Miracle-dz/UniFAR-FTUs huggingface dataset:
Visual Analysis of Multi-run Spatio-temporal Simulation Data

Multi-run simulations are widely used to investigate how the simulated processes evolve depending on varying initial conditions in different fields of sciences, such as astrophysics, ballistics, and oceanography. This kind of experiments is typically executed using high-performance computers and generates a large amount of data to analyze. The main goals of this work are an efficient visualization of multi-run time-varying spatial data, pairwise and ensemble-wise comparison of simulations, as well as simulation feature detection and investigation, and exploration and classification of simulation results. Also, this work aims generalization of developing approaches to be applicable for data of any spatial configuration and of a multi-field nature. This work introduces a number of approaches and tools, which can significantly improve an analysis of multi-run time-varying spatial data on all data aggregation levels from a field distribution of an single time frame up to overview of the whole simulations ensemble. To investigate a single-field spatial data a new isocontour based similarity measure is introduced. For an interactive visualization and for detailed comparative analysis of multi-field spatial data algorithms for a splat-based progressive rendering of continuous scatterplots are developed. For a comparative visualization of multi-run and multi-field spatio-temporal simulation data a new visualization technique, called multi-run similarity plots, is introduced. For an overview of a multi-run and multi-field spatio-temporal simulation data on a highest aggregation levels two histogram based visualizations are proposed. Finally, a scheme of a top-down analysis of a multi-run spatio-temporal simulation data is introduced. In this work an application on the real world data sets, results of a user study and evaluation by the domain experts, as well as detailed discussions about scalability of the methods, their efficiency and restrictions, are presented.
Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome

The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth. ABSTRACT Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield. Using a microbiome inoculation strategy, we studied how the belowground microbiome of Populus deltoides changes in response to diverse environmental conditions, including water limitation, light limitation (shading), and metal toxicity. While plant responses to treatments in terms of growth, photosynthesis, gene expression and metabolite profiles were varied, we identified a core set of bacterial genera that change in abundance in response to host stress. The results of this study indicate substantial structure in the plant microbiome community and identify potential drivers of the phytobiome response to stress. IMPORTANCE The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth.
Dosage‐dependent non‐linear effect of l‐dopa on human motor cortex plasticity

The neuromodulator dopamine affects learning and memory formation and their likely physiological correlates, long‐term depression and potentiation, in animals and humans. It is known from animal experiments that dopamine exerts a dosage‐dependent, inverted U‐shaped effect on these functions. However, this has not been explored in humans so far. In order to reveal a non‐linear dose‐dependent effect of dopamine on cortical plasticity in humans, we explored the impact of 25, 100 and 200 mg of l‐dopa on transcranial direct current (tDCS)‐induced plasticity in twelve healthy human subjects. The primary motor cortex served as a model system, and plasticity was monitored by motor evoked potential amplitudes elicited by transcranial magnetic stimulation. As compared to placebo medication, low and high dosages of l‐dopa abolished facilitatory as well as inhibitory plasticity, whereas the medium dosage prolonged inhibitory plasticity, and turned facilitatory plasticity into inhibition. Thus the results show clear non‐linear, dosage‐dependent effects of dopamine on both facilitatory and inhibitory plasticity, and support the assumption of the importance of a specific dosage of dopamine optimally suited to improve plasticity. This might be important for the therapeutic application of dopaminergic agents, especially for rehabilitative purposes, and explain some opposing results in former studies.
Long-Term Effects of Continuous Positive Airway Pressure on Blood Pressure and Prognosis in Hypertensive Patients with Coronary Heart Disease and Obstructive Sleep Apnea : A Randomized Controlled Trial

Obstructive sleep apnea (OSA) is a common disorder characterized by repetitive partial (hypopnea) or complete (apnea) occlusion of the upper airway during sleep, which is caused by collapse of the pharyngeal airway and results in sleep fragmentation and oxyhemoglobin desaturation.1 A study by Kiely and colleagues has shown that >20% of hypertensive patients exhibit OSA, whereas the prevalence of hypertension in the setting of OSA is >50%. 2 One study confirms that OSA is an important identifiable cause of hypertension.3 OSA is considered as one of the most common risk factors of resistant hypertension.4,5 The estimated prevalence of OSA among male patients with coronary artery disease (CAD) is 37%. 6 A previous study has suggested that OSA significantly increases cardiovascular morbidity and mortality, especially in patients with preexisting cardiovascular disease.7 Several studies8–13 have found that continuous positive airway pressure (CPAP) reduces systolic blood pressure (SBP) and diastolic blood pressure (DBP) in patients with OSA. Additionally, some articles have reported that there is a protective effect of CPAP therapy against death from cardiovascular disease in patients with severe OSA.14,15 Other studies have not demonstrated that CPAP has an antihypertensive effect.16,17 However, relevant studies have a relative short study duration, with few extending longer than 1 year. In our opinion, they are not sufficient to detect the real effects of CPAP on blood pressure (BP). Based on our Long-Term Effects of Continuous Positive Airway Pressure on Blood Pressure and Prognosis in Hypertensive Patients with Coronary Heart Disease and Obstructive Sleep Apnea: A Randomized Controlled Trial
Molecular types of Cryptococcus gattii/Cryptococcus neoformans species complex from clinical and environmental sources in Nairobi, Kenya

