Miracle-dz/UniFAR-FTUs huggingface dataset:
Models and simulations of variable-density flow in fractured porous media

We develop a numerical technique for variable-density flow in fractured porous media, in which fractures are (d − 1)-dimensional manifolds, with d being the dimension of the ambient space. The PDEs of variable-density flow are firstly presented in the same form for both the fractures and the enclosing medium. Then, the equations defined in the fractures are averaged along the fracture width and formulated in (d − 1)-dimensions. The resulting PDEs are solved together with those defined in the enclosing medium, which maintain their d-dimensional form. The discretisation of the coupled system of d-and (d − 1)-dimensional PDEs follows a finite-volume method requiring a special construction of the discretisation grid, obtained by the algorithm explained in this paper. The accuracy of our technique is tested by comparing the produced results with those obtained in simulations in which the fractures maintain dimension d. In all simulations the fractured medium is three-dimensional.
Preparation of nata de coco-based carboxymethylcellulose coating and its effect on the post-harvest life of bell pepper (Capsicum annuum l.) fruits

Carboxymethyl cellulose from nata de coco, referred to as carboxymethyl-nata (CMN), was prepared by two cycles of mercerization and etherification. Coatings containing 1% and 2% CMN were applied on bell peppers to evaluate the effect of the polysaccharide coating on the post-harvest life of the fruits. The fruits were stored at 25°C. During storage, the color change in CMN-coated fruits was slower than in the control and blank fruits (coated with additives only). CMN-coated fruits maintained firmness and had lower weight loss, total soluble solids content and titratable acidity than the control and blank. Antioxidant activity and total phenolic content increased from day 0 to day 15. CMN-coated fruits had lower total phenolic content than the control and blank at day 15. Values at day 15 did not indicate the retardation of antioxidant activity in the 1% CMN-coated fruits. Results indicated that CMN coatings reduced the rate of ripening.
AMF1 (GPS2) Modulates p53 Transactivation

ABSTRACT We have reported that the papillomavirus E2 protein binds the nuclear factor AMF1 (also called G-protein pathway suppressor 2 or GPS2) and that their interaction is necessary for transcriptional activation by E2. It has also been shown that AMF1 can influence the activity of cellular transcription factors. These observations led us to test whether AMF1 regulates the functions of p53, a critical transcriptional activator that integrates stress signals and regulates cell cycle and programmed cell death. We report that AMF1 associates with p53 in vivo and in vitro and facilitates the p53 response by augmenting p53-dependent transcription. Overexpression of AMF1 in U2OS cells increases basal level p21WAF1/CIP1 expression and causes a G1 arrest. U2OS cells stably overexpressing AMF1 show increased apoptosis upon exposure to UV irradiation. These data demonstrate that AMF1 modulates p53 activities.
A monoclonal antibody to human immunodeficiency virus type 1 which mediates cellular cytotoxicity and neutralization

Monoclonal antibodies (MAbs) were raised against human immunodeficiency virus type 1 gp120. One MAb, P4/D10, was found to mediate highly efficient antibody-dependent cellular cytotoxicity and virus neutralization. The reactivity was located to a major neutralizing region (amino acids 304 to 323) on gp120. Five other MAbs with a similar epitopic reactivity did not show any antibody-dependent cellulan cytotoxicity activity but had a virus-neutralizing capacity.
Cell-to-Cell Transfer of Bacterial Outer Membrane Lipoproteins

Myxococcus xanthus cells can glide forward by retracting type IV pili. Tgl, an outer membrane lipoprotein, is necessary to assemble pili. Tgl mutants can be transiently “stimulated” if brought into end-to-end contact with tgl+ donor cells. By separating the stimulated recipient cells from donor cells, we found that Tgl protein was transferred from the donors to the rescued recipient cells. Mutants lacking CglB lipoprotein, which is part of a second gliding engine, could also be stimulated, and CglB protein was transferred from donor to recipient cells. The high transfer efficiency of Tgl and CglB proteins suggests that donor and recipient cells briefly fuse their outer membranes.
Antibody constructs in cancer therapy

