Miracle-dz/UniFAR-FTUs huggingface dataset:
Conserved enhancer and silencer elements responsible for differential Adh transcription in Drosophila cell lines

The distal promoter of Adh is differentially expressed in Drosophila tissue culture cell lines. After transfection with an exogenous Adh gene, there was a specific increase in distal alcohol dehydrogenase (ADH) transcripts in ADH-expressing (ADH+) cells above the levels observed in transfected ADH-nonexpressing (ADH-) cells. We used deletion mutations and a comparative transient-expression assay to identify the cis-acting elements responsible for enhanced Adh distal transcription in ADH+ cells. DNA sequences controlling high levels of distal transcription were localized to a 15-base-pair (bp) region nearly 500 bp upstream of the distal RNA start site. In addition, a 61-bp negative cis-acting element was found upstream from and adjacent to the enhancer. When this silencer element was deleted, distal transcription increased only in the ADH+ cell line. These distant upstream elements must interact with the promoter elements, the Adf-1-binding site and the TATA box, as they only influenced transcription when at least one of these two positive distal promoter elements was present. Internal deletions targeted to the Adf-1-binding site or the TATA box reduced transcription in both cell types but did not affect the transcription initiation site. Distal transcription in transfected ADH- cells appears to be controlled primarily through these promoter elements and does not involve the upstream regulatory elements. Evolutionary conservation in distantly related Drosophila species suggests the importance of these upstream elements in correct developmental and tissue-specific expression of ADH.
Air pollution, weather and ischaemic cerebral and cardiac events: some methodological considerations

To the Editor I read with great interest the recent paper by Henrotin et al on evidence for the role of short-term exposure to ozone on ischaemic cerebral and cardiac events from the Dijon Vascular Project.1 The paper addressed the analysis procedure and considerations and presented findings on the relationship between air pollution and ischaemic cerebral and cardiac events in a large population-based setting. However, a few …
Localizing partial discharge in power transformers by combining acoustic and different electrical methods

The reliability of electrical systems depends on the quality and availability of the power apparatus. Power transformers are important nodes in the electrical power grid. Common reasons for breakdown are problems in the insulation system. Detecting partial discharge in the insulation system of a power transformer at an early stage reduces the risk of total breakdown of power apparatus. One method to detect partial discharge is the acoustic measurement. With this technique a detection and localization of partial discharge is possible by placing acoustic sensors on the surface of the transformer tank. The low level of electrical interferences from outside the measurement setup constitutes one of the strengths of this method. A further advantage is the ability of identifying the position of the partial discharge source, which is needed to estimate the risk and to enable a fast and effective repair.
Inflammation-induced up-regulation of TLR2 expression in human endothelial cells is independent of differential methylation in the TLR2 promoter CpG island

Toll-like receptors play an important role in endothelial inflammation; however, little is known on the mechanisms regulating their expression. Differential promoter DNA methylation is an increasingly recognized mechanism that determines a switch between gene silencing and gene transcription. We hypothesized that epigenetic mechanisms are involved in the regulation of endothelial TLR2 expression because of the localization of the TLR2 promoter on a CpG-island. Resting human umbilical vein endothelial cells (HUVECs) displayed rather low TLR2 mRNA expression, while a strong expression increase occurred under inflammatory conditions. We examined the TLR2 promoter methylation pattern in resting HUVECs and compared it to cells treated either with the inflammatory cytokine TNF-α or the DNA-demethylating agent 5-azacytidine. DNA bisulfite conversion was followed by either genomic sequencing or single nucleotide primer extension (SNuPE) HPLC. Results of both techniques showed a low- or non-methylated TLR2 promoter in resting HUVECs and no alteration of the methylation pattern under inflammatory conditions. Whereas 5-azacytidine significantly increased the mRNA expression of the epigenetically regulated gene H19, TLR2 expression was not affected. Taken together, employing different methodological approaches, our data show no implication of methylation pattern changes in inflammatory induction of TLR2 expression in human endothelial cells.
The microstructure, local indium composition and photoluminescence in green‐emitting InGaN/GaN quantum wells