Cryptococcal meningitis infections cause high mortality rates among HIV‐infected patients in Sub‐Saharan Africa. The high incidences of cryptococcal infections may be attributed to common environmental sources which, if identified, could lead to institution of appropriate control strategies. To determine the genotypes of Cryptococcus gattii/C. neoformans‐ species complex from Nairobi, Kenya, 123 clinical and environmental isolates were characterised. Typing was done using orotidine monophosphate pyrophosphorylase (URA5) gene restriction fragment length polymorphism (URA5‐RFLP). The majority of the isolates [105/123; 85.4%] were C. neoformans genotype (AFLPI/VNI) and 1.6% AFLP1A/VNB/VNII, whereas (13%) were C. gattii (AFLP4/VGI). This is the first report on the genotypes of C. gattii/C. neoformans species complex from clinical and environmental sources in Nairobi, Kenya and the isolation of C. gattii genotype AFLP4/VGI from the environment in Kenya.
A retrospective study on the clinical presentation and treatment outcome of melasma in a tertiary dermatological referral centre in Singapore.

BACKGROUND This is a retrospective study on the epidemiology of 205 patients with melasma seen in a tertiary dermatological referral centre in Singapore. PATIENTS The mean age of the 205 patients with melasma was 42.3 years with a female preponderance of 21:1 female to male ratio. There were proportionally more Chinese with melasma than the other races compared to the racial distribution of patients attending our clinic. Ninety percent of our patients had skin type III or IV. The mean age of onset of melasma was 37.6 years. Most sought treatment only 5 years after the appearance of their melasma. Forty-six percent of melasma were light brown, the majority of which were distributed on the malar areas (89%). More than 2/3 had epidermal melasma. Eighty-eight percent had mild localised melasma (occurring on < 20% of the total facial area). Only 26.8% of our patients reported sun exposure, 25 (12.1%) reported pregnancy and 27 (13.1%) reported oral contraceptives as precipitating factors. A positive family history of melasma was observed in 21 (10.2%) patients. Sunscreen forms the backbone in the treatment of melasma in our patients. Most patients were prescribed a sunscreen together with hydroquinone containing bleaching cream (54%) as first line treatment. Patients with epidermal type of melasma responded slightly better to treatment than those with dermal type of melasma (28% experienced > 25% reduction in pigmentation compared to 16% respectively (n.s.)). CONCLUSION Overall, 53% of our patients experienced some reduction of pigmentation with 28% experiencing > 25% reduction and 7% experiencing > 75% reduction. In 40%, the pigmentation remained stable with treatment. Treatment of melasma remains an enigma. More studies need to be undertaken to improve treatment response to alleviate the psychosocial impact melasma has on the patient.
Randomized trial of intake of fat, fiber, and beta carotene to prevent colorectal adenomas.

BACKGROUND Epidemiologic evidence of associations between the high intake of fat and low intake of dietary fiber, beta carotene, and other dietary constituents and the risk of colorectal neoplasia has been inconsistent and has not provided a sufficient basis for recommendations concerning the dietary prevention of large-bowel cancer in humans. PURPOSE We conducted a clinical trial to assess the effects on the incidence of adenomas of reducing dietary fat to 25% of total calories and supplementing the diet with 25 g of wheat bran daily and a capsule of beta carotene (20 mg daily). METHODS We performed a randomized, partially double-blinded, placebo-controlled factorial trial in which half the patients were assigned to each intervention, resulting in seven intervention groups and one control group. Eligibility criteria included histologic confirmation of at least one colorectal adenoma and confidence expressed by the colonoscopist that all polyps had been removed. Dietary changes were individually initiated and monitored by dietitians and research nurses. At surveillance colonoscopy, the size and location of all polyps were recorded, and their histology was later centrally reviewed. Among 424 patients who were randomly assigned in the trial, 13 were found to be ineligible upon histologic review. Among the remaining 411, complete outcome data were collected from 390 at 24 months and from 306 at 48 months. All P values are from two-sided tests of statistical significance. RESULTS There was no statistically significant prevention of total new adenomas with any of the interventions. We found a statistically non-significant reduced risk of large adenomas (> or = 10 mm) with the low-fat intervention: At 24 months, the odds ratio (OR) adjusted for potential confounders = 0.4 and 95% confidence interval (CI) = 0.1-1.1; at 48 months, OR = 0.3 and 95% CI = 0.1-1.0. Less and statistically nonsignificant reductions in the risk of large adenomas were found with wheat bran: At 24 months, OR = 0.8 and 95% CI = 0.3-2.2; at 48 months, OR = 0.8 and 95% CI = 0.3-2.5. Patients on the combined intervention of low fat and added wheat bran had zero large adenomas at both 24 and 48 months, a statistically significant finding (P = .03). CONCLUSIONS Because only small numbers of patients were studied, our finding that the combination of fat reduction and a supplement of wheat bran reduced the incidence of large adenomas in this randomized, controlled trial must be treated with caution. The results do suggest, however, that these interventions may reduce the transition from smaller to larger adenomas, a step that may critically define those adenomas most likely to progress to malignancy.
Performance Optimization of 3D Lattice Boltzmann Flow Solver on a GPU

