Miracle-dz/UniFAR-FTUs huggingface dataset:
Developmental activation of the capability to undergo checkpoint-induced apoptosis in the early zebrafish embryo.

In this study, we demonstrate the developmental activation, in the zebrafish embryo, of a surveillance mechanism which triggers apoptosis to remove damaged cells. We determine the time course of activation of this mechanism by exposing embryos to camptothecin, an agent which specifically inhibits topoisomerase I within the DNA replication complex and which, as a consequence of this inhibition, also produces strand breaks in the genomic DNA. In response to an early (pre-gastrula) treatment with camptothecin, apoptosis is induced at a time corresponding approximately to mid-gastrula stage in controls. This apoptotic response to a block of DNA replication can also be induced by early (pre-MBT) treatment with the DNA synthesis inhibitors hydroxyurea and aphidicolin. After camptothecin treatment, a high proportion of cells in two of the embryo's three mitotic domains (the enveloping and deep cell layers), but not in the remaining domain (the yolk syncytial layer), undergoes apoptosis in a cell-autonomous fashion. The first step in this response is an arrest of the proliferation of all deep- and enveloping-layer cells. These cells continue to increase in nuclear volume and to synthesize DNA. Eventually they become apoptotic, by a stereotypic pathway which involves cell membrane blebbing, "margination" and fragmentation of nuclei, and cleavage of the genomic DNA to produce a nucleosomal ladder. Fragmentation of nuclei can be blocked by the caspase-1,4,5 inhibitor Ac-YVAD-CHO, but not by the caspase-2,3,7[, 1] inhibitor Ac-DEVD-CHO. This suggests a functional requirement for caspase-4 or caspase-5 in the apoptotic response to camptothecin. Recently, Xenopus has been shown to display a developmental activation of the capability for stress- or damaged-induced apoptosis at early gastrula stage. En masse, our experiments suggest that the apoptotic responses in zebrafish and Xenopus are fundamentally similar. Thus, as for mammals, embryos of the lower vertebrates exhibit the activation of surveillance mechanisms, early in development, to produce the selective apoptosis of damaged cells.
Drosophila small heat shock protein CryAB ensures structural integrity of developing muscles, and proper muscle and heart performance

Molecular chaperones, such as the small heat shock proteins (sHsps), maintain normal cellular function by controlling protein homeostasis in stress conditions. However, sHsps are not only activated in response to environmental insults, but also exert developmental and tissue-specific functions that are much less known. Here, we show that during normal development the Drosophila sHsp CryAB [L(2)efl] is specifically expressed in larval body wall muscles and accumulates at the level of Z-bands and around myonuclei. CryAB features a conserved actin-binding domain and, when attenuated, leads to clustering of myonuclei and an altered pattern of sarcomeric actin and the Z-band-associated actin crosslinker Cheerio (filamin). Our data suggest that CryAB and Cheerio form a complex essential for muscle integrity: CryAB colocalizes with Cheerio and, as revealed by mass spectrometry and co-immunoprecipitation experiments, binds to Cheerio, and the muscle-specific attenuation of cheerio leads to CryAB-like sarcomeric phenotypes. Furthermore, muscle-targeted expression of CryABR120G, which carries a mutation associated with desmin-related myopathy (DRM), results in an altered sarcomeric actin pattern, in affected myofibrillar integrity and in Z-band breaks, leading to reduced muscle performance and to marked cardiac arrhythmia. Taken together, we demonstrate that CryAB ensures myofibrillar integrity in Drosophila muscles during development and propose that it does so by interacting with the actin crosslinker Cheerio. The evidence that a DRM-causing mutation affects CryAB muscle function and leads to DRM-like phenotypes in the fly reveals a conserved stress-independent role of CryAB in maintaining muscle cell cytoarchitecture. Summary: dCryAB, a heat shock protein, displays stress-independent expression in Drosophila muscles and interacts with the actin crosslinker filamin to ensure proper muscle cytoarchitecture.
A mutation in the short 5'-proximal open reading frame on Rous sarcoma virus RNA alters virus production

The 5'-proximal open reading frame on Rous sarcoma virus RNA encodes a seven-amino-acid peptide and is conserved in all avian sarcoma-leukosis retroviruses. Ribosome-binding site analysis in intact chick cells showed that the 5'-proximal AUG codon is a strong site for initiation of translation in vivo. Removal of the 5'-proximal AUG codon by site-specific mutagenesis resulted in a virus with a reduced ability either to replicate or to transform a population of chicken embryo fibroblasts. These results establish a procedure for determining sites of ribosome binding and initiation of translation on mRNAs in intact eucaryotic cells and strongly suggest that the 5'-proximal open reading frame (or its AUG codon) on Rous sarcoma virus RNA has an important role in regulating viral activity.
Gossiping With Multiple Messages

