Miracle-dz/UniFAR-FTUs huggingface dataset:
Recherche de proteines associees a la morphodynamique de l'appareil de golgi dans les cellules vegetales

L'objectif de ce travail est d'identifier des proteines associees a la morphodynamique de l'appareil de golgi dans les cellules vegetales. Trois groupes de proteines ont ainsi ete etudies : 1) des proteines associees aux membranes golgiennes. Nous definissons deux anticorps monoclonaux, mac254 et mac266, comme des marqueurs du golgi a l'echelle optique. Une etude comparative avec jim84, seul monoclonal reconnu comme marqueur du golgi, montre que tous ces anticorps decrivent differentes sous-familles de proteines portant toutes des branchements sucre de type lewis a. De plus, un marquage differentiel de surfaces cellulaires suggere une regulation de l'exportation des proteines reconnues fonction de l'environnement cellulaire. 2) des proteines candidates a la regulation du mouvement des unites golgiennes dans le cytoplasme. Nous avons initie une etude sur les proteines rho et les proteines de type myosine et spectrine qui pourraient jouer un role entre la dynamique de l'actine et les mouvements golgiens. Les resultats ne permettent pas d'identifier de myosine ou de spectrine participant au mouvement golgien. Ils soulignent la difficulte d'etudier les proteines rho par des approches classiques de toxines. Par contre ils indiquent qu'une petite proteine de 18 kda reconnue par les anticorps animaux anti-rac1 est associee aux membranes golgiennes, probablement par la face cis du golgi. 3) un complexe proteique, le coatomere, connu dans la cellule animale pour initier le bourgeonnement de vesicules mantelees de type copi a partir des membranes golgiennes. Nous avons mis en evidence une proteine de 100 kda reconnue par des anticorps anti--cop, associee aux membranes golgiennes. Une analyse par spectrometrie de masse definit cette proteine comme une -cop vegetale. Au moins deux autres proteines, qui pourraient etre associees a -cop et former un complexe de type coatomere, ont ete visualisees : -cop et -cop. Enfin la surexpression de arf1, petite proteine g en charge du recrutement du coatomere sur la membrane golgienne, retarde notamment son developpement. Une quatrieme partie reprend ces experiences dans un modele cellulaire a croissance apicale, le tube pollinique. Ces donnees sont discutees dans le contexte de la regulation de la morphodynamique du golgi.
Family Communication During the Cancer Experience

The family is often the primary support unit for the cancer patient. We are beginning to understand the impact of a cancer diagnosis on the family, but we are still far from understanding the complex process of how and why information is communicated within families during and after a cancer diagnosis. As survival rates increase and treatments become more complex, understanding how to improve communication processes within the family will become even more vital to supporting families and improving patient outcomes. In this article, we present the results of a 2-hour working group convened during a cancer communications workshop held at the 2008 Society of Behavioral Medicine meeting. During the session, an interdisciplinary group of investigators met and discussed the current state of the science with respect to familial communication during the cancer experience. We focused our discussion on four general areas: current state of the research, theoretical perspectives, methodological perspectives, and areas for future research and intervention in order to understand family communication in this context. Currently, most research has focused on couples and caregivers, mainly in the context of breast cancer. More research is needed into a wider array of cancers and expanding our theoretical foundations into understanding communication between other family members and approaching the family as a unit. Finally, we conclude with recommendations for three content areas to focus future research and intervention development efforts, namely, (1) familial life course, (2) technological advances, and (3) changing structure of the family.
Modulation of the Binding of Matrix Gla Protein (MGP) to Bone Morphogenetic Protein-2 (BMP-2)

