Miracle-dz/UniFAR-FTUs huggingface dataset:
Network analysis of gene lists for finding reproducible prognostic breast cancer gene signatures

Many genome-scale studies in molecular biology deliver results in the form of a ranked list of gene names, accordingly to some scoring method. There is always the question how many top-ranked genes to consider for further analysis, for example, in order creating a diagnostic or predictive gene signature for a disease. This question is usually approached from a statistical point of view, without considering any biological properties of top-ranked genes or how they are related to each other functionally. Here we suggest a new method for selecting a number of genes in a ranked gene list such that this set forms the Optimally Functionally Enriched Network (OFTEN), formed by known physical interactions between genes or their products. The method allows associating a network with the gene list, providing easier interpretation of the results and classifying the genes or proteins accordingly to their position in the resulting network. We demonstrate the method on four breast cancer datasets and show that 1) the resulting gene signatures are more reproducible from one dataset to another compared to standard statistical procedures and 2) the overlap of these signatures has significant prognostic potential. The method is implemented in BiNoM Cytoscape plugin (http://binom.curie.fr).
Frequencies in the Kolakoski Sequence

The classical Kolakoski sequence K = (Kn) ∞ n=1 is the unique sequence on the alphabet {1, 2} de ned as the sequence of its own symbols' run lengths starting with a 1. The classical Kolakoski sequence was rst studied in a work by Oldenburger [1], where it appears as the unique solution to the problem of a trajectory on the alphabet {1, 2} which is identical to its exponent trajectory. The name of the Kolakoski sequence, however, originates from [2, 3]. In the On-Line Encyclopedia of Integer Sequences [4], the Kolakoski sequence has entry number A000002. The rst letters of K are K = 1 2 2 1 1 2 1 . | / \ / \ | | / \ | K = 1 2 2 1 1 2 1 2 2 1 . (1)
Analysis of the human serological response to proteins of Chlamydia trachomatis

Sera from individuals with culture-proven genital infection with Chlamydia trachomatis were analyzed for the presence of antibodies to chlamydial proteins by an immunoelectrophoretic transfer method. Protein antigens from representative strains of the 15 known serotypes were resolved by gel electrophoresis and transferred to a nitrocellulose solid support before being probed with serum. Sera from infected patients reacted with many different proteins. Most of these sera reacted with a 60,000- and a 62,000-molecular-weight protein which were present in each of the C. trachomatis serotypes and clinical isolates analyzed. In contrast, reactions with the major outer membrane protein were frequently observed but were usually weak. Sera from control groups of children, cloistered nuns, and college women, who were presumed not to have had prior chlamydial infections, did not usually have antibodies against the 60,000- or 62,000-molecular-weight protein, but did react with the major outer membrane protein and a 29,000-molecular-weight protein. These observations may have implications for the development of serodiagnostic tests as well as the identification of candidate antigens for vaccine development.
The Ecological Genetics of Speciation

Ecological interactions and the natural selection they cause play a prominent causal role in biological diversification and speciation. As a discipline, ecological genetics integrates the two components of adaptive evolution (natural selection and genetic variability) to study the mechanisms of evolution. Ecological genetics is a fruitful approach to the study of how reproductive isolation can evolve under natural selection. The essence of this way of thinking and the ways in which it can be used to address persistent open questions in speciation are discussed.
Faster construction of asymptotically good unit-cost error correcting codes in the RAM model

Assuming we are in a Word-RAM model with word size $w$, we show that we can construct in $o(w)$ time an error correcting code with a constant relative positive distance that maps numbers of $w$ bits into $\Theta(w)$-bit numbers, and such that the application of the error-correcting code on any given number $x\in[0,2^w-1]$ takes constant time. Our result improves on a previously proposed error-correcting code with the same properties whose construction time was exponential in $w$.
Effects of ampicillin and corticosteroids on brain water content, cerebrospinal fluid pressure, and cerebrospinal fluid lactate levels in experimental pneumococcal meningitis.

