Miracle-dz/UniFAR-FTUs huggingface dataset:
Stochastic Lagrangian Trajectory Modeling of Surface Drifters Deployed during the Deepwater Horizon Oil Spill

Lagrangian trajectory models have been demonstrated to be a useful tool in oil spill response. Despite the improvements in this kind of models, surface drift prediction remains a difficult task plagued with uncertainties. This work presents a Stochastic Lagrangian Trajectory Model (SLTM) that quantifies the uncertainties in trajectory simulations and defines the most likely search area of possible trajectories. The methodology includes the following steps: 1) Numerical scheme based on the transport equation in Lagrangian form; (2) Parameter estimation process, which includes: (i) time independent parameter estimation based on the maximum likelihood method and (ii) time dependent parameter estimation through autoregressive moving average; (3) Monte Carlo simulation of multiple trajectories based on the joint probability distribution function and the temporal dependency model. The model is used to simulate the trajectories of surface drifters deployed in the Gulf of Mexico during the Deepwater Horizon oil spill incident using surface currents provided by the Global model HYCOM. A set of drifters was selected to estimate the model parameters and another one for simulation and validation. Observed drifter trajectories were compared with the modeled trajectories obtained with the deterministic and the SLTM approaches. After 5 days of simulation the root mean squared error of Lagrangian separation distance was found to be 115 km and 37 km for the deterministic approach and the best simulation of the SLTM, respectively. Moreover, actual trajectories were in the areas where the model predicted that the drifter was likely to go through, showing the capabilities of the SLTM for oil spill trajectory modelling and search and rescue applications.
A Two-Dimensional Data Distribution Method for Parallel Sparse Matrix-Vector Multiplication

A new method is presented for distributing data in sparse matrix-vector multiplication. The method is two-dimensional, tries to minimize the true communication volume, and also tries to spread the computation and communication work evenly over the processors. The method starts with a recursive bipartitioning of the sparse matrix, each time splitting a rectangular matrix into two parts with a nearly equal number of nonzeros. The communication volume caused by the split is minimized. After the matrix partitioning, the input and output vectors are partitioned with the objective of minimizing the maximum communication volume per processor. Experimental results of our implementation, Mondriaan, for a set of sparse test matrices show a reduction in communication volume compared to one-dimensional methods, and in general a good balance in the communication work. Experimental timings of an actual parallel sparse matrix-vector multiplication on an SGI Origin 3800 computer show that a sufficiently large reduction in communication volume leads to savings in execution time.
Refinement Algebra with Explicit Probabilism

Refinement algebra provides axioms for the stepwise removal of abstraction, in the form of demonic nondeterminism, in a first-order system that supports reasoning about loops. It has been extended by Solin and Meinecke to computations involving implicit probabilistic choices: demonic nondeterminism then satisfies weaker properties. In this paper their axiom system is extended to capture explicit probabilistic choices. The first form is an unquantified probabilistic choice; the second is a partial quantified probabilistic choice (from which the usual binary probabilistic choice can be recovered). The new refinement algebra is sound with respect to 1-bounded expectation transformers, the premier model of probabilistic computations, but also with respect to a new model introduced here to capture more directly partial quantified computations. In this setting a `normal form' result of Kozen is proved, replacing multiple loops with a single loop that does the same job; and the extent to which the two forms of loop have the same expected number of steps to termination is considered. Being entirely first-order, the new refinement algebra is targeted to automation.
Interaction of Complement Factor H and Fibulin3 in Age-Related Macular Degeneration

