Miracle-dz/UniFAR-FTUs huggingface dataset:
Marginalized zero‐inflated negative binomial regression with application to dental caries

The zero‐inflated negative binomial regression model (ZINB) is often employed in diverse fields such as dentistry, health care utilization, highway safety, and medicine to examine relationships between exposures of interest and overdispersed count outcomes exhibiting many zeros. The regression coefficients of ZINB have latent class interpretations for a susceptible subpopulation at risk for the disease/condition under study with counts generated from a negative binomial distribution and for a non‐susceptible subpopulation that provides only zero counts. The ZINB parameters, however, are not well‐suited for estimating overall exposure effects, specifically, in quantifying the effect of an explanatory variable in the overall mixture population. In this paper, a marginalized zero‐inflated negative binomial regression (MZINB) model for independent responses is proposed to model the population marginal mean count directly, providing straightforward inference for overall exposure effects based on maximum likelihood estimation. Through simulation studies, the finite sample performance of MZINB is compared with marginalized zero‐inflated Poisson, Poisson, and negative binomial regression. The MZINB model is applied in the evaluation of a school‐based fluoride mouthrinse program on dental caries in 677 children. Copyright © 2015 John Wiley & Sons, Ltd.
Stability of periodic solutions of periodic cellular neural networks with delays and impulsive perturbations

In this paper, we consider the dynamics of an artificial periodic cellular neural networks with time delays and impulsive control. Sufficient conditions are obtained for the stability of a unique periodic solution. The results extend earlier ones where impulse is absent. Further, the influences of the impulsive effect are investigated by using computer simulation method. These results are helpful to design globally asymptotically stable and periodic oscillatory cellular neural networks with time delay and impulsive perturbations.
Social Capital, Perceived Economic Affluence, and Smoking During Adolescence: A Cross-Sectional Study

ABSTRACT Background: Smoking is among the health risk behaviors taken up by many adolescents with lifelong consequences and associations with multiple health risk behaviors. Smoking and smoking initiation in adolescence involves an interaction between micro-, meso-, and macro systems, including neighborhoods and the greater community. Objectives: To examine the associations of individual social and economic capital with self-reported health, life satisfaction, and smoking behavior in adolescents. Methods: Using a multistage random sampling of junior high school students (16–18 years old) in Crete, Greece, 703 adolescents (90.2% 16 years old; 55.6% girls, participation rate 84.2%) completed an anonymous questionnaire based on HBSC study and the Youth Social Capital Scale (YSCS) during April–June 2008. Multiple logistic regression models were performed adjusted for potential confounders. Results: Adolescents with high participation in their neighborhoods and communities (higher structural social capital) displayed lower odds for daily smoking; those feeling unsafe (lower cognitive social capital) were at greater odds of daily smoking. Adolescents with less friends and acquaintances had lower odds of having tried tobacco products. Smoking was not related to any economic capital variables (perceived affluence, paternal and maternal employment status). Adolescents with low/medium versus high total social capital were at higher odds for low life satisfaction and fair/bad versus excellent self-rated health. Conclusions/Importance: Social capital theory may provide a better understanding in identifying the social context that is protective or harmful to adolescents' smoking. Public health organizations at all levels need to incorporate social capital theory in their interventions.
A score-informed shift-invariant extension of complex matrix factorization for improving the separation of overlapped partials in music recordings

Similar to non-negative matrix factorization (NMF), complex matrix factorization (CMF) can be used to decompose a given music recording into individual sound sources. In contrast to NMF, CMF models both the magnitude and phase of a source, which can improve the separation of overlapped partials. However, the shift-invariance for spectral templates enabling NMF-based methods to efficiently model vibrato in music is not available with CMF. Further, the estimation of an entire phase matrix for each source results in a high number of parameters in CMF, which often leads to poor local minima. In this paper we show that score information provides a source of prior knowledge rich enough to stabilize the CMF parameter estimation, without sacrificing its expressive power. As a second contribution, we present a shift-invariant extension to CMF bringing the vibrato-modeling capabilities of NMF to CMF. As our experiments demonstrate our proposed method consistently improves the separation quality for overlapped partials compared to score-informed NMF.
Full-duplex transmission in phy and mac layers for 5G mobile wireless networks

