Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the antioxidant response of Nicotiana benthamiana to infection with two strains of Pepper mild mottle virus

The present study was carried out to investigate the role of reactive oxygen species (ROS) metabolism in symptom development and pathogenesis in Nicotiana benthamiana plants upon infection with two strains of Pepper mild mottle virus, the Italian (PMMoV-I) and the Spanish (PMMoV-S) strains. In this host, it has been shown that PMMoV-I is less virulent and plants show the capability to recover 21 d after inoculation. Analyses of oxidative stress biomarkers, ROS-scavenging enzyme activities, and antioxidant compounds were conducted in plants at different post-infection times. Only PMMoV-I stimulated a defence response through: (i) up-regulation of different superoxide dismutase isozymes; (ii) maintenance of adequate levels of three peroxiredoxins (2-Cys Prx, Prx IIC, and Prx IIF); and (iii) adjustments in the glutathione pool to maintain the total glutathione content. Moreover, there was an increase in the level of oxidized glutathione and ascorbate in the recovery phase of PMMoV-I-infected plants. The antioxidant response and the extent of oxidative stress in N. benthamiana plants correlates to: (i) the severity of the symptoms elicited by either strain of PMMoV; and (ii) the high capacity of PMMoV-I-infected plants for symptom recovery and delayed senescence, compared with PMMoV-S-infected plants.
Polar auxin transport: an early invention

In higher plants, cell-to-cell polar auxin transport (PAT) of the phytohormone auxin, indole-3-acetic acid (IAA), generates maxima and minima that direct growth and development. Although IAA is present in all plant phyla, PAT has only been detected in land plants, the earliest being the Bryophytes. Charophyta, a group of freshwater green algae, are among the first multicellular algae with a land plant-like phenotype and are ancestors to land plants. IAA has been detected in members of Charophyta, but its developmental role and the occurrence of PAT are unknown. We show that naphthylphthalamic acid (NPA)-sensitive PAT occurs in internodal cells of Chara corallina. The relatively high velocity (at least 4–5 cm/h) of auxin transport through the giant (3–5 cm) Chara cells does not occur by simple diffusion and is not sensitive to a specific cytoplasmic streaming inhibitor. The results demonstrate that PAT evolved early in multicellular plant life. The giant Chara cells provide a unique new model system to study PAT, as Chara allows the combining of real-time measurements and mathematical modelling with molecular, developmental, cellular, and electrophysiological studies.
Triplet spike time dependent plasticity in a floating-gate synapse

Synapses plays an important role of learning in a neural network; the learning rules which modify the synaptic strength based on the timing difference between the pre- and post-synaptic spike occurrence is termed as Spike Time Dependent Plasticity (STDP). This paper describes the compact implementation of a synapse using single floating-gate (FG) transistor (and two additional high voltage transistors) that can store a weight in a non-volatile manner and demonstrate the triplet STDP (T-STDP) learning rule developed to explain biologically observed plasticity. We describe a mathematical procedure to obtain control voltages for the FG device for T-STDP and also show measurement results, from a FG synapse fabricated in TSMC 0. 35μm CMOS process to support the theory.
An Alternative and Effective HIV Vaccination Approach Based on Inhibition of Antigen Presentation Attenuators in Dendritic Cells

Background Current efforts to develop HIV vaccines that seek to stimulate immune responses have been disappointing, underscoring the inability of natural immune responses to control HIV-1 infection. Here we tested an alternative strategy to induce anti-HIV immune responses by inhibiting a host's natural immune inhibitor. Methods and Findings We used small interfering RNA (siRNA) to inhibit suppressor of cytokine signaling (SOCS) 1, a key negative regulator of the JAK/STAT pathway, and investigated the effect of this silencing on the ability of dendritic cells (DCs) to induce anti-HIV-1 immunity. We found that SOCS1-silenced DCs broadly induced enhanced HIV-1 envelope (Env)-specific CD8+ cytotoxic T lymphocytes and CD4+ T helper cells, as well as antibody responses, in mice. Importantly, SOCS1-silenced DCs were more resistant to HIV Env-mediated suppression and were capable of inducing memory HIV Env-specific antibody and T cell responses. SOCS1-restricted signaling, as well as production of proinflammatory cytokines such as interleukin-12 by DCs, play a critical role in regulating the anti-HIV immune response. Furthermore, the potency of HIV DNA vaccination is significantly enhanced by coimmunization with SOCS1 siRNA expressor DNA. Conclusions This study demonstrates that SOCS1 functions as an antigen presentation attenuator to control both HIV-1-specific humoral and cellular responses. This study represents the first, to our knowledge, attempt to elicit HIV-specific T cell and antibody responses by inhibiting a host's antigen presentation attenuator, which may open a new and alternative avenue to develop effective therapeutic and prophylactic HIV vaccines.
Arbitrarily varying wiretap channels with finite coordination resources

