Miracle-dz/UniFAR-FTUs huggingface dataset:
Shifts in coastal Antarctic marine microbial communities during and after melt water-related surface stratification.

Antarctic coastal waters undergo major physical alterations during summer. Increased temperatures induce sea-ice melting and glacial melt water input, leading to strong stratification of the upper water column. We investigated the composition of micro-eukaryotic and bacterial communities in Ryder Bay, Antarctic Peninsula, during and after summertime melt water stratification, applying community fingerprinting (denaturing gradient gel electrophoresis) and sequencing analysis of partial 18S and 16S rRNA genes. Community fingerprinting of the eukaryotic community revealed two major patterns, coinciding with a period of melt water stratification, followed by a period characterized by regular wind-induced breakdown of surface stratification. During the first stratified period, we observed depth-related differences in eukaryotic fingerprints while differences in bacterial fingerprints were weak. Wind-induced breakdown of the melt water layer caused a shift in the eukaryotic community from an Actinocyclus sp. - to a Thalassiosira sp. -dominated community. In addition, a distinct transition in the bacterial community was found, but with a few days' delay, suggesting a response to the changes in the eukaryotic community rather than to the mixing event itself. Sequence analysis revealed a shift from an Alpha- and Gammaproteobacteria to a Cytophaga-Flavobacterium-Bacteroides-dominated community under mixed conditions. Our results show that melt water stratification and the transition to nonstabilized Antarctic surface waters may have an impact not only on micro-eukaryotic but also bacterial community composition.
Action of different gamma interferons on mouse leukemic cells resistant to alpha and beta interferons

Phytohemagglutinin-induced interferon-gamma (IFN-gamma) was reported to act on mouse leukemic L1210 R cells resistant to IFN-alpha and -beta. Results reported here show that these cells are also sensitive to various preparations of murine IFN-gamma derived from different sources and purified to different degrees and that lymphokines present in the preparations are not involved in the antiviral effect of IFN. In addition, IFN-gamma preparation increases concanavalin A binding to L1210 S and L1210 R cells indicating that the sensitivity of L1210 R cells to IFN-gamma is not limited to its antiviral effect.
Surface Plasmon Resonance sensors based on polymer optical fiber

Surface Plasmon Resonance (SPR) is a powerful technique for directly sensing in biological studies, chemical detection and environmental pollution monitoring. In this paper, we present polymer optical fiber application in SPR sensors, including wavelength interrogation SPR sensor and surface enhanced Raman scattering (SERS) probe. Polymer optical fiber (POF) is used to effectively couple the incident light from light source, and collect reflective light into spectrometer. It also makes the sensing system more flexible and reliable. Gold nanorods with 30 nm long axis and average aspect ratios 3:1 are synthesized using seed-mediated growth method. Combining Au nanorods with POF, we can easily realize fiber SERS sensor. Long-period fiber gratings are fabricated on single mode polymer optical fiber with 120 um period and 50% duty cycle. The polarization characteristic of this kind of birefringent grating is studied. Theoretical analysis shows this type grating has two separated polarization peaks, and it will be advantageous in SPR sensing applications.
Conference Report - Management of HIV-Associated Lipoatrophy: Emerging Data in Clinical Context

