Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Markers Predict Survival in Glioma Patients*

Glioblastoma multiforme (GBM) is a genomically complex and aggressive primary adult brain tumor, with a median survival time of 12–14 months. The heterogeneous nature of this disease has made the identification and validation of prognostic biomarkers difficult. Using reverse phase protein array data from 203 primary untreated GBM patients, we have identified a set of 13 proteins with prognostic significance. Our protein signature predictive of glioblastoma (PROTGLIO) patient survival model was constructed and validated on independent data sets and was shown to significantly predict survival in GBM patients (log-rank test: p = 0.0009). Using a multivariate Cox proportional hazards, we have shown that our PROTGLIO model is distinct from other known GBM prognostic factors (age at diagnosis, extent of surgical resection, postoperative Karnofsky performance score (KPS), treatment with temozolomide (TMZ) chemoradiation, and methylation of the MGMT gene). Tenfold cross-validation repetition of our model generation procedure confirmed validation of PROTGLIO. The model was further validated on an independent set of isocitrate dehydrogenase wild-type (IDHwt) lower grade gliomas (LGG)—a portion of these tumors progress rapidly to GBM. The PROTGLIO model contains proteins, such as Cox-2 and Annexin 1, involved in inflammatory response, pointing to potential therapeutic interventions. The PROTGLIO model is a simple and effective predictor of overall survival in glioblastoma patients, making it potentially useful in clinical practice of glioblastoma multiforme.
Abundance and Diversity of Hydrogenotrophic Microorganisms in the Infant Gut before the Weaning Period Assessed by Denaturing Gradient Gel Electrophoresis and Quantitative PCR

Delivery mode (natural vs. cesarean) and feeding type (breast vs. formula feeding) are relevant factors for neonatal gut colonization. Biomolecular methods have shown that the ecological structure of infant microbiota is more complex than previously proposed, suggesting a relevant presence of unculturable bacteria. It has also been postulated that among unculturable bacteria, hydrogenotrophic populations might play a key role in infant health. Sulfate-reducing bacteria (SRB), acetogens, and methanogenic archaea use hydrogenotrophic pathways within the human colon. However, to date, few studies have reported detection of hydrogenotrophic microorganisms in newborns, possibly because of limitations on available group-specific, culture-independent quantification procedures. In the present work, we analyzed 16 fecal samples of healthy babies aged 1–6 months by means of quantitative PCR (qPCR) targeting the 16S rRNA or metabolic functional genes and by denaturing gradient gel electrophoresis (DGGE). qPCR data showed quantifiable levels of methanogens, SRB, and acetogens in all samples, indicating that the relative abundances of these microbial groups were not affected by delivery mode (natural vs. caesarian). DGGE revealed a high prevalence of the Blautia genus within the acetogenic bacteria despite strong interindividual variability. Our preliminary results suggest that hydrogenotrophic microorganisms, which have been a neglected group to date, should be included in future ecological and metabolic studies evaluating the infant intestinal microbiota.
A method for prolonged survival of primary cell lines

SummaryWe have established a means for prolonged survival of primary cell cultures and establishment of continuous cell lines without genetic manipulations. Primary cultures of granulosa cells degenerate rapidly in vitro by a spontaneous onset of apoptotic cell death. Earlier attempts to circumvent this limitation have included transformation with oncogenes, spontaneous immortalization of primary cultures, and chemical carcinogenesis. We have found that addition of a complex of growth-promoting compounds, carrier proteins, and factors isolated from porcine follicular fluid to standard culture medium allows, reproducibly, the establishment of continuous porcine primary granulosa cell lines with genetic stability. This same supplement allows the prolonged survival of primary cell cultures derived from adult rat ovaries. The rat ovary primary cultures consisted of mixed phenotypes, including epithelial, neuron-like, and mesenchymal cell types. Numerous cells stain positive for alkaline phosphatase in these cultures. Other primary cell lines were established from embryonic rat liver and from adult rat lungs, using the same supplement. The survival effect is reversible because cells degenerate when the supplement is removed. Therefore, the cell lines have neither acquired properties of a tumor cell line nor have they been immortalized by a virus infection. We expect that our approach will open the door to prolonged survival of other primary cell types.
Unidirectional theta replication of the structurally stable Enterococcus faecalis plasmid pAM beta 1.