Whereas over 85% of human cancers are solid tumors, of the 8 monoclonal antibodies (mAbs) currently approved for cancer therapy, 25% are directed at solid tumor surface antigens (Ags). This shortfall may be due to barriers to achieving adequate exposure in solid tumors. Advancements in tumor biology, protein engineering, and theoretical modeling of macromolecular transport are currently enabling identification of critical physical properties for antitumor Abs. It is now possible to structurally modify Abs or even replace full Abs with a plethora of Ab constructs. These constructs include Fab and Fab′2 fragments, scFvs, multivalent scFvs (e.g., diabodies and tribodies), minibodies (e.g., scFv‐CH3 dimers), bispecific Abs, and camel variable functional heavy chain domains. The purpose of the article is to provide investigators with a conceptual framework for exploiting the recent scientific advancements. The focus is on 2 properties that govern tumor exposure: 1) physical properties that enable penetration of and retention by tumors, and 2) favorable plasma pharmacokinetics. It is demonstrated that manipulating molecular size, charge, valence, and binding affinity can optimize these properties. These manipulations hold the key to promoting tumor exposure and to ultimately creating successful Ab therapies for solid tumors. Cancer 2007. © 2006 American Cancer Society.
Design of a compact 4-port MIMO antenna system

Multiple-input-multiple-output (MIMO) technology will be used by future generation mobile networks to achieve very high data rates in both the uplink and downlink channels. MIMO is based on the use of multiple antenna systems within the mobile terminal as well as the base station. Such antenna systems are required to fit within the hand-held terminal which occupies a small size. Antenna integration is one of the major challenges because strong mutual coupling occurs between closely spaced array elements in compact arrays. In this paper, a novel design of 4-port compact MIMO antenna system with reduced mutual coupling is presented. The proposed decoupling network consists of reactive elements, the values of which can be calculated by eigenmode analysis. Design procedures and equations are proposed.
Convolved Gaussian process priors for multivariate regression with applications to dynamical systems

In this thesis we address the problem of modeling correlated outputs using Gaussian process priors. Applications of modeling correlated outputs include the joint prediction of pollutant metals in geostatistics and multitask learning in machine learning. Defining a Gaussian process prior for correlated outputs translates into specifying a suitable covariance function that captures dependencies between the different output variables. Classical models for obtaining such a covariance function include the linear model of coregionalization and process convolutions. We propose a general framework for developing multiple output covariance functions by performing convolutions between smoothing kernels particular to each output and covariance functions that are common to all outputs. Both the linear model of coregionalization and the process convolutions turn out to be special cases of this framework. Practical aspects of the proposed methodology are studied in this thesis. They involve the use of domain-specific knowledge for defining relevant smoothing kernels, efficient approximations for reducing computational complexity and a novel method for establishing a general class of nonstationary covariances with applications in robotics and motion capture data.Reprints of the publications that appear at the end of this document, report case studies and experimental results in sensor networks, geostatistics and motion capture data that illustrate the performance of the different methods proposed.
Sensor Web Technologies for NASA Earth Science

Recent technological advancements in microelectronics, wireless communications, intelligent systems and networking have led to the conceptualized notion of a "web" of sensors, interconnected and interacting with one another to provide observations and measurements of geophysical phenomena, and routing data (or information) directly to researchers, scientists and other destinations (including forecast models and data archives). This is the concept that we call the "sensor web. " A vision for NASA sensor webs for Earth science is to enable "on-demand sensing of a broad array of environmental and ecological phenomena across a wide range of spatial and temporal scales, from a heterogeneous suite of sensors both in situ and in orbit. " This paper takes a high level view of sensor webs, describing their characteristics and giving examples of how NASA sees these systems contributing to our knowledge of the world in which we live. Examples of sensor web prototypes and research highlights will be presented from some of the research projects recently funded by the NASA Earth Science Technology Office and currently underway in universities, industries and NASA research centers throughout the country. The paper concludes by imagining how sensor webs will be used in the future and describing the key research technologies that will be needed to fully realize this vision.
Dimensional Interaction in Distance Judgment

