Miracle-dz/UniFAR-FTUs huggingface dataset:
TP53 and MYC gene alterations independently predict poor prognosis in breast cancer patients

We intended to establish the frequency of exon‐specific TP53 gene alterations and the relation to patient and tumor characteristics and clinical outcome of patients with breast cancer. By using polymerase chain reaction‐single‐strand conformation polymorphism analysis (PCR‐SSCP) and sequencing techniques, TP53 gene alterations were found in 59 (32%) of the 187 samples studied. Most of the TP53 changes (37%) were observed in exon 7. In patients with known follow up (median, 107 months), there was no significant association of the frequency of TP53 mutation with menopausal or nodal status, tumor size, or progesterone receptor status. TP53 gene alterations were more frequently present in estrogen receptor (ER)‐negative (ER−) tumors (P = 0.04) and in tumors with an amplified HER2/NEU oncogene (P = 0.03). Univariate analysis showed that patients with a mutated TP53 in their primary tumors had shorter relapse‐free (P = 0.01) and overall (P = 0.03) survival. Patients with a TP53 gene mutation in exon 8 may be identified as having a particularly rapid rate of relapse. In Cox multivariate regression analysis, which included age, menopausal status, lymph node status, tumor size, steroid‐hormone‐receptor status, and oncogene amplifications, both TP53 gene alteration and MYC amplification independently predicted poor prognosis, with relative hazard rates for TP53 and MYC of 1.8 and 1.6, respectively, in analysis for relapse‐free survival and of 1.7 and 1.6, respectively, in analysis for overall survival. Genes Chromosom Cancer 16:170–179 (1996). © 1996 Wiley‐Liss, Inc.
Phosphorus use efficiency in common bean (Phaseolus vulgaris L.) as related to compatibility of association among arbuscular mycorrhizal fungi and rhizobia

The tripartite symbiosis of common bean ( Phaseolus vulgaris L.) recombinant inbred line (RIL) 147 with rhizobia and arbuscular mycorrhizal fungi (AMF) was assessed in sand culture by comparing the effects of three AMF species on the mycorrhizal root colonization, rhizobial nodulation, plant growth and phosphorus use efficiency for symbiotic nitrogen fixation. Although Glomus intraradices well colonized roots of RIL147, Gigaspora rosea and Acaulospora mellea weakly colonized roots-plants. Higher colonization by Glomus was also obtained by contact with mycorrhized Stylosanthes guianensis . Significant differences among colonization and nodulation of the roots and growth were found between AMF species. Although the results showed that the double inoculation, especially with Glomus , induced a significant increase in all parameters whatever the AMF treatments in comparison to the control. In addition, the combined inoculation of Glomus and CIAT899 strains resulted in significantly higher nitrogen and phosphorus accumulation of common bean plants and improved phosphorus use efficiency compared with their controls which were not dually inoculated. It was concluded that phosphorus use efficiency for plant growth and nitrogen fixation could be improved by compatibility with arbuscular mycorrhizal fungi, rhizobial strain and common bean genotype, same under P limited. Key words : Acaulospora mellea, arbuscular mycorrhizal fungi, Glomus intraradices , Gigaspora rosea , nitrogen fixation, Phaseolus vulgaris , phosphorus, rhizobia, Stylosanthes guianensis , symbiosis.
A novel lightweight authentication scheme for heterogeneous wireless sensor networks in the context of Internet of Things

The evolution of Internet of Things (IoT) is changing traditional perceptions of the current Internet towards a vision of smart objects interacting with each other. Wireless Sensor Networks play an important role and support different applications domains in the IoT environment. However, security issues are the major obstacle for their deployment. Among these issues, authentication of the different interconnected entities. In this paper, we are interested to the case of the interconnection of a sensor node with a remote user. We propose a new lightweight authentication scheme adapted to the resource constrained environment. This scheme allows both of the sensor and the remote user to authenticate each other in order to secure the communication. Our scheme uses nonces, exclusive-or operations, and Keyed-Hash message authentication to check the integrity of the different exchanges. The proposed method stands out in that it provides authentication with less energy consumption, and it terminates with a session key agreement between the sensor node and the remote user. To assess our scheme, we carry out a performance and security analysis. The obtained results show that our scheme saves energy, and provides a resistance against different types of attacks.
Experimental inoculation of pigs with pandemic H1N1 2009 virus and HI cross‐reactivity with contemporary swine influenza virus antisera

