Miracle-dz/UniFAR-FTUs huggingface dataset:
DE NOVO INTRAOCULAR RETINOBLASTOMA DEVELOPMENT AFTER CHEMOTHERAPY IN PATIENTS WITH HEREDITARY RETINOBLASTOMA

Objective: Identification of incidence and risk factors for recurrence of de novo retinoblastomas after chemotherapy treatment in patients with hereditary retinoblastoma. Methods: A retrospective, case–control study of 32 patients (50 eyes) with sporadic or familial bilateral retinoblastomas was conducted. Patients received a systemic chemotherapy regimen applying three courses of a combination of three drugs (including vincristine, etoposide, carboplatin, or cyclophosphamide) followed by additional local therapy. The primary outcome analyzed was the development of retinoblastomas, probably arising as the cause of a new mutational event (de novo) after completion of chemotherapy treatment. Results: Patients were treated with an average of 5.8 ± 1.8 chemotherapy courses (4.6 ± 2.4-year follow-up time). Development of de novo tumors occurred in 48% of the treated eyes. These tumors occurred during chemotherapy treatment or within 7 months of chemotherapy completion. No de novo tumors developed in patients older than 3.2 years. Children who developed de novo tumors were significantly younger at the time of diagnosis (6.7 ± 6.3 months vs 14.4 ± 11.4 months, P < 0.001), and had a significantly lower number of tumors per eye at treatment begin (2.6 ± 2.3 tumors vs 4.3 ± 6.4 tumors, P < 0.001). The difference of the total numbers of retinoblastomas that developed per eye between the patients that developed de novo retinoblastomas during or after chemotherapy and patients who did not was not statistically significant (4.9 ± 2.7 and 4.3 ± 6.4, respectively, P = 0.8). No eye was lost because of de novo retinoblastoma development, and 92% of the eyes were preserved. Conclusions: De novo retinoblastomas developed both during and after completion of chemotherapy treatment. Younger children were at a significantly higher risk for developing de novo intraocular retinoblastomas. Good tumor control and eye preservation rates were achieved with regular and frequent control examinations in addition to the immediate treatment of de novo retinoblastomas.
Deep-sea coral amino acid archives of marine ecosystem function in east and southeast Australian waters

The research presented here uses deep-sea bamboo corals (Family Isididae) to reconstruct ecosystem dynamics in southeast Australian waters over the past 50-100 years. The work is divided into two complimentary research themes: methodological considerations and case studies that apply amino acid compound specific isotope analysis (AA-CSIA) to specimens from three regions: the subtropical Lord Howe Rise, and temperate to subantarctic Tasmanian waters. These case studies test the central thesis that Australian marine ecosystems are sensitive to documented oceanographic change. First, improvements to the graphite preparation for radiocarbon analysis are presented. These improvements minimized sampling requirements and enabled routine analysis of less than 100 micrograms of carbon. Optimized protocols reduced sample requirements from 2.5 milligrams to 100 micrograms of coral protein, significantly improving the resolving power of the reconstructions. To improve the spatial resolution of the study, it was necessary to test for artefacts of preservation method from different coral collections. Preservation method had no effect on the composition of radiocarbon, AA stable carbon and nitrogen isotopes or elemental ratios in either the organic or carbonate fractions. However, minimal alteration to organic bulk carbon isotopes, and a significant offset in carbonate lattice Ba:Ca after storage in ethanol were observed. The differing distribution of AA between coral families has significant implications for how deep-sea coral isotope proxies are applied to decipher paleoclimate. Multivariate analyses demonstrated first, the need to consider tissue-specific fractionation before applying pre-existing trophodynamic parameters to coral protein, and second, that the carbon and nitrogen isotopic composition of several amino acids show promise as diagnostic biomarkers of dominant algal clades in surface waters. Second, the isotopic composition of deep-sea corals was used to track or trace the provenance and fate of organic matter produced in surface waters. On the Lord Howe Rise, reconstructions indicate that the input of nitrogen fixation to the ‘new’ nitrogen budget varies significantly (approximately 60 per cent) on timescales comparable to variability in wind and flow regime of the South Pacific Gyre and East Australian Current, respectively. It is hypothesized that a surface community shift toward diazatrophs occurs during decreased wind over the Gyre when flow is favoured along the Tasman Front. South of the Tasman Front, three distinct surface community
Association Between 18F-Fluoro-2-Deoxy-d-Glucose Uptake Values and Tumor Vitality: Prognostic Value of Positron Emission Tomography in Early-Stage Non-small Cell Lung Cancer

