Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-reflective boundary conditions for incompressible free surface fluids

We have developed a novel approach to open-boundaries for fluid animations. More specifically we present a highly efficient energy absorbing boundary condition for the incompressible Navier-Stokes equations in the prescence of a free surface. Our work extends and adapts a Perfectly Matched Layer (PML) approach [Berenger 1994; Johnson 2007], recently developed for the Navier-Stokes equations, to free surfaces in the context fluid animations. We show how our PML boundary condition is able to effectively eliminate reflections generated by the presence of solid boundaries in the simulation domain, and that our method is far superior to simpler approaches for reducing wave reflection. Furthermore, we have adapted our theoretical PML model to work with the Stable-Fluids Eulerian Navier-Stokes solver commonly used in computer graphics. Finally, we show that the cost of deploying our method in terms of memory and additional computations is small, and for a given quality significantly less than other known methods.
Transcranial light affects plasma monoamine levels and expression of brain encephalopsin in the mouse

ABSTRACT Encephalopsin (OPN3) belongs to the light-sensitive transmembrane receptor family mainly expressed in the brain and retina. It is believed that light affects mammalian circadian rhythmicity only through the retinohypothalamic tract, which transmits light information to the suprachiasmatic nucleus in the hypothalamus. However, it has been shown that light penetrates the skull. Here, we present the effect of transcranial light treatment on OPN3 expression and monoamine concentrations in mouse brain and other tissues. Mice were randomly assigned to control group, morning-light group and evening-light group, and animals were illuminated transcranially five times a week for 8 min for a total of 4 weeks. The concentrations of OPN3 and monoamines were analysed using western blotting and HPLC, respectively. We report that transcranial light treatment affects OPN3 expression in different brain areas and plasma/adrenal gland monoamine concentrations. In addition, when light was administered at a different time of the day, the response varied in different tissues. These results provide new information on the effects of light on transmitters mediating mammalian rhythmicity. Summary: Light exposure via ear canals has a significant effect on brain encephalopsin expression and plasma and adrenal gland monoamine production in the mouse.
Estimating Bacterial Diversity for Ecological Studies: Methods, Metrics, and Assumptions

Methods to estimate microbial diversity have developed rapidly in an effort to understand the distribution and diversity of microorganisms in natural environments. For bacterial communities, the 16S rRNA gene is the phylogenetic marker gene of choice, but most studies select only a specific region of the 16S rRNA to estimate bacterial diversity. Whereas biases derived from from DNA extraction, primer choice and PCR amplification are well documented, we here address how the choice of variable region can influence a wide range of standard ecological metrics, such as species richness, phylogenetic diversity, β-diversity and rank-abundance distributions. We have used Illumina paired-end sequencing to estimate the bacterial diversity of 20 natural lakes across Switzerland derived from three trimmed variable 16S rRNA regions (V3, V4, V5). Species richness, phylogenetic diversity, community composition, β-diversity, and rank-abundance distributions differed significantly between 16S rRNA regions. Overall, patterns of diversity quantified by the V3 and V5 regions were more similar to one another than those assessed by the V4 region. Similar results were obtained when analyzing the datasets with different sequence similarity thresholds used during sequences clustering and when the same analysis was used on a reference dataset of sequences from the Greengenes database. In addition we also measured species richness from the same lake samples using ARISA Fingerprinting, but did not find a strong relationship between species richness estimated by Illumina and ARISA. We conclude that the selection of 16S rRNA region significantly influences the estimation of bacterial diversity and species distributions and that caution is warranted when comparing data from different variable regions as well as when using different sequencing techniques.
A Synaptic Explanation of Suppression in Visual Cortex

