Miracle-dz/UniFAR-FTUs huggingface dataset:
An Integrative Analysis of Meningioma Tumors Reveals the Determinant Genes and Pathways of Malignant Transformation

Meningiomas are frequent central nervous system neoplasms which despite their predominant benignity, show sporadically malignant behaviour. Type 2 Neurofibromatosis and polymorphisms in several genes have been associated with meningioma risk and are probably involved in its pathogenesis. Although GWAS studies have found loci related to meningioma risk, little is known about the factors determining malignant transformation. Thus, this study is aimed to identify the genomic and transcriptomic factors influencing evolution from benignity towards aggressive phenotypes. By applying an integrative bioinformatics pipeline combining public information on a wealth of biological layers of complexity (from genetic polymorphisms to protein interactions), this study identified a module of co-expressed genes highly correlated with tumor stage and statistically linked to several genomic regions (module Quantitaive Trait Loci, mQTLs). Ontology analysis of the transcription hub genes identified microtubule-associated cell cycle processes as key drivers of such network. mQTLs and SNPs associated with meningioma stage were replicated in an alternative meningioma cohort, and integration of these results with up-to-date scientific literature and several databases retrieved a list of genes and pathways with a potentially important role in meningioma malignancy. As a result, cytoskeleton and cell-cell adhesion pathways, calcium channels and glutamate receptors, as well as oxidoreductse and Endoplasmic Reticulum Associated Degradation (ERAD) pathways were found to be the most important and redundant findings associated to meningioma progression. This study presents an integrated view of the pathways involved in meningioma malignant conversion and paves the way for the development of new research lines that will improve our understanding of meningioma biology.
Basic FGF regulates interstitial collagenase gene expression in human smooth muscle cells

Basic fibroblast growth factor (bFGF) is a mitogenic factor that is implicated in smooth muscle cell growth in atherosclerosis and vascular restenosis. In this study, we examined the effect of bFGF on the expression of the interstitial collagenase gene in human vascular smooth muscle cells. Results from Northern transfer analysis showed that bFGF increased collagenase mRNA levels greater than threefold as early as 24 h. Collagenase pre‐mRNA levels were elevated approximately threefold by bFGF, according to RT‐PCR analysis. Transient transfections of the smooth muscle cells with a 4.4‐kb human collagenase promoter‐CAT reporter gene, however, failed to show upregulation of the promoter activity by bFGF. Interestingly, transfections with deleted fragments containing promoter sequences from ‐1047 to ‐2271 resulted in modest stimulation of the collagenase‐CAT promoter activity by bFGF. bFGF did not alter the stability of the collagenase mRNA, as demonstrated by degradation studies. The enhanced collagenase mRNA levels elicited by bFGF were reflected in increased amounts of collagenase protein that were detected by Western blot analysis. In summary, bFGF upregulates the interstitial collagenase expression, resulting in turnover of the extracellular matrix, an event that could facilitate smooth muscle cell migration and proliferation during the early stages of atherosclerosis and restenosis. J. Cell. Biochem. 65:32–41. © 1997 Wiley‐Liss, Inc.
Two‐dimensional analysis of myocardial protein expression following myocardial ischemia and reperfusion in rabbits