Numerous bacterial replicons remain poorly characterized due to difficulties in localization of the replication origin. We have circumvented this problem in the characterization and fine mapping of the origin of plasmid pAM beta 1 by exploiting the Bacillus subtilis termination signal, terC. In terC‐containing derivatives, theta‐form molecules with two invariant endpoints accumulate. The endpoints, which correspond to plasmid origin and terC, were mapped with single‐nucleotide precision. Analysis of the replication intermediates of wild‐type molecules by two‐dimensional gel electrophoresis confirmed the location of the plasmid origin. Our results demonstrate that pAM beta 1 replication proceeds unidirectionally by a theta mechanism. This work confirms the use of termination signals to localize origins, suggests that termination in B. subtilis occurs by a mechanism similar to that of Escherichia coli and establishes that in addition to rolling circle replicating plasmids, Gram positive bacteria harbour plasmids which replicate by a theta mechanism.
FEM based modeling of tunable BAW resonators with Ba0.8Sr0.2TiO3

In this paper, a finite element method and multiphysics based 3D modeling of tunable ferroelectric thin film resonator taking the advantages of electrostrictive and piezoelectric effects of Ba0.8Sr0. 2TiO3 thin film. DC electrical field dependency of the dielectric permittivity and elasticity coefficients can control the resonances in the thin film. The resonator has a series resonant frequency of 4.33 GHz and parallel resonance at 4.43 GHz with applied DC voltage of 2 V. The electromechanical coupling coefficient is measured at 5.4% and increased to be 8% with the biasing voltage at 8V.
A sliding‐window weighted linkage disequilibrium test

Multilocus linkage disequilibrium (LD) tests that consider inter‐marker (LD) are more powerful than single‐locus tests when disease etiology is contributed simultaneously by several linked and correlated loci. However, inclusion of redundant non‐informative markers may result in reduced testing power and/or inflated false‐positive rate, therefore selection of proper marker sets is important in such tests. We introduce a unified LD test based on a convenient marker‐selection procedure (sliding window) combined with an adjustment approach (marker weighting) to dilute the impact of nuisance markers on tests. The proposed procedure includes several conventional p‐value combination methods as its special cases. Simulation studies were performed to evaluate the impact of inclusion of nuisance markers and performance of the procedure. The results showed that testing power was often inversely proportional to the quantity of nuisance markers. Among a class of p‐value combination methods, the product p‐value method had the highest testing power. P‐value truncation somewhat reduced the testing power but controlled the false‐positive rate well. Compared with conventional unweighted approaches, the weighted strategy alleviated the false‐positive rate and/or increased testing power when nuisance markers were included. Analyses of two authentic data sets for psoriasis and Alzheimer's disease using our proposed method confirmed previous findings. Genet. Epidemiol. 2006. © 2006 Wiley‐Liss, Inc.
The Making of a Generation: The Children of the 1970s in Adulthood

In an effort to provide answers to the overarching question “of how a generation is made,” Andres and Wyn offer readers theoretical, conceptual, and policy insights based on the aspirations and trajectories of Canadian and Australian children born in the 1970s. The main premise of the book is that secondary-school graduates of the late 1980s and 1990s found themselves confronting significant economic uncertainty, workplace restructuring, and social change. Despite being more educated than their predecessors, these young adults entered new labour markets that were deregulated and precarious. As such, the authors convincingly argue that children of the 1970s “bore the brunt” of neoliberal educational and labour policies as they negotiated the significant social and economic transformations of the 1990s.
Optimized design of filter for transformerless three-level photovoltaic grid-connected inverter

