Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of zonula occludens‐1 (ZO‐1) and the transcription factor ZO‐1‐associated nucleic acid‐binding protein (ZONAB)–MsY3 in glial cells and colocalization at oligodendrocyte and astrocyte gap junctions in mouse brain

The PDZ domain‐containing protein zonula occludens‐1 (ZO‐1) interacts with several members of the connexin (Cx) family of gap junction‐forming proteins and has been localized to gap junctions, including those containing Cx47 in oligodendrocytes. We now provide evidence for ZO‐1 expression in astrocytes in vivo and association with astrocytic connexins by confocal immunofluorescence demonstration of ZO‐1 colocalization with astrocytic Cx30 and Cx43, and by ZO‐1 coimmunoprecipitation with Cx30 and Cx43. Evidence for direct interaction of Cx30 with ZO‐1 was obtained by pull‐down assays that indicated binding of Cx30 to the second of the three PDZ domains in ZO‐1. Further, we investigated mouse Y‐box transcription factor MsY3, the canine ortholog of which has been termed ZO‐1‐associated nucleic acid‐binding protein (ZONAB) and previously reported to interact with ZO‐1. By immunofluorescence using specific antimouse ZONAB antibody, ZONAB was found to be associated with oligodendrocytes throughout mouse brain and spinal cord, and to be colocalized with oligodendrocytic Cx47 and Cx32 as well as with astrocytic Cx43. Our results extend the CNS cell types that express the multifunctional protein ZO‐1, demonstrate an additional connexin (Cx30) that directly interacts with ZO‐1, and show for the first time the association of a transcription factor (ZONAB) with ZO‐1 localized to oligodendrocyte and astrocyte gap junctions. Given previous observations that ZONAB and ZO‐1 in combination regulate gene expression, our results suggest roles of glial gap junction‐mediated anchoring of signalling molecules in a wide variety of glial homeostatic processes.
Use of chemical clamps in denaturing gradient gel electrophoresis: application in the detection of the most frequent Mediterranean beta-thalassemic mutations.

Institut National de la Sant~ et de la Recherche M~dicale (INSERM) U 129, Institut Cochin de Genetique Moleculaire (ICGM), 75014, Paris Cedex, France The most frequent molecular defects in genetic diseases are represented by point mutations. There is an increasing need for practical, efficient, and inexpensive ways to explore mutations responsible for these diseases. PCR has solved the problem of the target. When the precise site of a point mutation is not known, it is necessary to first determine the region harboring the defect. Six methods are currently available: single-strand conformation polymorphisms (SSCP), chemical cleavage, RNase mismatch cleavage, reaction of DNA heteroduplexes with a water-soluble carbodiimide, direct sequencing, and denaturing gradient gel electrophoresis (DGGE). To be used routinely, a method must be safe, simple, and of reasonable cost. The first five methods involve unsafe reagents (chemicals and radioactivity), but in some cases are relatively inexpensive. The last method, DGGE, is safe but very expensive, because of the high cost of the long GC sequence (from 30 to 80 nucleotides) that must be attached to the 5' end of one of the primers. In addition, with such a clamp, the yield of primer is reduced drastically, increasing the cost of experiments. Chemical clamps (AppligEne, Strasbourg, France) have been designed recently, allowing these difficulties to be overcome. Instead of adding a long GC-rich tail, the end of the DNA fragment can be stabilized by covalently linking both strands with a chemical agent. The best such agent currently available is psoralen (furocoumarin), (1) a photoactivatable intercalating agent. When irradiated, this intercalated polycyclic compound becomes covalently linked to the 5-6 double bonds of the complementary strands (particularly thymine). The substance is chemically fixed by the manufacturer (AppligEne) to the 5' end (including two adenines) of the primer to be clamped. This procedure represents a very attractive alternative to GC clamping, especially as most laboratories in the world do not have an oligonucleotide synthesizer. To extend this method, we tested it on known mutations responsible for [3-thalassemia in the Mediterranean region. This disease is the most common recessive inherited disorder in Mediterranean populations, (2~ and in the last few years the molecular basis of [3-thalassemia in this area, as well as in other populations, has been largely defined by cloning and sequencing or oligonucleotide analysis. More than 110 different mutations, heterogeneously distributed, have been reported to cause this disease. (3,4~ Here, we propose the use of chemical clamps in combination with the DGGE method for a single-assay diagnosis of the most frequent [3-thalassemic mutations encountered in Mediterranean countries. (s~
Interaction of SOS2 with Nucleoside Diphosphate Kinase 2 and Catalases Reveals a Point of Connection between Salt Stress and H2O2 Signaling in Arabidopsis thaliana

