Miracle-dz/UniFAR-FTUs huggingface dataset:
Universality in the merging dynamics of parametric active contours: a study in MRI based lung segmentation

Measurement of lung ventilation is one of the most reliable techniques in diagnosing pulmonary diseases. The time-consuming and bias-prone traditional methods using hyperpolarized H3He and 1H magnetic resonance imageries have recently been improved by an automated technique based on ‘multiple active contour evolution’. This method involves a simultaneous evolution of multiple initial conditions, called ‘snakes’, eventually leading to their ‘merging’ and is entirely independent of the shapes and sizes of snakes or other parametric details. The objective of this paper is to show, through a theoretical analysis, that the functional dynamics of merging as depicted in the active contour method has a direct analogue in statistical physics and this explains its ‘universality’. We show that the multiple active contour method has an universal scaling behaviour akin to that of classical nucleation in two spatial dimensions. We prove our point by comparing the numerically evaluated exponents with an equivalent thermodynamic model.
Genetic linkage map of Coflea canephora : effect of segregation distortion and analysis of recombination rate in male and female meioses d ?

Two complementary segregating plant populations of Coffea canepltora were produced from the same clone. One population (DH) comprised 92 doubled haploids derived from female gametes, while the other population (TC) was a test cross consisting of 44 individuals derived from male gametes. Based on the DH population, a genetic linkage map comprising 160 loci was constructed. Eleven linkage groups that putatively correspond to the 11 gametic chromosomes of C. canephora were identified. The mapped loci included more than 40 specific sequence-tagged site markers, either single-copy RFLP probes or microsatellites, that could serve as standard landmarks in coffee-genome analyses. Furthermore, comparisons for segregation distortion and recombination frequency between the two populations were performed. Although segregation distortions were observed in both populations, the frequency of loci exhibiting a very pronounced degree of distortion was especially high in the DH population. This observation is consistent with the hypothesis of strong zygotic selection among the DH population. The recombination frequencies in both populations were found to be almost indistinguishable. These results offer evidence in favour of the lack of significant sex differences in recombination in C. canephora.
Designing software architectures to achieve quality attribute requirements

In order to have a software architecture design method that achieves quality attribute requirements several aspects of the method must be in place. First there must be some way to specify quality attribute requirements so that it can be determined whether the designed architecture can achieve them. Secondly, there must be some way for modularising the knowledge associated with quality attributes so that the design method does not need to know how to reason about all of the multiplicity of quality attributes that exist. Finally, there must be some way for managing the interactions among the quality attributes so that either the requirements can be satisfied or the ones that cannot be satisfied are identified. The authors describe a structure called a 'reasoning framework' as a modularisation of quality attribute knowledge. The requirements that the architecture must satisfy are specified as concrete quality attribute scenarios. Each reasoning framework provides mechanisms that will transform the architecture with respect to a given quality attribute theory. Within a reasoning framework, the authors distinguish between an architectural model and a quality attribute model and characterise the actions that a reasoning framework undertakes as basic architectural transformations. Finally, the process of identifying interactions among reasoning frameworks is begun so that conflicting requirements can be managed. The use of reasoning frameworks is situated inside an existing architectural design method so that a useful method exists while the open issues of designing to achieve quality attribute requirements are resolved.
Crosstalk between Oxidative Stress and SIRT1: Impact on the Aging Process

Increased oxidative stress has been associated with the aging process. However, recent studies have revealed that a low-level oxidative stress can even extend the lifespan of organisms. Reactive oxygen species (ROS) are important signaling molecules, e.g., being required for autophagic degradation. SIRT1, a class III protein deacetylase, is a crucial cellular survival protein, which is also involved in combatting oxidative stress. For instance, SIRT1 can stimulate the expression of antioxidants via the FoxO pathways. Moreover, in contrast to ROS, SIRT1 inhibits NF-κB signaling which is a major inducer of inflammatory responses, e.g., with inflammasome pathway. Recent studies have demonstrated that an increased level of ROS can both directly and indirectly control the activity of SIRT1 enzyme. For instance, ROS can inhibit SIRT1 activity by evoking oxidative modifications on its cysteine residues. Decreased activity of SIRT1 enhances the NF-κB signaling, which supports inflammatory responses. This crosstalk between the SIRT1 and ROS signaling provokes in a context-dependent manner a decline in autophagy and a low-grade inflammatory phenotype, both being common hallmarks of ageing. We will review the major mechanisms controlling the signaling balance between the ROS production and SIRT1 activity emphasizing that this crosstalk has a crucial role in the regulation of the aging process.
Prevalence, Supplementation, and Impact of Vitamin D Deficiency in Multiple Myeloma Patients