The responses of neurons in the primary visual cortex (V1) are suppressed by mask stimuli that do not elicit responses if presented alone. This suppression is widely believed to be mediated by intracortical inhibition. As an alternative, we propose that it can be explained by thalamocortical synaptic depression. This explanation correctly predicts that suppression is monocular, immune to cortical adaptation, and occurs for mask stimuli that elicit responses in the thalamus but not in the cortex. Depression also explains other phenomena previously ascribed to intracortical inhibition. It explains why responses saturate at high stimulus contrast, whereas selectivity for orientation and spatial frequency is invariant with contrast. It explains why transient responses to flashed stimuli are nonlinear, whereas spatial summation is primarily linear. These results suggest that the very first synapses into the cortex, and not the cortical network, may account for important response properties of V1 neurons.
Design's processional character

In this paper, we examine the ideas behind and reactions to a prototype online tool designed, in-house, for an art college's interaction design department. The web-based prototype, the Digital Scrapbook, was initially intended as a tool for tutors to oversee their students' work. However, our ongoing discussions with the department's members indicate that it is more interesting to its target audience for a variety of other reasons, including its role in design inspiration; group representation and collaboration; and as a repository for documenting the creative process. We speculate on the reasons behind this by further reflecting on the reactions to the tool. We come to the conclusion that members of the department value the Digital Scrapbook because it is seen to reflect the processional character of design. That is, we suggest the system is seen as promising because it reveals the often messy, unintended and meandering routes design can follow. In closing, we suggest how we might support further ways of displaying design's processional character and discuss the broader implications of displaying collective processes.
Regional Myocardial Blood Flow in Lambs with Concentric Right Ventricular Hypertrophy

Chronically hypertrophied right ventricles function normally under high systolic pressures, whereas normal right ventricles fail when they are acutely subjected to similar pressures. This phenomenon may be partly due to adaptation of the coronary circulation as well as to hypertrophy. Knowledge of the magnitude and distribution of coronary blood flow and the degree of coronary vascular reserve are important in understanding the function of hypertrophied myocardium. We studied these variables in 16 awake, 5–12-week-old, tranquilized lambs; 9 of the lambs had had their main pulmonary artery banded at 2 days of age. Pressures, cardiac output, and coronary blood flow (radioactive microsphere method) were measured at rest and during two stress states—isoproterenol and dextran infusion. Ventricular function was similar in control and banded lambs. We found significant right ventricular hypertension and both right ventricular and septal hypertrophy in the banded lambs. Total coronary blood flow per gram was slightly higher in banded lambs in all states, and right ventricular flow per gram was significantly elevated at rest and during isoproterenol infusion. Right ventricular coronary resistance per gram was significantly lower in banded lambs in all states. These changes demonstrate that hypertrophied right ventricular tissue is not ischemic at rest, since there is vascular reserve. The changes also raise the question of increased vascularity in hypertrophied myocardium. Right ventricular oxygen supply per unit oxygen demand was increased in banded lambs at rest and during isoproterenol infusion. This finding suggests that hypertrophied myocardium has inefficient oxygen utilization, low oxygen extraction, or both.
Better Language Models with Model Merging

This paper investigates model merging, a technique for deriving Markov models from text or speech corpora. Models are derived by starting with a large and specific model and by successively combining states to build smaller and more general models. We present methods to reduce the time complexity of the algorithm and report on experiments on deriving language models for a speech recognition task. The experiments show the advantage of model merging over the standard bigram approach. The merged model assigns a lower perplexity to the test set and uses considerably fewer states.
A NEW HYBRID APPROACH FOR LEGAL AMOUNT RECOGNITION

This paper presents a new hybrid approach for legal amount recognition o n Italian bankchecks. It exploits the consideration that a legal amount can be described as a sequence of 'core' groups of words s eparated b y suitable 'separator' words. Therefore, an analytical strategy is used to perform amount segmentation into 'core' groups of words that are then recognized according to a global approach. For this purpose, lexical and syntactical a-priori knowledge of the domain o f application is used both for amount segmentation and recognition. The experimental results demonstrate the effectiveness of the new approach.
Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12