ABSTRACT SOS2, a class 3 sucrose-nonfermenting 1-related kinase, has emerged as an important mediator of salt stress response and stress signaling through its interactions with proteins involved in membrane transport and in regulation of stress responses. We have identified additional SOS2-interacting proteins that suggest a connection between SOS2 and reactive oxygen signaling. SOS2 was found to interact with the H2O2 signaling protein nucleoside diphosphate kinase 2 (NDPK2) and to inhibit its autophosphorylation activity. A sos2-2 ndpk2 double mutant was more salt sensitive than a sos2-2 single mutant, suggesting that NDPK2 and H2O2 are involved in salt resistance. However, the double mutant did not hyperaccumulate H2O2 in response to salt stress, suggesting that it is altered signaling rather than H2O2 toxicity alone that is responsible for the increased salt sensitivity of the sos2-2 ndpk2 double mutant. SOS2 was also found to interact with catalase 2 (CAT2) and CAT3, further connecting SOS2 to H2O2 metabolism and signaling. The interaction of SOS2 with both NDPK2 and CATs reveals a point of cross talk between salt stress response and other signaling factors including H2O2.
Hypertension and the kidney.

A rise in "effective" blood volume and extracellular fluid volume encourages a rise in blood pressure and peripheral resistance, especially if there is renal-mass deficiency. Such a rise diminishes the effectiveness of antihypertensive drugs. An inappropriately high cardiac output leads to high arterial pressure and raised peripheral resistance partly through whole-body "autoregulation" of blood flow. Since this rise in resistance brings the high cardiac output back toward normal, the initial stimulus of the high cardiac output may be difficult to recognize. The kidney has a pivotal role in the hypertensive process through (1) regulation of extracellular fluid volume and (2) probable elaboration of both prohypertensive and antihypertensive humoral agents. Secretion of renin and prostaglandins E 2 and F 2α is established. Other antihypertensive lipid humoral agents may also be elaborated. The kidney probably participates fundamentally in most hypertensive syndromes.
Selective expression of Bhlhb5 in subsets of early‐born interneurons and late‐born association neurons in the spinal cord

Accumulating evidence has suggested that the basic helix‐loop‐helix transcription factors play important roles in controlling neuronal fate specification and differentiation in the developing central nervous system. In this study, we report a detailed immunological study on the expression of Bhlhb5 in embryonic mouse spinal cord with a newly developed antibody. At the early stage of neural development, Bhlhb5 is specifically expressed in dI6 dorsal interneurons and in V1 and V2 ventral interneurons. At late stages of development, Bhlhb5 expression is detected in a subset of late‐born dorsal association interneurons that migrate into the uppermost layer of the dorsal horn. Developmental Dynamics 236:829–835, 2007. © 2007 Wiley‐Liss, Inc.
Competitive and Synergistic Interactions of G Protein β2 and Ca2+ Channel β1b Subunits with Cav2.1 Channels, Revealed by Mammalian Two-hybrid and Fluorescence Resonance Energy Transfer Measurements*

