Miracle-dz/UniFAR-FTUs huggingface dataset:
Retrieving the Green’s function in an open system by cross correlation : A comparison of approaches (L)

We compare two approaches for deriving the fact that the Green’s function in an arbitrary inhomogeneous open system can be obtained by cross correlating recordings of the wave field at two positions. One approach is based on physical arguments, exploiting the principle of time-reversal invariance of the acoustic wave equation. The other approach is based on Rayleigh’s reciprocity theorem. Using a unified notation, we show that the result of the time-reversal approach can be obtained as an approximation of the result of the reciprocity approach.
Adaptive Solution for Blind Equalization and Carrier-Phase Recovery of Square-QAM

In this letter, we adaptively optimize the equalizer output energy to obtain a joint blind equalization and carrier-phase recovery solution. The resulting (multimodulus) update algorithm possesses a particular zero-memory Bussgang-type nonlinearity. We provide evidence of good performance, in comparison to existing adaptive methods, like RCA, MMA and CMA, through computer simulations for higher-order quadrature amplitude modulation signalling on symbol- and fractionally-spaced channels.
Dynamic NURBS with geometric constraints for interactive sculpting

This article develops a dynamic generalization of the nonuniform rational B-spline (NURBS) model. NURBS have become a defacto standard in commercial modeling systems because of their power to represent free-form shapes as well as common analytic shapes. To date, however, they have been viewed as purely geometric primitives that require the user to manually adjust multiple control points and associated weights in order to design shapes. Dynamic NURBS, or D-NURBS, are physics-based models that incorporate mass distributions, internal deformation energies, and other physical quantities into the popular NURBS geometric substrate. Using D-NURBS, a modeler can interactively sculpt curves and surfaces and design complex shapes to required specifications not only in the traditional indirect fashion, by adjusting control points and weights, but also through direct physical manipulation, by applying simulated forces and local and global shape constraints. D-NURBS move and deform in a physically intuitive manner in response to the user's direct manipulations. Their dynamic behavior results from the numerical integration of a set of nonlinear differential equations that automatically evolve the control points and weights in response to the applied forces and constraints. To derive these equations, we employ Lagrangian mechanics and a finite-element-like discretization. Our approach supports the trimming of D-NURBS surfaces using D-NURBS curves. We demonstrate D-NURBS models and constraints in applications including the rounding of solids, optimal surface fitting to unstructured data, surface design from cross sections, and free-form deformation. We also introduce a new technique for 2D shape metamorphosis using constrained D-NURBS surfaces.
Selectively Impaired Associative Learning in Older People with Cognitive Decline

Older people with declining cognitive function typically display deficits in declarative memory processes, often most evident on tests of associative learning (AL). The hippocampal formation (HF) is thought to be critically involved in the encoding and retrieval of such associations, consistent with neuroimaging findings that the HF is damaged in early stages of neurodegenerative disease and in older people with AL impairments. In the clinic, older people with cognitive decline commonly report difficulties associating names with faces. However, we have observed that such people are particularly impaired on tests requiring the association of novel stimuli. In Experiment 1, a series of AL tasks were administered to older people with cognitive decline to determine whether they were impaired at simply making associations, or at making associations between novel stimuli. In Experiment 2, we measured HF function in these subjects by administering an AL task designed to differentiate between HF-damaged and HF-intact individuals. Our experimental protocols were guided by a computational model of HF function in AL described by Gluck and Myers (1997). Older people with cognitive decline displayed impaired performance on tasks designed to be highly dependent upon intact HF function, including a task in which novel patterns and spatial locations were to be associated. These results suggest that the AL impairments observed in older people with cognitive decline may be due to HF dysfunction.
A Edge Detection Method for Microcalfication Clusters in Mammograms

