Miracle-dz/UniFAR-FTUs huggingface dataset:
Super-Resolution Delay-Doppler Estimation for OFDM Passive Radar

In this paper, we consider the problem of joint delay-Doppler estimation of moving targets in a passive radar that makes use of orthogonal frequency-division multiplexing communication signals. A compressed sensing algorithm is proposed to achieve supper resolution and better accuracy, using both the atomic norm and the <inline-formula> <tex-math notation="LaTeX">$\ell _1$</tex-math></inline-formula>-norm. The atomic norm is used to manifest the signal sparsity in the continuous domain. Unlike previous works that assume the demodulation to be error free, we explicitly introduce the demodulation error signal whose sparsity is imposed by the <inline-formula><tex-math notation="LaTeX"> $\ell _1$</tex-math></inline-formula>-norm. On this basis, the delays and Doppler frequencies are estimated by solving a semidefinite program (SDP) which is convex. We also develop an iterative method for solving this SDP via the alternating direction method of multipliers where each iteration involves closed-form computation. Simulation results are presented to illustrate the high performance of the proposed algorithm.
Comparative Analysis of HIV-1 and Murine Leukemia Virus Three-Dimensional Nuclear Distributions

ABSTRACT Recent advances in fluorescence microscopy allow three-dimensional analysis of HIV-1 preintegration complexes in the nuclei of infected cells. To extend this investigation to gammaretroviruses, we engineered a fluorescent Moloney murine leukemia virus (MLV) system consisting of MLV-integrase fused to enhanced green fluorescent protein (MLV-IN-EGFP). A comparative analysis of lentiviral (HIV-1) and gammaretroviral (MLV) fluorescent complexes in the nuclei of infected cells revealed their different spatial distributions. This research tool has the potential to achieve new insight into the nuclear biology of these retroviruses.
Antimicrobial effectiveness of chitosan-essential oil coated plastic films against foodborne pathogens

In this study, antimicrobial efficacy of polypropylene (PP) films coated with chitosan solutions (2% wt/v) and chitosan solutions enriched with essential oils (EOs) against Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli O157:H7 were evaluated on Kashar cheese slices. Oregano and clove oils were incorporated into film solutions at 1% (v/v). Inoculated cheese samples were wrapped with films and stored at 4°C for 14 days. Antimicrobial effectiveness of films against each of three pathogens was measured by plate counts performed on 1, 7, and 14 days of storage. It was found that the antimicrobial effectiveness of all film types against three pathogens were statistically significant (p < 0.05), with films containing oregano oil showed greater antimicrobial effect on pathogens than films containing clove oil. Results suggest that chitosan is an ideal biopolymer for coating onto PP films, and EOs have the potential to be used in antimicrobial coated plastic film prepared from biopolymers.
The Response of Heterotrophic Prokaryote and Viral Communities to Labile Organic Carbon Inputs Is Controlled by the Predator Food Chain Structure

Factors controlling the community composition of marine heterotrophic prokaryotes include organic-C, mineral nutrients, predation, and viral lysis. Two mesocosm experiments, performed at an Arctic location and bottom-up manipulated with organic-C, had very different results in community composition for both prokaryotes and viruses. Previously, we showed how a simple mathematical model could reproduce food web level dynamics observed in these mesocosms, demonstrating strong top-down control through the predator chain from copepods via ciliates and heterotrophic nanoflagellates. Here, we use a steady-state analysis to connect ciliate biomass to bacterial carbon demand. This gives a coupling of top-down and bottom-up factors whereby low initial densities of ciliates are associated with mineral nutrient-limited heterotrophic prokaryotes that do not respond to external supply of labile organic-C. In contrast, high initial densities of ciliates give carbon-limited growth and high responsiveness to organic-C. The differences observed in ciliate abundance, and in prokaryote abundance and community composition in the two experiments were in accordance with these predictions. Responsiveness in the viral community followed a pattern similar to that of prokaryotes. Our study provides a unique link between the structure of the predator chain in the microbial food web and viral abundance and diversity.
Direct activation of chordoblasts by retinoic acid is required for segmented centra mineralization during zebrafish spine development