Introduction: The prognostic value of quantitative 18F-fluoro-2-deoxy-d-glucose (FDG) uptake on positron emission tomography (PET) is controversial in unselected patients with non-small cell lung cancer (NSCLC). We assessed the in vivo FDG uptake, measured as maximum pixel standardized uptake value (SUVmax), in stages I and II NSCLC for its prognostic value and association with in vitro quantitative morphology of tumor vitality. Methods: Prospective FDG-PET data were available in 91 consecutive patients operated for pathologic stages I and II NSCLC. Quantitative morphology was performed of tumor architecture, tumor cell density and immunohistochemical biomarkers for apoptosis (caspase-3), cell proliferation (Ki-67), hypoxia (HIF-1α), cellular pH regulation (carbonic anhydrase IX [CAIX]), and microvessel density (CD31). Results: SUVmax ≥ median and SUVmax partial volume corrected for lesion size (PVC SUVmax) ≥ median were associated with an increased risk of death in univariable analysis. After correcting for stage, tumor size and age in multivariable analysis, only PVC SUVmax ≥ median remained significant. The strong significant association between tumor size and SUVmax weakened after PVC, suggesting that an important amount of SUVmax can be simply explained by tumor size, which is less in case for PVC SUVmax that associates more to the tumor cell density. In multivariable logistic regression analysis, a PVC SUVmax ≥ median could be explained by high Ki-67 and high-CAIX length density. Conclusion: PVC SUVmax has a prognostic value in completely resected stages I and II NSCLC. A high-quantitative FDG uptake is associated with characteristics of tumor vitality such as high tumor cell density, high cell proliferation, and extracellular acidosis.
Journal of Graph Algorithms and Applications a Polynomial Time Algorithm for Finding Nash Equilibria in Planar Win-lose Games

Two-player win-lose games have a simple directed graph representation. Exploiting this, we develop graph theoretic techniques for finding Nash equilibria in such games. In particular, we give a polynomial time algorithm for finding a Nash equilibrium in a two-player win-lose game whose graph representation is planar.
Chemical-biogeographic survey of secondary metabolism in soil

Significance A comparative analysis of conserved domain fragments amplified from nonribosomal peptide and polyketide-type gene clusters present in diverse soil microbiomes revealed a link between soil type, species composition, and biosynthetic richness, as well as an unexpected conservation of the meta-secondary metabolome present within microbiomes from similar soil types. Although the functional consequences of these enrichment patterns is not yet clear, it suggests that similar soil types contain functionally related collections of secondary metabolites that likely play conserved roles in the ecology of these soils. This work provides a model for the large-scale extension of molecular phylogenetic-type analyses directly to the study, characterization, and comparison of secondary metabolite biosynthetic gene clusters that remain hidden in diverse soil microbiomes. In this study, we compare biosynthetic gene richness and diversity of 96 soil microbiomes from diverse environments found throughout the southwestern and northeastern regions of the United States. The 454-pyroseqencing of nonribosomal peptide adenylation (AD) and polyketide ketosynthase (KS) domain fragments amplified from these microbiomes provide a means to evaluate the variation of secondary metabolite biosynthetic diversity in different soil environments. Through soil composition and AD- and KS-amplicon richness analysis, we identify soil types with elevated biosynthetic potential. In general, arid soils show the richest observed biosynthetic diversity, whereas brackish sediments and pine forest soils show the least. By mapping individual environmental amplicon sequences to sequences derived from functionally characterized biosynthetic gene clusters, we identified conserved soil type–specific secondary metabolome enrichment patterns despite significant sample-to-sample sequence variation. These data are used to create chemical biogeographic distribution maps for biomedically valuable families of natural products in the environment that should prove useful for directing the discovery of bioactive natural products in the future.
Identification of unusual Chlamydia pecorum genotypes in Victorian koalas (Phascolarctos cinereus) and clinical variables associated with infection.