We report the complete sequence of ER2796, a laboratory strain of Escherichia coli K-12 that is completely defective in DNA methylation. Because of its lack of any native methylation, it is extremely useful as a host into which heterologous DNA methyltransferase genes can be cloned and the recognition sequences of their products deduced by Pacific Biosciences Single-Molecule Real Time (SMRT) sequencing. The genome was itself sequenced from a long-insert library using the SMRT platform, resulting in a single closed contig devoid of methylated bases. Comparison with K-12 MG1655, the first E. coli K-12 strain to be sequenced, shows an essentially co-linear relationship with no major rearrangements despite many generations of laboratory manipulation. The comparison revealed a total of 41 insertions and deletions, and 228 single base pair substitutions. In addition, the long-read approach facilitated the surprising discovery of four gene conversion events, three involving rRNA operons and one between two cryptic prophages. Such events thus contribute both to genomic homogenization and to bacteriophage diversification. As one of relatively few laboratory strains of E. coli to be sequenced, the genome also reveals the sequence changes underlying a number of classical mutant alleles including those affecting the various native DNA methylation systems.
Mitochondrial DNA Intraspecific Variability in Sergentomyia minuta (Diptera: Psychodidae)

ABSTRACT Recently, there has been growing interest in analysis of the geographical variation between populations of different Phlebotomus spp. and American sand flies by comparing the sequences of various genes. However, little is known about the genetic structure of the genus Sergentomyia França & Parrot. No study has been carried out on Sergentomyia minuta Rondani. Most authors recognize this as a species with a high degree of morphological polymorphism, and some suspect that there are two subspecies: Se. minuta minuta Rondani in Europe, having about 40 horizontal cibarial teeth (sticks aligned along a straight line in the cibarial cavity), and Se. minuta parroti Adler & Theodor in North Africa, having about 70 cibarial teeth. Here we analyzed phylogeographic patterns using cytochrome b (Cytb) and cytochrome C oxidase I mtDNA for 29 populations from 10 countries: Algeria, Cyprus, France (continental and Corsica), Greece (continental and Crete), Malta, Montenegro, Morocco, Portugal (continental and Atlantic Savage Islands), Spain, and Tunisia. We analyzed intra- and interpopulation patterns of genetic diversity. Our results from Bayesian inference showed a complex genetic structure of Se. minuta with four haplogroups including many different haplotypes. One haplogroup includes all the specimens from North Africa. A second haplogroup includes a few specimens from the south of France, Spain, and one from Portugal. The third includes many specimens from southern France, all the specimens from Corsica, one from Spain, and all specimen from Portugal except one. A fourth branch includes specimens from the Balkans, Malta, Crete, Cyprus, and curiously some from the Atlantic Savage Islands; settlement of the latter population remains unexplained. However, our results suggest that the settlement of the Mediterranean basin could have occurred at the same time for Se. minuta and both Phlebotomus perniciosus Newstead and Phlebotomus ariasi Tonnoir. The spatial distribution of haplotypes was congruent with phylogenetic findings.
Partial discharges in lapped polymer taped insulation impregnated with supercritical helium

Apparatus has been designed and constructed to evaluate the high-voltage parameters of lapped cable models impregnated with supercritical helium for pressures up to 1.5 MPa and for temperatures to 4.2 K. The tape materials studied are as follows: high-density polythene, Valeron (cross-laminated polythene film), polypropylene, Nylon 11 and polysulphone with limited tests using polycarbonate. These were selected on previously published parameters related to mechanical properties, lappability and low loss. The variation of the maximum value of discharge with applied alternating voltage is obtained, and also the variation of inception stress (1 pC and 5 pC) with helium density and pressure. Although most attention has been given to tapes wrapped on a stainless-steel electrode, the influence of various conductor screens has also been investigated.In an AC superconducting cable the attainment of the highest possible inception stress is important, and the order of merit of the materials investigated is: Valeron, polypropylene, high-density polythene, polysulphpne and, finally, Nylon 11.
Gastrointestinal Stromal Tumors with Internal Tandem Duplications in 3′ End of KIT Juxtamembrane Domain Occur Predominantly in Stomach and Generally Seem to Have a Favorable Course

