Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial Suppression of RNA Polymerase II-Dependent Host Gene Expression

Asymptomatic bacteriuria (ABU) is a bacterial carrier state in the urinary tract that resembles commensalism at other mucosal sites. ABU strains often lack the virulence factors that characterize uropathogenic Escherichia coli (E. coli) strains and therefore elicit weak innate immune responses in the urinary tract. In addition, ABU strains are active modifiers of the host environment, which they influence by suppressing RNA polymerase II (Pol II)-dependent host gene expression. In patients inoculated with the ABU strain E. coli 83972, gene expression was markedly reduced after 24 h (>60% of all regulated genes). Specific repressors and activators of Pol II-dependent transcription were modified, and Pol II Serine 2 phosphorylation was significantly inhibited, indicating reduced activity of the polymerase. This active inhibition included disease–associated innate immune response pathways, defined by TLR4, IRF-3 and IRF-7, suggesting that ABU strains persist in human hosts by active suppression of the antibacterial defense. In a search for the mechanism of inhibition, we compared the whole genome sequences of E. coli 83972 and the uropathogenic strain E. coli CFT073. In addition to the known loss of virulence genes, we observed that the ABU strain has acquired several phages and identified the lytic Prophage 3 as a candidate Pol II inhibitor. Intact phage particles were released by ABU during in vitro growth in human urine. To address if Prophage 3 affects Pol II activity, we constructed a Prophage 3 negative deletion mutant in E. coli 83972 and compared the effect on Pol II phosphorylation between the mutant and the E. coli 83972 wild type (WT) strains. No difference was detected, suggesting that the Pol II inhibitor is not encoded by the phage. The review summarizes the evidence that the ABU strain E. coli 83972 modifies host gene expression by inhibition of Pol II phosphorylation, and discusses the ability of ABU strains to actively create an environment that enhances their persistence.
Advances on III-V on Silicon DBR and DFB Lasers for WDM Optical Interconnects and Associated Heterogeneous Integration 200mm-Wafer-Scale Technology

In the absence of practically efficient lasers achievable directly in Silicon or other group IV materials, Si-photonic transmitter sources must be made by "Hybrid integration" of III-V chips or "Heterogeneous integration" with III-V gain materials. "Hybrid integration" technologies consist in integrating processed (and finished) chips in a photonic microsystem. One commercial solution (from LUXTERA) makes use of a InP-bulk- processed laser-chip [3]. The laser chip is attached to the PIC, and its light is coupled into the PIC- waveguide by means of a lens, followed by an optical isolator, and a mirror for directing the light to a surface grating coupler in the Si-PIC. Other approaches (from KOTURA/ORACLE) consist in but-coupling a III-V- semiconductor reflective-SOA to the PIC-3μm- thick-Si-waveguide that comprises a Bragg-mirror for defining the laser cavity [4]. This forms an external-cavity DBR laser, with reported Waveguide-Coupled Wall-Plug-Efficiencies (WC-WPE) for the uncooled lasers of up to 9.5% at powers of 6 mW. In spite of the good demonstrated performances, this solution requires an accurate alignment between the R-SOA and the Si-PIC, limiting the capability for a low cost fabrication. As a more economical route that we opted for, "Heterogeneous integration" technologies were proposed [5], [6] together with new laser architectures. An InP-wafer having the III-V-gain- layers grown on top is bonded with loose alignment requirements (~50μm), the III-V gain-layers facing down to the bottom Silicon-On- Insulator (SOI) wafer on which silicon waveguides are pre- processed. In a more economical route, the InP-substrate having the laser III-V-gain- layers on top is first diced, and the dies are bonded where needed. Then the InP-substrate is removed, and the laser process is continued on the remaining III-V gain epi-layers, in a regular wafer level process flow. Putting the expensive III-V-gain material only where needed saves on cost. In addition to lower cost, photonic integration promises improved reliability and performances and reduced footprints over discrete components systems. This paper will report on our recent advances on both, 1) the developed III-V on Silicon lasers (DBR and DFB types) built up from heterogeneous integration, and, 2) the development of the integration technology for processing the lasers on 200mm-wafers, with industrial CMOS tools at very low cost.
Validation of the end-expired method for measuring carboxyhaemoglobin levels for the use in occupational and environmental exposure studies