23. 20. Walker UA, Langmann P, Miehle N, Zilly M, Klinker H, Petschner F. Beneficial effects of oral uridine in mitochondrial toxicity. AIDS. 2004;18:1085-1086. Abstract 21. Sutinen J, Walker UA, Sevastianova K, Hakkinen AM, Ristola M, Yki-Jarvinen H. Uridine supplementation increases subcutaneous fat in patients with HAART -associated lipodystrophy (HAL) -a randomized, placebo-controlled trial. Program and abstracts of the 7th International Workshop on Adverse Events and Lipodystrophy in HIV; November 13-16, 2006; Dublin, Ireland. Abstract 7. 22. Pozniak AL, Gallant JE, Dejesus E, et al, for the Study 934 Group. Tenofovir disoproxil fumarate, emtricitabine, and efavirenz versus fixed-dose zidovudine/lamivudine and efavirenz in antiretroviral-naive patients: virologic, immunologic, and morphologic changes: a 96-week analysis. J Acquir Immune Defic Syndr. 2006 [Epub ahead of print]. 23. Mallon PWG, Miller J, Kovacic JC, et al. Effects of pravastatin on body composition and markers of cardiovascular disease in HIV-infected men: a randomised, placebo-controlled study. AIDS. 2006;20:1003-1010. Abstract 24. Boccara F, Caron M, Auclair M, Capeau J. Irbesartan, an angiotensin II receptor I blocker, prevents the adverse effects of HIV antiretrovirals on adipocyte functions. Program and abstracts of the 8th International Workshop on Adverse Drug Reactions and Lipodystrophy in HIV; September 24-26, 2006; San Francisco, California. Abstract 7 25. Khatami H, Mulligan K, Schwarz J, et al. Effects of leptin treatment on glucose and lipid metabolism and fat distribution in HIV-infected patients with lipoatrophy and hypoleptinemia. Program and abstracts of the 8th International Workshop on Adverse Drug Reactions and Lipodystrophy in HIV; September 24-26, 2006; San Francisco, California. Abstract 21. Expert Column Cosmetic Interventions for HIVAssociated Lipoatrophy Graeme J. Moyle, MD, MBBS
Pre-attack symptomatology and temperament as predictors of children's responses to the September 11 terrorist attacks.

BACKGROUND The aims of this study were to assess the psychological response of children following the September 11, 2001 terrorist attacks in New York and Washington, DC and to examine prospective predictors of children's post-attack responses. METHOD Children's responses were assessed in a community sample of children in Seattle, Washington, participating in an ongoing study. Symptomatology and temperament assessed prior to the attacks were examined as prospective predictors of post-attack post-traumatic stress (PTS), anxiety, depression and externalizing problems. RESULTS Children demonstrated PTS symptoms and worries at levels comparable to those in children directly experiencing disasters, with 77% of children reporting being worried, 68% being upset by reminders, and 39% having upsetting thoughts. The most common PTS symptom cluster was re-experiencing, and 8% of children met criteria consistent with PTSD. African-American children reported more avoidant PTS symptoms and being more upset by the attacks than European-American children. Girls reported being more upset than boys. Prior internalizing, externalizing, social competence and self-esteem were related to post-attack PTS; and child inhibitory control, assessed prior to the 9/11 attacks, demonstrated a trend towards an association with post-attack PTS symptoms controlling for prior levels of symptomatology. PTS predicted child-report anxiety and conduct problem symptoms at follow-up, approximately 6 months after 9/11. CONCLUSIONS Children experiencing a major disaster at a distance or indirectly through media exposure demonstrated worries and PTS symptoms suggesting that communities need to attend to children's mental health needs in response to national or regional disasters. Pre-disaster symptomatology or low self-regulation may render children more vulnerable in response to a disaster, and immediate post-disaster responses predict subsequent symptomatology. These variables might be used in the identification of children in need of intervention.
Late improvement of regional wall motion after the subacute phase of myocardial infarction treated by acute PTCA in a 6-month follow-up.

BACKGROUND The aim of this follow-up study was to investigate the late effects of acute coronary angioplasty (PTCA) on regional wall motion after the subacute phase of myocardial infarction (MI). METHODS AND RESULTS Seventeen patients were investigated initially at a median of 11 days and again at 6 months after acute PTCA for myocardial infarction (< 8 hours after onset of symptoms) by cardiac magnetic resonance imaging. Corresponding short-axis slices encompassing the left ventricle (LV) were acquired using a standard cine MR for regional wall motion analysis and using delayed contrast enhanced magnetic resonance imaging (ceMRI) for infarct size quantification. The infarct size was similar in the subacute phase and the 6 month follow-up (20.8 and 21.9%, respectively; n.s.). Regional wall motion improved significantly in the area of hyperenhancement [percentage wall thickening (PWT) 21.9% and 37.9%, p < 0.05] in contrast to remote normal myocardium (46.4% and 38.4%; n.s.). Regional wall motion was significantly poorer in transmural compared with nontransmural MI in the subacute stage, and a late improvement could only be observed in transmural MI. CONCLUSION Transmural areas of hyperenhancement displayed significant late long-term improvement of regional wall motion after acute PTCA, possibly related to prolonged stunning compared with nontransmural areas.
Computation of a high‐resolution MRI 3D stereotaxic atlas of the sheep brain

