Miracle-dz/UniFAR-FTUs huggingface dataset:
Complex Morlet Wavelet Analysis of the DNA Frequency Chaos Game Signal and Revealing Specific Motifs of Introns in C.elegans

Nowadays, studying introns is becoming a very promising field in the genomics. Even though they play a role in the dynamic regulation of gene and in the organism's evolution, introns have not attracted enough attention like exons did; especially of digital signal processing researchers. Thus, we focus on analysis of the C.elegans introns. In this paper, we propose the complex Morlet wavelet analysis to investigate introns' characterization in the C.elegans genes. However, catching the change in frequency response with respect to time of the gene sequences is hindered by their presence in the form of strings of characters. This can only be counteracted by assigning numerical values to each of the DNA characters. This operation defines the so called "DNA coding approach". In this context, we propose a new coding technique based on the Frequency Chaos Game Representation (FCGR) that we name the "Frequency Chaos Game Signal" (FCGS). Results of the complex Morlet wavelet Analysis applied to the Celegans FCGS are showing a very distinguished texture. The visual interpretation of the colour scalograms is proved to be an efficient tool for revealing significant information about intronic sequences.
Alpha-1 antitrypsin Pi*Z gene frequency and Pi*ZZ genotype numbers worldwide: an update

In alpha-1 antitrypsin deficiency (AATD), the Z allele is present in 98% of cases with severe disease, and knowledge of the frequency of this allele is essential from a public health perspective. However, there is a remarkable lack of epidemiological data on AATD worldwide, and many of the data currently used are outdated. Therefore, the objective of this study was to update the knowledge of the frequency of the Z allele to achieve accurate estimates of the prevalence and number of Pi*ZZ genotypes worldwide based on studies performed according to the following criteria: 1) samples representative of the general population, 2) AAT phenotyping characterized by adequate methods, and 3) measurements performed using a coefficient of variation calculated from the sample size and 95% confidence intervals. Studies fulfilling these criteria were used to develop maps with an inverse distance weighted (IDW)-interpolation method, providing numerical and graphical information of Pi*Z distribution worldwide. A total of 224 cohorts from 65 countries were included in the study. With the data provided by these cohorts, a total of 253,404 Pi*ZZ were estimated worldwide: 119,594 in Europe, 91,490 in America and Caribbean, 3,824 in Africa, 32,154 in Asia, 4,126 in Australia, and 2,216 in New Zealand. In addition, the IDW-interpolation maps predicted Pi*Z frequencies throughout the world even in some areas that lack real data. In conclusion, the inclusion of new well-designed studies and the exclusion of the low-quality ones have significantly improved the reliability of results, which may be useful to plan strategies for future research and diagnosis and to rationalize the therapeutic resources available.
Ionizing Radiation Potentiates Dihydroartemisinin-Induced Apoptosis of A549 Cells via a Caspase-8-Dependent Pathway

This report is designed to explore the molecular mechanism by which dihydroartemisinin (DHA) and ionizing radiation (IR) induce apoptosis in human lung adenocarcinoma A549 cells. DHA treatment induced a concentration- and time-dependent reactive oxygen species (ROS)-mediated cell death with typical apoptotic characteristics such as breakdown of mitochondrial membrane potential (Δψm), caspases activation, DNA fragmentation and phosphatidylserine (PS) externalization. Inhibition of caspase-8 or -9 significantly blocked DHA-induced decrease of cell viability and activation of caspase-3, suggesting the dominant roles of caspase-8 and -9 in DHA-induced apoptosis. Silencing of proapoptotic protein Bax but not Bak significantly inhibited DHA-induced apoptosis in which Bax but not Bak was activated. In contrast to DHA treatment, low-dose (2 or 4 Gy) IR induced a long-playing generation of ROS. Interestingly, IR treatment for 24 h induced G2/M cell cycle arrest that disappeared at 36 h after treatment. More importantly, IR synergistically potentiated DHA-induced generation of ROS, activation of caspase-8 and -3, irreparable G2/M arrest and apoptosis, but did not enhance DHA-induced loss of Δψm and activation of caspase-9. Taken together, our results strongly demonstrate the remarkable synergistic efficacy of combination treatment with DHA and low-dose IR for A549 cells in which IR potentiates DHA-induced apoptosis largely by enhancing the caspase-8-mediated extrinsic pathway.
Continuous versus Intermittent β-Lactam Infusion in Severe Sepsis. A Meta-analysis of Individual Patient Data from Randomized Trials.