In this work, we analyse the microstructure and local chemical composition of green‐emitting InxGa1–xN/GaN quantum well (QW) heterostructures in correlation with their emission properties. Two samples of high structural quality grown by metalorganic vapour phase epitaxy (MOVPE) with a nominal composition of x = 0.15 and 0.18 indium are discussed. The local indium composition is quantitatively evaluated by comparing scanning transmission electron microscopy (STEM) images to simulations and the local indium concentration is extracted from intensity measurements. The calculations point out that the measured indium fluctuations may be correlated to the large width and intensity decrease of the PL emission peak.
Will Mandated Minimum Nurse Staffing Ratios Lead to Better Patient Outcomes?

Background: Mandatory hospital nurse staffing ratios are under consideration in a number of states without strong empirical evidence of the optimal ratio. Objective: To determine whether increases in medical-surgical licensed nurse staffing levels are associated with improvements in patient outcomes for hospitals having different baseline staffing levels. Research Design: Cross-sectional and fixed-effects regression analyses using a 1993–2001 panel of patient and hospital data from California. Splines define 4 staffing ratios. Subjects: Adult acute myocardial infarction (AMI) (n = 348,720) and surgical failure to rescue (FTR) (n = 109,066) patients discharged between 1993 and 2001 from 343 California acute care general hospitals. Measures: Patient outcomes are 30-day AMI mortality and surgical FTR; 4 baseline staffing levels—4 to 7 patients per licensed nurse [registered nurses (RN) and licensed vocational nurses (LVN)]. Results: Significant cross-sectional associations between higher nurse staffing and AMI mortality are reduced in the fixed-effects analyses. Improvements in outcomes were smaller in hospitals with higher baseline staffing: for each RN and RN + LVN increase, respectively, AMI mortality declined by 0.71 (P < 0.05) and by 2.75 percentage points for hospitals with more than 7 patients per nurse compared with 0.19 (P = NS) and 0.28 percentage points (P < 0.05) in hospitals with more than 4 patients per nurse. Significant cross-sectional associations between higher nurse staffing and FTR were not found in the fixed-effects analyses. Conclusions: Strong diminishing returns to nurse staffing improvements and lack of significant evidence that staffing uniformly increases improve outcomes raise questions about the likely cost-effectiveness of implementing state-wide mandatory nurse staffing ratios.
DNA repair gene XRCC 1 and XRCC 3 polymorphisms and their association with chronic myelogenous leukemia

Chronic myelogenous leukemia (CML) is a type of leukemia originating from hematopoietic stem cells characterized by unregulated proliferation of myeloid cells. Leukemic cells carry the chromosome, a translocation between one chromosome 9 and one chromosome 22. This chromosome has the fusion gene which consists of fragments of the breakpoint cluster region (BCR) and abelson murine leukemia (ABL) genes. The chimeric BCR-ABL oncogene encoding the p210 or p190 fusion protein exhibits a constitutively high tyrosine kinase activity.
Stable swarming by mutual interactions of Attraction/Alignment/Repulsion

In this paper we present a general decentralized controller for a swarm of agents with a dynamic topology to move in a given environment. The controller utilizes the hypothesis of attraction/alignment/repulsion (A/A/R) interactions which is widely used to model fish schools in mathematical biology community.We assume that during the swarm¿s motion, each agent can sense and interact with its neighbors via mutual A/A/R interactions, while following the gradient force of the environment. The environment is assumed to have identical effects on all agents. With the assumption of connected graph, we show that the controller makes the velocities of all swarm members asymptotically converge to a common value. The contributions of this paper are two folds. First, the controller is general and works for any specific function of the A/A/R interactions. In other words, this paper analytically proves the common A/A/R model of fish schools in the literature. Second, all the information needed by the controller can be locally sensed, therefore, communication modules and associated problems (such as communication noise and time delay) are avoided. Simulation results are presented to verify the controller.
Kalman Filter-based navigation system for the Amphibious Spherical Robot