As the fourth-generation (4G) standards have been successfully deployed in all 4G-based wireless communication industries and mobile devices, research attention and the efforts of academia and industry have already moved onto fifth-generation (5G) technologies. While the frequency-division duplexing (FDD) and timedivision duplexing (TDD) are widely used in 4G mobile wireless networks, they have their inherent deficiencies of low spectrum efficiency because FDD and TDD are both based on the half-duplex transmission mode. To overcome these problems existing in 4G systems, in this article we propose novel wireless full-duplex transmission schemes in both the PHY and MAC layers for 5G mobile wireless networks to significantly increase the spectrum efficiency. In particular, we first develop the wireless fullduplex model for both bidirectional transmission and unidirectional transmission, respectively, taking into account self-interference mitigation. Then we analyze the traditional half-duplex FDD and TDD modes and show the superiority of the wireless full-duplex mode over the halfduplex FDD and TDD modes, respectively. Using our developed wireless full-duplex model, we develop and evaluate the efficient full-duplex power allocation scheme at the PHY layer. Corresponding to full-duplex transmission at the PHY layer, we also develop and analyze the fullduplex MAC protocol at the MAC layer to implement full-duplex transmission over the entire 5G mobile wireless network architecture. Through simulation experiments we show that our proposed schemes can significantly enhance spectrum efficiency for 5G mobile wireless networks.
Vascularization of the human fetal retina: roles of vasculogenesis and angiogenesis.

PURPOSE To characterize the topography of and the cellular processes that underlie vascularization of the human retina. METHODS The vasculature of human eyes obtained from fetuses ranging in age from 14 to 38 weeks of gestation (WG) was examined in Nissl-stained, whole-mount preparations and by anti-CD34 immunohistochemistry. RESULTS The first event in retinal vascularization, apparent before 15 WG, was the migration of large numbers of spindle-shaped mesenchymal precursor cells from the optic disc. These cells proliferated and differentiated to produce cords of endothelial cells. By 15 WG, some cords were already patent and formed an immature vascular tree in the inner retinal layers that was centered on the optic disc. These processes are consistent with vessel formation by vasculogenesis. Angiogenesis then increased the vascular density of this immature plexus and extended it peripherally and temporally. Maturation of the plexus was characterized by substantial remodeling, which involved the withdrawal of endothelial cells into neighboring vascular segments. The outer plexus was formed as a result of the extension of capillary-sized buds from the existing inner vessels, a process that began around the incipient fovea between 25 and 26 WG. CONCLUSIONS These observations suggest that the formation of primordial vessels in the central retina is mediated by vasculogenesis, whereas angiogenesis is responsible for increasing vascular density and peripheral vascularization in the inner retina. In contrast, the outer plexus and the radial peripapillary capillaries are formed by angiogenesis only. These mechanisms of retinal vascularization appear similar to those of vascularization of the central nervous system during development.
Diagnostic value of microRNAs in asbestos exposure and malignant mesothelioma: systematic review and qualitative meta-analysis

