Miracle-dz/UniFAR-FTUs huggingface dataset:
Parameterization of SWIM Mobility Model Using Contact Traces

Opportunistic networks (OppNets) are focused to exploit direct, localised communications which occur in a peer-to-peer manner mostly based on people's movements and their contact durations. Therefore, the use of realistic mobility models is critical to evaluate the data dissemination in OppNets. One of the mobility models that is available in OMNeT++ which can be used to mimic human movement patterns is Small Worlds in Motion (SWIM). The SWIM model is based on the intuition that humans often visit nearby locations and if the visited location is far away, then it is probably due to the popularity of the location. As an alternative to mobility of a node, pairwise contact probabilities are also used to evaluate the data dissemination in OppNets. Pairwise contact probabilities can be used to predict that a node will be met by a particular node. These probabilities can be derived in many ways. One of the ways is to calculate the average probability with which a node will meet another particular node at any point of time. Another way is to calculate the probability with which a node will meet another based on the time of day. The way of calculating pairwise contact probability depends on the scenario. In this work, the pairwise contact probabilities obtained from the real traces are used to tune the parameters of the SWIM mobility model. The traces and the SWIM model are compared in terms of contact durations, inter-contact times and, number of pairwise contacts. How to decide SWIM parameters using real contact traces are being addressed.
Identification of mouse type‐2‐like astrocytes: Demonstration of glutamate and GABA transmitter activated responses

We have identified mouse type‐2‐like astrocytes and examined some of their electrophysiological properties. Cultures were prepared from P4 mouse neopallia. We demonstrate that mouse type‐2‐like astrocytes can be identified using the following criteria: presence of glial fibrillary acidic protein (GFAP), presence of chondroitin sulfate polysaccharide, and presence of γ‐aminobutyric acid (GABA). A2B5‐binding is not a sufficient criterion to identify O2A lineage cells in mouse neopallial glial cultures since the monoclonal antibody A2B5 binds not only to O2A lineage cells but also to a subpopulation of large, flat type‐1‐like astrocytes. Mouse type‐2‐like astrocytes have resting membrane potentials of −76.2 ± 2.1 mV—i.e., similar to that of mouse type‐1‐like astrocytes. The input resistance of 44.2 ± 0.5 MΩ is an order of magnitude greater than that of type‐1‐like astrocytes suggesting the type‐2‐like astrocytes are not extensively electrically coupled either to each other or to type‐1‐like astrocytes. Glutamate application caused an 8.8 ± 1.7 mV depolarization of type‐2‐like astrocytes. Application of glutamate to barium treated astrocytes caused a fast depolarization with a peak amplitude of 21.4 ± 1.8 mV; the cells repolarized from this peak by about 10 mV and upon removal of glutamate returned to its pre‐glutamate value. Application of GABA caused a transient depolarization of 14.0 ± 1.7 mV. The presence of barium resulted in a steady‐state GABA‐induced depolarization of 10.3 ± 2.0 mV. Neither SITS nor β‐alanine interfered with the amplitude of the glutamate and GABA responses. © 1992 Wiley‐Liss, Inc.
DNA Immunization with Japanese Encephalitis Virus Nonstructural Protein NS1 Elicits Protective Immunity in Mice

ABSTRACT Japanese encephalitis virus (JEV), a mosquito-borne flavivirus, is a zoonotic pathogen that is prevalent in some Southeast Asian countries and causes acute encephalitis in humans. To evaluate the potential application of gene immunization to JEV infection, we characterized the immune responses from mice intramuscularly injected with plasmid DNA encoding JEV glycoproteins, including the precursor membrane (prM) plus envelope (E) proteins and the nonstructural protein NS1. When injected with the plasmid expressing prM plus E, 70% of the immunized mice survived after a lethal JEV challenge, whereas when immunized with the plasmid expressing NS1, 90% of the mice survived after a lethal challenge. As a control, the mice immunized with the DNA vector pcDNA3 showed a low level (40%) of protection, suggesting a nonspecific adjuvant effect of the plasmid DNA. Despite having no detectable neutralizing activity, the NS1 immunization elicited a strong antibody response exhibiting cytolytic activity against JEV-infected cells in a complement-dependent manner. By contrast, immunization with a construct expressing a longer NS1 protein (NS1′), containing an extra 60-amino-acid portion from the N terminus of NS2A, failed to protect mice against a lethal challenge. Biochemical analyses revealed that when individually expressed, NS1 but not NS1′ could be readily secreted as a homodimer in large quantity and could also be efficiently expressed on the cell surface. Interestingly, when NS1 and NS1′ coexisted in cells, the level of NS1 cell surface expression was much lower than that in cells expressing NS1 alone. These data imply that the presence of partial NS2A might have a negative influence on an NS1-based DNA vaccine. The results herein clearly illustrate that immunization with DNA expressing NS1 alone is sufficient to protect mice against a lethal JEV challenge.
Long-term UHF RiverSonde river velocity observations at Castle Rock, Washington and Threemile Slough, California