Carbon monoxide is one of the most common toxins encountered in work settings, the gas being emitted in situations where there is incomplete combustion of carboncontaining substances. Its acute and chronic health effects have been well-documented. While identification of dangerous situations and evaluation of control measures are conducted by environmental monitoring, the body burden due to inhalation of carbon monoxide is measured by an individual's blood carboxyhaemoglobin level. Carboxyhaemoglobin level can be measured directly from a blood sample or, indirectly, by measuring the end-expired carbon monoxide level and using the charts provided to read the corresponding carboxyhaemoglobin level. As the end-expired method is not an intervention method, and is therefore easy to conduct, it Is being used widely in epidemiological studies and it could also be used for Individual measurements. This study presents a better statistical method for validating the end-expired method than the correlation method used and described in previous studies.
A Methodology for Modeling Dynamic and Static Power Consumption for Multicore Processors

System designers and application programmersmust consider trade-offs between performance and energy. Making energy-aware decisions when designing an application or runtime system requires quantitative information about power consumed by different processor components. We present a methodology to model static and dynamic power consumption of individual cores and the uncore components, and we validate our power model for both sequential and parallel benchmarks at different voltage-frequency pairs on an Intel Haswell platform. Our power models yield the following insights about energy-efficient scaling. (1) We show that uncore energy accounts for up to 74% of total energy. In particular, uncore static energy can be as high as 61% of total energy, potentially making it a major source of energy inefficiency. (2) We find that the frequency at which an application expends the lowest energy depends on how memory-bound it is. (3) We demonstrate that even though using more cores may improve performance, the energy consumed by stalled cores during serial portions of theprogram can make using fewer cores more energy-efficient.
Free radicals and chemiluminescence as products of the spontaneous oxidation of sulfide in seawater, and their biological implications.

The discovery of symbioses between marine invertebrates and sulfide-oxidizing bacteria at deep-sea hydrothermal vents and in other high-sulfide marine environments has stimulated research into the adaptations of metazoans to potentially toxic concentrations of sulfide. Most of these studies have focused on a particular action of sulfide--its disruption of aerobic metabolism by the inhibition of mitochondrial respiration--and on the adaptations of sulfide-tolerant animals to avoid this toxic effect (1). We propose that sulfidic environments impose another, hitherto over-looked type of toxicity: exposure to free radicals of oxygen, which may be produced during the spontaneous oxidation of sulfide, thus imposing an oxidative stress. Here we present evidence that oxygen- and sulfur-centered free radicals are produced during the oxidation of sulfide in seawater, and we propose a reaction pathway for sulfide oxidation that is consistent with our observations. We also show that chemiluminescence at visible wavelengths occurs during sulfide oxidation, providing a possible mechanism for the unexplained light emission from hydrothermal vents (2, 3).
The Relationship Between Creativity and Attention in Adults

Creativity is a valuable attribute that involves the generation of original ideas; attention is a vital function that facilitates information selection. There is some evidence that creative people may have poorer attention and are generally more distracted than others, and this distractibility is thought to enable the production of novel ideas. Previous research has largely supported this relationship between creativity and attention, yet they are both multifaceted constructs that can be measured in numerous ways. Using multiple measures of each construct, the aim of this study was to examine which features of creativity and attention might be related in a group of 100 adults (18–80 years, M = 26.9, SD = 11.5). Figural divergent-thinking (DT) originality was positively related to self-reported concentration; yet no other relationships were found. Results suggest that there is no consistent relationship between creativity and attention, and past studies that linked creativity to attention, having used just one or two measures, may be premature in their conclusions.
Optimality Theory and Human Sentence Processing: Towards a Cross-Modular Analysis of Coordination