Robust and performing navigation systems for Autonomous Underwater Vehicles (AUVs) play a discriminant role towards the success of complex underwater missions. This paper presents a new design and development of a low-cost INS (Inertial Navigation System) using Miro-Electro-Mechanical-System (MEMS) inertial sensor and the pressure sensor (PS). The intensive pre-processing and modeling MEMES sensor's primitive, noisy motion data are outline, these techniques transform the erroneous motion data into practical motion indicators illustrated in 3D position, 3D velocity and 3D orientation. INS acts as a dead reckoning device. The pressure sensor is used to detect the depth data of underwater Vehicles. The quality of the filtering algorithm for the estimation of the AUV navigation state strongly affects the performance of the overall system. In this paper, the authors present adapt the Kalman Filter (KF) approach. Experiments were conducted to improve the navigation system performance of the INS and PS installed on the Amphibious Spherical Robot III (ASR III) for motion and attitude estimation. Lastly the experiment results are evaluated and verified using the sensor data from the navigation system.
Efficiency and accuracy enhanced super resolved channel estimation

This paper presents a novel approach to substantially improve the efficiency as well as the accuracy of maximum likelihood based super resolved channel estimation. Ordinary maximum likelihood methods suffer from considerable computational complexity as hundreds of coupled discrete waves have to be estimated simultaneously. Standard methods are either very slow in convergence when parameters are correlated (e.g. SAGE) or suffer from estimation errors as waves are not sufficiently decoupled. This problem is solved by modifying the likelihood function by introducing windowing of both the measurement data and the corresponding model. In this way waves are fully decoupled for fairly small separations in parameter space making it possible to perform local maximization of the corresponding modified likelihood. Moreover, as the waves are decupled a corresponding reduction of complexity is possible by clipping data which is outside the coupling distance relative to the waves subject to parameter estimation. In the case of e.g. 1000 channel frequency samples a 100-fold reduction is possible.
Humanoid fall avoidance from randomly directed disturbances

When humanoid robots are pushed they risk falling and damaging themselves. Preemptive fall avoidance strategies are becoming popular and usually involve measures such as actively actuating the ankles, the hips or even taking steps. Deciding which strategy to take can be determined based on a stability region-known as the decision surface-drawn on a phase plot of the robot's state. Unfortunately, the decision surface is limited to disturbances emanating from the sagittal or coronal planes. This paper addresses this limitation by proposing a decision hypersurface for a hip strategy, which is used for the prediction of limiting states for recovery from disturbances in any orientation. A second contribution is the extension of the hip strategies for humanoid fall avoidance to disturbances in random directions. Both, strategies and decision hypersurfaces are tested on the Webots simulator then implemented on a real humanoid robot.
PREFIX CONTINUITY AND GLOBAL ADDRESS AUTOCONFIGURATION IN IPV 6 AD HOC NETWORKS

Ad hoc networks are formed by the spontaneous collaboration of wireless nodes when no networking infrastructure is available. When communication to the Internet is desired, one or more nodes must act as gateways for the ad hoc network. In this case, global addressing of ad hoc nodes is required. This article presents a protocol which can be used by an ad hoc node to dynamically select a gateway and create an associated IPv6 global address. The core of our proposal is the concept ofprejix continuity. By building and maintaining a forest of logical spanning trees, our proposal ensures that there exists, between a node A and its gateway G, a path of nodes such that each node on this path uses the same prefix P as the node A and its gateway G. This concept results in an organized ad hoc network, in the sense that sub-networks (with respect to prefixes) are automatically created and dynamically maintained when multiple gateways are available. Moreover, the concept of prefix continuity ensures that each subnetwork forms a connected graph of nodes which all use an identical prefix. In contrast to traditional wired networks, this feature is not trivial in ad hoc networks. +The initial (long) version of this paper, as originally submitted and accepted for the MedHocNet'O5 workshop, is available at http://cn.cs. unibas.ch/pub/ t ~ a r t of this work was carried out during the tenure of an ERClM fellowship (see http://w.ercim.org for details). K. A1 Agha, I. Gue'rin Lassous and G. Pujolle
UNIVERSITY OF MIAMI GROWTH PERFORMANCE OF ADULT FLORIDA POMPANO , Trachinotus carolinus , FED SEMI-PURIFIED DIETS WITH GRADED LEVELS OF METHIONINE By