Edge is one of the most important characteristics of microcalcifications, edge detection of microcalcification clusters has a great significance in computer-aided diagnosis system for the automatic detection of clustered microcalcifications in digitized mammograms. A lot of algorithms have been suggested for extracting medical image edges, however, few of them are well suited for edge extraction of microcalcifications due to obtaining discontinuous edges, or continuous edges with more over-detection points. In this paper, we propose a new method for clustered microcalcifications edge detection by integrating Kirsch edge operator, edge linking with Markov model. First, initial edges are extracted by employing kirsch edge operator. Then, we thin the initial edges and fill many gaps in the edge image using edge linking technique. Finally, closed boundaries of microcalcifications are obtained based on Markov model. The experiments demonstrate that our algorithm can obtain closed boundaries with less over-detection points. Keywords-edge detection; kirsch edge operator; markov model; mammogram
Increased Endoplasmic Reticulum Stress and Decreased Proteasomal Function in Lafora Disease Models Lacking the Phosphatase Laforin

Background Lafora progressive myoclonus epilepsy (Lafora disease; LD) is a fatal autosomal recessive neurodegenerative disorder caused by loss-of-function mutations in either the EPM2A gene, encoding the dual specificity phosphatase laforin, or the EPM2B gene, encoding the E3-ubiquitin ligase malin. Previously, we and others have shown that both proteins form a functional complex that regulates glycogen synthesis by a novel mechanism involving ubiquitination and proteasomal degradation of at least two proteins, glycogen synthase and R5/PTG. Since laforin and malin localized at the endoplasmic reticulum (ER) and their regulatory role likely extend to other proteins unrelated to glycogen metabolism, we postulated that their absence may also affect the ER-unfolded protein response pathway. Methodology/Principal Findings Here, we demonstrate that siRNA silencing of laforin in Hek293 and SH-SY5Y cells increases their sensitivity to agents triggering ER-stress, which correlates with impairment of the ubiquitin-proteasomal pathway and increased apoptosis. Consistent with these findings, analysis of tissue samples from a LD patient lacking laforin, and from a laforin knockout (Epm2a-/-) mouse model of LD, demonstrates constitutive high expression levels of ER-stress markers BIP/Grp78, CHOP and PDI, among others. Conclusions/Significance We demonstrate that, in addition to regulating glycogen synthesis, laforin and malin play a role protecting cells from ER-stress, likely contributing to the elimination of unfolded proteins. These data suggest that proteasomal dysfunction and ER-stress play an important role in the pathogenesis of LD, which may offer novel therapeutic approaches for this fatal neurodegenerative disorder.
Experimental Evaluation of LTAG-Based Features for Semantic Role Labeling

This paper proposes the use of Lexicalized Tree-Adjoining Grammar (LTAG) formalism as an important additional source of features for the Semantic Role Labeling (SRL) task. Using a set of one-vs-all Support Vector Machines (SVMs), we evaluate these LTAG-based features. Our experiments show that LTAG-based features can improve SRL accuracy significantly. When compared with the best known set of features that are used in state of the art SRL systems we obtain an improvement in F-score from 82.34% to 85.25%.
Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates

The use of plant growth promoting bacterial inoculants as live microbial biofertilizers provides a promising alternative to chemical fertilizers and pesticides. Inorganic phosphate solubilization is one of the major mechanisms of plant growth promotion by plant associated bacteria. This involves bacteria releasing organic acids into the soil which solubilize the phosphate complexes converting them into ortho-phosphate which is available for plant up-take and utilization. The study presented here describes the ability of endophytic bacteria to produce gluconic acid (GA), solubilize insoluble phosphate, and stimulate the growth of Pisum sativum L. plants. This study also describes the genetic systems within three of these endophyte strains thought to be responsible for their effective phosphate solubilizing abilities. The results showed that many of the endophytic strains produced GA (14–169 mM) and have moderate to high phosphate solubilization capacities (~400–1300 mg L−1). When inoculated into P. sativum L. plants grown in soil under soluble phosphate limiting conditions, the endophytes that produced medium-high levels of GA displayed beneficial plant growth promotion effects.
Nodal gap structure and order parameter symmetry of the unconventional superconductor UPt3

