Miracle-dz/UniFAR-FTUs huggingface dataset:
Light and electron microscopy of the photoreceptors in the retina of the red‐eared slider, Pseudemys scripta elegans

The six different types of photoreceptor in the retina of the turtle Pseudemys scripta elegans have been studied by light and electron microscopy. Fresh whole‐mount retina, in which the oil droplet colors of the photoreceptors could be seen, was compared with fixed tissue cut in the vertical plane. The red single cone (large red oil droplet) is largest in diameter and, in electron microscopy (EM) views, has the least opaque oil droplet. It also has a vacuolated paraboloid and a cone pedicle that ends at the intermediate level of the outer plexiform layer (OPL). The green single cone (yellow medium‐size oil droplet) has a thinner inner segment and uniformly vacuolated paraboloid. Its cone pedicle ends at the same level as that of red cones. The blue cone (small colorless oil droplet) has an obliquely running axon joining cell body to cone pedicle that lies innermost in the OPL. Double cones are recognizable by their adherent cell bodies and inner segments. The accessory member (green cone) lacks an oil droplet but has a distinct large paraboloid while the principal member (red cone) has an oil droplet (orange) lying more distal than oil droplets of other cone types. The axons of the double cones are separated by glia but have closely apposed pedicles ending above those of the single cones in the outermost level of the OPL. Rod photoreceptors have a large outer segment, no oil droplet, and a lowlying cell body continuous with the pedicle, which ends, like those of the double cones, at the outermost level of the OPL.
Dynamic Modeling of Cortisol Reduction after Inhaled Administration of Fluticasone Propionate

Fluticasone propionate (FP) is a new corticosteroid that has been developed for the treatment of asthma. The compound has a very high receptor affinity, 18 times that of dexamethasone. After inhalation, FP is systemically available because of inhaled bioavailability. In healthy subjects this may lead to measurable systemic effects, such as cortisol reduction. A clinical study was conducted in 12 healthy volunteers to determine the systemic effects after inhaled administration of single 500‐μg, 1,000‐μg, and 2,000‐μg doses of FP. Blood samples were collected over a 24‐hour period after administration. Concentrations of FP and cortisol were measured in plasma by immunoassay. Cortisol reduction was chosen as the pharmacodynamic parameter. A novel linear release rate model was used to parameterize the cortisol data. The pharmacokinetics of FP were linear over the dose range studied. The cortisol release parameters were determined from baseline data (before drug administration). Based on these results, the E50 values for cortisol reduction were then determined for each dose of FP. The average E50 was 0.134 ng/mL for total FP concentrations and 0.013 ng/mL for unbound FP concentrations; these results were not dose dependent. These in vivo pharmacodynamic values measured in healthy subjects are in good agreement with the relatively high receptor affinity of FP.
Cross-Project Defect Prediction With Respect To Code Ownership Model: An Empirical Study

The paper presents an analysis of 83 versions of industrial, open-source and academic projects. We have empirically evaluated whether those project types constitute separate classes of projects with regard to defect prediction. Statistical tests proved that there exist significant dierences between the models trained on the aforementioned project classes. This work makes the next step towards cross-project reusability of defect prediction models and facilitates their adoption, which has been very limited so far.
Extending Systematic Case Study Method: Generating and Testing Hypotheses About Therapeutic Factors Through Comparisons of Successful and Unsuccessful Cases

This commentary focuses on two case comparison studies, one by Burckell and McMain (2011) on Dialectical Behavior Therapy for borderline personality disorder, and one by Watson et al. (2011) and Goldman et al. (2011) on Emotion-Focused Therapy for depression. The associated case comparison method, which evaluates and contrasts one successful case against one unsuccessful case that are both conducted in similar conditions, provides a unique opportunity for deepening our understanding of therapeutic change. Both therapies are integrative approaches that are clinically state-of-the art and empirically supported, and that have been drawing considerable attention from practitioners and researchers. In this commentary, I first discuss the case comparison method by reviewing previous such approaches, I then examine each pair of case studies with a focus on (a) findings on factors influencing success and limited success, and (b) methodological issues associated with the application of this unique method. Finally, I end my commentary with a suggestion for conducting case comparison studies.
ITEM2VEC: Neural item embedding for collaborative filtering