A study was made of the effects of antibiotics and corticosteroids on parameters that reflect brain dysfunction and potential neurological damage in experimental pneumococcal meningitis in rabbits. Brain water content was 398 +/- 10 g/100 g dry weight in normal rabbits and 410 +/- 11 g in rabbits after 24 hr of infection (P less than .001). Cerebrospinal fluid (CSF) lactate levels increased from 16.3 +/- 3.4 mg/dl to 69.5 +/- 28.2 mg/dl (P less than .001), and CSF pressure increased by +8.3 +/- 3.6 mm Hg (P less than .005) over the same interval. Antibiotic therapy with ampicillin sterilized CSF and normalized CSF pressure and brain water content in all animals within 24 hr, while CSF lactate levels remained elevated. Administration of methyl prednisolone, 30 mg/kg, or dexamethasone, 1 mg/kg, 15 and 22 hr after infection completely reversed the development of brain edema, but only dexamethasone also significantly reduced the increase in CSF lactate level (43.8 +/- 12.3 mg/dl) and CSF pressure (+1.8 +/- 2.7 mm Hg). Methyl prednisolone did not significantly affect pressure or lactate levels.
Effect of Changes in the Structure of a Social Network on Emotion Contagion

Agent-based support systems are used to help people with developing and maintaining a healthy lifestyle. Interventions on the social network of an individual could play a role in achieving behaviour change. In this paper, a method for finding effective network interventions to influence specific individuals is proposed. The effect of these interventions was analysed by simulating the diffusion of emotional values about intentions and goals in a social network. Experiments showed that changing connections closer to the target have a larger influence than changing connections further from the target node. A comparison of the effect of the proposed interventions with all possible interventions showed that they are among the most optimal possible interventions. Finally, it was shown that nodes with fewer connections are easier to influence. The proposed interventions could form the basis for a support system that focus on affecting the social interaction between people in an online social network.
Easy, fast, and energy-efficient object detection on heterogeneous on-chip architectures

We optimize a visual object detection application (that uses Vision Video Library kernels) and show that OpenCL is a unified programming paradigm that can provide high performance when running on the Ivy Bridge heterogeneous on-chip architecture. We evaluate different mapping techniques and show that running each kernel where it fits the best and using software pipelining can provide 1.91 times higher performance and 42% better energy efficiency. We also show how to trade accuracy for energy at runtime. Overall, our application can perform accurate object detection at 40 frames per second (fps) in an energy-efficient manner.
Resonant Nanocantilever Chemical Vapor Sensors

Chemical vapor sensors are used in a wide variety of fields such as security, environmental monitoring, the food and beverage industry, and healthcare to detect disease biomarkers on exhaled breath. An electronic nose is composed of an array of cross-responsive chemical vapor sensors, in which every sensor responds to a varying degree to each chemical vapor, creating a "fingerprint" for that vapor. Incorporating an electronic nose into a highly-miniaturized vapor detection system, capable of bringing near laboratory-quality analysis into the field, requires the use of extremely small, fast, and sensitive sensors. One option is resonant nanocantilevers, which respond to changes in mass and stiffness by shifts in resonant frequency, and are capable of detecting mass-loading at the attogram (10-18 g) level in ambient conditions. To determine whether nanocantilevers can be used in an electronic nose, an array of five nanocantilevers, wherein each sensor was coated with a different dropcast polymer film (2-10 nm thick), were exposed to seven chemical vapors with a range of functional groups. The array successfully discriminated between all vapors, indicating that sensor responses were dominated by vapor absorption into polymer films, and not by non-specific physisorption. The thinness of the polymer film, combined with the small vapor capture area of the nanocantilevers, resulted in lower sensitivity than desired, limiting their effectiveness. To overcome this challenge, surface initiated atom transfer radical polymerization (SI-ATRP) was used to grow a 100 nm thick, uniform films of poly(methylmethacrylate) (PMMA), poly(methyl acrylate) (PMA), and poly(n-butyl methacrylate) (PBMA) on nanocantilevers. The thick polymer films absorbed more vapor, significantly increasing nanocantilever sensitivity. To determine the relative roles of mass loading and stiffness change on nanocantilever sensor response, SI-ATRP was combined with chromium masking, enabling polymer film growth to be localized to either the clamped end (sensitive to stiffness) or the free end (sensitive to mass-loading) of the nanocantilevers. These experiments revealed that changes in stiffness, induced by vapor absorption into the polymer films, dominated the sensor responses, and not mass-loading as was initially assumed. This work demonstrated that an array resonant nanocantilevers can be successfully used a sensitive, nanoscale electronic nose.
Reduced ligand affinity leads to an impaired function of the adenosine A2A receptor of human granulocytes in sepsis

