Miracle-dz/UniFAR-FTUs huggingface dataset:
Induction of angiogenic cytokine expression in cultured RPE by ingestion of oxidized photoreceptor outer segments.

PURPOSE Normal aging is associated with accumulation of lipofuscin pigment in the retinal pigment epithelium (RPE). This may occur as a result of phagocytosis and incomplete degradation of oxidized photoreceptor outer segments (POS). This study was undertaken to determine whether phagocytosis of UV-irradiated POS (artificial lipofuscin) would increase expression in the RPE of various chemotactic and angiogenic cytokines. METHODS ARPE-19 cells were exposed to latex beads (0.76 micro m), naïve bovine POS, and UV-irradiated POS (Ox-POS; 2 x 10(7)/mL), and supernatants were collected at 18 and 36 hours. The supernatants were assayed for IL-8, monocyte chemotactic protein-(MCP)-1, and TNF-alpha by ELISA. Protein synthesis and NFkappaB activity were inhibited by actinomycin D and SN50, respectively. Phagocytosis and generation of intracellular reactive oxygen species were assessed by flow cytometry. Confocal and electron microscopy studies were also performed to verify phagocytosis and cellular integrity. RESULTS IL-8 and MCP-1 levels were decreased in the naïve POS group (IL-8: 473.76 +/- 66.9 pg/mL, P = 0.0005; MCP-1: 550.1 +/- 21.8 pg/mL, P = 0.0001), but were increased in the Ox-POS group (IL-8: 1348.8 +/- 164.9 pg/mL; MCP-1: 1772.28 +/- 65.19 pg/mL) compared with the control (IL-8: 741.09 +/- 39.8 pg/mL; MCP-1: 1413.47 +/- 38.4 pg/mL) and latex bead groups (data not shown). TNF-alpha levels were not affected. At 12 hours (but not at 6 hours), ROS were increased in the Ox-POS group. The cytokine increases observed were dependent on de novo protein synthesis and were NF-kappaB dependent. CONCLUSIONS Ingestion by RPE of oxidized bovine POS stimulates expression of the chemotactic and angiogenic factors IL-8 and MCP-1 that have the capability to promote angiogenesis directly, or indirectly through the accumulation of immune cells such as macrophages, which themselves may release angiogenic promoters and degrade Bruch's membrane. This may be of significance in the development of exudative AMD.
HYPOXIC PRECONDITIONING INDUCES DELAYED CARDIOPROTECTION THROUGH P38 MAPK-MEDIATED CALRETICULIN UPREGULATION

The protective mechanisms of hypoxic preconditioning (HPC) involve the mitigation of cellular calcium overload in cardiomyocytes. The sarcoplasmic reticulum (SR) chaperone calreticulin (CRT) plays an important role in regulating calcium homeostasis and is upregulated by HPC. The goal of this study was to show whether the late cardioprotection of HPC is mediated by calreticulin upregulation and to demonstrate whether the calreticulin induction is mediated by p38 MAPK phosphorylation. Hypoxic preconditioning was induced by hypoxemic hypoxic exposure by a 24-h period of normoxic reoxygenation before undergoing LAD occlusion in rats or hypoxia/reoxygenation (H/R) in cardiomyocytes. Ca2+ uptake and release of the SR vesicles was determined by use of 45Ca2+ and the Millipore filtration technique. Western blotting analysis was used to detect calreticulin expression and activity of p38 MAPK. Hypoxic preconditioning induced calreticulin upregulation and attenuated H/R injury in neonatal cardiomyocytes and myocardial ischemia injury by increasing calcium uptake and reducing calcium release in SR. Hearts from the HPC group were more resistant to sustained ischemia and had much stronger phosphorylation of p38 MAPK than sham operation. Inhibition of p38 MAPK with SB202190 (a selective p38 MAPK inhibitor) abolished the calreticulin upregulation and cardioprotection by HPC. Hypoxic preconditioning upregulates calreticulin expression through a p38 MAPK signaling pathway and protects cardiomyocytes from H/R (and ischemia) injury.
GENERATION AND APPLICATION OF COPOLYMER BASED POLYACRYLAMIDE MICROBEADS (CBPmB) USING MICROFLUIDIC PLATFORM