RATIONALE Optimization of β-lactam antibiotic dosing for critically ill patients is an intervention that may improve outcomes in severe sepsis. OBJECTIVES In this individual patient data meta-analysis of critically ill patients with severe sepsis, we aimed to compare clinical outcomes of those treated with continuous versus intermittent infusion of β-lactam antibiotics. METHODS We identified relevant randomized controlled trials comparing continuous versus intermittent infusion of β-lactam antibiotics in critically ill patients with severe sepsis. We assessed the quality of the studies according to four criteria. We combined individual patient data from studies and assessed data integrity for common baseline demographics and study endpoints, including hospital mortality censored at 30 days and clinical cure. We then determined the pooled estimates of effect and investigated factors associated with hospital mortality in multivariable analysis. MEASUREMENTS AND MAIN RESULTS We identified three randomized controlled trials in which researchers recruited a total of 632 patients with severe sepsis. The two groups were well balanced in terms of age, sex, and illness severity. The rates of hospital mortality and clinical cure for the continuous versus intermittent infusion groups were 19.6% versus 26.3% (relative risk, 0.74; 95% confidence interval, 0.56-1.00; P = 0.045) and 55.4% versus 46.3% (relative risk, 1.20; 95% confidence interval, 1.03-1.40; P = 0.021), respectively. In a multivariable model, intermittent β-lactam administration, higher Acute Physiology and Chronic Health Evaluation II score, use of renal replacement therapy, and infection by nonfermenting gram-negative bacilli were significantly associated with hospital mortality. Continuous β-lactam administration was not independently associated with clinical cure. CONCLUSIONS Compared with intermittent dosing, administration of β-lactam antibiotics by continuous infusion in critically ill patients with severe sepsis is associated with decreased hospital mortality.
Iterative Source–Channel Decoding With Reduced Error Floors

Audio-visual source encoders for digital mobile communications extract parameters that-due to delay and complexity constraints-exhibit some residual redundancy. This residual redundancy can be exploited by iterative source-channel decoding (ISCD) to improve the robustness against transmission noise by performing soft parameter detection as part of the decoding process. Systems employing ISCD at the receiving end often exhibit an observable error floor. While this error floor can be tolerated in some cases, it is often desirable to perfectly reconstruct the source codec parameters. In this paper, we explain the reasons for the error floor and propose two solutions for realizing ISCD systems with optimized error floor performance while maintaining the desired near-capacity waterfall behavior. All approaches aim at optimizing the distance properties of the (redundant) mapping of bit patterns to the source codec parameters. In some cases, especially if small quantizer code books are employed, good mappings cannot be found-in this case, the novel multi-dimensional bit mapping allows to reduce the error floor after decoding.
Serum neutrophil gelatinase-associated lipocalin levels are correlated with the complexity and the severity of atherosclerosis in acute coronary syndrome

Objective: Neutrophil gelatinase-associated lipocalin (NGAL) is a novel inflammatory marker that is released from neutrophils. In this study, we evaluated the correlation between serum NGAL level and clinical and angiographic risk scores in patients diagnosed with non-ST elevation acute coronary syndrome (NSTE-ACS). Methods: Forty-seven random NSTE-ACS patients and 45 patients with normal coronary arteries (NCA) who underwent coronary angiography were enrolled in the study. GRACE risk score and SYNTAX and Gensini risk scores were used, respectively, for the purpose of clinical risk assessment and angiographic risk scoring. Serum NGAL level was measured via ELISA in peripheral blood samples obtained from the patients at the time of admission. Results: Serum NGAL level was significantly higher in the NSTE-ACS group compared to the control group (112.3±49.6 ng/mL vs. 58.1±24.3 ng/mL, p<0.001). There was a significant positive correlation between serum NGAL levels and the GRACE (r=0.533 and p<0.001), SYNTAX (r=0.395 and p=0.006), and Gensini risk scores (r=0.575 and p<0.001). The intermediate-high SYNTAX (>22) group had statistically significantly higher serum NGAL levels compared to the low SYNTAX (≤22) group (143±29.5 ng/mL vs. 98.7±43.2 ng/mL, p=0.001). Conclusion: NGAL level was positively correlated with lesion complexity and severity of coronary artery disease in patients with NSTE-ACS. Serum NGAL levels on admission are associated with increased burden of atherosclerosis in patients with NSTE-ACS.
Asset Allocation in a Value-at-Risk Framework