Spanning a broad range of physical systems, complex symmetry breaking is widely recognized as a hallmark of competing interactions. This is exemplified in superfluid 3He which has multiple thermodynamic phases with spin and orbital quantum numbers S = 1 and L = 1, that emerge on cooling from a nearly ferromagnetic Fermi liquid. The heavy fermion compound UPt3 exhibits similar behavior clearly manifest in its multiple superconducting phases. However, consensus as to its order parameter symmetry has remained elusive. Our small angle neutron scattering measurements indicate a linear temperature dependence of the London penetration depth characteristic of nodal structure of the order parameter. Our theoretical analysis is consistent with assignment of its symmetry to an L = 3 odd parity state for which one of the three thermodynamic phases in non-zero magnetic field is chiral.
Rapid intracellular turnover of adenovirus 5 early region 1A proteins

The half-life of the adenovirus 5 early region 1A (E1A) proteins was examined in productively infected and transformed cells. In HeLa cells infected with adenovirus 5, the half-life of the E1A proteins was approximately 30 min; in the transformed 293 cells, the constitutively expressed E1A proteins had a half-life of approximately 120 min. In HeLa cells, the E1A proteins produced by an adenovirus mutant that expresses only the 13S mRNA had a half-life of about 35 min; E1A proteins produced by a mutant that express only the 12S mRNA had a half-life of about 80 min. This difference in the stability of these two classes of E1A proteins helps explain why the steady-state level of the 12S class is usually equal to or greater than that of the 13S class, despite the fact that the concentration of the 13S mRNA is about four times greater than the concentration of the 12S mRNA.
Overexpression of Sirt7 Exhibits Oncogenic Property and Serves as a Prognostic Factor in Colorectal Cancer

Purpose: Sirtuins play an important role in cancer development. Sirt7, as a member of this family, is frequently overexpressed in certain carcinomas, but the oncogenic mechanism is seldom reported. In this study, Sirt7 was characterized for its role in colorectal cancer aggressiveness and underlying molecular mechanisms. Experimental Design: Quantitative PCR, Western blotting, and immunohistochemistry were performed to study Sirt7 expression in a cohort of colorectal cancer tissues and non-tumor tissues and cells. A series of in vitro and in vivo assays was performed to elucidate the function of Sirt7 in colorectal cancer and its underlying mechanisms. Association between the Sirt7 signature and survival was examined using Kaplan–Meier analysis and log-rank tests. Results: The Sirt7 protein level significantly correlated with tumor stage (P = 0.029), lymph node metastasis (P = 0.046), and poor patient survival (P < 0.05). Sirt7 knockdown significantly inhibited colorectal cancer cell proliferation, colony formation, and motility. Ectopic Sirt7 expression promoted colony formation, induced a more invasive phenotype, and accelerated cell growth both in vitro and in vivo. Moreover, Sirt7 enhanced MAPK pathway activity concomitantly with p-ERK and p-MEK upregulation. In Sirt7-overexpressing cells, the mesenchymal markers vimentin and fibronectin were upregulated, and the epithelial markers E-cadherin and β-catenin were downregulated, which was linked to enhanced invasion by colorectal cancer cells. Conclusion: Our findings suggest that Sirt7 plays an important role in the development and progression of human colorectal cancer and functions as a valuable marker of colorectal cancer prognosis. Clin Cancer Res; 20(13); 3434–45. ©2014 AACR.
Quantifying the Analyzability of Software Architectures

The decomposition of a software system into components is a major decision in any software architecture, having a strong influence on many of its quality aspects. A system's analyzability, in particular, is influenced by its decomposition into components. But into how many components should a system be decomposed to achieve optimal analyzability? And how should the elements of the system be distributed over those components? In this paper, we set out to find answers to these questions with the support of a large repository of industrial and open source software systems. Based on our findings, we designed a metric which we call Component Balance. In a case study we show that the metric provides pertinent results in various evaluation scenarios. In addition, we report on an empirical study that demonstrates that the metric is strongly correlated with ratings for analyzability as given by experts.
An Event-Related fMRI Investigation of Implicit Semantic Priming