Age-related macular degeneration (AMD) is a major cause of vision loss. It is associated with development of characteristic plaque-like deposits (soft drusen) in Bruch’s membrane basal to the retinal pigment epithelium (RPE). A sequence variant (Y402H) in short consensus repeat domain 7 (SCR7) of complement factor H (CFH) is associated with risk for “dry” AMD. We asked whether the eye-targeting of this disease might be related to specific interactions of CFH SCR7 with proteins expressed in the aging human RPE/choroid that could contribute to protein deposition in drusen. Yeast 2-hybrid (Y2H) screens of a retinal pigment epithelium/choroid library derived from aged donors using CFH SCR7 baits detected an interaction with EFEMP1/Fibulin 3 (Fib3), which is the locus for an inherited macular degeneration and also accumulates basal to macular RPE in AMD. The CFH/Fib3 interaction was validated by co-immunoprecipitation of native proteins. Quantitative Y2H and ELISA assays with different recombinant protein constructs both demonstrated higher affinity for Fib3 for the disease-related CFH 402H variant. Immuno-labeling revealed colocalization of CFH and Fib3 in globular deposits within cholesterol-rich domains in soft drusen in two AMD donors homozygous for CFH 402H (H/H). This pattern of labeling was quite distinct from those seen in examples of eyes with Y/Y and H/Y genotypes. The CFH 402H/Fib3 interaction could contribute to the development of pathological aggregates in soft drusen in some patients and as such might provide a target for therapeutic intervention in some forms of AMD.
Dynamic coalition formation for efficient sleep time allocation in wireless sensor networks using cooperative game theory

This paper proposes a dynamic coalition formation algorithm for efficient sleep time allocation in a wireless sensor network (WSN) deployed to localize targets based on cooperation among the nodes. The sleep time allocation problem is formulated as a non-convex cooperative game and the concept of the core is exploited to solve this problem. In this formulation, determinant of the Cramér-Rao lower bound (CRLB) is used to evaluate the accuracy of estimations. Finally, an algorithm is proposed based on a best-reply rule which converges to the core with probability one if the core of the game is non-empty.
In vivo antioxidant properties of vitamin e and chromium in cold-stressed Japanese quails

An experiment was conducted to determine if vitamin E (α-tocopherol acetate) and chromium (chromium picolinate, Cr Pic) supplementation attenuate the negative effects of cold stress on egg production, egg quality, serum metabolites, and antioxidant status in Japanese quails (Coturnix coturnix japonica). One hundred and fifty laying Japanese quails (50-day-old) were divided into five groups, 30 birds per group. The laying quails kept at 6°C for 12 h/d (08.00 p.m. to 08.00 a.m.) were fed either a basal diet (low temperature-basal diet, CS group) or the basal diet supplemented with either 400 μg of Cr/kg of diet (Cr group), 250 mg of α-tocopherol-acetate per kg of diet (Vit. E group) or 400 μg of Cr plus 250 mg of α-tocopherol-acetate per kg of diet (Vit. E + Cr group) while quails kept at 18°C were fed a basal diet (thermo-neutral-basal diet, TN group). Performance and egg quality were significantly reduced in CS group compared with TN group. Supplemental chromium and vitamin E significantly increased live weight change, egg production, and improved feed efficiency in cold-stressed laying hens compared with the group fed the basal diet at 6°C. Egg production and egg weight were also greater (P < 0.05) in each supplemental group compared with the CS group. However, a combination of vitamin E and chromium, rather than each separately, provided the greatest performance. Supplemental vitamin E and chromium also increased serum vitamin C and E but, decreased malondialdehyde (MDA) concentrations (P < 0.05); the combination of vitamin E and chromium resulted in the highest levels of serum vitamin C and E within the cold-stressed quails. Results of the present study indicate that combined antioxidant supplements increased performance, egg quality and serum antioxidant levels while lowering MDA in cold-stressed quails.
A proteomic analysis of erythromycin resistance in Streptococcus pneumoniae

Streptococcus pneumoniae is a significant human pathogen which is an important cause of pneumonia and bacteraemia. Over the past few years the incidence of antibiotic resistance among clinical isolates of S. pneumoniae has increased. Penicillin resistance is now widespread and the frequency of isolates that are resistant to erythromycin has risen. Erythromycin resistance in S. pneumoniae follows two basic patterns. The MLS erythromycin‐resistant phenotype is due to the enzymatic methylation of ribosomal RNA that blocks erythromycin binding to the ribosome. Alternatively, in isolates of the M phenotype, a more recently documented mechanism, resistance is associated with an active efflux process that reduces intracellular levels of erythromycin. We used two‐dimensional electrophoresis to examine the proteins synthesised by erythromycin‐susceptible and ‐resistant S. pneumoniae. Erythromycin‐resistant S. pneumoniae with the M phenotype showed a significantly increased synthesis of a 38 500 Dalton (pI 6.27) protein compared to susceptible isolates. Peptide mass mapping was used to identify the 38 500 Dalton protein as glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH). It was demonstrated that S. pneumoniae synthesised at least three forms of GAPDH that differed in their isoelectric points. The form of GAPDH possessing the most basic pI showed the increased synthesis in the erythromycin‐resistant S. pneumoniae isolates. Alterations in the synthesis of GAPDH were only found for those erythromycin‐resistant isolates possessing the M phenotype. S. pneumoniae isolates with the MLS phenotype were indistinguishable from the susceptible strains using the analytical conditions employed for the current study. The possible role of GAPDH in erythromycin resistance of S. pneumoniae is considered.
Myeloperoxidase Expression as a Potential Determinant of Parthenolide-Induced Apoptosis in Leukemia Bulk and Leukemia Stem Cells

