Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Methylation-Related Chromatin Remodeling in Activity-Dependent Bdnf Gene Regulation

In conjunction with histone modifications, DNA methylation plays critical roles in gene silencing through chromatin remodeling. Changes in DNA methylation perturb neuronal function, and mutations in a methyl-CpG–binding protein, MeCP2, are associated with Rett syndrome. We report that increased synthesis of brain-derived neurotrophic factor (BDNF) in neurons after depolarization correlates with a decrease in CpG methylation within the regulatory region of the Bdnf gene. Moreover, increased Bdnf transcription involves dissociation of the MeCP2–histone deacetylase–mSin3A repression complex from its promoter. Our findings suggest that DNA methylation–related chromatin remodeling is important for activity-dependent gene regulation that may be critical for neural plasticity.
Comparing Children’s Performance on and Preference for a Number-Line Estimation Task

Tablet computers (tablets) are positioned to be powerful, innovative, effective, and motivating research and assessment tools. We addressed two questions critical for evaluating the appropriateness of using tablets to study number-line estimation, a skill associated with math achievement and argued to be central to numerical cognition. First, is performance with paper and pencil comparable with performance on a tablet? Second, is comparability affected by students’ preference for one method of presentation? Thirty-two students in Grade 6 estimated targets on a number line; half estimated with paper and pencil and half with a tablet. For both presentation methods, students’ performance was comparable. Students liked both presentation conditions equally but, when asked to choose, most students preferred the tablet. Preference did not influence comparability of results across presentation methods. Finally, students’ reasons for their preferences were explored, along with implications for using tablet applications in research and educational assessment.
Morphology, Morphogenesis, and Molecular Phylogeny of Paraparentocirrus sibillinensis n. gen., n. sp., a “Stylonychine Oxytrichidae” (Ciliophora, Hypotrichida) Without Transverse Cirri

A terrestrial oxytrichid ciliate Paraparentocirrus sibillinensis n. gen., n. sp. , which was found in soil samples of a beech forest stand within the National Park of Sibillini Mountains, Italy, was investigated using live observation and protargol impregnation. The morphology of interphase, morphogenesis, and molecular phylogeny inferred from SSU rDNA sequences of this ciliate were studied. Paraparentocirrus n. gen., is mainly characterized by a semirigid body, an undulating membrane in the Oxytricha pattern, six fronto‐ventral (FV) rows, the absence of transverse cirri, one right and one left row of marginal cirri, four dorsal kineties, two dorsomarginal rows, and caudal cirri at the end of dorsal kinety 4. During morphogenesis, oral primordia develop through the proliferation of basal bodies from some cirri of FV rows 4 and 5, and FV row 6 takes part in the anlagen formation of the proter. The dorsal morphogenesis was typical of oxytrichids, with simple fragmentation of dorsal kinety 3, and the dorsomarginal rows developed from the right marginal row. Phylogenetic analyses based on the SSU rDNA sequences support the classification of this new genus in the stylonychines.
Tackling the ordinal and imbalance nature of a melanoma image classification problem

Melanoma is a type of cancer that usually occurs on the skin. Early detection is crucial for ensuring five-year survival (which varies between 15% and 99% depending on the melanoma stage). Melanoma severity is typically diagnosed by invasive methods (e.g. a biopsy). In this paper, we propose an alternative system combining image analysis and machine learning for detecting melanoma presence and severity. The 86 features selected consider the shape, colour, pigment network and texture of the melanoma. As opposed to previous studies that have focused on distinguishing melanoma and non-melanoma images, our work considers a finer-grain classification problem using five categories: benign lesions and 4 different stages of melanoma. The dataset presents two main characteristics that are approached by specific machine learning methods: 1) the classes representing melanoma severity follow a natural order, and 2) the dataset is imbalanced, where benign lesions clearly outnumber melanoma ones. Different nominal and ordinal classifiers are considered, one of them being based on an ordinal cascade decomposition method. The cascade method is shown to obtain good performance for all classes, while respecting and exploiting the order information. Moreover, we explore the alternative of applying a class balancing technique, presenting good synergy with the ordinal and nominal methods.
Modeling, dynamics and optimal control of Ebola virus spread