The wiretap channel models secure communication in the presence of a non-legitimate eavesdropper who has to be kept ignorant. In this paper, the arbitrarily varying wiretap channel (AVWC) is studied, in which the channel to both legitimate receiver and eavesdropper may vary in an unknown and arbitrary manner from channel use to channel use. It has been shown that for AVCs coordination between the transmitter and legitimate receiver based on common randomness (CR) is indispensable for reliable communication. Approaches taken so far yield CR-assisted strategies where the needed amount of CR increases unbounded with the block length. In this paper, it is shown that if we allow for a small but non-vanishing average probability of error and information leakage (in terms of weak secrecy), the amount of CR is always finite and independent of the block length. The corresponding secrecy capacity equals the one with asymptotically vanishing performance requirements. Furthermore, it is shown that the average decoding error at the eavesdropper can be made arbitrarily close to 1 regardless of the applied decoding strategy.
Cloning, localization and focus formation at DNA damage sites of canine XLF

Understanding the molecular mechanisms of DNA double-strand break (DSB) repair processes, especially nonhomologous DNA-end joining (NHEJ), is critical for developing next-generation radiotherapies and chemotherapeutics for human and animal cancers. The localization, protein-protein interactions and post-translational modifications of core NHEJ factors, such as human Ku70 and Ku80, might play critical roles in controlling NHEJ activity. XRCC4-like factor (XLF) is a core NHEJ factor and plays a key role in the Ku-dependent NHEJ repair process in human cells. Recently, companion animals, such as canines, have been proposed to be a good model for many aspects of cancer research, including the development of chemotherapeutics. However, the localization and regulation of core NHEJ factors in canine cells have not been elucidated. Here, we show that the localization of canine XLF changes dynamically during the cell cycle. EYFP-canine XLF localizes in the nuclei of interphase cells and accumulates immediately at microirradiated DSB sites. The structure of a putative human XLF nuclear localization signal (NLS) and a putative 14-3-3 binding motif are evolutionarily conserved in canine, chimpanzee and mouse XLF. However, the putative β-TRCP-recognizable degron of human XLF is not conserved in canine and mouse. Additionally, some vital human XLF phosphorylation sites, including the ATM major phosphorylation site (S251), are not conserved in canine XLF. Our findings might be useful for the study of the molecular mechanisms of NHEJ in canine cells and for the development of new radiosensitizers that target XLF.
Black-box optimization benchmarking the IPOP-CMA-ES on the noisy testbed: comparison to the BIPOP-CMA-ES

We benchmark the IPOP-CMA-ES on the noisy testbed of the BBOB 2010 workshop. The performances of the IPOP-CMA-ES are compared to those of the BIPOP-CMA-ES. Both algorithms are shown to perform comparably on the BBOB noisy testbed.
Takala Pulmonary capillary pressures during the acute respiratory distress syndrome

