Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved enrichment and proteomic identification of outer membrane proteins from a Gram‐negative bacterium: Focus on Caulobacter crescentus

Efforts to characterize proteins found in the outer membrane (OM) of Gram‐negative bacteria have been steadily increasing due to the promise of expanding our understanding of fundamental bacterial processes such as cell adhesion or cell wall biogenesis as well as the promise of finding potential vaccine‐ or drug‐targets for virulent bacteria. We have developed a mass spectrometry‐compatible experimental strategy that resulted in increased coverage of the OM proteome of a model organism, Caulobacter crescentus. The specificity of the OM enrichment step was improved by using detergent solubilization of the protein pellet, low‐density cell culture conditions, and a surface‐layer deficient cell line. Additionally, efficient gel‐assisted digestion, high‐resolution RP/RP‐MS/MS, and rigorous bioinformatic analysis led to the identification of 234 proteins using strict identification criteria (≥two unique peptides per protein; peptide false discovery rate <2%). Eighty‐four of the detected proteins were predicted to localize to the OM or extracellular space. These results represent ∼70% coverage of the predicted OM/extracellular proteome of C. crescentus. This analytical approach, which considers important experimental variables not previously explored in published OM protein studies, can be applied to other OM proteomic endeavors “as is” or with slight modification and should improve the large‐scale study of this especially challenging subproteome.
Invisibility and Cloaking Based on Scattering Cancellation

Advances in material synthesis and in metamaterial technology offer new venues to tailor the electromagnetic properties of devices, which may go beyond conventional limits in a variety of fields and applications. Invisibility and cloaking are perhaps one of the most thought‐provoking possibilities offered by these new classes of advanced materials. Here, recently proposed solutions for invisibility and cloaking using metamaterials, metasurfaces, graphene and/or plasmonic materials in different spectral ranges are reviewed and highlighted. The focus is primarily on scattering‐cancellation approaches, describing material challenges, venues and opportunities for the plasmonic and the mantle cloaking techniques, applied to various frequency windows and devices. Analogies, potentials and relevant opportunities of these concepts are discussed, their potential realization and the underlying technology required to verify these phenomena are reviewed with an emphasis on the material aspects involved. Finally, these solutions are compared with other popular cloaking techniques.
Physiology and Pathophysiology of Sleep Apnea Disorders of glucose metabolism in sleep apnea

Punjabi, Naresh M. , and Vsevolod Y. Polotsky. Disorders of glucose metabolism in sleep apnea. J Appl Physiol 99: 1998–2007, 2005; doi:10.1152/ japplphysiol.00695. 2005. —Sleep is a complex behavioral state that occupies onethird of the human life span. Although viewed as a passive condition, sleep is a highly active and dynamic process. The sleep-related decrease in muscle tone is associated with an increase in resistance to airflow through the upper airway. Partial or complete collapse of the airway during sleep can lead to the occurrence of apneas and hypopneas during sleep that define the syndrome of sleep apnea. Sleep apnea has become pervasive in Western society, affecting 5% of adults in industrialized countries. Given the pandemic of obesity, the prevalence of Type 2 diabetes mellitus and metabolic syndrome has also increased dramatically over the last decade. Although the role of sleep apnea in cardiovascular disease is uncertain, there is a growing body of literature that implicates sleep apnea in the pathogenesis of altered glucose metabolism. Intermittent hypoxemia and sleep fragmentation in sleep apnea can trigger a cascade of pathophysiological events, including autonomic activation, alterations in neuroendocrine function, and release of potent proinflammatory mediators such as tumor necrosis factorand interleukin-6. Epidemiologic and experimental evidence linking sleep apnea and disorders of glucose metabolism is reviewed and discussed here. Although the cause-and-effect relationship remains to be determined, the available data suggest that sleep apnea is independently associated with altered glucose metabolism and may predispose to the eventual development of Type 2 diabetes mellitus.
Journal of Graph Algorithms and Applications Geometric Simultaneous Embeddings of a Graph and a Matching