Summary Matrix Gla protein (MGP) is an inhibitor of calcification of the arterial wall but the mechanism of inhibition has not been resolved. Since chondrogenesis has been identified in calcified arteries from MPG null mice, we hypothesized that locally produced MGP might inhibit calcification by neutralizing the known effect of bone morphogenetic proteins (BMPs) as promotors of chondrogenesis and bone formation. As the first step to test this hypothesis, we demonstrate that MGP is a binding protein for 125I-BMP-2. Optimal binding is dependent on metals which suggests that the metal binding Gla region in MGP is involved. MGP is shown to undergo a Ca++ induced conformational change despite the presence of the γ-carboxylase binding site being part of the mature protein sequence. The data propose that MGP matures earlier in the secretory pathway than other vitamin K-dependent proteins. Antibodies were used in an attempt to identify MGP in bovine serum. Conformational specific MGP antibodies were shown to also recognize the Gla region in prothrombin and factor X but did not identify MGP in serum. This finding is supported by electrophoresis data which demonstrate the absence of MGP among Ba-citrate absorbed vitamin K-dependent serum proteins. We conclude that MGP does not exist in normal bovine serum.
Jule G. Charney, 1917-1981

Jule Gregory Charney, Alfred P. Sloan Professor of Meteorology at the Massachusetts Institute of Technology, died June 16, 1981, at the Sidney Farber Cancer Institute. He was the leading world figure in meteorology ever since he and John von Neumann first introduced the electronic computer into weather prediction in 1950.
Speeding Up the Convergence of Online Heuristic Search and Scaling Up Offline Heuristic Search

Heuristic search algorithms are popular Artificial Intelligence methods for solving the shortest-path problem. This research contributes new heuristic search algorithms that are either faster or scale up to larger problems than existing algorithms. Our contributions apply to both online and offline tasks. For online tasks, existing real-time heuristic search algorithms learn better informed heuristic values and sometimes eventually converge to a shortest path by repeatedly executing the action leading to a successor state with a minimum cost-to-goal estimate. In contrast, we claim that real-time heuristic search converges faster to a shortest path when it always selects an action leading to a state with a minimum f-value (i.e., a minimum estimate of the cost of a shortest path from start to goal via the state), just like in the offline A* search algorithm. We support this claim by implementing this new non-trivial action-selection rule in FALCONS and by showing empirically that FALCONS significantly reduces the number of actions to convergence of a state-of-the-art real-time search algorithm. For offline tasks, we scale up two best-first search approaches. First, a greedy variant of A* called WA* is known (1) to consume less memory to find solutions of equal cost when it is diversified (i.e., when it performs expansions in parallel), as in KWA*; and (2) to solve larger problems when it is committed (i.e., when it chooses the state to expand next among a fixed-size subset of the set of generated but unexpanded states), as in MSC-WA*. We claim that WA* solves even larger problems when it is enhanced with both diversity and commitment. We support this claim with our MSC-KWA* algorithm. Second, it is known that breadth-first search solves larger problems when it prunes unpromising states, resulting in the beam search algorithm. We claim that beam search quickly solves even larger problems when it is enhanced with backtracking based on limited discrepancy search. We support this claim with our BULB algorithm. We demonstrate the improved scaling of MSC-KWA* and BULB empirically in three standard benchmark domains. Finally, we apply anytime variants of BULB to the multiple sequence alignment problem in biology.
New image analysis tool to study biomass and morphotypes of three major bacterioplankton groups in an alpine lake

We present an image analysis routine to de- termine the contribution of distinct morphotypes to the total abundance and biomass (carbon) of freshwater bac- terioplankton and to the fraction of cells detected by fluorescence in situ hybridization via catalyzed reporter deposition (CARD-FISH). The method was tested on bacterial assemblages from an alpine lake (Piburger See, Austria) at characteristic time points during the lim- nological year. Although on average 51% of 4',6'-di- amidino-2-phenylindole (DAPI)-stained objects were hy- bridized with the oligonucleotide probe EUB I-III, we detected on average 80% of total biomass determined from DAPI staining. The assemblage was numerically dominated by cocci and rods <0.6 µm (mean cell volume = 0.024 µm 3 ). Only a minor part of these morphotypes could be hybridized (18 and 50%, respectively). In con- trast, larger rods (0.087 µm 3 ), cocci (0.155 µm 3 ) and vibrio-shaped cells (0.073 µm 3 ) showed much higher probabilities to be detected by CARD-FISH. These mor- photypes per se formed the highest contribution to total biomass, which explained the high detection efficiency of biomass with CARD-FISH. In addition, we determined the seasonal dynamics of morphotype distributions within 3 distinct phylogenetic lineages. Actinobacteria were predominately small rods and cocci, whereas bac- teria from the Cytophaga -Flavobacterium-Bacteroides group formed mainly large rods, cocci and filaments. Be- taproteobacteria showed the highest morphological vari- ability. Within all lineages, distinct spatio-temporal dy- namics of dominant morphotypes were observed. Thus, the approach presented here will allow for more detailed studies of the amount of carbon bound by different bac- terial taxa. This is of relevance as distinct lineages can contribute much more to total bacterial biomass than to total bacterioplankton abundance.
Short vegetation influence on surface parameter estimations