Accepted: 10 September 2003 Published online: 29 October 2003 © Springer-Verlag 2003 Abstract Objectives: (1)To describe the evolution of pulmonary capillary pressure (Pcap) and of the pressure drop across the pulmonary venous bed from early to established acute respiratory distress syndrome (ARDS), (2) to assess Pcap under different levels of positive end-expiratory pressure (PEEP) and (3) to compare the visual method and a mathematical model to determine Pcap. Design: Prospective, intervention study. Setting: Intensive care unit in a teaching institution. Patients: Nine ARDS patients, according to the ARDS Consensus Conference criteria. Interventions: Pulmonary arterial pressures were measured during routine respiratory mechanics measurements throughout ARDS. Four PEEP levels (6, 9, 12 and 15 cmH2O) were studied. Measurements and results: Pulmonary artery occlusions were made in triplicate at each PEEP level. Pcap was determined for every occlusion trace by three observers (visual method) and a mathematical model. Diastolic pulmonary artery pressure (PAPd) and pulmonary artery occlusion pressure (PAOP) were measured. The visually determined Pcap showed a bias of 2.5±2.1 mmHg as compared to the mathematical estimation. PAPd, Pcap and PAOP tended to decrease from early to late ARDS (p=0.128, 0.265, 0.121). Pcap−PAOP (6.3±2.7 mmHg) did not change throughout ARDS. Higher PEEP levels were associated with increased PAPd, Pcap and PAOP, as well as with larger Pcap−PAOP throughout ARDS. Conclusions: Pulmonary capillary pressure cannot be predicted from PAOP during early and established ARDS. The high variability in Pcap−PAOP increases the risk for underestimation of filtration pressures and consequently the risk for lung edema. Pcap can be estimated at the bedside by either the visual or mathematical methods.
An Alternative Conception of Tree-Adjoining Derivation

The precise formulation of derivation for tree-adjoining grammars has important ramifications for a wide variety of uses of the formalism, from syntactic analysis to semantic interpretation and statistical language modeling. We argue that the definition of tree-adjoining derivation must be reformulated in order to manifest the proper linguistic dependencies in derivations. The particular proposal is both precisely characterizable, through a compilation to linear indexed grammars, and computationally operational, by virtue of an efficient algorithm for recognition and parsing.
DC-SIGN on B Lymphocytes Is Required For Transmission of HIV-1 to T Lymphocytes

Infection of T cells by HIV-1 can occur through binding of virus to dendritic cell (DC)-specific ICAM-3 grabbing nonintegrin (DC-SIGN) on dendritic cells and transfer of virus to CD4+ T cells. Here we show that a subset of B cells in the blood and tonsils of normal donors expressed DC-SIGN, and that this increased after stimulation in vitro with interleukin 4 and CD40 ligand, with enhanced expression of activation and co-stimulatory molecules CD23, CD58, CD80, and CD86, and CD22. The activated B cells captured and internalized X4 and R5 tropic strains of HIV-1, and mediated trans infection of T cells. Pretreatment of the B cells with anti–DC-SIGN monoclonal antibody blocked trans infection of T cells by both strains of HIV-1. These results indicate that DC-SIGN serves as a portal on B cells for HIV-1 infection of T cells in trans. Transmission of HIV-1 from B cells to T cells through this DC-SIGN pathway could be important in the pathogenesis of HIV-1 infection.
Mometasone Furoate Improves Nasal and Ocular Symptoms of Seasonal Allergic Rhinitis in Adolescents

Seasonal allergic rhinitis (SAR) is common in adolescents. However, few studies have investigated the effectiveness of intranasal corticosteroids (INSs) for nasal and ocular symptoms of SAR solely in adolescents. The purpose of this study was to determine the safety and efficacy of the INS mometasone furoate nasal spray (MFNS) in adolescents; a post hoc analysis was conducted of adolescents who had participated in a study with adults. Data were analyzed retrospectively for subjects aged 12–17 years with moderate or severe SAR randomized to mometasone furoate, 200 meg once daily (n = 86), or placebo (n = 82) for 15 days in a multicenter, double-blind, placebo-controlled study. Symptom scores (0 = none to 3 = severe) were recorded in diaries twice daily. End points included changes from baseline in total nasal symptom score (TNSS), individual nasal symptom score (rhinorrhea, congestion, itching, and sneezing), and total ocular symptom score (TOSS). Over 15 days, a significantly greater decrease from baseline in mean TNSS was observed in subjects receiving mometasone furoate (–2.47; −28.8%) compared with those receiving placebo (–0.9; −9.6%; p < 0.001). Significant improvement versus placebo was seen for each full day of treatment. Mometasone furoate significantly improved individual nasal symptoms (p ≤ 0.03) and TOSS (p = 0.011) versus placebo. The incidence of adverse events was similar for both treatment groups. MFNS, 200 meg once daily, is an effective and well-tolerated treatment for symptoms of SAR in adolescents.
Tetrahedral Mesh Generation Based on Contours