Given that parthenolide (PTL) is an effective antileukemic agent, identifying molecular markers that predict response to PTL is important. We evaluated the role of myeloperoxidase (MPO) in determining the sensitivity of leukemia cells to PTL-induced apoptosis. In this study, the level of PTL-induced generation of reactive oxygen species (ROS) and apoptosis was significantly higher in the MPO-high leukemia cell lines compared with the MPO-low leukemia cell lines. Pretreatment of MPO-high leukemia cells with a MPO-specific inhibitor, 4-aminobenzoic acid hydrazide, or a MPO-specific small interfering RNA (siRNA) abrogated the PTL-induced ROS generation and apoptosis, indicating that MPO plays a crucial role in PTL-induced apoptosis in leukemia cells. PTL-induced apoptosis was accompanied by down-regulation of nuclear factor-κB, Bcl-xL, Mcl-1, X-linked inhibitor of apoptosis protein, and survivin and selectively observed in primary acute myeloid leukemia (AML) cells expressing higher levels of MPO (≥50%) while sparing both AML cells with lower MPO and normal CD34-positive (CD34+) normal bone marrow cells. The extent of PTL-induced apoptosis of the CD34+CD38− cell fraction was significantly greater in the MPO-high AML cases, compared with the MPO-low AML (P < 0.01) and normal CD34+ marrow cells (P < 0.01). Nonobese diabetic/severe combined immunodeficient human leukemia mouse model also revealed that PTL preferentially targets the MPO-high AML cells. Our data suggest that MPO plays a crucial role in determining the susceptibility of leukemia cells to PTL-induced apoptosis. PTL can be considered a promising leukemic stem cell-targeted therapy for AML expressing high levels of MPO.
Analysis of lip motion due to the influence of vocalization

Lip motion features such as changes in lip width and length provide important information for authenticating personal identification or recognizing lip motions as commands. An interface based on lip motion features is practical because it can be operated without touching the device. In this study, we analyze changes in the motion features of lips due to the influence of vocalization We analyze five features: aspect ratio, horizontal length displacement, vertical length displacement, lip area, and vocalization The results show that the variation in the breadth and longitudinal width without vocalization has a tendency to increase as compared that with vocalization. Moreover, the number of image frames involved in a non-vocalized command is longer by 19.9%, on average.
Effect of Brefeldin A on the Structure of the Golgi Apparatus and on the Synthesis and Secretion of Proteins and Polysaccharides in Sycamore Maple (Acer pseudoplatanus) Suspension-Cultured Cells