Long-term, non-contact river velocity measurements have been made using a UHF RiverSonde system for several months at each of two locations having quite different flow characteristics. Observations were made on the Cowlitz River at Castle Rock, Washington from October 2003 to June 2004, where the unidirectional flow of the river ranged from about 1.0 to 3.5 m/s. The radar velocity was highly correlated with the stage height which was continually measured by the U. S. Geological Survey. The profile of the along-channel velocity across the water channel also compared favorably with in-situ measurements performed by the Survey. The RiverSonde was moved to Threemile Slough, in central California, in September 2004 and has been operating there for several months. At Threemile Slough, which connects the Sacramento and San Joaquin Rivers, the flow is dominated by tidal effects and reverses direction four times per day, with a maximum speed of about 0.8 m/s in each direction. Water level and water velocity are continually measured by the Survey at the Threemile Slough site, with velocity recorded every 15 minutes from measurements made by an ultrasonic velocity meter (UVM). Over a period of several months, the radar and UVM velocity measurements have been highly correlated, with a coefficient of determination R/sup 2/ of 0.976.
Structure-Function Analysis of Severe Acute Respiratory Syndrome Coronavirus RNA Cap Guanine-N7-Methyltransferase

ABSTRACT Coronaviruses possess a cap structure at the 5′ ends of viral genomic RNA and subgenomic RNAs, which is generated through consecutive methylations by virally encoded guanine-N7-methyltransferase (N7-MTase) and 2′-O-methyltransferase (2′-O-MTase). The coronaviral N7-MTase is unique for its physical linkage with an exoribonuclease (ExoN) harbored in nonstructural protein 14 (nsp14) of coronaviruses. In this study, the structure-function relationships of the N7-MTase were analyzed by deletion and site-directed mutagenesis of severe acute respiratory syndrome coronavirus (SARS-CoV) nsp14. The results showed that the ExoN domain is closely involved in the activity of the N7-MTase, suggesting that coronavirus N7-MTase is different from all other viral N7-MTases, which are separable from other structural domains located in the same polypeptide. Two of the 12 critical residues identified to be essential for the N7-MTase were located at the N terminus of the core ExoN domain, reinforcing a role of the ExoN domain in the N7-MTase activity of nsp14. The other 10 critical residues were distributed throughout the N7-MTase domain but localized mainly in the S-adenosyl-l-methionine (SAM)-binding pocket and key structural elements of the MTase fold of nsp14. The sequence motif DxGxPxA (amino acids [aa] 331 to 338) was identified as the key part of the SAM-binding site. These results provide insights into the structure and functional mechanisms of coronaviral nsp14 N7-MTase.
Real Solving for Positive Dimensional Systems

Finding one point on each semi-algebraically connected component of a real algebraic variety, or at least deciding if such a variety is empty or not, is a fundamental problem of computational real algebraic geometry. Although numerous studies have been done on the subject, only a small number of efficient implementations exist.In this paper, we propose a new efficient and practical algorithm for computing such points. By studying the critical points of the restriction to the variety of the distance function to one well chosen point, we show how to provide a set of zero-dimensional systems whose zeros contain at least one point on each semi-algebraically connected component of the studied variety, without any assumption either on the variety (smoothness or compactness for example) or on the system of equations which define it.From the output of our algorithm, one can then apply, for each computed zero-dimensional system, any symbolic or numerical algorithm for counting or approximating the real solutions. We report some experiments using a set of pure exact methods. The practical efficiency of our method is due to the fact that we do not apply any infinitesimal deformations, unlike the existing methods based on a similar strategy.
A Meta-Analysis of the RTI Literature for Children at Risk for Reading Disabilities