We develop a method to construct tetrahedral mesh from contours in this paper. Each tetrahedron is generated under the supervision of the defined quality measure standard. This method reduces possibility of intersection between the segment and the triangle. Intersection test is sufficiently analyzed to guarantee that there is no overlap between tetrahedrons.
Analysis of wear, wear particles, and reduced inflammatory potential of vitamin E ultrahigh-molecular-weight polyethylene for use in total joint replacement

Vitamin E (VE) has been added to ultrahigh-molecular-weight polyethylene (UHMWPE) acetabular cups and tibial trays primarily to reduce oxidative damage to the polymer. The aim of this study was to investigate the relative wear rates of UHMWPE-containing VE compared with virgin UHMWPE. The ability of VE to reduce the amount of inflammatory cytokines produced from stimulated peripheral blood mononuclear cells (PBMNCs) was also investigated. Stimulation was achieved by exposure of PBMNCs to either lipoplysaccharide (LPS) or VE-containing UHMWPE (VE-UHMWPE). In the present study, results showed that the wear rates of UHMWPE with or without VE were not significantly different. Particles generated by UHMWPE with and without VE were not significantly different in size distribution. The production of osteolytic mediators, tumor necrosis factor-alpha, interleukin 1β (IL-β), IL-6, and IL-8 were significantly reduced in (PBMNCs) stimulated with either LPS + VE compared with LPS or VE-UHMWPE particles compared to virgin UHMWPE particles. This trend was also observed when VE was added as a liquid to UHMWPE wear particle-stimulated PBMNCs. The exact mechanism of how VE affects the release of inflammatory mediators from particle-stimulated macrophages is not yet understood. It is likely to involve the anti-inflammatory and/or antioxidant effects of VE.
Hormone Replacement Therapy, Percent Mammographic Density, and Sensitivity of Mammography

Objective: We examine to what extent the lower mammographic sensitivity found in hormone replacement therapy (HRT) users can be explained by any association of HRT use with higher mammographic density and more difficult to detect cancers. Methods: We used logistic regression to estimate the odds of a false-negative screen (a breast cancer diagnosed in the 24 months after a negative screening examination) for HRT users and to estimate, and adjust for, mammographic density (measured on a continuous scale, blinded, using a reliable, computer-assisted method), tumor characteristics (size, grade, and morphology), and potential confounders (age, symptom status, family history, and prior screening) among women ages ≥55 years who attended BreastScreen Victoria for first round screening mammography in 1994 and 1995 (1,086 breast cancers) and for subsequent round screening (471 breast cancers) in 1995 and 1996. Results: After adjusting for confounders, HRT users were more likely to have a false-negative screen [first round: odds ratio (OR), 1.99; 95% confidence interval (95% CI), 1.4-2.9; subsequent round: OR, 2.29; 95% CI, 1.4-3.8]. This effect was modestly attenuated by adjusting for mammographic density (first round: OR, 1.54; 95% CI, 1.0-2.3; subsequent round: OR, 1.97; 95% CI, 1.2-3.3). Adjusting for tumor characteristics resulted in a modest increase in the odds of a false negative at first round but had no effect at subsequent round. Conclusions: Mammographic density only partly explains the effect of HRT on sensitivity. Further research needs to clarify whether hyperemic breast tissue changes affect cancer detectability in HRT users as well as the possibility that the quality of mammography may be poor in some HRT users.
Degeneration of the Olfactory Guanylyl Cyclase D Gene during Primate Evolution

Background The mammalian olfactory system consists of several subsystems that detect specific sets of chemical cues and underlie a variety of behavioral responses. Within the main olfactory epithelium at least three distinct types of chemosensory neurons can be defined by their expression of unique sets of signal transduction components. In rodents, one set of neurons expresses the olfactory-specific guanylyl cyclase (GC)-D gene (Gucy2d, guanylyl cyclase 2d) and other cell-type specific molecules. GC-D-positive neurons project their axons to a small group of atypical “necklace” glomeruli in the olfactory bulb, some of which are activated in response to suckling in neonatal rodents and to atmospheric CO2 in adult mice. Because GC-D is a pseudogene in humans, signaling through this system appears to have been lost at some point in primate evolution. Principal Findings Here we used a combination of bioinformatic analysis of trace-archive and genome-assembly data and sequencing of PCR-amplified genomic DNA to determine when during primate evolution the functional gene was lost. Our analysis reveals that GC-D is a pseudogene in a large number of primate species, including apes, Old World and New World monkeys and tarsier. In contrast, the gene appears intact and has evolved under purifying selection in mouse, rat, dog, lemur and bushbaby. Conclusions These data suggest that signaling through GC-D-expressing cells was probably compromised more than 40 million years ago, prior to the divergence of New World monkeys from Old World monkeys and apes, and thus cannot be involved in chemosensation in most primates.
Cell-Free miR-27a, a Potential Diagnostic and Prognostic Biomarker for Gastric Cancer