Many Collaborative Filtering (CF) algorithms are item-based in the sense that they analyze item-item relations in order to produce item similarities. Recently, several works in the field of Natural Language Processing (NLP) suggested to learn a latent representation of words using neural embedding algorithms. Among them, the Skip-gram with Negative Sampling (SGNS), also known as word2vec, was shown to provide state-of-the-art results on various linguistics tasks. In this paper, we show that item-based CF can be cast in the same framework of neural word embedding. Inspired by SGNS, we describe a method we name item2vec for item-based CF that produces embedding for items in a latent space. The method is capable of inferring item-item relations even when user information is not available. We present experimental results that demonstrate the effectiveness of the item2vec method and show it is competitive with SVD.
Alzheimer's Disease Detection in Brain Magnetic Resonance Images Using Multiscale Fractal Analysis

We present a new automated system for the detection of brain magnetic resonance images (MRI) affected by Alzheimer's disease (AD). The MRI is analyzed by means of multiscale analysis (MSA) to obtain its fractals at six different scales. The extracted fractals are used as features to differentiate healthy brain MRI from those of AD by a support vector machine (SVM) classifier. The result of classifying 93 brain MRIs consisting of 51 images of healthy brains and 42 of brains affected by AD, using leave-one-out cross-validation method, yielded 99.18% ± 0.01 classification accuracy, 100% sensitivity, and 98.20% ± 0.02 specificity. These results and a processing time of 5.64 seconds indicate that the proposed approach may be an efficient diagnostic aid for radiologists in the screening for AD.
DNA damage signaling assessed in individual cells in relation to the cell cycle phase and induction of apoptosis

Reviewed are the phosphorylation events reporting activation of protein kinases and the key substrates critical for the DNA damage signaling (DDS). These DDS events are detected immunocytochemically using phospho-specific Abs; flow cytometry or image-assisted cytometry provide the means to quantitatively assess them on a cell by cell basis. The multiparameter analysis of the data is used to correlate these events with each other and relate to the cell cycle phase, DNA replication and induction of apoptosis. Expression of γH2AX as a possible marker of induction of DNA double strand breaks is the most widely studied event of DDS. Reviewed are applications of this multiparameter approach to investigate constitutive DDS reporting DNA damage by endogenous oxidants byproducts of oxidative phosphorylation. Also reviewed are its applications to detect and explore mechanisms of DDS induced by variety of exogenous agents targeting DNA such as exogenous oxidants, ionizing radiation, radiomimetic drugs, UV light, DNA topoisomerase I and II inhibitors, DNA crosslinking drugs and variety of environmental genotoxins. Analysis of DDS induced by these agents provides often a wealth of information about mechanism of induction and the type of DNA damage (lesion) and is reviewed in the context of cell cycle phase specificity, DNA replication, and induction of apoptosis or cell senescence. Critically assessed is interpretation of the data as to whether the observed DDS events report induction of a particular type of DNA lesion.
Cancer mortality at very old ages

Mortality rates of all malignant neoplastic diseases combined and of most individual kinds of cancer increase with age through most of the human life span. What happens to cancer mortality rates near the end of the life span has not been described previously. People age 85 years and older are commonly considered as a single category; however information is available for cancer mortality of patients older than 85 years in 4 age groups, each covering 5‐year spans.
Negative Feelings Exacerbate Hostile Attributions of Intent in Highly Aggressive Boys

Tested the hypothesis that aggressive boys' tendency to attribute hostile intentions to peers is exacerbated in a negative emotional state. Twenty-nine highly aggressive boys in special education, 12 moderately aggressive boys in regular education, and 16 nonaggressive boys in regular education inferred peers' intentions in 8 vignettes concerning ambiguous provocation by peers. Mild negative emotions were induced by unjust loss of a manipulated computer game. Half the vignettes were completed in this negative emotional state. After completion of all vignettes, the game was played again and won to reinduce positive feelings. Self-ratings of feelings obtained throughout the study showed the manipulations consecutively induced negative and positive feelings. Negative feelings increased hostile attribution of intent in the highly aggressive group. Highly and moderately aggressive boys responded more aggressively than nonaggressive boys.
AMP-Activated Protein Kinase–Deficient Mice Are Resistant to the Metabolic Effects of Resveratrol