ABSTRACT Zebrafish mutants with increased retinoic acid (RA) signaling due to the loss of the RA-inactivating enzyme Cyp26b1 develop a hyper-mineralized spine with gradually fusing vertebral body precursors (centra). However, the underlying cellular mechanisms remain incompletely understood. Here, we show that cells of the notochord epithelium named chordoblasts are sensitive to RA signaling. Chordoblasts are uniformly distributed along the anteroposterior axis and initially generate the continuous collagenous notochord sheath. However, subsequently and iteratively, subsets of these cells undergo further RA-dependent differentiation steps, acquire a stellate-like shape, downregulate expression of the collagen gene col2a1a, switch on cyp26b1 expression and trigger metameric sheath mineralization. This mineralization fails to appear upon chordoblast-specific cell ablation or RA signal transduction blockade. Together, our data reveal that, despite their different developmental origins, the activities and regulation of chordoblasts are very similar to those of osteoblasts, including their RA-induced transition from osteoid-producing cells to osteoid-mineralizing ones. Furthermore, our data point to a requirement for locally controlled RA activity within the chordoblast layer in order to generate the segmented vertebral column. Highlighted Article: Retinoic acid induces locally controlled morphological and transcriptional changes in chordoblasts that lead to segmental notochord sheath mineralization, identifying chordoblasts as key skeletogenic cells during chordacentrum development in zebrafish.
Clone Detection for Ecore Metamodels using N-grams

Increasing model-driven engineering use leads to an abundance of models and metamodels in academic and industrial practice. A key technique for the management and maintenance of those artefacts is model clone detection, where highly similar (meta-)models and (meta-)model fragments are mined from a possibly large amount of data. In this paper we extend the SAMOS framework (Statistical Analysis of MOdelS) to clone detection on Ecore metamodels, using the framework’s n-gram feature extraction, vector space model and clustering capabilities. We perform a case analysis on Ecore metamodels obtained by applying an exhaustive set of single mutations to assess the precision/sensitivity of our technique with respect to various types of mutations. Using mutation analysis, we also briefly evaluate MACH, a comparable UML clone detection tool.
A Slotted Photonic Crystal Nanobeam Cavity for Simultaneous Attainment of Ultra-High Q-Factor and Sensitivity

An optical refractive index (RI) sensor is proposed based on a slotted photonic crystal nanobeam cavity. Three rows of parabolic-tapered air-holes are used to design the cavity and an embedded narrow slot is used to obtain a highly localized optical field in a low refractive index region in order to produce a strong light matter interaction. The number and the radii of the air holes, the width of the slot, and the number of rows are optimized to address the most challenging issue of RI sensor design, i.e. to obtain a high Q-factor and sensitivity, simultaneously. The plane wave expansion method has been used to facilitate the design procedure and a 3-D finite difference time domain method has been used to obtain the simulation outcome. The outcomes for the optimized cavity show an ultra-high Q-factor <inline-formula> <tex-math notation="LaTeX">$\sim 4.3\times 10^{7}$ </tex-math></inline-formula> along with a sensitivity ~975 nm/RIU at a wavelength 1534 nm, for which the figure-of-merit is calculated as <inline-formula> <tex-math notation="LaTeX">$2.73\times 10^{7}$ </tex-math></inline-formula>. However, the slot-width can be varied to obtain a Q-factor of <inline-formula> <tex-math notation="LaTeX">$8\times 10^{7}$ </tex-math></inline-formula> and sensitivity of 1100 nm/RIU individually. The device also has an ultra-small mode volume of the order of 0.0253 <inline-formula> <tex-math notation="LaTeX">$(\lambda /n)^{3}$ </tex-math></inline-formula>. Hence, all together, the sensor is expected to be a promising candidate for the lab-on-chip sensor application.
Effects of Lipopolysaccharide Core Sugar Deficiency on Colanic Acid Biosynthesis in Escherichia coli