In this paper we develop an asset allocation model which allocates assets by maximising expected return subject to the constraint that the expected maximum loss should meet the Value-at-Risk limits set by the risk manager. Similar to the mean-variance approach a performance index like the Sharpe index is constructed. Furthermore it is shown that the model nests the mean-variance approach in case of normally distributed expected returns. We provide an empirical analysis using two assets: US stocks and bonds. The results highlight the influence of non-normal characteristics of the expected return distribution on the optimal asset allocation.
Effects of Lattice Types on GaN-Based Photonic Crystal Surface-Emitting Lasers

GaN-based photonic crystal (PC) surface emitting lasers with different lattice types including hexagonal, square, and honeycomb lattice were fabricated and characterized. Laser characteristics including threshold conditions, lasing spectra, polarization, and divergence angle of devices with different lattice have been studied and discussed. The threshold energy density of the device with honeycomb, hexagonal, and square lattice was measured to be approximately 1.6, 2.3, and 3.8 mJ/cm2 at room temperature, showing superior characteristics of applying honeycomb as PC lattice patterns. Moreover, the experimental results were matched well to the theoretical prediction using the multiple scattering method. Finally, the laser characteristics of devices with three lattice types such as divergence angle and degree of polarization (DOP) were analyzed and discussed. The device with honeycomb lattice shows low threshold, high DOP of 86%, and low divergence angle of 1.3° among three lattice types, demonstrating its potential in the future surface emitting laser sources.
Inducible expression of insulin receptors on T lymphocyte clones

This study demonstrates that the insulin receptors are expressed on the surface of some T cell clones after specific antigenic stimulation. The insulin receptors on these lymphocytes are physicochemically similar to insulin receptors present on cells which express the receptors constitutively (adipocytes, hepatocytes, etc.). The kinetics of expression of insulin receptors on cloned, noncytotoxic T cells after specific antigenic stimulation closely parallels that of [3H]thymidine incorporation in such cultures.
Whisper: Tracing the Spatiotemporal Process of Information Diffusion in Real Time

When and where is an idea dispersed? Social media, like Twitter, has been increasingly used for exchanging information, opinions and emotions about events that are happening across the world. Here we propose a novel visualization design, “Whisper”, for tracing the process of information diffusion in social media in real time. Our design highlights three major characteristics of diffusion processes in social media: the temporal trend, social-spatial extent, and community response of a topic of interest. Such social, spatiotemporal processes are conveyed based on a sunflower metaphor whose seeds are often dispersed far away. In Whisper, we summarize the collective responses of communities on a given topic based on how tweets were retweeted by groups of users, through representing the sentiments extracted from the tweets, and tracing the pathways of retweets on a spatial hierarchical layout. We use an efficient flux line-drawing algorithm to trace multiple pathways so the temporal and spatial patterns can be identified even for a bursty event. A focused diffusion series highlights key roles such as opinion leaders in the diffusion process. We demonstrate how our design facilitates the understanding of when and where a piece of information is dispersed and what are the social responses of the crowd, for large-scale events including political campaigns and natural disasters. Initial feedback from domain experts suggests promising use for today's information consumption and dispersion in the wild.
The spectra of nonnegative integer matrices via formal power series