Lattice Boltzmann Method (LBM) is a powerful numerical simulation method of the fluid flow. With its data parallel nature, it is a promising candidate for a parallel implementation on a GPU. The LBM, however, is heavily data intensive and memory bound. In particular, moving the data to the adjacent cells in the streaming computation phase incurs a lot of uncoalesced accesses on the GPU which affects the overall performance. Furthermore, the main computation kernels of the LBM use a large number of registers per thread which limits the thread parallelism available at the run time due to the fixed number of registers on the GPU. In this paper, we develop high performance parallelization of the LBM on a GPU by minimizing the overheads associated with the uncoalesced memory accesses while improving the cache locality using the tiling optimization with the data layout change. Furthermore, we aggressively reduce the register uses for the LBM kernels in order to increase the run-time thread parallelism. Experimental results on the Nvidia Tesla K20 GPU show that our approach delivers impressive throughput performance: 1210.63 Million Lattice Updates Per Second (MLUPS).
Silicone Augmentation Rhinoplasty in an Oriental Population

Aesthetic augmentation rhinoplasty is gaining in popularity among Oriental populations. Despite being widely criticized in the literature, silicone implants remain the most commonly used as a result of their ease of application and lack of donor site morbidity. The authors present 355 consecutive Chinese patients who underwent silicone augmentation rhinoplasty from January 1999 to April 2003. During a mean follow-up period of 160 days, 28 patients (7.9%) developed major complications that required either removal or revision of the implant. The patients who had received the largest volume implants had the highest extrusion and infection rates, indicating that overaugmentation is the main cause. The authors hypothesize that the lower complication rates in Oriental compared with white populations is primarily the result of structural differences in the soft tissue envelope of the nose. In our series of patients, nasal augmentation with silicone implants proved to be effective and safe.
Variations of OCT measurements corrected for the magnification effect according to axial length and refractive error in children

Purpose: The aim of this paper was to examine the distribution of macular, retinal nerve fiber layer (RNFL) thickness and optic disc parameters of myopic and hyperopic eyes in comparison with emmetropic control eyes and to investigate their variation according to axial length (AL) and spherical equivalent (SE) in healthy children. Methods: This study included 293 pairs of eyes of 293 children (145 boys and 148 girls), ranging in age from 6 to 17 years. Subjects were divided according to SE in control (emmetropia, 99 children), myopia (100 children) and hyperopia (94 children) groups and according to axial AL in 68 short ( 25.00mm, 36). Macular parameters, RNFL thickness and optic disc morphology were assessed by the CirrusTM HD-OCT. AL was measured using the IOL-Master system. Littmann’s formula was used for calculating the corrected AL-related ocular magnification. Results: Mean age (±SD) was 10.84±3.05 years; mean (±SD) SE was +0.14±0.51 D (range from −8.75 to +8.25 D) and mean AL (±SD) was 23.12±1.49. Average RNFL thickness, average macular thickness and macular volume decreased as AL and myopia increased. No correlations between AL/SE and optic disc parameters were found after correcting for magnification effect. Conclusions: AL and refractive error affect measurements of macular and RNFL thickness in healthy children. To make a correct interpretation of OCT measurements, ocular magnification effect should be taken into account by clinicians or OCT manufacturers.
Pulsed lavage in wound cleansing.