OBJECTIVE Resveratrol, a natural polyphenolic compound that is found in grapes and red wine, increases metabolic rate, insulin sensitivity, mitochondrial biogenesis, and physical endurance and reduces fat accumulation in mice. Although it is thought that resveratrol targets Sirt1, this is controversial because resveratrol also activates 5′ AMP-activated protein kinase (AMPK), which also regulates insulin sensitivity and mitochondrial biogenesis. Here, we use mice deficient in AMPKα1 or -α2 to determine whether the metabolic effects of resveratrol are mediated by AMPK. RESEARCH DESIGN AND METHODS Mice deficient in the catalytic subunit of AMPK (α1 or α2) and wild-type mice were fed a high-fat diet or high-fat diet supplemented with resveratrol for 13 weeks. Body weight was recorded biweekly and metabolic parameters were measured. We also used mouse embryonic fibroblasts deficient in AMPK to study the role of AMPK in resveratrol-mediated effects in vitro. RESULTS Resveratrol increased the metabolic rate and reduced fat mass in wild-type mice but not in AMPKα1−/− mice. In the absence of either AMPKα1 or -α2, resveratrol failed to increase insulin sensitivity, glucose tolerance, mitochondrial biogenesis, and physical endurance. Consistent with this, the expression of genes important for mitochondrial biogenesis was not induced by resveratrol in AMPK-deficient mice. In addition, resveratrol increased the NAD-to-NADH ratio in an AMPK-dependent manner, which may explain how resveratrol may activate Sirt1 indirectly. CONCLUSIONS We conclude that AMPK, which was thought to be an off-target hit of resveratrol, is the central target for the metabolic effects of resveratrol.
Serum lipoproteins in the diabetes control and complications trial/epidemiology of diabetes intervention and complications cohort: associations with gender and glycemia.

OBJECTIVE To relate the nuclear magnetic resonance (NMR)-determined lipoprotein profile, conventional lipid and apolipoprotein measures, and in vitro oxidizibility of LDL with gender and glycemia in type 1 diabetes. RESEARCH DESIGN AND METHODS In the 1997-1999 Diabetes Control and Complications Trial/Epidemiology of Diabetes Intervention and Complications (DCCT/EDIC) cohort, serum from 428 women and 540 men were characterized by conventional lipids, NMR, apolipoprotein levels, and LDL susceptibility to in vitro oxidation. Simple and partial correlation coefficients were calculated for each lipoprotein-related parameter versus gender, with and without covariates (age, diabetes duration, concurrent HbA(1c), DCCT randomization, hypertension, BMI, waist-to-hip ratio, and albuminuria). For concurrent HbA(1c), data were analyzed as above, exchanging gender for HbA(1c). Associations were significant if P < 0.05. RESULTS Although men and women had similar total and LDL cholesterol and triglycerides, men exhibited the following significant percent differences in NMR profiles versus women: small VLDL 41; IDL -30; medium LDL 39; small LDL 21; large HDL -32; small HDL 35; LDL particle concentration 4; VLDL and HDL diameters -8 and -4, respectively. Small VLDL, small HDL, medium LDL (women only), small LDL (men only), and LDL particle concentration were positively correlated, and HDL size was inversely correlated, with concurrent HbA(1c). NMR profile was unrelated to prior DCCT randomization. Susceptibility of LDL to oxidation was unrelated to gender and glycemia. CONCLUSIONS Male gender and poor glycemia are associated with a potentially more atherogenic NMR lipoprotein profile. Neither gender nor glycemia influence LDL oxidation in vitro.
Myeloid-Derived Suppressor Cells are Generated during Retroviral Transduction of Murine Bone Marrow