Background Asbestos is a harmful and exceptionally persistent natural material. Malignant mesothelioma (MM), an asbestos-related disease, is an insidious, lethal cancer that is poorly responsive to current treatments. Minimally invasive, specific, and sensitive biomarkers providing early and effective diagnosis in high-risk patients are urgently needed. MicroRNAs (miRNAs, miRs) are endogenous, non-coding, small RNAs with established diagnostic value in cancer and pollution exposure. A systematic review and a qualitative meta-analysis were conducted to identify high-confidence miRNAs that can serve as biomarkers of asbestos exposure and MM. Methods The major biomedical databases were systematically searched for miRNA expression signatures related to asbestos exposure and MM. The qualitative meta-analysis applied a novel vote-counting method that takes into account multiple parameters. The most significant miRNAs thus identified were then subjected to functional and bioinformatic analysis to assess their biomarker potential. Results A pool of deregulated circulating and tissue miRNAs with biomarker potential for MM was identified and designated as “mesomiRs” (MM-associated miRNAs). Comparison of data from asbestos-exposed and MM subjects found that the most promising candidates for a multimarker signature were circulating miR-126-3p, miR-103a-3p, and miR-625-3p in combination with mesothelin. The most consistently described tissue miRNAs, miR-16-5p, miR-126-3p, miR-143-3p, miR-145-5p, miR-192-5p, miR-193a-3p, miR-200b-3p, miR-203a-3p, and miR-652-3p, were also found to provide a diagnostic signature and should be further investigated as possible therapeutic targets. Conclusion The qualitative meta-analysis and functional investigation confirmed the early diagnostic value of two miRNA signatures for MM. Large-scale, standardized validation studies are needed to assess their clinical relevance, so as to move from the workbench to the clinic.
A Scoping Review of Health Outcomes Examined in Randomized Controlled Trials Using Guided Imagery

Introduction: Guided imagery involves the controlled visualization of detailed mental images. This integrative health technique is used for healing, health maintenance, or the treatment of specific conditions. Guided imagery is an integral part of mindfulness meditation, hypnosis, and various relaxation exercises. However, evidence to support the widespread use and dissemination of guided imagery interventions has been lacking. The purposes of this scoping review were to document the scope of health outcomes and disease processes examined by guided imagery researchers and the journal outlets where this work has been published. Secondary purposes were to review the efficacy of guided imagery, risk of bias from studies published in selected integrative health journals, and gain feedback from clinicians in a practiced-based research network about potential barriers for use in clinical settings. Methods: Ten bibliographic databases were searched for randomized controlled trials (RCTs) published between 1960 and 2013 that included adult participants. Descriptive and analytic methods were employed to document the journal outlets, diseases, and health outcomes investigated. Results: Three hundred twenty RCTs that included more than 17,979 adult participants were reviewed. The published studies appeared in 216 peer-reviewed journals from diverse disciplines largely representing psychology, the sport sciences, rehabilitation, nursing, and medicine. Major outcomes observed were coping with pain, stroke recovery, anxiety, coping with stress, and sport skills. Practitioner feedback from the practiced-based research network revealed some interest but skepticism and time constraints were discussed as barriers. Conclusions: Ongoing research and creative dissemination techniques are warranted.
Mesenchymal Wnt/β-catenin signaling limits tooth number

ABSTRACT Tooth agenesis is one of the predominant developmental anomalies in humans, usually affecting the permanent dentition generated by sequential tooth formation and, in most cases, caused by mutations perturbing epithelial Wnt/β-catenin signaling. In addition, loss-of-function mutations in the Wnt feedback inhibitor AXIN2 lead to human tooth agenesis. We have investigated the functions of Wnt/β-catenin signaling during sequential formation of molar teeth using mouse models. Continuous initiation of new teeth, which is observed after genetic activation of Wnt/β-catenin signaling in the oral epithelium, was accompanied by enhanced expression of Wnt antagonists and a downregulation of Wnt/β-catenin signaling in the dental mesenchyme. Genetic and pharmacological activation of mesenchymal Wnt/β-catenin signaling negatively regulated sequential tooth formation, an effect partly mediated by Bmp4. Runx2, a gene whose loss-of-function mutations result in sequential formation of supernumerary teeth in the human cleidocranial dysplasia syndrome, suppressed the expression of Wnt inhibitors Axin2 and Drapc1 in dental mesenchyme. Our data indicate that increased mesenchymal Wnt signaling inhibits the sequential formation of teeth, and suggest that Axin2/Runx2 antagonistic interactions modulate the level of mesenchymal Wnt/β-catenin signaling, underlying the contrasting dental phenotypes caused by human AXIN2 and RUNX2 mutations. Summary: Using mouse models to investigate serial tooth formation reveals that contrasting changes in tooth number associated with human mutations in AXIN2 and RUNX2 result from modulation of Wnt/β-catenin signaling in dental mesenchyme.
Solid‐State Characterization of Amorphous Dispersions

