 1 year and were largely because of higher readmission rates. Conclusions—Survivors of an in-hospital cardiac arrest have frequent readmissions and high follow-up inpatient costs. Readmissions and inpatient costs were higher in certain subgroups, including patients of younger age and black race.
Role of Tetanus Neurotoxin Insensitive Vesicle-Associated Membrane Protein (Ti-Vamp) in Vesicular Transport Mediating Neurite Outgrowth

How vesicular transport participates in neurite outgrowth is still poorly understood. Neurite outgrowth is not sensitive to tetanus neurotoxin thus does not involve synaptobrevin-mediated vesicular transport to the plasma membrane of neurons. Tetanus neurotoxin-insensitive vesicle-associated membrane protein (TI-VAMP) is a vesicle-SNARE (soluble N-ethylmaleimide-sensitive fusion protein [NSF] attachment protein [SNAP] receptor), involved in transport to the apical plasma membrane in epithelial cells, a tetanus neurotoxin-resistant pathway. Here we show that TI-VAMP is essential for vesicular transport-mediating neurite outgrowth in staurosporine-differentiated PC12 cells. The NH2-terminal domain, which precedes the SNARE motif of TI-VAMP, inhibits the association of TI-VAMP with synaptosome-associated protein of 25 kD (SNAP25). Expression of this domain inhibits neurite outgrowth as potently as Botulinum neurotoxin E, which cleaves SNAP25. In contrast, expression of the NH2-terminal deletion mutant of TI-VAMP increases SNARE complex formation and strongly stimulates neurite outgrowth. These results provide the first functional evidence for the role of TI-VAMP in neurite outgrowth and point to its NH2-terminal domain as a key regulator in this process.
Hypoxia tolerance in elasmobranchs. I. Critical oxygen tension as a measure of blood oxygen transport during hypoxia exposure

SUMMARY The critical O2 tension of whole-animal O2 consumption rate (), or Pcrit, is the water PO2 (PwO2) at which an animal transitions from an oxyregulator to an oxyconformer. Although Pcrit is a popular measure of hypoxia tolerance in fishes because it reflects the capacity for O2 uptake from the environment at low PwO2, little is known about the interrelationships between Pcrit and blood O2 transport characteristics and increased use of anaerobic metabolism during hypoxia exposure in fishes, especially elasmobranchs. We addressed this knowledge gap using progressive hypoxia exposures of two elasmobranch species with differing hypoxia tolerance. The Pcrit of the hypoxia-tolerant epaulette shark (Hemiscyllium ocellatum, 5.10±0.37 kPa) was significantly lower than that of the comparatively hypoxia-sensitive shovelnose ray (Aptychotrema rostrata, 7.23±0.40 kPa). Plasma [lactate] was elevated above normoxic values at around Pcrit in epaulette sharks, but increased relative to normoxic values at PwO2 below Pcrit in shovelnose rays, providing equivocal support for the hypothesis that Pcrit is associated with increased anaerobic metabolism. The , arterial PO2 and arterial blood O2 content (CaO2) were similar between the two species under normoxia and decreased in both species with progressive hypoxia, but as PwO2 declined, epaulette sharks had a consistently higher and CaO2 than shovelnose rays, probably due to their significantly greater in vivo haemoglobin (Hb)–O2 binding affinity (in vivo Hb–O2 P50=4.27±0.57 kPa for epaulette sharks vs 6.35±0.34 kPa for shovelnose rays). However, at PwO2 values representing the same percentage of each species' Pcrit (up to ∼175% of Pcrit), Hb–O2 saturation and CaO2 were similar between species. These data support the hypothesis that Hb–O2 P50 is an important determinant of Pcrit and suggest that Pcrit can predict Hb–O2 saturation and CaO2 during hypoxia exposure, with a lower Pcrit being associated with greater O2 supply at a given PwO2 and consequently better hypoxia tolerance. Thus, Pcrit is a valuable predictor of environmental hypoxia tolerance and hypoxia exposures standardized at a given percentage of Pcrit will yield comparable levels of arterial hypoxaemia, facilitating cross-species comparisons of responses to hypoxia.
[Pyr1]Apelin-13(1–12) Is a Biologically Active ACE2 Metabolite of the Endogenous Cardiovascular Peptide [Pyr1]Apelin-13