Chlamydia pecorum infection is a threat to the health of free-ranging koalas (Phascolarctos cinereus) in Australia. Utilizing an extensive sample archive we determined the prevalence of C. pecorum in koalas within six regions of Victoria, Australia. The ompA genotypes of the detected C. pecorum were characterized to better understand the epidemiology of this pathogen in Victorian koalas. Despite many studies in northern Australia (i.e. Queensland and New South Wales), prior Chlamydia studies in Victorian koalas are limited. We detected C. pecorum in 125/820 (15 %) urogenital swabs, but in only one ocular swab. Nucleotide sequencing of the molecular marker C. pecorum ompA revealed that the majority (90/114) of C. pecorum samples typed were genotype B. This genotype has not been reported in northern koalas. In general, Chlamydia infection in Victorian koalas is associated with milder clinical signs compared with infection in koalas in northern populations. Although disease pathogenesis is likely to be multifactorial, the high prevalence of genotype B in Victoria may suggest it is less pathogenic. All but three koalas had C. pecorum genotypes unique to southern koala populations (i.e. Victoria and South Australia). These included a novel C. pecorum ompA genotype and two genotypes associated with livestock. Regression analysis determined that significant factors for the presence of C. pecorum infection were sex and geographical location. The presence of 'wet bottom' in males and the presence of reproductive tract pathology in females were significantly associated with C. pecorum infection, suggesting variation in clinical disease manifestations between sexes.
A Rodent Model of Dynamic Facial Reanimation Using Functional Electrical Stimulation

Facial paralysis can be a devastating condition, causing disfiguring facial droop, slurred speech, eye dryness, scarring and blindness. This study investigated the utility of closed-loop functional electric stimulation (FES) for reanimating paralyzed facial muscles in a quantitative rodent model. The right buccal and marginal mandibular branches of the rat facial nerve were transected for selective, unilateral paralysis of whisker muscles. Microwire electrodes were implanted bilaterally into the facial musculature for FES and electromyographic (EMG) recording. With the rats awake and head-fixed, whisker trajectories were tracked bilaterally with optical micrometers. First, the relationship between EMG and volitional whisker movement was quantified on the intact side of the face. Second, the effect of FES on whisker trajectories was quantified on the paralyzed side. Third, closed-loop experiments were performed in which the EMG signal on the intact side triggered FES on the paralyzed side to restore symmetric whisking. The results demonstrate a novel in vivo platform for developing control strategies for neuromuscular facial prostheses.
Regulation of bFGF gene expression and subcellular distribution of bFGF protein in adrenal medullary cells

Basic fibroblast growth factor (bFGF), a potent mitogenic/neurotrophic factor, controls the development and plasticity of many types of neural cells. In adrenal chromaffin cells, the appearance of bFGF protein coincided with the establishment of functional innervation, suggesting induction by trans-synaptic signals. In cultured bovine adrenal medullary cells Western blot analysis revealed 18-, 23-, and 24-kD bFGF isoforms in the cytosolic and nuclear fractions. Stimulation of acetylcholine nicotinic receptors or hormonal angiotensin II receptors or the direct stimulation of adenylate cyclase with forskolin or protein kinase C (PKC) with PMA increased the content of all bFGF isoforms. Increases in the levels of intracellular bFGF did not result in detectable presence of bFGF proteins in culture medium. Instead, bFGF proteins accumulated in the cytoplasm or the nucleus depending on whether PKC or cAMP pathways were activated. The long-term nuclear forskolin-induced accumulation of bFGF was prevented by cycloheximide or by antisense bFGF oligonucleotide and was also accompanied by an increase in bFGF mRNA. We used luciferase reporter plasmids containing the human bFGF promoter to show that the induction of bFGF resulted from transcriptional activation of the bFGF gene and was mediated by regulatory sequences located upstream from its transcription start site. Stimulation of bFGF gene expression by forskolin and PMA was synergistic and was mediated through different promoter regions. The results suggest that stimulation by cAMP and PKC is mediated through novel cis elements. The regulation of bFGF protein content also involves posttranscriptional mechanisms since changes in the levels of individual bFGF isoforms were different depending on whether cells were treated with carbachol or angiotensin II, forskolin, or PMA. The present study indicates that bFGF is an intracrine cytoplasmic-nuclear factor, whose expression is regulated by trans-synaptic and hormonal stimuli and which may act as a direct mediator of genomic responses to afferent stimulation.
A Flexible Kernel for Adaptive Mesh Refinement on GPU