Several inversion models [1] estimate roughness and soil moisture of bare surfaces. In the case of vegetated areas, the soil moisture is underestimated by inversion algorithms due to the sensitivity of the polarimetric scattering to the vegetation. In order to estimate soil moisture under vegetation, this paper analyzes the influence of scattering through short plant layer at L- band for which the scattering is very sensitive to soil parameters. The potential to classify the short vegetation influence using the so-called Single and Double bounce Eigenvalue Relative Difference (SDERD) and the Luneburg randomness parameter pr [2], is addressed so as to observe. Moreover, the short vegetation backscattering is empirically modeled basing on the radiative transfer first order method [3]. The data used are at L-band from the airborne E-SAR system of the German Aerospace Center (DLR) and the testsite is the Ailing city in Germany.
Semianalytical Derivation of Phytoplankton, CDOM, and Detritus Absorption Coefficients From the Landsat 8/OLI Reflectance in Coastal Waters

The Operational Land Imager (OLI) onboard Landsat 8 has potential for mapping the water bio ‐ optical properties with high spatial resolution. Landsat 8/OLI generates the remote sensing re ﬂ ectance ( R rs ) at four visible bands ( λ 1 ‐ 4 = 443, 482, 561, and 655 nm) and is lack of a 412 ‐ nm band commonly included for ocean color sensors. This spectral con ﬁ guration has limited the use of Landsat 8/OLI re ﬂ ectance product for analytical derivation of light absorption coef ﬁ cients of phytoplankton, colored dissolved organic matter (CDOM), and detritus. In this study, we proposed a hybrid approach to ﬁ ll this gap. First, we developed an algorithm to estimate the re ﬂ ectance in a virtual band centered at λ 0 = 412 nm from the OLI re ﬂ ectance spectra R rs ( λ 1 ‐ 4 ). Both the estimated R rs ( λ 0 ) and measured R rs ( λ 1 ‐ 4 ) were then used together to retrieve the water component absorption coef ﬁ cients with existing algorithms including the quasi ‐ analytical algorithm. We assessed the model performance using in situ measurements from the global waters. It was found that the proposed approach could estimate R rs (412) with a median absolute percentage difference of ~9%. The subsequent retrievals of the component absorption coef ﬁ cients were satisfactorily accurate, with median absolute percentage difference roughly equal to 35%, 40%, and 60% for phytoplankton, CDOM, and detritus, respectively. The results suggest the feasibility to generate analytically the component absorption coef ﬁ cients from the Landsat 8/OLI re ﬂ ectance.
Fault Recovery in Discrete-Event Systems using Observer-Based Supervisors

In this paper, we study the synthesis of fault recovery procedures in discrete—event systems, following a state—based approach. It is assumed that the faults are unobservable but can be diagnosed within a bounded delay. A modular switching supervisory scheme is proposed to satisfy the system design specifications. The design consists of observer-based supervisor modules. One of the modules enforces design specifications during the normal mode of operation and after a fault occurs but before the fault is diagnosed. The rest of the modules are designed for recovery from faults — one module for each fault. When a fault is diagnosed, the corresponding recovery module takes sole control of the plant. The issue of the nonblocking property of the system under supervision is also studied.
The next admissible set