Linking the capacitor neutral point of LCL filter to the DC midpoint for transformerless three-level photovoltaic inverter has an advantage of leakage current reduction. But it also brings large current virtual value and low-frequency resonance of bridge-side current, which leads to the reduction of the system efficiency and stability. Aiming at these problems, the common and differential mode model of three-level grid-connected inverter was constructed. Based on the equivalent model, the mechanism of the two problems was analyzed and a optimized design scheme was proposed. In the scheme, the capacitor of LCL filter was divided to two parts and the neutral point of the smaller one was linked to the DC midpoint. Then, the design principle of the improved LCL filter parameter was proposed based on bridge-side current ripple and common mode voltage source spectrum analysis. The problems of the system efficiency and stability reduction were solved when this proposed scheme was adopted. Feasibility and effectiveness of the optimized scheme are validated by experimental results.
Two-step stimulation of B lymphocytes to enter DNA synthesis: synergy between anti-immunoglobulin antibody and cytochalasin on expression of c-myc and a G1-specific gene

Previously we demonstrated that stimulation of resting murine splenic B lymphocytes with goat anti-mouse immunoglobulin antibody (GaMIg) plus cytochalasin D (CD) led to DNA synthesis; GaMIg and CD added simultaneously, or GaMIg added before CD, induced this response (T. L. Rothstein, J. Immunol. 136:813-816, 1986). Cells similarly treated with GaMIg or CD alone did not enter S phase. Here we have measured the effects of this two-signal stimulation on the c-myc, 2F1, and gamma-actin genes. The expression of these growth-related genes is known to change either during the G0-to-G1 transition or in the G1 phase of the cell cycle. For the 2F1 and c-myc genes, neither the GaMIg nor CD stimulus alone led to a prolonged increase in mRNA levels, whereas GaMIg plus CD allowed for continuous elevated expression of these genes. Furthermore, GaMIg pretreatment rendered expression of the c-myc and 2F1 genes susceptible to subsequent action by CD. In contrast, CD alone was sufficient to produce changes in gamma-actin gene expression. Thus there are synergistic effects of competence- and progressionlike factors on the expression of the c-myc and 2F1 genes, and these effects correlate with the progression of B lymphocytes to DNA synthesis.
Exploring Proxemics for Human-Drone Interaction

We present a human-centered designed social drone aiming to be used in a human crowd environment. Based on design studies and focus groups, we created a prototype of a social drone with a social shape, face and voice for human interaction. We used the prototype for a proxemic study, comparing the required distance from the drone humans could comfortably accept compared with what they would require for a nonsocial drone. The social shaped design with greeting voice added decreased the acceptable distance markedly, as did present or previous pet ownership, and maleness. We also explored the proximity sphere around humans with a social shaped drone based on a validation study with variation of lateral distance and heights. Both lateral distance and the higher height of 1.8 m compared to the lower height of 1.2 m decreased the required comfortable distance as it approached.
Closed-form scheduling policies for delay-sensitive traffic over fading channels

Next-generation wireless networks for personal communication services should be designed to transfer delay-sensitive (possibly, heavy-tailed distributed) bursty traffic flows over energy-limited buffer-equipped faded connections. In this scenario, a still open question concerns the closed-form design of scheduling policies minimizing the average transfer-delay under constraints on both average and peak energies. The key-point of the novel approach we follow consists in the minimization (on a per step basis) of the queue-length averaged over the fading statistics and conditioned on the queue occupancy at the previous step. We prove that, under the considered energy constraints, the scheduler retains two optimality properties. First, its stability region is the maximal admissible one. Second, the scheduler also minimizes the unconditional average queue-length (over both queue and link state statistics). Finally, we explicitly derive the optimal scheduler expressions and performances for some systems of practical interest.
Cognitive learning in neural networks using fuzzy systems

Adaptation and recognition problem in multipurpose environments is always called as one of the most important and useful problems between the recognition algorithms and mechanisms. One popular approach is using mechanisms which are trying to train the recognition system on a targeted pattern, to concentrating all the capacity of recognition system onto recognition or prediction process. Cognitive structures are among these intelligence learning solutions. Since cognitive structures used in living organisms have shown their eligibility on recognition and classification with appropriate accuracy, utilizing of these structures is rational. This paper proposes three cognitive principles based on neural network as a universal approximator. First a central control unit, a fuzzy system, will be shown to determine the adaptation rate for a target sample. Second, a minimal optimization will be performing for each sample. Third, a recognition system is going to use for recognition in sort of different environments.
Deep metric learning for multi-labelled radiographs