Presynaptic Ca2+ channels are inhibited by metabotropic receptors. A possible mechanism for this inhibition is that G protein βγ subunits modulate the binding of the Ca2+ channel β subunit on the Ca2+ channel complex and induce a conformational state from which channel opening is more reluctant. To test this hypothesis, we analyzed the binding of Ca2+ channel β and G protein β subunits on the two separate binding sites, i.e. the loopI–II and the C terminus, and on the full-length P/Q-type α12. 1 subunit by using a modified mammalian two-hybrid system and fluorescence resonance energy transfer (FRET) measurements. Analysis of the interactions on the isolated bindings sites revealed that the Ca2+ channel β1b subunit induces a strong fluorescent signal when interacting with the loopI–II but not with the C terminus. In contrast, the G protein β subunit induces FRET signals on both the C terminus and loopI–II. Analysis of the interactions on the full-length channel indicates that Ca2+ channel β1b and G protein β subunits bind to the α1 subunit at the same time. Coexpression of the G protein increases the FRET signal between α1/β1b FRET pairs but not for α1/β1b FRET pairs where the C terminus was deleted from the α1 subunit. The results suggest that the G protein alters the orientation and/or association between the Ca2+ channel β and α12. 1 subunits, which involves the C terminus of the α1 subunit and may corresponds to a new conformational state of the channel.
Biomonitoring with the comet assay of Greek greenhouse workers exposed to pesticides

The pesticides in use in Greek greenhouses include a number of agents known to be mutagens and carcinogens. In the present study, we evaluated whether occupational exposure of agricultural workers to a complex mixture of pesticides resulted in a significant increase in DNA damage in human peripheral blood lymphocytes (PBLs). A total of 116 healthy individuals were divided into groups based on exposure to pesticides, smoking status, and gender. Alkaline comet assays performed on PBLs from these individuals indicated no statistically significant differences in basal DNA damage between the study groups. In addition, exposure of PBLs to a dose of hydrogen peroxide led to a similar degree of DNA damage and subsequent repair for all the study populations. The results of the study indicate that the agricultural workers who participated in this study had no detectable increase in DNA damage or alteration in the cellular response to DNA damage. Environ. Mol. Mutagen. Environ. Mol. Mutagen. 41:104–110, 2003. © 2003 Wiley‐Liss, Inc.
Enhancement of muscle fibers in ultrasound images using Gabor filters

In this study, the Gabor filter bank technique was applied to the biceps and gastrocnemius ultrasound images to longitudinally enhance the coherently oriented and hyperechoic perimysiums regions. The method involved three steps, orientation field estimation, frequency map computation and Gabor filtering. The method was evaluated using a simulated image distorted with multiplicative speckle noises, where the “muscles” were arranged in a bipennate fashion with a central “aponeurosis”. After the enhancement using the proposed method, most of the original hyperechoic bands in the simulated image could be recovered and the noises in other locations were greatly reduced. The proposed method was also tested on biceps sonograms collected from 4 healthy adult subjects. Based on the filtering results, the hyperechoic regions, especially the fibroadipose septas, could be enhanced in several aspects, such as the completion of broken but coherently oriented regions. It is believed that the proposed method have potentials in assisting the visualization of strongly oriented patterns in ultrasound images and especially the quantitative estimation of muscle thickness, muscle fiber pennation angle and fascicle length.
Nutritional Anemia in Developing Countries