We report that the generation of Copolymer Based Polyacrylamide Microbeads (CBPmB) could be covalently cross-linked with acrydite modified oligomer by placing on droplet based microfluidic platform. Acrydite oligomers are exposed on the surface of microbeads, they are used to amplification of single strand DNA (ssDNA) used aptamer-sensor and aptafilter, diagnostic tools, formatting some modified oligomer and DNA SELEX.
An Access Delay Model for IEEE 802.11e EDCA

We analyze the MAC access delay of the IEEE 802.11e EDCA mechanism under saturation. We develop a detailed analytical model to evaluate the influence of all EDCA differentiation parameters, namely AIFS, CWmin, CWmax and TXOP limit, as well as the backoff multiplier beta. Explicit expressions for the mean, standard deviation and generating function of the access delay distribution are derived. By applying numerical inversion on the generating function, we are able to efficiently compute values of the distribution. Comparison with simulation confirms the accuracy of our analytical model over a wide range of operating conditions. We derive simple asymptotics and approximations for the mean and standard deviation of the access delay, which reveal the salient model parameters for performance under different differentiation mechanisms. We also use the model to numerically study the differentiation performance and find that beta differentiation, though rejected during the standardization process, is an effective differentiation mechanism that has some advantages over the other mechanisms.
An Improved Fst Estimator

The fixation index F st plays a central role in ecological and evolutionary genetic studies. The estimators of Wright (F^st1), Weir and Cockerham (F^st2), and Hudson et al. (F^st3) are widely used to measure genetic differences among different populations, but all have limitations. We propose a minimum variance estimator F^stm using F^st1 and F^st2. We tested F^stm in simulations and applied it to 120 unrelated East African individuals from Ethiopia and 11 subpopulations in HapMap 3 with 464,642 SNPs. Our simulation study showed that F^stm has smaller bias than F^st2 for small sample sizes and smaller bias than F^st1 for large sample sizes. Also, F^stm has smaller variance than F^st2 for small F st values and smaller variance than F^st1 for large F st values. We demonstrated that approximately 30 subpopulations and 30 individuals per subpopulation are required in order to accurately estimate F st.
Benchmarking to improve the quality of cystic fibrosis care

Purpose of review Benchmarking involves the ascertainment of healthcare programs with most favorable outcomes as a means to identify and spread effective strategies for delivery of care. The recent interest in the development of patient registries for patients with cystic fibrosis (CF) has been fueled in part by an interest in using them to facilitate benchmarking. This review summarizes reports of how benchmarking has been operationalized in attempts to improve CF care. Recent findings Although certain goals of benchmarking can be accomplished with an exclusive focus on registry data analysis, benchmarking programs in Germany and the United States have supplemented these data analyses with exploratory interactions and discussions to better understand successful approaches to care and encourage their spread throughout the care network. Summary Benchmarking allows the discovery and facilitates the spread of effective approaches to care. It provides a pragmatic alternative to traditional research methods such as randomized controlled trials, providing insights into methods that optimize delivery of care and allowing judgments about the relative effectiveness of different therapeutic approaches.
Joint blind source separation of multidimensional components: Model and algorithm

This paper deals with joint blind source separation (JBSS) of multidimensional components. JBSS extends classical BSS to simultaneously resolve several BSS problems by assuming statistical dependence between latent sources across mixtures. JBSS offers some significant advantages over BSS, such as identifying more than one Gaussian white stationary source within a mixture. Multidimensional BSS extends classical BSS to deal with a more general and more flexible model within each mixture: the sources can be partitioned into groups exhibiting dependence within a given group but independence between two different groups. Motivated by various applications, we present a model that is inspired by both extensions. We derive an algorithm that achieves asymptotically the minimal mean square error (MMSE) in the estimation of Gaussian multidimensional components. We demonstrate the superior performance of this model over a two-step approach, in which JBSS, which ignores the multidimensional structure, is followed by a clustering step.
Physicians and electronic health records: a statewide survey.