The enhanced release of reactive oxygen species by excessively activated polymorphonuclear leucocytes (PMN) is a key step in the pathogenesis of sepsis. Potent action of adenosine in inhibiting cytotoxic PMN functions has been documented. Recent data, however provide evidence that in sepsis a diminished capability of adenosine to inhibit the generation of oxygen radicals by PMN occurs. Here, we investigated the underlying mechanisms in an in vitro sepsis model and in PMN of sepsis patients. We report that lipopolysaccharide (LPS)‐incubation of human PMN elicited the same increase in the half‐maximal inhibitory concentration (IC50) of adenosine as observed in patients with septic shock. Coupling to adenylyl cyclase was impaired as well, as indicated by a decreased potency of adenosine to stimulate cyclic adenosine monophosphate (cAMP) accumulation. Ligand‐binding studies conducted with native, LPS‐stimulated PMN, and with PMN of sepsis patients revealed that, despite an increased adenosine A2A receptor (A2AR) expression, the receptor function declines due to a diminished ligand‐binding affinity most likely caused by allosteric modulators within the inflammatory environment. A2AR function obviously is highly dependent upon the cellular environment and thus, further functional characterization of A2AR responses in sepsis may be a promising approach to develop new adenosine or A2AR agonists based therapeutic strategies.
NCP: Finishing Flows Even More Quickly

The transmission control protocol (TCP) is the major transport layer protocol in the Internet today. TCP and its variants have the drawback of not knowing the explicit rate share of flows at bottleneck links. The Rate Control Protocol (RCP) is a major clean slate congestion control protocol which has been recently proposed to address these drawbacks. RCP tries to get explicit knowledge of flow shares at bottleneck links. However, RCP under or over estimates the number of active flows which it needs to obtain the flow fair rate share. This causes under or over utilization of bottleneck link capacity. This in turn can result in very high queue length and packet drops which translate into a high average file completion time (AFCT). In this paper we present the design and analysis of a Network congestion Control Protocol (NCP). NCP can give flows their fair share rates and hence resulting in the minimum AFCT. Unlike RCP, NCP can also use accurate formula to calculate the number of flows sharing a network link. This enables NCP to assign fair share rates to flows without over or under-utilization of bottleneck link capacities. Simulation results confirm the design goals of NCP in achieving minimum AFCT when compared with RCP.
Interaction of TGFβ and BMP Signaling Pathways during Chondrogenesis

TGFβ and BMP signaling pathways exhibit antagonistic activities during the development of many tissues. Although the crosstalk between BMP and TGFβ signaling pathways is well established in bone development, the relationship between these two pathways is less well defined during cartilage development and postnatal homeostasis. We generated hypomorphic mouse models of cartilage-specific loss of BMP and TGFβ signaling to assess the interaction of these pathways in postnatal growth plate homeostasis. We further used the chondrogenic ATDC5 cell line to test effects of BMP and TGFβ signaling on each other's downstream targets. We found that conditional deletion of Smad1 in chondrocytes resulted in a shortening of the growth plate. The addition of Smad5 haploinsufficiency led to a more severe phenotype with shorter prehypertrophic and hypertrophic zones and decreased chondrocyte proliferation. The opposite growth plate phenotype was observed in a transgenic mouse model of decreased chondrocytic TGFβ signaling that was generated by expressing a dominant negative form of the TGFβ receptor I (ΔTβRI) in cartilage. Histological analysis demonstrated elongated growth plates with enhanced Ihh expression, as well as an increased proliferation rate with altered production of extracellular matrix components. In contrast, in chondrogenic ATDC5 cells, TGFβ was able to enhance BMP signaling, while BMP2 significantly reduces levels of TGF signaling. In summary, our data demonstrate that during endochondral ossification, BMP and TGFβ signaling can have antagonistic effects on chondrocyte proliferation and differentiation in vivo. We also found evidence of direct interaction between the two signaling pathways in a cell model of chondrogenesis in vitro.
Utilisation de profils utilisateurs pour l'accès à une bibliothèque numérique. (Using user'profiles for accessing a digital library)