An old problem in matrix theory is to determine the n-tuples of complex numbers which can occur as the spectrum of a matrix with nonnegative entries (see [BP94, Chapter 4] or [Min88, Chapter VII]). Authors have studied the case where the ntuple is comprised of real numbers [Bor95, Cia68, Fri78, Kel71, Per53, Sal72, Sou83, Sul49], the case where the matrices under consideration are symmetric [Fie74, JLL96], and the general problem [Joh81, LM99, LL79, Rea94, Rea96, Wuw97]. Various necessary conditions and sufficient conditions have been provided, but a complete characterization is known for real n-tuples only for n ≤ 4 [Kel71, Sul49] and for complex n-tuples only for n ≤ 3 [LL79]. Motivated by symbolic dynamics, Boyle and Handelman refocused attention on the nonzero part of the spectrum by making the following “Spectral Conjecture” [BH91, BH93] (see also [Boy93, §8] and [LM95, Chapter 11]). Below, a matrix A is primitive if all entries of A are nonnegative and for some n, all entries of A are strictly positive. Also,
Percutaneous Vertebroplasty: A New Serial Injection Technique to Minimize Cement Leak

Study Design This is a prospective cohort study. Purpose This study discusses a new technique for injecting cement in the affected vertebrae. Overview of Literature Since introduction of vertebroplasty to clinical practice, the cement leak is considered the most frequent and hazardous complication. In literature, the cement extravasation occurred in 26%-97% of the cases. Methods A hundred and twenty-three patients underwent vertebroplasty using the serial injection technique. The package of the cement powder and the solvent was divided into five equal parts. Each part of the powder and the solvent was mixed as a single dose and injected to the affected vertebra. The duration between subsequent injections was 10 minutes. Each injection consisted of 1-1.5 mL of cement. Results This new technique gives the surgeon enough time to make multiple separate injections using the same package. The time interval between injections hardens the cement just enough so that it does not get displaced by the next cement injection. This technique gives time to the preceding injected cement to seal off the cracks and cavities in the vertebra, and subsequently leads to a significant decrease in cement leak (p<0.001), as compared to literature. Conclusions This study demonstrates a previously unreported technique for vertebroplasty that adds more safety to the procedure by significantly decreasing cement leak. It also makes the surgeon more relaxed due to time intervals, giving him more self-confidence whilst performing the procedure.
Algorithm for the Computation of the Generalized Fresnel Integral

The generalized Fresnel Integral appears as a canonical function in the uniform ray field representation of several high-frequency diffraction mechanisms, such as double wedge or vertex diffraction. Here we propose an algorithm for its calculation which is valid both for real and imaginary arguments as required for treating the general case in the uniform geometrical theory of diffraction framework.
The Specifics of Coping: Parents of Daughters With Anorexia Nervosa

In this article, the authors report on an interview study in which parents described the coping strategies they used to deal with the demands of having a daughter diagnosed with anorexia nervosa. They compare parents’ accounts with commonly used categorizations in quantitative studies of parental coping and adjustment. The study indicates that parents attribute multiple, complex, and unique motives to their actions that problematize quantitative constructions of types of coping. Parents often defined their actions differently and reported using coping strategies that were not considered or measured by the most widely used quantitative coping instruments. The analysis indicates that when the focus is on understanding and assisting parental coping in particular circumstances, situated, contextspecific analyses are necessary to design measures that accurately reflect parents’ coping efforts.
Disentangling the complex of Lichenothelia species from rock communities in the desert

Rock-inhabiting fungi (RIF) are melanized, meristematic fungi which dwell on and within rocks and have adapted to withstand harsh conditions in extreme habitats worldwide. Their morphological and genetic diversity remained unknown for a long time, but in the past few years culture-dependent and molecular phylogenetic approaches have contributed to uncovering the species richness of these otherwise very inconspicuous fungi. Only a few taxa of RIF develop both sexual reproductive structure (fertile stromata and/or pycnidia) and show multiple life styles, interacting with algae and lichen thalli in different ways. The genus Lichenothelia is one of these: It is characterized by fertile stromata and pycnidia and by species which can grow on and within exposed rocks, optionally associating with algae, with some species also being lichenicolous. The genus Lichenothelia includes up to now 25 species and form a monotypic family (Lichenotheliaceae) and order (Lichenotheliales) in Dothideomycetes. Here we focused on a group of Lichenothelia taxa distributed in the hot arid region of the Sonoran and Mojave Deserts in the Joshua Tree National Park in California. We performed molecular and morphological analyses and culture isolation and considered the ecology of the environmental samples to disentangle five species. We present the revision of two species already described, Lichenothelia calcarea and L. convexa, and introduce three new taxa to science, L. arida, L. umbrophila and L. umbrophila var. pullata.
Exponential Synchronization of Complex Networks of Linear Systems and Nonlinear Oscillators: A Unified Analysis