We present a flexible GPU kernel for adaptive on‐the‐fly refinement of meshes with arbitrary topology. By simply reserving a small amount of GPU memory to store a set of adaptive refinement patterns, on‐the‐fly refinement is performed by the GPU, without any preprocessing nor additional topology data structure. The level of adaptive refinement can be controlled by specifying a per‐vertex depth‐tag, in addition to usual position, normal, color and texture coordinates. This depth‐tag is used by the kernel to instanciate the correct refinement pattern, which will map a refined connectivity on the input coarse polygon. Finally, the refined patch produced for each triangle can be displaced by the vertex shader, using any kind of geometric refinement, such as Bezier patch smoothing, scalar valued displacement, procedural geometry synthesis or subdivision surfaces. This refinement engine does neither require multipass rendering nor any use of fragment processing nor special preprocess of the input mesh structure. It can be implemented on any GPU with vertex shading capabilities.
PC based precision timing without GPS

A highly accurate monitoring solution for active network measurement is provided without the need for GPS, based on an alternative software clock for PC's running Unix. With respect to clock rate, it's performance exceeds common GPS and NTP synchronized software clock accuracy. It is based on the TSC register counting CPU cycles and offers a resolution of around 1ns, a rate stability of 0.1PPM equal to that of the underlying hardware, and a processing overhead well under 1µs per timestamp. It is scalable and can be run in parallel with the usual clock. It is argued that accurate rate, and not synchronised offset, is the key requirement of a clock for network measurement. The clock requires an accurate estimation of the CPU cycle period. Two calibration methods which do not require a reference clock at the calibration point are given. To the TSC clock we add timestamping optimisations to create two high accuracy monitors, one based on Linux and the other on Real-Time Linux. The TSC-RT-Linux monitor has offset fluctuations of the order of 1µs. The clock is ideally suited for high precision active measurement.
Antibiotic Susceptibility Patterns of Pseudomonas Corneal Ulcers in Contact Lens Wearers

Purpose: To evaluate the resistance or susceptibility of Pseudomonas aeruginosa, the most common pathogen in contact lens keratitis and corneal ulcer, to different antibiotic regimens. Materials and Methods: This cross-sectional study included all patients with recently diagnosed contact lens corneal ulcer whose culture results were positive for P. aeruginosa, from March 2009 to March 2010. The empirical antibiotic therapy was changed to appropriate antibiotics according to the culture results, provided that satisfactory clinical improvement was not achieved with the initial antibiotic regimen. The overall sensitivity or resistance of P. aeruginosa to the most commonly used antibiotics was assessed based on the results of the antibiograms. Results: Fifty-two patients (43 females and 9 males) were included. Forty-five patients (86%) were wearing cosmetic contact lenses, while 7 patients (14%) were using therapeutic contact lenses. Thirty-nine patients (75%) were hospitalized and13 patients (25%) were followed up through an outpatient clinic. Thirty patients (58%) had central ulcers, whereas 22 patients (42%) had peripheral ulcers. Twelve patients (23%) had hypopyon in their first exam. The mean time to diagnose the ulcer after the last time wearing was 2 days (range: 12 hours to 5 days). AMT was required for 10 patients (19%). Based on the antibiograms, PA was shown to be sensitive in 100% of cases to ceftazidime and ciprofloxacin. Amikacin, imipenem, and gentamicin were the second most effective antibiotics. Conclusion: P. aeruginosa was highly sensitive to ceftazidime, ciprofloxacin, and amikacin. All cases were resistant to cefazolin. Resistance to multiple antibiotics might be a significant concern in patients with corneal ulcers. In referral centers dealing with corneal ulcers, the initial antibiotic regimens should be changed from time to time to prevent this phenomenon.
INVESTIGATION OF THE MULTI-SCALE INTERACTIONS BETWEEN AN OFFSHORE WIND TURBINE WAKE AND THE OCEAN-SEDIMENT DYNAMICS IN A INDEALIZED FRAMEWORK