Participants decided under speed stress whether or not the horizontal distances between pairs of frontal locations exceeded a criterion distance. The error rate reflected parallel effects of the horizontal and vertical distance between the locations. Whereas dimensional interaction in perceptual judgment has previously been attributed either to the perception of the stimulus or to the response decision concerning the stimulus, here dimensional interaction was attributed to the process of distance assessment regarding the test locations. Under the proposed account, the horizontal distance between the locations could not be assessed independently of the vertical distance. Only the overall distance between the locations could be assessed. However, because the horizontal and vertical positions of the locations could be independently assessed, the horizontal distance between the locations was available to the extent that the vertical positions of the locations were weighted so as to minimize vertical distance prior to the assessment of overall distance. In support of this account, parallel effects of horizontal and vertical distance were not observed when participants decided whether or not pairs of locations had the same horizontal position.
An Efficient Approach for Image Filtering by Directional Neighborhood with wavelets

Image Processing refers to the use of algorithm to perform processing on digital image. Microscopic images like some microorganism images contain different type of noises which reduce the quality of the images. Removing noise is a difficult task. Noise removal is an issue of image processing. Images containing noise degrade the quality of the images. Removing noise is an important processing task. After removing noise from the images, the visual effect will not be proper. This paper presents an approach to de-noise based on averaging of pixels in 5X5 window and wavelets is proposed.
Off-diagonal long-range order, oblique confinement, and the fractional quantum Hall effect.

Demonstration de l'existence d'un nouveau type d'ordre a longue distance non diagonal dans l'etat fondamental de l'effet Hall quantique fractionnaire, basee sur l'application de la transformation de jauge de Wilczek pour la connexion de m tubes de flux quantifies aux particules avec un facteur de remplissage fractionnaire de 1/m. Analogie avec le confinement oblique
Mutagenesis Studies of the H5 Influenza Hemagglutinin Stem Loop Region*

Background: The stem loop region of influenza hemagglutinin plays a critical role in viral entry. Results: Novel site-directed mutants of the H5 hemagglutinin stem loop region were generated and characterized. Conclusion: The sensitivity of the stem loop region to mutation underscores its importance to function and attractiveness as a site for therapeutic intervention. Significance: Antibodies and drug-like molecules targeting the stem loop region of hemagglutinin are promising antivirals. Influenza outbreaks, particularly the pandemic 1918 H1 and avian H5 strains, are of high concern to public health. The hemagglutinin envelope protein of influenza plays a critical role in viral entry and thus is an attractive target for inhibition of virus entry. The highly conserved stem loop region of hemagglutinin has been shown to undergo critically important conformational changes during the entry process and, moreover, to be a site for inhibition of virus entry by antibodies, small proteins, and small drug-like molecules. In this work we probe the structure-function properties of the H5 hemagglutinin stem loop region by site-directed mutagenesis. We find that most mutations do not disrupt expression, proteolytic processing, incorporation into virus, or receptor binding; however, many of the mutations disrupt the entry process. We further assess the effects of mutations on inhibition of entry by a neutralizing monoclonal antibody (C179) and find examples of increased and decreased sensitivity to the antibody, consistent with the antibody binding site observed by x-ray crystallography. In addition, we tested the sensitivity of the mutants to MBX2329, a small molecule inhibitor of influenza entry. Interestingly, the mutants exhibit increased and decreased sensitivities to MBX2329, which gives further insight into the binding site of the compound on HA and potential mechanisms of escape. Finally, we have modeled the binding site of MBX2329 using molecular dynamics and find that the resulting structure is in good agreement with the mutagenesis results. Together these studies underscore the importance of the stem loop region to HA function and suggest potential sites for therapeutic intervention of influenza entry.
Prevalence of psychiatric disorder and the need for psychiatric care in Northern Ireland