As described in earlier chapters, anemia is characterized by an insufficient concentration of the protein hemoglobin in the circulation, causing a lack of oxygen transporting capacity. Hemoglobin is the principal component of red blood cells, erythrocytes, and is synthesised in the bone marrow with iron as the key oxygen binding site. Before discussing causes and consequences of nutritional anemia in developing countries, it is important to consider briefly how anemia is diagnosed. Anemia can be diagnosed clinically, for example by looking at the paleness of the skin or mucosa or by a history of weakness and dizziness. This clinical assessment is often the only method available in resource-poor settings, but unfortunately has a low sensitivity and specificity (Critchley and Bates 2005). A more direct and thus more sensitive and specific approach is to measure hemoglobin concentrations in the blood, using one of many different techniques in blood samples obtained by either finger prick or vena-puncture. The obtained values are then compared to those from a matching, normal population, using pre-defined cut-offs for anemia. It is important to realize that different cut-off thresholds are used for different situations. For example, there are different cut-off points for young children, pregnant women, non-pregnant women and men, as well as ethnic differences and differences between smokers and non-smokers. Moreover, altitude affects hemoglobin concentrations and hence cut-offs for anemia. Therefore, it is very important to select the correct reference population for the subjects studied. Cut-off thresholds are normally chosen as the point at which 2.5% of the normal population (or 2 standard deviations) has a value that is lower. Hence, in a normal population, 2.5% of the people will be anemic according to this definition. From an epidemiological viewpoint, this means that if a survey finds a prevalence of anemia close to 2.5%, the studied population can be regarded as normal. From an individual viewpoint however, if a subject from that same population was diagnosed with anemia, s/he would not regard this as normal, would like to know the cause, and if indicated, s/he would like to be treated! Moreover, cut-offs are certainly not absolute or unequivocal, rather, they should be regarded as a proposed value that is accepted by consensus, and are sometimes challenged if found insufficiently accurate. For example, there is currently discussion regarding the cut-off for anemia in infants. Domellof et al. have proposed more precise, stratified cut-off thresholds for anemia at hemoglobin
Observation of high and low frequency muscle fatigue by means of 31P nuclear magnetic resonance.

The changes in energy metabolites and corresponding force curves were studied during muscle fatigue with respect to excitation frequency (20 and 50Hz) for contracting muscle in situ and by means of 31P nuclear magnetic resonance (NMR) technique in vitro. The rat hind limb muscle group was stimulated via the tibial nerve by 0.5ms duration square pulses at different frequencies for a period of three minutes. The force signals recorded during repeated experiments were fed through an A/D converter and averaged by the use of a desk-top computer. 31P-NMR spectra were recorded from gastrochemius and soleus muscle of resting and after stimulation. Results indicated that 1) Iarge and significant decreases in high energy phosphate compounds (e.g., creatine phosphate and adenosine triphosphate (ATP)) were observed during prolonged electric stimulation at 50Hz in both the gastrocnemius and soleus muscles, 2) during 20Hz stimulation, muscle fiber type dependent changes in energy metabolites were observed: i. e. , the gastrocnemius manifested a significant decline in creatine phosphate and ATP contents (p<0.01) while the soleus hardly showed any such changes, and 3) these metabolite changes occurring during different frequency stimulations were well reflected upon the rate of force decline in such that the calculated time constant for force fatigue during 50Hz stimulation was significantly shorter than obtained during 20Hz stimulation (p<0.01). The observed difference in the force fatigue time constants could be, at least in part, explained by the difference in the rate of ATP hydrolysis (e.g., the energy cost for contraction, Ca++ diffusion and uptake, ATP-linked sodium-potassium pump). It was suggested that force fatigue may ultimately be due to a failure of the rate of energy supply to meet demand, but the precise expression of this defect might vary, such that failure of membrane excitation and/or activation may predominate over failure of the energy supply.
On the stability of MIMO EWMA run-to-run controllers with metrology delay

As production requirements in semiconductor manufacturing continue to escalate, it is rarely possible to perform quality measurements on a product before subsequent process operations are performed. This delay between manufacturing and metrology coupled with inaccurate process models can lead to closed-loop instabilities. This paper investigates the effect of metrology delay on the closed-loop stability of a multiple input-multiple output exponentially weighted moving average run-to-run controller. The generalized Routh-Hurwitz stability criteria are used to derive the necessary and sufficient conditions for stability. A sufficient condition for stability is then derived for systems with any length of metrology delay. This condition states that if all of the eigenvalues of a model-mismatch matrix fall inside a circle with unit radius and centered at {1,0} on the complex plane, then the closed-loop system is stable.
Spectral plot properties: Towards a qualitative classification of networks

We introduce a tentative classification scheme for empirical networks based on global qualitative properties detected through the spectrum of the Laplacian of the graph underlying the network. Our method identifies several distinct types of networks across different domains of applications, indicates hidden regularity properties and provides evidence for processes like node duplication behind the evolution or construction of a given class of networks.
Mouse Jagged1 Physically Interacts with Notch2 and Other Notch Receptors