This article synthesizes the literature comparing at-risk children designated as responders and low responders to interventions in reading. The central question addressed in this review is whether individual differences in reading-related skills at pretest predict responders at posttest across a variety of interventions and sets of criteria for determining responding and low responding. A total of 13 studies met criteria for the meta-analysis, yielding 107 weighted effect sizes (ESs) at posttest (M = .76, SE = .03, 95% confidence interval [CI] =.71, .81) and 108 weighted ESs at pretest (M = 1.02, SE = .03, CI = 1.02, 1.13). The results showed that the magnitude of ES between responders and low responders increased from pretest to posttest on measures of reading (e.g., real word identification = 1.06 vs. 1.53, word attack = 1.10 vs. 1.28, and passage comprehension, 0.45 vs. 1.43). Hierarchical linear modeling indicated that overall posttest ESs were significantly moderated by pretest scores as well as the type of measure administered, whereas no significant moderating effects were found for number of weeks of intervention, length of sessions, number of sessions, type of intervention (one-to-one vs. small group instruction), and criteria for defining responders (cutoff, scores, discrepancy, benchmark). Overall, the synthesis suggested that regardless of type of treatment and identification criteria, response-to-intervention (RTI) conditions were not effective in mitigating learner characteristics related to pretest conditions.
Cell Growth Arrest by Nucleotides, Nucleosides and Bases as a Tool for Improved Production of Recombinant Proteins

Arresting cell growth and thus decreasing cell division potentially lessens the chance for genetic drift in the cell population; this would be of utmost importance for the consistent production of biopharmaceuticals during long periods. The drawback of the addition of well‐known synchronizing agents, such as chemotherapeutics, is that they cause a disproportionate accumulation of cellular constituents, leading to cell death. The use of compounds that are naturally synthesized by the cell, as is the case of nucleotides, nucleosides, and bases (Nt/Ns/B), is shown in this work to be a promising tool. The addition of purines and pyrimidines was tested using a CHO cell line producing the secreted form of the human placental alkaline phosphatase enzyme (SEAP). From the chemical alternatives tested, AMP was the most promising compound for protein production improvement; it reduced cell growth and maintained the culture with high cell viability for long periods, while increasing SEAP specific productivity 3‐fold. The use of CHO and BHK mammalian cells producing Factor VII and the use of a insect cell line (Sf9) showed that the effect of AMP addition seems to be independent of the r‐protein and cell line. With the addition of AMP, accumulation of cells at the S phase was accompanied by an increase of the protein specific productivity. Addition of known synchronizing drugs (aphidicolin and doxorubicin) and application of environmental cell growth arrest strategies (depletion of nutrients and byproduct accumulation) showed also to effectively arrest CHO cell growth. A careful look onto cell cycle distribution in the different scenarios created, shows whether it is important to consider r‐protein expression dependency upon cell cycle in process optimization and operation strategies.
Small scale integrated Sachs-Wolfe effect.

The integrated Sachs-Wolfe (ISW) effect can be an important factor in the generation of cosmic microwave background anisotropies on all scales, especially in a reionized curvature- or \ensuremath{\Lambda}-dominated universe. We present a simple analytic treatment of the ISW effect, which is analogous to thick last scattering surface techniques for the Doppler effect, that compares quite well with the full numerical calculations. The power spectrum of temperature fluctuations due to the small scale ISW effect has a wave number dependence ${\mathit{k}}^{\mathrm{\ensuremath{-}}5}$ times that of the matter power spectrum.
Signatures for Network Coding