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. GISTs express KIT and have KIT mutations. Majority of these mutations cluster in the 5′ end of the KIT juxtamembrane domain. Little is known about the clinicopathological profile of GIST carrying internal tandem duplications in the 3′ end of KIT juxtamembrane domain (ITDs in the 3′ KIT-JM). In this study, 500 immunohistochemically KIT-positive GISTs were screened for this type of mutation, and 18 cases were identified (3.6%). The majority of the ITDs consisted of 1 to 18 codon duplications, with Tyr578, Asp579, and Leu576 being the most commonly duplicated codons. There were 14 gastric (78%), 2 small intestinal (11%), and 2 anal (11%) primary tumors diagnosed in 12 females and 6 males with median age of 71 years. The frequency of IDTs in gastric GISTs was 6.5% and was only 0.5% in intestinal GISTs. There was a strong female predominance (79%) among the patients with gastric tumors. Histologically, 16 GISTs were spindle cell, and 2 had epithelioid morphology. The sizes of primary tumors varied from 1 to >20 cm. Based on the combination of tumor size and mitotic activity, six tumors were classified as benign or probably benign, eight as having uncertain malignant potential, and only four as malignant. Follow-up data available in 17 patients confirmed the malignant course of disease in 3 cases. Only one of the tumors classified as potentially malignant metastasized, although the follow-up was limited in some cases. In summary, the great majority of GISTs with ITDs in the 3′ KIT-JM were mitotically inactive tumors occurring predominantly in the stomach and that seemed to have a favorable course. This suggests that presence of these IDTs may define a clinicopathologically favorable subset of GISTs. The consequence of these mutations to KIT signaling should be investigated.
Artonin E Induces Apoptosis via Mitochondrial Dysregulation in SKOV-3 Ovarian Cancer Cells

Artonin E is a prenylated flavonoid isolated from the stem bark of Artocarpus elasticus Reinw. (Moraceae). This study aimed to investigate the apoptotic mechanisms induced by artonin E in a metastatic human ovarian cancer cell line SKOV-3 in vitro. MTT assay, clonogenic assay, acridine orange and propidium iodide double staining, cell cycle and annexin V analyses were performed to explore the mode of artonin E-induced cell death at different time points. DNA laddering, activation of caspases-3, -8, and -9, multi-parametric cytotoxicity-3analysis by high-content screening, measurement of reactive oxygen species generation, and Western blot were employed to study the pathways involved in the apoptosis. MTT results showed that artonin E inhibited the growth of SKOV-3 cells, with IC50 values of 6.5±0. 5μg/mL after 72 h treatment, and showed less toxicity toward a normal human ovarian cell lineT1074, with IC50 value of 32.5±0. 5μg/mL. Results showed that artonin E induced apoptosis and cell cycle arrest at the S phase. This compound also promoted the activation of caspases-3, -8, and -9. Further investigation into the depletion of mitochondrial membrane potential and release of cytochrome c revealed that artonin E treatment induced apoptosis via regulation of the expression of pro-survival and pro-apoptotic Bcl-2 family members. The expression levels of survivin and HSP70 proteins were also down regulated in SKOV-3 cells treated with artonin E. We propose that artonin E induced an antiproliferative effect that led to S phase cell cycle arrest and apoptosis through dysregulation of mitochondrial pathways, particularly the pro- and anti-apoptosis signaling pathways.
Pulmonary function of adolescents from Tripura, a North-eastern state of India