In this paper we describe generalizations of several approaches to the hyperarithmetic hierarchy, show how they are related to the Kripke-Platek theory of admissible ordinals and sets, and study conditions under which the various approaches remain equivalent. To put matters in some perspective, let us first review various approaches to the theory of hyperarithmetic sets. For most purposes, it is convenient to first define the semi-hyperarithmetic (semi-HA) subsets of N. A set is then said to be hyperarithmetic (HA) if both it and its complement are semi-HA. A total number-theoretic function is HA if its graph is HA.
ETE: a customizable approach to measuring end-to-end response times and their components in distributed systems

Detecting and resolving performance problems in distributed systems often requires measurements of end-to-end ("finger tip to eyeball") response times. Existing approaches embed transaction definitions in instrumentation codes. As a result, service providers (e.g., ISPs) cannot tailor transaction definitions to the usage patterns of their customers. We propose a new approach-ETE (end-to-end)-in which transaction definitions are externalized so that they can be customized. This is accomplished by having instrumentation generate events (not transactions) and employing a separate component-the transaction generator-that uses external definitions of transactions to construct response time measurements from event streams. ETE provides measurements of both end-to-end response times and their components. The latter reflect delays for services within distributed systems (e.g., name resolution service). We have used ETE to measure response times for Web transactions, terminal emulators, and Lotus Notes.
Multi-Neighborhood Convolutional Networks

We explore the role of scale for improved feature learning in convolutional networks. We propose multi-neighborhood convolutional networks, designed to learn image features at different levels of detail. Utilizing nonlinear scale-space models, the proposed multineighborhood model can effectively capture fine-scale image characteristics (i.e., appearance) using a small-size neighborhood, while coarse-scale image structures (i.e., shape) are detected through a larger neighborhood. The experimental results demonstrate the superior performance of the proposed multi-scale multi-neighborhood models over their single-scale counterparts.
Calibration of very fast TLP transients

A calibration methodology for transient analysis of voltage and current waveforms during VFTLP testing is presented. An OPEN, SHORT and LOAD calibration are required to de-embed the probe needles and system parasitics. This enables the use of non-RF probes for VFTLP measurements, resulting in a lower cost and higher measurement flexibility for VFTLP testing.
Adaptive imaging using the generalized coherence factor

Sound-velocity inhomogeneities degrade both spatial and contrast resolutions. This paper proposes a new adaptive imaging technique that uses the generalized coherence factor (GCF) to reduce the focusing errors resulting from the sound-velocity inhomogeneities. The GCF is derived from the spatial spectrum of the received aperture data after proper receive delays have been applied. It is defined as the ratio of the spectral energy within a prespecified low-frequency range to the total energy. It is demonstrated that the low-frequency component of the spectrum corresponds to the coherent portion of the received data, and that the high-frequency component corresponds to the incoherent portion. Hence, the GCF reduces to the coherence factor defined in the literature if the prespecified low-frequency range is restricted to DC only. In addition, the GCF is also an index of the focusing quality and can be used as a weighting factor for the reconstructed image. The efficacy of the GCF technique is demonstrated for focusing errors resulting from the sound-velocity inhomogeneities. Simulations and real ultrasound data are used to evaluate the efficacy of the proposed GCF technique. The characteristics of the GCF, including the effects of the signal-to-noise ratio and the number of channels, are also discussed. The GCF technique also is compared with the correlation-based technique and the parallel adaptive receive compensation algorithm; the improvement in image quality obtained with the proposed technique rivals that of the latter technique. In the presence of a displaced phase screen, this proposed technique also outperforms the correlation-based technique. Computational complexity and implementation issues also are addressed.
Use of Modular Substrates Demonstrates Mechanistic Diversity and Reveals Differences in Chaperone Requirement of ERAD*