ABSTRACT When 10 Escherichia coli mutant strains with defects in lipopolysaccharide (LPS) core biosynthesis were grown on agar medium at 30°C, four of them, the ΔwaaF, ΔwaaG, ΔwaaP, and ΔwaaB strains, formed mucoid colonies, while the other six, the ΔwaaU, ΔwaaR, ΔwaaO, ΔwaaC, ΔwaaQ, and ΔwaaY strains, did not. Using light microscopy with tannin mordant staining, the presence of exopolysaccharide around the cells of the mutants that formed mucoid colonies could be discerned. The ΔwaaF mutant produced the largest amounts of exopolysaccharide, regardless of whether it was grown on agar or in liquid medium. The exopolysaccharide was isolated from the liquid growth medium of ΔwaaF cells, hydrolyzed, and analyzed by high-performance liquid chromatography with an ion-exchange column, and the results indicated that the exopolysaccharide was consistent with colanic acid. When the key genes related to the biosynthesis of colanic acid, i.e., wza, wzb, wzc, and wcaA, were deleted in the ΔwaaF background, the exopolysaccharide could not be produced any more, further confirming that it was colanic acid. Colanic acid could not be produced in strains in which rcsA, rcsB, rcsD, or rcsF was deleted in the ΔwaaF background, but a reduced level of colanic acid production was detected when the rcsC gene was deleted, suggesting that a change of lipopolysaccharide structure in ΔwaaF cells might be sensed by the RcsCDB phosphorelay system, leading to the production of colanic acid. The results demonstrate that E. coli cells can activate colanic acid production through the RcsCDB phosphorelay system in response to a structural deficiency of lipopolysaccharide. IMPORTANCE Lipopolysaccharide and colanic acid are important forms of exopolysaccharide for Escherichia coli cells. Their metabolism and biological significance have been investigated, but their interrelation with the cell stress response process is not understood. This study demonstrates, for the first time, that E. coli cells can activate colanic acid production through the RcsCDB phosphorelay system in response to a structural change of lipopolysaccharide, suggesting that bacterial cells can monitor the outer membrane integrity, which is essential for cell survival and damage repair.
Multi-view Graph Embedding with Hub Detection for Brain Network Analysis

Multi-view graph embedding and hub detection have both become widely studied problems in the area of graph learning. Both graph embedding and hub detection relate to the node clustering structure of graphs. The multi-view graph embedding usually implies the node clustering structure of the graph based on the multiple views, while hubs are the boundary-spanning nodes across different node clusters in the graph and thus may potentially influence the clustering structure of the graph. However, none of the existing works considered joint learning the multi-view embeddings and the hubs from multi-view graph data. In this paper, we propose to incorporate the hub detection task into the multi-view graph embedding framework so that the two tasks could benefit from each other. Specifically, we propose an auto-weighted framework of Multi-view Graph Embedding with Hub Detection (MVGE-HD) for brain network analysis. The MVGE-HD framework learns a unified graph embedding across all the views while reducing the potential influence of the hubs on blurring the boundaries between node clusters in the graph, thus leading to a clear and discriminative node clustering structure for the graph. We apply MVGE-HD on two real multi-view brain network datasets (i.e., HIV and Bipolar). The experimental results demonstrate the superior performance of the proposed framework in brain network analysis for clinical investigation and application.
Melatonin-independent Photoperiodic Entrainment of the Circannual TSH Rhythm in the Pars Tuberalis of the European Hamster