In this paper we propose a model of human sentence processing that is based on Optimality Theory (OT). In contrast to most other OT approaches to language processing, we use constraints from OT semantics rather than OT syntax to address on-line comprehension. We illustrate the workings of our model by investigating the processing of coordinated structures. The psycholinguistic evidence that is currently available suggests that the on-line comprehension of coordination is influenced by constraints from many different information sources: pragmatics, discourse semantics, lexical semantics, and syntax. The model we propose formalizes this cross-modular interaction of constraints, and yields concrete predictions with respect to both intermediate parsing preferences and final interpretations. Our ultimate aim is to develop a model of processing performance is that at the same time a fully functional model of linguistic competence.
Reconsidering Common Ground: Examining Clark's Contribution Theory in the OR

The constructs of "common ground" and "grounding" are frequently invoked in the CSCW literature as a mechanism by which participants engaged in joint activity coordinate their respective understandings of matters at hand. These constructs arise from a model of conversation developed by Herbert Clark and sometimes referred to as "contribution theory. " We describe here the basic features of this theory and attempt to apply it in analyzing a fragment of enacted interaction. The interaction was recorded during an abdominal surgery performed with the aid of an endoscopic camera. We encountered difficulties, however, in applying contribution theory as an analytic framework within this concrete setting. We found further that the notion of common ground represents a confusing metaphor rather than a useful explanatory mechanism. We conclude with a suggestion that researchers in the future seek ways of constructing descriptions of joint activity that do not rely on the troublesome notions of grounding and common ground. Such words insert a name in place of a problem, and let it go at that; they pull out no plums, and only say, "What a big boy am I! " Dewey and Bentley (1991)
Knocking on elders' door: investigating the functional and emotional geography of their domestic space

The domestic environment is more than a place where to live. It is a territory of meaning, a place where pleasure, affect and aesthetics are deeply interwoven with the functional and utilitarian dimensions. With the aging process, the home is progressively invested with new meanings and functions, and becomes the emotional center of older people's life. This paper presents a user study based on cultural probes on how domestic spaces are managed and perceived by older adults, uncovering some of the complex interrelations among the daily activities, objects and meanings revolving around the home. The findings provide suggestions on how the dimensions of remembrance, perception of safety and environmental stability may affect the design of domestic technology for elderly people.
Nonlinear enhancement and segmentation algorithm for the detection of age-related macular degeneration (AMD) in human eye's retina

Assessment of the risk for the development of age related macular degeneration requires reliable detection of retinal abnormalities that are considered as precursors of the disease. A typical sign for the latter are the so-called drusen, which appear as abnormal white-yellow deposits on the retina. This paper presents a novel segmentation algorithm for automatic detection of abnormalities in images of the human eye's retina, acquired from a depth-vision camera. Conventional image processing techniques are sensitive to non-uniform illumination and nonhomogeneous background, which obstructs the derivation of reliable results for a large set of different images. Homomorphic filtering and a multilevel variant of histogram equalization are used for non-uniform illumination compensation and enhancement. We develop a novel segmentation technique, the histogram-teased adaptive local thresholding (HALT), to detect drusen in retina images by extracting the useful information without being affected by the presence of other structures. We provide experimental results from the application of our technique to real images, where certain abnormalities (drusen) have slightly different characteristics from the background and are hard to be segmented by other conventional techniques.
Morphologic and biochemical analysis of the intracellular trafficking of the Alzheimer beta/A4 amyloid precursor protein

