Miracle-dz/UniFAR-FTUs huggingface dataset:
Trends in bacterial pathogens of lower respiratory tract infections.

OBJECTIVES This study was conducted to determine the bacterial aetiology of lower respiratory tract infections in this environment as well as update the clinicians in the various antimicrobial alternatives available in the treatment. METHODS Between September 2002 and February 2005, 157 bacterial pathogens from 556 patients with lower respiratory tract infections were isolated from sputum specimens, and subjected to susceptibility testing, using standard bacteriologic techniques. RESULTS Out of the 556 cases, only 150 (27%) had an established bacterial aetiology. One pathogen was demonstrated in 143 (95.3%) patients and seven (4.7%) had mixed infections. The most prevalent single pathogen was Klebsiella pneumoniae (38%) while the most prevalent bacterial combination was Klebsiella and Pseudomonas species (2%). Isolates of Klebsiella pneumoniae were susceptible to ciprofloxacin, gentamicin and ceftriaxone. CONCLUSIONS Bacteriological diagnosis and antibiotic resistance surveillance are indispensable in the effective management of lower respiratory tract infections.
Mitigating the mobile agent malicious host problem by using communication patterns

Purpose – This paper seeks to describe an approach to mitigate the unsoluble malicious host problem.Design/methodology/approach – By using obfuscation as a component of communication patterns and their switching in an environment of cooperating agents the malicious host can be detected and the attacked agents can be deleted.Findings – Finds that the information about the detected malicious host can be used further, e.g. to prevent another mobile agent from visiting this host.Originality/value – This paper will be helpful to people involved in information management and computer security issues.
An algorithm for automatic respiratory state classifications using tracheal sound analysis

Analyzing the breathing data to classify the respiratory states has various applications in the areas of drug overdose and medical diagnosis of several other respiratory medical conditions. Tracheal sounds have shown to provide accurate breathing data with high signal to noise ratio for measuring air flow. The heartbeat signal is a source of interference for the tracheal sound measurements and hence is often filtered out prior to the tracheal sound data analysis. Filtering the heartbeat signal, however, removes a part of the tracheal sound data along with its energy and statistical information. We propose an algorithm to classify the respiratory states from the tracheal sound data despite the presence of heartbeat signals. This algorithm uses the data histogram as well as the data autocorrelation function (ACF) for feature extractions, and shows that these features, when used by a Softmax classifier, can properly discriminate among breathing conditions with classification rates exceeding 97%.
The UL6 Gene Product Forms the Portal for Entry of DNA into the Herpes Simplex Virus Capsid

ABSTRACT During replication of herpes simplex virus type 1 (HSV-1), viral DNA is synthesized in the infected cell nucleus, where DNA-free capsids are also assembled. Genome-length DNA molecules are then cut out of a larger, multigenome concatemer and packaged into capsids. Here we report the results of experiments carried out to test the idea that the HSV-1 UL6 gene product (pUL6) forms the portal through which viral DNA passes as it enters the capsid. Since DNA must enter at a unique site, immunoelectron microscopy experiments were undertaken to determine the location of pUL6. After specific immunogold staining of HSV-1 B capsids, pUL6 was found, by its attached gold label, at one of the 12 capsid vertices. Label was not observed at multiple vertices, at nonvertex sites, or in capsids lacking pUL6. In immunoblot experiments, the pUL6 copy number in purified B capsids was found to be 14.8 ± 2.6. Biochemical experiments to isolate pUL6 were carried out, beginning with insect cells infected with a recombinant baculovirus expressing the UL6 gene. After purification, pUL6 was found in the form of rings, which were observed in electron micrographs to have outside and inside diameters of 16.4 ± 1.1 and 5.0 ± 0.7 nm, respectively, and a height of 19.5 ± 1.9 nm. The particle weights of individual rings as determined by scanning transmission electron microscopy showed a majority population with a mass corresponding to an oligomeric state of 12. The results are interpreted to support the view that pUL6 forms the DNA entry portal, since it exists at a unique site in the capsid and forms a channel through which DNA can pass. The HSV-1 portal is the first identified in a virus infecting a eukaryote. In its dimensions and oligomeric state, the pUL6 portal resembles the connector or portal complexes employed for DNA encapsidation in double-stranded DNA bacteriophages such as φ29, T4, and P22. This similarity supports the proposed evolutionary relationship between herpesviruses and double-stranded DNA phages and suggests the basic mechanism of DNA packaging is conserved.
Aneuploidy detection in porcine embryos using fluorescence in situ hybridization