Many radiological studies can reveal the presence of several co-existing abnormalities, each one represented by a distinct visual pattern. In this article we address the problem of learning a distance metric for plain radiographs that captures a notion of "radiological similarity": two chest radiographs are considered to be similar if they share similar abnormalities. Deep convolutional neural networks (DCNs) are used to learn a low-dimensional embedding for the radiographs that is equipped with the desired metric. Two loss functions are proposed to deal with multi-labelled images and potentially noisy labels. We report on a large-scale study involving over 745,000 chest radiographs whose labels were automatically extracted from free-text radiological reports through a natural language processing system. Using 4,500 validated exams, we demonstrate that the methodology performs satisfactorily on clustering and image retrieval tasks.
Differential Effects of Ebselen on Neutrophil Recruitment, Chemokine, and Inflammatory Mediator Expression in a Rat Model of Lipopolysaccharide-Induced Pulmonary Inflammation

We postulated that the seleno-organic compound ebselen would attenuate neutrophil recruitment and activation after aerosolized challenge with endotoxin (LPS) through its effect as an antioxidant and inhibitor of gene activation. Rats were given ebselen (1–100 mg/kg i.p.) followed by aerosolized LPS exposure (0.3 mg/ml for 30 min). Airway inflammatory indices were measured 4 h postchallenge. Bronchoalveolar lavage (BAL) fluid cellularity and myeloperoxidase activity were used as a measure of neutrophil recruitment and activation. RT-PCR analysis was performed in lung tissue to assess gene expression of TNF-α, cytokine-induced neutrophil chemoattractant-1 (CINC-1), macrophage-inflammatory protein-2 (MIP-2), ICAM-1, IL-10, and inducible NO synthase. Protein levels in lung and BAL were also determined by ELISA. Ebselen pretreatment inhibited neutrophil influx and activation as assessed by BAL fluid cellularity and myeloperoxidase activity in cell-free BAL and BAL cell homogenates. This protective effect was accompanied by a significant reduction in lung and BAL fluid TNF-α and IL-1β protein and/or mRNA levels. Ebselen pretreatment also prevented lung ICAM-1 mRNA up-regulation in response to airway challenge with LPS. This was not a global effect of ebselen on LPS-induced gene expression, because the rise in lung and BAL CINC-1 and MIP-2 protein levels were unaffected as were lung mRNA expressions for CINC-1, MIP-2, IL-10, and inducible NO synthase. These data suggest that the anti-inflammatory properties of ebselen are achieved through an inhibition of lung ICAM-1 expression possibly through an inhibition of TNF-α and IL-1β, which are potent neutrophil recruiting mediators and effective inducers of ICAM-1 expression.
A Comparative Live Evaluation of Multileaving Methods on a Commercial cQA Search

We present one of the world's first attempts to examine the feasibility of multileaving evaluation of document rankings on a large scale commercial community Question Answering (cQA) service. As a natural enhancement of interleaving evaluation, multileaving merges more than two input rankings into one and measures the search user satisfaction of each input ranking on the basis of user clicks on the multileaved ranking. We evaluated the adequateness of two major multileaving methods, team draft multileaving (TDM) and optimized multileaving (OM), proposing their practical implementation for live services. Our experimental results demonstrated that multileaving methods could precisely evaluate the effectiveness of five rankings with different quality by using clicks from real users. Moreover, we concluded that OM is more efficient than TDM by observing that most of the evaluation results with OM converged after showing multileaved rankings around 40,000 times and an in-depth analysis of their characteristics.
Mutual Productivity Spillovers in Slovakia: Absorptive Capacity, the Technology Gap, and Nonlinear Effects