Abnormal metabolic processing of the beta/A4 amyloid precursor protein (APP) has been implicated in the pathogenesis of Alzheimer disease. Several aspects of normal APP processing have been elucidated, but the precise cellular trafficking of APP remains unclear. To investigate APP trafficking pathways further, we have examined the subcellular distribution of APP in rat brain tissue and a variety of cultured cell types, and correlated this distribution with the biochemical processing of APP. In immunofluorescence microscopy of rat brain sections, APP immunoreactivity was concentrated in the Golgi complex and in proximal axon segments. In addition, a lower level of punctate fluorescence was visible throughout the neuropil. By immunoelectron microscopy of rat brain tissue fragments, APP was found associated with Golgi elements and with medium-sized, invaginated vesicles in both axons and dendrites. Prominent localization of APP to the Golgi complex was also found in primary cultures of rat hippocampal neurons and in non- neuronal cell lines. When cultured cells were treated with brefeldin A (BFA), APP immunoreactivity changed from a Golgi-like to an endoplasmic reticulum-like distribution. No APP was detected in the BFA-induced reticulum identified by the transferrin receptor, indicating that concentration of APP in the Golgi does not reflect recycling between the trans-Golgi network and early endosomal system. In immunoblots of BFA-treated cells, there was an accumulation of full-length APP and inhibition of APP secretory processing. Treatment with phorbol ester resulted in a marked elevation of APP secretion, but no obvious redistribution of APP immunoreactivity was apparent at the light microscope level. The lysosomotropic drug chloroquine induced accumulation of APP in cell lysates, as seen by immunoblotting. Immunofluorescence microscopy of chloroquine-treated cells demonstrated a colocalization of APP with the lysosomal marker Igp 120, whereas no colocalization was seen in untreated cells. Taken together, these results support a scheme in which APP is concentrated in the Golgi complex as it travels through the central vacuolar system en route to the plasma membrane for secretion of its amino-terminal domain and/or to lysosomes for degradation.
GRB 060218 and GRBs associated with supernovae Ib/c

Context. The Swift satellite has given continuous data in the range 0.3–150 keV from 0 s to 10 6 s for GRB 060218 associated with SN2006aj. This Gamma-Ray Burst (GRB) which has an unusually long duration (T90 ∼ 2100 s) fulfills the Amati relation. These data offer the opportunity to probe theoretical models for GRBs connected with Supernovae (SNe). Aims. We plan to fit the complete γ- and X-ray light curves of this long duration GRB, including the prompt emission, in order to clarify the nature of the progenitors and the astrophysical scenario of the class of GRBs associated with SNe Ib/c. Methods. We apply our “fireshell” model based on the formation of a black hole, giving the relevant references. It is characterized by the precise equations of motion and equitemporal surfaces and by the role of thermal emission. Results. The initial total energy of the electron-positron plasma E tot± = 2.32 × 10 50 erg has a particularly low value, similar to the other GRBs associated with SNe. For the first time, we observe a baryon loading B = 10 −2 which coincides with the upper limit for the dynamical stability of the fireshell. The effective CircumBurst Medium (CBM) density shows a radial dependence ncbm ∝ r −α with 1.0 < α < 1.7 and monotonically decreases from 1 to 10 −6 particles/cm 3 . This behavior is interpreted as being due to a fragmentation in the fireshell. Analogies with the fragmented density and filling factor characterizing Novae are outlined. The fit presented is particularly significant in view of the complete data set available for GRB 060218 and of the fact that it fulfills the Amati relation. Conclusions. We fit GRB 060218, usually considered as an X-Ray Flash (XRF), as a “canonical GRB” within our theoretical model. The smallest possible black hole, formed by the gravitational collapse of a neutron star in a binary system, is consistent with the especially low energetics of the class of GRBs associated with SNe Ib/c. We provide the first evidence for a fragmentation in the fireshell. This fragmentation is crucial in explaining both the unusually large T90 and the consequently inferred abnormally low value of the CBM effective density.
Performance Evaluation of Cloud Infrastructure using Complex Workloads