MicroRNAs (miRNAs) have been demonstrated to play an important role in carcinogenesis. Previous studies revealed that miRNAs are present in human plasma in a remarkably stable form that is protected from endogenous RNase activity. In this study, we measured the plasma expression levels of three miRNAs (miR-21, miR-27a, and miR-155) to investigate the usefulness of miRNAs for gastric cancer detection. We initially examined plasma miRNA expression levels in a screening cohort consisting of 15 patients with gastric cancer and 15 healthy controls from Korean population, using TaqMan quantitative real-time polymerase chain reaction. We observed that the expression level of miR-27a was significantly higher in patients with gastric cancer than in healthy controls, whereas the miR-21 and miR-155a expression levels were not significantly higher in the patients with gastric cancer. Therefore, we further validated the miR-27a expression level in 73 paired gastric cancer tissues and in a validation plasma cohort from 35 patients with gastric cancer and 35 healthy controls. In both the gastric cancer tissues and the validation plasma cohort, the miR-27a expression levels were significantly higher in patients with gastric cancer. Receiver-operator characteristic (ROC) analysis of the validation cohort, revealed an area under the ROC curve value of 0.70 with 75% sensitivity and 56% specificity in discriminating gastric cancer. Thus, the miR-27a expression level in plasma could be a useful biomarker for the diagnosis and/or prognosis of gastric cancer.
Localization algorithm based on difference estimation for wireless sensor networks in Pervasive Computing Environment

In order to suppress effectively the effects of RSSI error to wireless sensor networks node localization's precision in pervasive computing environment, individual diversity difference coefficient, distance difference coefficient and distance difference localization equation is defined based on the analysis of the models of maximum likelihood estimation and RSSI. The closest beaconing node to object node as reference node corrects measure distance based on RSSI by difference method. A distance difference localization algorithm is put forward through combining difference correction method and maximum likelihood estimation method. This localization algorithm needn't additional hardware spending, easy to be realized and its localization error is less than 2.5 m, therefore it is fit for localization of WSN node whose operation ability and power supply are restricted.
Using cache memory to reduce processor-memory traffic

The importance of reducing processor-memory bandwidth is recognized in two distinct situations: single board computer systems and microprocessors of the future. Cache memory is investigated as a way to reduce the memory-processor traffic. We show that traditional caches which depend heavily on spatial locality (look-ahead) for their performance are inappropriate in these environments because they generate large bursts of bus traffic. A cache exploiting primarily temporal locality (look-behind) is then proposed and demonstrated to be effective in an environment where process switches are infrequent. We argue that such an environment is possible if the traffic to backing store is small enough that many processors can share a common memory and if the cache data consistency problem is solved. We demonstrate that such a cache can indeed reduce traffic to memory greatly, and introduce an elegant solution to the cache coherency problem.
Decoupled Plant and Insect Diversity After the End-Cretaceous Extinction

Food web recovery from mass extinction is poorly understood. We analyzed insect-feeding damage on 14,999 angiosperm leaves from 14 latest Cretaceous, Paleocene, and early Eocene sites in the western interior United States. Most Paleocene floras have low richness of plants and of insect damage. However, a low-diversity 64.4-million-year-old flora from southeastern Montana shows extremely high insect damage richness, especially of leaf mining, whereas an anomalously diverse 63.8-million-year-old flora from the Denver Basin shows little damage and virtually no specialized feeding. These findings reveal severely unbalanced food webs 1 to 2 million years after the end-Cretaceous extinction 65.5 million years ago.