Previous work by our group showed that transferring bone marrow cells transduced with an autoantigen into nonmyeloablated mice with experimental autoimmune encephalomyelitis induced immune tolerance and improved symptoms of the disease. Because this effect occurred in the absence of molecular chimerism, we hypothesized that the cells responsible did not have repopulating ability and that they were not mediating central but peripheral tolerance mechanisms. In the present study, we analyzed the immunophenotype of the cells that are generated in the transduction cultures and we evaluated the immunosuppressive activity of the main cell subpopulations produced. We show that both granulocytic (CD11b+ Gr-1hi) and monocytic (CD11b+Gr-1lo) myeloid-derived suppressor cells (G- and M-MDSCs, respectively) are generated during standard 4-day γ-retroviral transduction cultures (representing about 25% and 40% of the total cell output, respectively) and that the effectively transduced cells largely consist of these two cell types. A third cell population representing about 15% of the transduced cells did not express CD45 or hematopoietic lineage markers and expressed mesenchymal stromal cell markers. Transduced total bone marrow cells and sorted M-MDSCs expressed arginase and inducible nitric oxide synthase activities, produced reactive oxygen species, and inhibited antigen-induced T-cell proliferation in vitro. Transgene-expressing MDSCs could be exploited therapeutically to induce tolerance in autoimmune diseases and in gene therapy protocols.
Performance of IEEE 802.15.4 beacon enabled PAN with uplink transmissions in non-saturation mode - access delay for finite buffers

In this work, we derive the probability distribution of access delay and calculate throughput of a personal area network operating under the IEEE standard 802.15. 4 in the beacon enabled mode. We model the network using the theory of discrete time Markov chains and M/G/1/K queues. The model considers acknowledged uplink transmission in non-saturation mode, and includes the impact of different parameters such as packet arrival rate, number of stations, the finite size of individual node buffers, packet size, and inactive period between the beacons. Our model also captures the problem of congestion at the beginning of the superframe due to multiple transmissions delayed from the previous superframe. The results show that average access delays, even for small buffer sizes, may be quite high if the throughput exceeds 50%, which can seriously affect applications with delay bounds. Values of throughput larger than 50% can be achieved at the expense of larger buffer sizes, which imposes implementation problems on devices with small memory resources.
Sublethal photic stress and the motility of RPE phagosomes and melanosomes.

PURPOSE To determine whether sublethal oxidative stress to the retinal pigment epithelium by visible light treatment affects the translocation of organelles, notably phagosomes and melanosomes. METHODS Isolated porcine melanosomes were phagocytized by ARPE-19 cells, then cultures were treated with blue light to generate reactive oxygen intermediates (ROIs) by endogenous retinal pigment epithelial (RPE) chromophores throughout the cytoplasm. Other melanosomes were preloaded with a photosensitizer before phagocytosis, and cells were light treated to generate ROIs specifically at the granule surface. Phagosome movement was analyzed by live cell imaging. Also analyzed were phagocytized black latex beads, phagocytized melanosomes pretreated to simulate age-related melanin photobleaching, and endogenous RPE melanosomes in primary cultures of porcine retinal pigment epithelium. RESULTS Sublethal blue light treatment slowed the movement of some, but not all, phagocytized melanosomes. All phagosomes slowed when ROIs were generated near the organelles through a photosensitized reaction. Melanosome photobleaching, which makes granules more photoreactive, increased the effects of blue light. Blue light treatment also slowed the motility of phagosomes containing latex beads and endogenous pigment granules. CONCLUSIONS Blue light-induced stress impairs phagosome motility in RPE cells but affects individual organelles differently, suggesting that the effects of mild oxidative injury vary with subcellular location. The mechanisms underlying slowed motility are at least partially local because slowing can be induced by a photosensitized reaction in the subdomain of the organelle and the magnitude of the slowing is greater when the phagosome contents are photoreactive. Photic stress may impair the movement and positioning of RPE organelles, which would have widespread consequences for maintaining a functionally efficient subcellular organization.
LTE over copper — Potential and limitations

The densification of mobile networks in order to meet increased capacity demands is ongoing, needed and costly. A few papers have been published based on the insight that the fixed broadband networks offer a multitude of sites, for instance our homes, for potential small cell deployment providing backhaul capacity and power without site costs. However, in order to reach economical large-scale benefits, we explore the case when radio systems are deployed in coexistence with DSL. In this paper, we establish the feasibility of such a concept under constraints invoked by state-of-the-art and emerging systems (3GPP, VDSL2 and G.fast) and make statements about the required architecture. We also point out that the enthusiasm of previously published results should be lowered a notch.
A dimensionless number for understanding the evolutionary dynamics of antigenically variable RNA viruses