The geometric simultaneous embedding problem asks whether two pla-nar graphs on the same set of vertices in the plane can be drawn using straight lines, such that each graph is plane. Geometric simultaneous embedding is a current topic in graph drawing and positive and negative results are known for various classes of graphs. So far only connected graphs have been considered. In this paper we present the first results for the setting where one of the graphs is a matching. In particular, we show that there exist a planar graph and a matching which do not admit a geometric simultaneous embedding. This strengthens an analogous negative result for a planar graph and a path. On the positive side, we describe algorithms that compute a geometric simultaneous embedding of a matching and a wheel, outerpath, or tree. Our drawing algorithms minimize the number of orientations used to draw the edges of the matching. Specifically, when embedding a matching and a tree, we can draw all matching edges horizontally. When embedding a matching and a wheel or an outerpath, we use only two orientations.
Regulation of the delta and alpha epithelial sodium channel (ENaC) by ubiquitination and Nedd8

The δ epithelial sodium channel (δENaC) is a proton‐activated, sodium‐selective, amiloride‐sensitive ion channel in the ENaC/degenerin family of ion channels involved in blood pressure regulation and mechanosensation. Other ENaC family members are subject to ubiquitin modification leading to internalization from the cell surface, and degradation of the channel. Here, we show that δENaC is also modified by ubiquitin on three intracellular lysine residues. Absence of these lysines abolished ubiquitin modification of δENaC and increased cell surface levels of δENaC. Although the HECT‐domain ubiquitin ligase Nedd4‐2 reduced amiloride‐sensitive current generated by δβγENaC‐containing channels, δENaC does not contain a binding site for Nedd4‐2; therefore, this effect is probably mediated by the βγENaC subunits. Nedd8, a ubiquitin‐like protein that regulates RING‐domain E3 ubiquitin ligases, promoted δENaC ubiquitination, decreased both the intracellular and cell surface δENaC populations, and decreased δβγENaC amiloride‐sensitive short circuit current (Isc‐amiloride) in a mammalian epithelium. Nedd8 also promoted α− and γENaC ubiquitination, decreased the cell surface pools, and decreased αβγENaC Isc‐amiloride. Conversely, XIAP, a single subunit RING E3 ligase, decreased ubiquitinated δENaC, increased the δENaC cell surface pool and increased δβγENaC Isc‐amiloride. Therefore δ− and α − βγENaC channel function may be influenced by RING‐domain E3 ubiquitin ligases. J. Cell. Physiol. 228: 2190–2201, 2013. © 2013 Wiley Periodicals, Inc.
My program is ok – am I? Computing freshmen's experiences of doing programming assignments

This article provides insight into how computing majors experience the process of doing programming assignments in their first programming course. This grounded theory study sheds light on the various processes and contexts through which students constantly assess their self-efficacy as a programmer. The data consists of a series of four interviews conducted with a purposeful sample of nine computer science majors in a research intensive state university in the United States. Use of the constant comparative method elicited two forms of results. First, we identified six stages of doing a programming assignment. Analysis captures the dimensional variation in students' experiences with programming assignments on a detailed level. We identified a core category resulting from students' reflected emotions in conjunction with self-efficacy assessment. We provide a descriptive model of how computer science majors build their self-efficacy perceptions, reported via four narratives. Our key findings are that some students reflect negative views of their efficacy, even after having a positive programming experience and that in other situations, students having negative programming experiences still have a positive outlook on their efficacy. We consider these findings in light of possible languages and support structures for introductory programming courses.
Effects of endogenous insulin-like growth factor binding protein-3 on cell cycle regulation in breast cancer cells