The neural basis underlying implicit semantic priming was investigated using event-related fMRI. Prime-target pairs were presented auditorily for lexical decision (LD) on the target stimulus, which was either semantically related or unrelated to the prime, or was a nonword. A tone task was also administered as a control. Behaviorally, all participants demonstrated semantic priming in the LD task. fMRI results showed that for all three conditions of the LD task, activation was seen in the superior temporal gyrus (STG), the middle temporal gyrus (MTG), and the inferior parietal lobe, with greater activation in the unrelated and nonword conditions than in the related condition. Direct comparisons of the related and unrelated conditions revealed foci in the left STG, left precentral gyrus, left and right MTGs, and right caudate, exhibiting significantly lower activation levels in the related condition. The reduced activity in the temporal lobe suggests that the perception of the prime word activates a lexical semantic network that shares common elements with the target word, and, thus, the target can be recognized with enhanced neural efficiency. The frontal lobe reductions most likely reflect the increased efficiency in monitoring the activation of lexical representations in the temporal lobe, making a decision, and planning the appropriate motor response.
Descriptive Epidemiology and Underlying Psychiatric Disorders among Hospitalizations with Self-Directed Violence

Background Suicide claims over one million lives worldwide each year. In the United States, 1 per 10,000 persons dies from suicide every year, and these rates have remained relatively constant over the last 20 years. There are nearly 25 suicide attempts for each suicide, and previous self-directed violence is a strong predictor of death from suicide. While many studies have focused on suicides, the epidemiology of non-fatal self-directed violence is not well-defined. Objective We used a nationally representative survey to examine demographics and underlying psychiatric disorders in United States (US) hospitalizations with non-fatal self-directed violence (SDV). Method International Classification of Disease, 9th Revision (ICD-9) discharge diagnosis data from the National Hospital Discharge Survey (NHDS) were examined from 1997 to 2006 using frequency measures and adjusted logistic regression. Results The rate of discharges with SDV remained relatively stable over the study time period with 4.5 to 5.7 hospitalizations per 10,000 persons per year. Excess SDV was documented for females, adolescents, whites, and those from the Midwest or West. While females had a higher likelihood of self-poisoning, both genders had comparable proportions of hospitalizations with SDV resulting in injury. Over 86% of the records listing SDV also included psychiatric disorders, with the most frequent being affective (57.8%) and substance abuse (37.1%) disorders. The association between psychiatric disorders and self-injury was strongest for personality disorders for both males (OR = 2.1; 95% CI = 1.3–3.4) and females (OR = 3.8; 95% CI = 2.7–5.3). Conclusion The NHDS provides new insights into the demographics and psychiatric morbidity of those hospitalized with SDV. Classification of SDV as self-injury or self-poisoning provides an additional parameter useful to epidemiologic studies.
Pathway Markers for Pro-resolving Lipid Mediators in Maternal and Umbilical Cord Blood: A Secondary Analysis of the Mothers, Omega-3, and Mental Health Study

The omega-3 fatty acids docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) are precursors to immune regulatory and specialized pro-resolving mediators (SPM) of inflammation termed resolvins, maresins, and protectins. Evidence for lipid mediator formation in vivo can be gained through evaluation of their 5-lipoxygenase (LOX) and 15-LOX metabolic pathway precursors and downstream metabolites. We performed a secondary blood sample analysis from 60 participants in the Mothers, Omega-3, and Mental Health study to determine whether SPM and SPM precursors are augmented by dietary EPA- and DHA-rich fish oil supplementation compared to soy oil placebo. We also aimed to study whether SPM and their precursors differ in early and late pregnancy or between maternal and umbilical cord blood. We found that compared to placebo supplementation, EPA- and DHA-rich fish oil supplementation increased SPM precursor 17-hydroxy docosahexaenoic acid (17-HDHA) concentrations in maternal and umbilical cord blood (P = 0.02). We found that the D-series resolvin pathway marker 17-HDHA increased significantly between enrollment and late pregnancy (P = 0.049). Levels of both 14-HDHA, a maresin pathway marker, and 17-HDHA were significantly greater in umbilical cord blood than in maternal blood (P < 0.001, both).
Mortality in heart failure patients