In contrast to human embryos, there are very few studies published on the frequency of chromosomal aneuploidy in farm animals. The objectives of this study were to apply a three-color fluorescent in situ hybridization (FISH) method for evaluating aneuploidy in porcine embryos using chromosome-specific DNA probes, establish baseline frequencies of aneuploidy in embryos and compare the results with our previous findings of aneuploidy in spermatozoa and oocytes. The embryos were collected from superovulated gilts, which were slaughtered 48 h after insemination. FISH was performed using probes specific for the centromeric regions of porcine chromosomes 1, 10 and Y. Altogether 403 blastomeres from 114 porcine embryos were successfully investigated. Diploidy was observed in 101 (88.6%) embryos, triploidy in 2 (1.8%) embryos, mosaicism/mixoploidy in 9 (7.9%) embryos, and trisomy for chromosomes 1 or 10 in 2 (1.8%) embryos. No blastomere showed aneuploidy for chromosome Y. These findings correspond with the frequencies of aneuploidy we have found previously in porcine germ cells.
Targeting mTOR in renal cell carcinoma

The mammalian target of rapamycin (mTOR) is clearly an important therapeutic target for advanced renal cell carcinoma (RCC), although its mechanisms of activation are not completely understood. In first‐line treatment of patients who have both advanced RCC and multiple risk factors for short survival, temsirolimus improves overall survival (OS) compared with interferon. In patients whose tumors have progressed after sunitinib and/or sorafenib therapy, everolimus improves progression‐free survival compared with placebo. Beyond the initial phase 3 studies demonstrating efficacy, many important questions remain in the clinical application of mTOR inhibition and in developing other inhibitors of PI3K/Akt/mTOR signaling. Important objectives of current and future clinical investigations include a more detailed description of the molecular pathology of RCC and identification of potential biomarkers that are predictive of tumor sensitivity to PI3K/Akt/mTOR targeted therapies. This information may identify other groups of RCC patients that are likely to benefit from inhibition of this signaling pathway. Additional questions concern mechanisms by which tumors become resistant to mTOR inhibitor therapy and how such resistance can be defeated. Possible mechanisms include the loss of feedback inhibition of insulin receptor substate/PI3K signaling resulting from the inhibition of mTOR complex 1 by rapamycin analogs and the activating phosphorylation of Akt by mTOR complex 2. Laboratory studies indicate that these resistance mechanisms could be countered by using other targeted agents in combination with mTOR inhibitors. Cancer 2009;115(10 suppl):2313‐20. © 2009 American Cancer Society.
Current Losses at the Front of Silicon Heterojunction Solar Cells

The current losses due to parasitic absorption in the indium tin oxide (ITO) and amorphous silicon (a-Si:H) layers at the front of silicon heterojunction solar cells are isolated and quantified. Quantum efficiency spectra of cells in which select layers are omitted reveal that the collection efficiency of carriers generated in the ITO and doped a-Si:H layers is zero, and only 30% of light absorbed in the intrinsic a-Si:H layer contributes to the short-circuit current. Using the optical constants of each layer acquired from ellipsometry as inputs in a model, the quantum efficiency and short-wavelength current loss of a heterojunction cell with arbitrary a-Si:H layer thicknesses and arbitrary ITO doping can be correctly predicted. A 4 cm2 solar cell in which these parameters have been optimized exhibits a short-circuit current density of 38.1 mA/cm2 and an efficiency of 20.8%.
Methodological Primitives for Phased Construction of Data Visualization Models