Myocardial ischemia and reperfusion injury (MI/R) can be related to leukocyte activation with subsequent release of cytokines and oxygen derived free radicals. Activation of the complement system has been implicated in the pathogenesis of myocardial ischemia and reperfusion injury. Inflammatory injury will subsequently result in cellular activation and protein synthesis. In the present study we analyzed the myocardial protein expression and its pattern following myocardial ischemia and reperfusion, with and without complement inhibition with the synthetic serine protease inhibitor Futhan/nafamstat mesilate (FUT‐175) known to inhibit classical and alternative complement pathway in a rabbit model of myocardial ischemia and reperfusion (60 min I+180 min R). FUT‐175 significantly reduced myocardial necrosis, i.e. creatine kinase release which were analyzed for the three groups (p<0.05). Similary, histological analysis demonstrated preservation of myocardial tissue injury and reduced leukocyte accumulation following FUT‐175 treatment. Further, the myocardial protein expression was analyzed by two‐dimensional gel electrophoresis following MI/R in the different groups. The protein patterns were evaluated by means of MELANIE III, a computer assisted gel analysis system. The biochemical identification of the proteins of interest was, achieved using nanohigh‐performance liquid chromatography/electrospray ionization‐tandem mass spectrometry. On average, 509 ± 25 protein spots were found on the gels. A pattern of 480 spots with identical positions was found on every gel of five animals of each group. We analyzed ten spots which were significantly altered (i.e., in eight spots we observed decreased protein expression and in two spots we observed increased expression, vehicle vs. sham), by using mass spectrometry. Superoxide dismutase precursor and αB‐crystallin were identified. We compared sham group vs. vehicle group and vehicle group vs. FUT‐175 treated animals. Expression of the two identified proteins decreased by half the amount in the vehicle group when compared to sham treated animals. Treatment with FUT‐175 preserved significantly superoxide dismutase precursor and αB‐crystallin protein expression when compared to vehicle animals. The results present marked differences in myocardial protein expression after ischemia and reperfusion and following treatment with the complement inhibitor FUT‐175. Our results illustrate the application of proteomics to discover possible new therapeutic targets or to detect unexpected effects of pharmacological inhibitors.
The Continuum of Serous Tumors of Low Malignant Potential and Low-Grade Serous Carcinomas of the Ovary

The role of serous tumors of low malignant potential (LMP) in the development of invasive epithelial cancer of the ovary is debatable. This review summarizes the current clinical, genetic, and genomic evidence for the existence of a continuum comprising both LMP serous tumors and low-grade serous ovarian carcinomas.
Sonar interpretation learned from laser data

Sensor interpretation in mobile robots often involves an inverse sensor model, which generates hypotheses on specific aspects of the robot's environment based on current sensor data. Building inverse sensor models for sonar sensor assemblies is a particularly difficult problem that has received much attention in the past few years. A common solution is to train neural networks using supervised learning. However, large amounts of training data are typically needed, consisting, for example, of scans of recorded sonar data which are labeled with manually constructed teacher maps. Obtaining these training data is an error-prone and time-consuming process. We suggest that it can be avoided if an additional sensor, like a laser scanner, is also available which can act as the feeding signal. We have successfully trained inverse sensor models for sonar interpretation using laser scan data. In this paper, we describe the procedure we used and the results we obtained.
Space-borne radar detection of orbital debris

Orbital debris in low-Earth-orbit (LEG) poses an increasing threat to the Space Station Freedom (SSF). A combined ground-based/on-orbit radar detection system can provide adequate warning to minimize the collision threat. The paper discusses the unique features on an on-board radar, its contributions to solving the problem, simulation results from modeling of atmospheric effects, and their perturbations upon propagation of debris trajectories, and associated effects of "time-staleness" of orbital parameters of the debris particles. <<ETX>>
Microsatellite Variation Within Three Populations of Inbred C57BL/6J Strain

The goal of this study was to investigate the genetic stability of the C57BL/6J (B6) inbred mouse strain maintained in different breeders. Three populations of B6, Pop1 and Pop2 purchased from Beijing and Pop3 purchased from Shanghai, were examined. Fifteen microsatellite loci reported to be polymorphic among inbred strains were amplified using FAM labeled primers and genotyped with ABI Prism 377 automated sequencer. Seven loci were found polymorphic, and all the loci were homozygous in all the three populations. The present study indicates that genetic variation occurs in different B6 populations although they are still inbred in each breeder. The mechanism of genetic variation is not well understood now, but it is very important to know the precise content of the B6 genome before use of this strain in research.
Optimizing Traffic Flow in Fixed Wireless

We consider the problem of optimizing traffic flow in a fixed network of wired and wireless links where some wireless links interfere with each other. The objective of the network oper- ator is to maximize the total amount of traffic carried. We present algorithms for computing traffic flow in in a mixed wired-wireless network to meet demand and maximize the total traffic carried. I. INTRODUCTION
ON THE TRUTH CONDITIONAL POTENTIAL OF NEGATIONS