Please cite this paper as: Vincent et al. (2010) Experimental inoculation of pigs with pandemic H1N1 2009 virus and HI cross‐reactivity with contemporary swine influenza virus antisera. Influenza and Other Respiratory Viruses 4(2), 53–60
cDNA Expression Analysis of a Human Radiosensitive-Radioresistant Cell Line Model Identifies Telomere Function as a Hallmark of Radioresistance

Abstract To achieve a more complete understanding of the molecular mechanisms underlying tumor radioresistance, we established a radioresistant cell line from the human larynx squamous cell carcinoma cell line Hep-2 after long-term radiation induction. The biological features of the resulting cell lines were characterized. cDNA microarray technology was used to measure the alterations of gene expression in the radioresistant cells. We found that certain genes associated with DNA repair, cell cycle, apoptosis, etc. were significantly changed. In particular, genes related to telomeres, such as POT1, were significantly altered. Radioresistant cells had higher telomerase activity and longer telomeres than their parental cells. Our research suggests that telomere function is a novel hallmark of cellular radiosensitivity, and the mechanistic link between telomere maintenance and radiosensitivity may involve the genes and pathways we implicated in this study.
Partitioning of Food Resources in Bathypelagic Micronekton in the Eastern Gulf of Mexico

A mid-water trawl survey conducted between depths of 1000 and 3000 m in the eastern Gulf of Mexico found 54% of the organisms collected were gonostomatid fishes. Lophogastrids within the family Eucopiidae were also common (17.3%), as were decapod shrimps within the families Oplophoridae and Benthesicymidae (9.9 and 7.1% respectively). We examined the gut contents of 14 prominent species from this assemblage to determine if available food resources were partitioned. Cluster analysis of stomach contents resulted in 4 clusters based on taxonomic composition and 3 based on prey size. Bristlemouth fishes (Gonostomatidae) of the genus Cyclothone and lophogastrids of the genus Eucopia were planktivorous, consuming smaller prey items such as copepods and ostra- cods. Decapods within the family Oplophoridae tended to be piscivorous and consumed relatively large prey. Dendrobranchiate shrimps appeared to regularly consume detrital material, although the contribution of such material to the overall diet could not be quantified. The hatchetfish Sternoptyx pseudobscura had a large proportion of shallow-living taxa in its diet despite being non-migratory. Many of the bathypelagic species were found to be more piscivorous than mesopelagic counterparts within the same family or genus. Dietary overlap in both prey size and taxonomic composition was rare, occurring only 16.5% of the time. The most prevalent pattern (~50% of species pairings) was overlap in neither diet category, suggesting the species partitioned food resources.
Behavioral persistence in captive bears : implications for reintroduction

We investigated the relationship between stereotypic behavior and abnormal behavioral persistence, a trait that could have potentially negative implications for reintroduction efforts, for 18 Asiatic black bears (Ursus thibetanus) and 11 Malayan sun bears (Helarctos malayanus) individually housed in a government confiscation facility in Thailand. Reintroduction or augmentation programs using captive-reared animals are typically less successful than those involving wild-reared conspecifics. One reason for this may lie in deficiencies in the behavior of captive animals. Attributes of stereotypy performance were quantified by observing bears from blinds. Mean stereotypy frequencies ranged between 0 and 51% (mean = 18%, SE = ? 3), of all observations, and stereotypy frequency increased with age. To assess behavioral persistence, 12 bears were trained in a spatial discrimination task; once a performance criterion had been met, further responses were unrewarded and the ability to cease responding was assessed. The number of trials for which bears continued responding without reward was positively related to stereotypy frequency. This finding suggests that captivity can exert subtle but potentially detrimental influences on behavioral control that could possibly be manifest even in non-stereotypic animals. In the wild, where behavior must be adaptive and flexible to meet fluctuating conditions, such behavioral deficiencies could help account for reduced survivorship of reintroduced subjects.
Cloning and Characterization of the cDNA for Human Airway Trypsin-like Protease*