The paper considers common methodological primitives for phased construction of data visualization models, which will help to create new graphical models of data security visualization, or will help to show advantages and disadvantages of existing models. The paper also considers examples of graphical models and additional tools, which allow to work with these models. The purpose of the paper is to form a comprehensive vision to create data security visualization models. The primitives classification and communication between them are suggested. On the base of identified primitives, graphical models and additional tools to work with graphical models, a methodology for constructing data security visualization models is provided. This methodology can be used for improving efficiency of existing models and for evaluating their effectiveness. The paper also considers a new visualization model for network security which was developed based on the proposed visualization process.
EEG as a means of communication: preliminary experiments in EEG analysis using neural networks

EEG analysis has played a key role in the modeling of the brain's cortical dynamics, but relatively little effort has been devoted to developing EEG as a limited means of communication. If several mental states can be reliably distinguished by recognizing patterns in EEG, then a paralyzed person could communicate to a device like a wheelchair by composing sequences of these mental states. EEG pattern recognition is a difficult problem and hinges on the success of finding representations of the EEG signals in which the patterns can be distinguished. In this article, we report on a study comparing three EEG representations, the raw signals, a reduced-dimensional representation using the K-L transform, and a frequency-based representation. Classification is performed with a two-layer neural network implemented on a CNAPS server (128 processor, SIMD architecture) by Adaptive Solutions, Inc. The best classification accuracy on untrained samples is 73% using the frequency-based representation.
Community photo collections

With the recent rise in popularity of Internet photo sharing sites, community photo collections-collections of images contributed by users online-have emerged as a powerful new type of image data set for computer vision and computer graphics research. Community photo collections are both a challenge and an opportunity: Compared to standard data sets captured under laboratory conditions, community photo collections show an extreme variability since the images were captured by a large number of photographers with various cameras and at different times. On the other hand, they are a tremendous resource since they give us access to a wide variety of images and associated meta information. In this talk, I will first give an overview over community photo collections. I will then describe several different projects done in my group that use community photo collections for reconstruction, rendering, and other purposes. Finally, I will close with an outlook on open research problems in the area.
Research and application of a new computational model of human vision system based on ridgelet transform

The properties and limitations of the human visual system (HVS) can be utilizing in many image processing, such as image compression, watermarking and image quality assessment. This paper addresses the issue of how to establish the computational model of HVS in image ridgelet transform domain. Utilizing the multi-channel spatial-frequency decomposition, we proposed a new visual model in ridgelet domain by taking into account the local band limited contrast, the frequency sensitivity and masking effecting of HVS. The proposed visual model can exactly evaluate the just noticeable distortion (JND) tolerance of HVS. Finally we demonstrated the performance of our model with the application in the field of image quality evaluation and digital watermarking. A perceptual criterion of image quality evaluation is proposed and a robust watermark in ridgelet domain is presented. Lots of experiments are shown the new computational model of HVS is very useful in such applications.
Low-noise variable-gain amplifier in 90-nm CMOS for TV on mobile

Presented is a low-noise variable-gain amplifier intended for handheld TV-on-mobile in the UHF band. The circuitry, implemented in 90-nm CMOS technology, is designed for compliance with MBRAI category 2 and 3 and for robustness against the high RF input levels caused by uplink signals from cellular and connectivity services integrated in the same handheld. The overall Noise Figure is kept low by employing lossless feedback in the VGA. The effect of a back- gate control to reduce the sensitivity of the amplifier characteristics to variations in supply voltage has been studied. The test chip realized exhibits 23 dB gain that can be stepped down with 2 dB resolution, 2.6 dB NF, a -5.4 dBm IIP3 at maximum gain and 40 mW power consumption at 1.2 V supply.
Mapping Medical Disasters: Ebola Makes Old Lessons, New

Abstract Disaster medicine is characterized by shortages of everything but patients. There are never enough beds, equipment, personnel, or supplies. In the 2014 Ebola epidemic, another scarcity was maps. The need for maps of the affected areas, and the ways the maps were used, serve to emphasize the way maps have always served in both disaster medicine and public health preparedness. Those lessons are reviewed here in the context of the Ebola epidemic. (Disaster Med Public Health Preparedness. 2015;0:1-8)
Chloroplast- or Mitochondria-Targeted DEAD-Box RNA Helicases Play Essential Roles in Organellar RNA Metabolism and Abiotic Stress Responses