A coupled two dimensional idealized numerical model of the ocean and sediment layers, forced by an offshore wind turbine wake is used to investigate the complex interactions between the wake, the ocean and the sediment layers, together with the retro-action on the wind energy. Results show that the turbine wake has an impact on both, the ocean and the sediment layers. The turbine wake impacts the ocean surface and generates instabilities or vortex streets for some parameter values. Shallow ocean layers (typically below 15m) are laminar. When water depth is higher, large scale instabilities are generated, leading to a turbulent dynamic in the ocean layer. The size of the generated vortices in the ocean increases with water depth and decreases with the quadratic-law bottom friction coefficient. Considering the morphodynamics three cases are observed, depending on whether the ocean dynamics is laminar (i), has a localized (ii) or domain wide (iii) turbulent behavior. In the first case, changes in seabed elevation are around a few millimeters per month. Results are similar for the localized turbulence case with small spatial variations. For the domain wide turbulence case (iii), instantaneous seabed changes are of the order of a few millimeters per month, whereas the transport averaged over several days decreases to a few tenths of millimeter per month. This behavior is easily explained by the oscillating local velocity which transports sediments back and forth. The above emphasizes that the water depth is a key parameter for the coupled atmosphere-ocean-sediment system around wind turbines. Furthermore, considering the ocean velocity in the atmospheric forcing at the ocean surface leads to a decrease of 4 % of the power lost by friction at the atmosphere-ocean interface. Ocean dynamics could thus have a non-negligible feedback on the wind power available for the turbines and its variability.
The Distribution of Toxoplasma gondii Cysts in the Brain of a Mouse with Latent Toxoplasmosis: Implications for the Behavioral Manipulation Hypothesis

Background The highly prevalent parasite Toxoplasma gondii reportedly manipulates rodent behavior to enhance the likelihood of transmission to its definitive cat host. The proximate mechanisms underlying this adaptive manipulation remain largely unclear, though a growing body of evidence suggests that the parasite-entrained dysregulation of dopamine metabolism plays a central role. Paradoxically, the distribution of the parasite in the brain has received only scant attention. Methodology/Principal Findings The distributions of T. gondii cysts and histopathological lesions in the brains of CD1 mice with latent toxoplasmosis were analyzed using standard histological techniques. Mice were infected per orally with 10 tissue cysts of the avirulent HIF strain of T. gondii at six months of age and examined 18 weeks later. The cysts were distributed throughout the brain and selective tropism of the parasite toward a particular functional system was not observed. Importantly, the cysts were not preferentially associated with the dopaminergic system and absent from the hypothalamic defensive system. The striking interindividual differences in the total parasite load and cyst distribution indicate a probabilistic nature of brain infestation. Still, some brain regions were consistently more infected than others. These included the olfactory bulb, the entorhinal, somatosensory, motor and orbital, frontal association and visual cortices, and, importantly, the hippocampus and the amygdala. By contrast, a consistently low incidence of tissue cysts was recorded in the cerebellum, the pontine nuclei, the caudate putamen and virtually all compact masses of myelinated axons. Numerous perivascular and leptomeningeal infiltrations of inflammatory cells were observed, but they were not associated with intracellular cysts. Conclusion/Significance The observed pattern of T. gondii distribution stems from uneven brain colonization during acute infection and explains numerous behavioral abnormalities observed in the chronically infected rodents. Thus, the parasite can effectively change behavioral phenotype of infected hosts despite the absence of well targeted tropism.
Video Segmentation and Structuring for Indexing Applications

This paper introduces a complete framework for temporal video segmentation. First, a computationally efficient shot extraction method is introduced, which adopts the normalized graph partition approach, enriched with a non-linear, multiresolution filtering of the similarity vectors involved. The shot boundary detection technique proposed yields high precision 90% and recall 95% rates, for all types of transitions, both abrupt and gradual. Next, for each detected shot, the authors construct a static storyboard by introducing a leap keyframe extraction method. The video abstraction algorithm is 23% faster than existing techniques for similar performances. Finally, the authors propose a shot grouping strategy that iteratively clusters visually similar shots under a set of temporal constraints. Two different types of visual features are exploited: HSV color histograms and interest points. In both cases, the precision and recall rates present average performances of 86%.