In communication networks, files commonly are separated into data packets and transmitted from the source node to a prescribed set of destination nodes by a method known as “store and forward”, in which data packets received are stored and then forwarded to the next node. Network coding has been proposed to replace the traditional “store and forward” model, and to improve the throughput and robustness of networks. With linear network coding, instead of copying and forwarding, intermediate nodes compute linear combinations of previously received information, and create and transmit a new packet to the next nodes. However, some malicious intermediate nodes may modify the data of packets and the recipients not can distinguish the corrupted packets from uncorrupted ones. This is known as a “pollution attack”. Homomorphic hashings and homomorphic signatures were proposed to provide cryptographic protection against pollution attacks. First, we present Krohn et al.’s homomorphic hashing schemes for rateless erasure codes. This paper presented six homomorphic signature schemes for network coding including three pairing-based homomorphic signature schemes, three RSA-based homomorphic signature schemes, and a signature scheme using a vector orthogonal to the message linear subspace. We then discuss and compare the memory and communication overhead of five of these homomorphic signature schemes. Finally, we point out flaws with some of these schemes, even though some security analysis has been presented, and we present solutions to prevent such attacks.
Intrinsic connections of macaque striate cortex: axonal projections of cells outside lamina 4C

We have exploited a technique for making small injections of horseradish peroxidase into single cortical laminae in order to study axonal projections in macaque striate cortex. In the preceding paper (Fitzpatrick, D., J. S. Lund, and G. G. Blasdel (1985) J. Neurosci. 5: 3329–3349) we examined the projections of cells in lamina 4C--cells that receive most of their input from the lateral geniculate nucleus. The present paper deals with the projections of neurons that lie outside of lamina 4C. Among our findings are several projections that previously had not been described in the monkey. These include: a strong and precise (point-to-point) projection from lamina 4B to lamina 2/3A, a reciprocal projection from 2/3A back to 4B, a definite projection from lamina 4B to 5B, as well as a prominent input to lamina 6 from 5B. In many cases, we find it possible to trace the flow of visual information through several “circuits” in striate cortex that have, as their output, projections to extrastriate cortex or to the brainstem. Our results offer additional insights in this regard since we are able, in many cases, to compare the lateral spreads of particular projections. These vary and can be separated into at least three categories: those that terminate in a precise, point-to-point, fashion, those that spread widely, and those that terminate in a laterally periodic fashion. In several cases we find evidence for a correlation between specific patterns of projection and known physiological differences between the topographies of laminae that are connected. In cases where two laminae possess similar topographies (for example, where both contain orderly maps for orientation) their interconnections appear precise, with little diffuse spread. In cases where two laminae are characterized by strikingly different topographies (where, for example, one contains an orderly map for orientation and the other a precise map for retinotopic position, but no specificity for orientation), the connections appear more diffuse.
Thoracic and abdominal SPECT-CT image fusion without external markers in endocrine carcinomas. The Group of Thyroid Tumoral Pathology of Champagne-Ardenne.

UNLABELLED Superimposition of SPECT and computed tomography (CT) slices from the thoracoabdominal region was achieved without the use of external markers for 14 studies in 13 patients with endocrine carcinoma. Technical feasibility and clinical validation of this retrospective fusion method were assessed. METHODS Patients had a history of thyroid cancer or of carcinoid tumor. To detect tumor sites, CT scan and dual-isotope tomoscintigraphy were performed, with 99mTc-hydroxymethylene diphosphonate for bone scintigraphy and with 111In-pentetreotide, 131I or 131I-metaiodobenzylguanidine for tumor scintigraphy (TS). A superimposition method previously developed for the pelvic region was adapted to the nonrigid thoraco-abdominal region. CT-bone scintigraphy and CT-TS superimposed images were obtained. Clinical validation of the information obtained from the superimposed images was obtained from surgery or follow-up imaging studies performed after clinical evolution of the disease process. RESULTS Reliable and reproducible registration was achieved in all patients. CT-TS superimposed images produced accurate localization of abnormal TS foci. Accuracy was limited primarily by variable relative displacements of the thoracoabdominal organs. For 10 sites in 8 patients, localization and/or characterization obtained from CT-TS images was confirmed by a reference technique. Superimposition enabled the localization of tumor sites that otherwise could not have been suspected from CT alone and allowed the characterization of CT suspicious masses and the confirmation of CT positive sites. Nonspecific tumor TS uptake sites were also localized. CONCLUSION With standard CT and dual-isotope SPECT acquisitions, SPECT-CT fusion is feasible in the thoracoabdominal region without the use of external markers. Fused images were validated in 8 patients for 10 sites. The use of this technique could probably improve the management and care of patients with endocrine carcinoma.
Elovl4 mRNA distribution in the developing mouse retina and phylogenetic conservation of Elovl4 genes.