This chapter reviews established and emerging analytical and physical techniques for the characterization of amorphous solid dispersions. The thermal analysis methods used in most reported studies of amorphous solid dispersions include differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), and isothermal microcalorimetry (ITC). Many of the commonly used polymers in amorphous solid dispersions are hydrophilic in nature and contain polar functional groups, and can absorb moisture from the atmosphere. In the pharmaceutical sciences, vibrational spectroscopic methods are generally used to probe molecular vibrations and phonon modes in crystalline substances. Solid-state nuclear magnetic resonance (SSNMR) analysis of mobility in amorphous solid dispersions is complementary to thermal analysis and dielectric spectroscopy techniques. Scanning electron microscopy (SEM) is widely used in the characterization of amorphous solid dispersions. Effective characterization plays a critical role in the development of pharmaceutical amorphous solid dispersions. Keywords: amorphous solid dispersions; crystalline nanosuspensions; polymers; scanning electron microscopy (SEM); solid-state nuclear magnetic resonance (SSNMR)
Saa3 is a key mediator of the protumorigenic properties of cancer-associated fibroblasts in pancreatic tumors

Significance Pancreatic ductal adenocarcinoma is one of the most malignant human tumors for which there are no efficacious therapeutic strategies. This tumor type is characterized by an abundant desmoplastic stroma that promotes tumor progression. Yet recent studies have shown that physical or genetic elimination of the stroma leads to more aggressive tumor development. Here, we decided to reprogram the stromal tissue by identifying and subsequently targeting genes responsible for their protumorigenic properties. Comparative transcriptome analysis revealed several genes overexpressed in cancer-associated fibroblasts compared with those present in normal pancreata. We provide genetic evidence that one of these genes, Saa3, plays a key role on the protumorigenic properties of the stroma, opening the door to the design of future therapeutic strategies. Pancreatic ductal adenocarcinoma (PDAC) is characterized by the presence of abundant desmoplastic stroma primarily composed of cancer-associated fibroblasts (CAFs). It is generally accepted that CAFs stimulate tumor progression and might be implicated in drug resistance and immunosuppression. Here, we have compared the transcriptional profile of PDGFRα+ CAFs isolated from genetically engineered mouse PDAC tumors with that of normal pancreatic fibroblasts to identify genes potentially implicated in their protumorigenic properties. We report that the most differentially expressed gene, Saa3, a member of the serum amyloid A (SAA) apolipoprotein family, is a key mediator of the protumorigenic activity of PDGFRα+ CAFs. Whereas Saa3-competent CAFs stimulate the growth of tumor cells in an orthotopic model, Saa3-null CAFs inhibit tumor growth. Saa3 also plays a role in the cross talk between CAFs and tumor cells. Ablation of Saa3 in pancreatic tumor cells makes them insensitive to the inhibitory effect of Saa3-null CAFs. As a consequence, germline ablation of Saa3 does not prevent PDAC development in mice. The protumorigenic activity of Saa3 in CAFs is mediated by Mpp6, a member of the palmitoylated membrane protein subfamily of the peripheral membrane-associated guanylate kinases (MAGUK). Finally, we interrogated whether these observations could be translated to a human scenario. Indeed, SAA1, the ortholog of murine Saa3, is overexpressed in human CAFs. Moreover, high levels of SAA1 in the stromal component correlate with worse survival. These findings support the concept that selective inhibition of SAA1 in CAFs may provide potential therapeutic benefit to PDAC patients.
Evaluation of Takagi-Sugeno-Kang fuzzy method in entropy-based detection of DDoS attacks