The yields and productivity of crops are greatly diminished by various abiotic stresses, including drought, cold, heat, and high salinity. Chloroplasts and mitochondria are cellular organelles that can sense diverse environmental stimuli and alter gene expression to cope with adverse environmental stresses. Organellar gene expression is mainly regulated at posttranscriptional levels, including RNA processing, intron splicing, RNA editing, RNA turnover, and translational control, during which a variety of nucleus-encoded RNA-binding proteins (RBPs) are targeted to chloroplasts or mitochondria where they play essential roles in organellar RNA metabolism. DEAD-box RNA helicases (RHs) are enzymes that can alter RNA structures and affect RNA metabolism in all living organisms. Although a number of DEAD-box RHs have been found to play important roles in RNA metabolism in the nucleus and cytoplasm, our understanding on the roles of DEAD-box RHs in the regulation of RNA metabolism in chloroplasts and mitochondria is only at the beginning. Considering that organellar RNA metabolism and gene expression are tightly regulated by anterograde signaling from the nucleus, it is imperative to determine the functions of nucleus-encoded organellar RBPs. In this review, we summarize the emerging roles of nucleus-encoded chloroplast- or mitochondria-targeted DEAD-box RHs in organellar RNA metabolism and plant response to diverse abiotic stresses.
Percutaneous coronary intervention for postcardiac arrest syndrome

Purpose of review Sudden cardiac arrest is a major cause of unexpected death, as well as a major clinical issue. Primary percutaneous coronary intervention (PCI) can drastically improve outcomes among patients with ST-elevation myocardial infarction without cardiac arrest. Recent studies reported that using emergency PCI to resuscitate patients has the potential to improve their outcomes. The purpose of this review is to elucidate the effects of PCI among resuscitated patients. Recent findings To the best of current understanding, no randomized clinical trial has assessed PCI for postcardiac arrest syndrome. Several observational studies suggested a positive effect of PCI for resuscitated out-of-hospital cardiac arrest (OHCA) patients, and a number of observational studies reported a limited beneficial effect. Several studies reported that a combination of therapeutic hypothermia and PCI may be feasible and effective. However, the presence of bias and unmeasured confounders in these studies may have affected the outcomes. Summary PCI for postcardiac arrest syndrome may improve outcomes of OHCA patients; however, randomized trials of PCI for postcardiac arrest syndrome are necessary to confirm this issue. Alternative cardiopulmonary resuscitation using venoarterial extracorporeal membrane oxygenation and PCI may have the potential to improve the outcomes of refractory cardiac arrest patients.
Evolutionary bilevel optimization (EBO)

Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage, and that copies bear this no<ce and the full cita<on on the first page. Copyrights for third-­‐party components of this work must be honored. For all other uses, contact the owner/author(s). Copyright is held by the author/owner(s). GECCO'14, July 12–16, 2014, Vancouver, BC, Canada. ACM 978-­‐1-­‐4503-­‐2662-­‐9/14/07. Ankur Sinha Post-Doctoral Researcher Aalto University School of Business Helsinki, Finland ankur.sinha@aalto.fi
Energy efficient networking: Avoiding a future energy crunch

Estimates suggest that in ten years backbone network traffic will increase by a factor of thirty, which will require a corresponding increase in network capacity. However, at the same time, as the traffic will continue to explosively increase, analyses also indicate that capacity scaling may be nearing an end for optical fibers, Silicon CMOS and cellular systems. Clearly this is undesirable and novel technical approaches are needed to address communications sustainability. In this paper we describe the problem and novel technical approaches to confront the issue.
IL-1 alpha regulates CXCL1, CXCL10 and ICAM1 in network form in oral keratinocytes.