Aims: Apelin is a predicted substrate for ACE2, a novel therapeutic target. Our aim was to demonstrate the endogenous presence of the putative ACE2 product [Pyr1]apelin-13(1–12) in human cardiovascular tissues and to confirm it retains significant biological activity for the apelin receptor in vitro and in vivo. The minimum active apelin fragment was also investigated. Methods and Results: [Pyr1]apelin-13 incubated with recombinant human ACE2 resulted in de novo generation of [Pyr1]apelin-13(1–12) identified by mass spectrometry. Endogenous [Pyr1]apelin-13(1–12) was detected by immunostaining in human heart and lung localized to the endothelium. Expression was undetectable in lung from patients with pulmonary arterial hypertension. In human heart [Pyr1]apelin-13(1–12) (pKi = 8.04 ± 0.06) and apelin-13(F13A) (pKi = 8.07 ± 0.24) competed with [125I]apelin-13 binding with nanomolar affinity, 4-fold lower than for [Pyr1]apelin-13 (pKi = 8.83 ± 0.06) whereas apelin-17 exhibited highest affinity (pKi = 9.63 ± 0.17). The rank order of potency of peptides to inhibit forskolin-stimulated cAMP was apelin-17 (pD2 = 10.31 ± 0.28) > [Pyr1]apelin-13 (pD2 = 9.67 ± 0.04) ≥ apelin-13(F13A) (pD2 = 9.54 ± 0.05) > [Pyr1]apelin-13(1–12) (pD2 = 9.30 ± 0.06). The truncated peptide apelin-13(R10M) retained nanomolar potency (pD2 = 8.70 ± 0.04) but shorter fragments exhibited low micromolar potency. In a β-arrestin recruitment assay the rank order of potency was apelin-17 (pD2 = 10.26 ± 0.09) >> [Pyr1]apelin-13 (pD2 = 8.43 ± 0.08) > apelin-13(R10M) (pD2 = 8.26 ± 0.17) > apelin-13(F13A) (pD2 = 7.98 ± 0.04) ≥ [Pyr1]apelin-13(1–12) (pD2 = 7.84 ± 0.06) >> shorter fragments (pD2 < 6). [Pyr1]apelin-13(1–12) and apelin-13(F13A) contracted human saphenous vein with similar sub-nanomolar potencies and [Pyr1]apelin-13(1–12) was a potent inotrope in paced mouse right ventricle and human atria. [Pyr1]apelin-13(1–12) elicited a dose-dependent decrease in blood pressure in anesthetized rat and dose-dependent increase in forearm blood flow in human volunteers. Conclusions: We provide evidence that ACE2 cleaves [Pyr1]apelin-13 to [Pyr1]apelin-13(1–12) and this cleavage product is expressed in human cardiovascular tissues. We have demonstrated biological activity of [Pyr1]apelin-13(1–12) at the human and rodent apelin receptor in vitro and in vivo. Our data show that reported enhanced ACE2 activity in cardiovascular disease should not significantly compromise the beneficial effects of apelin based therapies for example in PAH.
Nonnegative approximations of nonnegative tensors

We study the decomposition of a nonnegative tensor into a minimal sum of outer product of nonnegative vectors and the associated parsimonious naïve Bayes probabilistic model. We show that the corresponding approximation problem, which is central to nonnegative PARAFAC, will always have optimal solutions. The result holds for any choice of norms and, under a mild assumption, even Brègman divergences. Copyright © 2009 John Wiley & Sons, Ltd.
Reduced inflammation in expanding populations of a neotropical bird species