Here, we studied 83 unselected multiple myeloma patients from December 2007 through December 2014. Lower 25(OH) D levels (<10 ng/mL) were associated with higher number of plasma cells in the bone marrow. Supplementation of vitamin D was accompanied with a significant increase in hemoglobin (11.8 to 12.3 p = .039), leukocyte (4.9 to 5.8 p = .011), and erythrocyte (3.8 to 4.0 p = .004) levels, while thrombocytes (200.5 to 175.2 p = .036) decreased. In conclusion, the present study found a high incidence of vitamin D deficiency and insufficiency in MM patients. In myeloma patients, vitamin D levels and supplementation should be more widely taken into account.
Extending Brain-Training to the Affective Domain: Increasing Cognitive and Affective Executive Control through Emotional Working Memory Training

So-called ‘brain-training’ programs are a huge commercial success. However, empirical evidence regarding their effectiveness and generalizability remains equivocal. This study investigated whether brain-training (working memory [WM] training) improves cognitive functions beyond the training task (transfer effects), especially regarding the control of emotional material since it constitutes much of the information we process daily. Forty-five participants received WM training using either emotional or neutral material, or an undemanding control task. WM training, regardless of training material, led to transfer gains on another WM task and in fluid intelligence. However, only brain-training with emotional material yielded transferable gains to improved control over affective information on an emotional Stroop task. The data support the reality of transferable benefits of demanding WM training and suggest that transferable gains across to affective contexts require training with material congruent to those contexts. These findings constitute preliminary evidence that intensive cognitively demanding brain-training can improve not only our abstract problem-solving capacity, but also ameliorate cognitive control processes (e.g. decision-making) in our daily emotive environments.
Characterization of HIV-Specific CD4+ T Cell Responses against Peptides Selected with Broad Population and Pathogen Coverage

CD4+ T cells orchestrate immunity against viral infections, but their importance in HIV infection remains controversial. Nevertheless, comprehensive studies have associated increase in breadth and functional characteristics of HIV-specific CD4+ T cells with decreased viral load. A major challenge for the identification of HIV-specific CD4+ T cells targeting broadly reactive epitopes in populations with diverse ethnic background stems from the vast genomic variation of HIV and the diversity of the host cellular immune system. Here, we describe a novel epitope selection strategy, PopCover, that aims to resolve this challenge, and identify a set of potential HLA class II-restricted HIV epitopes that in concert will provide optimal viral and host coverage. Using this selection strategy, we identified 64 putative epitopes (peptides) located in the Gag, Nef, Env, Pol and Tat protein regions of HIV. In total, 73% of the predicted peptides were found to induce HIV-specific CD4+ T cell responses. The Gag and Nef peptides induced most responses. The vast majority of the peptides (93%) had predicted restriction to the patient’s HLA alleles. Interestingly, the viral load in viremic patients was inversely correlated to the number of targeted Gag peptides. In addition, the predicted Gag peptides were found to induce broader polyfunctional CD4+ T cell responses compared to the commonly used Gag-p55 peptide pool. These results demonstrate the power of the PopCover method for the identification of broadly recognized HLA class II-restricted epitopes. All together, selection strategies, such as PopCover, might with success be used for the evaluation of antigen-specific CD4+ T cell responses and design of future vaccines.
Machine learning methods for locating re-entrant drivers from electrograms in a model of atrial fibrillation