This article analyzes traditional productivity spillovers from foreign to local firms and reverse productivity spillovers from local to foreign firms. It argues that the extent of mutual productivity spillovers depends on absorptive capacity and the technology gap. The authors’ hypotheses were tested with panel data on Slovak firms for the period 2003–12. Traditional productivity spillovers through output were found to be positive, but the spillover effects through capital were mostly negative. The effect of the technology gap on productivity spillovers was conducive. Nonlinear effects were found in services and high-tech industries. Reverse productivity spillovers through capital were positive in the manufacturing industries.
Coping in Cyberspace: The Impact of Internet Use on the Ability of HIV-Positive Individuals to Deal with Their Illness

The human immunodeficiency virus (HIV) poses one of the greatest health threats of modern times. The Internet provides unparalleled access to resources that can assist individuals coping with HIV infection. Despite the promise of online resources to help individuals manage and cope with their illness, few studies have investigated the impact of their use. Those that have looked primarily at Internet use from a group perspective. These studies were usually 'bounded' as well, focusing on electronic support groups or highly structured computer-based support systems that offer select users prescribed resource options. Little is known about how individuals who are on their 'own' - without access to these services - use the vast, unstructured array of resources available through the Internet. The purpose of this study was to investigate the impact of Internet use on the coping ability of HIV-positive individuals. This research study employed a descriptive qualitative design that used in depth, semi structured, face-to-face interviews for data collection. The sample of 10 purposefully selected HIV-positive individuals reflected diversity in gender, age, race, education, employment, number of years living with HIV, and Internet use. Data analysis guided by the constant comparative method revealed that the impact of Internet use on coping ability involved three themes: The Internet promotes empowerment, augments social support, and facilitates helping others.
A new load balancing mechanism for improved video delivery over Wireless Mesh Networks

Wireless Mesh Networks (WMNs) are becoming increasingly popular and user demand for high-quality rich media services is continuously growing. Despite the fact that WMNs offer significant flexibility, they suffer in respect to Quality of Service (QoS) provisioning. This paper proposes a novel mechanism for providing enhanced QoS support to video services in multi-hop WMNs. The mechanism makes use of an innovative hybrid hierarchical architecture which combines centralized and distributed approaches. The proposed solution relies on performance monitoring at WMN nodes and performs load balancing by off-loading traffic from the highest loaded nodes to less loaded neighbours. Simulation-based results presented outline the performance of our proposed mechanism in terms of QoS metrics (delay, throughput, packet losses and PSNR) in different network load scenarios. The results clearly demonstrate how our proposed mechanism outperforms the traditional OLSR protocol in terms of QoS performance.
The JAK-STAT Pathway Is Critical in Ventilator-Induced Diaphragm Dysfunction

Mechanical ventilation (MV) is one of the lynchpins of modern intensive-care medicine and is life saving in many critically ill patients. Continuous ventilator support, however, results in ventilation-induced diaphragm dysfunction (VIDD) that likely prolongs patients’ need for MV and thereby leads to major associated complications and avoidable intensive care unit (ICU) deaths. Oxidative stress is a key pathogenic event in the development of VIDD, but its regulation remains largely undefined. We report here that the JAK-STAT pathway is activated in MV in the human diaphragm, as evidenced by significantly increased phosphorylation of JAK and STAT. Blockage of the JAK-STAT pathway by a JAK inhibitor in a rat MV model prevents diaphragm muscle contractile dysfunction (by ̃85%, p < 0.01). We further demonstrate that activated STAT3 compromises mitochondrial function and induces oxidative stress in vivo, and, interestingly, that oxidative stress also activates JAK-STAT. Inhibition of JAK-STAT prevents oxidative stress-induced protein oxidation and polyubiquitination and recovers mitochondrial function in cultured muscle cells. Therefore, in ventilated diaphragm muscle, activation of JAK-STAT is critical in regulating oxidative stress and is thereby central to the downstream pathogenesis of clinical VIDD. These findings establish the molecular basis for the therapeutic promise of JAK-STAT inhibitors in ventilated ICU patients.