Aujourd'hui, les bibliotheques numeriques deviennent de plus en plus populaires. Ces bibliotheques fournissent plusieurs services pour leurs utilisateurs. Le service de recherche d'information est un service indispensable pour ces bibliotheques. La personnalisation de ce service pour mieux repondre aux exigences des utilisateurs est une approche qui attire beaucoup d'attention de la communaute scientifique. Plusieurs systemes de recherche d'information personnalisee actuels ont choisi de re-trier les resultats d'un moteur de recherche en prenant en compte les similarites entre ces resultats et le profil utilisateur afin de rendre des resultats plus pertinents pour les utilisateurs. Cependant, la plupart de ces systemes n'utilise que les approches basees sur le contenu textuel pour ce but. Dans nos travaux, nous proposons d'utiliser egalement des methodes basees sur les citations telles que la methode des co-citations et la methode du couplage bibliographique pour calculer les similarites document-profil. Nous etudions la performance de la methode des co-citations avec differentes bases de donnees bibliographiques. Nous utilisons egalement differentes fonctions de combinaison pour combiner les scores individuels. Les approches proposees ont ete validees par des experimentations sur une collection de test utilisee dans INEX 2005.
Influence of polyaniline/multiwalled carbon nanotube composites on alkyd coatings against the corrosion of carbon steel alloy

Abstract Polyaniline (PANI) and its composites with multiwalled carbon nanotubes (MWCNTs) were synthesized by chemical oxidative polymerization. High-resolution transmission electron microscopy (HR-TEM), thermogravimetric analysis (TGA), and Raman spectroscopy were used to characterize the investigated compounds. The synthesized composite is formulated as pigments in alkyd resin with different pigment-binder (P/B) ratios and investigated as anticorrosive coatings on carbon steel in 1 m HCl using potentiodynamic polarization and electrochemical impedance spectroscopy (EIS) techniques. The protection mechanism of PANI occurred through the barrier and passivation effect on the carbon steel surface. The encapsulation and dispersion of MWCNTs into the PANI matrix promoted the anticorrosive efficiency of the alkyd coating.
Mirror Buckling Transitions in Freestanding Graphene Membranes Induced through Scanning Tunneling Microscopy

Graphene has the ability to provide for a technological revolution. First isolated and characterized in 2004, this material shows promise in the field of flexible electronics. The electronic properties of graphene can be tuned by controlling the shape of the membrane. Of particular interest in this endeavor are the thermal ripples in graphene membranes. Years of theoretical work by such luminaries as Lev Landau, Rudolf Peierls, David Mermin and Herbert Wagner have established that 2D crystals should not be thermodynamically stable. Experimental research on thin films has supported this finding. Yet graphene exists, and freestanding graphene films have been grown on large scales. It turns out that coupling between the bending and stretching phonons can stabilize the graphene in a flat, albeit rippled phase. These ripples have attracted much attention, and recent work has shown how to arrange these ripples in a variety of configurations. In this thesis, I will present work done using a scanning tunneling microscope (STM) to interact with freestanding graphene membranes. First I will present STM images of freestanding graphene and show how these images show signs of distortion under the electrostatic influence of the STM tip. This electrostatic attraction between the STM tip and the graphene sample can be used to pull on the graphene sample. At the same time, by employing Joule heating in order to heat graphene using the tunneling current, and exploiting the negative coefficient of thermal expansion, a repulsive thermal load can be generated. By repeatedly pulling on the graphene using the electrostatic potential, while sequentially increasing the setpoint current we can generate a thermal mirror buckling event. Slowly heating the graphene using the tunneling current, prepares a small convex region of graphene under the tip. By increasing thermal stress, as well as pulling using the out of plane electrostatic force, the graphene suddenly and irreversibly switches the sign of its curvature. This event is discovered using STM measurements and supplemented by molecular dynamics simulations. Finally, I will show how to characterize this transition using the famed Ising model. The ripples are modeled as individual Ising spins, which at low temperature exhibit antiferromagnetic coupling. By heating the graphene membrane, the strain increases, changing the antiferromagnetic coupling to ferromagnetic coupling, which characterizes the irreversible transition from a soft, flexible state to a rigid configuration.
Is Epilepsy a Preventable Disorder? New Evidence from Animal Models