Previously we isolated a trypsin-like enzyme designated human airway trypsin-like protease from the sputum of patients with chronic airway diseases. This paper describes the cDNA cloning, characterization of the primary protein structure deduced from the cDNA, and gene expression of this enzyme in various human tissues. We obtained an entire 1517-base pair sequence of cDNA with an open reading frame encoding a polypeptide with 418-amino acid residues. The polypeptide consisted of a 232-residue catalytic region and a 186-residue noncatalytic region with a hydrophobic putative transmembrane domain near the NH2 terminus. The polypeptide was suggested to be a type II integral membrane protein in which the COOH-terminal catalytic region is extracellular. Therefore, this protein is thought to be synthesized as a membrane-bound precursor and to mature to a soluble and active protease by limited proteolysis. It showed 29–38% identity in the sequence of the catalytic region with human hepsin, enteropeptidase, acrosin, and mast cell tryptase. The noncatalytic region had little similarity to other known proteins. In Northern blot analysis a transcript of 1.9 kilobases was detectable most prominently in the trachea among 17 human tissues examined.
Complexin Regulates the Closure of the Fusion Pore during Regulated Vesicle Exocytosis*

Membrane fusion during exocytosis and throughout the cell is believed to involve members of the SNARE (solubleN-ethylmaleimide-sensitive fusion protein attachment protein receptors) family of proteins. The assembly of these proteins into a four-helix bundle may be part of the driving force for bilayer fusion. Regulated exocytosis in neurons and related cell types is specialized to be fast and Ca2+-dependent suggesting the involvement of other regulatory proteins specific for regulated exocytosis. Among these are the complexins, two closely related proteins that bind only to the assembled SNARE complex. We have investigated the function of complexin by analysis of single vesicle release events in adrenal chromaffin cells using carbon fiber amperometry. These cells express complexin II, and overexpression of this protein modified the kinetics of vesicle release events so that their time course was shortened. This effect depended on complexin interaction with the SNARE complex as introduction of a mutation of Arg-59, a residue that interacts with synaptobrevin in the SNARE complex, abolished its effects. The data are consistent with a function for complexin in stabilizing an intermediate of the SNARE complex to allow kiss-and-run recycling of the exocytosed vesicle.
Exploitation of harmonic signals generated by the UHF RFID chips: New promises for the radio frequency identification technology

The Ultra High Frequencies (UHF) Radio Frequency Identification (RFID) chips generate harmonic signals due to their nonlinear circuits. Usually these harmonic signals are seen as harmful because they are considered as efficiency losses or potential sources of disturbing signals. This paper overviews several recent works demonstrating that the harmonic signals produced by the UHF RFID chips could be source of new capabilities for the tags.
Data interpretation: using probability

• Ensure that a sample is random • Use observations of a sample to judge the features of the population • Plan the study: this includes the appropriate analysis • Establish a hypothesis: usually that there is no difference • Estimate the probability that the observed data could have occurred by chance • Consider the probabilities of more extreme data as well • If you find ‘no difference’ this is no DETECTABLE difference • Absence of evidence is NOT evidence of absence
Preliminary Investigation of IBR in Buffaloe ( Bubalusbubalis ) and Cattle ( Cross Bred ) in Baghdad / Iraq . *

Infectious bovine rhinotracheitis (IBR) is an economically important disease of cattle and buffaloes, and causes abortions, infertility, meningeal encephalitisو and keratoconjunctivitis. The aim of the study was to determine seroprevelence of the IBRantibodiesin two herds, 26buffaloes and 21 cow related agriculture research office and veterinarymedicine college respectively in Baghdad, these animals did not take any vaccination program against the disease.For the serum samples tested with enzyme-linked immunosoarbentassay(ELISA) used specifically for detection IBR antibodiessurvelence, which was apartof survey for detection of the disease in cattle &buffaloe in Baghdad. The results showed the highest seropositivity percentage in buffaloes 65.36%(17:26), while in cattle showed the lowest seropositivity 4.7%(1:21). These results showed that buffaloes are more susceptable than cattle to the infection in this study.
The University of Minnesota Biocatalysis/Biodegradation Database: the first decade