Adaptation of biological rhythms to a seasonal environment in circannual mammals is achieved via the synchronization of intrinsic circannual rhythms to the external year by photoperiod. In mammals, the photoperiodic information is integrated to seasonal physiology via the pineal hormone melatonin regulation of pars tuberalis (PT) TSHβ expression and its downstream control of hypothalamic dio2 gene expression. In the circannual European hamster, however, photoperiodic entrainment of the circannual clock is possible in pinealectomized animals. The present study explores whether the TSHβ expression in the PT and the downstream hypothalamic pathways are regulated by photoperiod in European hamsters in the absence of melatonin. All animals were kept on an accelerated photoperiodic regime, which compressed the natural year to a 6-month cycle. Sham-operated European hamsters and half of the pinealectomized European hamsters entrained their annual cycle in reproduction, body weight, and activity pattern to this cycle, whereas the other half of the pinealectomized animals followed only each second cycle. In all animals, PT TSHβ and hypothalamic dio2 expressions were higher in hamsters displaying a summer physiological state than in those in winter state. Moreover, in agreement with their seasonal state, reproductive animals (summer state) showed higher expression of rfrp and lower expression of kiss1—genes encoding central regulators of the reproductive axis—than those animals in reproductive quiescence (winter state), indicating the hypothalamic integration of the photoperiodic signal even in pinealectomized animals. The appropriate occurrence of a well-characterized activity pattern indicative of a so-called sensitive phase to short photoperiod suggested that the SCN constructs the melatonin-independent photoperiodic message. This message is sufficient to entrain the circannual rhythm in TSHβ expression in the PT and the downstream hypothalamic neuroendocrine pathway through a yet unknown pathway. These results reinforce the hypothesis that the PT is the site for the integration of circannual and photoperiodic information.
Online Self-Help as an Add-On to Inpatient Psychotherapy: Efficacy of a New Blended Treatment Approach

Background: Depression is one of the most frequent and costly mental disorders. While there is increasing evidence for the efficacy of online self-help to improve depression or prevent relapse, there is little evidence in blended care settings, especially combined with inpatient face-to-face psychotherapy. Therefore, we evaluated whether an evidence-based online self-help program improves the efficacy of inpatient psychotherapy. Methods: A total of 229 depressed patients were randomly allocated either to an online self-help program (intervention group [IG]; Deprexis) or an active control group (CG; weekly online information on depression) in addition to inpatient psychodynamic psychotherapy. Both groups had access to their respective experimental intervention for 12 weeks, regardless of inpatient treatment duration. Reduction of depressive symptoms, as measured with the Beck Depression Inventory-II, was the primary outcome at the end of the intervention (T2). Results: Depressive symptoms were statistically significantly lower in the IG compared to the active CG at T2 with a moderate between-group effect size of d = 0.44. The same applied to anxiety (d = 0.33), quality of life (d = 0.34), and self-esteem (d = 0.38) at discharge from inpatient treatment (T1). No statistically significant differences were found regarding dysfunctional attitudes (d = 0.14) and work ability (d = 0.08) at T1. Conclusions: This is the first evidence for blended treatment combining online self-help with inpatient psychotherapy. The study opens new and promising avenues for increasing the efficacy of inpatient psychotherapy. Future studies should determine how integration of online self-help into the therapeutic process can be developed further.
Modelling a batch biofilm passive aeration process using an activated sludge process and a biofilm process

Biofilm-based passive aeration systems (PAS) have attracted recent attention as alternative energy efficient and low maintenance technologies for the treatment of municipal wastewater. However the modelling of biofilm-based PAS offers unique challenges for modellers particularly where new technologies are not easily modelled using existing commercial modelling software. However, if the modeller is concerned only with modelling the effluent from the system it may be possible to model these technologies using “surrogate” unit process systems (e.g. using an activated sludge process to model a biofilm process). The pumped flow biofilm reactor (PFBR); a batch biofilm technology, is one such example of a passive aeration system. The PFBR is a two reactor technology that employs a unique hydraulic regime and enables aerobic, anoxic and anaerobic conditions to be sequenced. Biofilm, growing on plastic media modules within the two reactors, is aerated passively as wastewater is moved alternately between the reactors during an aeration sequence. Thus as the two reactors empty and fill a number of times during a typical aeration sequence, the biofilm is exposed, in turn, to atmospheric air and wastewater. Furthermore while the PFBR has many of the features of a sequencing batch reactor the fill and discharge from the system typically take place in Reactors 1 and 2 respectively. GPS-X is modular, multi-purpose commercial software that can be used to simulate various wastewater treatment processes. As a relatively new technology a predictive model for the PFBR system has yet to be developed. Indeed for novel passive aeration systems in general, it can be time consuming and difficult to develop new models that accurately describe performance. In this study, using the PFBR as a case study of a biofilm-based PAS, a predictive model, developed using the modelling package GPS-X (Hydromatis Inc.), is presented. The model, which aims to simulate effluent quality only, was developed by modifying standard activated sludge sequencing batch reactor processes. The model was calibrated using experimental data obtained from a laboratory PFBR study. The model was then applied to a second set of independent laboratory data, obtained by operating the PFBR under an alternative wastewater loading regime. The results showed excellent correlation between experimental and modelled effluent results. While future work will focus on developing a unique model for the PFBR (and similar technologies) this study presents an alternative means to efficiently develop initial predictive models for novel passive aeration systems. Presented by the 1 author at the IWA 9th International Conference on Biofilm Reactors 2013. Paris, France. 28 – 31 May 2013 Abstract associated with Chapter 4.associated with Chapter 4.
Acoustic Emission of Fiber Reinforced Plastics