Infrastructure as a Service (IaaS) is a delivery model of cloud computing, which provides the ability to users to acquire and release resources according to their demand and pay according to their usage. Resources are provisioned from the cloud as Virtual Machines (VMs), many of which can be deployed on a single computing node, realizing a multi-tenancy model. While virtualization and multi-tenancy are two sources of workload-execution overhead that have been studied in the past, we still need a thorough, empirical investigation of the joint impact of these overheads, on workload execution. Additionally, commercial and private IaaS providers offer mechanisms that facilitate the lease and use of single infrastructure resources, but to execute multi-job workloads IaaS users still need to select adequate provisioning and allocation policies to instantiate resources and map computational jobs to them. Even though some studies on the policies employed in cloud environments already exist, current and potential IaaS users need deeper insight on the achieved performance and incurred cost of the used policies, derived through empirical investigation. In this work, we address these problems with the use of SkyMark, a performance analysis framework for IaaS clouds. SkyMark has three key features: ? rst, it is designed to analyze IaaS deployments through a sequence of automated tests and the subsequent automated analysis of results. Second, it can analyze the impact of individual provisioning and allocation policies to the performance of the workload execution. Lastly, it is able to generate complex workloads, stressing any of the compute, memory and disk components. With the use of SkyMark, we ? rst study the overheads that the cloud software stack imposes to the workload execution. Subsequently, we analyze the performance and cost of six provisioning and three allocation policies through experimentation in three IaaS environments, including Amazon EC2.
On the Evaluation of the Conversational Speech Quality in Telecommunications

We propose an objective method to assess speech quality in the conversational context by taking into account the talking and listening speech qualities and the impact of delay. This approach is applied to the results of four subjective tests on the effects of echo, delay, packet loss, and noise. The dataset is divided into training and validation sets. For the training set, a multiple linear regression is applied to determine a relationship between conversational, talking, and listening speech qualities and the delay value. The multiple linear regression leads to an accurate estimation of the conversational scores with high correlation and low error between subjective and estimated scores, both on the training and validation sets. In addition, a validation is performed on the data of a subjective test found in the literature which confirms the reliability of the regression. The relationship is then applied to an objective level by replacing talking and listening subjective scores with talking and listening objective scores provided by existing objective models, fed by speech signals recorded during the subjective tests. The conversational model achieves high performance as revealed by comparison with the test results and with the existing standard methodology "E-model," presented in the ITU-T (International Telecommunication Union) Recommendation G.107.
Near-uniform range partition approach for increased partitioning in large database

Database partitioning technique which adopts "divide and conquer" method can efficiently simplify the complexity of managing massive data and improve the performance of the system, especially the range partitioning. The traditional range partitioning approach brings heavy burden to the system without an increased partitioning algorithm, so it does not adapt to the partitioning in the realtime data environment. To speed up the partitioning algorithm, the current partitioning technology is well studied and three effective range partitioning algorithms for the massive data are proposed, which based on allowing the fluctuation of data amount in each range of partitions. At last, some experiments and applications show that the proposed algorithms are more effective and efficient to partitioning and re-partitioning tables in the large database or real-time environment.
Interaction frequency as a surrogate for the total effect of animal mutualists on plants

We evaluate whether species interaction frequency can be used as a surrogate for the total effect of a species on another. Because interaction frequency is easier to estimate than per-interaction effect, using interaction frequency as a surrogate of total effect could facilitate the large-scale analysis of quantitative patterns of species-rich interaction networks. We show mathematically that the correlation between interaction frequency (I ) and total effect (T ) becomes more strongly positive the greater the variation of I relative to the variation of per-interaction effect (P ) and the greater the correlation between I and P. A meta-analysis using data on I, P and T for animal pollinators and seed dispersers visiting plants shows a generally strong, positive relationship between T and I, in spite of no general relationship between P and I. Thus, frequent animal mutualists usually contribute the most to plant reproduction, regardless of their effectiveness on a per-interaction basis.