PURPOSE Stargardt-like macular dystrophy (STGD3) is an autosomal dominant form of early onset macular degeneration. The disease causing gene ELOVL4 encodes a protein that belongs to a family of proteins functioning in elongation of long chain fatty acids. The purpose of this study is to characterize cross-species conservation of ELOVL4 and investigate its mRNA distribution in the developing mouse eye. METHODS Bovine and porcine orthologs of the human ELOVL4 gene were cloned using RT-PCR method. EST and HTGS databases were searched for orthologs of ELOVL4. Cross-species alignments were performed using ClustalW. In situ hybridizations using murine Elovl4 probes were performed on frozen sections of mouse eyes. RESULTS Elovl4 orthologs from mammalian to invertebrate species share strong sequence homology with human ELOVL4 at the amino acid level, suggesting functional conservation of Elovl4 during evolution. Expression of Elovl4 in mouse retina begins at E15 during embryogenesis and persists in postnatal stages. However, Elovl4 is predominantly expressed in the retinal ganglion cells at P1-P3, followed by predominant expression in the outer nuclear layer at P7, with its final expression enriched in inner segments of photoreceptors. CONCLUSIONS Elovl4 expression in developing retina follows a dynamic pattern. It switches from predominant ganglion cell expression in embryonic and early postnatal development to predominant expression in the photoreceptor inner segments in later stages. Phylogenetic analysis reveals strong conservation of Elovl4 among different species throughout the vertebrate subphylum consistent with our hypothesis that ELOVL4 performs a fundamentally important function.
Poly[[μ2-1,4-bis(4,5-dihydro-1,3-oxazol-2-yl)benzene-κ2 N:N′]di-μ2-chlorido-cadmium]

In the title coordination polymer, [CdCl2(C12H12N2O2)]n, the CdII ion, situated on an inversion center, is coordinated by four bridging Cl atoms and two N atoms from two 1,4-bis(4,5-dihydro-1,3-oxazol-2-yl)benzene (L) ligands in a distorted octahedral geometry. Each L ligand also lies across an inversion center and bridges two CdII ions, forming infinite two-dimensional rectangular layers running parallel to (010).
Herpes Simplex Virus 1 Infection Induces Activation and Subsequent Inhibition of the IFI16 and NLRP3 Inflammasomes

ABSTRACT Inflammasomes are multiprotein complexes that recognize pathogens and pathogen- or danger-associated molecular patterns. They induce the maturation and secretion of powerful proinflammatory interleukin-1B (IL-1β), IL-18, and IL-33 cytokines, which in turn activate expression of other immune genes and lymphocyte recruitment to the site of primary infection, thereby controlling invading pathogens. Inflammasomes are comprised of cytoplasmic sensor molecules, such as NLRP3 and AIM2 or nuclear sensor IFI16, the adaptor protein ASC (apoptosis-associated speck-like protein containing CARD), and the effector protein procaspase-1. Herpes simplex virus 1 (HSV-1), a ubiquitous virus that infects humans and establishes life-long latency, has evolved numerous mechanisms to evade host detection and immune responses. Here, we show that early during in vitro infection of human foreskin fibroblasts (2 to 4 h), HSV-1 induced the activation of the IFI16 and NLRP3 inflammasomes and maturation of IL-1β. Independent of viral gene expression, IFI16 recognized the HSV-1 genome in infected cell nuclei, relocalized, and colocalized with ASC in the cytoplasm. However, HSV-1 specifically targeted IFI16 for rapid proteasomic degradation at later times postinfection, which was dependent on the expression of ICP0, an immediate early protein of HSV-1. In contrast, NLRP3, AIM2, and ASC levels were not decreased. Also, caspase-1 was “trapped” in actin clusters at later time points that likely blocked the NLRP3/IFI16 inflammasome activity. In addition, the secretion of mature IL-1β was inhibited. These results suggest that though the host cell responds to HSV-1 infection by IFI16 and NLRP3 inflammasomes early during infection, HSV-1 has evolved mechanisms to shut down these responses to evade the proinflammatory consequences.