We present a mathematical analysis of the early detection of Ebola virus. The propagation of the virus is analysed by using a Susceptible, Infected, Recovered (SIR) model. In order to provide useful predictions about the potential transmission of the virus, we analyse and simulate the SIR model with vital dynamics, by adding demographic effects and an induced death rate. Then, we compute the equilibria of the model. The numerical simulations confirm the theoretical analysis. Our study describes the 2015 detection of Ebola virus in Guinea, the parameters of the model being identified from the World Health Organization data. Finally, we consider an optimal control problem of the propagation of the Ebola virus, minimizing the number of infected individuals while taking into account the cost of vaccination.
Local coordination verses systemic disregulation: complexities in leukocyte recruitment revealed by local and systemic activation of TLR4 in vivo

The recruitment of leukocytes to a tissue is a critical step in the inflammatory response. Toll‐like receptor 4 (TLR4) is an important receptor involved in the initiation of inflammatory responses. Administration of the ligand for TLR4, lipopolysaccharide, is often used to model inflammation—local responses to stimuli within a specific tissue and systemic responses such as those observed during endotoxic or septic shock. Here, we review work, which demonstrates that in response to local activation of TLR4, highly coordinated and multistep processes are initiated, ultimately resulting in the leukocyte’s arrival at the inflamed tissue. In contrast, systemic activation of TLR4 results in nonspecific accumulation of leukocytes within the lung capillaries and liver sinusoids through mechanisms profoundly different than those involved in local tissue recruitment. Contrary to current dogma, leukocyte accumulation in the lung is dependent on endothelial rather than leukocyte activation. Finally, we discuss recent evidence suggesting that activation of leukocytes through TLR4, although still in the circulation, effectively paralyzes inflammatory cells, rendering them incapable of appropriate trafficking to inflamed tissues.
Thermal Land Surface Emissivity Retrieved From SEVIRI/Meteosat

The methodologies used by the Satellite Application Facility on Land Surface Analysis (Land SAF) for retrieving emissivity are presented here. In the first approach, i.e., the vegetation cover method (VCM), the land surface emissivity (EM) is computed for Spinning Enhanced Visible and Infrared Imager (SEVIRI) infrared channels and for the 3- to 14- range using information on the pixel fraction of vegetation cover (FVC). The VCM uses a lookup table, which takes into account the channel's spectral response function, and laboratory reflectance spectra for different materials. The accuracy of the VCM depends on the reliability of FVC and the land cover classification. The EM for SEVIRI split-window channels is primarily used as an internal product by Land SAF for land surface temperature (LST) estimations. However, sensitivity studies show that LST often fails to meet the required accuracy of 2 K over desert and semiarid regions, where the VCM is unable to model the EM spatial variability, which is mostly associated with soil composition. Moreover, it is also over such areas where the atmosphere is generally dry that the impact of EM uncertainties on LST is largest. A second approach to determine the EM for SEVIRI split-window channels is currently being tested. This methodology allows the simultaneous retrieval of LST and channel EMs with the assumption that the latter remain constant. The channel EMs are then averaged over a 22-day period to filter out the noise in the retrievals. A first analysis of the maps obtained for an area within Northern Africa shows spatial patterns with features also present in the surface albedo.
A Framework for Assessing the Vulnerability of Communities in the Canadian Arctic to Risks Associated with Climate Change

Adaptation to climate change is recognized as an important policy issue by international bodies such as the United Nations and by various national governments. Initiatives to identify adaptation needs and to improve adaptive capacity increasingly start with an assessment of the vulnerability of the system of interest, in terms of who and what are vulnerable, to what stresses, in what way, and what capacity exists to adapt to changing risks. Notwithstanding the scholarship on climate change itself, there are few studies on the nature of Arctic communities' vulnerability to climate-change risks. We review existing literature on implications of climate change for Arctic communities, develop a conceptual model of vulnerability, and present an analytical approach to assessing climate hazards and coping strategies in Arctic communities. Vulnerability is conceptualized as a function of exposure to climatic stresses and the adaptive capacity to cope with these stresses. The analytical framework employs place-specific case studies involving community residents and integrates information from multiple sources, both to document current exposures and adaptations and to characterize future exposures and adaptive capacity.
Molecular Mechanism Responsible for Fibronectin-controlled Alterations in Matrix Stiffness in Advanced Chronic Liver Fibrogenesis*