The Delta/Serrate/LAG-2 (DSL) domain containing proteins are considered to be ligands for Notch receptors. However, the physical interaction between DSL proteins and Notch receptors is poorly understood. In this study, we cloned a cDNA for mouse Jagged1 (mJagged1). To identify the receptor interacting with mJagged1 and to gain insight into its binding characteristics, we established two experimental systems using fusion proteins comprising various extracellular parts of mJagged1, a “cell” binding assay and a “solid-phase” binding assay. mJagged1 physically bound to mouse Notch2 (mNotch2) on the cell surface and to a purified extracellular portion of mNotch2, respectively, in a Ca2+-dependent manner. Scatchard analysis of mJagged1 binding to BaF3 cells and to the soluble Notch2 protein demonstrated dissociation constants of 0.4 and 0.7 nm, respectively, and that the number of mJagged1-binding sites on BaF3 is 5,548 per cell. Furthermore, deletion mutant analyses showed that the DSL domain of mJagged1 is a minimal binding unit and is indispensable for binding to mNotch2. The epidermal growth factor-like repeats of mJagged1 modulate the affinity of the interaction, with the first and second repeats playing a major role. Finally, solid-phase binding assay showed that Jagged1 binds to Notch1 and Notch3 in addition to Notch2, suggesting that mJagged1 is a ligand for multiple Notch receptors.
Long‐term survivor mixture model with random effects: application to a multi‐centre clinical trial of carcinoma

A mixture model incorporating long‐term survivors has been adopted in the field of biostatistics where some individuals may never experience the failure event under study. The surviving fractions may be considered as cured. In most applications, the survival times are assumed to be independent. However, when the survival data are obtained from a multi‐centre clinical trial, it is conceived that the environmental conditions and facilities shared within clinic affects the proportion cured as well as the failure risk for the uncured individuals. It necessitates a long‐term survivor mixture model with random effects. In this paper, the long‐term survivor mixture model is extended for the analysis of multivariate failure time data using the generalized linear mixed model (GLMM) approach. The proposed model is applied to analyse a numerical data set from a multi‐centre clinical trial of carcinoma as an illustration. Some simulation experiments are performed to assess the applicability of the model based on the average biases of the estimates formed. Copyright © 2001 John Wiley & Sons, Ltd.
Reusability through Value Based Software Repository

Profitability is prime goal of every software organization. In the recent years, software development paradigm has vastly changed due to rapidly changing business requirements. Now customers demand for their desired products to be delivered in a minimal timeframe. To cater for these demands, different rapid development techniques termed as agile development and reusability phenomena are introduced in the software industry. With the help of reusable components, developing and deploying software products can be much easier and economical. Such approaches can help save cost and working hours so that the developing company can utilize its scare resources on other projects. But achieving accurate and precise reusability is not a piece of cake because along with economical and time saving benefits it comes with some shortcomings, such as it can increase the system complexity, can harm the architecture, degrade quality of the system etc. A proper storage facility of reusable components is required where an organization can save its important data and retrieve it when required. A wide range of standard repositories are used in various organizations for this purpose where important data is stored and retrieved. But in reality, every repository contains huge volumes of data and mostly no proper business standards of storing mechanism are applied. Though there are some repository maintaining software available in the market, but they only provide mechanism for storing artifacts. Maintaining the huge data volumes necessitates providing ample search assistance and putting in place precise reusable components suggestion procedure; therefore, researchers have to sift through loads of volumes of data within the repository for locating the intended component. In this paper, we discuss a novel concept of Central Value Based Software Repository (CBVSR). The proposed approach can assist users in finding the more appropriate artifact as it provides the best possible match against the user query. Proper standards have been followed in storing, deleting, amending and discarding data from the CBVSR. Data quality, security and integrity have been taken care of and indexing, tagging and classification are performed to provide technical assistance to developers.