BACKGROUND Electronic health records (EHRs) allow for a variety of functions, ranging from visit documentation to laboratory test ordering, but little is known about physicians' actual use of these functions. METHODS We surveyed a random sample of 1884 physicians in Massachusetts by mail and assessed availability and use of EHR functions, predictors of use, and the relationships between EHR use and physicians' perceptions of medical practice. RESULTS A total of 1345 physicians responded to the survey (71.4% response rate), and 387 (28.8%) reported that their practice had adopted EHRs. More than 80% of physicians with EHRs reported having the ability to view laboratory reports (84.8%) and document visits electronically (84.0%), but considerably fewer reported being able to order laboratory tests electronically (46.8%) or transmit prescriptions to a pharmacy electronically (44.7%). Fewer than half of the physicians who had systems with clinical decision support, transmittal of electronic prescriptions, and radiology order entry actually used these functions most or all of the time. Compared with physicians who had not adopted EHRs, EHR users reported more positive views of the effects of computers on health care; there were no significant differences in these attitudes between high and low users of EHRs. Overall, about 1 in 4 physicians reported dissatisfaction with medical practice; there was no difference in this measure by EHR adoption or use. CONCLUSIONS There is considerable variability in the functions available in EHRs and in the extent to which physicians use them. Future work should emphasize factors that affect the use of available functions.
Cognitive Biases in Software Engineering: A Systematic Mapping Study

One source of software project challenges and failures is the systematic errors introduced by human cognitive biases. Although extensively explored in cognitive psychology, investigations concerning cognitive biases have only recently gained popularity in software engineering research. This paper therefore systematically maps, aggregates and synthesizes the literature on cognitive biases in software engineering to generate a comprehensive body of knowledge, understand state-of-the-art research and provide guidelines for future research and practise. Focusing on bias antecedents, effects and mitigation techniques, we identified 65 articles (published between 1990 and 2016), which investigate 37 cognitive biases. Despite strong and increasing interest, the results reveal a scarcity of research on mitigation techniques and poor theoretical foundations in understanding and interpreting cognitive biases. Although bias-related research has generated many new insights in the software engineering community, specific bias mitigation techniques are still needed for software professionals to overcome the deleterious effects of cognitive biases on their work.
The genetic architecture of male colour differences between a sympatric Lake Malawi cichlid species pair

The genetic basis of traits involved in reproductive isolation is a key parameter in models of sympatric speciation by sexual selection, a potential mechanism driving the explosive radiation of East African cichlids. Analysis of hybrid crosses between two sympatric Lake Malawi cichlid species, representing the extremes of the extant colour distribution, generated Castle–Wright estimates of four to seven loci controlling colour differences. Segregation patterns deviated from a purely additive model with a significant contribution from dominance, and possibly also epistasis. Evidence was found for a strong influence of autosomal loci. As departures from simple additive variation could effect the operation of models of sympatric speciation, dominance and epistasis should not be neglected.
Algorithms for fast vector quantization

This paper shows that if one is willing to relax the requirement of finding the true nearest neighbor, it is possible to achieve significant improvements in running time and at only a very small loss in the performance of the vector quantizer. The authors present three algorithms for nearest neighbor searching: standard and priority k-d tree search algorithms and a neighborhood graph search algorithm in which a directed graph is constructed for the point set and edges join neighboring points. <<ETX>>
The Serotonergic Central Nervous System of the Drosophila Larva: Anatomy and Behavioral Function

The Drosophila larva has turned into a particularly simple model system for studying the neuronal basis of innate behaviors and higher brain functions. Neuronal networks involved in olfaction, gustation, vision and learning and memory have been described during the last decade, often up to the single-cell level. Thus, most of these sensory networks are substantially defined, from the sensory level up to third-order neurons. This is especially true for the olfactory system of the larva. Given the wealth of genetic tools in Drosophila it is now possible to address the question how modulatory systems interfere with sensory systems and affect learning and memory. Here we focus on the serotonergic system that was shown to be involved in mammalian and insect sensory perception as well as learning and memory. Larval studies suggested that the serotonergic system is involved in the modulation of olfaction, feeding, vision and heart rate regulation. In a dual anatomical and behavioral approach we describe the basic anatomy of the larval serotonergic system, down to the single-cell level. In parallel, by expressing apoptosis-inducing genes during embryonic and larval development, we ablate most of the serotonergic neurons within the larval central nervous system. When testing these animals for naïve odor, sugar, salt and light perception, no profound phenotype was detectable; even appetitive and aversive learning was normal. Our results provide the first comprehensive description of the neuronal network of the larval serotonergic system. Moreover, they suggest that serotonin per se is not necessary for any of the behaviors tested. However, our data do not exclude that this system may modulate or fine-tune a wide set of behaviors, similar to its reported function in other insect species or in mammals. Based on our observations and the availability of a wide variety of genetic tools, this issue can now be addressed.
Federal Reserve Bank of New York Staff Reports CoVaR