Fibrosis is characterized by extracellular matrix (ECM) remodeling and stiffening. However, the functional contribution of tissue stiffening to noncancer pathogenesis remains largely unknown. Fibronectin (Fn) is an ECM glycoprotein substantially expressed during tissue repair. Here we show in advanced chronic liver fibrogenesis using a mouse model lacking Fn that, unexpectedly, Fn-null livers lead to more extensive liver cirrhosis, which is accompanied by increased liver matrix stiffness and deteriorated hepatic functions. Furthermore, Fn-null livers exhibit more myofibroblast phenotypes and accumulate highly disorganized/diffuse collagenous ECM networks composed of thinner and significantly increased number of collagen fibrils during advanced chronic liver damage. Mechanistically, mutant livers show elevated local TGF-β activity and lysyl oxidase expressions. A significant amount of active lysyl oxidase is released in Fn-null hepatic stellate cells in response to TGF-β1 through canonical and noncanonical Smad such as PI3 kinase-mediated pathways. TGF-β1-induced collagen fibril stiffness in Fn-null hepatic stellate cells is significantly higher compared with wild-type cells. Inhibition of lysyl oxidase significantly reduces collagen fibril stiffness, and treatment of Fn recovers collagen fibril stiffness to wild-type levels. Thus, our findings indicate an indispensable role for Fn in chronic liver fibrosis/cirrhosis in negatively regulating TGF-β bioavailability, which in turn modulates ECM remodeling and stiffening and consequently preserves adult organ functions. Furthermore, this regulatory mechanism by Fn could be translated for a potential therapeutic target in a broader variety of chronic fibrotic diseases.
Tile Complexity of Linear Assemblies

Self-assembly is fundamental to both biological processes and nanoscience. Key features of self-assembly are its probabilistic nature and local programmability. These features can be leveraged to design better self-assembled systems. The conventional tile assembly model (TAM) developed by Winfree using Wang tiles is a powerful, Turing-universal theoretical framework which models varied self-assembly processes. A particular challenge in DNA nanoscience is to form linear assemblies or rulers of a specified length using the smallest possible tile set, where any tile type may appear more than once in the assembly. The tile complexity of a linear assembly is the cardinality of the tile set that produces it. These rulers can then be used as components for construction of other complex structures. While square assemblies have been extensively studied, many questions remain about fixed length linear assemblies, which are more basic constructs yet fundamental building blocks for molecular architectures. In this wo.
Endovascular Repair of Blunt Popliteal Arterial Injuries

Objective To evaluate the feasibility and effectiveness of endovascular repair for blunt popliteal arterial injuries. Materials and Methods A retrospective analysis of seven patients with clinical suspicion of popliteal arterial injuries that were confirmed by arteriography was performed from September 2009 to July 2014. Clinical data included demographics, mechanism of injury, type of injury, location of injury, concomitant injuries, time of endovascular procedures, time interval from trauma to blood flow restoration, instrument utilized, and follow-up. All patients were male (mean age of 35.9 ± 10.3 years). The type of lesion involved intimal injury (n = 1), partial transection (n = 2), complete transection (n = 2), arteriovenous fistula (n = 1), and pseudoaneurysm (n = 1). All patients underwent endovascular repair of blunt popliteal arterial injuries. Results Technical success rate was 100%. Intimal injury was treated with a bare-metal stent. Pseudoaneurysm and popliteal artery transections were treated with bare-metal stents. Arteriovenous fistula was treated with bare-metal stent and coils. No perioperative death and procedure-related complication occurred. The average follow-up was 20.9 ± 2.3 months (range 18–24 months). One patient underwent intra-arterial thrombolysis due to stent thrombosis at 18 months after the procedure. All limbs were salvaged. Stent migration, deformation, or fracture was not found during the follow-up. Conclusion Endovascular repair seems to be a viable approach for patients with blunt popliteal arterial injuries, especially on an emergency basis. Endovascular repair may be effective in the short-term. Further studies are required to evaluate the long-term efficacy of endovascular repair.
Optimization and Validation of Methods for Mapping of the Radiofrequency Transmit Field at 3T