Epilepsy accounts for 0.5% of the global burden of disease, and primary prevention of epilepsy represents one of the three 2007 NINDS Epilepsy Research Benchmarks. In the past decade, efforts to understand and intervene in the process of epileptogenesis have yielded fruitful preventative strategies in animal models.This article reviews the current understanding of epileptogenesis, introduces the concept of a “critical period” for epileptogenesis, and examines strategies for epilepsy prevention in animal models of both acquired and genetic epilepsies. We discuss specific animal models, which may yield important insights into epilepsy prevention including kindling, poststatus epilepticus, prolonged febrile seizures, traumatic brain injury, hypoxia, the tuberous sclerosis mouse model, and the WAG/Rij rat model of primary generalized epilepsy. Hopefully, further investigation of antiepileptogenesis in animal models will soon enable human therapeutic trials to be initiated, leading to long-term epilepsy prevention and improved patient quality of life.
Detection of Human JC Polyomavirus DNA in Patients with Solid Tumors by Semi-Nested Polymerase Chain Reaction

Background: JCV is a DNA polyomavirus identified in human cancers. In Egypt, very limited data about presence of JC polyomavirus in immunocompromised cancer patients. Here, we investigated JCV infection and viral DNA load in Egyptian patients with different tumors and its possible correlation with outcome of the disease. Patients and Methods: Fifty blood samples were collected from cancer patients with different solid tumors, and 20 blood samples were collected from apparently healthy individuals as a control group. All samples were subjected to detection of JC polyomavirus by seminested PCR (snPCR) assay using primers targeting large T antigen and real time PCR to measure viral load. Results: The sensitivity level of snPCR assay was 100 copies/ul for JC polyomavirus, while the sensitivity level of quantitative PCR assay was found to be 10 copies/ul. Our snPCR assay was highly specific. JC polyomovirus DNA could be detected in 6 of 51 (11.8%) patients with solid tumors, but none of control was positive for JC polyomavirus DNA. Median viral load was found to be 200 copies/ul of serum. Conclusion: Elevation of JC polyomaviruses copies in patients with different human cancers suggesting its correlation with pathogenesis of disease, but further analysis is required on a larger scale to confirm such findings. [Samah Aly Loutfy, Lamiaa Hussein, EL-Chaimaa Bilal Mohamed, Salem Eid Salem Mohamed Emad Abd ElMoniem Abada, Entsar Abd El-Moniem Ahmed, Amira H.Soliman. Detection of Human JC Polyomavirus DNA in Patients with Solid Tumors by Semi-Nested Polymerase Chain Reaction. Life Sci J 2014;11(12):918-927]. (ISSN:1097-8135). http://www.lifesciencesite. com. 160
Collective information structure model for Information Security Risk Assessment (ISRA)

Purpose – Information security has become an essential entity for organizations across the globe to eliminate the possible risks in their organizations by conducting information security risk assessment (ISRA). However, the existence of numerous different types of risk assessment methods, standards, guidelines and specifications readily available causes the organizations to face the daunting tasks in determining the most suitable method that would augur well in meeting their needs. Therefore, to overcome this tedious process, this paper suggests collective information structure model for ISRA. Design/methodology/approach – The proposed ISRA model was developed by deploying a questionnaire using close-ended questions administrated to a group of information security practitioners in Malaysia (N = 80). The purpose of the survey was to strengthen and add more relevant additional features to the existing framework, as it was developed based on secondary data. Findings – Previous comparative and analyzed studie.