This paper investigates the dissemination of multiple pieces of information in large networks where users contact each other in a random uncoordinated manner, and users upload one piece per unit time. The underlying motivation is the design and analysis of piece selection protocols for peer-to-peer networks which disseminate files by dividing them into pieces. We first investigate one-sided protocols, where piece selection is based on the states of either the transmitter or the receiver. We show that any such protocol relying only on pushes, or alternatively only on pulls, is inefficient in disseminating all pieces to all users. We propose a hybrid one-sided piece selection protocol-INTERLEAVE-and show that by using both pushes and pulls it disseminates k pieces from a single source to n users in 9(k + log n) time, while obeying the constraint that each user can upload at most one piece in one unit of time, with high probability for large n. An optimal, unrealistic, centralized protocol would take k + log2 n time in this setting. For a soft upload constraint, the finishing time of INTERLEAVE is, with high probability, at most 3.2(k + log n). Moreover, efficient dissemination is also possible if the source implements forward erasure coding, and users push the latest released coded pieces (but do not pull). We also investigate two-sided protocols where piece selection is based on the states of both the transmitter and the receiver. We show that it is possible to disseminate n pieces to n users in n + O(log n) time, starting from an initial state where each user has a unique piece.
Comparison of Brain Volumes between Single and Multiple Foundresses in the Paper Wasp Polistes dominulus

Queens of the paper wasp Polistes dominulus have the option to found nests in spring alone or together with other queens. In the latter case a dominance hierarchy is established among the cofoundresses with the dominant wasp getting the major share of the reproductive output of the nest. The different reproductive strategies of an individual wasp will necessitate different behaviors. We measured the volumes of brain structures as a potential indicator of differential use and elaboration of a number of brain structures. We found a significant increase in the volume of the antennal lobe in members of multiple foundress associations in comparison to single foundresses. The volume of the collar, a substructure of the calyx of the mushroom body, was also significantly larger, especially in the dominant queen of a foundress association. No significant differences between dominant or subordinate wasps in regard to volume of the measured brain substructures were found.
Measuring the Business Value of Electronic Supply Chain Collaboration: The Case of Electronic Invoicing

In the last decade, supply chain management has changed its focus, centring now on value creation, by taking into consideration the recent trends of partners integration and implementation of internet technologies. Within this context, this paper presents measurable results regarding the business value of supply chain collaboration practices enabled by e-commerce technologies. The presented research addresses electronic supply chain collaboration by examining the case of electronic invoicing (the electronic exchange of invoice data between supply chain partners) as a type of collaborative message-based system. The paper presents the quantitative and qualitative results of a series of case studies from the grocery retail sector. The results indicate considerable cost savings, especially as the extent of collaboration increases. Additionally, qualitative results from the interviews are provided, supporting suggestions for future research.
Evaluation of five antibiotics on larval gut bacterial diversity of Plutella xylostella (Lepidoptera: Plutellidae)

Larvae of the diamondback moth, Plutella xylostella L. (Lepidoptera: Plutellidae), have rich microbial communities inhabiting the gut, and these bacteria contribute to the fitness of the pest. In this study we evaluated the effects of five antibiotics (rifampicin, ampicillin, tetracycline, streptomycin sulfate and chloramphenicol) on the gut bacterial diversity of P. xylostella larvae. We screened five different concentrations for each antibiotic in a leaf disc assay, and found that rifampicin and streptomycin sulfate at 3 mg/mL significantly reduced the diversity of the bacterial community, and some bacterial species could be rapidly eliminated. The number of gut bacteria in the rifampicin group and streptomycin sulfate group decreased more rapidly than the others. With the increase of antibiotic concentration, the removal efficiency was improved, whereas toxic effects became more apparent. All antibiotics reduced larval growth and development, and eventually caused high mortality, malformation of the prepupae, and hindered pupation and adult emergence. Among the five antibiotics, tetracycline was the most toxic and streptomycin sulfate was a relatively mild one. Some dominant bacteria were not affected by feeding antibiotics alone. Denaturing gradient gel electrophoresis graph showed that the most abundant and diverse bacteria in P. xylostella larval gut appeared in the cabbage feeding group, and diet change and antibiotics intake influenced gut flora abundance. Species diversity was significantly reduced in the artificial diet and antibiotics treatment groups. After feeding on the artificial diet with rifampicin, streptomycin sulfate and their mixture for 10 days, larval gut bacteria could not be completely removed as detected with the agarose gel electrophoresis method.
Optimization of a retrospective technique for respiratory-gated high speed micro-CT of free-breathing rodents