Background This is the first report on the epidemiology of psychiatric disorders and needs for psychiatric treatment in the District of Derry, Northern Ireland. Aims To assess the prevalence of psychiatric disorder and the needs for treatment in the general population of Derry. Method The sample was drawn at random with a two-phase design using the General Health Questionnaire (GHQ–28) during the first phase, and the Schedules for Clinical Assessment in Neuropsychiatry (SCAN) with the Needs for Care Assessment (NFCAS–C) in the second phase. Results The second phase (n=307) gave a weighted 1-month prevalence of hierarchically ordered ICD–10 psychiatric disorders of 7.5% and a 1-year prevalence of 12.2%. The equivalent prevalences for depressive disorders were 2.4% and 6.0%, respectively, and those for anxiety states were 3.5% and 3.7%. Only a quarter of needs for treatment were met, with the situation being better for depression than for anxiety. Conclusions The rates of psychiatric disorder in Derry were even higher than those reported by a similar survey in inner London. This almost certainly reflects the very high levels of social deprivation in the District. Needs for treatment were often unmet.
Coding theorems of quantum information theory

Coding theorems and (strong) converses for memoryless quantum communication channels and quantum sources are proved: for the quantum source the coding theorem is reviewed, and the strong converse proven. For classical information transmission via quantum channels we give a new proof of the coding theorem, and prove the strong converse, even under the extended model of nonstationary channels. As a by-product we obtain a new proof of the famous Holevo bound. Then multi-user systems are investigated, and the capacity region for the quantum multiple access channel is determined. The last chapter contains a preliminary discussion of some models of compression of correlated quantum sources, and a proposal for a program to obtain operational meaning for quantum conditional entropy. An appendix features the introduction of a notation and calculus of entropy in quantum systems.
Thalamic activation in photic myoclonus

Regional cerebral blood flow (rCBF) during photic myoclonus was studied by means of positron emission tomography in a 51‐year‐old male patient suffering from MERRF (myoclonic epilepsy with ragged‐red fibres). Frequencies of 3 Hz and 5 Hz flash stimulation were used. Both frequencies elicited paroxysmal EEG‐abnormalities but only the higher frequency induced generalized myoclonic jerks. We found a left dominated significant increase of rCBF in the thalamus during myoclonus. The thalamic asymmetry was significant when tested with an ROI approach. The myoclonic activity was accompanied by significantly increased activity in the supplementary motor cortex (SMA). Decreases in rCBF were seen in the limbic, temporal and occipital areas during photic stimulation at both flash frequencies, more expressed during myoclonus. The findings observed in this patient indicate a thalamic focus for photic myoclonus in MERRF. We suggest that photic stimulation induced an abnormal discharge in the thalamus, which was fed forwards via thalamo‐cortical connections to the precentral motor cortex, to produce the muscle jerks.
Amantadine Resistance among Porcine H1N1, H1N2, and H3N2 Influenza A Viruses Isolated in Germany between 1981 and 2001

This study was designed to gain insight into amantadine susceptibility of porcine influenza A viruses isolated in Germany between 1981 and 2001. The 12 studied H1N1, H1N2, and H3N2 porcine influenza virus strains were isolated in chicken eggs and passaged once in MDCK cells. Plaque reduction assays were applied to examine virus susceptibility to amantadine. Genotyping was used to confirm drug resistance. In the results of these antiviral studies, only 3 of the 12 isolates were shown to be amantadine-susceptible. All resistant strains contained the AA substitutions G16E, S31N, and R77Q in the membrane protein 2 (M2). Additionally, L27A was detected in two H1N1 strains. S31N and/or L27A are well-known amino acid substitutions in M2 that confer amantadine resistance. The role of the pig as an intermediate host of avian and human influenza A viruses, the possible involvement of genetic reassortment, and the high incidence of naturally amantadine-resistant porcine influenza A viruses suggest a real risk of emergence of amantadine resistant human viruses. Therefore, drug susceptibility monitoring appears to be warranted for effective application of those drugs.
Testing interconnects for noise and skew in gigahertz SoCs