of a thesis at the University of Miami. Thesis supervised by Professor Daniel D. Benetti. No. of pages in text. (35) Replacement of fishmeal with soy-based protein alternatives has produced the need to determine nutritional requirements of aquaculture species to appropriately formulate and supplement aquafeeds. Compared to fishmeal, soybean meal is deficient in methionine, an essential amino acid. Thus, the methionine requirement of a high-value and soy-tolerant species, the Florida pompano (Trachinotus carolinus) at a near harvestable size (>200 g) was evaluated. Six semi-purified, isonitrogenous and isocaloric, experimental diets were formulated based on the whole-body amino acid (AA) profile of the Florida pompano with incremental inclusions of methionine (0.5, 0.7, 0.9, 1.1, 1.3, and 1.5 g 100 g diet–1). Three tanks were randomly assigned per diet and stocked with 11 fish per tank averaging a total of 2290.3 ± 13.86 g initial biomass. Fish were fed twice daily at 900 h and 1500 h to satiation for 58 days. Pompano from all treatments, including the lowest and highest inclusions of methionine exhibited normal behavior, appearance, and weight gain throughout the duration of the experiment. There were no discernable trends (neither increasing nor decreasing) among growth parameters across all methionine inclusion levels. No significant differences (p > 0.05) were observed among treatments for mean daily intake (MDI), weight gain ratio (WGR), specific growth rate (SGR), energy intake (EI), protein intake (PI), feed efficiency (FE), and hepatosomatic index (HSI). Significant differences were apparent (p < 0.05) for average weight gain (AWG), average daily gain (ADG), protein efficiency ratio (PER), and feed conversion ratio (FCR) with substandard values for fish fed Diet 4 (1.1 g 100 g diet–1) compared to the other diets. These results suggest that near-harvestable size Florida pompano perform well with respect to growth at the lowest methionine inclusion of 0.5 g / 100 g diet. Further research is required to confirm these findings.
Stable Pose Estimation with a Motion Model in Real-Time Application

Estimation of a object pose from camera is a well-developing topic in computer vision. In theory, the pose from a calibrated camera can be uniquely determined. But in practice, most of the real-time pose estimation algorithms suffer from pose ambiguity due to low accuracy of the target object. We think that pose ambiguity¡Xtwo distinct local minima of the according error function¡Xexist because of the phenomenon of geometric illusions. Both of the ambiguous poses are plausible. After obtaining the solution of two minima (pose candidates), we develop a real-time algorithm for stable pose estimation of a target objects with a motion model. In the experimental results, the proposed algorithm diminish the significance of pose jumping and pose jittering effectively. To the best of our knowledge, this is the first work to solve the pose ambiguity problem with motion model in real-time application.
Memory and Common Ground Processes in Language Use

During communication, we form assumptions about what our communication partners know and believe. Information that is mutually known between the discourse partners-their common ground-serves as a backdrop for successful communication. Here we present an introduction to the focus of this topic, which is the role of memory in common ground and language use. Two types of questions emerge as central to understanding the relationship between memory and common ground, specifically questions having to do with the representation of common ground in memory, and the use of common ground during language processing.
Reply to O'Brien et al.

Across Atlantic ice (AAI) sets out specifically to propose an alternative hypothesis of early human entry into the Americas and to stimulate research (Stanford & Bradley 2012: 16). O'Brien et al.'s response (above) primarily contains an unsupported dismissal of the evidence and these ideas. Unfortunately, to date, no work equivalent to AAI has been presented for any other Clovis origin hypothesis; this would be most welcome, especially from those who critique and reject the Solutrean hypothesis with unsupported assertions. For convenience we respond to each of O'Brien et al.'s critiques in the order in which they appear.
The statistics of polarization-dependent loss in a recirculating loop