As the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, ) starts its second decade, it includes information on over 900 compounds, over 600 enzymes, nearly 1000 reactions and about 350 microorganism entries. Its Biochemical Periodic Tables have grown to include biological information for almost all stable, non-noble-gas elements (). Its Pathway Prediction System (PPS) () is now an internationally recognized, open system for predicting microbial catabolism of organic compounds. Graphical display of PPS rules, a stand-alone version of the PPS and guidance for PPS users are being developed. The next decade should see the PPS, and the UM-BBD on which it is based, find increasing use by national and international government agencies, commercial organizations and educational institutions.
Asymmetrical Low-Voltage Ride Through of Brushless Doubly Fed Induction Generators for the Wind Power Generation

Compared with the Doubly fed induction generators (DFIG), the brushless doubly fed induction generator (BDFIG) has a commercial potential for wind power generation due to its lower cost and higher reliability. In the most recent grid codes, wind generators are required to be capable of riding through low voltage faults. As a result of the negative sequence, induction generators response differently in asymmetrical voltage dips compared with the symmetrical dip. This paper gave a full behavior analysis of the BDFIG under different types of the asymmetrical fault and proposed a novel control strategy for the BDFIG to ride through asymmetrical low voltage dips without any extra hardware such as crowbars. The proposed control strategies are experimentally verified by a 250-kW BDFIG.
Induction of FoxP3+CD4+25+ Regulatory T Cells Following Hemopoietic Stem Cell Transplantation: Role of Bone Marrow-Derived Facilitating Cells12

The establishment of donor cell lineages following allogeneic bone marrow transplantation is frequently associated with the development of graft-vs-host disease (GVHD). The identification of cell populations that are capable of supporting allogeneic stem cell (SC) engraftment and the induction of tolerance without inducing GVHD could expand the use of this therapy. CD8+TCR− facilitating cells (FC) have been shown to promote allogeneic SC engraftment with resulting transplantation tolerance across complete MHC barriers without inducing GVHD. Although donor reconstitution in SC plus FC recipients is associated with the induction of regulatory T cell-associated factors, it is not known whether an induction of regulatory T cells and subsequent tolerance is a direct effect of the FC. The current study demonstrates that 1) SC plus FC transplantation results in the induction of donor CD4+25+ regulatory T cells and that FC are present in the spleen of recipients before the induction of these cells, 2) activation of FC with CpG-oligodeoxynucleotide promotes CD4+25− T cell differentiation into CD4+25+ regulatory T cells in vitro, as demonstrated by cytokine and forkhead/winged helix transcription factor (FoxP3) gene and protein expression, and 3) direct contact between FC and CD4+25− T cells is required for FoxP3+CD4+25+ regulatory T cell induction and is dependent on CD86 expression on FC. This is the first report to demonstrate a mechanism for FC in the induction of regulatory T cells following allogeneic SC plus FC transplantation. The transplantation of donor FC may provide an alternative approach to permit clinical SC engraftment and induction of transplantation tolerance in the future.
Molecular Mechanism of 17-Allylamino-17-demethoxygeldanamycin (17-AAG)-induced AXL Receptor Tyrosine Kinase Degradation*