Brefeldin A (BFA), a specific inhibitor of Golgi-mediated secretion in animal cells, has been used to study the organization of the secretory pathway and the function of the Golgi apparatus in plant cells. To this end, we have employed a combination of electron microscopical, immunocytochemical, and biochemical techniques to investigate the effects of this drug on the architecture of the Golgi apparatus as well as on the secretion of proteins and complex cell wall polysaccharides in sycamore maple (Acer pseudoplatanus) suspension-cultured cells. We have used 2.5 and 7.5 [mu]g/mL of BFA, which is comparable to the 1 to 10 [mu]g/mL used in experiments with animal cells. Electron micrographs of high-pressure frozen and freeze-substituted cells show that although BFA causes swelling of the endoplasmic reticulum cisternae, unlike in animal cells, it does not induce the disassembly of sycamore maple Golgi stacks. Instead, BFA induces the formation of large clusters of Golgi stacks, an increase in the number of trans-like Golgi cisternae, and the accumulation in the cytoplasm of very dense vesicles that appear to be derived from trans Golgi cisternae. These vesicles contain large amounts of xyloglucan (XG), the major hemicellulosic cell wall polysaccharide, as shown by immunocytochemical labeling with anti-XG antibodies. All of these structural changes disappear within 120 min after removal of the drug. In vivo labeling experiments using [3H]leucine demonstrate that protein secretion into the culture medium, but not protein synthesis, is inhibited by approximately 80% in the presence of BFA. In contrast, the incorporation of [3H]fucose into N-linked glycoproteins, which occurs in trans-Golgi cisternae, appears to be affected to a greater extent than the incorporation of[3H]xylose, which has been localized to medial Golgi cisternae. BFA also affects secretion of complex polysaccharides as evidenced by the approximate 50% drop in incorporation of [3H]xylose and [3H]fucose into cell wall hemicelluloses. Taken together, these findings suggest that at concentrations of 2.5 to 7.5 [mu]g/mL BFA causes the following major changes in the secretory pathway of sycamore maple cells: (a) it inhibits the transport of secretory proteins to the cell surface by about 80% and of hemicelluloses by about 50%; (b) it changes the patterns of glycosylation of N-linked glycoproteins and hemicelluloses; (c) it reduces traffic between trans Golgi cisternae and secretory vesicles; (d) it produces a major block in the transport of XG-containing, dense secretory vesicles to the cell surface; and (e) it induces the formation of large aggregates of Golgi stacks in the vicinity of the nucleus, possibly mediated by the fusion of Golgi matrix zones. Thus, although the Golgi apparatus of plant and animal cells share many functional and structural characteristics, the plant Golgi apparatus possesses properties that make its response to BFA unique.
Adding Inverse Kinematics for Providing Live Feedback in a Serious Game-Based Rehabilitation System

In this paper, we present a serious game-based framework for providing live feedback to a patient performing a rehabilitation therapy for the purpose of assisting a patient in correct therapeutic steps and obtaining high quality therapy data for further analysis. The game environment uses forward kinematics to receive the live sensory data from two 3D motion tracking sensors and uses inverse kinematics to analyze the sensory data stream in real-time. A subject performs a rehabilitation therapy prescribed by the physician and using both forward and inverse kinematics the system validates the angular and rotational positions of the joints with respect to the correct therapeutic posture and provides live feedback to the subject. As a proof of concept, we have developed an open source web-based framework that can be easily adopted for inhome therapy, without the assistance of a therapist. Finally, we share our initial test result, which is encouraging.
A Generative Probabilistic OCR Model

In this paper, we present a generative probabilistic optical character recognition (OCR) model that describes an end-to-end process from generation of the true word sequence to the noisy output of an OCR system. The model is designed for use in error correction in a postprocessing framework, treating the OCR system as a black-box. The focus of the system is to make OCR output more useful for computer usage. We present a £nitestate machine based implementation of the model, and demonstrate its ability to signi£cantly reduce word and character error rates.
Leukocyte Recruitment to the Inflamed Glomerulus: A Critical Role for Platelet-Derived P-Selectin in the Absence of Rolling1

The renal glomerulus is one of the few sites within the microvasculature in which leukocyte recruitment occurs in capillaries. However, due to the difficulty of directly visualizing the glomerulus, the mechanisms of leukocyte recruitment to glomerular capillaries are poorly understood. To overcome this, we rendered murine kidneys hydronephrotic to allow the visualization of the functional glomerular microvasculature during an inflammatory response. These experiments demonstrated that following infusion of anti-glomerular basement membrane (GBM) Ab, leukocytes became adherent in glomerular capillaries via a process of immediate arrest, without undergoing prior detectable rolling. However, despite the absence of rolling, this recruitment involved nonredundant roles for the P-selectin/P-selectin glycoprotein ligand-1 and β2 integrin/ICAM-1 pathways, suggesting that a novel form of the multistep leukocyte adhesion cascade occurs in these vessels. Anti-GBM Ab also increased glomerular P-selectin expression and induced a P-selectin-independent increase in platelet accumulation. Moreover, platelet depletion prevented both the increase in glomerular P-selectin, and the leukocyte recruitment induced by anti-GBM Ab. Furthermore, depletion of neutrophils and platelets also prevented the increase in urinary protein excretion induced by anti-GBM Ab, indicating that their accumulation in glomeruli contributed to the development of renal injury. Finally, infusion of wild-type platelets into P-selectin-deficient mice restored the ability of glomeruli in these mice to support leukocyte adhesion. Together, these data indicate that anti-GBM Ab-induced leukocyte adhesion in glomeruli occurs via a novel pathway involving a nonrolling interaction mediated by platelet-derived P-selectin.
Human Bladder Uroepithelial Cells Synergize with Monocytes to Promote IL-10 Synthesis and Other Cytokine Responses to Uropathogenic Escherichia coli