The sheep model was first used in the fields of animal reproduction and veterinary sciences and then was utilized in fundamental and preclinical studies. For more than a decade, magnetic resonance (MR) studies performed on this model have been increasingly reported, especially in the field of neuroscience. To contribute to MR translational neuroscience research, a brain template and an atlas are necessary. We have recently generated the first complete T1‐weighted (T1W) and T2W MR population average images (or templates) of in vivo sheep brains. In this study, we 1) defined a 3D stereotaxic coordinate system for previously established in vivo population average templates; 2) used deformation fields obtained during optimized nonlinear registrations to compute nonlinear tissues or prior probability maps (nlTPMs) of cerebrospinal fluid (CSF), gray matter (GM), and white matter (WM) tissues; 3) delineated 25 external and 28 internal sheep brain structures by segmenting both templates and nlTPMs; and 4) annotated and labeled these structures using an existing histological atlas. We built a quality high‐resolution 3D atlas of average in vivo sheep brains linked to a reference stereotaxic space. The atlas and nlTPMs, associated with previously computed T1W and T2W in vivo sheep brain templates and nlTPMs, provide a complete set of imaging space that are able to be imported into other imaging software programs and could be used as standardized tools for neuroimaging studies or other neuroscience methods, such as image registration, image segmentation, identification of brain structures, implementation of recording devices, or neuronavigation. J. Comp. Neurol. 525:676–692, 2017. © 2016 Wiley Periodicals, Inc.
A Trust-Region Approach to the Regularization of Large-Scale Discrete Forms of Ill-Posed Problems

We consider large-scale least squares problems where the coefficient matrix comes from the discretization of an operator in an ill-posed problem, and the right-hand side contains noise. Special techniques known as regularization methods are needed to treat these problems in order to control the effect of the noise on the solution. We pose the regularization problem as a quadratically constrained least squares problem. This formulation is equivalent to Tikhonov regularization, and we note that it is also a special case of the trust-region subproblem from optimization. We analyze the trust-region subproblem in the regularization case and we consider the nontrivial extensions of a recently developed method for general large-scale subproblems that will allow us to handle this case. The method relies on matrix-vector products only, has low and fixed storage requirements, and can handle the singularities arising in ill-posed problems. We present numerical results on test problems, on an inverse interpolation problem with field data, and on a model seismic inversion problem with field data.
Acute myocarditis

Myocarditis is defined as inflammation of the myocardium accompanied by myocellular necrosis. Acute myocarditis must be considered in patients who present with recent onset of cardiac failure or arrhythmia. Often there is a history of an antecedent flu-like illness. Fulminant myocarditis is a distinct entity characterized by sudden onset of severe congestive heart failure or cardiogenic shock, usually following a flu-like illness. Giant cell myocarditis is a rare, frequently fatal disorder of unknown origin characterized by presence of giant cell inflammatory infiltrate in the myocardium. In recent years we have made good progress in understanding the causes, pathogenesis, natural history, diagnosis, and treatment of myocarditis. However, our knowledge is still far from complete. New information that extends our understanding of myocarditis is being reported constantly. This review summarizes recent advances in myocarditis, with an emphasis on the literature during the last year.
Competitive wireless energy transfer bidding: A game theoretic approach

Wireless or RF energy transfer will be capable of supplying energy to mobile nodes for packet transmission without physical battery changing or replacement. In this paper, we consider the network in which the access point can transfer wireless energy to the nodes and the nodes use that energy to transmit packets. The nodes can send requests (i.e., bids) to the access point for transferring wireless energy. As the access point adopts auction mechanism for wireless energy transfer, we formulate a noncooperative game to analyze the competitive wireless energy transfer bidding of the nodes. The Nash equilibrium is considered to be a solution of the game. To reach the Nash equilibrium, the nodes as players can adapt their strategies based on stochastic response dynamic. The Markov chain is used to analyze the properties of the game (e.g., convergence). The numerical results clearly show the convergence of the bidding strategy adaptation of the nodes toward the Nash equilibrium.
Identifying Domain-Specific Cognitive Strategies for Software Engineering