Heart failure (HF) is a clinical syndrome, which is becoming a major public health problem in recent decades, due to its increasing prevalence, especially in the developed countries, mostly due to prolonged lifespan of the general population as well as the increased of HF patients. The HF treatment, particularly, new pharmacological and non-pharmacological agents, has markedly improved clinical outcomes of patients with HF including increased life expectancy and improved quality of life. However, despite the facts that mortality in HF patients has decreased, it still remains unacceptably high. This review of summarizes the evidence to date about the mortality of HF patients. Despite the impressive achievements in the pharmacological and non-pharmacological treatment of HF patients which has undeniably improved the survival of these patients, the mortality still remains high particularly among elderly, male and African-American patients. Patients with HF and reduced ejection fraction have higher mortality rates, most commonly due to cardiovascular causes, compared with patients HF and preserved ejection fraction.
Ventilation heterogeneity in the acinar and conductive zones of the normal ageing lung

Rationale Small airways function studies in lung disease have used three promising multiple breath washout (MBW) derived indices: indices of ventilation heterogeneity in the acinar (Sacin) and conductive (Scond) lung zones, and the lung clearance index (LCI). Since peripheral lung structure is known to change with age, ventilation heterogeneity is expected to be affected too. However, the age dependence of the MBW indices of ventilation heterogeneity in the normal lung is unknown. Objectives The authors systematically investigated Sacin, Scond or LCI as a function of age, testing also the robustness of these relationships across two laboratories. Methods MBW tests were performed by never-smokers (50% men) in the age range 25–65 years, with data gathered across two laboratories (n=120 and n=60). For comparison with the literature, the phase III slopes from classical single breath washout tests were also acquired in one group (n=120). Measurements and main results All three MBW indices consistently increased with age, representing a steady worsening of ventilation heterogeneity in the age range 25–65. Age explained 7–16% of the variability in Sacin and Scond and 36% of the variability in LCI. There was a small but significant gender difference only for Sacin. Classical single breath washout phase III slopes also showed age dependencies, with gender effects depending on the normalisation method used. Conclusions With respect to the clinical response, age is a small but consistent effect that needs to be factored in when using the MBW indices for the detection of small airways abnormality in disease.
Sources and Secondary Production of Organic Aerosols in the Northeastern United States during WINTER

Most intensive field studies investigating aerosols have been conducted in summer, and thus, wintertime aerosol sources and chemistry are comparatively poorly understood. An aerosol mass spectrometer was flown on the National Science Foundation/National Center for Atmospheric Research C‐130 during the Wintertime INvestigation of Transport, Emissions, and Reactivity (WINTER) 2015 campaign in the northeast United States. The fraction of boundary layer submicron aerosol that was organic aerosol (OA) was about a factor of 2 smaller than during a 2011 summertime study in a similar region. However, the OA measured in WINTER was almost as oxidized as OA measured in several other studies in warmer months of the year. Fifty‐eight percent of the OA was oxygenated (secondary), and 42% was primary (POA). Biomass burning OA (likely from residential heating) was ubiquitous and accounted for 33% of the OA mass. Using nonvolatile POA, one of two default secondary OA (SOA) formulations in GEOS‐Chem (v10‐01) shows very large underpredictions of SOA and O/C (5×) and overprediction of POA (2×). We strongly recommend against using that formulation in future studies. Semivolatile POA, an alternative default in GEOS‐Chem, or a simplified parameterization (SIMPLE) were closer to the observations, although still with substantial differences. A case study of urban outflow from metropolitan New York City showed a consistent amount and normalized rate of added OA mass (due to SOA formation) compared to summer studies, although proceeding more slowly due to lower OH concentrations. A box model and SIMPLE perform similarly for WINTER as for Los Angeles, with an underprediction at ages <6 hr, suggesting that fast chemistry might be missing from the models.