According to Partee (1991) and Hajicova/Partee/Sgall (1998), the meaning of natural language sentences corresponds to the tripartite structure. Scope relations within the sentence meaning may effect different readings of DPs. The essential point is the syntactic position of a DP relative to the position of the (possible) sentence negation. It can be shown that the scope of negation coincides with the domain of prosodic focus. The semantic counterpart of focus is the critical meaning of the sentence or - speaking with Roberts (1996) - its partial answer. Scope relations within the sentence yield complex, nested function-argument structures. The resultant operations mapping properties onto individuals mark the structural precondition for DP-readings, e.g. for the specific reading of indefinite DPs. The presentation regards German data as well as data from Czech, which has no overt article system. The movement of DPs out of the prosodically unmarked focus, i.e. the focus of new information, results in the specific DP-reading, at least in the reading of the DP as an individual term: Petr si autoi koupil ti 'Peter cari bought ti' (= Peter bought the car). The presentation illuminates the semantic composition of sentence meaning with respect to its interaction with the lexical, prosodic, and syntactic level.
An adaptive end-to-end QoS management for multimedia applications over wireless ATM network

The provision of multimedia application services over mobile wireless network is a very challenging problem. One major problem encountered is the maintenance of the QoS satisfaction for every application running over the network. Wireless ATM (WATM), as one of the next generation wireless system, is expected to provide such a service. After reviewing four current projects dealing with QoS management in the wireless network, this paper presents our approach to deliver an alternative solution to the problem, which is called AdQoS (adaptive QoS). This system introduces some improvements over the other systems. The comparison among the techniques are presented and discussed.
CPrefSQL-Tool: Uma Ferramenta Web para Consultas com Suporte a Contextos e Preferências do Usuário

In an ubiquitous computing scenario users access to databases will not occur at a unique context, and consequently their expectation when query- ing data will vary according to a multitude of parameters including location, time and surrounding influences. In this article we present CPrefSQL-Tool, a web tool allowing to execute queries and filter the results according to the user preferences and contexts. Some of the functionalities of the CPrefSQL-Tool are: (1) queries may be specified either by using standard SQL commands or by us- ing CPrefSQL, an extension of SQL with specific operators for computing the top k and the most preferred tuples according to a set of contextual preference rules; (2) preference rules are easily specified by means of a simple and intu- itive interface; (3) queries are executed by using the CPrefSQL query processor; (4) the filtered results of a query execution are traceable and explained on user demand.
Mast cells migrate, but do not degranulate, in response to fractalkine, a membrane‐bound chemokine expressed constitutively in diverse cells of the skin

Mast cells (MC) are anatomically located near nerves and blood vessels in skin and the gastrointestinal tract and tend to localize within certain cutaneous tumors such as neurofibromas. However, the molecular mechanisms by which MC home to these sites are not well characterized. Fractalkine (FK) is a membrane‐bound CX3C chemokine that displays constitutive expression in dendritic cells as well as in non‐hematopoietic tissues including mammalian brain. Here we show that FK is constitutively expressed by skin endothelial cells, dermal dendrocytes and cells within neurofibromas. By reverse transcription‐PCR, FK receptor, CX3CR1, is expressed by cultured murine bone marrow‐derived MC (BMMC) of both connective tissue and mucosal phenotypes. Non‐activated human dermal MC isolated from neonatal foreskin similarly demonstrated CX3CR1 expression. In chemotaxis assays, FK attracted MC with maximal migration occurring between 25 – 125 ng / ml. BMMC were not stimulated to release proinflammatory mediators in the presence of FK as measured by granule‐associated β‐hexosaminidase release. Thus, CX3CR1 is expressed by MC and effectively mediates chemotaxis without inducing degranulation. We propose that the constitutive expression of FK on certain cells in the skin may be a factor in the tissue‐specific homing of MC.
Mutational analysis of the PTEN gene in gliomas: Molecular and pathological correlations