Due to the rapidly changing nature of today's work environment, software engineering (SE) students are required to have self-regulated learning (SRL) and problem solving skills. Previous research suggests that training students in the use of domain-specific cognitive strategies and using scaffolded instruction for strategy training improves students' SRL and problem solving task performance. In order to identify SE-specific cognitive strategies, we conducted a survey of advanced-level SE students. We then conducted a pre-test and post-test experiment with one control and two treatment groups, to analyze the effectiveness of identified strategies in improving students' task performance. The control group was not exposed to any strategies, while one treatment group was instructed verbally in the use of strategies and the other was trained using a newly developed scaffolded strategy training module. The results of the experiment demonstrate significant improvement in post-test task performance for both treatment groups, with a further increase in performance for those undertaking the training module.
Non-Coaxial Plasticity Constitutive Modeling of Sands

Classical coaxial plasticity constitutive models implicate an inevitable limitation that directions for principal stress and that for principal plastic strain increment are always coaxial. They are not capable of simulating non-coaxial phenomena during the rotation of principal stress axis. In this paper, a three-dimensional, non-coaxial plasticity constitutive model for sands with a modification of Lade angle dependent shape function is introduced to describe the non-coaxial behavior under principal axes rotation. A series of numerical simulations of hollow cylindrical torsional shear tests are performed. The results show that the proposed constitutive model can predict the variations of principal plastic strain increment directions with principal stress directions reasonably.
A Dynamic Explanation of The Hybrid Effect

A theoretical analysis has been performed to evaluate the dynamic stress concentration factor in hybrid composites composed of low elongation (LE) and high elongation (HE) fibers. At a fracture of a fiber, the present model predicts two stress waves propagating along each fiber in the hybrid. The phase difference of the dynamic responses contributed by these waves at the middle section of a fiber immediately adjacent to a fiber breakage is controll ed by the fiber mass per unit length. The magnitude of the dynamic responses is determined by the fiber extensional stiffness. The study concludes that hybrid effect always exists in a beneficial manner and the case of the parent LE fiber composite provides the upper bound for the dynamic stress concen tration factor in hybrids. The validity of the approximations made in the derivations has been examined.
Jointly sparse vector recovery via reweighted ℓ1 minimization

An iterative reweighted algorithm is proposed for the recovery of jointly sparse vectors from multiple-measurement vectors (MMV). The proposed MMV algorithm is an extension of the iterative reweighted ℓ1 algorithm for single measurement problems. The proposed algorithm (M-IRL1) is demonstrated to outperform non-reweighted MMV algorithms under noiseless measurements. A regularization of the M-IRL1 algorithm is also proposed to accommodate noise. The ability to robustly handle noise is demonstrated through an electromagnetic induction application.
Streptolysin O and its Co-Toxin NAD-glycohydrolase Protect Group A Streptococcus from Xenophagic Killing