High tissue insulin-like growth factor binding protein-3 (IGFBP-3) expression in breast cancers is associated in some studies with rapid growth and poor outcome. This study examined the effects of endogenous IGFBP-3 in Hs578T breast cancer cells, which are IGF-unresponsive and grow aggressively despite relatively high IGFBP-3 expression. IGFBP-3 downregulation using siRNA was associated with increases in DNA synthesis, the percentage of cells in S phase and viable cell numbers, accompanied by increases in cyclins A and D1, a decrease in p27 expression, and increased phosphorylation of retinoblastoma (Rb) on Ser795. Downregulation of IGFBP-3 inhibited extracellular signal-regulated kinase (ERK) activation and cell migration in a monolayer wound healing assay. These results indicate that endogenous IGFBP-3 is anti-proliferative and pro-migratory in Hs578T cells and that these effects are IGF-independent. Poor outcome in breast tumours expressing high levels of IGFBP-3 may be due to the effects of IGFBP-3 on cell migration rather than cell growth.
Toward Scalable Hybrid Stores

Data centric applications often use heterogeneous datasets: some very large while others of moderate size, some highly structured (e.g., relations) while others complex structured (e.g., graphs) or little structured (e.g., log data). Facing them is a variety of storage systems but none of which is the best for all, at all times. We present Estocada, an architecture we are currently developing to efficiently handle highly heterogeneous datasets based on a dynamic set of potentially very different data stores. Estocada provides to the ap- plication layer access to each dataset in its native format, while hosting them internally in a set of potentially overlapping fragments, possibly distributed across heterogeneous stores. At the core of Estocada lie powerful view-based rewriting and view selection algorithms to marry correctness with high performance.
Multiple solutions to the l1-optimal control problem and its dual linear programming problem

This paper explores the consequences for the l/sup 1/-optimal controller of the dual linear programming problem having multiple solutions, for linear time-invariant single-input/single-output systems. When the dual problem has multiple solutions, all solutions yield the same set of optimal controllers. If these multiple solutions comprise an entire face of the constraint region, there is a single optimal controller. Thus, if the constraint region is two-dimensional, the primal and dual problems cannot both have multiple solutions. An example is given with a three dimensional constraint region where both problems have multiple solutions.
Quantitative analysis of in-field defects in image sensor arrays

Growth of pixel density and sensor array size increases the likelihood of developing in-field pixel defects. An ongoing study on defect development in imagers has now provided us sufficient data to be able to quantify characteristics of defect growth. Preliminary investigations have shown that defects are distributed randomly and the closest distance between two defective pixels is approximately 79-340 pixels apart. Furthermore, from an observation of 98 cluster-free defects, the diameter of the defect is estimated to be less than 2.3% of a pixel size at 99% confidence level. The fact that no defect clusters were found in the study of various digital cameras allows us to conclude that defects are not likely to be related to material degradation or imperfect fabrication but are due to environmental stress such as radiation. Furthermore, as verified by a statistical study, the absence of defect clustering provides information on the size of defects and insight into the nature of the defect development.
Coupling Cortical Neurons through Electronic Memristive Synapse

Functional coupling live neurons through artificial synapses is the primary requirement for their implementation as prosthetic devices or in building hybrid networks. Here, the first evidence of unidirectional, activity dependent, coupling of two live neurons in brain slices via organic memristive devices (OMD) is demonstrated. ODM is a polymeric electrochemical element, which has two terminals for the connection in electrical circuits and which displays hysteresis and rectifying features. OMD coupling is characterized by nonlinear relationships determined by the instantaneous values of OMD resistance that can be controlled by the neuronal activity, and the excitation threshold in the postsynaptic neuron. OMD coupling also has the spike‐timing features similar to that of the natural excitatory synapses. Also, OMD‐synapses support synchronized delta‐oscillations in the two‐neuron network. It is proposed that OMD‐synapses may enable realization of prosthetic synapses and building hybrid neuronal networks endowed with a capacity of learning, memory, and computation.
The Structure Lacuna