Antigenically variable RNA viruses are significant contributors to the burden of infectious disease worldwide. One reason for their ubiquity is their ability to escape herd immunity through rapid antigenic evolution and thereby to reinfect previously infected hosts. However, the ways in which these viruses evolve antigenically are highly diverse. Some have only limited diversity in the long-run, with every emergence of a new antigenic variant coupled with a replacement of the older variant. Other viruses rapidly accumulate antigenic diversity over time. Others still exhibit dynamics that can be considered evolutionary intermediates between these two extremes. Here, we present a theoretical framework that aims to understand these differences in evolutionary patterns by considering a virus's epidemiological dynamics in a given host population. Our framework, based on a dimensionless number, probabilistically anticipates patterns of viral antigenic diversification and thereby quantifies a virus's evolutionary potential. It is therefore similar in spirit to the basic reproduction number, the well-known dimensionless number which quantifies a pathogen's reproductive potential. We further outline how our theoretical framework can be applied to empirical viral systems, using influenza A/H3N2 as a case study. We end with predictions of our framework and work that remains to be done to further integrate viral evolutionary dynamics with disease ecology.
Soccer athletes are superior to non-athletes at perceiving soccer-specific and non-sport specific human biological motion

Recent studies have shown that athletes’ domain specific perceptual-cognitive expertise can transfer to everyday tasks. Here we assessed the perceptual-cognitive expertise of athletes and non-athletes using sport specific and non-sport specific biological motion perception (BMP) tasks. Using a virtual environment, university-level soccer players and university students’ non-athletes were asked to perceive the direction of a point-light walker and to predict the trajectory of a masked-ball during a point-light soccer kick. Angles of presentation were varied for orientation (upright, inverted) and distance (2 m, 4 m, 16 m). Accuracy and reaction time were measured to assess observers’ performance. The results highlighted athletes’ superior ability compared to non-athletes to accurately predict the trajectory of a masked soccer ball presented at 2 m (reaction time), 4 m (accuracy and reaction time), and 16 m (accuracy) of distance. More interestingly, experts also displayed greater performance compared to non-athletes throughout the more fundamental and general point-light walker direction task presented at 2 m (reaction time), 4 m (accuracy and reaction time), and 16 m (reaction time) of distance. In addition, athletes showed a better performance throughout inverted conditions in the walker (reaction time) and soccer kick (accuracy and reaction time) tasks. This implies that during human BMP, athletes demonstrate an advantage for recognizing body kinematics that goes beyond sport specific actions.
Sinks of Light Elements in Stars - Part III (Invited Paper)

The fragile light elements lithium, beryllium, and boron are easily destroyed in stellar interiors, and are thus superb probes of physical processes occuring in the outer stellar layers. The light elements are also excellent tracers of the chemical evolution of the Galaxy, and can test big bang nucleosynthesis (BBN). These inter-related topics are reviewed with an emphasis on stellar physics. In Part I (presented by CPD), an overview is given of the physical processes which can modify the surface abundances of the light elements, with emphasis on Population I dwarfs - convection; gravitational settling, thermal diffusion, and radiative levitation; slow mixing induced by gravity waves or rotation. We will discuss the increasingly large body of data which begin to enable us to discern the relative importance of these mechanisms in Population I main sequence stars. In Part II (presented by MHP), discussion is extended to the issue of whether or not the halo Li plateau is depleted, and includes the following topics: Li dispersion in field and globular cluster stars, Li production vs. destruction in Li-rich halo stars, and constraints from 6Li. Also discussed are trends with metal abundance and Teff and implications for chemical evolution and BBN. In Part III (presented by CC), evidence is reviewed that suggests that in situ mixing occurs in evolved low mass Population I and Population II stars. Theoretical mechanisms that can create such mixing are discussed, as well as their implications in stellar yields.