Urinary tract infections are a major source of morbidity for women and the elderly, with Uropathogenic Escherichia coli (UPEC) being the most prevalent causative pathogen. Studies in recent years have defined a key anti-inflammatory role for Interleukin-10 (IL-10) in urinary tract infection mediated by UPEC and other uropathogens. We investigated the nature of the IL-10-producing interactions between UPEC and host cells by utilising a novel co-culture model that incorporated lymphocytes, mononuclear and uroepithelial cells in histotypic proportions. This co-culture model demonstrated synergistic IL-10 production effects between monocytes and uroepithelial cells following infection with UPEC. Membrane inserts were used to separate the monocyte and uroepithelial cell types during infection and revealed two synergistic IL-10 production effects based on contact-dependent and soluble interactions. Analysis of a comprehensive set of immunologically relevant biomarkers in monocyte-uroepithelial cell co-cultures highlighted that multiple cytokine, chemokine and signalling factors were also produced in a synergistic or antagonistic fashion. These results demonstrate that IL-10 responses to UPEC occur via multiple interactions between several cells types, implying a complex role for infection-related IL-10 during UTI. Development and application of the co-culture model described in this study is thus useful to define the degree of contact dependency of biomarker production to UPEC, and highlights the relevance of histotypic co-cultures in studying complex host-pathogen interactions.
Training Melanoma Detection in Photographs Using the Perceptual Expertise Training Approach

Summary Although a deadly form of skin cancer, melanoma is treatable if detected early. However, current rule-based training practices in melanoma detection are not effective. We assessed an innovative technique to train melanoma detection using the perceptual expertise principles. Participants in the training group were trained to categorize melanoma and benign lesions to 95% accuracy. Participants in the control group received no training. Prior to testing all participants reviewed the ABCDE rules. Training was evaluated by the pre and post tests using the Melanoma Detection Test where participants categorized images of melanoma and benign lesions. As compared to the control group, the training group showed significant improvement in melanoma detection and became less liberal (i.e., bias toward categorizing a lesion as melanoma), and both improvements maintained a week after the training. These findings indicate that perceptual expertise training is a promising approach to train melanoma detection.Copyright © 2016 John Wiley & Sons, Ltd.
Age, Tumor Characteristics, and Treatment Regimen as Event Predictors in Ewing: A Children's Oncology Group Report

Purpose. To associate baseline patient characteristics and relapse across consecutive COG studies. Methods. We analyzed risk factors for LESFT patients in three randomized COG trials. We evaluated age at enrollment, primary site, gender, tumor size, and treatment (as randomized). We estimated event-free survival (EFS, Kaplan-Meier) and compared risk across groups (log-rank test). Characteristics were assessed by proportional hazards regression with the characteristic of interest as the only component. Confidence intervals (CI) for RR were derived. Factors related to outcome at level 0.05 were included in a multivariate regression model. Results. Between 12/1988 and 8/2005, 1444 patients were enrolled and data current to 2001, 2004, or 2008 were used. Patients were with a median age of 12 years (0–45), 55% male and 88% Caucasian. The 5-year EFS was 68.3% ± 1.3%. In univariate analysis age, treatment, and tumor location were identified for inclusion in the multivariate model, and all remained significant (p < 0.01). Since tumor size was not collected in the last study, the other two were reanalyzed. This model identified age, treatment, tumor location, and tumor size as significant predictors. Conclusion. Age > 18 years, pelvic tumor, size > 8 cms, and chemotherapy without ifosfamide/etoposide significantly predict worse outcome. AEWS0031 is NCT00006734, INT0091 and INT0054 designed before 1993 (unregistered).