MRI techniques such as quantitative imaging and parallel transmit require precise knowledge of the radio‐frequency transmit field (B 1+ ). Three published methods were optimized for robust B 1+ mapping at 3T in the human brain: three‐dimensional (3D) actual flip angle imaging (AFI), 3D echo‐planar imaging (EPI), and two‐dimensional (2D) stimulated echo acquisition mode (STEAM). We performed a comprehensive comparison of the methods, focusing on artifacts, reproducibility, and accuracy compared to a reference 2D double angle method. For the 3D AFI method, the addition of flow‐compensated gradients for diffusion damping reduced the level of physiological artifacts and improved spoiling of transverse coherences. Correction of susceptibility‐induced artifacts alleviated image distortions and improved the accuracy of the 3D EPI imaging method. For the 2D STEAM method, averaging over multiple acquisitions reduced the impact of physiological noise and a new calibration method enhanced the accuracy of the B 1+ maps. After optimization, all methods yielded low noise B 1+ maps (below 2 percentage units), of the nominal flip angle value (p.u.) with a systematic bias less than 5 p.u. units. Full brain coverage was obtained in less than 5 min. The 3D AFI method required minimal postprocessing and showed little sensitivity to off‐resonance and physiological effects. The 3D EPI method showed the highest level of reproducibility. The 2D STEAM method was the most time‐efficient technique. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Softstar: Heuristic-Guided Probabilistic Inference

Recent machine learning methods for sequential behavior prediction estimate the motives of behavior rather than the behavior itself. This higher-level abstraction improves generalization in different prediction settings, but computing predictions often becomes intractable in large decision spaces. We propose the Softstar algorithm, a softened heuristic-guided search technique for the maximum entropy inverse optimal control model of sequential behavior. This approach supports probabilistic search with bounded approximation error at a significantly reduced computational cost when compared to sampling based methods. We present the algorithm, analyze approximation guarantees, and compare performance with simulation-based inference on two distinct complex decision tasks.
AN ITERATED LOCAL SEARCH FOR THE VEHICLE ROUTING PROBLEM WITH CONFLICTS

The Vehicle Routing Problem (VRP) is a classical problem for which several exact and approximation methods were proposed. In real life applications, such as in Hazardous Material transportation, transported items may be incompatible. This variant of routing problems represents a new problem for which only few heuristic methods have been developed. This paper introduces this extension called the Vehicle Routing Problem with Conflicts (VRPC) which is NP-hard since it generalizes the VRP which is known to be NP-hard. This study presents a mathematical model and an Iterated Local Search metaheuristic (ILS) for this new problem. The ILS improves the results obtained by the constructive heuristics developed by us in a previous work.
Morphologic Features of Congenital Acetabular Dysplasia: One in Six is Retroverted

It generally is thought that in congenital hip dysplasia, the opening of the acetabulum lies in excessive anteversion from the sagittal plane. Although this is true for the majority of patients, we found that one in six patients with acetabular dysplasia has retroversion in which the superior ⅓ of the acetabulum faces posterolaterally. Our method of analysis depends mainly on one true orthograde view of the pelvis. This view can be obtained easily and has the advantage of allowing the surgeon to adjust the correction during surgery. In the dysplastic hip with acetabular retroversion, realignment osteotomy still may be done but the corrective maneuvers are different.
Exopolysaccharide Produced by Lactobacillus Plantarum Induces Maturation of Dendritic Cells in BALB/c Mice