The PTEN gene, recently identified on chromosome 10q23, has been proposed to be a candidate tumor suppressor gene inactivated in multiple cancers including glial tumors. We investigated 47 glioblastomas (GBM), 14 anaplastic astrocytomas (AA), 6 non‐pilocytic low‐grade astrocytomas (LGA), 21 low‐grade and anaplastic oligodendrogliomas (O) and oligoastrocytomas (OA), and 3 ependymomas (E) for mutation of the PTEN gene using denaturing gradient gel electrophoresis (DGGE) followed by DNA sequencing. These tumors have been previously screened for loss of heterozygosity (LOH) on chromosome 10q, p53 mutations and EGFR amplification. Overall, PTEN mutations, detected in 14 of 91 tumors, were present in 13 of 47 GBM and 1 of 14 AA. In contrast, mutations were absent in other glioma subtypes (0/30). In all informative cases, PTEN mutations occurred in tumors showing LOH on chromosome 10q, confirming the inactivation of this gene by a 2‐hit mechanism. No correlation was observed between the presence of PTEN mutation and p53 mutation and EGFR amplification. Our results indicate that biallelic PTEN inactivation plays an important role in the pathogenesis of high‐grade astrocytomas as a late event. Moreover, they suggest that PTEN alterations are equally involved in the 2 glioblastoma pathways defined by the presence of EGFR amplification and p53 mutation. Finally, correlation analysis with clinical data did not show that PTEN mutation was linked to survival of the patients. Int. J. Cancer (Pred. Oncol.): 84:150–154, 1999. © 1999 Wiley‐Liss, Inc.
Efeito do uso de enzimas sobre o desempenho e metabolismo de poedeiras

The effect of the addition of multienzymatic complex on performance and metabolism of laying hens was estimated. Two hundred and sixteen Bovans Goldline hens were assigned to a completely randomized design, with 12 replicates of 6 birds per unit and three experimental treatments arranged as follows: positive control (PC), negative control (NC), NC + Rovabio® Max (100 g/t). The positive control diets were formulated to contain adequate levels of nutrients according to the recommendations of the Brazilian tables. Diets of NC and NC + Rovabio® Max were calculated with reduced contents of nutrients present in the nutritional contribution of the enzyme complex evaluated according to the recommendations from the manufacturer. The parameters evaluated were: feed intake, egg production, egg weight, egg mass, feed:gain ratio (per g of egg mass and per dozen of egg) in the period from 24 to 36 weeks of age. In the metabolism trial, feed intake and total excreta production per replicate were measured to determine the metabolizable energy values (apparent ME and apparent Nitrogen Corrected MEn), metabolizability coefficients of gross energy and nitrogen retention and P and Ca balance. When compared to hens fed both negative and positive control diets, the addition of Rovabio® Max to the NC diet improved the hen day egg production an the feed:gain ratio (kg/dz). The reduction in the levels of nutritional diets resulted in lower ME and MEn values. The supplementation of the enzyme complex to diets with lower nutritional levels improved the ME values, resulting in values similar to those presented by hens fed PC diet. The addition of the enzyme complex to the NC diet increase P retention and resulte in lower P excretion when compared to the hens fed NC diet. Layers fed PC diet show higher P intake, excretion and retention.
The Reproductive Behaviour and the Nature of Sexual Selection in Scatophaga Stercoraria L. (Diptera : Scatophagidae)