Group A Streptococcus (Streptococcus pyogenes or GAS) causes pharyngitis, severe invasive infections, and the post-infectious syndromes of glomerulonephritis and rheumatic fever. GAS can be internalized and killed by epithelial cells in vitro, a process that may contribute to local innate defense against pharyngeal infection. Secretion of the pore-forming toxin streptolysin O (SLO) by GAS has been reported to stimulate targeted autophagy (xenophagy) upon internalization of the bacteria by epithelial cells. Whereas this process was associated with killing of GAS in HeLa cells, studies in human keratinocytes found SLO production enhanced intracellular survival. To reconcile these conflicting observations, we now report in-depth investigation of xenophagy in response to GAS infection of human oropharyngeal keratinocytes, the predominant cell type of the pharyngeal epithelium. We found that SLO expression was associated with prolonged intracellular survival; unexpectedly, expression of the co-toxin NADase was required for this effect. Enhanced intracellular survival was lost upon deletion of NADase or inactivation of its enzymatic activity. Shortly after internalization of GAS by keratinocytes, SLO-mediated damage to the bacteria-containing vacuole resulted in exposure to the cytosol, ubiquitination of GAS and/or associated vacuolar membrane remnants, and engulfment of GAS in LC3-positive vacuoles. We also found that production of streptolysin S could mediate targeting of GAS to autophagosomes in the absence of SLO, a process accompanied by galectin 8 binding to damaged GAS-containing endosomes. Maturation of GAS-containing autophagosome-like vacuoles to degradative autolysosomes was prevented by SLO pore-formation and by SLO-mediated translocation of enzymatically active NADase into the keratinocyte cytosol. We conclude that SLO stimulates xenophagy in pharyngeal keratinocytes, but the coordinated action of SLO and NADase prevent maturation of GAS-containing autophagosomes, thereby prolonging GAS intracellular survival. This novel activity of NADase to block autophagic killing of GAS in pharyngeal cells may contribute to pharyngitis treatment failure, relapse, and chronic carriage.
Noncontact, Low-Frequency Ultrasound Therapy Enhances Neovascularization and Wound Healing in Diabetic Mice

Background: Chronic wounds are a major source of morbidity for patients and represent a significant health burden. Implementing noninvasive techniques that accelerate healing of these wounds would provide great benefit. Ultrasound appears to be an effective modality for the treatment of chronic wounds in humans. MIST Therapy is a noncontact, low-frequency ultrasound treatment delivered through a saline mist. A variety of mechanisms have been proposed to explain the efficacy of ultrasound therapy, but the underlying molecular and cellular pathways impacted by this technique remain unclear. The in vivo effect of noncontact, low-frequency ultrasound was therefore examined in a humanized excisional wound model. Methods: The treatment group received noncontact, low-frequency ultrasound therapy three times per week, whereas the control group received a standard dressing change. Wounds were photographed at regular intervals to calculate healing kinetics. Wound tissue was harvested and processed for histology, quantitative polymerase chain reaction, and enzyme-linked immunosorbent assay. Results: The MIST group demonstrated significantly accelerated wound healing, with 17.3 days to wound closure compared with 24 days in the controls (p < 0.05). This improvement became evident by day 9, with healing evidenced by significantly decreased mean wound area relative to original size (68 percent versus 80 percent; p < 0.01). Expression of markers of neovascularization (stromal cell-derived factor 1, vascular endothelial growth factor, and CD31) was also increased in the wound beds of noncontact, low-frequency ultrasound–treated mice compared with controls. Conclusion: Noncontact, low-frequency ultrasound treatment improves neovascularization and wound closure rates in excisional wounds for diabetic mice, likely because of the stimulated release of angiogenic factors.
Does Day Length Affect Winter Bird Distribution? Testing the Role of an Elusive Variable

Differences in day length may act as a critical factor in bird biology by introducing time constraints in energy acquisition during winter. Thus, differences in day length might operate as a main determinant of bird abundance along latitudinal gradients. This work examines the influence of day length on the abundance of wintering crested tits (Lophophanes cristatus) in 26 localities of Spanish juniper (Juniperus thurifera) dwarf woodlands (average height of 5 m) located along a latitudinal gradient in the Spanish highlands, while controlling for the influence of food availability, minimum night temperature, habitat structure and landscape characteristics. Top regression models in the AIC framework explained 56% of variance in bird numbers. All models incorporated day length as the variable with the highest magnitude effect. Food availability also played an important role, although only the crop of ripe juniper fruits, but not arthropods, positively affected crested tit abundance. Differences in vegetation structure across localities had also a strong positive effect (average tree height and juniper tree density). Geographical variation in night temperature had no influence on crested tit distribution, despite the low winter temperatures reached in these dwarf forests. This paper demonstrates for the first time that winter bird abundance increases with day length after controlling for the effect of other environmental variables. Winter average difference in day length was only 10.5 minutes per day along the 1°47′ latitudinal interval (190 km) included in this study. This amount of time, which reaches 13.5 h accumulated throughout the winter season, appears to be large enough to affect the long-term energy budget of small passerines during winter and to shape the distribution of winter bird abundance under restrictive environmental conditions.