Because most nondestructive test methods are not suitable for use with plastics, and in light of the poor performance record of FRP structures, a practical nondestructive test could be of great value. The paper reports results of a series of tests designed to evaluate the suitability of acoustic emission for testing of FRP structures. In order to characterize FRP, tensile and flexural tests were carried out using various FRP constructions and a range of load levels. In addition, a test of a full-size FRP reactor was undertaken. The tests demonstrate that level of emission, first damage, Kaiser effect, emission during a load hold, amplitude spectrum, and the effect of different frequencies on wave attenuation provide useful information on the structural integrity of FRP. Recommendations for future test work are presented with an assessment of the applicability of acoustic emission for nondestructive testing of FRP structures.
Microelectromechanical systems. Fabrication and characterization of microcantilevers

Microelectromechanical systems (MEMS) technologies can be used to produce from the simplest structures to the most complex devices and systems. Due to their many applications in various fields, MEMS have turned into one of the most researched areas in microtechnology. In this context, this project was developed in an attempt to produce one of most used structures in MEMS sensing devices microcantilevers. Several microfabrication techniques were combined to fabricate this type of structures on the top layer of silicon of a silicon-on-insulator (SOI) wafer. After the microcantilevers had been successfully created, an experiment was set up to verify the microcantilevers ability to bend. Here, a voltage was applied between the top and bottom layers of silicon of the SOI wafer. It was then observed that the microcantilevers were deflected all the way to the bottom silicon layer by the electrostatic force acting between them, given that a current was detected when a certain value of applied voltage was reached.
Quality of Life, Mood, and Prognostic Understanding in Patients with Metastatic Breast Cancer.

BACKGROUND Although breast cancer is the second leading cause of cancer-related mortality in women in the United States, few studies focus on the supportive care needs of patients living with metastatic breast cancer (MBC). OBJECTIVE We studied quality of life (QOL), depression, anxiety, and prognostic understanding of patients with MBC. DESIGN We conducted a cross-sectional study of 140 patients with MBC, stratified by receipt of endocrine therapy or chemotherapy. MEASUREMENTS We evaluated anxiety and depression using the Hospital Anxiety and Depression Scale (HADS). We assessed QOL using the Functional Assessment of Cancer Therapy-Breast (FACT-B), specifically measuring the FACT-B Trial Outcome Index (TOI), which includes physical and functional well-being and breast cancer-specific symptoms. Higher FACT-B TOI scores represent better QOL. We used a 12-item questionnaire to assess patients' perceptions of their prognosis and goals of therapy. RESULTS Compared to those taking endocrine therapy (n = 40), patients receiving chemotherapy (n = 100) reported lower scores on the FACT-B TOI (66.1 versus 72.5, p < 0.01) and more depression symptoms (HADS-D >7; 22% versus 7.5%, p = 0.03). Higher scores on the FACT-B TOI were associated with lower depression (β, -0.16; p < 0.01) and anxiety (β, -0.11; p < 0.01), and patients who reported frequent prognostic conversations with their oncologists had less depression (β, -1.28; p < 0.01). Thirty-nine percent (54/140) reported that their cancer was likely curable. CONCLUSION Patients with MBC, particularly those treated with chemotherapy, may benefit from interventions to address their physical, functional, and breast cancer-related symptoms. Many do not report accurate prognostic understanding, and more frequent prognostic conversations might address this information gap.