The detection of distributed denial of service (DDoS) attacks based on internet traffic anomalies is a method which is general in nature and can detect unknown or zero-day attacks. One of the statistical characteristics used for this purpose is network traffic entropy: a sudden change in entropy may indicate a DDoS attack. However, this approach often gives false positives, and this is the main obstacle to its wider deployment within network security equipment. In this paper, we propose a new, two-step method for detection of DDoS attacks. This method combines the approaches of network traffic entropy and the TakagiSugeno-Kang fuzzy system. In the first step, the detection process calculates the entropy distribution of the network packets. In the second step, the TakagiSugeno-Kang fuzzy system (TSK-FS) method is applied to these entropy values. The performance of the TSK-FS method is compared with that of the typically used approach, in which cumulative sum (CUSUM) change point detection is applied directly to entropy time series. The results show that the TSK-FS DDoS detector reaches enhanced sensitivity and robustness in the detection process, achieving a high true-positive detection rate and a very low false-positive rate. As it is based on entropy, this combined method retains its generality and is capable of detecting various types of attack.
Prognostic value of plasma levels of HIF-1a and PGC-1a in breast cancer

Cellular adaptive mechanisms are crucial for tumorigenesis and a common feature in solid tumor progression. Hypoxia-inducible factor-1α (HIF-1α) facilitates the biological response to hypoxia, advancing angiogenesis and metastatic potential of the tumor. The peroxisome proliferator–activated receptor γ coactivators 1α (PGC-1α) enhances mitochondrial biogenesis, favored by migratory/invasive cancer cells. We conducted a prospective, long-term follow up study to determine whether HIF-1α and PGC-1α can be implemented as predictive biomarker in breast cancer. HIF-1α and PGC-1α plasma concentrations were measured in patients and in healthy controls by enzyme linked immune sorbent assay. Breast cancer patients had significantly higher HIF-1α and PGC-1α levels, which correlated with clinicopathological features, overall with more aggressive cancer characteristics. Disease free and overall survival of breast cancer patients with high HIF-1α and PGC-1α were significantly poorer than in patients with low plasma levels. In multivariate analysis, high amount of PGC-1α showed independent prognostic value. Our data suggests that HIF-1α and PGC-1α may be promising, noninvasive, biomarkers with a high potential for future clinical implication to identify subgroups of patients with poorer prognosis and to indicate early, subclinical metastasis.
Patterning of thick polymeric substrates for the fabrication of microfluidic devices

Plasma etching is investigated as an alternative technology to soft lithography for the fabrication of microfluidic devices. First, soft lithography was employed for the fabrication of microchannels in poly-dimethylsiloxane (PDMS), for use in a biosensor for protein and DNA detection. Then, a plasma etching process was investigated and optimized with respect to etch rate maximization for PDMS and PMMA substrates. Preliminary results for deep pattern transfer to these polymeric substrates with an Al etch mask are shown.
Source finding in linear polarization for LOFAR, and SKA predecessor surveys, using Faraday moments

The optimal source-finding strategy for linear polarization data is an unsolved problem, with many inhibitive factors imposed by the technically challenging nature of polarization observations. Such an algorithm is essential for Square Kilometre Array (SKA) pathfinder surveys, such as the Multifrequency Snapshot Sky Survey with the LOw Frequency ARray (LOFAR), as data volumes are significant enough to prohibit manual inspection. We present a new strategy of 'Faraday Moments' for source-finding in linear polarization with LOFAR, using the moments of the frequency-dependent full-Stokes data (i.e. the mean, standard deviation, skewness, and excess kurtosis). Through simulations of the sky, we find that moments can identify polarized sources with a high completeness: 98.5 per cent at a signal to noise of 5. While the method has low reliability, rotation measure (RM) synthesis can be applied per candidate source to filter out instrumental and spurious detections. This combined strategy will result in a complete and reliable catalogue of polarized sources that includes the full sensitivity of the observational bandwidth. We find that the technique can reduce the number of pixels on which RM Synthesis needs to be performed by a factor of ≈1 × 10 5 for source distributions anticipated with modern radio telescopes. Through tests on LOFAR data, we find that the technique works effectively in the presence of diffuse emission. Extensions of this method are directly applicable to other upcoming radio surveys such as the POlarization Sky Survey of the Universe's Magnetism with the Australia Square Kilometre Array Pathfinder, and the SKA itself.