We propose a measure for systemic risk: CoVaR, the value at risk (VaR) of financial institutions conditional on other institutions being in distress. We define an institution’s (marginal) contribution to systemic risk as the difference between CoVaR and the financial system’s VaR. From our estimates of CoVaR for characteristic-sorted portfolios of publicly traded financial institutions, we quantify the extent to which characteristics such as leverage, size, and maturity mismatch predict systemic risk contribution. We argue for macro-prudential regulation based on the degree to which such characteristics forecast systemic risk contribution.
Inhibition by recombinant SLPI and half‐SLPI (Asn55‐Ala107) of elastase and cathepsin G activities: consequence for neutrophil‐platelet cooperation

1 The capacity of recombinant human secretory leukocyte proteinase inhibitor (SLPI) to inhibit human leukocyte elastase (HLE) and cathespin G (Cat G) was investigated and compared with a recombinant truncated form (carboxyl‐terminal domain, Asn55‐Ala107) called 1/2 SLPI. 2 Both compounds were efficient when tested against enzymatic activities of purified HLE and Cat G indicating that the HLE‐ and Cat G‐inhibitory sites were preserved in the truncated form. SLPI and 1/2 SLPI also affected platelet activation induced by 0.2 μm Cat G (IC50 = 112 ± 13 nm for SLPI and 280 ± 12 nm for 1/2 SLPI). 3 The effects of SLPI and 1/2 SLPI were then tested against polymorphonuclear neutrophil (PMN)‐mediated platelet activation, a cell‐to‐cell interaction mediated by HLE and Cat G released from PMN. In this experimental system, addition of SLPI or 1/2 SLPI before N‐formyl‐Met‐Leu‐Phe (fMLP) led to the inhibition of the resulting platelet activation. As was the case for Cat G enzymatic activity and Cat G‐induced platelet activation, SLPI was more efficient than 1/2 SLPI (IC50 = 676 ± 69 nm vs 1121 ± 150 nm). 4 The ratio of the IC50 against PMN‐mediated platelet activation compared to purified Cat G‐mediated platelet activation was 6.03 for SLPI and 4.32 for 1/2 SLPI. This difference may be due to the smaller size of the truncated form which could allow this molecule to diffuse more easily between PMN and platelets. 5 In conclusion, 1/2 SLPI could be a promising candidate in the treatment of pathological states linked to inflammation in which participation of HLE and Cat G has been evoked.
Field emission study of strain controlled ZnO nanowire arrays via a hydrothermal technique

We report a novel approach to the rational fabrication of high quality strain controlled wurtzite ZnO nanowire arrays on conductive silicon and ITO substrates by a facile hydrothermal method. The quality of the ZnO nanowire arrays is dramatically improved by hanging the substrate above from the bottom of the Teflon lined autoclave. For comparison, the field emission device performance of the ZnO nanowire arrays grown under different experimental processes is investigated. The low turn-on voltage (1.9 V/μm) from field emission measurement was observed from ZnO nanowire arrays grown by substrate hanging growth procedure.
Scalar fields, bent branes, and RG flow

This work deals with braneworld scenarios driven by real scalar fields with standard dynamics. We show how the first-order formalism which exists in the case of four dimensional Minkowski space-time can be extended to de Sitter or anti-de Sitter geometry in the presence of several real scalar fields. We illustrate the results with some examples, and we take advantage of our findings to investigate renormalization group flow. We have found symmetric brane solutions with four-dimensional anti-de Sitter geometry whose holographically dual field theory exhibits a weakly coupled regime at high energy.
Improved analysis and evaluation of real-time semaphore protocols for P-FP scheduling