The objective of this study was to develop a technique for dynamic respiratory imaging using retrospectively gated high-speed micro-CT imaging of free-breathing mice. Free-breathing C57Bl6 mice were scanned using a dynamic micro-CT scanner, comprising a flat-panel detector mounted on a slip-ring gantry. Projection images were acquired over ten complete gantry rotations in 50 s, while monitoring the respiratory motion in synchrony with projection-image acquisition. Projection images belonging to a selected respiratory phase were retrospectively identified and used for 3D reconstruction. The effect of using fewer gantry rotations—which influences both image quality and the ability to quantify respiratory function—was evaluated. Images reconstructed using unique projections from six or more gantry rotations produced acceptable images for quantitative analysis of lung volume, CT density, functional residual capacity and tidal volume. The functional residual capacity (0.15 ± 0.03 mL) and tidal volumes (0.08 ± 0.03 mL) measured in this study agree with previously reported measurements made using prospectively gated micro-CT and at higher resolution (150 µm versus 90 µm voxel spacing). Retrospectively gated micro-CT imaging of free-breathing mice enables quantitative dynamic measurement of morphological and functional parameters in the mouse models of respiratory disease, with scan times as short as 30 s, based on the acquisition of projection images over six gantry rotations.
Aminopyrine demethylation measured by breath analysis in cirrhosis

The method of measuring the rate of aminopyrine demethylation by breath analysis was assessed in 23 normal subjects and 20 patients with cirrhosis. Carbon 14 aminopyrine specifically labeled at the two N‐methyl groups was administered by mouth in a dose of 9 mg/kg, including a total radioactivity of 2 μCi. The decay of the specific activity of 14C02 in breath (kb) was found to correlate (r = 0.91) with the disappearance of aminopyrine from plasma (Kp). In normal volunteers, kb was 22.4%/hr; in patients with alcoholic and nonalcoholic cirrhosis it was depressed to 8.4%/hr (p < 0.001). The degree of functional impairment found with the breath test was similar to the sulfobromophthalein (BSP) disappearance curve and the galactose elimination capacity. Although many questions relating to the aminopyrine breath test remain open, our data confirm and extend previous studies of 14CO2 breath analysis after 14C‐aminopyrine administration. It is concluded that it represents a simple and noninvasive procedure which quantitatively reflects the microsomal function of the cirrhotic liver.
the Neonatal Rat Barrel Cortex In Vivo Network Mechanisms of Spindle-Burst Oscillations in

You might find this additional information useful. This article cites 68 articles, 34 of which you can access free at: http://jn.physiology. org/cgi/content/full/97/1/692#BIBL Updated information and services including high-resolution figures, can be found at: http://jn.physiology. org/cgi/content/full/97/1/692 Additional material and information about Journal of Neurophysiology can be found at: http://www.the-aps.org/publications/jn This information is current as of February 6, 2007 . € American Physiological Society. ISSN: 0022-3077, ESSN: 1522-1598. Visit our website at http://www.the-aps.org/.
Electronic Reprint Applied Crystallography New Developments in the Atsas Program Package for Small-angle Scattering Data Analysis Applied Crystallography New Developments in the Atsas Program Package for Small-angle Scattering Data Analysis

Author(s) of this paper may load this reprint on their own web site or institutional repository provided that this cover page is retained. Republication of this article or its storage in electronic databases other than as specified above is not permitted without prior permission in writing from the IUCr. Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents papers on the application of crystallographic techniques and on the related apparatus and computer software. For many years, the Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering papers and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published. New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high-and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented.
Growth hormone-releasing hormone as an agonist of the ghrelin receptor GHS-R1a

Ghrelin synergizes with growth hormone-releasing hormone (GHRH) to potentiate growth hormone (GH) response through a mechanism not yet fully characterized. This study was conducted to analyze the role of GHRH as a potential ligand of the ghrelin receptor, GHS-R1a. The results show that hGHRH(1–29)NH2 (GHRH) induces a dose-dependent calcium mobilization in HEK 293 cells stably transfected with GHS-R1a an effect not observed in wild-type HEK 293 cells. This calcium rise is also observed using the GHRH receptor agonists JI-34 and JI-36. Radioligand binding and cross-linking studies revealed that calcium response to GHRH is mediated by the ghrelin receptor GHS-R1a. GHRH activates the signaling route of inositol phosphate and potentiates the maximal response to ghrelin measured in inositol phosphate turnover. The presence of GHRH increases the binding capacity of 125I-ghrelin in a dose dependent-fashion showing a positive binding cooperativity. In addition, confocal microscopy in CHO cells transfected with GHS-R1a tagged with enhanced green fluorescent protein shows that GHRH activates the GHS-R1a endocytosis. Furthermore, the selective GHRH-R antagonists, JV-1–42 and JMR-132, act also as antagonists of the ghrelin receptor GHS-R1a. Our findings suggest that GHRH interacts with ghrelin receptor GHS-R1a, and, in consequence, modifies the ghrelin-associated intracellular signaling pathway. This interaction may represent a form of regulation, which could play a putative role in the physiology of GH regulation and appetite control.
I/O-Aware Deadline Miss Ratio Management in Real-Time Embedded Databases