Mapping resolution has recently been identified as a key limitation in successfully locating the drivers of atrial fibrillation (AF). Using a simple cellular automata model of AF, we demonstrate a method by which re-entrant drivers can be located quickly and accurately using a collection of indirect electrogram measurements. The method proposed employs simple, out-of-the-box machine learning algorithms to correlate characteristic electrogram gradients with the displacement of an electrogram recording from a re-entrant driver. Such a method is less sensitive to local fluctuations in electrical activity. As a result, the method successfully locates 95.4% of drivers in tissues containing a single driver, and 95.1% (92.6%) for the first (second) driver in tissues containing two drivers of AF. Additionally, we demonstrate how the technique can be applied to tissues with an arbitrary number of drivers. In its current form, the techniques presented are not refined enough for a clinical setting. However, the methods proposed offer a promising path for future investigations aimed at improving targeted ablation for AF.
Adenocarcinomas with Widespread Microsatellite Instability Genetic and Clinical Features of Human Pancreatic Ductal Updated

The incidences of microsatellite instability (MSI) and underlying DNA mismatch repair (MMR) defects in pancreatic carcinogenesis have not been well established. We analyzed 100 sporadic and 3 hereditary pancreatic ductal adenocarcinomas for MSI, and high-frequency MSI (MSI-H) and low-frequency MSI (MSI-L) tumors were further analyzed for frameshift mutations of possible target genes and for promoter methylation and mutation of DNA MMR genes, including hMLH1, hMSH2, hMSH3, and hMSH6 genes. Among the 100 sporadic tumors, 13 (13%) were MSI-H, 13 (13%) were MSI-L, and 74 (74%) were microsatellite stable (MSS) tumors. All of the three hereditary tumors from hereditary nonpolyposis colorectal cancer (HNPCC) patients were MSI-H. MSI-H tumors were significantly associated with poor differentiation and the presence of wild-typeK-RASand p53genes. Patients with MSI-H tumors had a significantly longer overall survival time than did those with MSI-L or MSS tumors (P 5 0.0057). Frameshift mutations ofhMSH3, hMLH3, BRCA-2,TGF-b type II receptor, andBAX genes were detected in MSI-H tumors. Hypermethylation of the hMLH1 promoter was observed in 6 (46%) of the 13 sporadic MSI-H tumors but not in any of the 3 hereditary MSI-H tumors or 13 MSI-L tumors. All of the 3 HNPCC cases had germ-line hMLH1 mutation accompanied by loss of heterogeneity or other mutation in the tumor. Our results suggest that pancreatic carcinomas with MSI-H represent a distinctive oncogenic pathway because they exhibit peculiar clinical, pathological, and molecular characteristics. Our results also suggest the principal involvement of epigenetic or genetic inactivation of the hMLH1 gene in the pathogenesis of pancreatic carcinoma with MSI-H.
Tourists intra-destination visits and transportation mode : a bivariate model

This paper investigates tourists' profile in relation to both intra-destination movement patterns and transportation mode choices at the destination through the use of bivariate probit models. The analysis is based on a field survey conducted among tourists visiting the Canton of Ticino, Switzerland. The results show a positive correlation between visiting more than one region and the use of private transportation at the destination. In particular, the two variables are explained by a mixed combination of independent variables; the transport mode choice of tourists can be well explained by demographics while destination movement patterns are rather influenced by trip characteristics. The introduction of activity participation and motivation increases consistently the fit of the model allowing a better understanding of tourist behaviour in relation to the spatial extent of the destination visited and to the transport mode selected. Finally, conclusions are drawn for policy implications in destination management and transport planning.
New method for culture of zona‐included or zona‐free embryos: The Well of the Well (WOW) system