Molecular symmetry is intimately connected with the classical concept of three-dimensional molecular structure. In a non-classical theory of wave-like interaction in four-dimensional space-time, both of these concepts and traditional quantum mechanics lose their operational meaning, unless suitably modified. A required reformulation should emphasize the importance of four-dimensional effects like spin and the symmetry effects of space-time curvature that could lead to a fundamentally different understanding of molecular symmetry and structure in terms of elementary number theory. Isolated single molecules have no characteristic shape and macro-biomolecules only develop robust three-dimensional structure in hydrophobic response to aqueous cellular media.
Observation of oscillations in coronal loops

High cadence TRACE data (JOP 83) in the 171 A bandpass are used to report on several examples of outward propagating oscillations in the footpoints of large diffuse coronal loop structures close to active regions. The disturbances travel outward with a propagation speed between 70 and 160 km s−1. The variations in intensity are of the order of 2%–4%, compared to the background brightness and these get weaker as the disturbance propagates along the structure. From a wavelet analysis at different positions along the structures, periods in the 200–400 seconds range are found. It is suggested that these oscillations are slow magneto-acoustic waves propagating along the loop, carrying an estimated energy flux of 4×102 ergs cm−2 s−1.
The Tumor Microenvironment and Cancer

Tumors are now recognized as structures of multiple cell types. It is increasingly appreciated that as the cancer progresses, the surrounding microenvironment is activated in support, coevolving through continuous paracrine communication and supporting carcinogenesis. Therefore, the characterization of these interactions, and the molecular identification of key mediators, will provide insights into tumor biology and suggest further novel therapeutic options. In this special issue, C. Roma-Rodrigues et al. reviewed the role of exosome in tumor microenvironment, especially the cancer derived exosomes in the development and progression of cancer through modulation of intercellular communication within the tumor microenvironment by the transfer of protein, lipid, and RNA cargo. S. L. Schlereth et al. reviewed the crosstalk between cancer cells and tumor microenvironment that involved in the process of lymphangiogenesis. They showed that lymphangiogenesis is regulated by cells of the tumor microenvironment, including cancer-associated fibroblasts, mesenchymal stem cells, dendritic cells, or macrophages. Therefore, targeting prolymphangiogenic tumor microenvironment may represent a promising therapeutic option for cancer metastasis. J. Zhou et al. reviewed that chemoattractant receptors, a family of seven transmembrane G protein coupled receptors (GPCRs) combined with their ligands, are involved in almost every step of tumor development and progression such as increasing tumor cell migration, invasion, and metastasis. Bone metastases remain as the major problem for cancer patients. Bone metastases account for decreased quality of life and ultimately death of prostate, breast, and lung cancer patients. In this issue, D. Buenrostro et al. reviewed that the bone microenvironment cells including the fibroblasts, osteoblasts, osteoclasts, immune cells, and others may interact with the tumor cells and promote tumor cells to metastasize to the bone and other sites. While A. Romano et al.'s review focused on the role of immunological dysregulation in multiple myeloma progression and their potential clinical implications as novel therapeutic target. We hope that this issue will help researchers understand the interactions between tumor cells and tumor microenvironment that mediate tumor progression and metastasis. We also hope that this special issue will initiate new discussions relating to the development of novel anticancer therapies or preventive strategies based on an understanding of the communication within the tumor microenvironment. Zhen Chen Zhiqiang Meng Lijun Jia Rutao Cui
Neurobiological model of obsessive–compulsive disorder: Evidence from recent neuropsychological and neuroimaging findings