Abstract The loss of regulating agents such as parasites is among the most important changes in biotic interactions experienced by populations established in newly colonized areas. Under a relaxed parasite pressure, individuals investing less in costly immune mechanisms might experience a selective advantage and become successful colonizers as they re‐allocate resources to other fitness‐related traits. Accordingly, a refinement of the evolution of increased competitive ability (EICA) hypothesis proposed that immunity of invasive populations has evolved toward a reduced investment in innate immunity, the most costly component of immunity, and an increased humoral immunity that is less costly. Biogeographical approaches comparing populations between native and expansion ranges are particularly relevant in exploring this issue, but remain very scarce. We conducted a biogeographical comparison between populations of Spectacled Thrush (Turdus nudigenis) from the native area (South America) and from the expansion range (Caribbean islands). First, we compared haemosporidian prevalence and circulating haptoglobin (an acute‐phase protein produced during inflammation). Second, we challenged captive birds from both ranges with Escherichia coli lipopolysaccharides (LPS) and measured postchallenge haptoglobin production and body mass change. Birds from the expansion range showed lower haemosporidian prevalence and lower levels of haptoglobin than birds from the native range. In addition, the inflammation elicited by LPS injection and its associated cost in terms of body mass loss were lower in birds from the expansion range than in birds from the native range. In accordance with the enemy release hypothesis, our results suggest that range expansion is associated with a reduced infection risk. Our study also supports the hypothesis that individuals from newly established populations have evolved mechanisms to dampen the inflammatory response and are in accordance with one prediction of the refined EICA hypothesis, proposed to understand biological invasions.
Exploring core based tree (CBT) in WDM networks

In this paper, we explore the routing and wavelength assignment problem for the CBT service in a WDM network where k sources need to send data to a common core node. We formally model the problem as a problem of finding k shortest lightpaths from sources to the core subject to the constraint of wavelength collision free. We define and study several subproblems, each addressing a different objective. For the feasibility and the minimum total cost problems of k shortest lightpaths, we show how the classical network flow algorithms can be modified and applied efficiently on the network flow model constructed on the transformed wavelength graph. For the minimum max-cost problem, we prove its NP-completeness and propose two efficient heuristic algorithms. Simulation results show that the proposed heuristic algorithms perform very close to the calculated lower bounds.
Tracking the Time-Varying Cortical Connectivity Patterns by Adaptive Multivariate Estimators

The directed transfer function (DTF) and the partial directed coherence (PDC) are frequency-domain estimators that are able to describe interactions between cortical areas in terms of the concept of Granger causality. However, the classical estimation of these methods is based on the multivariate autoregressive modelling (MVAR) of time series, which requires the stationarity of the signals. In this way, transient pathways of information transfer remains hidden. The objective of this study is to test a time-varying multivariate method for the estimation of rapidly changing connectivity relationships between cortical areas of the human brain, based on DTF/PDC and on the use of adaptive MVAR modelling (AMVAR) and to apply it to a set of real high resolution EEG data. This approach will allow the observation of rapidly changing influences between the cortical areas during the execution of a task. The simulation results indicated that time-varying DTF and PDC are able to estimate correctly the imposed connectivity patterns under reasonable operative conditions of signal-to-noise ratio (SNR) ad number of trials. An SNR of Ave and a number of trials of at least 20 provide a good accuracy in the estimation. After testing the method by the simulation study, we provide an application to the cortical estimations obtained from high resolution EEG data recorded from a group of healthy subject during a combined foot-lips movement and present the time-varying connectivity patterns resulting from the application of both DTF and PDC. Two different cortical networks were detected with the proposed methods, one constant across the task and the other evolving during the preparation of the joint movement.
On the Maximum Tolerable Noise for Reliable Computation by Formulas

It is shown that if a formula is constructed from noisy 2-input NAND gates, with each gate failing independently with probability E, then reliable computation can or cannot take place according as /spl epsiv/ is less than or greater than /spl epsiv//sub 0/=(3-/spl radic/7)/4=0.08856.
Investigating combination HIV prevention: isolated interventions or complex system