Culture of mammalian zygotes individually and in small groups results in lower developmental rates than culture of large groups. Zona‐free zygotes also have impaired developmental potential in current culture systems. This paper describes a new approach to resolve the problems, the Well of the Well (WOW) system. Small wells (WOWs) were formed in four‐well dishes by melting the bottom with heated steel rods. The WOWs were then rinsed, the wells were filled with medium, and the embryos were placed into the WOWs. To test the value of the WOW system a 3 × 3 factorial experiment was performed. Bovine presumptive zygotes were cultured from day 1 to day 7 (day 0: day of insemination) using three modules (single embryos, embryo groups of five, or single zona‐digested embryos) and three different culture systems (400 μl medium, 200 μl drops, or WOWs). An additional control group consisted of 40 to 50 embryos cultured in 400 μl medium. The WOW system resulted in higher blastocyst/oocyte rates for all three modules (single: 59%; group of five: 61%; single zona‐digested: 53%) than the culture in drops or in wells (P < 0.05 for all). The developmental rate was independent of the number of WOWs per well. The cell number of blastocysts cultured in the WOW system did not differ from that of the controls. Apart from its theoretical value in revealing the role of different factors influencing embryo development in vitro, the WOW system may have immediate practical consequences in certain areas of mammalian embryo production. Mol Reprod Dev 55:256–264, 2000. © 2000 Wiley‐Liss, Inc.
The packing density of a supramolecular membrane protein cluster is controlled by cytoplasmic interactions

Molecule clustering is an important mechanism underlying cellular self-organization. In the cell membrane, a variety of fundamentally different mechanisms drive membrane protein clustering into nanometre-sized assemblies. To date, it is unknown whether this clustering process can be dissected into steps differentially regulated by independent mechanisms. Using clustered syntaxin molecules as an example, we study the influence of a cytoplasmic protein domain on the clustering behaviour. Analysing protein mobility, cluster size and accessibility to myc-epitopes we show that forces acting on the transmembrane segment produce loose clusters, while cytoplasmic protein interactions mediate a tightly packed state. We conclude that the data identify a hierarchy in membrane protein clustering likely being a paradigm for many cellular self-organization processes. DOI: http://dx.doi. org/10.7554/eLife.20705. 001
Prognostic Significance of Tumor-infiltrating CD8+ or CD3+ T Lymphocytes and Interleukin-2 Expression in Radically Resected Non-small Cell Lung Cancer

Background: Altered immunoresponse is associated with tumorigenesis and cancer progression. This study assessed the levels of tumor-infiltrating CD3+ or CD8+ T lymphocytes and interleukin-2 (IL-2) protein in radically resected non-small cell lung cancer (NSCLC) tissues to predict overall survival (OS) of the patients. Methods: Paraffin-embedded tissue specimens from 129 NSCLC patients were retrospectively collected for immunostaining of CD8+, CD3+, and IL-2 expression. Clinicopathological and survival data were collected and analyzed using the Chi-squared test, Kaplan–Meier curves, and the log-rank test or the Cox regression model. Results: The data showed a significant inverse association between CD8+ T lymphocyte levels and IL-2 expression (r = −0.927; P = 0.000) and between the levels of CD8+ and CD3+ T lymphocytes (r = −0.722; P = 0.000), but a positive association between CD3+ T lymphocyte levels and IL-2 expression (r = 0.781; P = 0.000) in NSCLC tissues. Furthermore, the levels of CD3+ and CD8+ T lymphocytes and IL-2 expression were associated with tumor stage (P = 0.023, 0.006, and 0.031, respectively) and the level of CD8+ T lymphocytes was associated with the patient gender (P = 0.024). In addition, the levels of CD8+ T lymphocytes were associated with an unfavorable 5-year OS, whereas patients with high levels of CD3+ T lymphocytes in tumor lesions and IL-2-expressing tumors had significantly better 5-year OS rates than patients with low levels. Conclusions: The levels of CD8+ T cells in tumor lesions and IL-2 expression were both independent predictors of OS for these NSCLC patients. Thus, the detection of tumor-infiltrating CD3+ or CD8+ T lymphocytes and IL-2 expression could be useful to predict the prognosis of radically resected NSCLC patients.
The Relationship between Technology Acceptance Model and Usability Test - Case of Performing E-learning Task with PDA