Obsessive–compulsive disorder (OCD) was previously considered refractory to most types of therapeutic intervention. There is now, however, ample evidence that selective serotonin reuptake inhibitors and behavior therapy are highly effective methods for treatment of OCD. Furthermore, recent neurobiological studies of OCD have found a close correlation between clinical symptoms, cognitive function, and brain function. A large number of previous neuroimaging studies using positron emission tomography, single‐photon emission computed tomography or functional magnetic resonance imaging (fMRI) have identified abnormally high activities throughout the frontal cortex and subcortical structures in patients with OCD. Most studies reported excessive activation of these areas during symptom provocation. Furthermore, these hyperactivities were decreased after successful treatment using either selective serotonin reuptake inhibitors or behavioral therapy. Based on these findings, an orbitofronto‐striatal model has been postulated as an abnormal neural circuit that mediates symptomatic expression of OCD. On the other hand, previous neuropsychological studies of OCD have reported cognitive dysfunction in executive function, attention, nonverbal memory, and visuospatial skills. Moreover, recent fMRI studies have revealed a correlation between neuropsychological dysfunction and clinical symptoms in OCD by using neuropsychological tasks during fMRI. The evidence from fMRI studies suggests that broader regions, including dorsolateral prefrontal and posterior regions, might be involved in the pathophysiology of OCD. Further, we should consider that OCD is heterogeneous and might have several different neural systems related to clinical factors, such as symptom dimensions. This review outlines recent neuropsychological and neuroimaging studies of OCD. We will also describe several neurobiological models that have been developed recently. Advanced findings in these fields will update the conventional biological model of OCD.
Improving the expressiveness of mobile robots

RoboX is a tour guide robot, designed to interact with visitors at Expo02, the Swiss National Exhibition. During five months, ten RoboXs will be in contact with about 4500 visitors per day. These peoples are not trained to autonomous robots and will be guided by the robots throughout an exhibition about robotics. The work exposed here was dedicated to make RoboX lifelike and credible in implementing an expression generator This generator uses the robot capacities in order to best express its internal state which is influenced by its sensor entries and the scenario of the guided tour To validate our approach, a short experiment was set UP in order to present results that include appreciations of people not used to robots.
A Simple , Low Cost , 3 D Scanning System Using the Laser Light-Sectioning Method

The use of 3D scanning systems for acquiring the external shape features of arbitrary objects has many applications in industry, computer graphics, and more recently, the biomedical field. The potential exists to expand the use of 3D models even further, by continuing to develop simpler, more cost effective systems. A simple, lost cost, 3D scanning system is presented which employs a laser light-sectioning technique. Results of a proof of concept experiment for the proposed system demonstrate the validity of the chosen approach. Directions for future work are also discussed.
Reestimation of Reified Rules in Semiring Parsing and Biparsing

We show that reifying the rules from hyperedge weights to first-class graph nodes automatically gives us rule expectations in any kind of grammar expressible as a deductive system, without any explicit algorithm for calculating rule expectations (such as the inside-outside algorithm). This gives us expectation maximization training for any grammar class with a parsing algorithm that can be stated as a deductive system, for free. Having such a framework in place accelerates turnover time for experimenting with new grammar classes and parsing algorithms---to implement a grammar learner, only the parse forest construction has to be implemented.
How to measure metacognition

The ability to recognize one's own successful cognitive processing, in e.g., perceptual or memory tasks, is often referred to as metacognition. How should we quantitatively measure such ability? Here we focus on a class of measures that assess the correspondence between trial-by-trial accuracy and one's own confidence. In general, for healthy subjects endowed with metacognitive sensitivity, when one is confident, one is more likely to be correct. Thus, the degree of association between accuracy and confidence can be taken as a quantitative measure of metacognition. However, many studies use a statistical correlation coefficient (e.g., Pearson's r) or its variant to assess this degree of association, and such measures are susceptible to undesirable influences from factors such as response biases. Here we review other measures based on signal detection theory and receiver operating characteristics (ROC) analysis that are “bias free,” and relate these quantities to the calibration and discrimination measures developed in the probability estimation literature. We go on to distinguish between the related concepts of metacognitive bias (a difference in subjective confidence despite basic task performance remaining constant), metacognitive sensitivity (how good one is at distinguishing between one's own correct and incorrect judgments) and metacognitive efficiency (a subject's level of metacognitive sensitivity given a certain level of task performance). Finally, we discuss how these three concepts pose interesting questions for the study of metacognition and conscious awareness.