Background: AXL is an established therapeutic target in various cancers. HSP90 chaperoning is critical in maintaining the stability of several oncogenic kinases. Results: HSP90 blockade by 17-AAG induced cytosolic mature AXL degradation via ubiquitin/proteasome pathway and impeded its membrane localization. Conclusion: AXL depends on HSP90 for its stability and membrane translocation. Significance: Targeting HSP90 would avail a strategy to counteract AXL. The receptor tyrosine kinase AXL is overexpressed in many cancer types including thyroid carcinomas and has well established roles in tumor formation and progression. Proper folding, maturation, and activity of several oncogenic receptor tyrosine kinases require HSP90 chaperoning. HSP90 inhibition by the antibiotic geldanamycin or its derivative 17-allylamino-17-demethoxygeldanamycin (17-AAG) causes destabilization of its client proteins. Here we show that AXL is a novel client protein of HSP90. 17-AAG induced a time- and dose-dependent down-regulation of endogenous or ectopically expressed AXL protein, thereby inhibiting AXL-mediated signaling and biological activity. 17-AAG-induced AXL down-regulation specifically affected fully glycosylated mature receptor present on cell membrane. By using biotin and [35S]methionine labeling, we showed that 17-AAG caused depletion of membrane-localized AXL by mediating its degradation in the intracellular compartment, thus restricting its exposure on the cell surface. 17-AAG induced AXL polyubiquitination and subsequent proteasomal degradation; under basal conditions, AXL co-immunoprecipitated with HSP90. Upon 17-AAG treatment, AXL associated with the co-chaperone HSP70 and the ubiquitin E3 ligase carboxyl terminus of HSC70-interacting protein (CHIP). Overexpression of CHIP, but not of the inactive mutant CHIP K30A, induced accumulation of AXL polyubiquitinated species upon 17-AAG treatment. The sensitivity of AXL to 17-AAG required its intracellular domain because an AXL intracellular domain-deleted mutant was insensitive to the compound. Active AXL and kinase-dead AXL were similarly sensitive to 17-AAG, implying that 17-AAG sensitivity does not require receptor phosphorylation. Overall our data elucidate the molecular basis of AXL down-regulation by HSP90 inhibitors and suggest that HSP90 inhibition in anticancer therapy can exert its effect through inhibition of multiple kinases including AXL.
Interactive Geometric Constraint Systems

Graphics and modeling systems allow users to place objects or primitives in space and permit the individual editing of these objects. A more powerful paradigm allows relationships expressed by constraints to be established and maintained between pairs of these primitives. For example, two lines might be constrained to be parallel or two points constrained to be coincident. These geometric constraints lead to a ``live'''' model in which design changes to one part of the model may induce changes elsewhere thus permitting the encoding of the designer''s intent into the model. Constraints may describe complex non-linear algebraic relationships between the parameters of a model. To provide constraint satisfaction and maintenance in an interactive environment requires extremely fast and general equation solving techniques. We have developed a system called MechEdit for the interactive editing and animation of planar linkages to demonstrate techniques applicable to general geometric constraint-solving problems. MechEdit combines analytic and iterative numerical techniques for constraint-system solving. A system of equations derived from a linkage is first examined and ordered based upon dependencies between parameters. Parameters that can be solved by propagating values are solved using backsubstitution. Among the remaining unsolved equations, a set of basic geometric reductions are used to identify parameters that can be solved analytically by combining pairs of equations. Finally, Newton-Raphson iteration is used to solve the remaining parameters. Singular value decomposition is used to solve systems of linear equations within the inner-loop of the Newton-Raphson iteration to provide quasi-physical motion for under-constrained and degenerate systems. By providing high-performance, interactive constraint maintenance and robust solving for complex systems, MechEdit demonstrates the power of constraints as a paradigm for specifying relationships between the primitives of a geometric model.
SUCCESSFUL PREGNANCY INDUCED BY HUMAN MENOPAUSAL GONADOTROPHIN IN A PATIENT WITH GROWTH HORMONE DEFICIENCY AND PRIMARY AMENORRHOEA: CASE REPORT

A patient with growth hormone deficiency and primary amenorrhoea became pregnant with the help of human menopausal gonadotrophin. Pregnancy was complicated only by abdominal discomfort due to her very small stature and by moderate oedema. She was delivered of healthy female twins by lower segment Caesarean section at the 37th week.
Long-term protection of mice from Lyme disease by vaccination with OspA

Mice vaccinated with recombinant outer surface protein A (OspA) have been shown to be protected from infection with Borrelia burgdorferi, the agent of Lyme disease, when sacrificed 14 days after challenge with an intradermal inoculum of the spirochete. To determine whether infection was not merely delayed and that protection was long-lasting, we sacrificed vaccinated mice 60, 120, and 180 days after challenge; and to determine whether vaccinated mice retained their immune state over long periods, we challenged mice with B. burgdorferi 60, 90, 120, and 150 days after vaccination. The results of both groups of experiments show that the mice remained free from infection and disease and extend the usefulness of OspA as a vaccine candidate for Lyme borreliosis.