Wound cleansing is an essential component of wound management used to facilitate the wound healing process.1,2 Several methods are available for use by the physical therapist to achieve wound cleansing.1–4 This update reviews the research examining the effects of pulsed lavage in wound cleansing and comparisons with more traditional methods of wound cleansing. Normal wound healing is characterized by 3 overlapping phases: inflammatory, proliferative or fibroplastic, and remodeling.5,6 Vascular and cellular responses to trauma occurring during the inflammatory phase remove infectious microorganisms, foreign materials, and necrotic tissue from the wound's surface. During the proliferative phase, tissue granulation and reepithelialization occur.5,6 Collagen fibers are deposited in the dermis of the skin during the remodeling phase to strengthen the healing wound. If the body's inflammatory response is inadequate to overcome surface microorganisms, a wound is predisposed to infection, delaying wound angiogenesis and granulation.7 In the 1950s, Liedberg et al8 showed that when bacterial concentrations of streptococci, pseudomonas, or staphylococci were greater than 100,000 organisms per gram in tissues, skin grafts on rabbits were destroyed. In 1969, Robson and Heggers9 summarized military and civilian studies examining the critical level of bacterial burden necessary to produce wound sepsis and failure to heal. They concluded that wound healing is possible only when bacterial counts are maintained at a concentration of 100,000 organisms per gram or less. Impediments to healing are not limited to the presence of microorganisms on the wound's surface. Winter,10 for example, suggested that the presence of eschar or scab in a dry wound delays wound epithelialization and contraction. Likewise, Constantine and Bolton11 surmised that the presence of necrotic tissue or eschar, within the wound or at the wound's margin, impedes wound contraction and closure. Elek …
Expression and function of decapentaplegic and thick veins during the differentiation of the veins in the Drosophila wing

The differentiation of the veins in the Drosophila wing involves the coordinate activities of several signal transduction pathways, including those mediated by the transmembrane receptors Torpedo and Notch. In this report, the role of the signalling molecule Decapentaplegic during vein differentiation has been analysed. It is shown that decapentaplegic is expressed in the pupal veins under the control of genes that establish vein territories in the imaginal disc. Decapentaplegic, acting through its receptor Thick veins, activates vein differentiation and restricts expression of both veinlet and the Notch-ligand Delta to the developing veins. Genetic combinations between mutations that increase or reduce Notch, veinlet and decapentaplegic activities suggest that the maintenance of the vein differentiation state during pupal development involves cross-regulatory interactions between these pathways.
Predictors of insufficient sweat production during confirmatory testing for cystic fibrosis

Michigan's Newborn Screening (NBS) Program began statewide screening for cystic fibrosis (CF) in October 2007. Confirmatory sweat testing is performed in infants having initial immunoreactive trypsinogen concentrations ≥99.8th percentile or ≥96th percentile and at least one CF mutation identified by DNA analysis. Some infants fail to produce a sufficient quantity of sweat (QNS—quantity not sufficient) to test for CF, meaning disease confirmation is delayed and sweat testing is later repeated. In this study, we evaluate predictors of QNS results. Information from the linked birth certificates and NBS diagnostic confirmation data were used. The study population was resident infants born in Michigan in 2008 who underwent a sweat test. Bivariate analyses revealed that preterm birth, low birth weight, CF care center, and race were significantly associated with QNS sweat testing results. Adjusted analyses indicated that preterm infants were 2.4 times more likely to have QNS results (95% CI 0.9, 6.4). When age at time of test, accounting for gestational age (gestational age at delivery plus postdelivery age of life = corrected age), was used in the multivariable model, infants <39 weeks were 7.4 times more likely to have QNS results (95% CI 2.5, 21.8). Waiting to sweat test until an infant is aged 39 weeks or more (corrected age) would likely reduce the rate of QNS results, thereby reducing the burden of repeat sweat testing on families and healthcare providers. Further research is necessary to understand the impact of potential delays in diagnosis/treatment relative to postponing sweat testing. Pediatr Pulmonol. 2011; 46:23–30. © 2010 Wiley‐Liss, Inc.
Virulence of human and bovine isolates of group B streptococci (types Ia and III) in experimental pregnant mouse models

Two experimental mouse models were tested for their suitability in measuring virulence of two human and two bovine isolates (types Ia and III) of group B streptococci. In the first model, the kinetics of the number of bacteria in the spleen, liver, and placenta of mice inoculated intravenously on day 16 of pregnancy were monitored for 48 h after infection. In the second model, lethality and abortion were recorded for mice inoculated on day 13 of pregnancy. Levels of colonization in spleens or livers and lethality were significantly greater (P less than 0.001) for human isolates than for bovine isolates. In contrast, no statistically significant differences in the ability to colonize placentas and to induce abortions were noted between human and bovine isolates. The results showed that pregnant mice were more sensitive than nonpregnant mice to a challenge with group B streptococci. The results also suggest that placental colonization and abortion could be a suitable mouse model in evaluating the virulence of human and bovine isolates of group B streptococci.