Objective: Spirometric evaluation of pulmonary function has been evolved as clinical tool in diagnosis, management, and follow-up of respiratory disorders. There are very few studies on normative reference values of pulmonary function parameters for adolescents from Tripura, a North-eastern state of India. The present study was aimed to evaluate pulmonary function and their predictors in male and female adolescents of Tripura. Materials and Methods: A total of 640 (320 from tribal and 320 non-tribal) healthy, non-smoking male and female school children (age 10-14 years) from four different districts of Tripura were randomly sampled for the study. The pulmonary function parameters analysed included forced vital capacity (FVC), forced expiratory volume in 1 second (FEV1), peak expiratory flow rate (PEFR), forced expiratory flow between 25% and 75% expired volume (FEF25-75%), ratio of FEV1/FVC and maximum voluntary ventilation (MVV). Results: The results revealed that body weight, body mass index (BMI), PEFR, FEF25-75% and MVV are significantly high among male tribal children in comparison to non-tribal children. Height, weight, waist-to-hip ratio (WHR), waist-to-height ratio (WHtR), PEFR and MVV were found to be significantly more in tribal girls. In case of adolescents from Tripura, most of the pulmonary function parameters correlated with anthropometric parameters of the subject like height, weight, BMI, WHR, and WHtR. Conclusion: From the present study, it can be concluded that both anthropometric and pulmonary function status of tribal and non-tribal adolescents from Tripura are comparable. The computed regression norms may be used to predict pulmonary function of adolescents from Tripura by using anthropometric indices.
NMF-based Target Source Separation Using Deep Neural Network

Non-negative matrix factorization (NMF) is one of the most well-known techniques that are applied to separate a desired source from mixture data. In the NMF framework, a collection of data is factorized into a basis matrix and an encoding matrix. The basis matrix for mixture data is usually constructed by augmenting the basis matrices for independent sources. However, target source separation with the concatenated basis matrix turns out to be problematic if there exists some overlap between the subspaces that the bases for the individual sources span. In this letter, we propose a novel approach to improve encoding vector estimation for target signal extraction. Estimating encoding vectors from the mixture data is viewed as a regression problem and a deep neural network (DNN) is used to learn the mapping between the mixture data and the corresponding encoding vectors. To demonstrate the performance of the proposed algorithm, experiments were conducted in the speech enhancement task. The experimental results show that the proposed algorithm outperforms the conventional encoding vector estimation scheme.
Seismic Performance of Reinforced Concrete Piers with Bond-Controlled Reinforcements

New seismic design codes for reinforced concrete (RC) bridges in Japan have resulted in difficulties in placing and compacting the concrete, which may cause construction defects in the concrete. Thus, it becomes important to find alternative methods of improving shear capacity and ductility to avoid relying primarily on shear reinforcements. This article reports on a study undertaken to examine how controlling the bond of the longitudinal reinforcements can improve seismic performance factors, such as shear strength and ductility, of reinforced concrete (RC) structures. The experiment employed fifteen, 300 x 300 mm square RC columns tested under reversed cyclic loading. The columns were of six different bond conditions, varying from perfect bond, with the use of ordinary deformed bars, to perfect unbond. The other test variables included the shear span-depth ratio, shear to flexural strength ratio, and the length of unbonded region. Results showed that the failure mode at the ultimate state could be changed from shear to flexure by reducing the bond strength of the longitudinal bars. Complete unbonding of the reinforcing bars in the column leads to a smaller amount of hysteretic energy absorption as compared with ordinary columns. This is due to the occurrence of wide flexural cracks in the column-footing joint. The test results also showed that RC columns reinforced with bond-controlled bars had significantly better shear strength and ductility than RC columns reinforced with ordinary bars.
Making meaning through joint activity in Computer-Supported Collaborative Learning (CSCL) settings: The interplay between content-related and activity-related talk

In the recent literature on CSCL which places the spotlight on participants' talk, there is a clear dichotomy between studies that focus on content-related talk and those that focus on off-topic or activity-related talk. In the approach adopted in this paper, based on the notion of educa- tional influence, the guiding hypothesis is that both forms of talk are close- ly linked in the collaborative dynamics and that activity-related talk, far from being irrelevant, has an essential role to play in promoting the collab- orative construction of knowledge. The paper empirically examines this hypothesis in four online collaborative learning situations. The results show that participants in small group situations requiring the preparation of a written product devote a major part of their discursive activity to ne- gotiating the form of organization of their joint activity and to making sure that all members are familiar with it. In contrast, the technological tools used in the collaborative situation do not seem to have an impact on the relative weight of the type of participants" talk, either content-related or ac- tivity-related.