Voltage distortion (noise) and delay violations (skew) contribute to the signal integrity loss and ultimately functional error, performance degradation and reliability problems. We present a BIST-based test methodology that includes two special cells to detect and measure noise and skew occurring on the interconnects of the gigahertz system-on-chips.
Multi-agent Deep Reinforcement Learning for Task Allocation in Dynamic Environment

: The task allocation problem in a distributed environment is one of the most challenging problems in a multi-agent system. We propose a new task allocation process using deep reinforcement learning that allows cooperating agents to act automatically and learn how to communicate with other neighboring agents to allocate tasks and share resources. Through learning capabilities, agents will be able to reason conveniently, generate an ap-propriate policy and make a good decision. Our experiments show that it is possible to allocate tasks using deep Q-learning and more importantly show the performance of our distributed task allocation approach.
Obstructor-A Is Required for Epithelial Extracellular Matrix Dynamics, Exoskeleton Function, and Tubulogenesis*

Background: The extracellular matrix (ECM) is essential for protection and development of epithelial tissues. Results: Obstructor-A (Obst-A) organizes a core complex with chitin modifiers and enzymes to protect ECM from premature degradation. Conclusion: Obst-A is required for growth control, tubulogenesis, wound healing, and epithelial integrity. Significance: This novel mechanism is crucial for understanding ECM dynamics of epithelial tissues. The epidermis and internal tubular organs, such as gut and lungs, are exposed to a hostile environment. They form an extracellular matrix to provide epithelial integrity and to prevent contact with pathogens and toxins. In arthropods, the cuticle protects, shapes, and enables the functioning of organs. During development, cuticle matrix is shielded from premature degradation; however, underlying molecular mechanisms are poorly understood. Previously, we identified the conserved obstructor multigene-family, which encodes chitin-binding proteins. Here we show that Obstructor-A is required for extracellular matrix dynamics in cuticle forming organs. Loss of obstructor-A causes severe defects during cuticle molting, wound protection, tube expansion and larval growth control. We found that Obstructor-A interacts and forms a core complex with the polysaccharide chitin, the cuticle modifier Knickkopf and the chitin deacetylase Serpentine. Knickkopf protects chitin from chitinase-dependent degradation and deacetylase enzymes ensure extracellular matrix maturation. We provide evidence that Obstructor-A is required to control the presence of Knickkopf and Serpentine in the extracellular matrix. We propose a model suggesting that Obstructor-A coordinates the core complex for extracellular matrix protection from premature degradation. This mechanism enables exoskeletal molting, tube expansion, and epithelial integrity. The evolutionary conservation suggests a common role of Obstructor-A and homologs in coordinating extracellular matrix protection in epithelial tissues of chitinous invertebrates.
A Combinatorial Library Strategy for the Rapid Humanization of Anticarcinoma BR96 Fab*

We have used a combinatorial mutagenesis strategy to humanize BR96, a monoclonal antibody that binds to the Lewis Y class of tumor antigens. This approach allows simultaneous assessment of hundreds of humanized variable regions to identify the molecules that best preserve affinity, thus overcoming the major drawback of current humanization procedures, the requirement to construct and analyze each humanized antibody separately. Murine residues of BR96 were mutated to human if they were solvent-exposed residues that did not participate in the formation of the antigen binding site and were not at the interface of the light and heavy chain. At positions that might be involved in binding to antigen, the choice between the murine and human residue was more difficult. Murine and human alternatives were incorporated into a combinatorial library at positions representing buried residues that might affect the structural integrity of the antigen binding site. By encoding this library of humanized BR96 Fabs in an M13 phage vector, we rapidly identified several candidates with nearly identical antigen binding, within 2-fold, of the chimeric Fab. Additional mutagenesis directed at sites suggested in the literature as potentially important for antigen binding in a similar anti-Lewis Y antibody yielded no further improvements.