Treatment as prevention has mobilized new opportunities in preventing HIV transmission and has led to bold new UNAIDS targets in testing, treatment coverage and transmission reduction. These will require not only an increase in investment but also a deeper understanding of the dynamics of combining behavioural, biomedical and structural HIV prevention interventions. High‐income countries are making substantial investments in combination HIV prevention, but is this investment leading to a deeper understanding of how to combine interventions? The combining of interventions involves complexity, with many strategies interacting with non‐linear and multiplying rather than additive effects.
NIST Cloud Computing Reference Architecture

This paper presents the first version of the NIST Cloud Computing Reference Architecture (RA). This is a vendor neutral conceptual model that concentrates on the role and interactions of the identified actors in the cloud computing sphere. Five primary actors were identified - Cloud Service Consumer, Cloud Service Provider, Cloud Broker, Cloud Auditor and Cloud Carrier. Their roles and activities are discussed in this report. A primary goal for generating this model was to give the United States Government (USG) a method for understanding and communicating the components of a cloud computing system for Federal IT executives, Program Managers and IT procurement officials.
Extended X-Ray Study of M49: The Frontier of the Virgo Cluster

The M49 group, residing outside the virial radius of the Virgo cluster, is falling onto the cluster from the south. We report results from deep XMM-Newton mosaic observations of M49. Its hot gas temperature is 0.8 keV at the group center and rises to 1.5 keV beyond the brightest group galaxy (BGG). The group gas extends to radii of ∼300 kpc to the north and south. The observations reveal a cold front ∼20 kpc north of the BGG center and an X-ray-bright stripped tail 70 kpc long and 10 kpc wide to the southwest of the BGG. We argue that the atmosphere of the infalling group was slowed by its encounter with the Virgo cluster gas, causing the BGG to move forward subsonically relative to the group gas. We measure declining temperature and metallicity gradients along the stripped tail. The tail gas can be traced back to the cooler and enriched gas uplifted from the BGG center by buoyant bubbles, implying that active galactic nucleus outbursts may have intensified the stripping process. We extrapolate to a virial radius of 740 kpc and derive a virial mass of 4.6 × 1013 M⊙ for the M49 group. Its group atmosphere appears truncated and deficient when compared with isolated galaxy groups of similar temperatures. If M49 is on its first infall to Virgo, the infall region of a cluster could have profound impacts on galaxies and groups that are being accreted onto galaxy clusters. Alternatively, M49 may have already passed through Virgo once.
Finite temperature optoelectronic properties of BAs from first principles

The high thermal conductivity of boron arsenide (BAs) makes it a promising material for optoelectronic applications in which thermal management is central. In this work, we study the finite temperature optoelectronic properties of BAs by considering both electron-phonon coupling and thermal expansion. The inclusion of electron-phonon coupling proves imperative to capture the temperature dependence of the optoelectronic properties of the material, while thermal expansion makes a negligible contribution due to the highly covalent bonding character of BAs. We predict that with increasing temperature the optical absorption onset is subject to a red shift, the absorption peaks become smoother, and the phonon-assisted absorption at energies below those of the optical gap has a coefficient that lies in the range $10^{-3}$ to $10^{-4}$ cm$^{-1}$. We also show that good agreement with the measured indirect band gap of BAs is only obtained if exact exchange, electron-phonon coupling, and spin-orbit coupling effects are all included in the calculations.
Bayesian Factor Analysis for Inference on Interactions

Abstract This article is motivated by the problem of inference on interactions among chemical exposures impacting human health outcomes. Chemicals often co-occur in the environment or in synthetic mixtures and as a result exposure levels can be highly correlated. We propose a latent factor joint model, which includes shared factors in both the predictor and response components while assuming conditional independence. By including a quadratic regression in the latent variables in the response component, we induce flexible dimension reduction in characterizing main effects and interactions. We propose a Bayesian approach to inference under this factor analysis for interactions (FIN) framework. Through appropriate modifications of the factor modeling structure, FIN can accommodate higher order interactions. We evaluate the performance using a simulation study and data from the National Health and Nutrition Examination Survey. Code is available on GitHub. Supplementary materials for this article are available online.