In this paper, we study the statistical distribution of the accumulated polarization-dependent loss (PDL) in a recirculating loop. The distribution is studied both via numerical simulations and with analytical theory and very good agreement is found between the two. In addition, we have experimentally obtained the probability density distribution for the PDL and, even in this case, we find good agreement with the predicted one. The mean accumulated PDL is found to grow linearly with the number of circulations N in contraposition to a straight-line system. Moreover, the statistical distribution tends to become uniformly distributed as N is increasing. Finally, the statistics of the PDL for a recirculating loop, when considering small values of PDL, is found to be equal to the statistics of the differential group delay for recirculating loops.
Geometric convergence of filters for hidden Markov models

Hidden Markov models have proved suitable for many in­ teresting applications which can be modelled using some unobservable finite state Markov process, influencing mea­ sured signals. This can be used to describe bursty telecom­ munications traffic, or the faults in a complicated systems, for modelling the activity in neurons, for modelling speech patterns, etc. In all these applications, one has to estimate the unobservable underlying state of the Markov process, using the observed signals. Optimal recursive filters are well known for this estimation problem. Recently risk sensitive filters for the same problem have also been ob­ tained. An important question in studying the quality of such filters is the rate at which arbitrarily assigned initial conditions are forgotten. In this paper we show that the effect of initial conditions on these filters dies out geomet­ rically fast under very reasonable observability assump­ tions. The proof is given in the simplest case of finite state space and of a finite, quantised, observations spacc. How­ ever the method can be extended to more general models by continuity arguments.
Identification and Characterization of hsa, the Gene Encoding the Sialic Acid-Binding Adhesin of Streptococcus gordonii DL1

ABSTRACT Oral colonization by Streptococcus gordonii, an important cause of subacute bacterial endocarditis, involves bacterial recognition of sialic acid-containing host receptors. The sialic acid-binding activity of this microorganism was previously detected by bacterium-mediated hemagglutination and associated with a streptococcal surface component identified as the Hs antigen. The gene for this antigen (hsa) has now been cloned in Escherichia coli, and its expression has been detected by colony immunoblotting with anti-Hs serum. Mutants of S. gordonii containing hsa inactivated by the insertion of an erythromycin resistance gene or deletion from the chromosome were negative for Hs-immunoreactivity, bacterium-mediated hemagglutinating activity, and adhesion to α2-3-linked sialoglycoconjugates. The deletion in the latter mutants was complemented by plasmid-borne hsa, resulting in Hs antigen production and the restoration of cell surface sialic acid-binding activity. The hsa gene encodes a 203-kDa protein with two serine-rich repetitive regions in its 2,178-amino-acid sequence. The first serine-rich region occurs within the amino-terminal region of the molecule, between different nonrepetitive sequences that may be associated with sialic acid binding. The second serine-rich region, which is much longer than the first, is highly repetitive, containing 113 dodecapeptide repeats with a consensus sequence of SASTSASVSASE. This long repetitive region is followed by a typical gram-positive cell wall anchoring region at the carboxyl-terminal end. Thus, the predicted properties of Hsa, which suggest an amino-terminal receptor-binding domain attached to the cell surface by a molecular stalk, are consistent with the identification of this protein as the sialic acid-binding adhesin of S. gordonii DL1.
Reliability Degradation Mechanisms of Horizontal Current Bipolar Transistor

The impact of the reverse-bias emitter-base stress and the mixed-mode stress on horizontal current bipolar transistor (HCBT) reliability characteristics is analyzed. Under the stress conditions, hot carriers are generated and injected toward silicon-oxide interfaces above and below HCBT's emitter n+ polysilicon region where the traps responsible for the base current and beta (β) degradations are formed. Different degradation rates of three HCBT structures measured under both stresses suggest various contributions of the top and bottom oxides to total damage. A larger contribution of the top interface under the reverse-bias emitter-base stress and of the bottom interface under the mixed-mode stress is determined. A lower doping concentration in the bottom part of the intrinsic transistor and a shorter emitter polysilicon predeposition oxide etching both reduce the generation of interface traps during stress tests. The time-dependent trap degradation simulations are run on the structures with the realistic doping profiles to explain the measured stress data on various HCBT structures.