In the past, most studies used Technology Acceptance Model (TAM) to test the degree of technology acceptance and usability test to measure the task performance respectively. However, the relationship between TAM and usability has not been addressed. In this paper, an E-learning task was tested and validated with PDA. The findings show that TAM seems more suitable for general purpose context and usability test seems more reasonable and consistency for task-based context.
Genetic characterization of 12 heterologous microsatellite markers for the giant tropical tree Cariniana legalis (Lecythidaceae)

Twelve microsatellite loci previously developed in the tropical tree Cariniana estrellensis were genetically characterized in Cariniana legalis. Polymorphisms were assessed in 28 C. legalis individuals found between the Pardo and Mogi-Guaçu River basins in the state of São Paulo, Brazil. Of the 12 loci, 10 were polymorphic and exhibited Mendelian inheritance. The allelic richness at each locus ranged from 2-11, with an average of 7 alleles per locus, and the expected heterozygosity ranged from 0.07-0.88. These loci showed a high probability of paternity exclusion. The characteristics of these heterologous microsatellite markers indicate that they are suitable tools for investigating questions concerning population genetics in C. legalis.
Is There Something Out There? Inferring Space from Sensorimotor Dependencies

This letter suggests that in biological organisms, the perceived structure of reality, in particular the notions of body, environment, space, object, and attribute, could be a consequence of an effort on the part of brains to account for the dependency between their inputs and their outputs in terms of a small number of parameters. To validate this idea, a procedure is demonstrated whereby the brain of a (simulated) organism with arbitrary input and output connectivity can deduce the dimensionality of the rigid group of the space underlying its input-output relationship, that is, the dimension of what the organism will call physical space.
Color photometric stereo for multicolored surfaces

We present a multispectral photometric stereo method for capturing geometry of deforming surfaces. A novel photometric calibration technique allows calibration of scenes containing multiple piecewise constant chromaticities. This method estimates per-pixel photometric properties, then uses a RANSAC-based approach to estimate the dominant chromaticities in the scene. A likelihood term is developed linking surface normal, image intensity and photometric properties, which allows estimating the number of chromaticities present in a scene to be framed as a model estimation problem. The Bayesian Information Criterion is applied to automatically estimate the number of chromaticities present during calibration. A two-camera stereo system provides low resolution geometry, allowing the likelihood term to be used in segmenting new images into regions of constant chromaticity. This segmentation is carried out in a Markov Random Field framework and allows the correct photometric properties to be used at each pixel to estimate a dense normal map. Results are shown on several challenging real-world sequences, demonstrating state-of-the-art results using only two cameras and three light sources. Quantitative evaluation is provided against synthetic ground truth data.
Host Plant-Associated Population Variation in the Carob Moth Ectomyelois ceratoniae in Iran: A Geometric Morphometric Analysis Suggests a Nutritional Basis.

Abstract The carob moth, Ectomyelois ceratoniae (Zeller, 1839) (Lepidoptera: Pyralidae), is the most important pest of pomegranate in Iran. As it has been rarely recorded on other host plants, control methods have mostly been focused on its populations on pomegranate. In this study, shapes and sizes of wings were compared in populations on 4 host plants (pomegranate, fig, pistachio and walnut) using a landmark-based geometric morphometric method, and analysis of partial warp scores and centroid sizes. The results showed significantly smaller wing size in populations on pomegranate and a significant host plant-associated shape difference among populations as a consequence of allometric growth. This suggests that the wing size and shape differences among test populations may not have a genetic basis and could happen because of differences in the nutritional content of host plants. The results of the analysis suggest that the female carob moth lays her eggs on host plants that provide suitable conditions for hatching. The larger size of moths on hosts other than pomegranate showed that some host plants such as fig, pistachio and walnut can provide for increased stored nutritional reserves by larvae that may result in more successful over-wintering and higher fecundity in adults. This suggests that in spite of the more extensive activity of carob moth on pomegranate in Iran, populations on other host plants can have an important effect on expanding pest population sizes in following years which should be considered in control methods.