Several suspension-based multiprocessor real-time locking protocols for partitioned fixed-priority (P-FP) scheduling have been proposed in prior work. These protocols differ in key design choices that affect implementation complexity, overheads, and worst-case blocking, and it is not obvious which is “best” when implemented in a real OS. In particular, should blocked tasks wait in FIFO or in priority order? Should tasks execute critical sections locally on their assigned processor, or should resource access be centralized on designated processors? This paper reports on a large-scale, overhead-aware schedulability study comparing four protocols, the MPCP, FMLP+, DPCP, and the DFLP, which together cover each of the four possible combinations. The results are based on a new, linear-programming-based blocking analysis technique, which is explained in detail and shown to offer substantial improvements over prior blocking bounds. The results reveal that priority queuing (MPCP, DPCP) is often preferable if the range of temporal constraints spans (at least) an order of magnitude, whereas FIFO queueing (FMLP+, DFLP) is preferable if the ratio of longest to shortest deadlines is small. Further, centralized resource access (DPCP, DFLP) is found to be preferable to local critical sections (MPCP, FMLP+) for high-contention workloads. Scheduling, cache, and locking overheads were accounted for as measured in LITMUSRT on two 8- and 16-core x86 platforms. In contrast to earlier LITMUSRT-based studies, no statistical outlier filtering was performed, owing to improved tracing support.
Alginates in Foods

Alginate has been widely investigated since it was first isolated and described in 1881 by Stanford (E.C.C Stanford, 1881) and has since become a vastly utilised polymer with a variety of applications. Alginate is not only exploited in the food industry, but also in the paper and textile industries, pharmaceutical and more recently, for biomedical applications. The versatility of alginate has led to it being a fairly well understood material and has been subject to a great number of systematic rheological investigations, information from which has been subsequently utilised in food applications. More recently, their “high value” pharmaceutical and biomedical applications have driven the development and understanding of alginate further. This chapter intends to provide a brief overview of the chemical properties of alginates and to review the influence of molecular structure on the physical, functional and more specifically, rheological properties which are exploited in food systems. Specific applications in foods are also covered which highlight the multi functional nature of alginate and its future potential.
The Mammalian Circadian Clock Gene Per2 Modulates Cell Death in Response to Oxidative Stress

Living in the earth’s oxygenated environment forced organisms to develop strategies to cope with the damaging effects of molecular oxygen known as reactive oxygen species (ROS). Here, we show that Per2, a molecular component of the mammalian circadian clock, is involved in regulating a cell’s response to oxidative stress. Mouse embryonic fibroblasts (MEFs) containing a mutation in the Per2 gene are more resistant to cytotoxic effects mediated by ROS than wild-type cells, which is paralleled by an altered regulation of bcl-2 expression in Per2 mutant MEFs. The elevated survival rate and alteration of NADH/NAD+ ratio in the mutant cells is reversed by introduction of the wild-type Per2 gene. Interestingly, clock synchronized cells display a time dependent sensitivity to paraquat, a ROS inducing agent. Our observations indicate that the circadian clock is involved in regulating the fate of a cell to survive or to die in response to oxidative stress, which could have implications for cancer development and the aging process.
Multi-modal imaging, model-based tracking, and mixed reality visualisation for orthopaedic surgery

Orthopaedic surgeons are still following the decades old workflow of using dozens of two-dimensional fluoroscopic images to drill through complex 3D structures, e.g. pelvis. This Letter presents a mixed reality support system, which incorporates multi-modal data fusion and model-based surgical tool tracking for creating a mixed reality environment supporting screw placement in orthopaedic surgery. A red–green–blue–depth camera is rigidly attached to a mobile C-arm and is calibrated to the cone-beam computed tomography (CBCT) imaging space via iterative closest point algorithm. This allows real-time automatic fusion of reconstructed surface and/or 3D point clouds and synthetic fluoroscopic images obtained through CBCT imaging. An adapted 3D model-based tracking algorithm with automatic tool segmentation allows for tracking of the surgical tools occluded by hand. This proposed interactive 3D mixed reality environment provides an intuitive understanding of the surgical site and supports surgeons in quickly localising the entry point and orienting the surgical tool during screw placement. The authors validate the augmentation by measuring target registration error and also evaluate the tracking accuracy in the presence of partial occlusion.