Lactobacillus plantarum (L. plantarum) exopolysaccharide (EPS) is an important bioactive component in fermented functional foods. However, there is a lack of data concerning the effects of L. plantarum EPS on maturation of mouse dendritic cells (DCs). In this study, we purified L. plantarum EPS and examined its effects on cytokines production by dendritic cells in serum and intestinal fluid of BALB/c mice, then investigated its effects on phenotypic and functional maturation of mouse bone marrow-derived dendritic cells (BMDCs). Cytokines (nitric oxide, IL-12p70, IL-10 and RANTES) in serum and intestinal fluid were analyzed by enzyme linked immunosorbent assay (ELISA) after the mice received EPS for 2, 5 and 7 days, respectively. DCs derived from bone marrow of BALB/c mouse were treated with EPS, then the phenotypic maturation of BMDCs was analyzed using flow cytometer and the functional maturation of BMDCs was analyzed by ELISA, and, lastly, mixed lymphocyte proliferation was performed. We found the molecular weight of purified EPS was approximately 2.4×106 Da and it was composed of ribose, rhamnose, arabinose, xylose, mannose, glucose and galactose in a molar ratio of 2:1:1:10:4:205:215. We observed that L. plantarum EPS enriched production of nitric oxide, IL-12p70 and RANTES, and decreased the secretion of IL-10 in the serum or intestinal fluid as well as in the supernatant of DCs treated with the EPS. The EPS also up-regulated the expression of MHC II and CD86 on DCs surface and promoted T cells to proliferate in vitro. Our data provide direct evidence to suggest that L. plantarum EPS can effectively induce maturation of DCs in mice.
Voronoi regions for binary linear block codes

The Voronoi regions of a block code govern many aspects of the code's performance on a Gaussian channel, and they are fundamental instruments in, for example, error probability analysis and soft-decision decoding. The article presents an efficient method for finding the boundaries of the Voronoi regions for an arbitrary binary linear block code. Two theoretical results together lead to the Voronoi regions. First, it is shown that the question of the Voronoi neighborship can be reduced into testing a simpler relation, called the Gabriel neighborship. Second, a fast method of recognising Gabriel neighbors is proposed. These results are finally employed to describe the Voronoi regions for the Golay codes and several BCH codes, including Hamming codes.
Association of Nutrition Parameters Including Bioelectrical Impedance and Systemic Inflammatory Response With Quality of Life and Prognosis in Patients With Advanced Non-Small-Cell Lung Cancer: A Prospective Study

Early identification and treatment of nutritional deficiencies can lead to improved outcomes in the quality of life (QoL) and survival of patients with nonsmall cell lung cancer (NSCLC). Noninvasive techniques are needed to evaluate changes in body composition as part of determining nutritional status. The aim of the study was to evaluate the association of nutritional parameters in health-related quality of life (HRQL) and survival in patients with advanced NSCLC. Chemotherapy-naïve patients with advanced NSCLC with good performance status Eastern Cooperative Oncology Group (ECOG) 0–2 were included prospectively in the study. We evaluated inflammatory parameters such as C-reactive protein, platelet/lymphocyte index, neutrophil/lymphocyte index, serum interleukin (IL)-6, and tumor necrosis factor-α, and nutritional variables such as body mass index (BMI) and serum albumin levels. Bioelectrical impedance analysis including phase angle was obtained before cisplatin-based chemotherapy was started. HRQL was assessed by application of the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire (QLQ)-C30 and QLQ-LC13 instruments at baseline. Overall survival (OS) was calculated with the Kaplan-Meier method and analyzed with log-rank and Cox proportional hazard models. One hundred nineteen patients were included. Mean BMI was 24.8 ± 4.5 kg/m2, average weight loss of patients was 8.4%, and median phase angle was 5.8°. Malnutrition measured by subjective global assessment (SGA), weight loss >10%, BMI >20 was associated with lower HRQL scales. Patients with ECOG 2, high content serum IL-6, lower phase angle, and malnutrition parameters showed lower OS; however, after multivariate analysis, only ECOG 2 [Hazard ratio (HR), 2.7; 95% confidence interval (95% CI), 1.5–4.7; P = 0.001], phase angle ≤5.8° (HR = 3.02; 95% CI: 1.2–7.11; P = 0.011), and SGA (HR = 2.7; 95% CI, 1.31–5.5; P = 0.005) were associated with poor survival. Patients were divided into low-, intermediate-, and high-risk groups according to regression coefficients; OS at 1 yr was 78.4, 53, and 13.8%, respectively. Malnutrition is associated with low HRQL and is an independent prognostic factor in advanced NSCLC. The results warrant prospective trials to evaluate the impact of different nutritional interventions on HRQL and survival.