A unified approach to the analysis of synchronization for complex dynamical networks, i.e., networks of partial-state coupled linear systems and networks of full-state coupled nonlinear oscillators, is introduced. It is shown that the developed analysis can be used to describe the difference between the state of each node and the weighted sum of the states of those nodes playing the role of leaders in the networks, thus making it feasible to consider the error dynamics for the whole network system. Different from the other various methods given in the existing literature, the analysis employed in this paper is demonstrated successfully in not only providing the consistent convergence analysis with much simpler form, but also explicitly specifying the convergence rate.
Clinical evaluation of and parental satisfaction with resin-faced stainless steel crowns.

PURPOSE This study evaluated the clinical success and parental acceptance of anterior primary dentition caries treatment with prefabricated resin-faced stainless steel crowns. METHODS A retrospective analysis of maxillary anterior primary dentition caries treatment using Whiter Biter II Crowns was performed. Each crown was evaluated for retention, fracture, interface failure, color match, marginal integrity, and surface texture. Parental satisfaction regarding the esthetics of the crowns was evaluated by survey. RESULTS Thirty-eight crowns were evaluated in 12 children. The average crown age at time of examination was 20.7 months. Three teeth were lost to trauma with all other crowns remaining intact. Twelve crowns (32%) showed loss of at least some facial resin. Nine crowns (24%) had complete loss of the resin facing. Overall parental satisfaction with the treatment was excellent, however, satisfaction with crown esthetics received the lowest rating. CONCLUSIONS While parental satisfaction with treatment of anterior primary dentition caries with prefabricated resin-faced stainless steel crowns is excellent, the high failure rate of the resin facings is problematic.
Gender Integration in Israeli Officer Training: Degendering and Regendering the Military

T his article examines the nature and meaning of gender integration in an officer training course in the Israeli military, in light of the hegemonic status of combat masculinity. The above quote is taken from an interview with Lieutenant Colonel Yoav Golan, a male battalion commander in the newly gender-integrated course. The quote starts by recognizing gender differences as legitimate: women’s crying no longer frightens him. However, in the same breath, Yoav recreates the gendered
Differential ability of a thiazolidinedione PPARγ agonist to attenuate cytokine secretion in primary microglia and macrophage‐like cells

Peroxisome proliferator‐activated receptor gamma (PPARγ) agonists are known to inhibit select pro‐inflammatory changes in models of CNS and systemic inflammation. Recent reports suggest that these anti‐inflammatory effects are due to mechanisms other than canonical nuclear receptor‐mediated transcriptional alteration. Using primary microglia and the monocytic cell line, THP‐1, we demonstrate that rosiglitazone, a PPARγ‐activating thiazolidinedione, decreases pro‐inflammatory cytokine secretion as measured by ELISA. Cells were pre‐treated with various thiazolidinediones, including rosiglitazone, prior to stimulation with lipopolysaccharide or phorbol 12‐myristate 13‐acetate (PMA) to stimulate cytokine production. Tumor necrosis factor alpha (TNFα) secretion was significantly inhibited in both primary microglia and THP‐1 cells differentiated for 72 h in the presence of PMA to induce a macrophage‐like phenotype. No reduction in TNFα secretion was observed in undifferentiated THP‐1 cells with rosiglitazone pre‐treatment. Electrophoretic mobility shift assay revealed no significant difference in PPARγ activation between PMA‐differentiated and undifferentiated THP‐1 cells. When PMA‐differentiated and undifferentiated THP‐1 cells were treated with the irreversible PPARγ antagonist, GW 9662, a significant, dose‐dependent decrease in TNFα secretion was observed. These results suggest that the anti‐inflammatory benefit of PPARγ ligands occur independently of classical PPARγ activation.