The endoplasmic reticulum (ER) harbors a protein quality control system, which monitors protein folding in the ER. Elimination of malfolded proteins is an important function of this protein quality control. Earlier studies with various soluble and transmembrane ER-associated degradation (ERAD) substrates revealed differences in the ER degradation machinery used. To unravel the nature of these differences we generated two type I membrane ERAD substrates carrying malfolded carboxypeptidase yscY (CPY*) as the ER-luminal ERAD recognition motif. Whereas the first, CT* (CPY*-TM), has no cytoplasmic domain, the second, CTG*, has the green fluorescent protein present in the cytosol. Together with CPY*, these three substrates represent topologically diverse malfolded proteins, degraded via ERAD. Our data show that degradation of all three proteins is dependent on the ubiquitin-proteasome system involving the ubiquitin-protein ligase complex Der3/Hrd1p-Hrd3p, the ubiquitin conjugating enzymes Ubc1p and Ubc7p, as well as the AAA-ATPase complex Cdc48-Ufd1-Npl4 and the 26S proteasome. In contrast to soluble CPY*, degradation of the membrane proteins CT* and CTG* does not require the ER proteins Kar2p (BiP) and Der1p. Instead, CTG* degradation requires cytosolic Hsp70, Hsp40, and Hsp104p chaperones.
Discrete-Time, Discrete-Frequency Reassignment Method

The reassignment method is a non-linear, postprocessing technique which cans improve the localization of a time-frequency distribution by moving its values according to a suitable vector field. The reassignment method’s scheme assumes that the energy distribution in the time-frequency plane resembles a mass distribution and moves each value of the time-frequency plane located at a point (tt,ff)to another point,(tt�,ff�), which is the center of gravity of the energy distribution in the area of (tt,ff). The result is a focused representation with very high intensity [11]. Duringthis research it was investigated and determined that the frequency reassignment corrections derived from the Flandrin reassignment method have undesired noise sensitivity at very small noise levels as well as undesired observed distortions. In order to address these issues, a novel approach was derived the discrete-time, discrete-frequency formulation of frequency reassignment. It is shown that in noise-free tone scenarios, this novel approach eliminates ambiguity and provides less distortion than the Flandrin reassignment method.
IWRM and the Nexus Approach: Versatile Concepts for Water Resources Education

Integrated Water Resources Management (IWRM) and the nexus approach are tools to identify solutions for water problems across interdependent sectors with interacting social and natural systems. Although both tools aim at solutions for complex water issues using an interdisciplinary approach, IWRM is a management process and the nexus approach is a systems tool to characterize problems. By clarifying their attributes and providing examples, instructors can use them to explain broad social problems and offer practical frameworks for problem-solving. Given their breadth, IWRM and the nexus approach can seem vague and attract criticism, but if they are replaced, the need for them will endure. The concepts are explained, and similarities between them are explored in the paper. Case study sources for them are identified, and the cases are classified by the processes of water resources management as applied across related sectors. How the concepts and their corresponding case studies can be used will vary by context. Suggestions are made for interdisciplinary instruction and discussions in disciplinary settings.
Identification of Genes Associated with the Long-Gut-Persistence Phenotype of the Probiotic Lactobacillus johnsonii Strain NCC533 Using a Combination of Genomics and Transcriptome Analysis

ABSTRACT Lactobacillus johnsonii strains NCC533 and ATCC 33200 (the type strain of this species) differed significantly in gut residence time (12 versus 5 days) after oral feeding to mice. Genes affecting the long gut residence time of the probiotic strain NCC533 were targeted for analysis. We hypothesized that genes specific for this strain, which are expressed during passage of the bacterium through the gut, affect the phenotype. When the DNA of the type strain was hybridized against a microarray of the sequenced NCC533 strain, we identified 233 genes that were specific for the long-gut-persistence isolate. Whole-genome transcription analysis of the NCC533 strain using the microarray format identified 174 genes that were strongly and consistently expressed in the jejunum of mice monocolonized with this strain. Fusion of the two microarray data sets identified three gene loci that were both expressed in vivo and specific to the long-gut-persistence isolate. The identified genes included LJ1027 and LJ1028, two glycosyltransferase genes in the exopolysaccharide synthesis operon; LJ1654 to LJ1656, encoding a sugar phosphotransferase system (PTS) transporter annotated as mannose PTS; and LJ1680, whose product shares 30% amino acid identity with immunoglobulin A proteases from pathogenic bacteria. Knockout mutants were tested in vivo. The experiments revealed that deletion of LJ1654 to LJ1656 and LJ1680 decreased the gut residence time, while a mutant with a deleted exopolysaccharide biosynthesis cluster had a slightly increased residence time.