Recently, cheap and large capacity non-volatile memory such as flash memory is rapidly replacing disks in embedded systems. While the access time of flash memory is highly predictable, deadline misses may occur if data objects in flash memory are not properly managed in real-time embedded databases. Buffer cache can be used to mitigate this problem. However, since the workload of a real-time database cannot be precisely predicted, it may not be feasible to provide enough buffer space to satisfy all timing constraints. Several deadline miss ratio management schemes have been proposed, but they do not consider I/O activities. In this paper, we present an I/O-aware deadline miss ratio management scheme in real-time embedded databases whose secondary storage is flash memory. We propose an adaptive I/O deadline assignment scheme, in which I/O deadlines are derived from up-to-date system status. We also present a deadline miss ratio management architecture where a control theory-based feedback control loop prevents resource overload both in I/O and CPU. A simulation study shows that our approach can effectively cope with both I/O and CPU overload to achieve the desired deadline miss ratio.
Discovering Host Genes Involved in the Infection by the Tomato Yellow Leaf Curl Virus Complex and in the Establishment of Resistance to the Virus Using Tobacco Rattle Virus-based Post Transcriptional Gene Silencing

The development of high-throughput technologies allows for evaluating gene expression at the whole-genome level. Together with proteomic and metabolomic studies, these analyses have resulted in the identification of plant genes whose function or expression is altered as a consequence of pathogen attacks. Members of the Tomato yellow leaf curl virus (TYLCV) complex are among the most important pathogens impairing production of agricultural crops worldwide. To understand how these geminiviruses subjugate plant defenses, and to devise counter-measures, it is essential to identify the host genes affected by infection and to determine their role in susceptible and resistant plants. We have used a reverse genetics approach based on Tobacco rattle virus-induced gene silencing (TRV-VIGS) to uncover genes involved in viral infection of susceptible plants, and to identify genes underlying virus resistance. To identify host genes with a role in geminivirus infection, we have engineered a Nicotiana benthamiana line, coined 2IRGFP, which over-expresses GFP upon virus infection. With this system, we have achieved an accurate description of the dynamics of virus replication in space and time. Upon silencing selected N. benthamiana genes previously shown to be related to host response to geminivirus infection, we have identified eighteen genes involved in a wide array of cellular processes. Plant genes involved in geminivirus resistance were studied by comparing two tomato lines: one resistant (R), the other susceptible (S) to the virus. Sixty-nine genes preferentially expressed in R tomatoes were identified by screening cDNA libraries from infected and uninfected R and S genotypes. Out of the 25 genes studied so far, the silencing of five led to the total collapse of resistance, suggesting their involvement in the resistance gene network. This review of our results indicates that TRV-VIGS is an exquisite reverse genetics tool that may provide new insights into the molecular mechanisms underlying plant infection and resistance to infection by begomoviruses.
Toxic shock syndrome: causes in people with burn wounds

Toxic shock syndrome (TSS) is a rare complication resulting from colonisation or infection with a toxin-producing strain of Staphylococcus aureus. It was first described in 1978 by Todd et al who saw seven cases of TSS in young children with similar symptoms (fever, vomiting, diarrhoea, rash) that progressed to disseminated intravascular coagulation, shock and multi-organ failure. It was soon confirmed in five of the seven cases, that the syndrome was a result of infection associated with S. aureus of phage group 1 (Todd et al, 1978). It was shown that toxic shock syndrome toxin-1 (TSST-1) was involved in the pathogenesis of the syndrome (Bergdoll et al, 1981; Schlievert et al, 1981; Bergdoll and Schlievert, 1984) and since then there have been reported cases associated with other staphylococcal exotoxins, namely enterotoxin A, B and C (SEA–C) (Yaqoob et al, 1990). In 1980, after a strict definition of TSS was devised by the Centers for Disease Control and Prevention in Atlanta, USA (Chesney et al, 1981), there were hundreds of notified TSS cases in young women associated with menstruation. Epidemiological studies in the US showed that this sudden increase was due to the introduction of a highly absorbent tampon containing carboxymethylcellulose, RelyTM, produced by Proctor and Gamble (Schlievert et al, 1984). Subsequently these were shown to increase production of TSST-1 by S. aureus in vitro (Lee et al, 1987) and were recalled and discontinued in 1980 which led to a subsequent decrease in the incidence of menstrual-related TSS (MTSS) (Schuchat and Broome, 1991) (Figure 1). In addition, details of TSS and symptoms were included in all packs of tampons, raising awareness of the risks with users. Tampons are now predominantly made of cotton and rayon (Schuchat and Broome, 1991).