Females in all stages of their reproductive cycle around dung are equally attractive in eliciting encounters from searching males. On contact, all females which still have eggs to lay are mated (or remated), generally (i.e. over 75%) in their first encounter. All such females copulate for a normal duration, irrespective of previous matings. However, females which have completed oviposition are much less attractive to males on contact and though about 35% of post-oviposition females copulate as a result of their first encounter, only about half of them will have begun genital contact even if allowed six encounters with males. The female behaviour does not appear to be involved in this effect. Matings with post-oviposition females last only 43% of the normal duration. This effect may be due at least in part to the side to side ('swaying') movement performed by the female. It is extremely rare in nature for females to oviposit without a male mounted in attendance (i.e. in the 'passive phase'), though females will do so quite readily if separated artificially. The female initiates separation only after all the egg batch is laid, and after separation she flies immediately upwards and away from the dropping. Female quiescence appears to be necessary for the male to adopt the passive phase; swaying during genital contact and immediately after precedes separation without a passive phase. Females remain quiescent if they still have eggs to lay (even when already mated) and fresh dung is present, though the continuous reception of fresh dung is not necessary. Females sway fairly persistently if they have completed oviposition or there is no dung stimulus. Most females examined on arrival at the dropping (and before being found by a male) already had sperm in their spermathecae, presumably from matings at previous ovipositions since all females mate on arrival at the dung and there are several successive batches of eggs. It is predicted that receptivity before all the eggs are laid may now be of selective advantage to the female. The performance of non-receptivity as exhibited by post-oviposition females involves the female in an average rejection delay of 2.7 min. per encounter. At the average density of searching males present on the dung this rejection delay time would involve the female in much more time waste than full receptivity, since after mating the passive male undertakes the rejection of other males during oviposition. Even allowing for time wasted in recopulation following take-over (i.e. when a second male takes possession of the female), a female with full receptivity would save about 50 min. per oviposition cycle compared to one showing rejection. The passive phase is presumably of advantage to the male in preventing further inseminations, sperm from which could compete with his own for the fertilisation of the female's eggs. After oviposition, the female initiates termination of the passive phase by swaying reactions which cause the male to dismount. She then flies from the dropping.
Blocking the Endogenous Increase in HSP 72 Increases Susceptibility to Hypoxia and Reoxygenation in Isolated Adult Feline Cardiocytes

Background Heat shock protein (HSP) 72 is a ubiquitous protein that is rapidly induced in response to stress and is thought to constitute an endogenous protective response. Previously, work has focused on the effect of overexpression of HSP 72 in various cell types. We were interested in testing the hypothesis that blocking the increase in HSP 72 that occurs in response to hypoxia or ischemia would be deleterious, thus showing that the endogenous response in cells, particularly cardiac cells, is an important line of defense against cell injury. Methods and Results Isolated adult feline cardiocytes were treated with a 14-mer phosphorothioate antisense (AS) to HSP 72 and then exposed to mild (8 hours) or severe (12 hours) hypoxia. With mild hypoxia, an increase in LDH release, a decrease in MTT uptake, and a decrease in live-to-dead ratios were seen in AS-treated cells compared with control cells and cells treated with the complementary sense sequence or with AS to major histocompatibility complex I. AS treatment converted mild hypoxic injury to a pattern of cell injury seen with severe injury. After severe hypoxia, all treatment groups showed an increase in LDH, a decrease in MTT uptake, and a decrease in live-to-dead ratios; AS-treated cells had the greatest increase in cell injury. AS treatment produced a 40% decrease in HSP 72 levels after hypoxia compared with control cells treated with hypoxia. A dose-response study showed inhibition of the increase in HSP 72 with as little as 5 μg (1.24 μmol/L) of AS. Conclusions (1) Blocking an increase in HSP 72 with AS increases the susceptibility of adult cardiac myocytes to hypoxic injury. (2) HSP 72 is an important part of the normal cell response to stress and is important in protecting cardiac myocytes from hypoxia and reoxygenation.
Transient High Affinity Binding of Tissue Factor Pathway Inhibitor−Factor Xa Complexes to Negatively Charged Phospholipid Membranes†

The interaction of tissue factor pathway inhibitor (TFPI), factor Xa, and TFPI−factor Xa complexes with negatively charged phospholipid membranes composed of 25 mol % phosphatidylserine and 75 mol % phosphatidylcholine was studied by ellipsometry. The binding of TFPI alone was negligible; factor Xa bound with moderate affinity, with a dissociation constant Kd = 42 nM. Formation of the TFPI−factor Xa complex drastically enhanced the affinity for phospholipid membranes, Kd = 5 nM, compared to that of either protein alone. TFPI1-161, a TFPI variant lacking the third Kunitz domain and the positively charged C-terminus did not enhance binding affinity of the factor Xa. Analysis of the kinetics of adsorption and desorption confirmed the equilibrium binding data, although upon longer residence at the lipid membrane the desorption rate of TFPI−factor Xa complexes became slower, indicating an increase in affinity with longer residence of the TFPI−factor Xa complexes at the membrane. In contrast, binding of TFPI−fa.