BACKGROUND Keratinocytes are the major constituent of epithelial cells at skin and mucosal surfaces such as oral mucosa. In our previous study, it was indicated that oral keratinocytes play active roles in oral mucosal adaptive immune response and an IL-alpha sub-network was identified. In the past decades IL-1, a revolutionarily ancient cytokine, has attracted our attention for its important roles in innate and adaptive immune responses. In this study we aim to show the IL-alpha sub-network in oral keratinocytes and explore its relevance in oral lichen planus (OLP). METHODS We first tested whether IL-1alpha regulated its sub-network genes including CXCL1, CXCL10, and ICAM1 mRNA levels in time and concentration dependent manners by real time PCR. Then we investigated the expression of IL-1alpha and CXCL1 in OLP tissues by immunohistochemical staining. RESULTS IL-1alpha regulated its sub-network genes including CXCL1, CXCL10, and ICAM1 mRNA levels in time dependent but not in concentration dependent manner. Immunohistochemistry studies showed that IL-1alpha and CXCL1 were expressed in OLP tissues, which were only detected in tissue transudate and whole unstimulated saliva in previous studies. CONCLUSIONS IL-1alpha regulates CXCL1, CXCL10, and ICAM1 in network form in oral keratinocytes. A complete characterization of the IL-1alpha sub-network will shed light on the exploration of IL-1 as the therapeutic target in OLP and help to illuminate the multiple regulatory functions of keratinocytes in oral mucosa or even in other mucosa sites.
Automatic Brain Mask Segmentation for Mono-modal MRI

In recent years, deep learning methods have gained promising results in different kinds of image processing tasks, such as image classification, semantic segmentation, image generation and so on. This paper focuses on the research of brain masking for monomodal MRI, structural MRI, which is the most commonly used by the clinic and research. The brain mask is a basic and essential tool for brain function analysis and voxel-based structural analysis. In this paper, we present an automatic method for brain masking which would match the brain atlas for the origin image and also extract the regions of interest (ROI), like Hippocampus. Our network is developed from the U-net and a coarse mask is added into the network, which is generated by the method of region seeds growing. The combination of coarse mask and origin input speeds up the localization of the network and also increases the segmentation accuracy. In this work, two groups of experiments have been carried out, the one to do the brain mask automatically for the whole brain and the other for the region of Hippocampus extraction. Finally we have gained 0.893 dice coefficient for Hippocampus and 0.865 for the whole brain regions in average.
Writing as a Knowledge-Constituting Process

This chapter argues that current problem-solving models of writing fail to capture the role writing has in constituting thought. It sketches a model of language production as a knowledge-constituting process, in which content can be generated by constraint satisfaction within a distributed semantic memory, and in which sequences of ideas can be produced by inhibitory feedback from preceding output. The model is then used to clarify: the distinctions between different forms of text production in writing, the relation between writing and discovery, and the interaction between explicit problem-solving processes and implicit knowledge-constituting processes during writing. It concludes by outlining the preliminary results of a study motivated by the model.
Increased Levels of Soluble LR11 in Cerebrospinal Fluid of Patients with Alzheimer Disease

Background: Recent genetic and pathological studies have suggested that a lipoprotein receptor, LR11, is intricately implicated in the pathogenesis of Alzheimer disease (AD). We have recently established a novel sandwich ELISA, which enabled the sensitive quantification of a soluble LR11 (sLR11). By this ELISA, we attempted to determine the difference in the levels of CSF sLR11 in AD patients. Methods: We examined CSF from 29 AD patients, 20 frontotemporal lobar degeneration patients and 27 age-matched control subjects. The CSF sLR11 level as well as the levels of tau and β-amyloid42 (Aβ42) were determined by sandwich ELISA. Results: The CSF tau level and tau/Aβ42 ratio were significantly increased (p < 0.01) in the AD patients. The CSF sLR11 level in the AD patients was significantly higher (p < 0.01) than that of the frontotemporal lobar degeneration patients and the controls. The APOE-Ε4-positive AD patients have higher sLR11 levels than the APOE-Ε4-negative patients (p < 0.01). Conclusions: These results suggest that the quantification of CSF sLR11 may serve as a biomarker of AD, although the diagnostic value for individual patients is limited. An elevated CSF sLR11 level in AD patients may be relevant to AD pathogenesis.